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Bateman NW, Abulez T, Soltis AR, McPherson A, Choi S, Garsed DW, Pandey A, Tian C, Hood BL, Conrads KA, Teng PN, Oliver J, Gist G, Mitchell D, Litzi TJ, Tarney CM, Crothers BA, Mhawech-Fauceglia P, Dalgard CL, Wilkerson MD, Pierobon M, Petricoin EF, Yan C, Meerzaman D, Bodelon C, Wentzensen N, Lee JSH, Huntsman DG, Shah S, Shriver CD, Phippen NT, Darcy KM, Bowtell DDL, Conrads TP, Maxwell GL. Author Correction: Proteogenomic analysis of enriched HGSOC tumor epithelium identifies prognostic signatures and therapeutic vulnerabilities. NPJ Precis Oncol 2024; 8:97. [PMID: 38710993 DOI: 10.1038/s41698-024-00588-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024] Open
Affiliation(s)
- Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
| | - Tamara Abulez
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Anthony R Soltis
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Andrew McPherson
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Seongmin Choi
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Dale W Garsed
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Ahwan Pandey
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Kelly A Conrads
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Pang-Ning Teng
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Glenn Gist
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Dave Mitchell
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Tracy J Litzi
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Christopher M Tarney
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Barbara A Crothers
- The Joint Pathology Center, Defense Health Agency, National Capital Region Medical Directorate, Silver Spring, MD, USA
| | - Paulette Mhawech-Fauceglia
- Department of Anatomic Pathology, Division of Gynecologic Pathology, University of Southern California, Los Angeles, CA, USA
| | - Clifton L Dalgard
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Matthew D Wilkerson
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Chunhua Yan
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Daoud Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Clara Bodelon
- Division of Cancer Epidemiology and Genetics National Cancer Institute, Rockville, MD, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics National Cancer Institute, Rockville, MD, USA
| | - Jerry S H Lee
- Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, USA
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Sohrab Shah
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Craig D Shriver
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Neil T Phippen
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA.
| | - G Larry Maxwell
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA.
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Kopelman ZA, Tian C, Tumas J, Phippen NT, Tarney CM, Hope ER, Winkler SS, Jokajtys S, Kucera CW, Chan JK, Richardson MT, Kapp DS, Hamilton CA, Leath CA, Jones NL, Rocconi RP, Farley JH, Secord AA, Cosgrove CM, Powell MA, Klopp A, Walker JL, Fleming GF, Bateman NW, Conrads TP, Maxwell GL, Darcy KM. Disease progression, survival, and molecular disparities in Black and White patients with endometrioid endometrial carcinoma in real-world registries and GOG/NRG oncology randomized phase III clinical trials. Gynecol Oncol 2024; 183:103-114. [PMID: 38593674 DOI: 10.1016/j.ygyno.2024.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024]
Abstract
OBJECTIVE Investigate racial disparities in outcomes and molecular features in Black and White patients with endometrioid endometrial carcinoma (EEC). METHODS Black and White patients diagnosed with EEC who underwent hysterectomy ± adjuvant treatment in SEER, National Cancer Database (NCDB), the Genomics Evidence Neoplasia Information Exchange (GENIE) project (v.13.0), and eight NCI-sponsored randomized phase III clinical trials (RCTs) were studied. Hazard ratio (HR) and 95% confidence interval (CI) were estimated for cancer-related death (CRD), non-cancer death (NCD), and all-cause death. RESULTS Black (n = 4397) vs. White (n = 47,959) patients in SEER had a HR (95% CI) of 2.04 (1.87-2.23) for CRD and 1.22 (1.09-1.36) for NCD. In NCDB, the HR (95% CI) for death in Black (n = 13,468) vs. White (n = 155,706) patients was 1.52 (1.46-1.58) dropping to 1.29 (1.23-1.36) after propensity-score matching for age, comorbidity, income, insurance, grade, stage, LVSI, and treatment. In GENIE, Black (n = 109) vs. White (n = 1780) patients had fewer PTEN, PIK3R1, FBXW7, NF1, mTOR, CCND1, and PI3K-pathway-related gene mutations. In contrast, TP53 and DNA-repair-related gene mutation frequency as well as tumor mutational burden-high status were similar in Black and White patients. In RCTs, Black (n = 187) vs. White (n = 2877) patients were more likely to have advanced or recurrent disease, higher grade, worse performance status and progressive disease. Risk of death in Black vs. White patients in RCTs was 2.19 (1.77-2.71) persisting to 1.32 (1.09-1.61) after matching for grade, stage, and treatment arm while balancing age and performance status. CONCLUSIONS Differences exist in clinical presentation, outcomes, and molecular features in Black vs. White patients with EEC in real-world registries and RCTs. Targeted-drug development, strategies to modify social determinants, and diverse inclusion in RCTs are approaches to reduce disparities.
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Affiliation(s)
- Zachary A Kopelman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Jordyn Tumas
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Neil T Phippen
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Christopher M Tarney
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Erica R Hope
- Division of Gynecologic Oncology, Department of Gynecologic Surgery and Obstetrics, Brooke Army Medical Center, San Antonio, TX, USA
| | - Stuart S Winkler
- Division of Gynecologic Oncology, Department of Gynecologic Surgery and Obstetrics, Brooke Army Medical Center, San Antonio, TX, USA
| | - Suzanne Jokajtys
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Calen W Kucera
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - John K Chan
- Palo Alto Medical Foundation, California Pacific Medical Center, Sutter Health, San Francisco, CA, USA
| | - Michael T Richardson
- Department of Obstetrics and Gynecology, University of California, Los Angeles School of Medicine, Los Angeles, CA, USA
| | - Daniel S Kapp
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Chad A Hamilton
- Gynecologic Oncology Section, Women's Services and The Ochsner Cancer Institute, Ochsner Health, New Orleans, LA, USA
| | - Charles A Leath
- Division of Gynecologic Oncology, University of Alabama at Birmingham, O'Neal Comprehensive Cancer Center, Birmingham, AL, USA
| | - Nathaniel L Jones
- Division of Gynecologic Oncology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Rodney P Rocconi
- Division of Gynecologic Oncology, Cancer Center & Research Institute, the University of Mississippi Medical Center, Jackson, MS, USA
| | - John H Farley
- Division of Gynecologic Oncology, Center for Women's Health, Cancer Institute, Dignity Health St. Joseph's Hospital and Medical Center, Phoenix, AZ, USA
| | | | - Casey M Cosgrove
- Division of Gynecologic Oncology, The Ohio State University, Columbus, OH, USA
| | - Matthew A Powell
- Division of Gynecologic Oncology, Siteman Cancer Center, Washington University, St Louis, MO, USA
| | - Ann Klopp
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joan L Walker
- Gynecologic Oncology Division, Stephenson Cancer Center, Oklahoma University Health Sciences Center, Oklahoma City, OK, USA
| | - Gini F Fleming
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Nicholas W Bateman
- Division of Gynecologic Oncology, Center for Women's Health, Cancer Institute, Dignity Health St. Joseph's Hospital and Medical Center, Phoenix, AZ, USA; The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - G Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, Falls Church, VA, USA.
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA.
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Randall J, Hunt AL, Nutcharoen A, Johnston L, Chouraichi S, Wang H, Winer A, Wadlow R, Huynh J, Davis J, Corgiat B, Bateman NW, Deeken JF, Petricoin EF, Conrads TP, Cannon TL. Quantitative proteomic analysis of HER2 protein expression in PDAC tumors. Clin Proteomics 2024; 21:24. [PMID: 38509475 PMCID: PMC10953162 DOI: 10.1186/s12014-024-09476-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Metastatic pancreatic adenocarcinoma (PDAC) is the third leading cause of cancer-related death in the United States, with a 5-year survival rate of only 11%, necessitating identification of novel treatment paradigms. Tumor tissue specimens from patients with PDAC, breast cancer, and other solid tumor malignancies were collected and tumor cells were enriched using laser microdissection (LMD). Reverse phase protein array (RPPA) analysis was performed on enriched tumor cell lysates to quantify a 32-protein/phosphoprotein biomarker panel comprising known anticancer drug targets and/or cancer-related total and phosphorylated proteins, including HER2Total, HER2Y1248, and HER3Y1289. RPPA analysis revealed significant levels of HER2Total in PDAC patients at abundances comparable to HER2-positive (IHC 3+) and HER2-low (IHC 1+ /2+ , FISH-) breast cancer tissues, for which HER2 screening is routinely performed. These data support a critical unmet need for routine clinical evaluation of HER2 expression in PDAC patients and examination of the utility of HER2-directed antibody-drug conjugates in these patients.
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Affiliation(s)
- Jamie Randall
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA
| | - Allison L Hunt
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, 3289 Woodburn Rd, Annandale, VA, 22042, USA
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Aratara Nutcharoen
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA
- Department of Pathology, Inova Fairfax Hospital, 3300 Gallows Road, Falls Church, VA, 22042, USA
| | - Laura Johnston
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA
| | - Safae Chouraichi
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA
| | - Hongkun Wang
- Department of Biostatistics, Bioinformatics, and Biomathematics, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Arthur Winer
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA
| | - Raymond Wadlow
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA
| | - Jasmine Huynh
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA
| | - Justin Davis
- Theralink Technologies, Inc., 15000 W 6th Ave, Golden, CO, 80401, USA
| | - Brian Corgiat
- Theralink Technologies, Inc., 15000 W 6th Ave, Golden, CO, 80401, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - John F Deeken
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, 20110, USA
| | - Thomas P Conrads
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, 3289 Woodburn Rd, Annandale, VA, 22042, USA
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Timothy L Cannon
- Inova Schar Cancer Institute, Inova Health System, 8081 Innovation Park Dr, Fairfax, VA, 22031, USA.
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Teng PN, Schaaf JP, Abulez T, Hood BL, Wilson KN, Litzi TJ, Mitchell D, Conrads KA, Hunt AL, Olowu V, Oliver J, Park FS, Edwards M, Chiang A, Wilkerson MD, Raj-Kumar PK, Tarney CM, Darcy KM, Phippen NT, Maxwell GL, Conrads TP, Bateman NW. ProteoMixture: A cell type deconvolution tool for bulk tissue proteomic data. iScience 2024; 27:109198. [PMID: 38439970 PMCID: PMC10910246 DOI: 10.1016/j.isci.2024.109198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/04/2023] [Accepted: 02/07/2024] [Indexed: 03/06/2024] Open
Abstract
Numerous multi-omic investigations of cancer tissue have documented varying and poor pairwise transcript:protein quantitative correlations, and most deconvolution tools aiming to predict cell type proportions (cell admixture) have been developed and credentialed using transcript-level data alone. To estimate cell admixture using protein abundance data, we analyzed proteome and transcriptome data generated from contrived admixtures of tumor, stroma, and immune cell models or those selectively harvested from the tissue microenvironment by laser microdissection from high grade serous ovarian cancer (HGSOC) tumors. Co-quantified transcripts and proteins performed similarly to estimate stroma and immune cell admixture (r ≥ 0.63) in two commonly used deconvolution algorithms, ESTIMATE or ConsensusTME. We further developed and optimized protein-based signatures estimating cell admixture proportions and benchmarked these using bulk tumor proteomic data from over 150 patients with HGSOC. The optimized protein signatures supporting cell type proportion estimates from bulk tissue proteomic data are available at https://lmdomics.org/ProteoMixture/.
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Affiliation(s)
- Pang-ning Teng
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Joshua P. Schaaf
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Tamara Abulez
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Brian L. Hood
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Katlin N. Wilson
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Tracy J. Litzi
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - David Mitchell
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Kelly A. Conrads
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Allison L. Hunt
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- Women’s Health Integrated Research Center, Women’s Service Line, Inova Health System, Falls Church, VA 22042, USA
| | - Victoria Olowu
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Fred S. Park
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Marshé Edwards
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - AiChun Chiang
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Matthew D. Wilkerson
- Center for Military Precision Health, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | | | - Christopher M. Tarney
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The John P. Murtha Cancer Center, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
| | - Kathleen M. Darcy
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
- The John P. Murtha Cancer Center, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
| | - Neil T. Phippen
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The John P. Murtha Cancer Center, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
| | - G. Larry Maxwell
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- Women’s Health Integrated Research Center, Women’s Service Line, Inova Health System, Falls Church, VA 22042, USA
- The John P. Murtha Cancer Center, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
| | - Thomas P. Conrads
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- Women’s Health Integrated Research Center, Women’s Service Line, Inova Health System, Falls Church, VA 22042, USA
- The John P. Murtha Cancer Center, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
| | - Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence and the Women’s Health Integrated Research Center, Annandale, VA 22003, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
- The John P. Murtha Cancer Center, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
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Bateman NW, Abulez T, Soltis AR, McPherson A, Choi S, Garsed DW, Pandey A, Tian C, Hood BL, Conrads KA, Teng PN, Oliver J, Gist G, Mitchell D, Litzi TJ, Tarney CM, Crothers BA, Mhawech-Fauceglia P, Dalgard CL, Wilkerson MD, Pierobon M, Petricoin EF, Yan C, Meerzaman D, Bodelon C, Wentzensen N, Lee JSH, Huntsman DG, Shah S, Shriver CD, Phippen NT, Darcy KM, Bowtell DDL, Conrads TP, Maxwell GL. Proteogenomic analysis of enriched HGSOC tumor epithelium identifies prognostic signatures and therapeutic vulnerabilities. NPJ Precis Oncol 2024; 8:68. [PMID: 38480868 PMCID: PMC10937683 DOI: 10.1038/s41698-024-00519-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 01/15/2024] [Indexed: 03/17/2024] Open
Abstract
We performed a deep proteogenomic analysis of bulk tumor and laser microdissection enriched tumor cell populations from high-grade serous ovarian cancer (HGSOC) tissue specimens spanning a broad spectrum of purity. We identified patients with longer progression-free survival had increased immune-related signatures and validated proteins correlating with tumor-infiltrating lymphocytes in 65 tumors from an independent cohort of HGSOC patients, as well as with overall survival in an additional 126 HGSOC patient cohort. We identified that homologous recombination deficient (HRD) tumors are enriched in pathways associated with metabolism and oxidative phosphorylation that we validated in independent patient cohorts. We further identified that polycomb complex protein BMI-1 is elevated in HR proficient (HRP) tumors, that elevated BMI-1 correlates with poor overall survival in HRP but not HRD HGSOC patients, and that HRP HGSOC cells are uniquely sensitive to BMI-1 inhibition.
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Affiliation(s)
- Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
| | - Tamara Abulez
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Anthony R Soltis
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Andrew McPherson
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Seongmin Choi
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Dale W Garsed
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Ahwan Pandey
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Kelly A Conrads
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Pang-Ning Teng
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Glenn Gist
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Dave Mitchell
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Tracy J Litzi
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Christopher M Tarney
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Barbara A Crothers
- The Joint Pathology Center, Defense Health Agency, National Capital Region Medical Directorate, Silver Spring, MD, USA
| | - Paulette Mhawech-Fauceglia
- Department of Anatomic Pathology, Division of Gynecologic Pathology, University of Southern California, Los Angeles, CA, USA
| | - Clifton L Dalgard
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Matthew D Wilkerson
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Chunhua Yan
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Daoud Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Clara Bodelon
- Division of Cancer Epidemiology and Genetics National Cancer Institute, Rockville, MD, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics National Cancer Institute, Rockville, MD, USA
| | - Jerry S H Lee
- Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, USA
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Sohrab Shah
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Craig D Shriver
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Neil T Phippen
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA.
| | - G Larry Maxwell
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA.
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6
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Sitler CA, Tian C, Hamilton CA, Richardson MT, Chan JK, Kapp DS, Leath CA, Casablanca Y, Washington C, Chappell NP, Klopp AH, Shriver CD, Tarney CM, Bateman NW, Conrads TP, Maxwell GL, Phippen NT, Darcy KM. Immuno-Molecular Targeted Therapy Use and Survival Benefit in Patients with Stage IVB Cervical Carcinoma in Commission on Cancer ®-Accredited Facilities in the United States. Cancers (Basel) 2024; 16:1071. [PMID: 38473428 DOI: 10.3390/cancers16051071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 02/27/2024] [Accepted: 03/03/2024] [Indexed: 03/14/2024] Open
Abstract
PURPOSE To investigate IMT use and survival in real-world stage IVB cervical cancer patients outside randomized clinical trials. METHODS Patients diagnosed with stage IVB cervical cancer during 2013-2019 in the National Cancer Database and treated with chemotherapy (CT) ± external beam radiation (EBRT) ± intracavitary brachytherapy (ICBT) ± IMT were studied. The adjusted hazard ratio (AHR) and 95% confidence interval (CI) for risk of death were estimated in patients treated with vs. without IMT after applying propensity score analysis to balance the clinical covariates. RESULTS There were 3164 evaluable patients, including 969 (31%) who were treated with IMT. The use of IMT increased from 11% in 2013 to 46% in 2019. Age, insurance, facility type, sites of distant metastasis, and type of first-line treatment were independently associated with using IMT. In propensity-score-balanced patients, the median survival was 18.6 vs. 13.1 months for with vs. without IMT (p < 0.001). The AHR was 0.72 (95% CI = 0.64-0.80) for adding IMT overall, 0.72 for IMT + CT, 0.66 for IMT + CT + EBRT, and 0.69 for IMT + CT + EBRT + ICBT. IMT-associated survival improvements were suggested in all subgroups by age, race/ethnicity, comorbidity score, facility type, tumor grade, tumor size, and site of metastasis. CONCLUSIONS IMT was associated with a consistent survival benefit in real-world patients with stage IVB cervical cancer.
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Affiliation(s)
- Collin A Sitler
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Chad A Hamilton
- Gynecologic Oncology Section, Women's Services and The Ochsner Cancer Institute, Ochsner Health, New Orleans, LA 70115, USA
| | - Michael T Richardson
- Department of Obstetrics and Gynecology, Los Angeles School of Medicine, University of California, Los Angeles, CA 90024, USA
| | - John K Chan
- Palo Alto Medical Foundation, California Pacific Medical Center, Sutter Health, San Francisco, CA 94010, USA
| | - Daniel S Kapp
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Charles A Leath
- Division of Gynecologic Oncology, University of Alabama at Birmingham, O'Neal Comprehensive Cancer Center, Birmingham, AL 35249, USA
| | - Yovanni Casablanca
- Gynecologic Oncology Division, Levine Cancer Institute, Atrium Health, Charlotte, NC 28204, USA
| | - Christina Washington
- Gynecologic Oncology Division, Stephenson Cancer Center, Oklahoma University Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Nicole P Chappell
- Gynecologic Oncology Division, GW Medical Faculty Associates, George Washington University, Washington, DC 20037, USA
| | - Ann H Klopp
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Craig D Shriver
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
| | - Christopher M Tarney
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA 22042, USA
| | - George Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA 22042, USA
| | - Neil T Phippen
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
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7
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Kucera CW, Chappell NP, Tian C, Richardson MT, Tarney CM, Hamilton CA, Chan JK, Kapp DS, Leath CA, Casablanca Y, Rojas C, Sitler CA, Wenzel L, Klopp A, Jones NL, Rocconi RP, Farley JH, O'Connor TD, Shriver CD, Bateman NW, Conrads TP, Phippen NT, Maxwell GL, Darcy KM. Survival disparities in non-Hispanic Black and White cervical cancer patients vary by histology and are largely explained by modifiable factors. Gynecol Oncol 2024; 184:224-235. [PMID: 38340648 DOI: 10.1016/j.ygyno.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
PURPOSE We investigated racial disparities in survival by histology in cervical cancer and examined the factors contributing to these disparities. METHODS Non-Hispanic Black and non-Hispanic White (hereafter known as Black and White) patients with stage I-IV cervical carcinoma diagnosed between 2004 and 2017 in the National Cancer Database were studied. Survival differences were compared using Cox modeling to estimate hazard ratio (HR) or adjusted HR (AHR) and 95% confidence interval (CI). The contribution of demographic, socioeconomic and clinical factors to the Black vs White differences in survival was estimated after applying propensity score weighting in patients with squamous cell carcinoma (SCC) or adenocarcinoma (AC). RESULTS This study included 10,111 Black and 43,252 White patients with cervical cancer. Black patients had worse survival than White cervical cancer patients (HR = 1.40, 95% CI = 1.35-1.45). Survival disparities between Black and White patients varied significantly by histology (HR = 1.20, 95% CI = 1.15-1.24 for SCC; HR = 2.32, 95% CI = 2.12-2.54 for AC, interaction p < 0.0001). After balancing the selected demographic, socioeconomic and clinical factors, survival in Black vs. White patients was no longer different in those with SCC (AHR = 1.01, 95% CI 0.97-1.06) or AC (AHR = 1.09, 95% CI = 0.96-1.24). In SCC, the largest contributors to survival disparities were neighborhood income and insurance. In AC, age was the most significant contributor followed by neighborhood income, insurance, and stage. Diagnosis of AC (but not SCC) at ≥65 years old was more common in Black vs. White patients (26% vs. 13%, respectively). CONCLUSIONS Histology matters in survival disparities and diagnosis at ≥65 years old between Black and White cervical cancer patients. These disparities were largely explained by modifiable factors.
