1
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Delgado-Coka LA, Roa-Peña L, Babu S, Horowitz M, Petricoin EF, Matrisian LM, Blais EM, Marchenko N, Allard FD, Akalin A, Jiang W, Larson BK, Hendifar AE, Picozzi VJ, Choi M, Shroyer KR, Escobar-Hoyos LF. Keratin 17 is a prognostic and predictive biomarker in pancreatic ductal adenocarcinoma. Am J Clin Pathol 2024:aqae038. [PMID: 38642081 DOI: 10.1093/ajcp/aqae038] [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: 12/23/2023] [Accepted: 04/05/2024] [Indexed: 04/22/2024] Open
Abstract
OBJECTIVES To determine the role of keratin 17 (K17) as a predictive biomarker for response to chemotherapy by defining thresholds of K17 expression based on immunohistochemical tests that could be used to optimize therapeutic intervention for patients with pancreatic ductal adenocarcinoma (PDAC). METHODS We profiled K17 expression, a hallmark of the basal molecular subtype of PDAC, by immunohistochemistry in 2 cohorts of formalin-fixed, paraffin-embedded PDACs (n = 305). We determined a K17 threshold of expression to optimize prognostic stratification according to the lowest Akaike information criterion and explored the potential relationship between K17 and chemoresistance by multivariate predictive analyses. RESULTS Patients with advanced-stage, low K17 PDACs treated using 5-fluorouracil (5-FU)-based chemotherapeutic regimens had 3-fold longer survival than corresponding cases treated with gemcitabine-based chemotherapy. By contrast, PDACs with high K17 did not respond to either regimen. The predictive value of K17 was independent of tumor mutation status and other clinicopathologic variables. CONCLUSIONS The detection of K17 in 10% or greater of PDAC cells identified patients with shortest survival. Among patients with low K17 PDACs, 5-FU-based treatment was more likely than gemcitabine-based therapies to extend survival.
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Affiliation(s)
- Lyanne A Delgado-Coka
- Departments of Pathology
- Departments of Preventative Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, US
| | - Lucia Roa-Peña
- Departments of Pathology
- Department of Pathology, School of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | | | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, VA, US
- Perthera, McLean, VA, US
| | - Lynn M Matrisian
- Scientific and Medical Affairs, Pancreatic Cancer Action Network, Manhattan Beach, CA, US
| | | | | | - Felicia D Allard
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, US
| | - Ali Akalin
- Department of Pathology, University of Massachusetts Memorial Medical Center, Worcester, MA, US
| | - Wei Jiang
- Department of Pathology, Anatomy and Cell Biology, Sidney Kimmel Cancer Center Thomas Jefferson University Hospital, Philadelphia, PA, US
| | - Brent K Larson
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, US
| | - Andrew E Hendifar
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, US
| | | | | | | | - Luisa F Escobar-Hoyos
- Departments of Pathology
- Departments of Therapeutic Radiology
- Departments of Molecular Biophysics and Biochemistry
- Department of Medicine, Division of Oncology, Yale University, New Haven, CT, US
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2
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Bylicky MA, Shankavaram U, Aryankalayil MJ, Chopra S, Naz S, Sowers AL, Choudhuri R, Calvert V, Petricoin EF, Eke I, Mitchell JB, Coleman CN. Multiomic-Based Molecular Landscape of FaDu Xenograft Tumors in Mice after a Combinatorial Treatment with Radiation and an HSP90 Inhibitor Identifies Adaptation-Induced Targets of Resistance and Therapeutic Intervention. Mol Cancer Ther 2024; 23:577-588. [PMID: 38359816 PMCID: PMC10985469 DOI: 10.1158/1535-7163.mct-23-0796] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/10/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
Treatments involving radiation and chemotherapy alone or in combination have improved patient survival and quality of life. However, cancers frequently evade these therapies due to adaptation and tumor evolution. Given the complexity of predicting response based solely on the initial genetic profile of a patient, a predetermined treatment course may miss critical adaptation that can cause resistance or induce new targets for drug and immunotherapy. To address the timescale for these evasive mechanisms, using a mouse xenograft tumor model, we investigated the rapidity of gene expression (mRNA), molecular pathway, and phosphoproteome changes after radiation, an HSP90 inhibitor, or combination. Animals received radiation, drug, or combination treatment for 1 or 2 weeks and were then euthanized along with a time-matched untreated group for comparison. Changes in gene expression occur as early as 1 week after treatment initiation. Apoptosis and cell death pathways were activated in irradiated tumor samples. For the HSP90 inhibitor and combination treatment at weeks 1 and 2 compared with Control Day 1, gene-expression changes induced inhibition of pathways including invasion of cells, vasculogenesis, and viral infection among others. The combination group included both drug-alone and radiation-alone changes. Our data demonstrate the rapidity of gene expression and functional pathway changes in the evolving tumor as it responds to treatment. Discovering these phenotypic adaptations may help elucidate the challenges in using sustained treatment regimens and could also define evolving targets for therapeutic efficacy.
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Affiliation(s)
- Michelle A. Bylicky
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Uma Shankavaram
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Molykutty J. Aryankalayil
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Sunita Chopra
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Sarwat Naz
- Radiation Biology Branch, National Cancer Institute, NIH, Bethesda, Maryland
| | - Anastasia L. Sowers
- Radiation Biology Branch, National Cancer Institute, NIH, Bethesda, Maryland
| | - Rajani Choudhuri
- Radiation Biology Branch, National Cancer Institute, NIH, Bethesda, Maryland
| | - Valerie Calvert
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | - Iris Eke
- Department of Radiation Oncology, Stanford University Medical School, Stanford, California
| | - James B. Mitchell
- Radiation Biology Branch, National Cancer Institute, NIH, Bethesda, Maryland
| | - C. Norman Coleman
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
- Radiation Research Program, National Cancer Institute, NIH, Rockville, Maryland
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3
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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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4
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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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Grants
- HU0001-16-2-0006 United States Department of Defense | Uniformed Services University of the Health Sciences (Uniformed Services University)
- HU0001-19-2-0031 United States Department of Defense | Uniformed Services University of the Health Sciences (Uniformed Services University)
- HU0001-20-2-0033 United States Department of Defense | Uniformed Services University of the Health Sciences (Uniformed Services University)
- HU0001-21-2-0027 United States Department of Defense | Uniformed Services University of the Health Sciences (Uniformed Services University)
- HU0001-18-2-0032 United States Department of Defense | Uniformed Services University of the Health Sciences (Uniformed Services University)
- HU0001-18-2-0032 United States Department of Defense | Uniformed Services University of the Health Sciences (Uniformed Services University)
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027 United States Department of Defense | Uniformed Services University of the Health Sciences (Uniformed Services University)
- HU0001-16-2-0006, HU0001-19-2-0031, HU0001-20-2-0033, and HU0001-21-2-0027 United States Department of