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Affiliation(s)
- Calen W Kucera
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Nicole P Chappell
- George Washington Medical Faculty Associates, George Washington Cancer Center, Washington, DC, USA
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Michael T Richardson
- Department of Obstetrics and Gynecology, University of California, Los Angeles School of Medicine, Los Angeles, CA. USA
| | - Christopher M Tarney
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Chad A Hamilton
- Gynecologic Oncology Section, Women's Services and The Ochsner Cancer Institute, Ochsner Health, New Orleans, LA, USA
| | - John K Chan
- Palo Alto Medical Foundation / California Pacific Medical Center /Sutter Health, San Francisco, CA, USA
| | - Daniel S Kapp
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Charles A Leath
- Division of Gynecologic Oncology, University of Alabama at Birmingham, O'Neal Comprehensive Cancer Center, Birmingham, AL, USA
| | - Yovanni Casablanca
- Division of Gynecologic Oncology, Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Christine Rojas
- Division of Gynecologic Oncology, Naval Medical Center Portsmouth, Portsmouth, VA, USA
| | - Collin A Sitler
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Lari Wenzel
- School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Ann Klopp
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nathaniel L Jones
- Division of Gynecologic Oncology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Rodney P Rocconi
- Division of Gynecologic Oncology, Cancer Center & Research Institute, the University of Mississippi Medical Center, Jackson, MS, USA
| | - John H Farley
- Division of Gynecologic Oncology, Center for Women's Health, Cancer Institute, Dignity Health St. Joseph's Hospital and Medical Center, Phoenix, AZ, USA
| | - Timothy D O'Connor
- Institute for Genome Sciences, Department of Medicine and Program in Personalized and Genomic Medicine, and Program in Health Equity and Population Health, University of Maryland School of Medicine, Baltimore, MD, USA; University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Craig D Shriver
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - Neil T Phippen
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - G Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
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8
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Winkler SS, Tian C, Casablanca Y, Bateman NW, Jokajtys S, Kucera CW, Tarney CM, Chan JK, Richardson MT, Kapp DS, Liao CI, Hamilton CA, Leath CA, Reddy M, Cote ML, O'Connor TD, Jones NL, Rocconi RP, Powell MA, Farley J, Shriver CD, Conrads TP, Phippen NT, Maxwell GL, Darcy KM. Racial, ethnic and country of origin disparities in aggressive endometrial cancer histologic subtypes. Gynecol Oncol 2024; 184:31-42. [PMID: 38277919 DOI: 10.1016/j.ygyno.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 01/28/2024]
Abstract
OBJECTIVE This study investigated the risk of an aggressive endometrial cancer (EC) diagnosis by race, ethnicity, and country of origin to further elucidate histologic disparities in non-Hispanic Black (NHB), Hispanic, Asian/Pacific Islander (API), American Indian/Alaskan Native (AIAN) vs. non-Hispanic White (NHW) patients, particularly in Hispanic or API subgroups. METHODS Patient diagnosed between 2004 and 2020 with low grade (LG)-endometrioid endometrial cancer (ECC) or an aggressive EC including grade 3 EEC, serous carcinoma, clear cell carcinoma, mixed epithelial carcinoma, or carcinosarcoma in the National Cancer Database were studied. The odds ratio (OR) and 95% confidence interval (CI) for diagnosis of an aggressive EC histology was estimated using logistic modeling. RESULTS There were 343,868 NHW, 48,897 NHB, 30,013 Hispanic, 15,015 API and 1646 AIAN patients. The OR (95% CI) for an aggressive EC diagnosis was 3.07 (3.01-3.13) for NHB, 1.08 (1.06-1.11) for Hispanic, 1.17 (1.13-1.21) for API and 1.07 (0.96-1.19) for AIAN, relative to NHW patients. Subset analyses by country of origin illustrated the diversity in the OR for an aggressive EC diagnosis among Hispanic (1.18 for Mexican to 1.87 for Dominican), Asian (1.14 Asian Indian-Pakistani to 1.48 Korean) and Pacific Islander (1.00 for Hawaiian to 1.33 for Samoan) descendants. Hispanic, API and AIAN patients were diagnosed 5-years younger that NHW patients, and the risk for an aggressive EC histology were all significantly higher than NHW patients after correcting for age. Insurance status was another independent risk factor for aggressive histology. CONCLUSIONS Risk of an aggressive EC diagnosis varied by race, ethnicity, and country of origin. NHB patients had the highest risk, followed by Dominican, South/Central American, Cuban, Korean, Thai, Vietnamese, and Filipino descendants.
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Affiliation(s)
- Stuart S Winkler
- Division of Gynecologic Oncology, Department of Gynecologic Surgery and Obstetrics, Brooke Army Medical Center, San Antonio, TX, USA
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | - Yovanni Casablanca
- Division of Gynecologic Oncology, Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | - Suzanne Jokajtys
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Calen W Kucera
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Christopher M Tarney
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - John K Chan
- Palo Alto Medical Foundation, California Pacific Medical Center, Sutter Health, San Francisco, CA, USA
| | - Michael T Richardson
- Department of Obstetrics and Gynecology, University of California, Los Angeles School of Medicine, Los Angeles, CA. USA
| | - Daniel S Kapp
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Cheng-I Liao
- Division of Obstetrics and Gynecology, Pingtung Veterans General Hospital, Pingtung, Taiwan
| | - Chad A Hamilton
- Gynecologic Oncology Section, Women's Services and The Ochsner Cancer Institute, Ochsner Health, New Orleans, LA, USA
| | - Charles A Leath
- Division of Gynecologic Oncology, University of Alabama at Birmingham, O'Neal Comprehensive Cancer Center, Birmingham, AL, USA
| | - Megan Reddy
- California Pacific Medical Center, San Francisco, CA, USA
| | - Michele L Cote
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Timothy D O'Connor
- Institute for Genome Sciences, Department of Medicine, Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Nathaniel L Jones
- Division of Gynecologic Oncology, Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Rodney P Rocconi
- Division of Gynecologic Oncology, Cancer Center & Research Institute, The University of Mississippi Medical Center, Jackson, MS, USA
| | - Matthew A Powell
- Division of Gynecologic Oncology, Siteman Cancer Center, Washington University, St Louis, MO, USA
| | - John Farley
- Division of Gynecologic Oncology, Center for Women's Health, Cancer Institute, Dignity Health St. Joseph's Hospital and Medical Center, Phoenix, AZ, USA
| | - Craig D Shriver
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - Neil T Phippen
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - G Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA.
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9
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Hunt AL, Bateman NW, Barakat W, Makohon-Moore SC, Abulez T, Driscoll JA, Schaaf JP, Hood BL, Conrads KA, Zhou M, Calvert V, Pierobon M, Loffredo J, Wilson KN, Litzi TJ, Teng PN, Oliver J, Mitchell D, Gist G, Rojas C, Blanton B, Darcy KM, Rao UNM, Petricoin EF, Phippen NT, Maxwell GL, Conrads TP. Mapping three-dimensional intratumor proteomic heterogeneity in uterine serous carcinoma by multiregion microsampling. Clin Proteomics 2024; 21:4. [PMID: 38254014 PMCID: PMC10804562 DOI: 10.1186/s12014-024-09451-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/14/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Although uterine serous carcinoma (USC) represents a small proportion of all uterine cancer cases, patients with this aggressive subtype typically have high rates of chemotherapy resistance and disease recurrence that collectively result in a disproportionately high death rate. The goal of this study was to provide a deeper view of the tumor microenvironment of this poorly characterized uterine cancer variant through multi-region microsampling and quantitative proteomics. METHODS Tumor epithelium, tumor-involved stroma, and whole "bulk" tissue were harvested by laser microdissection (LMD) from spatially resolved levels from nine USC patient tumor specimens and underwent proteomic analysis by mass spectrometry and reverse phase protein arrays, as well as transcriptomic analysis by RNA-sequencing for one patient's tumor. RESULTS LMD enriched cell subpopulations demonstrated varying degrees of relatedness, indicating substantial intratumor heterogeneity emphasizing the necessity for enrichment of cellular subpopulations prior to molecular analysis. Known prognostic biomarkers were quantified with stable levels in both LMD enriched tumor and stroma, which were shown to be highly variable in bulk tissue. These USC data were further used in a comparative analysis with a data generated from another serous gynecologic malignancy, high grade serous ovarian carcinoma, and have been added to our publicly available data analysis tool, the Heterogeneity Analysis Portal ( https://lmdomics.org/ ). CONCLUSIONS Here we identified extensive three-dimensional heterogeneity within the USC tumor microenvironment, with disease-relevant biomarkers present in both the tumor and the stroma. These data underscore the critical need for upfront enrichment of cellular subpopulations from tissue specimens for spatial proteogenomic analysis.
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Grants
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027, and HU0001-22-2-0016 Defense Health Agency
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Affiliation(s)
- Allison L Hunt
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Rd, Suite 375, Annandale, VA, 22042, USA
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
- Department of Surgery, The John P. Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Waleed Barakat
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Sasha C Makohon-Moore
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Tamara Abulez
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Jordan A Driscoll
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Joshua P Schaaf
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Kelly A Conrads
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Ming Zhou
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Rd, Suite 375, Annandale, VA, 22042, USA
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Valerie Calvert
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Jeremy Loffredo
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Katlin N Wilson
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Tracy J Litzi
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Pang-Ning Teng
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Dave Mitchell
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Glenn Gist
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Christine Rojas
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Brian Blanton
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
- Department of Surgery, The John P. Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Uma N M Rao
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Neil T Phippen
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
- Department of Surgery, The John P. Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - G Larry Maxwell
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Rd, Suite 375, Annandale, VA, 22042, USA
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- Department of Surgery, The John P. Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Thomas P Conrads
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Rd, Suite 375, Annandale, VA, 22042, USA.
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.
- Department of Surgery, The John P. Murtha Cancer Center Research Program, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.
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10
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Buddenkotte T, Rundo L, Woitek R, Escudero Sanchez L, Beer L, Crispin-Ortuzar M, Etmann C, Mukherjee S, Bura V, McCague C, Sahin H, Pintican R, Zerunian M, Allajbeu I, Singh N, Sahdev A, Havrilesky L, Cohn DE, Bateman NW, Conrads TP, Darcy KM, Maxwell GL, Freymann JB, Öktem O, Brenton JD, Sala E, Schönlieb CB. Deep learning-based segmentation of multisite disease in ovarian cancer. Eur Radiol Exp 2023; 7:77. [PMID: 38057616 PMCID: PMC10700248 DOI: 10.1186/s41747-023-00388-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 09/21/2023] [Indexed: 12/08/2023] Open
Abstract
PURPOSE To determine if pelvic/ovarian and omental lesions of ovarian cancer can be reliably segmented on computed tomography (CT) using fully automated deep learning-based methods. METHODS A deep learning model for the two most common disease sites of high-grade serous ovarian cancer lesions (pelvis/ovaries and omentum) was developed and compared against the well-established "no-new-Net" framework and unrevised trainee radiologist segmentations. A total of 451 CT scans collected from four different institutions were used for training (n = 276), evaluation (n = 104) and testing (n = 71) of the methods. The performance was evaluated using the Dice similarity coefficient (DSC) and compared using a Wilcoxon test. RESULTS Our model outperformed no-new-Net for the pelvic/ovarian lesions in cross-validation, on the evaluation and test set by a significant margin (p values being 4 × 10-7, 3 × 10-4, 4 × 10-2, respectively), and for the omental lesions on the evaluation set (p = 1 × 10-3). Our model did not perform significantly differently in segmenting pelvic/ovarian lesions (p = 0.371) compared to a trainee radiologist. On an independent test set, the model achieved a DSC performance of 71 ± 20 (mean ± standard deviation) for pelvic/ovarian and 61 ± 24 for omental lesions. CONCLUSION Automated ovarian cancer segmentation on CT scans using deep neural networks is feasible and achieves performance close to a trainee-level radiologist for pelvic/ovarian lesions. RELEVANCE STATEMENT Automated segmentation of ovarian cancer may be used by clinicians for CT-based volumetric assessments and researchers for building complex analysis pipelines. KEY POINTS • The first automated approach for pelvic/ovarian and omental ovarian cancer lesion segmentation on CT images has been presented. • Automated segmentation of ovarian cancer lesions can be comparable with manual segmentation of trainee radiologists. • Careful hyperparameter tuning can provide models significantly outperforming strong state-of-the-art baselines.
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Affiliation(s)
- Thomas Buddenkotte
- Department, of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Department for Diagnostic and Interventional Radiology and Nuclear Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- jung diagnostics GmbH, Hamburg, Germany
| | - Leonardo Rundo
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
- Department of Information and Electrical Engineering and Applied Mathematics, University of Salerno, Fisciano, Italy
| | - Ramona Woitek
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, Danube Private University, Krems, Austria
| | - Lorena Escudero Sanchez
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | - Lucian Beer
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University Vienna, Vienna, Austria
| | - Mireia Crispin-Ortuzar
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Christian Etmann
- Department, of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - Subhadip Mukherjee
- Department, of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| | - Vlad Bura
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
- Department of Radiology and Medical Imaging, County Clinical Emergency Hospital, Cluj-Napoca-Napoca, Romania
| | - Cathal McCague
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
| | - Hilal Sahin
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
- Department of Radiology, Tepecik Training and Research Hospital, Izmir, Turkey
| | - Roxana Pintican
- Department of Radiology and Medical Imaging, County Clinical Emergency Hospital, Cluj-Napoca-Napoca, Romania
- Department of Radiology, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca-Napoca, Romania
| | - Marta Zerunian
- Department of Medical-Surgical and Translational Medicine-Radiology Unit, Sapienza University of Rome, Sant'Andrea Hospital, Rome, Italy
| | - Iris Allajbeu
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Naveena Singh
- Department of Clinical Pathology, Barts Health NHS Trust, London, UK
| | - Anju Sahdev
- Department of Radiology, Barts Health NHS Trust, London, UK
| | | | - David E Cohn
- Departmant of Obstetrics and Gynecology, Division of Gynecologic Oncology, Ohio State University Comprehensive Cancer Center, Ohio State University College of Medicine, Columbus, OH, USA
| | - Nicholas W Bateman
- Department of Obstetrics and Gynecology, Gynecologic Cancer Center of Excellence, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University, Bethesda, MD, USA
| | - Thomas P Conrads
- Department of Obstetrics and Gynecology, Gynecologic Cancer Center of Excellence, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University, Bethesda, MD, USA
- Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, Falls Church, VA, USA
- Inova Center for Personalized Health, Inova Schar Cancer Institute, Falls Church, VA, USA
| | - Kathleen M Darcy
- Department of Obstetrics and Gynecology, Gynecologic Cancer Center of Excellence, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University, Bethesda, MD, USA
| | - G Larry Maxwell
- Department of Obstetrics and Gynecology, Gynecologic Cancer Center of Excellence, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University, Bethesda, MD, USA
- Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, Falls Church, VA, USA
| | - John B Freymann
- Cancer Imaging Informatics Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ozan Öktem
- Department of Mathematics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - James D Brenton
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Evis Sala
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
- Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, UK.
- Dipartimento Di Scienze Radiologiche Ed Ematologiche, Universita Cattolica del Sacro Cuore, Rome, Italy.
- Dipartimento Diagnostica Per Immagini, Radioterapia Oncologica Ed Ematologia, Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.
| | - Carola-Bibiane Schönlieb
- Department, of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
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11
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McGee JP, Su P, Durbin KR, Hollas MAR, Bateman NW, Maxwell GL, Conrads TP, Fellers RT, Melani RD, Camarillo JM, Kafader JO, Kelleher NL. Author Correction: Automated imaging and identification of proteoforms directly from ovarian cancer tissue. Nat Commun 2023; 14:7946. [PMID: 38040721 PMCID: PMC10692193 DOI: 10.1038/s41467-023-43898-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2023] Open
Affiliation(s)
- John P McGee
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Pei Su
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | | | | | - Nicholas W Bateman
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
- Department of Gynecologic Surgery and Obstetrics and the Gynecologic Cancer Center of Excellence, John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - G Larry Maxwell
- Department of Gynecologic Surgery and Obstetrics and the Gynecologic Cancer Center of Excellence, John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - Thomas P Conrads
- Department of Gynecologic Surgery and Obstetrics and the Gynecologic Cancer Center of Excellence, John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, Falls Church, VA, USA
| | | | - Rafael D Melani
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Jeannie M Camarillo
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jared O Kafader
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Neil L Kelleher
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA.
- Proteomics Center of Excellence, Evanston, IL, USA.
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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12
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Corvigno S, Badal S, Spradlin ML, Keating M, Pereira I, Stur E, Bayraktar E, Foster KI, Bateman NW, Barakat W, Darcy KM, Conrads TP, Maxwell GL, Lorenzi PL, Lutgendorf SK, Wen Y, Zhao L, Thaker PH, Goodheart MJ, Liu J, Fleming N, Lee S, Eberlin LS, Sood AK. In situ profiling reveals metabolic alterations in the tumor microenvironment of ovarian cancer after chemotherapy. NPJ Precis Oncol 2023; 7:115. [PMID: 37923835 PMCID: PMC10624842 DOI: 10.1038/s41698-023-00454-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 09/26/2023] [Indexed: 11/06/2023] Open
Abstract
In this study, we investigated the metabolic alterations associated with clinical response to chemotherapy in patients with ovarian cancer. Pre- and post-neoadjuvant chemotherapy (NACT) tissues from patients with high-grade serous ovarian cancer (HGSC) who had poor response (PR) or excellent response (ER) to NACT were examined. Desorption electrospray ionization mass spectrometry (DESI-MS) was performed on sections of HGSC tissues collected according to a rigorous laparoscopic triage algorithm. Quantitative MS-based proteomics and phosphoproteomics were performed on a subgroup of pre-NACT samples. Highly abundant metabolites in the pre-NACT PR tumors were related to pyrimidine metabolism in the epithelial regions and oxygen-dependent proline hydroxylation of hypoxia-inducible factor alpha in the stromal regions. Metabolites more abundant in the epithelial regions of post-NACT PR tumors were involved in the metabolism of nucleotides, and metabolites more abundant in the stromal regions of post-NACT PR tumors were related to aspartate and asparagine metabolism, phenylalanine and tyrosine metabolism, nucleotide biosynthesis, and the urea cycle. A predictive model built on ions with differential abundances allowed the classification of patients' tumor responses as ER or PR with 75% accuracy (10-fold cross-validation ridge regression model). These findings offer new insights related to differential responses to chemotherapy and could lead to novel actionable targets.
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Grants
- P50 CA217685 NCI NIH HHS
- R01 CA193249 NCI NIH HHS
- R35 CA209904 NCI NIH HHS
- This work was supported, in part, by the MD Anderson Ovarian Cancer Moon Shot, CPRIT (RP180381), SPORE in ovarian cancer (CA217685), CA193249, CA209904, and CA193249-S1 from the National Institutes of Health, the Ovarian Cancer Research Alliance, the American Cancer Society, the Dunwoody Fund, and the Frank McGraw Memorial Chair in Cancer Research, the Foundation for Women’s cancer, Amy Krouse Rosenthal Foundation and Judy’s Mission to End Ovarian Cancer Foundation Research Grant for Early Detection of Ovarian Cancer. We acknowledge the Research Medical Library at MD Anderson Cancer Center for editing the text. For the GYN-COE collection, the collection and banking of these specimens and data were funded by awards HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027 from the Uniformed Services University of the Health Sciences from the Defense Health Program to the Henry M Jackson Foundation (HJF) for the Advancement of Military Medicine Inc. Gynecologic Cancer Center of Excellence Program (PI: Yovanni Casablanca, Co-PI: G. Larry Maxwell
- the Foundation for Women’s cancer, Amy Krouse Rosenthal Foundation and Judy’s Mission to End Ovarian Cancer Foundation Research Grant for Early Detection of Ovarian Cancer
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Affiliation(s)
- Sara Corvigno
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sunil Badal
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | | | - Michael Keating
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Igor Pereira
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Elaine Stur
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Emine Bayraktar
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Katherine I Foster
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Waleed Barakat
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - G Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Susan K Lutgendorf
- Departments of Psychological and Brain Sciences, Obstetrics and Gynecology, and Urology, University of Iowa, Iowa City, IA, USA
| | - Yunfei Wen
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Li Zhao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Premal H Thaker
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Washington University, St. Louis, MO, USA
| | - Michael J Goodheart
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, University of Iowa, Iowa City, IA, USA
| | - Jinsong Liu
- Department of Anatomic Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicole Fleming
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sanghoon Lee
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Livia S Eberlin
- Department of Surgery, Baylor College of Medicine, Houston, TX, USA.
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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13
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Hunt AL, Khan I, Wu AML, Makohon-Moore SC, Hood BL, Conrads KA, Abulez T, Ogata J, Mitchell D, Gist G, Oliver J, Wei D, Chung MA, Rahman S, Bateman NW, Zhang W, Conrads TP, Steeg PS. The murine metastatic microenvironment of experimental brain metastases of breast cancer differs by host age in vivo: a proteomic study. Clin Exp Metastasis 2023:10.1007/s10585-023-10233-7. [PMID: 37917186 DOI: 10.1007/s10585-023-10233-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/07/2023] [Indexed: 11/04/2023]
Abstract
Breast cancer in young patients is known to exhibit more aggressive biological behavior and is associated with a less favorable prognosis than the same disease in older patients, owing in part to an increased incidence of brain metastases. The mechanistic explanations behind these findings remain poorly understood. We recently reported that young mice, in comparison to older mice, developed significantly greater brain metastases in four mouse models of triple-negative and luminal B breast cancer. Here we have performed a quantitative mass spectrometry-based proteomic analysis to identify proteins potentially contributing to age-related disparities in the development of breast cancer brain metastases. Using a mouse hematogenous model of brain-tropic triple-negative breast cancer (MDA-MB-231BR), we harvested subpopulations of tumor metastases, the tumor-adjacent metastatic microenvironment, and uninvolved brain tissues via laser microdissection followed by quantitative proteomic analysis using high resolution mass spectrometry to characterize differentially abundant proteins potentially contributing to age-dependent rates of brain metastasis. Pathway analysis revealed significant alterations in signaling pathways, particularly in the metastatic microenvironment, modulating tumorigenesis, metabolic processes, inflammation, and neuronal signaling. Tenascin C (TNC) was significantly elevated in all laser microdissection (LMD) enriched compartments harvested from young mice relative to older hosts, which was validated and confirmed by immunoblot analysis of whole brain lysates. Additional in vitro studies including migration and wound-healing assays demonstrated TNC as a positive regulator of tumor cell migration. These results provide important new insights regarding microenvironmental factors, including TNC, as mechanisms contributing to the increased brain cancer metastatic phenotype observed in young breast cancer patients.
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Affiliation(s)
- Allison L Hunt
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Rd, Annandale, VA, 22042, USA
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Imran Khan
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Building 37, Room 1126, Bethesda, MD, 20892, USA
| | - Alex M L Wu
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Building 37, Room 1126, Bethesda, MD, 20892, USA
- Zymeworks Inc, Vancouver, BC, V5T 1G4, Canada
| | - Sasha C Makohon-Moore
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Kelly A Conrads
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Tamara Abulez
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Jonathan Ogata
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Dave Mitchell
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Glenn Gist
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
| | - Debbie Wei
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Building 37, Room 1126, Bethesda, MD, 20892, USA
| | - Monika A Chung
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Building 37, Room 1126, Bethesda, MD, 20892, USA
- Rutgers New Jersey Medical School, 185 S Orange Ave, Newark, NJ, 07103, USA
| | - Samiur Rahman
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Building 37, Room 1126, Bethesda, MD, 20892, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, 6720A Rockledge Drive, Suite 100, Bethesda, MD, 20817, USA
- Department of Surgery, The John P. Murtha Cancer Center Research Program, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Wei Zhang
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Building 37, Room 1126, Bethesda, MD, 20892, USA
| | - Thomas P Conrads
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Rd, Annandale, VA, 22042, USA.
- Gynecologic Cancer Center of Excellence and the Women's Health Integrated Research Center, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.
- Department of Surgery, The John P. Murtha Cancer Center Research Program, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.
| | - Patricia S Steeg
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Building 37, Room 1126, Bethesda, MD, 20892, USA.
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14
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McGee JP, Su P, Durbin KR, Hollas MAR, Bateman NW, Maxwell GL, Conrads TP, Fellers RT, Melani RD, Camarillo JM, Kafader JO, Kelleher NL. Automated imaging and identification of proteoforms directly from ovarian cancer tissue. Nat Commun 2023; 14:6478. [PMID: 37838706 PMCID: PMC10576781 DOI: 10.1038/s41467-023-42208-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 09/28/2023] [Indexed: 10/16/2023] Open
Abstract
The molecular identification of tissue proteoforms by top-down mass spectrometry (TDMS) is significantly limited by throughput and dynamic range. We introduce AutoPiMS, a single-ion MS based multiplexed workflow for top-down tandem MS (MS2) directly from tissue microenvironments in a semi-automated manner. AutoPiMS directly off human ovarian cancer sections allowed for MS2 identification of 73 proteoforms up to 54 kDa at a rate of <1 min per proteoform. AutoPiMS is directly interfaced with multifaceted proteoform imaging MS data modalities for the identification of proteoform signatures in tumor and stromal regions in ovarian cancer biopsies. From a total of ~1000 proteoforms detected by region-of-interest label-free quantitation, we discover 303 differential proteoforms in stroma versus tumor from the same patient. 14 of the top proteoform signatures are corroborated by MSI at 20 micron resolution including the differential localization of methylated forms of CRIP1, indicating the importance of proteoform-enabled spatial biology in ovarian cancer.
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Affiliation(s)
- John P McGee
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Pei Su
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | | | | | - Nicholas W Bateman
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
- Department of Gynecologic Surgery and Obstetrics and the Gynecologic Cancer Center of Excellence, John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - G Larry Maxwell
- Department of Gynecologic Surgery and Obstetrics and the Gynecologic Cancer Center of Excellence, John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - Thomas P Conrads
- Department of Gynecologic Surgery and Obstetrics and the Gynecologic Cancer Center of Excellence, John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, Falls Church, VA, USA
| | | | - Rafael D Melani
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Jeannie M Camarillo
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jared O Kafader
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Neil L Kelleher
- Departments of Molecular Biosciences, Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA.
- Proteomics Center of Excellence, Evanston, IL, USA.
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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15
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Teng PN, Barakat W, Tran SM, Tran ZM, Bateman NW, Conrads KA, Wilson KN, Oliver J, Gist G, Hood BL, Zhou M, Maxwell GL, Leggio L, Conrads TP, Lee MR. Brain proteomic atlas of alcohol use disorder in adult males. Transl Psychiatry 2023; 13:318. [PMID: 37833300 PMCID: PMC10575941 DOI: 10.1038/s41398-023-02605-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/16/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Alcohol use disorder (AUD) affects transcriptomic, epigenetic and proteomic expression in several organs, including the brain. There has not been a comprehensive analysis of altered protein abundance focusing on the multiple brain regions that undergo neuroadaptations occurring in AUD. We performed a quantitative proteomic analysis using a liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of human postmortem tissue from brain regions that play key roles in the development and maintenance of AUD, the amygdala (AMG), hippocampus (HIPP), hypothalamus (HYP), nucleus accumbens (NAc), prefrontal cortex (PFC) and ventral tegmental area (VTA). Brain tissues were from adult males with AUD (n = 11) and matched controls (n = 16). Across the two groups, there were >6000 proteins quantified with differential protein abundance in AUD compared to controls in each of the six brain regions. The region with the greatest number of differentially expressed proteins was the AMG, followed by the HYP. Pathways associated with differentially expressed proteins between groups (fold change > 1.5 and LIMMA p < 0.01) were analyzed by Ingenuity Pathway Analysis (IPA). In the AMG, adrenergic, opioid, oxytocin, GABA receptor and cytokine pathways were among the most enriched. In the HYP, dopaminergic signaling pathways were the most enriched. Proteins with differential abundance in AUD highlight potential therapeutic targets such as oxytocin, CSNK1D (PF-670462), GABAB receptor and opioid receptors and may lead to the identification of other potential targets. These results improve our understanding of the molecular alterations of AUD across brain regions that are associated with the development and maintenance of AUD. Proteomic data from this study is publicly available at www.lmdomics.org/AUDBrainProteomeAtlas/ .
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Affiliation(s)
- Pang-Ning Teng
- Women's Health Integrated Research Center, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Waleed Barakat
- Women's Health Integrated Research Center, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Sophie M Tran
- Women's Health Integrated Research Center, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Zoe M Tran
- Women's Health Integrated Research Center, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Nicholas W Bateman
- Women's Health Integrated Research Center, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Kelly A Conrads
- Women's Health Integrated Research Center, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Katlin N Wilson
- Women's Health Integrated Research Center, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Julie Oliver
- Women's Health Integrated Research Center, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Glenn Gist
- Women's Health Integrated Research Center, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Brian L Hood
- Women's Health Integrated Research Center, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Ming Zhou
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - G Larry Maxwell
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - Lorenzo Leggio
- Clinical Psychoneuroendocrinology and Neuropsychopharmacology Section, Translational Addiction Medicine Branch, National Institute on Drug Abuse and National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Baltimore, Bethesda, Maryland, USA
- Medication Development Program, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
- Center for Alcohol and Addiction Studies, Department of Behavioral and Social Sciences, School of Public Health, Brown University, Providence, Rhode Island, USA
- Division of Addiction Medicine, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Neuroscience, Georgetown University Medical Center, Washington, DC, USA
| | - Thomas P Conrads
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA.
| | - Mary R Lee
- Veterans Affairs Medical Center, Washington, DC, USA.
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16
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Ao W, Kim HI, Tommarello D, Conrads KA, Hood BL, Litzi T, Abulez T, Teng PN, Dalgard CL, Zhang X, Wilkerson MD, Darcy KM, Tarney CM, Phippen NT, Bakkenist CJ, Maxwell GL, Conrads TP, Risinger JI, Bateman NW. Metronomic dosing of ovarian cancer cells with the ATR inhibitor AZD6738 leads to loss of CDC25A expression and resistance to ATRi treatment. Gynecol Oncol 2023; 177:60-71. [PMID: 37639904 DOI: 10.1016/j.ygyno.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/07/2023] [Accepted: 08/13/2023] [Indexed: 08/31/2023]
Abstract
OBJECTIVE ATR kinase inhibitors promote cell killing by inducing replication stress and through potentiation of genotoxic agents in gynecologic cancer cells. To explore mechanisms of acquired resistance to ATRi in ovarian cancer, we characterized ATRi-resistant ovarian cancer cells generated by metronomic dosing with the clinical ATR inhibitor AZD6738. METHODS ATRi-resistant ovarian cancer cells (OVCAR3 and OV90) were generated by dosing with AZD6738 and assessed for sensitivity to Chk1i (LY2603618), PARPi (Olaparib) and combination with cisplatin or a CDK4/6 inhibitor (Palbociclib). Models were characterized by diverse methods including silencing CDC25A in OV90 cells and assessing impact on ATRi response. Serum proteomic analysis of ATRi-resistant OV90 xenografts was performed to identify circulating biomarker candidates of ATRi-resistance. RESULTS AZD6738-resistant cell lines are refractory to LY2603618, but not to Olaparib or combinations with cisplatin. Cell cycle analyses showed ATRi-resistant cells exhibit G1/S arrest following AZD6738 treatment. Accordingly, combination with Palbociclib confers resistance to AZD6738. AZD6738-resistant cells exhibit altered abundances of G1/S phase regulatory proteins, including loss of CDC25A in AZD6738-resistant OV90 cells. Silencing of CDC25A in OV90 cells confers resistance to AZD6738. Serum proteomics from AZD6738-resistant OV90 xenografts identified Vitamin D-Binding Protein (GC), Apolipoprotein E (APOE) and A1 (APOA1) as significantly elevated in AZD6738-resistant backgrounds. CONCLUSIONS We show that metronomic dosing of ovarian cancer cells with AZD6738 results in resistance to ATR/ Chk1 inhibitors, that loss of CDC25A expression represents a mechanism of resistance to ATRi treatment in ovarian cancer cells and identify several circulating biomarker candidates of CDC25A low, AZD6738-resistant ovarian cancer cells.
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Affiliation(s)
- Wei Ao
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA
| | - Hong Im Kim
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University Grand Rapids, MI, USA
| | - Domenic Tommarello
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA
| | - Kelly A Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA
| | - Tracy Litzi
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA
| | - Tamara Abulez
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA
| | - Pang-Ning Teng
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA
| | - Clifton L Dalgard
- The American Genome Center, Department of Anatomy Physiology and Genetics, Collaborative Health Initiative Research Program, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Xijun Zhang
- The American Genome Center, Department of Anatomy Physiology and Genetics, Collaborative Health Initiative Research Program, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Matthew D Wilkerson
- The American Genome Center, Department of Anatomy Physiology and Genetics, Collaborative Health Initiative Research Program, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA; The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA
| | - Christopher M Tarney
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA
| | - Neil T Phippen
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA
| | - Christopher J Bakkenist
- Departments of Radiation Biology and Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - G Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, 3300 Gallows Rd. Falls Church, VA 22042, USA
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, 3300 Gallows Rd. Falls Church, VA 22042, USA
| | - John I Risinger
- Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University Grand Rapids, MI, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Bethesda, MD 20817, USA; The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda 20889, MD, USA.
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17
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Hunt AL, Nutcharoen A, Randall J, Papazian A, Deeken J, Maxwell GL, Bateman NW, Petricoin EF, Benyounes A, Conrads TP, Cannon TL. Integration of Multi-omic Data in a Molecular Tumor Board Reveals EGFR-Associated ALK-Inhibitor Resistance in a Patient With Inflammatory Myofibroblastic Cancer. Oncologist 2023:7187076. [PMID: 37255276 PMCID: PMC10400139 DOI: 10.1093/oncolo/oyad129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/14/2023] [Indexed: 06/01/2023] Open
Abstract
Inflammatory myofibroblastic tumors (IMTs) are intermediate-grade mesenchymal neoplasms commonly characterized by chromosomal rearrangements causing constitutive activation of anaplastic lymphoma kinase (ALK) and/or ALK mutations causing reduced sensitivity to ALK tyrosine kinase inhibitors (TKI). We present a patient with an IMT who initially responded to first-line alectinib, but who later suffered disease relapse and presently survives with moderate residual disease after receiving second-line lorlatinib. Biopsy specimens were analyzed using next generation sequencing (DNA-seq and RNA-seq) and reverse phase protein microarray (RPPA) as part of an institutional Molecular Tumor Board (MTB) study. An EML4-ALK rearrangement and EGFR activation (pEGFRY1068) were present in both the primary and recurrent tumors, while a secondary ALK I1171N mutation was exclusive to the latter. EGFR signaling in the background of a secondary ALK mutation is correlated with reduced ALK TKI sensitivity in vitro, implicating an important mechanism of drug resistance development in this patient. The RPPA results also critically demonstrate that ALK signaling (ALKY1604) was not activated in the recurrent tumor, thereby indicating that standard-of-care use of third- or fourth-line ALK TKI would not likely be efficacious or durable. These results underscore the importance of real-time clinical integration of functional protein drug target activation data with NGS in the MTB setting for improving selection of patient-tailored therapy.
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Affiliation(s)
- Allison L Hunt
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Annandale, VA, USA
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | | | - Jamie Randall
- Inova Schar Cancer Institute, Inova Health System, Fairfax, VA, USA
| | - Alyssa Papazian
- Inova Schar Cancer Institute, Inova Health System, Fairfax, VA, USA
| | - John Deeken
- Inova Schar Cancer Institute, Inova Health System, Fairfax, VA, USA
| | - G Larry Maxwell
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Annandale, VA, USA
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University, Bethesda, MD, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
- Theralink Technologies, Inc., Golden, CO, USA
| | - Amin Benyounes
- Inova Schar Cancer Institute, Inova Health System, Fairfax, VA, USA
| | - Thomas P Conrads
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Annandale, VA, USA
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University, Bethesda, MD, USA
| | - Timothy L Cannon
- Inova Schar Cancer Institute, Inova Health System, Fairfax, VA, USA
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18
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Stur E, Peng F, Teng PN, Bayraktar E, Hu M, Corvigno S, Brown DJ, Lee S, Moore KN, Bateman NW, Darcy KM, Maxwell GL, Conrads T, Fleming N, Navin N, Wang L, Sood AK. Abstract 5782: The dynamic immune behavior of primary and metastatic tumors of ovarian cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-5782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Background: Despite advances in cancer diagnosis and therapy, high-grade serous ovarian cancer (HGSC) is often diagnosed when spread to multiple intraperitoneal areas; it is prone to metastasize to adipose-rich tissues such as the omentum. To gain a deeper understanding of the molecular determinants of the HGSC milieu, we carried out a single-cell analysis of primary and metastatic tumors of HGSC. Thus, our aim is to identify molecular mechanisms that lead to immunosuppressive mechanisms of HGSC in primary and metastatic tumors of HGSC.
Methods: Fresh HGSC surgical samples from 19 patients were collected right after surgery, dissociated, and then frozen. For single-cells analysis, cells were sorted by a viability dye and CD45+/- populations followed by Single cell 10 × 3’v3 protocol (10X Genomics) and sequenced using the NovaSeq6000 S2 sequencer. Cell Ranger toolkit v3.1.0 (10x Genomics) was applied for data processing, followed by further downstream analysis using multiple packages from R Package Seurat.
Results: To elucidate the cellular heterogeneity of HGSC, we analyzed 100,480 cells, including epithelial, lymphoid, and myeloid populations; these were identified and represented across all patients. We explored the epithelial compartment further, including a total of 21,144 cells. Given the importance of metastatic lesions for the treatment and outcome of patients with HGSC, we examined expression programs among primary and omentum tumors as well treated and untreated tumors. The major differences between primary and omental metastatic tumors included enrichment of EMT pathways and angiogenesis, as well as a decrease in the IFNα and IFNγ response in the omentum. IFNα and IFNγ response pathways were also upregulated in primary treated (P-NACT) tumors, when compared with primary untreated (P-UT) tumors. To explore the immune compartment, we clustered the immune cells across patients in 28 sub-clusters, including 19 sub-clusters of T-cells and Natural Killer cells. Altogether, the immune infiltration on P-UT indicated an immune infiltrate environment and the composition of P-UT was highly enriched in lymphoid cells with a late stage of differentiation. This finding was also demonstrated by the analysis of T cell trajectories, with a clear definition that CD8 and CD4 cells from P-UT tumors are in a late/final and exhausted stage of differentiation, while post-NACT tumors (independent of tissue type) are in early stages (naïve/central memory). The measurement of a dysfunctional score showed that P-UT tumors have the highest scores, indicating a potential increase in tumor reactivity in P-UT tumors.
Conclusions: Collectively, these data indicate that HGSC primary and omentum tumors are very distinct niches for immune cells, with primary being much more dysfunctional than omentum tissue, which could indicate that the application of immunotherapies would have different impacts in variable niches of HGSC.
Citation Format: Elaine Stur, Fuduan Peng, Pang-ning Teng, Emine Bayraktar, Min Hu, Sara Corvigno, David J. Brown, Sanghoon Lee, Kathleen N. Moore, Nicholas W. Bateman, Kathleen M. Darcy, George L. Maxwell, Thomas Conrads, Nicole Fleming, Nicholas Navin, Linghua Wang, Anil K. Sood. The dynamic immune behavior of primary and metastatic tumors of ovarian cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5782.
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Affiliation(s)
- Elaine Stur
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Fuduan Peng
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Pang-ning Teng
- 2Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Emine Bayraktar
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Min Hu
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Sara Corvigno
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - David J. Brown
- 3Stephenson Cancer Center at the University of Oklahoma Health Sciences Center/Sarah Cannon Research Institute, Oklahoma City, OK
| | - Sanghoon Lee
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Kathleen N. Moore
- 3Stephenson Cancer Center at the University of Oklahoma Health Sciences Center/Sarah Cannon Research Institute, Oklahoma City, OK
| | | | | | | | - Thomas Conrads
- 2Uniformed Services University of the Health Sciences, Bethesda, MD
| | - Nicole Fleming
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Nicholas Navin
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Linghua Wang
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Anil K. Sood
- 1The University of Texas, MD Anderson Cancer Center, Houston, TX
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19
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Kucera CW, Tian C, Tarney CM, Presti C, Jokajtys S, Winkler SS, Casablanca Y, Bateman NW, Mhawech-Fauceglia P, Wenzel L, Hamilton CA, Chan JK, Jones NL, Rocconi RP, O’Connor TD, Farley JH, Shriver CD, Conrads TP, Phippen NT, Maxwell GL, Darcy KM. Factors Associated With Survival Disparities Between Non-Hispanic Black and White Patients With Uterine Cancer. JAMA Netw Open 2023; 6:e238437. [PMID: 37067801 PMCID: PMC10111180 DOI: 10.1001/jamanetworkopen.2023.8437] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/02/2023] [Indexed: 04/18/2023] Open
Abstract
Importance Disparities in survival exist between non-Hispanic Black (hereafter, Black) and non-Hispanic White (hereafter, White) patients with uterine cancer. Objective To investigate factors associated with racial disparities in survival between Black and White patients with uterine cancer. Design, Setting, and Patients This cohort study used data from the National Cancer Database on 274 838 Black and White patients who received a diagnosis of uterine cancer from January 1, 2004, to December 31, 2017, with follow-up through December 2020. Statistical analysis was performed in July 2022. Main Outcomes and Measures Overall survival by self-reported race and evaluation of explanatory study factors associated with hazard ratio (HR) reduction for Black vs White patients. A propensity scoring approach was applied sequentially to balance racial differences in demographic characteristics, comorbidity score, neighborhood income, insurance status, histologic subtype, disease stage, and treatment. Results The study included 32 230 Black female patients (mean [SD] age at diagnosis, 63.8 [10.0] years) and 242 608 White female patients (mean [SD] age at diagnosis, 63.5 [10.5] years) and had a median follow-up of 74.0 months (range, 43.5-113.8 months). Black patients were more likely than White patients to have low income (44.1% vs 14.0%), be uninsured (5.7% vs 2.6%), present with nonendometrioid histologic characteristics (46.1% vs 21.6%), have an advanced disease stage (34.1% vs 19.8%), receive first-line chemotherapy (33.8% vs 18.2%), and have worse 5-year survival (58.6% vs 78.5%). Among patients who received a diagnosis at younger than 65 years of age, the HR for death for Black vs White patients was 2.43 (95% CI, 2.34-2.52) in a baseline demographic-adjusted model and 1.29 (95% CI, 1.23-1.35) after balancing other factors. Comorbidity score, neighborhood income, insurance status, histologic subtype, disease stage, treatment, and unexplained factors accounted for 0.8%, 7.2%, 11.5%, 53.1%, 5.8%, 1.2%, and 20.4%, respectively, of the excess relative risk (ERR) among the younger Black vs White patients. Among patients 65 years or older, the HR for death for Black vs White patients was 1.87 (95% CI, 1.81-1.93) in the baseline model and 1.14 (95% CI, 1.09-1.19) after balancing other factors. Comorbidity score, neighborhood income, insurance status, histologic subtype, disease stage, treatment, and unexplained factors accounted for 3.0%, 7.5%, 0.0%, 56.2%, 10.6%, 6.9%, and 15.8%, respectively, of the ERR among Black vs White patients aged 65 years or older. Conclusions and Relevance This study suggests that histologic subtype was the dominant factor associated with racial survival disparity among patients with uterine cancer, while insurance status represented the main modifiable factor for women younger than 65 years. Additional studies of interactions between biology and social determinants of health are merited.
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Affiliation(s)
- Calen W. Kucera
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, Maryland
| | - Christopher M. Tarney
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Cassandra Presti
- Department of Obstetrics and Gynecology, Inova Fairfax Hospital, Falls Church, Virginia
| | - Suzanne Jokajtys
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Stuart S. Winkler
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Yovanni Casablanca
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, Maryland
| | - Paulette Mhawech-Fauceglia
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- Aurora Diagnostics, LMC Pathology Services, Las Vegas, Nevada
| | - Lari Wenzel
- Department of Medicine, School of Medicine, University of California, Irvine
- Department of Public Health, School of Medicine, University of California, Irvine
| | - Chad A. Hamilton
- Gynecologic Oncology Section, Women’s Services and The Ochsner Cancer Institute, Ochsner Health, New Orleans, Louisiana
| | - John K. Chan
- Gynecologic Oncology Division, Palo Alto Medical Foundation/California Pacific Medical Center/Sutter Health, San Francisco
| | - Nathaniel L. Jones
- Division of Gynecologic Oncology, the Mitchell Cancer Institute, University of South Alabama, Mobile
| | - Rodney P. Rocconi
- Division of Gynecologic Oncology, the University of Alabama at Birmingham, Infirmary Cancer Care, Infirmary Health, Mobile
| | - Timothy D. O’Connor
- Institute for Genome Sciences, Department of Medicine, Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore
- Program in Health Equity and Population Health, University of Maryland School of Medicine, Baltimore
- The University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore
| | - John H. Farley
- Division of Gynecologic Oncology, Dignity Health Cancer Institute, Dignity Health St Joseph’s Hospital and Medical Center, Phoenix, Arizona
| | - Craig D. Shriver
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Thomas P. Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- Women’s Health Integrated Research Center, Inova Women’s Service Line, Inova Health System, Falls Church, Virginia
| | - Neil T. Phippen
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
| | - G. Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- Women’s Health Integrated Research Center, Inova Women’s Service Line, Inova Health System, Falls Church, Virginia
| | - Kathleen M. Darcy
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, Maryland
- The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, Maryland
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20
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Burdett NL, Willis MO, Alsop K, Hunt AL, Pandey A, Hamilton PT, Abulez T, Liu X, Hoang T, Craig S, Fereday S, Hendley J, Garsed DW, Milne K, Kalaria S, Marshall A, Hood BL, Wilson KN, Conrads KA, Pishas KI, Ananda S, Scott CL, Antill Y, McNally O, Mileshkin L, Hamilton A, Au-Yeung G, Devereux L, Thorne H, Bild A, Bateman NW, Maxwell GL, Chang JT, Conrads TP, Nelson BH, Bowtell DDL, Christie EL. Multiomic analysis of homologous recombination-deficient end-stage high-grade serous ovarian cancer. Nat Genet 2023; 55:437-450. [PMID: 36849657 DOI: 10.1038/s41588-023-01320-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/26/2023] [Indexed: 03/01/2023]
Abstract
High-grade serous ovarian cancer (HGSC) is frequently characterized by homologous recombination (HR) DNA repair deficiency and, while most such tumors are sensitive to initial treatment, acquired resistance is common. We undertook a multiomics approach to interrogate molecular diversity in end-stage disease, using multiple autopsy samples collected from 15 women with HR-deficient HGSC. Patients had polyclonal disease, and several resistance mechanisms were identified within most patients, including reversion mutations and HR restoration by other means. We also observed frequent whole-genome duplication and global changes in immune composition with evidence of immune escape. This analysis highlights diverse evolutionary changes within HGSC that evade therapy and ultimately overwhelm individual patients.
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Affiliation(s)
- Nikki L Burdett
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Department of Medical Oncology, Eastern Health, Box Hill, Victoria, Australia
| | | | - Kathryn Alsop
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Allison L Hunt
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, Annandale, Victoria, USA
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Ahwan Pandey
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Tamara Abulez
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Xuan Liu
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center, Houston, TX, USA
| | - Therese Hoang
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Stuart Craig
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sian Fereday
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Joy Hendley
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Dale W Garsed
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Katy Milne
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Shreena Kalaria
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Ashley Marshall
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Katlin N Wilson
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Kelly A Conrads
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Kathleen I Pishas
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Sumitra Ananda
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Medical Oncology, Western Health, St Albans, Victoria, Australia
- Department of Medicine, Western Health, The University of Melbourne, St Albans, Victoria, Australia
- Epworth Healthcare, East Melbourne, Victoria, Australia
| | - Clare L Scott
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Yoland Antill
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
- Cabrini Health, Malvern, Victoria, Australia
- Department of Medical Oncology, Peninsula health, Frankston, Victoria, Australia
| | - Orla McNally
- The Royal Women's Hospital, Parkville, Victoria, Australia
- Department of Obstetrics and Gynaecology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Linda Mileshkin
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Anne Hamilton
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- The Royal Women's Hospital, Parkville, Victoria, Australia
| | - George Au-Yeung
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Lisa Devereux
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Heather Thorne
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrea Bild
- Department of Medical Oncology and Therapeutics, City of Hope Comprehensive Cancer Center, Monrovia, CA, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University, Bethesda, MD, USA
| | - G Larry Maxwell
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, Annandale, Victoria, USA
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University, Bethesda, MD, USA
| | - Jeffrey T Chang
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center, Houston, TX, USA
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University, Bethesda, MD, USA
| | - Brad H Nelson
- Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Elizabeth L Christie
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.
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21
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Wong KK, Bateman NW, Ng CW, Tsang YTM, Sun CS, Celestino J, Nguyen TV, Malpica A, Hillman RT, Zhang J, Futreal PA, Rojas C, Conrads KA, Hood BL, Dalgard CL, Wilkerson MD, Phippen NT, Conrads TP, Maxwell GL, Sood AK, Gershenson DM. Integrated multi-omic analysis of low-grade ovarian serous carcinoma collected from short and long-term survivors. J Transl Med 2022; 20:606. [PMID: 36528667 PMCID: PMC9758924 DOI: 10.1186/s12967-022-03820-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Low-grade serous ovarian cancer (LGSOC) is a rare disease that occurs more frequently in younger women than those with high-grade disease. The current treatment is suboptimal and a better understanding of the molecular pathogenesis of this disease is required. In this study, we compared the proteogenomic analyses of LGSOCs from short- and long-term survivors (defined as < 40 and > 60 months, respectively). Our goal was to identify novel mutations, proteins, and mRNA transcripts that are dysregulated in LGSOC, particularly in short-term survivors. METHODS Initially, targeted sequencing of 409 cancer-related genes was performed on 22 LGSOC and 6 serous borderline ovarian tumor samples. Subsequently, whole-genome sequencing analysis was performed on 14 LGSOC samples (7 long-term survivors and 7 short-term survivors) with matched normal tissue samples. RNA sequencing (RNA-seq), quantitative proteomics, and phosphoproteomic analyses were also performed. RESULTS We identified single-nucleotide variants (SNVs) (range: 5688-14,833 per sample), insertion and deletion variants (indels) (range: 880-1065), and regions with copy number variants (CNVs) (range: 62-335) among the 14 LGSOC samples. Among all SNVs and indels, 2637 mutation sites were found in the exonic regions. The allele frequencies of the detected variants were low (median12%). The identified recurrent nonsynonymous missense mutations included KRAS, NRAS, EIF1AX, UBR5, and DNM3 mutations. Mutations in DNM3 and UBR5 have not previously been reported in LGSOC. For the two samples, somatic DNM3 nonsynonymous missense mutations in the exonic region were validated using Sanger sequencing. The third sample contained two missense mutations in the intronic region of DNM3, leading to a frameshift mutation detected in RNA transcripts in the RNA-seq data. Among the 14 LGSOC samples, 7754 proteins and 9733 phosphosites were detected by global proteomic analysis. Some of these proteins and signaling pathways, such as BST1, TBXAS1, MPEG1, HBA1, and phosphorylated ASAP1, are potential therapeutic targets. CONCLUSIONS This is the first study to use whole-genome sequencing to detect somatic mutations in LGSOCs with matched normal tissues. We detected and validated novel mutations in DNM3, which were present in 3 of the 14 samples analyzed. Additionally, we identified novel indels, regions with CNVs, dysregulated mRNA, dysregulated proteins, and phosphosites that are more prevalent in short-term survivors. This integrated proteogenomic analysis can guide research into the pathogenesis and treatment of LGSOC.
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Affiliation(s)
- Kwong-Kwok Wong
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Nicholas W. Bateman
- grid.414467.40000 0001 0560 6544Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD USA ,grid.201075.10000 0004 0614 9826Henry M. Jackson Foundation for Advancement of Military Medicine, Inc., Bethesda, MD USA
| | - Chun Wai Ng
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Yvonne T. M. Tsang
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Charlotte S. Sun
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Joseph Celestino
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Tri V. Nguyen
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Anais Malpica
- grid.240145.60000 0001 2291 4776Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - R. Tyler Hillman
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - Jianhua Zhang
- grid.240145.60000 0001 2291 4776Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - P. Andrew Futreal
- grid.240145.60000 0001 2291 4776Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Christine Rojas
- grid.414467.40000 0001 0560 6544Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD USA
| | - Kelly A. Conrads
- grid.414467.40000 0001 0560 6544Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD USA ,grid.201075.10000 0004 0614 9826Henry M. Jackson Foundation for Advancement of Military Medicine, Inc., Bethesda, MD USA
| | - Brian L. Hood
- grid.414467.40000 0001 0560 6544Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD USA ,grid.201075.10000 0004 0614 9826Henry M. Jackson Foundation for Advancement of Military Medicine, Inc., Bethesda, MD USA
| | - Clifton L. Dalgard
- grid.265436.00000 0001 0421 5525Department of Anatomy, Physiology and Genetics and Center for Military Precision Health, Uniformed Services University of the Health Sciences, Bethesda, MD USA
| | - Matthew D. Wilkerson
- grid.265436.00000 0001 0421 5525Department of Anatomy, Physiology and Genetics and Center for Military Precision Health, Uniformed Services University of the Health Sciences, Bethesda, MD USA
| | - Neil T. Phippen
- grid.414467.40000 0001 0560 6544Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD USA
| | - Thomas P. Conrads
- grid.414629.c0000 0004 0401 0871Women’s Health Integrated Research Center at Inova Health System, Women’s Service Line, Inova Fairfax Medical Campus, Falls Church, VA USA ,grid.414467.40000 0001 0560 6544Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD USA
| | - George L. Maxwell
- grid.414629.c0000 0004 0401 0871Women’s Health Integrated Research Center at Inova Health System, Women’s Service Line, Inova Fairfax Medical Campus, Falls Church, VA USA ,grid.414467.40000 0001 0560 6544Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD USA
| | - Anil K. Sood
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
| | - David M. Gershenson
- grid.240145.60000 0001 2291 4776Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Room T4-3900, Clinical Research Building, 1515 Holcombe Boulevard, Houston, TX 77030 USA
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22
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Garsed DW, Pandey A, Fereday S, Kennedy CJ, Takahashi K, Alsop K, Hamilton PT, Hendley J, Chiew YE, Traficante N, Provan P, Ariyaratne D, Au-Yeung G, Bateman NW, Bowes L, Brand A, Christie EL, Cunningham JM, Friedlander M, Grout B, Harnett P, Hung J, McCauley B, McNally O, Piskorz AM, Saner FAM, Vierkant RA, Wang C, Winham SJ, Pharoah PDP, Brenton JD, Conrads TP, Maxwell GL, Ramus SJ, Pearce CL, Pike MC, Nelson BH, Goode EL, DeFazio A, Bowtell DDL. The genomic and immune landscape of long-term survivors of high-grade serous ovarian cancer. Nat Genet 2022; 54:1853-1864. [PMID: 36456881 PMCID: PMC10478425 DOI: 10.1038/s41588-022-01230-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 10/17/2022] [Indexed: 12/03/2022]
Abstract
Fewer than half of all patients with advanced-stage high-grade serous ovarian cancers (HGSCs) survive more than five years after diagnosis, but those who have an exceptionally long survival could provide insights into tumor biology and therapeutic approaches. We analyzed 60 patients with advanced-stage HGSC who survived more than 10 years after diagnosis using whole-genome sequencing, transcriptome and methylome profiling of their primary tumor samples, comparing this data to 66 short- or moderate-term survivors. Tumors of long-term survivors were more likely to have multiple alterations in genes associated with DNA repair and more frequent somatic variants resulting in an increased predicted neoantigen load. Patients clustered into survival groups based on genomic and immune cell signatures, including three subsets of patients with BRCA1 alterations with distinctly different outcomes. Specific combinations of germline and somatic gene alterations, tumor cell phenotypes and differential immune responses appear to contribute to long-term survival in HGSC.
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Affiliation(s)
- Dale W Garsed
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.
| | - Ahwan Pandey
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sian Fereday
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Catherine J Kennedy
- The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
| | - Kazuaki Takahashi
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo, Japan
| | - Kathryn Alsop
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Phineas T Hamilton
- The Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - Joy Hendley
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Yoke-Eng Chiew
- The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
| | - Nadia Traficante
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Pamela Provan
- The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
| | | | - George Au-Yeung
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Nicholas W Bateman
- Women's Health Integrated Research Center, Gynecologic Cancer Center of Excellence, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Leanne Bowes
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- The Royal Women's Hospital, Parkville, Victoria, Australia
| | - Alison Brand
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
| | - Elizabeth L Christie
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Michael Friedlander
- Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Paul Harnett
- The University of Sydney, Sydney, New South Wales, Australia
- Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia
| | - Jillian Hung
- The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
| | - Bryan McCauley
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Orla McNally
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- The Royal Women's Hospital, Parkville, Victoria, Australia
- Department of Obstetrics and Gynaecology, The University of Melbourne, Parkville, Victoria, Australia
| | - Anna M Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Flurina A M Saner
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Obstetrics and Gynecology, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Robert A Vierkant
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Chen Wang
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Stacey J Winham
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Thomas P Conrads
- Women's Health Integrated Research Center, Gynecologic Cancer Center of Excellence, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - George L Maxwell
- Women's Health Integrated Research Center, Gynecologic Cancer Center of Excellence, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - Susan J Ramus
- School of Clinical Medicine, Faculty of Medicine and Health, University of NSW, Sydney, New South Wales, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, University of NSW, Sydney, New South Wales, Australia
| | - Celeste Leigh Pearce
- Department of Epidemiology and Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Malcolm C Pike
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brad H Nelson
- The Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Ellen L Goode
- Division of Epidemology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Anna DeFazio
- The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- The University of Sydney, Sydney, New South Wales, Australia
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, New South Wales, Australia
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.
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23
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Penick ER, Bateman NW, Rojas C, Magana C, Conrads K, Zhou M, Hood BL, Wang G, Parikh N, Huang Y, Darcy KM, Casablanca Y, Mhawech-Fauceglia P, Conrads TP, Maxwell GL. Proteomic alterations associated with residual disease in neoadjuvant chemotherapy treated ovarian cancer tissues. Clin Proteomics 2022; 19:35. [PMID: 36195845 PMCID: PMC9531351 DOI: 10.1186/s12014-022-09372-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Optimal cytoreduction to no residual disease (R0) correlates with improved disease outcome for high-grade serous ovarian cancer (HGSOC) patients. Treatment of HGSOC patients with neoadjuvant chemotherapy, however, may select for tumor cells harboring alterations in hallmark cancer pathways including metastatic potential. This study assessed this hypothesis by performing proteomic analysis of matched, chemotherapy naïve and neoadjuvant chemotherapy (NACT)-treated HGSOC tumors obtained from patients who had suboptimal (R1, n = 6) versus optimal (R0, n = 14) debulking at interval debulking surgery (IDS). METHODS Tumor epithelium was harvested by laser microdissection from formalin-fixed, paraffin-embedded tissues from matched, pre- and post-NACT treated tumors for twenty HGSOC patients and analyzed by quantitative mass spectrometry-based proteomics. RESULTS Differential analysis of patient matched pre- and post-NACT treated tumors revealed proteins associated with cell survival and metabolic signaling to be significantly altered in post-NACT treated tumor cells. Comparison of pre-NACT treated tumors from suboptimal (R1) versus optimally (R0) debulked patients identified proteins associated with tumor cell viability and invasion signaling enriched in R1 patients. We identified five proteins altered between R1 and R0 patients in pre- NACT treated tumors that significantly correlated with PFS in an independent cohort of HGSOC patients, including Fermitin family homolog 2 (FERMT2), a protein elevated in R1 that correlated with disease progression in HGSOC patients (multivariate Cox HR = 1.65, Wald p = 0.022) and increased metastatic potential in solid-tumor malignancies. CONCLUSIONS This study identified distinct proteome profiles in patient matched pre- and post-NACT HGSOC tumors that correlate with NACT resistance and that may predict residual disease status at IDS that collectively warrant further pre-clinical investigation.
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Affiliation(s)
- Emily R Penick
- Women's Health Integrated Research Center, Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Nicholas W Bateman
- Women's Health Integrated Research Center, Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.,Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD, 20817, USA
| | - Christine Rojas
- Women's Health Integrated Research Center, Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Cuauhtemoc Magana
- Department of Anatomic Pathology, Division of Gynecologic Pathology, University of Southern California, Los Angeles, CA, 9007, USA
| | - Kelly Conrads
- Women's Health Integrated Research Center, Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD, 20817, USA
| | - Ming Zhou
- Women's Health Integrated Research Center, Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.,Women's Health Integrated Research Center, Women's Service Line, Inova Health System, 3289 Woodburn Rd, Falls Church, VA, 22003, USA
| | - Brian L Hood
- Women's Health Integrated Research Center, Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD, 20817, USA
| | - Guisong Wang
- Women's Health Integrated Research Center, Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD, 20817, USA
| | - Niyati Parikh
- Women's Health Integrated Research Center, Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD, 20817, USA
| | - Ying Huang
- Women's Health Integrated Research Center, Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD, 20817, USA
| | - Kathleen M Darcy
- Women's Health Integrated Research Center, Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.,Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD, 20817, USA
| | - Yovanni Casablanca
- Women's Health Integrated Research Center, Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA.,Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Paulette Mhawech-Fauceglia
- Department of Anatomic Pathology, Division of Gynecologic Pathology, University of Southern California, Los Angeles, CA, 9007, USA
| | - Thomas P Conrads
- Women's Health Integrated Research Center, Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA. .,Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA. .,Women's Health Integrated Research Center, Women's Service Line, Inova Health System, 3289 Woodburn Rd, Falls Church, VA, 22003, USA.
| | - G Larry Maxwell
- Women's Health Integrated Research Center, Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA. .,Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA. .,Women's Health Integrated Research Center, Women's Service Line, Inova Health System, 3289 Woodburn Rd, Falls Church, VA, 22003, USA.
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Handley KF, Sims TT, Bateman NW, Glassman D, Foster KI, Lee S, Yao J, Yao H, Fellman BM, Liu J, Lu Z, Conrads KA, Hood BL, Barakat W, Zhao L, Zhang J, Westin SN, Celestino J, Rangel KM, Badal S, Pereira I, Ram PT, Maxwell GL, Eberlin LS, Futreal PA, Bast RC, Fleming ND, Conrads TP, Sood AK. Classification of High-Grade Serous Ovarian Cancer Using Tumor Morphologic Characteristics. JAMA Netw Open 2022; 5:e2236626. [PMID: 36239936 PMCID: PMC9568802 DOI: 10.1001/jamanetworkopen.2022.36626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
IMPORTANCE Despite similar histologic appearance among high-grade serous ovarian cancers (HGSOCs), clinical observations suggest vast differences in gross appearance. There is currently no systematic framework by which to classify HGSOCs according to their gross morphologic characteristics. OBJECTIVE To develop and characterize a gross morphologic classification system for HGSOC. DESIGN, SETTING, AND PARTICIPANTS This cohort study included patients with suspected advanced-stage ovarian cancer who presented between April 1, 2013, and August 5, 2016, to the University of Texas MD Anderson Cancer Center, a large referral center. Patients underwent laparoscopic assessment of disease burden before treatment and received a histopathologic diagnosis of HGSOC. Researchers assigning morphologic subtype and performing molecular analyses were blinded to clinical outcomes. Data analysis was performed between April 2020 and November 2021. EXPOSURES Gross tumor morphologic characteristics. MAIN OUTCOMES AND MEASURES Clinical outcomes and multiomic profiles of representative tumor samples of type I or type II morphologic subtypes were compared. RESULTS Of 112 women (mean [SD] age 62.7 [9.7] years) included in the study, most patients (84% [94]) exhibited a predominant morphologic subtype and many (63% [71]) had a uniform morphologic subtype at all involved sites. Compared with those with uniform type I morphologic subtype, patients with uniform type II morphologic subtype were more likely to have a favorable Fagotti score (83% [19 of 23] vs 46% [22 of 48]; P = .004) and thus to be triaged to primary tumor reductive surgery. Similarly, patients with uniform type II morphologic subtype also had significantly higher mean (SD) estimated blood loss (639 [559; 95% CI, 391-887] mL vs 415 [527; 95% CI, 253-577] mL; P = .006) and longer mean (SD) operative time (408 [130; 95% CI, 350-466] minutes vs 333 [113; 95% CI, 298-367] minutes; P = .03) during tumor reductive surgery. Type I tumors had enrichment of epithelial-mesenchymal transition (false discovery rate [FDR] q-value, 3.10 × 10-24), hypoxia (FDR q-value, 1.52 × 10-5), and angiogenesis pathways (FDR q-value, 2.11 × 10-2), whereas type II tumors had enrichment of pathways related to MYC signaling (FDR q-value, 2.04 × 10-9) and cell cycle progression (FDR q-value, 1.10 × 10-5) by integrated proteomic and transcriptomic analysis. Abundances of metabolites and lipids also differed between the 2 morphologic subtypes. CONCLUSIONS AND RELEVANCE This study identified 2 novel, gross morphologic subtypes of HGSOC, each with unique clinical features and molecular signatures. The findings may have implications for triaging patients to surgery or chemotherapy, identifying outcomes, and developing tailored therapeutic strategies.
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Affiliation(s)
- Katelyn F. Handley
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Morsani College of Medicine, University of South Florida, Tampa
- Department of Gynecologic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Travis T. Sims
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Nicholas W. Bateman
- Women’s Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Health System, Falls Church, Virginia
- Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Deanna Glassman
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Katherine I. Foster
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Sanghoon Lee
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston
| | - Jun Yao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston
| | - Bryan M. Fellman
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston
| | - Jinsong Liu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston
| | - Zhen Lu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston
| | - Kelly A. Conrads
- Women’s Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Health System, Falls Church, Virginia
- Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Brian L. Hood
- Women’s Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Health System, Falls Church, Virginia
- Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Waleed Barakat
- Women’s Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Health System, Falls Church, Virginia
- Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Li Zhao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Shannon N. Westin
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Joseph Celestino
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Kelly M. Rangel
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston
| | - Sunil Badal
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Igor Pereira
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Prahlad T. Ram
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston
| | - George L. Maxwell
- Women’s Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Health System, Falls Church, Virginia
- Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Livia S. Eberlin
- Department of Surgery, Baylor College of Medicine, Houston, Texas
| | - P. Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Robert C. Bast
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston
| | - Nicole D. Fleming
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston
| | - Thomas P. Conrads
- Women’s Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Health System, Falls Church, Virginia
- Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Anil K. Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston
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Casablanca Y, Wang G, Lankes HA, Tian C, Bateman NW, Miller CR, Chappell NP, Havrilesky LJ, Wallace AH, Ramirez NC, Miller DS, Oliver J, Mitchell D, Litzi T, Blanton BE, Lowery WJ, Risinger JI, Hamilton CA, Phippen NT, Conrads TP, Mutch D, Moxley K, Lee RB, Backes F, Birrer MJ, Darcy KM, Maxwell GL. Improving Risk Assessment for Metastatic Disease in Endometrioid Endometrial Cancer Patients Using Molecular and Clinical Features: An NRG Oncology/Gynecologic Oncology Group Study. Cancers (Basel) 2022; 14:cancers14174070. [PMID: 36077609 PMCID: PMC9454742 DOI: 10.3390/cancers14174070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/29/2022] [Accepted: 08/11/2022] [Indexed: 12/31/2022] Open
Abstract
Objectives: A risk assessment model for metastasis in endometrioid endometrial cancer (EEC) was developed using molecular and clinical features, and prognostic association was examined. Methods: Patients had stage I, IIIC, or IV EEC with tumor-derived RNA-sequencing or microarray-based data. Metastasis-associated transcripts and platform-centric diagnostic algorithms were selected and evaluated using regression modeling and receiver operating characteristic curves. Results: Seven metastasis-associated transcripts were selected from analysis in the training cohorts using 10-fold cross validation and incorporated into an MS7 classifier using platform-specific coefficients. The predictive accuracy of the MS7 classifier in Training-1 was superior to that of other clinical and molecular features, with an area under the curve (95% confidence interval) of 0.89 (0.80-0.98) for MS7 compared with 0.69 (0.59-0.80) and 0.71 (0.58-0.83) for the top evaluated clinical and molecular features, respectively. The performance of MS7 was independently validated in 245 patients using RNA sequencing and in 81 patients using microarray-based data. MS7 + MI (myometrial invasion) was preferrable to individual features and exhibited 100% sensitivity and negative predictive value. The MS7 classifier was associated with lower progression-free and overall survival (p ≤ 0.003). Conclusion: A risk assessment classifier for metastasis and prognosis in EEC patients with primary tumor derived MS7 + MI is available for further development and optimization as a companion clinical support tool.
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Affiliation(s)
- Yovanni Casablanca
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
| | - Guisong Wang
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Heather A. Lankes
- Gynecologic Oncology Group Statistical and Data Management Center, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Caela R. Miller
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
| | - Nicole P. Chappell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
| | | | - Amy Hooks Wallace
- Division of Gynecologic Oncology, Duke University, Durham, NC 27710, USA
| | - Nilsa C. Ramirez
- Gynecologic Oncology Group Tissue Bank, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - David S. Miller
- Division of Gynecologic Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Dave Mitchell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Tracy Litzi
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - Brian E. Blanton
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
| | - William J. Lowery
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
| | - John I. Risinger
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, 333 Bostwick Ave., NE, Grand Rapids, MI 49503, USA
| | - Chad A. Hamilton
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- Women’s Health Integrated Research Center, Women’s Service Line, Inova Health System, Falls Church, VA 22042, USA
| | - Neil T. Phippen
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- Women’s Health Integrated Research Center, Women’s Service Line, Inova Health System, Falls Church, VA 22042, USA
| | - Thomas P. Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- Women’s Health Integrated Research Center, Women’s Service Line, Inova Health System, Falls Church, VA 22042, USA
| | - David Mutch
- Division of Gynecologic Oncology, Washington University, St. Louis, MO 63110, USA
| | - Katherine Moxley
- Department of OB/GYN, Section of Gyn Oncology, University of Oklahoma University Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Roger B. Lee
- Department of GYN/ONC, Tacoma General Hospital, Tacoma, WA 98405, USA
| | - Floor Backes
- Division of Gynecologic Oncology, Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Michael J. Birrer
- P. Rockefeller Cancer Institute, Women’s Gynecologic Cancer Clinic, Little Rock, AR 72205, USA
| | - Kathleen M. Darcy
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- The Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
- Correspondence: (K.M.D.); (G.L.M.)
| | - George Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD 20889, USA
- Women’s Health Integrated Research Center, Women’s Service Line, Inova Health System, Falls Church, VA 22042, USA
- Correspondence: (K.M.D.); (G.L.M.)
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Nolin AC, Tian C, Hamilton CA, Casablanca Y, Bateman NW, Chan JK, Cote ML, Shriver CD, Powell MA, Phippen NT, Conrads TP, Maxwell GL, Darcy KM. Conditional estimates for uterine serous cancer: Tools for survivorship counseling and planning. Gynecol Oncol 2022; 166:90-99. [PMID: 35624045 DOI: 10.1016/j.ygyno.2022.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/06/2022] [Accepted: 05/14/2022] [Indexed: 11/04/2022]
Abstract
OBJECTIVES Develop conditional survival and risk-assessment estimates for uterine serous carcinoma (USC) overall and stratified by stage as tools for annual survivorship counseling and care planning. METHODS Patients in the National Cancer Data Base diagnosed between 2004 and 2014 with stage I-IV USC were eligible. Individuals missing stage or survival data or with multiple malignancies were excluded. Five-year conditional survival was estimated using the stage-stratified Kaplan-Meier method annually during follow-up. A standardized mortality ratio (SMR) estimated the proportion of observed to expected deaths in the U.S. adjusted for year, age, and race. The relationships between prognostic factors and survival were studied using multivariate Cox modeling at diagnosis and conditioned on surviving 5-years. RESULTS There were 14,575 participants, including 43% with stage I, 8% with stage II, 29% with stage III, and 20% with stage IV USC. Five-year survival at diagnosis vs. after surviving 5-years was 52% vs. 75% overall, 77% vs. 81% for stage I, 57% vs. 72% for stage II, 40% vs. 66% for stage III, and 17% vs. 60% for stage IV USC, respectively (P < 0.0001). Incremental improvements in 5-year conditional survival and reductions in SMR tracked with annual follow-up and higher stage. The adjusted risk of death at diagnosis vs. after surviving 5-years was 1.15 vs. 1.40 per 5-year increase of age, 1.26 vs. 1.68 for Medicaid insurance, 3.92 vs. 2.48 for stage III disease, and 6.65 vs. 2.79 for stage IV disease, respectively (P < 0.0001). CONCLUSION In USC, the evolution of conditional survival permits annual reassessments of prognosis to tailor survivorship counseling and care planning.
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Affiliation(s)
- Angela C Nolin
- Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, Falls Church, VA, USA
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Chad A Hamilton
- Gynecologic Oncology Section, Women's Services and The Ochsner Cancer Institute, Ochsner Health, New Orleans, LA, USA
| | - Yovanni Casablanca
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - John K Chan
- Palo Alto Medical Foundation, California Pacific Medical Center, Sutter Health, San Francisco, CA, USA
| | - Michele L Cote
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Karmanos Cancer Institute, Population Studies, and Disparities Research Program, Detroit, MI, USA
| | - Craig D Shriver
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Matthew A Powell
- Division of Gynecologic Oncology, Siteman Cancer Center, Washington University, St Louis, MO, USA
| | - Neil T Phippen
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - G Larry Maxwell
- Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA; Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA.
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Mitchell D, Hunt AL, Conrads KA, Hood BL, Makohon-Moore SC, Rojas C, Maxwell GL, Bateman NW, Conrads TP. Industrialized, Artificial Intelligence-guided Laser Microdissection for Microscaled Proteomic Analysis of the Tumor Microenvironment. J Vis Exp 2022. [DOI: 10.3791/64171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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28
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Zhu Q, Wang J, Yu H, Hu Q, Bateman NW, Long M, Rosario S, Schultz E, Dalgard CL, Wilkerson MD, Sukumar G, Huang RY, Kaur J, Lele SB, Zsiros E, Villella J, Lugade A, Moysich K, Conrads TP, Maxwell GL, Odunsi K. Whole-Genome Sequencing Identifies PPARGC1A as a Putative Modifier of Cancer Risk in BRCA1/2 Mutation Carriers. Cancers (Basel) 2022; 14:2350. [PMID: 35625955 PMCID: PMC9139302 DOI: 10.3390/cancers14102350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/03/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
While BRCA1 and BRCA2 mutations are known to confer the largest risk of breast cancer and ovarian cancer, the incomplete penetrance of the mutations and the substantial variability in age at cancer onset among carriers suggest additional factors modifying the risk of cancer in BRCA1/2 mutation carriers. To identify genetic modifiers of BRCA1/2, we carried out a whole-genome sequencing study of 66 ovarian cancer patients that were enriched with BRCA carriers, followed by validation using data from the Pan-Cancer Analysis of Whole Genomes Consortium. We found PPARGC1A, a master regulator of mitochondrial biogenesis and function, to be highly mutated in BRCA carriers, and patients with both PPARGC1A and BRCA1/2 mutations were diagnosed with breast or ovarian cancer at significantly younger ages, while the mutation status of each gene alone did not significantly associate with age of onset. Our study suggests PPARGC1A as a possible BRCA modifier gene. Upon further validation, this finding can help improve cancer risk prediction and provide personalized preventive care for BRCA carriers.
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Affiliation(s)
- Qianqian Zhu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Jie Wang
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Han Yu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Qiang Hu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA; (N.W.B.); (T.P.C.); (G.L.M.)
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA;
| | - Mark Long
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Spencer Rosario
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Emily Schultz
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.W.); (H.Y.); (Q.H.); (M.L.); (S.R.); (E.S.)
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA; (C.L.D.); (M.D.W.)
- Department of Anatomy Physiology and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Matthew D. Wilkerson
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA; (C.L.D.); (M.D.W.)
- Department of Anatomy Physiology and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Gauthaman Sukumar
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA;
- Department of Anatomy Physiology and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Ruea-Yea Huang
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (R.-Y.H.); (A.L.)
| | - Jasmine Kaur
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.K.); (S.B.L.); (E.Z.)
| | - Shashikant B. Lele
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.K.); (S.B.L.); (E.Z.)
| | - Emese Zsiros
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.K.); (S.B.L.); (E.Z.)
| | - Jeannine Villella
- Division of Gynecologic Oncology, Lenox Hill Hospital/Northwell Health Cancer Institute, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New York, NY 11549, USA;
| | - Amit Lugade
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (R.-Y.H.); (A.L.)
| | - Kirsten Moysich
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Thomas P. Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA; (N.W.B.); (T.P.C.); (G.L.M.)
- Women’s Health Integrated Research Center, Women’s Service Line, Inova Health System, 3289 Woodburn Rd, Annandale, VA 22003, USA
| | - George L. Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA; (N.W.B.); (T.P.C.); (G.L.M.)
- Women’s Health Integrated Research Center, Women’s Service Line, Inova Health System, 3289 Woodburn Rd, Annandale, VA 22003, USA
| | - Kunle Odunsi
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (R.-Y.H.); (A.L.)
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (J.K.); (S.B.L.); (E.Z.)
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL 60637, USA
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Bateman NW, Tarney CM, Abulez TS, Hood BL, Conrads KA, Zhou M, Soltis AR, Teng PN, Jackson A, Tian C, Dalgard CL, Wilkerson MD, Kessler MD, Goecker Z, Loffredo J, Shriver CD, Hu H, Cote M, Parker GJ, Segars J, Al-Hendy A, Risinger JI, Phippen NT, Casablanca Y, Darcy KM, Maxwell GL, Conrads TP, O'Connor TD. Peptide ancestry informative markers in uterine neoplasms from women of European, African, and Asian ancestry. iScience 2021; 25:103665. [PMID: 35036865 PMCID: PMC8753123 DOI: 10.1016/j.isci.2021.103665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/29/2021] [Accepted: 12/17/2021] [Indexed: 02/07/2023] Open
Abstract
Characterization of ancestry-linked peptide variants in disease-relevant patient tissues represents a foundational step to connect patient ancestry with disease pathogenesis. Nonsynonymous single-nucleotide polymorphisms encoding missense substitutions within tryptic peptides exhibiting high allele frequencies in European, African, and East Asian populations, termed peptide ancestry informative markers (pAIMs), were prioritized from 1000 genomes. In silico analysis identified that as few as 20 pAIMs can determine ancestry proportions similarly to >260K SNPs (R2 = 0.99). Multiplexed proteomic analysis of >100 human endometrial cancer cell lines and uterine leiomyoma tissues combined resulted in the quantitation of 62 pAIMs that correlate with patient race and genotype-confirmed ancestry. Candidates include a D451E substitution in GC vitamin D-binding protein previously associated with altered vitamin D levels in African and European populations. pAIMs will support generalized proteoancestry assessment as well as efforts investigating the impact of ancestry on the human proteome and how this relates to the pathogenesis of uterine neoplasms.
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Affiliation(s)
- Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA,Corresponding author 3289 Woodburn Rd, Suite 375, Annandale, VA 22003;
| | - Christopher M. Tarney
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Tamara S. Abulez
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - Brian L. Hood
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - Kelly A. Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - Ming Zhou
- Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, 3300 Gallows Road, Falls Church, VA 22042, USA
| | - Anthony R. Soltis
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA,The American Genome Center; Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Pang-Ning Teng
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - Amanda Jackson
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - Clifton L. Dalgard
- The American Genome Center; Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA,Department of Anatomy Physiology and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Matthew D. Wilkerson
- The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA,The American Genome Center; Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA,Department of Anatomy Physiology and Genetics, Uniformed Services University, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Michael D. Kessler
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Zachary Goecker
- University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jeremy Loffredo
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Craig D. Shriver
- The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Hai Hu
- The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA
| | | | - Glendon J. Parker
- University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - James Segars
- Johns Hopkins University Medical Center, Baltimore, MD 21218, USA
| | - Ayman Al-Hendy
- The University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - John I. Risinger
- Department of Obstetrics and Gynecology, Michigan State University, East Lansing, MI 48824, USA
| | - Neil T. Phippen
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Yovanni Casablanca
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Kathleen M. Darcy
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Dr., Suite 100, Bethesda, MD 20817, USA
| | - G. Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, 3300 Gallows Road, Falls Church, VA 22042, USA
| | - Thomas P. Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA,Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, 3300 Gallows Road, Falls Church, VA 22042, USA
| | - Timothy D. O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA,Program in Personalize and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA,Marlene and Stewart Greenebaum Comprehensive Cancer, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Cobb LP, Siamakpour-Reihani S, Zhang D, Qin X, Owzar K, Zhou C, Conrads TP, Maxwell GL, Darcy KM, Bateman NW, Litzi T, Bae-Jump V, Secord AA. Obesity and altered angiogenic-related gene expression in endometrial cancer. Gynecol Oncol 2021; 163:320-326. [PMID: 34538531 PMCID: PMC11018267 DOI: 10.1016/j.ygyno.2021.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/12/2021] [Accepted: 08/14/2021] [Indexed: 11/22/2022]
Abstract
OBJECTIVES Evaluate association between obesity and angiogenic-related gene expression in endometrial cancer (EC). Evaluate interaction between diet and metformin on angiogenic-related gene expression. METHODS We evaluated the association between 168 human angiogenic-related genes and body mass index (BMI) in the TCGA Uterine Corpus Endometrial Carcinoma cohort (endometrioid endometrial cancer (EEC) cohort n = 290, and copy number high cohort n = 55), an independent validation cohort from Gynecologic Cancer Center of Excellence (GYN-COE) (n = 62) and corresponding 185 homologous mouse genes in an LKB1fl/flp53fl/fl mouse model of EC (n = 20). Mice received 60% of calories from fat in a high-fat diet (HFD), mimicking diet-induced obesity, versus 10% of calories from fat in a low-fat diet (LFD). After tumor growth, HFD (n = 5) and LFD (n = 5) mice were treated with metformin (200 mg/kg/day) or control. Whole transcriptome analysis of mouse tumors was performed using RNA-Seq. RESULTS At a false-discovery rate of 10%, twenty-one angiogenic-related genes were differentially expressed with respect to BMI when adjusting for grade in the TCGA EEC cohort. Evaluation of these genes in the mouse model control group revealed association between increased Edil3 expression in HFD versus LFD mice (2.5-fold change (FC); unadjusted p = 0.03). An interaction was observed for expression of Edil3 between diet and metformin treatment (unadjusted p = 0.009). Association between BMI and increased expression of EDIL3 was validated in one of four EDIL3 probesets in the GYN-COE cohort (p = 0.0011, adjusted p = 0.0342). CONCLUSIONS Obesity may promote tumor progression via differential modulation of angiogenic pathways in EEC. Our exploratory findings demonstrated that EDIL3 may be a candidate gene of interest.
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Affiliation(s)
- Lauren Patterson Cobb
- Department of Gynecologic Oncology and Reproductive Medicine, MD Anderson Cancer Center, Houston, TX, USA; Division of Gynecology Oncology, Department of Obstetrics and Gynecology, Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.
| | - Sharareh Siamakpour-Reihani
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Duke University Medical Center, USA
| | - Dadong Zhang
- Bioinformatics Shared Resource, Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Xiaodi Qin
- Bioinformatics Shared Resource, Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Kouros Owzar
- Bioinformatics Shared Resource, Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA; Duke Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, USA
| | - Chunxiao Zhou
- Division of Gynecologic Oncology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA
| | - G Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA; Inova Schar Cancer Institute, Inova Center for Personalized Health, Falls Church, VA, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | - Tracy Litzi
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, USA
| | - Victoria Bae-Jump
- Division of Gynecologic Oncology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Angeles Alvarez Secord
- Division of Gynecology Oncology, Department of Obstetrics and Gynecology, Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
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31
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Hunt AL, Bateman NW, Barakat W, Makohon-Moore S, Hood BL, Conrads KA, Zhou M, Calvert V, Pierobon M, Loffredo J, Litzi TJ, Oliver J, Mitchell D, Gist G, Rojas C, Blanton B, Robinson EL, Odunsi K, Sood AK, Casablanca Y, Darcy KM, Shriver CD, Petricoin EF, Rao UN, Maxwell GL, Conrads TP. Extensive three-dimensional intratumor proteomic heterogeneity revealed by multiregion sampling in high-grade serous ovarian tumor specimens. iScience 2021; 24:102757. [PMID: 34278265 PMCID: PMC8264160 DOI: 10.1016/j.isci.2021.102757] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/19/2021] [Accepted: 06/17/2021] [Indexed: 12/15/2022] Open
Abstract
Enriched tumor epithelium, tumor-associated stroma, and whole tissue were collected by laser microdissection from thin sections across spatially separated levels of ten high-grade serous ovarian carcinomas (HGSOCs) and analyzed by mass spectrometry, reverse phase protein arrays, and RNA sequencing. Unsupervised analyses of protein abundance data revealed independent clustering of an enriched stroma and enriched tumor epithelium, with whole tumor tissue clustering driven by overall tumor "purity." Comparing these data to previously defined prognostic HGSOC molecular subtypes revealed protein and transcript expression from tumor epithelium correlated with the differentiated subtype, whereas stromal proteins (and transcripts) correlated with the mesenchymal subtype. Protein and transcript abundance in the tumor epithelium and stroma exhibited decreased correlation in samples collected just hundreds of microns apart. These data reveal substantial tumor microenvironment protein heterogeneity that directly bears on prognostic signatures, biomarker discovery, and cancer pathophysiology and underscore the need to enrich cellular subpopulations for expression profiling.
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Affiliation(s)
- Allison L. Hunt
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Road, Annandale, VA 22042, USA
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Suite 100, Bethesda, MD 20817, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Waleed Barakat
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Suite 100, Bethesda, MD 20817, USA
| | - Sasha Makohon-Moore
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Suite 100, Bethesda, MD 20817, USA
| | - Brian L. Hood
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Suite 100, Bethesda, MD 20817, USA
| | - Kelly A. Conrads
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Suite 100, Bethesda, MD 20817, USA
| | - Ming Zhou
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Road, Annandale, VA 22042, USA
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Valerie Calvert
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Jeremy Loffredo
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Suite 100, Bethesda, MD 20817, USA
| | - Tracy J. Litzi
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Suite 100, Bethesda, MD 20817, USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Suite 100, Bethesda, MD 20817, USA
| | - Dave Mitchell
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Suite 100, Bethesda, MD 20817, USA
| | - Glenn Gist
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Suite 100, Bethesda, MD 20817, USA
| | - Christine Rojas
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Brian Blanton
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Emma L. Robinson
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Road, Annandale, VA 22042, USA
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Kunle Odunsi
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Anil K. Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Yovanni Casablanca
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Suite 100, Bethesda, MD 20817, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Kathleen M. Darcy
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Suite 100, Bethesda, MD 20817, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Craig D. Shriver
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Uma N.M. Rao
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 6720A Rockledge Drive, Suite 100, Bethesda, MD 20817, USA
| | - G. Larry Maxwell
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Road, Annandale, VA 22042, USA
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
| | - Thomas P. Conrads
- Women's Health Integrated Research Center, Inova Women's Service Line, Inova Health System, 3289 Woodburn Road, Annandale, VA 22042, USA
- Gynecologic Cancer Center of Excellence, Department of Gynecologic Surgery and Obstetrics, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD 20889, USA
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Xuan Y, Bateman NW, Gallien S, Goetze S, Zhou Y, Navarro P, Hu M, Parikh N, Hood BL, Conrads KA, Loosse C, Kitata RB, Piersma SR, Chiasserini D, Zhu H, Hou G, Tahir M, Macklin A, Khoo A, Sun X, Crossett B, Sickmann A, Chen YJ, Jimenez CR, Zhou H, Liu S, Larsen MR, Kislinger T, Chen Z, Parker BL, Cordwell SJ, Wollscheid B, Conrads TP. Standardization and harmonization of distributed multi-center proteotype analysis supporting precision medicine studies. Nat Commun 2020; 11:5248. [PMID: 33067419 PMCID: PMC7568553 DOI: 10.1038/s41467-020-18904-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 09/16/2020] [Indexed: 02/02/2023] Open
Abstract
Cancer has no borders: Generation and analysis of molecular data across multiple centers worldwide is necessary to gain statistically significant clinical insights for the benefit of patients. Here we conceived and standardized a proteotype data generation and analysis workflow enabling distributed data generation and evaluated the quantitative data generated across laboratories of the international Cancer Moonshot consortium. Using harmonized mass spectrometry (MS) instrument platforms and standardized data acquisition procedures, we demonstrate robust, sensitive, and reproducible data generation across eleven international sites on seven consecutive days in a 24/7 operation mode. The data presented from the high-resolution MS1-based quantitative data-independent acquisition (HRMS1-DIA) workflow shows that coordinated proteotype data acquisition is feasible from clinical specimens using such standardized strategies. This work paves the way for the distributed multi-omic digitization of large clinical specimen cohorts across multiple sites as a prerequisite for turning molecular precision medicine into reality.
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Affiliation(s)
- Yue Xuan
- Thermo Fisher Scientific GmbH, Hanna-Kunath Str. 11, Bremen, 28199, Germany.
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, 20889, MD, USA
| | - Sebastien Gallien
- Thermo Fisher Scientific, Paris, France.,Thermo Fisher Scientific, Precision Medicine Science Center, Cambridge, MA, USA
| | - Sandra Goetze
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Yue Zhou
- Thermo Fisher Scientific Co. Ltd, Shanghai, China
| | - Pedro Navarro
- Thermo Fisher Scientific GmbH, Hanna-Kunath Str. 11, Bremen, 28199, Germany
| | - Mo Hu
- Thermo Fisher Scientific Co. Ltd, Shanghai, China
| | - Niyati Parikh
- Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, 20889, MD, USA
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, 20889, MD, USA
| | - Kelly A Conrads
- Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, 20889, MD, USA
| | - Christina Loosse
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Bunsen-Kirchhoff-Straße 11, 44139, Dortmund, Germany
| | - Reta Birhanu Kitata
- Institute of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Sander R Piersma
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
| | - Davide Chiasserini
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands.,Stoller Biomarker Discovery Centre, Institute of Cancer Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Hongwen Zhu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Guixue Hou
- BGI-SHENZHEN, Beishan Road, Yantian District, Shenzhen, 518083, Guangdong, China
| | - Muhammad Tahir
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, DK-5230, Denmark
| | - Andrew Macklin
- Princess Margaret Cancer Centre, 101 College Street PMCRT 9-807, Toronto, ON, M5G 1L7, Canada
| | - Amanda Khoo
- Princess Margaret Cancer Centre, 101 College Street PMCRT 9-807, Toronto, ON, M5G 1L7, Canada
| | - Xiuxuan Sun
- National Translational Science Center for Molecular Medicine, Xi'an, 710032, China.,Department of Cell Biology, School of Basic Medicine, Air Force Medical University, Xi'an, 710032, China
| | - Ben Crossett
- Sydney Mass Spectrometry, The University of Sydney, NSW, 2006, Sydney, Australia
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Bunsen-Kirchhoff-Straße 11, 44139, Dortmund, Germany.,Medizinische Fakultät, Medizinisches Proteom-Center (MPC), Ruhr-Universität Bochum, 44801, Bochum, Germany.,Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, AB243FX, Scotland, UK
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Connie R Jimenez
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, De Boelelaan 1117, 1081 HV, Amsterdam, the Netherlands
| | - Hu Zhou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Siqi Liu
- BGI-SHENZHEN, Beishan Road, Yantian District, Shenzhen, 518083, Guangdong, China
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, DK-5230, Denmark
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, 101 College Street PMCRT 9-807, Toronto, ON, M5G 1L7, Canada
| | - Zhinan Chen
- National Translational Science Center for Molecular Medicine, Xi'an, 710032, China.,Department of Cell Biology, School of Basic Medicine, Air Force Medical University, Xi'an, 710032, China
| | - Benjamin L Parker
- School of Life and Environmental Science, The University of Sydney, NSW, 2006, Sydney, Australia
| | - Stuart J Cordwell
- School of Life and Environmental Science, The University of Sydney, NSW, 2006, Sydney, Australia
| | - Bernd Wollscheid
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Thomas P Conrads
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, 3289 Woodburn Bldg, Annandale, VA, 22003, USA.
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33
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Soltis AR, Bateman NW, Conrads TP, Dalgard CL, Hu H, Franks TJ, Liu J, Meerzaman D, Petricoin EF, Chen Q, Yan C, Zhang X, Turner CE, Shriver CD, Moskaluk CA, Browning RF, Wilkerson MD. Abstract 5893: Comprehensive proteogenomic analysis and classification of lung adenocarcinoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Lung adenocarcinoma is a highly lethal tumor that displays extensive molecular heterogeneity of which deep characterization may drive therapeutic development and improve clinical outcomes. Through the Applied Proteogenomics Organizational Learning and Outcomes (APOLLO) research network, we utilized five molecular profiling technologies (DNA whole genome sequencing, RNA sequencing, total and phospho-proteomics by mass spectrometry, and reverse phase protein arrays [RPPA]) to characterize a longitudinally-annotated cohort of 87 lung adenocarcinomas. Through whole genome sequencing, we identified molecular signatures from patterns of somatic SNVs, indels, and large structural alterations that stratified tumors into three groups associated with patient smoke exposures. We also identified TP53, EGFR, KRAS, and STK11 as recurrently mutated genes, which together represent 80% of the cohort, in addition to genes mutated in smaller cohort subsets (e.g. RBM10), fusion genes, and pathogenic germline variants. To characterize tumor proteomes, we quantified >7,000 proteins and >10,000 phosphopeptides by mass spectrometry and >300 species by RPPA. Matched RNAs and proteins were typically positively correlated across samples (median ρ = 0.49). Through quantitative trait loci analyses, we identified genes whose RNA and protein expression levels were significantly modified by somatic mutations. We then classified tumors into RNA expression subtypes and found coordinated proteogenomic alterations and distinct clinical associations: terminal respiratory unit subtype – EGFR mutations and RNA/protein overexpression, acinar histology, non-smokers; proximal-proliferative subtype – STK11 mutations and RNA/protein underexpression, high smoking signature; proximal-inflammatory subtype – high tumor mutational burden. We also identified phospho-peptide signatures associated with these subtypes, including downregulation of CDK1/2 targets in terminal respiratory unit tumors. Protein co-expression network analysis discovered biologically-diverse pathway activities of the RNA expression subtypes. To interrogate somatic mutations in the context of molecular pathways, we projected DNA alterations onto known interaction networks and identified four subtypes with markedly distinct proteomic and microenvironment characteristics. Finally, several molecular characteristics were found to significantly predict patient outcomes, including RNA expression subtype classification against metastasis-free survival. Thus, our integrative, proteogenomic characterization of lung adenocarcinoma uncovered novel tumor biology and identified potential molecular markers for predicting patient outcomes. The views expressed in this abstract are solely of the authors and do not reflect the official policy of the Departments of Army/Navy/Air Force, Department of Defense, USUHS, HJF, or U.S. Government.
Citation Format: Anthony R. Soltis, Nicholas W. Bateman, Thomas P. Conrads, Clifton L. Dalgard, Hai Hu, Teri J. Franks, Jianfang Liu, Daoud Meerzaman, Emanuel F. Petricoin, Qingrong Chen, Chunhua Yan, Xijun Zhang, Clesson E. Turner, The APOLLO Research Network, Craig D. Shriver, Christopher A. Moskaluk, Robert F. Browning, Matthew D. Wilkerson. Comprehensive proteogenomic analysis and classification of lung adenocarcinoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5893.
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Affiliation(s)
- Anthony R. Soltis
- 1The American Genome Center, Uniformed Services University; Henry Jackson Foundation, Bethesda, MD
| | - Nicholas W. Bateman
- 2Women's Service Line at Inova Fairfax Medical Campus; Gynecologic Cancer Center of Excellence at Uniformed Services University; Henry Jackson Foundation, Falls Church, VA
| | - Thomas P. Conrads
- 3Women's Service Line at Inova Fairfax Medical Campus; Gynecologic Cancer Center of Excellence at Uniformed Services University, Falls Church, VA
| | - Clifton L. Dalgard
- 4The American Genome Center, Uniformed Services University, Bethesda, MD
| | - Hai Hu
- 5Chan Soon-Siong Institute of Molecular Medicine at Windber, Windber, PA
| | - Teri J. Franks
- 6Joint Pathology Center, Department of Defense, Silver Spring, MD
| | - Jianfang Liu
- 5Chan Soon-Siong Institute of Molecular Medicine at Windber, Windber, PA
| | - Daoud Meerzaman
- 7Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD
| | - Emanuel F. Petricoin
- 8Center for Applied Proteomics and Molecular Medicine at George Mason University, Manassas, VA
| | - Qingrong Chen
- 7Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD
| | - Chunhua Yan
- 7Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD
| | - Xijun Zhang
- 1The American Genome Center, Uniformed Services University; Henry Jackson Foundation, Bethesda, MD
| | - Clesson E. Turner
- 9John P. Murtha Cancer Center Research Program at Uniformed Services University, Bethesda, MD
| | - Craig D. Shriver
- 9John P. Murtha Cancer Center Research Program at Uniformed Services University, Bethesda, MD
| | | | - Robert F. Browning
- 9John P. Murtha Cancer Center Research Program at Uniformed Services University, Bethesda, MD
| | - Matthew D. Wilkerson
- 1The American Genome Center, Uniformed Services University; Henry Jackson Foundation, Bethesda, MD
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34
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Millard M, Appleton KM, Elrod A, Bateman NW, Abulez T, Conrads K, Hood B, Conrads TP, Holmes LM, DesRochers TM. Abstract 6018: The perfused 3DKUBE™ rare tumor assay models in vivo drug response. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-6018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Models that accurately reflect patient drug response are essential for the clinical design of personalized treatment plans and necessary for preclinical drug development. The advancement of predictive models for rare tumor types is impeded in part, by the relative scarcity of fresh tumor tissue available for study. To address the problem of tissue availability we have developed a label-free, combined functional and chemical selection method for the isolation of rare tumor cancer stem cells (CSC) and circulating tumor cells (CTC) from primary patient tissue and blood. Enriched cells were expanded as 3D microtumors under optimized conditions, validated as CSC through in vivo tumorigenesis studies, and characterized by correlative genomic, proteomic/phosphoproteomic, and phenomic analysis. We found isolation and expansion by this method yielded a source of primary cells suitable for live, cell-based predictive drug screening in multiple rare tumor derived models of neuroendocrine and mesenchymal origin, including locally or regionally advanced and metastatic SCLC, recurrent Merkel Cell Carcinoma, recurrent osteosarcoma and dermatofibrosarcoma protuberans. The 3DKUBE™ rare tumor assay was performed using validated CSCs cultured as perfused 3D microtumors (pMTs). Drug studies using the perfused, 3DKUBE™ rare tumor assay modeled individual patient response better than CSC-based or 3D static microtumor-based drug screens and thus demonstrate the effectiveness of this platform for predictive modeling of individual patient drug response. Taken together, this system provides a means of performing ex vivo drug response experiments on very small tissue samples, including core biopsies, with relevant results for patients.
Citation Format: Melissa Millard, Kathryn M. Appleton, Ashley Elrod, Nicholas W. Bateman, Tamara Abulez, Kelly Conrads, Brian Hood, Thomas P. Conrads, Lillia M. Holmes, Teresa M. DesRochers. The perfused 3DKUBE™ rare tumor assay models in vivo drug response [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6018.
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Affiliation(s)
| | | | | | - Nicholas W. Bateman
- 2Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation for the Advancement of Military Medicine, Annandale, VA
| | - Tamara Abulez
- 2Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation for the Advancement of Military Medicine, Annandale, VA
| | - Kelly Conrads
- 2Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation for the Advancement of Military Medicine, Annandale, VA
| | - Brian Hood
- 2Gynecologic Cancer Center of Excellence, Henry M. Jackson Foundation for the Advancement of Military Medicine, Annandale, VA
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35
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Lee S, Zhao L, Westin SN, Bateman NW, Jazaeri AA, Fleming ND, Lu KH, Coleman RL, Mills GB, Zhang J, Conrads TP, Maxwell GL, Futreal PA, Sood AK. Abstract 2510: High-depth whole genome sequencing of clinically-annotated high-grade serous ovarian cancers. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-2510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Prior molecular characterization efforts for high-grade serous ovarian cancer (HGSOC) were restricted to those who had upfront surgical debulking with variable treatment paradigms. Thus, we sought to examine molecular and cellular differences between clinically defined groups (tumor tissues from patients who had complete gross resection (CGR) versus those who were triaged to neoadjuvant chemotherapy (NACT) and experienced either excellent or poor response.
Methods: Tumor biopsies were collected from three patient groups managed under a systematic surgical algorithm: CGR after primary surgery (R0, n=10); poor tumor response to NACT (NACT-PR, n=10); excellent tumor response to NACT (NACT-ER, n=10). Primary and multiple metastatic tumor sites per each patient were obtained pre-treatment and subjected to comprehensive omics analyses including high-pass whole-genome (WGS) and targeted deep DNA sequencing.
Results: An average of 71 nonsynonymous somatic mutations from each sample for 75 samples with high-purity tumors (≥75%) by WGS were identified from each sample for the entire cohort. Fourteen ovarian-cancer-associated genes were found mutated in our patient cohort and, as expected, the most frequently mutated gene was TP53 in both primary and metastatic sites in all three groups. TP53 nonsense mutations were exclusively identified in the NACT-ER (36.0%) and NACT-PR groups (15.4%), while in the R0 group most TP53 mutations were missense mutations (62.5%). Nonsense mutations in CSMD3 and PIK3CA were exclusively identified in both primary and metastatic sites in the NACT-PR group. The most frequent copy number variations (CNVs) in the R0 were copy number gain/loss of CSMD3 (67%) and copy number loss of NF1 (54%) and CDK12 (50%) in both primary and metastatic sites. Interestingly, copy number losses of NF1 were significantly lower in the NACT groups (18%, p=0.002), especially in the NACT-PR (8%, p=0.0004), when compared to the R0 group (54%). We also identified significant less observation of chromothripsis-like patterns, and a significantly higher level of strong-binding neoantigens in the R0 than in the NACT groups.
Conclusions: Our findings using HGSOC samples obtained from patients treated on a prospective algorithm identified distinct molecular abnormalities, and could have prognostic and therapeutic implications for patients with HGSOC.
Citation Format: Sanghoon Lee, Li Zhao, Shannon N. Westin, Nicholas W. Bateman, Amir A. Jazaeri, Nicole D. Fleming, Karen H. Lu, Robert L. Coleman, Gordon B. Mills, Jianhua Zhang, Thomas P. Conrads, George L. Maxwell, P. Andrew Futreal, Anil K. Sood. High-depth whole genome sequencing of clinically-annotated high-grade serous ovarian cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2510.
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Affiliation(s)
| | - Li Zhao
- 1UT MD Anderson Cancer Center, Houston, TX
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36
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Beer L, Sahin H, Bateman NW, Blazic I, Vargas HA, Veeraraghavan H, Kirby J, Fevrier-Sullivan B, Freymann JB, Jaffe CC, Brenton J, Miccó M, Nougaret S, Darcy KM, Maxwell GL, Conrads TP, Huang E, Sala E. Integration of proteomics with CT-based qualitative and radiomic features in high-grade serous ovarian cancer patients: an exploratory analysis. Eur Radiol 2020; 30:4306-4316. [PMID: 32253542 PMCID: PMC7338824 DOI: 10.1007/s00330-020-06755-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 01/21/2020] [Accepted: 02/17/2020] [Indexed: 11/24/2022]
Abstract
OBJECTIVES To investigate the association between CT imaging traits and texture metrics with proteomic data in patients with high-grade serous ovarian cancer (HGSOC). METHODS This retrospective, hypothesis-generating study included 20 patients with HGSOC prior to primary cytoreductive surgery. Two readers independently assessed the contrast-enhanced computed tomography (CT) images and extracted 33 imaging traits, with a third reader adjudicating in the event of a disagreement. In addition, all sites of suspected HGSOC were manually segmented texture features which were computed from each tumor site. Three texture features that represented intra- and inter-site tumor heterogeneity were used for analysis. An integrated analysis of transcriptomic and proteomic data identified proteins with conserved expression between primary tumor sites and metastasis. Correlations between protein abundance and various CT imaging traits and texture features were assessed using the Kendall tau rank correlation coefficient and the Mann-Whitney U test, whereas the area under the receiver operating characteristic curve (AUC) was reported as a metric of the strength and the direction of the association. P values < 0.05 were considered significant. RESULTS Four proteins were associated with CT-based imaging traits, with the strongest correlation observed between the CRIP2 protein and disease in the mesentery (p < 0.001, AUC = 0.05). The abundance of three proteins was associated with texture features that represented intra-and inter-site tumor heterogeneity, with the strongest negative correlation between the CKB protein and cluster dissimilarity (p = 0.047, τ = 0.326). CONCLUSION This study provides the first insights into the potential associations between standard-of-care CT imaging traits and texture measures of intra- and inter-site heterogeneity, and the abundance of several proteins. KEY POINTS • CT-based texture features of intra- and inter-site tumor heterogeneity correlate with the abundance of several proteins in patients with HGSOC. • CT imaging traits correlate with protein abundance in patients with HGSOC.
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MESH Headings
- Abdominal Cavity/diagnostic imaging
- Adaptor Proteins, Signal Transducing/metabolism
- Aged
- Aged, 80 and over
- Aldehyde Oxidoreductases/metabolism
- Antigens, Neoplasm/metabolism
- Carcinoma, Ovarian Epithelial/diagnostic imaging
- Carcinoma, Ovarian Epithelial/metabolism
- Carcinoma, Ovarian Epithelial/secondary
- Cytokines/metabolism
- Female
- Gene Expression Profiling
- Glucose-6-Phosphate Isomerase/metabolism
- Humans
- LIM Domain Proteins/metabolism
- Mesentery/diagnostic imaging
- Middle Aged
- Neoplasm Grading
- Neoplasm Proteins/metabolism
- Neoplasms, Cystic, Mucinous, and Serous/diagnostic imaging
- Neoplasms, Cystic, Mucinous, and Serous/metabolism
- Neoplasms, Cystic, Mucinous, and Serous/secondary
- Omentum/diagnostic imaging
- Ovarian Neoplasms/diagnostic imaging
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/pathology
- Peritoneal Neoplasms/diagnostic imaging
- Peritoneal Neoplasms/metabolism
- Peritoneal Neoplasms/secondary
- Pilot Projects
- Proteomics
- ROC Curve
- Retrospective Studies
- Tomography, X-Ray Computed/methods
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Affiliation(s)
- Lucian Beer
- Department of Radiology, Cancer Research UK Cambridge Center, Cambridge, CB2 0QQ, UK
| | - Hilal Sahin
- Department of Radiology, Cancer Research UK Cambridge Center, Cambridge, CB2 0QQ, UK
| | - Nicholas W Bateman
- Department of Obstetrics and Gynecology, Gynecologic Cancer Center of Excellence, Walter Reed National Military Medical Center, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - Ivana Blazic
- Department of Radiology, Clinical Hospital Center Zemun, Vukova 9, Belgrade, 11080, Serbia
| | - Hebert Alberto Vargas
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Harini Veeraraghavan
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Justin Kirby
- Cancer Imaging Informatics Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Brenda Fevrier-Sullivan
- Cancer Imaging Informatics Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - John B Freymann
- Cancer Imaging Informatics Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - C Carl Jaffe
- Department of Radiology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - James Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, Cambridgeshire, UK
- Cancer Research UK Cambridge Centre, Cambridge, Cambridgeshire, UK
| | - Maura Miccó
- Dipartimento Diagnostica per Immagini, Radiologia Diagnostica e Interventistica Generale, Area Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Rome, Italy
| | - Stephanie Nougaret
- Department of Radiology, Montpellier Cancer Institute, INSERM, University of Montpellier, Montpellier, France
| | - Kathleen M Darcy
- Department of Obstetrics and Gynecology, Gynecologic Cancer Center of Excellence, Walter Reed National Military Medical Center, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
| | - G Larry Maxwell
- Department of Obstetrics and Gynecology, Gynecologic Cancer Center of Excellence, Walter Reed National Military Medical Center, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, 3300 Gallows Rd., Falls Church, VA, 22042, USA
| | - Thomas P Conrads
- Department of Obstetrics and Gynecology, Gynecologic Cancer Center of Excellence, Walter Reed National Military Medical Center, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University, 8901 Wisconsin Avenue, Bethesda, MD, 20889, USA
- Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, 3300 Gallows Rd., Falls Church, VA, 22042, USA
- Inova Center for Personalized Health, Inova Schar Cancer Institute, 3300 Gallows Rd., Falls Church, VA, 22042, USA
| | - Erich Huang
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Evis Sala
- Department of Radiology, Cancer Research UK Cambridge Center, Cambridge, CB2 0QQ, UK.
- Department of Radiology, University of Cambridge, Box 218, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
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37
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Liu Y, Lear TB, Verma M, Wang KZ, Otero PA, McKelvey AC, Dunn SR, Steer E, Bateman NW, Wu C, Jiang Y, Weathington NM, Rojas M, Chu CT, Chen BB, Mallampalli RK. Chemical inhibition of FBXO7 reduces inflammation and confers neuroprotection by stabilizing the mitochondrial kinase PINK1. JCI Insight 2020; 5:131834. [PMID: 32493843 DOI: 10.1172/jci.insight.131834] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 04/23/2020] [Indexed: 01/01/2023] Open
Abstract
Mitochondrial quality control is mediated by the PTEN-induced kinase 1 (PINK1), a cytoprotective protein that is dysregulated in inflammatory lung injury and neurodegenerative diseases. Here, we show that a ubiquitin E3 ligase receptor component, FBXO7, targets PINK1 for its cellular disposal. FBXO7, by mediating PINK1 ubiquitylation and degradation, was sufficient to induce mitochondrial injury and inflammation in experimental pneumonia. A computational simulation-based screen led to the identification of a small molecule, BC1464, which abrogated FBXO7 and PINK1 association, leading to increased cellular PINK1 concentrations and activities, and limiting mitochondrial damage. BC1464 exerted antiinflammatory activity in human tissue explants and murine lung inflammation models. Furthermore, BC1464 conferred neuroprotection in primary cortical neurons, human neuroblastoma cells, and patient-derived cells in several culture models of Parkinson's disease. The data highlight a unique opportunity to use small molecule antagonists that disrupt PINK1 interaction with the ubiquitin apparatus to enhance mitochondrial quality, limit inflammatory injury, and maintain neuronal viability.
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Affiliation(s)
- Yuan Liu
- Department of Medicine, the Acute Lung Injury Center of Excellence.,The McGowan Institute for Regenerative Medicine
| | - Travis B Lear
- Department of Medicine, the Acute Lung Injury Center of Excellence.,Department of Environmental and Occupational Health, Graduate School of Public Health, and
| | - Manish Verma
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kent Zq Wang
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - P Anthony Otero
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | - Sarah R Dunn
- Department of Medicine, the Acute Lung Injury Center of Excellence
| | - Erin Steer
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | | | - Yu Jiang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Mauricio Rojas
- Department of Medicine, the Acute Lung Injury Center of Excellence
| | - Charleen T Chu
- The McGowan Institute for Regenerative Medicine.,Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Ophthalmology.,The Pittsburgh Institute for Neurodegenerative Diseases
| | - Bill B Chen
- Department of Medicine, the Acute Lung Injury Center of Excellence.,Vascular Medicine Institute, and
| | - Rama K Mallampalli
- Department of Medicine, the Acute Lung Injury Center of Excellence.,Department of Cell Biology and.,Medical Specialty Service Line, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
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Lee S, Zhao L, Rojas C, Bateman NW, Yao H, Lara OD, Celestino J, Morgan MB, Nguyen TV, Conrads KA, Rangel KM, Dood RL, Hajek RA, Fawcett GL, Chu RA, Wilson K, Loffredo JL, Viollet C, Jazaeri AA, Dalgard CL, Mao X, Song X, Zhou M, Hood BL, Banskota N, Wilkerson MD, Te J, Soltis AR, Roman K, Dunn A, Cordover D, Eterovic AK, Liu J, Burks JK, Baggerly KA, Fleming ND, Lu KH, Westin SN, Coleman RL, Mills GB, Casablanca Y, Zhang J, Conrads TP, Maxwell GL, Futreal PA, Sood AK. Molecular Analysis of Clinically Defined Subsets of High-Grade Serous Ovarian Cancer. Cell Rep 2020; 31:107502. [PMID: 32294438 PMCID: PMC7234854 DOI: 10.1016/j.celrep.2020.03.066] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 01/02/2020] [Accepted: 03/19/2020] [Indexed: 12/30/2022] Open
Abstract
The diversity and heterogeneity within high-grade serous ovarian cancer (HGSC), which is the most lethal gynecologic malignancy, is not well understood. Here, we perform comprehensive multi-platform omics analyses, including integrated analysis, and immune monitoring on primary and metastatic sites from highly clinically annotated HGSC samples based on a laparoscopic triage algorithm from patients who underwent complete gross resection (R0) or received neoadjuvant chemotherapy (NACT) with excellent or poor response. We identify significant distinct molecular abnormalities and cellular changes and immune cell repertoire alterations between the groups, including a higher rate of NF1 copy number loss, and reduced chromothripsis-like patterns, higher levels of strong-binding neoantigens, and a higher number of infiltrated T cells in the R0 versus the NACT groups.
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Affiliation(s)
- Sanghoon Lee
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Li Zhao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christine Rojas
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Nicholas W Bateman
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Olivia D Lara
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph Celestino
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Margaret B Morgan
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tri V Nguyen
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kelly A Conrads
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Kelly M Rangel
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert L Dood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Richard A Hajek
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gloria L Fawcett
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Randy A Chu
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Katlin Wilson
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Jeremy L Loffredo
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Coralie Viollet
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Amir A Jazaeri
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Clifton L Dalgard
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Xizeng Mao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ming Zhou
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Brian L Hood
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Nirad Banskota
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Matthew D Wilkerson
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Jerez Te
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Anthony R Soltis
- The American Genome Center, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | | | | | | | - Agda Karina Eterovic
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jinsong Liu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared K Burks
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keith A Baggerly
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicole D Fleming
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Karen H Lu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shannon N Westin
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert L Coleman
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yovanni Casablanca
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Thomas P Conrads
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - George L Maxwell
- Women's Health Integrated Research Center at Inova Health System, Women's Service Line, Inova Fairfax Medical Campus, Falls Church, VA, USA; Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Hunt AL, Pierobon M, Baldelli E, Oliver J, Mitchell D, Gist G, Bateman NW, Larry Maxwell G, Petricoin EF, Conrads TP. The impact of ultraviolet- and infrared-based laser microdissection technology on phosphoprotein detection in the laser microdissection-reverse phase protein array workflow. Clin Proteomics 2020; 17:9. [PMID: 32165870 PMCID: PMC7061469 DOI: 10.1186/s12014-020-09272-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/20/2020] [Indexed: 12/13/2022] Open
Abstract
Reversible protein phosphorylation represents a key mechanism by which signals are transduced in eukaryotic cells. Dysregulated phosphorylation is also a hallmark of carcinogenesis and represents key drug targets in the precision medicine space. Thus, methods that preserve phosphoprotein integrity in the context of clinical tissue analyses are crucially important in cancer research. Here we investigated the impact of UV laser microdissection (UV LMD) and IR laser capture microdissection (IR LCM) on phosphoprotein abundance of key cancer signaling protein targets assessed by reverse-phase protein microarray (RPPA). Tumor epithelial cells from consecutive thin sections obtained from four high-grade serous ovarian cancers were harvested using either UV LMD or IR LCM methods. Phosphoprotein abundances for ten phosphoproteins that represent important drug targets were assessed by RPPA and revealed no significant differences in phosphoprotein integrity from those obtained using higher-energy UV versus the lower-energy IR laser methods.
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Affiliation(s)
- Allison L. Hunt
- Women’s Service Line, Inova Health System, 3300 Gallows Rd., Falls Church, VA 22042 USA
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA USA
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 720A Rockledge Drive, Suite 100, Bethesda, MD 20817 USA
| | - Dave Mitchell
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 720A Rockledge Drive, Suite 100, Bethesda, MD 20817 USA
| | - Glenn Gist
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 720A Rockledge Drive, Suite 100, Bethesda, MD 20817 USA
| | - Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., 720A Rockledge Drive, Suite 100, Bethesda, MD 20817 USA
| | - G. Larry Maxwell
- Women’s Service Line, Inova Health System, 3300 Gallows Rd., Falls Church, VA 22042 USA
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA USA
| | - Thomas P. Conrads
- Women’s Service Line, Inova Health System, 3300 Gallows Rd., Falls Church, VA 22042 USA
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, 8901 Wisconsin Avenue, Bethesda, MD 20889 USA
- 3289 Woodburn Rd, Suite 375, Annandale, VA 22003 USA
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40
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Rojas C, Tian C, Powell MA, Chan JK, Bateman NW, Conrads TP, Rocconi RP, Jones NL, Shriver CD, Hamilton CA, Maxwell GL, Casablanca Y, Darcy KM. Racial disparities in uterine and ovarian carcinosarcoma: A population-based analysis of treatment and survival. Gynecol Oncol 2020; 157:67-77. [PMID: 32029291 DOI: 10.1016/j.ygyno.2020.01.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/31/2019] [Accepted: 01/07/2020] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To investigate racial disparities in uterine carcinosarcoma (UCS) and ovarian carcinosarcoma (OCS) in Commission on Cancer®-accredited facilities. METHODS Non-Hispanic Black (NHB) and non-Hispanic White (NHW) women in the National Cancer Database diagnosed with stage I-IV UCS or OCS between 2004 and 2014 were eligible. Differences by disease site or race were compared using Chi-square test and multivariate Cox analysis. RESULTS There were 2830 NHBs and 7366 NHWs with UCS, and 280 NHBs and 2586 NHWs with OCS. Diagnosis of UCS was more common in NHBs (11.5%) vs. NHWs (3.7%) and increased with age (P < .0001). OCS diagnosis remained <5% in both races and all ages. NHBs with UCS or OCS were more common in the South and more likely to have a comorbidity score ≥ 1, low neighborhood income and Medicaid or no insurance (P < .0001). Diagnosis at stage II-IV was more common in NHBs than NHWs with UCS but not OCS. NHBs with both UCS and OCS were less likely to undergo surgery and to achieve no gross residual disease with surgery (P = .002). Risk of death in NHB vs. NHW patients with UCS was 1.38 after adjustment for demographic factors and dropped after sequential adjustment for comorbidity score, neighborhood income, insurance status, stage and treatment by 4%, 16%, 7%, 19% and 10%, respectively, leaving 43.5% of the racial disparity in survival unexplained. In contrast, risk of death in NHBs vs. NHWs with OCS was 1.19 after adjustment for demographic factors and became insignificant after adjustment for comorbidity. Race was an independent prognostic factor in UCS but not in OCS. CONCLUSIONS Racial disparities exist in characteristics, treatment and survival in UCS and OCS with distinctions that merit additional research.
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Affiliation(s)
- Christine Rojas
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA.
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA.
| | - Matthew A Powell
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA.
| | - John K Chan
- Palo Alto Medical Foundation, California Pacific Medical Center, Sutter Health, San Francisco, CA, USA.
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA.
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Department of Obstetrics and Gynecology, Inova Fairfax Hospital, Falls Church, VA, USA.
| | - Rodney P Rocconi
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA.
| | - Nathaniel L Jones
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA.
| | - Craig D Shriver
- John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA.
| | - Chad A Hamilton
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Department of Obstetrics and Gynecology, Inova Fairfax Hospital, Falls Church, VA, USA; Inova Schar Cancer Institute, Inova Center for Personalized Health, Falls Church, VA, USA.
| | - G Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Department of Obstetrics and Gynecology, Inova Fairfax Hospital, Falls Church, VA, USA; Inova Schar Cancer Institute, Inova Center for Personalized Health, Falls Church, VA, USA.
| | - Yovanni Casablanca
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA.
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA; John P Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Walter Reed National Military Medical Center, Bethesda, MD, USA.
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41
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Bateman NW, Teng PN, Hope E, Hood BL, Oliver J, Ao W, Zhou M, Wang G, Tommarello D, Wilson K, Litzy T, Conrads KA, Hamilton CA, Darcy KM, Casablanca Y, Maxwell GL, Bae-Jump V, Conrads TP. Jupiter microtubule-associated homolog 1 (JPT1): A predictive and pharmacodynamic biomarker of metformin response in endometrial cancers. Cancer Med 2019; 9:1092-1103. [PMID: 31808620 PMCID: PMC6997075 DOI: 10.1002/cam4.2729] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 10/26/2019] [Accepted: 10/28/2019] [Indexed: 01/02/2023] Open
Abstract
Preoperative use of metformin in obese women with endometrioid endometrial cancer (EEC) reduces tumor proliferation and inhibits the mammalian target of rapamycin pathway, though is only effective in select cases. This study sought to identify a predictive and/or pharmacodynamic proteomic signature of metformin response to tailor its pharmacologic use. Matched pre‐ and post‐metformin‐treated tumor tissues from a recently completed preoperative window trial of metformin in EEC patients (ClinicalTrials.gov: NCT01911247) were analyzed by mass spectrometry (MS)‐based proteomic and immunohistochemical analyses. Jupiter microtubule‐associated homolog 1 (JPT1) was significantly elevated in metformin responders (n = 13) vs nonresponders (n = 7), and found to decrease in abundance in metformin responders following treatment; observations that were verified by immunohistochemical staining for JPT1. Metformin response and loss of JPT1 were assessed in RL95‐2 and ACI‐181 endometrial cancer (EC) cell lines. We further identified that silencing of JPT1 abundance does not alter cellular response to metformin or basal cell proliferation, but that JPT1 abundance does decrease in response to metformin treatment in RL95‐2 and ACI‐181 EC cell lines. These data suggest that JPT1 represents a predictive and pharmacodynamic biomarker of metformin response that, if validated in larger patient populations, may enable preoperative EEC patient stratification to metformin treatment and the ability to monitor patient response.
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Affiliation(s)
- Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Pang-Ning Teng
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Erica Hope
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Wei Ao
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Ming Zhou
- Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, Falls Church, VA, USA
| | - Guisong Wang
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Domenic Tommarello
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Katlin Wilson
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Tracy Litzy
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Kelly A Conrads
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Chad A Hamilton
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | - Yovanni Casablanca
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - George Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, Falls Church, VA, USA
| | - Victoria Bae-Jump
- University of North Carolina at Chapel Hill, Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Chapel Hill, NC, USA
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,The John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, Falls Church, VA, USA
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42
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Liu S, Matsuzaki J, Wei L, Tsuji T, Battaglia S, Hu Q, Cortes E, Wong L, Yan L, Long M, Miliotto A, Bateman NW, Lele SB, Chodon T, Koya RC, Yao S, Zhu Q, Conrads TP, Wang J, Maxwell GL, Lugade AA, Odunsi K. Efficient identification of neoantigen-specific T-cell responses in advanced human ovarian cancer. J Immunother Cancer 2019; 7:156. [PMID: 31221207 PMCID: PMC6587259 DOI: 10.1186/s40425-019-0629-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/30/2019] [Indexed: 12/20/2022] Open
Abstract
Background Efficient identification of neoantigen-specific T-cell responses in epithelial ovarian cancer (EOC) remains a challenge. Existing investigations of spontaneous T-cell response to tumor neoepitope in EOC have taken the approach of comprehensive screening all neoantigen candidates, with a validation rate of 0.5–2%. Methods Whole-exome and transcriptome sequencing analysis of treatment-naive EOC patients were performed to identify neoantigen candidates, and the immunogenicity of prioritized neoantigens was evaluated by analyzing spontaneous neoantigen-specfic CD4+ and CD8+ T-cell responses in the tumor and/or peripheral blood. The biological relevance of neoantigen-specific T-cell lines and clones were analyzed by evaluating the capacity of autologous ovarian tumor recognition. Genetic transfer of T-cell receptor (TCR) from these neoantigen-specific T-cell clones into peripheral blood T-cells was conducted to generate neoepitope-specific T-cells. The molecular signature associated with positive neoantigen T-cell responses was investigated, and the impacts of expression level and lymphocyte source on neoantigen identification were explored. Results Using a small subset of prioritized neoantigen candidates, we were able to detect spontaneous CD4+ and/or CD8+ T-cell responses against neoepitopes from autologous lymphocytes in half of treatment-naïve EOC patients, with a significantly improved validation rate of 19%. Tumors from patients exhibiting neoantigen-specific T-cell responses exhibited a signature of upregulated antigen processing and presentation machinery, which was also associated with favorable patient survival in the TCGA ovarian cohort. T-cells specific against two mutated cancer-associated genes, NUP214 and JAK1, recognized autologous tumors. Gene-engineering with TCR from these neoantigen-specific T-cell clones conferred neoantigen-reactivity to peripheral T-cells. Conclusions Our study demonstrated the feasibility of efficiently identifying both CD4+ and CD8+ neoantigen-specific T-cells in EOC. Autologous lymphocytes genetically engineered with tumor antigen-specific TCR can be used to generate cells for use in the personalized adoptive T-cell transfer immunotherapy. Electronic supplementary material The online version of this article (10.1186/s40425-019-0629-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
| | - Junko Matsuzaki
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
| | - Lei Wei
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Takemasa Tsuji
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Sebastiano Battaglia
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Eduardo Cortes
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Laiping Wong
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Mark Long
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Anthony Miliotto
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, 20889, USA
| | - Shashikant B Lele
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Thinle Chodon
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Richard C Koya
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, 20889, USA.,Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, Falls Church, VA, 22003, USA.,Inova Schar Cancer Institute, Falls Church, VA, 22003, USA
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - George L Maxwell
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, 20889, USA.,Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, Falls Church, VA, 22003, USA
| | - Amit A Lugade
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Kunle Odunsi
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA. .,Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
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Wang KZ, Otero PA, Steer E, Bateman NW, Wu C, Shih Y, Hsueh Y, Chu CT. PINK1 activates PKA to promote VCP‐P47 complex‐mediated dendritogenesis. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.662.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | | | - Yu‐Tzu Shih
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | - Yi‐Ping Hsueh
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
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Kessler MD, Bateman NW, Conrads TP, Maxwell GL, Dunning Hotopp JC, O’Connor TD. Ancestral characterization of 1018 cancer cell lines highlights disparities and reveals gene expression and mutational differences. Cancer 2019; 125:2076-2088. [PMID: 30865299 PMCID: PMC6541501 DOI: 10.1002/cncr.32020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/15/2019] [Indexed: 12/11/2022]
Abstract
Background Although cell lines are an essential resource for studying cancer biology, many are of unknown ancestral origin, and their use may not be optimal for evaluating the biology of all patient populations. Methods An admixture analysis was performed using genome‐wide chip data from the Catalogue of Somatic Mutations in Cancer (COSMIC) Cell Lines Project to calculate genetic ancestry estimates for 1018 cancer cell lines. After stratifying the analyses by tissue and histology types, linear models were used to evaluate the influence of ancestry on gene expression and somatic mutation frequency. Results For the 701 cell lines with unreported ancestry, 215 were of East Asian origin, 30 were of African or African American origin, and 453 were of European origin. Notable imbalances were observed in ancestral representation across tissue type, with the majority of analyzed tissue types having few cell lines of African American ancestral origin, and with Hispanic and South Asian ancestry being almost entirely absent across all cell lines. In evaluating gene expression across these cell lines, expression levels of the genes neurobeachin line 1 (NBEAL1), solute carrier family 6 member 19 (SLC6A19), HEAT repeat containing 6 (HEATR6), and epithelial cell transforming 2 like (ECT2L) were associated with ancestry. Significant differences were also observed in the proportions of somatic mutation types across cell lines with varying ancestral proportions. Conclusions By estimating genetic ancestry for 1018 cancer cell lines, the authors have produced a resource that cancer researchers can use to ensure that their cell lines are ancestrally representative of the populations they intend to affect. Furthermore, the novel ancestry‐specific signal identified underscores the importance of ancestral awareness when studying cancer. Preclinical cancer cell line research is often conducted without an awareness of ancestral background, which results in incongruities between the genetic backgrounds of used cell lines and the patient populations they are intended to represent. By calculating genetic ancestry for 1018 common cancer cell lines and identifying ancestry‐specific expression and somatic mutation patterns, the importance of ancestral awareness is emphasized, and a resource is provided that can be used by cancer researchers to ensure that their cell lines are ancestrally representative of the populations they aim to impact.
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Affiliation(s)
- Michael D. Kessler
- Institute for Genome SciencesUniversity of Maryland School of MedicineBaltimoreMaryland
- Department of MedicineUniversity of Maryland School of MedicineBaltimoreMaryland
- Program in Personalized and Genomic MedicineUniversity of Maryland School of MedicineBaltimoreMaryland
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer CenterBaltimoreMaryland
| | - Nicholas W. Bateman
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology and the John P. Murtha Cancer CenterUniformed Services University of the Health Sciences and Walter Reed National Military Medical CenterBethesdaMaryland
- Inova Schar Cancer Institute, Inova Center for Personalized HealthFairfaxVirginia
| | - Thomas P. Conrads
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology and the John P. Murtha Cancer CenterUniformed Services University of the Health Sciences and Walter Reed National Military Medical CenterBethesdaMaryland
- Inova Schar Cancer Institute, Inova Center for Personalized HealthFairfaxVirginia
- Department of Obstetrics and GynecologyInova Fairfax Medical CampusFalls ChurchVirginia
| | - George L. Maxwell
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology and the John P. Murtha Cancer CenterUniformed Services University of the Health Sciences and Walter Reed National Military Medical CenterBethesdaMaryland
- Inova Schar Cancer Institute, Inova Center for Personalized HealthFairfaxVirginia
- Department of Obstetrics and GynecologyInova Fairfax Medical CampusFalls ChurchVirginia
| | - Julie C. Dunning Hotopp
- Institute for Genome SciencesUniversity of Maryland School of MedicineBaltimoreMaryland
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer CenterBaltimoreMaryland
- Department of Microbiology and ImmunologyUniversity of Maryland School of MedicineBaltimoreMaryland
| | - Timothy D. O’Connor
- Institute for Genome SciencesUniversity of Maryland School of MedicineBaltimoreMaryland
- Department of MedicineUniversity of Maryland School of MedicineBaltimoreMaryland
- Program in Personalized and Genomic MedicineUniversity of Maryland School of MedicineBaltimoreMaryland
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer CenterBaltimoreMaryland
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Wang KZQ, Steer E, Otero PA, Bateman NW, Cheng MH, Scott AL, Wu C, Bahar I, Shih YT, Hsueh YP, Chu CT. PINK1 Interacts with VCP/p97 and Activates PKA to Promote NSFL1C/p47 Phosphorylation and Dendritic Arborization in Neurons. eNeuro 2018; 5:ENEURO.0466-18.2018. [PMID: 30783609 PMCID: PMC6377406 DOI: 10.1523/eneuro.0466-18.2018] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/06/2018] [Accepted: 12/10/2018] [Indexed: 01/06/2023] Open
Abstract
While PTEN-induced kinase 1 (PINK1) is well characterized for its role in mitochondrial homeostasis, much less is known concerning its ability to prevent synaptodendritic degeneration. Using unbiased proteomic methods, we identified valosin-containing protein (VCP) as a major PINK1-interacting protein. RNAi studies demonstrate that both VCP and its cofactor NSFL1C/p47 are necessary for the ability of PINK1 to increase dendritic complexity. Moreover, PINK1 regulates phosphorylation of p47, but not the VCP co-factor UFD1. Although neither VCP nor p47 interact directly with PKA, we found that PINK1 binds and phosphorylates the catalytic subunit of PKA at T197 [PKAcat(pT197)], a site known to activate the PKA holoenzyme. PKA in turn phosphorylates p47 at a novel site (S176) to regulate dendritic complexity. Given that PINK1 physically interacts with both the PKA holoenzyme and the VCP-p47 complex to promote dendritic arborization, we propose that PINK1 scaffolds a novel PINK1-VCP-PKA-p47 signaling pathway to orchestrate dendritogenesis in neurons. These findings highlight an important mechanism by which proteins genetically implicated in Parkinson's disease (PD; PINK1) and frontotemporal dementia (FTD; VCP) interact to support the health and maintenance of neuronal arbors.
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Affiliation(s)
- Kent Z. Q. Wang
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Erin Steer
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - P. Anthony Otero
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Nicholas W. Bateman
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Mary Hongying Cheng
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Ana Ligia Scott
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Christine Wu
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Ivet Bahar
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Yu-Tzu Shih
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan 11529
| | - Yi-Ping Hsueh
- Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan 11529
| | - Charleen T. Chu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
- Pittsburgh Institute for Neurodegenerative Diseases, McGowan Institute for Regenerative Medicine, Center for Protein Conformational Diseases and Center for Neuroscience at the University of Pittsburgh, Pittsburgh, PA 15213
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Bateman NW, Conrads TP. Recent advances and opportunities in proteomic analyses of tumour heterogeneity. J Pathol 2018; 244:628-637. [PMID: 29344964 DOI: 10.1002/path.5036] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/04/2018] [Accepted: 01/05/2018] [Indexed: 01/27/2023]
Abstract
Solid tumour malignancies comprise a highly variable admixture of tumour and non-tumour cellular populations, forming a complex cellular ecosystem and tumour microenvironment. This tumour heterogeneity is not incidental, and is known to correlate with poor patient prognosis for many cancer types. Indeed, non-malignant cell populations, such as vascular endothelial and immune cells, are known to play key roles supporting and, in some cases, driving aggressive tumour biology, and represent targets of emerging therapeutics, such as antiangiogenesis and immune checkpoint inhibitors. The biochemical interplay between these cellular populations and how they contribute to molecular tumour heterogeneity remains enigmatic, particularly from the perspective of the tumour proteome. This review focuses on recent advances in proteomic methods, namely imaging mass spectrometry, single-cell proteomic techniques, and preanalytical sample processing, that are uniquely positioned to enable detailed analysis of discrete cellular populations within tumours to improve our understanding of tumour proteomic heterogeneity. This review further emphasizes the opportunity afforded by the application of these techniques to the analysis of tumour heterogeneity in formalin-fixed paraffin-embedded archival tumour tissues, as these represent an invaluable resource for retrospective analyses that is now routinely accessible, owing to recent technological and methodological advances in tumour tissue proteomics. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,The John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,The John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Inova Schar Cancer Institute, Inova Center for Personalized Health, Falls Church, VA, USA
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Bateman NW, Dubil EA, Wang G, Hood BL, Oliver JM, Litzi TA, Gist GD, Mitchell DA, Blanton B, Phippen NT, Tian C, Zahn CM, Cohn DE, Havrilesky LJ, Berchuck A, Shriver CD, Darcy KM, Hamilton CA, Conrads TP, Maxwell GL. Race-specific molecular alterations correlate with differential outcomes for black and white endometrioid endometrial cancer patients. Cancer 2017; 123:4004-4012. [PMID: 28654152 DOI: 10.1002/cncr.30813] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/28/2017] [Accepted: 05/03/2017] [Indexed: 12/16/2022]
Abstract
BACKGROUND The objective of this study was to identify molecular alterations associated with disease outcomes for white and black patients with endometrioid endometrial cancer (EEC). METHODS EEC samples from black (n = 17) and white patients (n = 13) were analyzed by proteomics (liquid chromatography-tandem mass spectrometry) and transcriptomics (RNA-seq). Coordinate alterations were validated with RNA-seq data from black (n = 49) and white patients (n = 216). Concordantly altered candidates were further tested for associations with race-specific progression-free survival (PFS) in black (n = 64) or white patients (n = 267) via univariate and multivariate Cox regression modeling and log-rank testing. RESULTS Discovery analyses revealed significantly altered candidate proteins and transcripts between black and white patients, suggesting modulation of tumor cell viability in black patients and cell death signaling in black and white patients. Eighty-nine candidates were validated as altered between these patient cohorts, and a subset significantly correlated with differential PFS. White-specific PFS candidates included serpin family A member 4 (SERPINA4; hazard ratio [HR], 0.89; Wald P value = .02), integrin subunit α3 (ITGA3; HR, 0.76; P = .03), and Bet1 Golgi vesicular membrane trafficking protein like (BET1L; HR, 0.48; P = .04). Black-specific PFS candidates included family with sequence similarity 228 member B (FAM228B; HR, 0.13; P = .001) and HEAT repeat containing 6 (HEATR6; HR, 4.94; P = .047). Several candidates were also associated with overall survival (SERPINA4 and ITGA3) as well as PFS independent of disease stage, grade and myometrial invasion (SERPINA4, BET1L and FAM228B). CONCLUSIONS This study has identified and validated molecular alterations in tumors from black and white EEC patients, including candidates significantly associated with altered disease outcomes within these patient cohorts. Cancer 2017;123:4004-12. © 2017 American Cancer Society.
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Affiliation(s)
- Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland.,John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Elizabeth A Dubil
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Guisong Wang
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Julie M Oliver
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Tracy A Litzi
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Glenn D Gist
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - David A Mitchell
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Brian Blanton
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Neil T Phippen
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | | | - David E Cohn
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, College of Medicine, Ohio State University, Columbus, Ohio
| | - Laura J Havrilesky
- Division of Gynecologic Oncology, Duke University Medical Center, Durham, North Carolina
| | - Andrew Berchuck
- Division of Gynecologic Oncology, Duke University Medical Center, Durham, North Carolina
| | - Craig D Shriver
- John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland.,John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Chad A Hamilton
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland.,John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland.,John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland.,Inova Schar Cancer Institute, Inova Center for Personalized Health, Falls Church, Virginia
| | - G Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland.,John P. Murtha Cancer Center, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, Maryland.,Inova Schar Cancer Institute, Inova Center for Personalized Health, Falls Church, Virginia.,Department of Obstetrics and Gynecology, Inova Fairfax Medical Campus, Falls Church, Virginia
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Tarney CM, Tian C, Wang G, Dubil EA, Bateman NW, Chan JK, Elshaikh MA, Cote ML, Schildkraut JM, Shriver CD, Conrads TP, Hamilton CA, Maxwell GL, Darcy KM. Impact of age at diagnosis on racial disparities in endometrial cancer patients. Gynecol Oncol 2017; 149:12-21. [PMID: 28800945 DOI: 10.1016/j.ygyno.2017.07.145] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 07/29/2017] [Accepted: 07/31/2017] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Although black patients with endometrial cancer (EC) have worse survival compared with white patients, the interaction between age/race has not been examined. The primary objective was to evaluate the impact of age at diagnosis on racial disparities in disease presentation and outcome in EC. METHODS We evaluated women diagnosed with EC between 1991 and 2010 from the Surveillance, Epidemiology, and End Results. Mutation status for TP53 or PTEN, or with the aggressive integrative, transcript-based, or somatic copy number alteration-based molecular subtype were acquired from the Cancer Genome Atlas. Logistic regression model was used to estimate the interaction between age and race on histology. Cox regression model was used to estimate the interaction between age and race on survival. RESULTS 78,184 white and 8518 black patients with EC were analyzed. Median age at diagnosis was 3-years younger for black vs. white patients with serous cancer and carcinosarcoma (P<0.0001). The increased presentation of non-endometrioid histology with age was larger in black vs. white patients (P<0.0001). The racial disparity in survival and cancer-related mortality was more prevalent in black vs. white patients, and in younger vs. older patients (P<0.0001). Mutations in TP53, PTEN and the three aggressive molecular subtypes each varied by race, age and histology. CONCLUSIONS Aggressive histology and molecular features were more common in black patients and older age, with greater impact of age on poor tumor characteristics in black vs. white patients. Racial disparities in outcome were larger in younger patients. Intervention at early ages may mitigate racial disparities in EC.
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Affiliation(s)
- Christopher M Tarney
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States; John P Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Guisong Wang
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Elizabeth A Dubil
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States; John P Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States; Gynecologic Oncology Division, Department of Obstetrics and Gynecology, Naval Medical Center Portsmouth, VA, United States
| | - Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States; John P Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - John K Chan
- Palo Alto Medical Foundation, California Pacific Medical Center, Sutter Health, San Francisco, CA, United States
| | - Mohamed A Elshaikh
- Department of Radiation Oncology, Henry Ford Hospital, Detroit, MI, United States
| | - Michele L Cote
- Oncology, Wayne State University, Karmanos Cancer Institute, Detroit, MI, United States
| | - Joellen M Schildkraut
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Craig D Shriver
- John P Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States; John P Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States; Inova Schar Cancer Institute, Inova Center for Personalized Health, Falls Church, VA, United States
| | - Chad A Hamilton
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States; John P Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - G Larry Maxwell
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States; John P Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States; Inova Schar Cancer Institute, Inova Center for Personalized Health, Falls Church, VA, United States; Department of Obstetrics and Gynecology, Inova Fairfax Hospital, Falls Church, VA, United States.
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Department of Obstetrics & Gynecology, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States; John P Murtha Cancer Center, Walter Reed National Military Medical Center, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.
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Bateman NW, Dubil E, Wang G, Hood BL, Litzi T, Oliver J, Darcy KM, Hamilton CA, Conrads TP, Maxwell GL. Abstract 5277: Proteome and transcriptome alterations in black endometrial cancer patients correlate with poor disease outcome. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-5277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Objective: Black endometrial cancer patients are more than twice as likely to die from their disease as White patients. This study sought to identify alterations in the proteome and transcriptome of primary tumor tissues from White and Black endometrioid endometrial cancer (EEC) patients associated with differential outcome.
Methods: An integrated proteomic and transcriptomic analysis (LC-MS/MS and RNA-seq) was performed on White (n=13) and Black (n=17) EEC patient tissues. Significant and concordantly altered protein and transcript candidates were validated against publicly available RNA-seq data (TCGA UCEC) from White (n=216) and Black (n=49) EEC patients. Validated candidates were further correlated with overall (OS, n=356 White and Black patients) and progression-free survival (PFS, n=331 White and Black patients) to identify candidates significantly associated with differential disease outcome. Alterations of outcome-associated candidates were validated in an independent cohort of White (n=115) and Black (n=17) EEC patient transcript expression data.
Results: We identified and validated 89 proteins and transcripts significantly altered between White vs Black EEC patients. Pathway analyses revealed candidates elevated in White EEC patients correlated with marked activation of molecular signaling pathways regulating viral infection, but inhibition of those regulating cell death and necrosis. Candidates elevated in Black EEC patients largely correlated with activation of cell viability and nucleic acid metabolism, but inhibition of cell death, glucose metabolism disorder and inflammatory signaling. Correlation with patient outcome measures revealed 11 candidates significantly associated with differential OS and 8 candidates with differential PFS in EEC patients. All outcome-associated candidates elevated in White patients significantly correlated with a low risk of poor OS and poor PFS (Hazard Ratio (HR) < 1, Wald p-value < 0.05). Conversely, the majority of outcome-associated candidates (88%) elevated in Black patients correlated with a high risk of poor OS and poor PFS (HR > 1, Wald p-value < 0.05). Several OS (27%) and PFS (75%) candidates remained significant after adjustment for disease stage and grade as well as myometrial invasion. Alteration trends for several OS (27%) and PFS (25%) candidates were validated in an independent cohort of White and Black EEC patients.
Conclusions: Our analyses identified and confirmed molecular alterations between White and Black EEC patients, including outcome-associated candidates largely supportive of better outcome in White patients, but poor outcome in Black patients. These findings define molecular alterations in White and Black EEC patients consistent with the historic disparity of poor outcome for Black patients warranting further investigation of these candidates in Black EEC disease pathology.
Citation Format: Nicholas W. Bateman, Elizabeth Dubil, Guisong Wang, Brian L. Hood, Tracy Litzi, Julie Oliver, Kathleen M. Darcy, Chad A. Hamilton, Thomas P. Conrads, George L. Maxwell. Proteome and transcriptome alterations in black endometrial cancer patients correlate with poor disease outcome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5277. doi:10.1158/1538-7445.AM2017-5277
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Affiliation(s)
| | | | - Guisong Wang
- 1Gynecologic Cancer Center of Excellence, Annandale, VA
| | - Brian L. Hood
- 1Gynecologic Cancer Center of Excellence, Annandale, VA
| | - Tracy Litzi
- 1Gynecologic Cancer Center of Excellence, Annandale, VA
| | - Julie Oliver
- 1Gynecologic Cancer Center of Excellence, Annandale, VA
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Teng PN, Bateman NW, Wang G, Litzi T, Blanton BE, Hood BL, Conrads KA, Ao W, Oliver KE, Darcy KM, McGuire WP, Paz K, Sidransky D, Hamilton CA, Maxwell GL, Conrads TP. Establishment and characterization of a platinum- and paclitaxel-resistant high grade serous ovarian carcinoma cell line. Hum Cell 2017; 30:226-236. [PMID: 28251557 DOI: 10.1007/s13577-017-0162-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/30/2017] [Indexed: 10/20/2022]
Abstract
High grade serous ovarian cancer (HGSOC) patients have a high recurrence rate after surgery and adjuvant chemotherapy due to inherent or acquired drug resistance. Cell lines derived from HGSOC tumors that are resistant to chemotherapeutic agents represent useful pre-clinical models for drug discovery. Here, we describe establishment of a human ovarian carcinoma cell line, which we term WHIRC01, from a patient-derived mouse xenograft established from a chemorefractory HGSOC patient who did not respond to carboplatin and paclitaxel therapy. This newly derived cell line is platinum- and paclitaxel-resistant with cisplatin, carboplatin, and paclitaxel half-maximal lethal doses of 15, 130, and 20 µM, respectively. Molecular characterization of this cell line was performed using targeted DNA exome sequencing, transcriptomics (RNA-seq), and mass spectrometry-based proteomic analyses. Results from exomic sequencing revealed mutations in TP53 consistent with HGSOC. Transcriptomic and proteomic analyses of WHIRC01 showed high level of alpha-enolase and vimentin, which are associated with cell migration and epithelial-mesenchymal transition. WHIRC01 represents a chemorefractory human HGSOC cell line model with a comprehensive molecular profile to aid future investigations of drug resistance mechanisms and screening of chemotherapeutic agents.
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Affiliation(s)
- Pang-Ning Teng
- Women's Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale, VA, USA
| | - Nicholas W Bateman
- Women's Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale, VA, USA.,The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD, USA.,Department of Obstetrics and Gynecology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Guisong Wang
- Women's Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale, VA, USA
| | - Tracy Litzi
- Women's Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale, VA, USA
| | - Brian E Blanton
- Women's Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale, VA, USA
| | - Brian L Hood
- Women's Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale, VA, USA
| | - Kelly A Conrads
- Women's Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale, VA, USA
| | - Wei Ao
- Women's Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale, VA, USA
| | - Kate E Oliver
- Gynecologic Oncology Service, Department of Obstetrics and Gynecology, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Kathleen M Darcy
- Women's Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale, VA, USA.,The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - William P McGuire
- Department of Internal Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Keren Paz
- Champions Oncology, Inc., Baltimore, MD, USA
| | - David Sidransky
- Otolaryngology-Head and Neck Surgery and Oncology, Johns Hopkins University, Baltimore, MD, USA
| | - Chad A Hamilton
- Women's Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale, VA, USA.,The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD, USA.,Gynecologic Oncology Service, Department of Obstetrics and Gynecology, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - G Larry Maxwell
- Women's Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale, VA, USA.,The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD, USA.,Department of Obstetrics and Gynecology, Inova Fairfax Hospital, Falls Church, VA, USA.,Inova Schar Cancer Institute, Inova Center for Personalized Health, Falls Church, VA, USA
| | - Thomas P Conrads
- Women's Health Integrated Research Center at Inova Health System, Gynecologic Cancer Center of Excellence, Annandale, VA, USA. .,The John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD, USA. .,Department of Obstetrics and Gynecology, Inova Fairfax Hospital, Falls Church, VA, USA. .,Department of Obstetrics and Gynecology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA. .,Inova Schar Cancer Institute, Inova Center for Personalized Health, Falls Church, VA, USA.
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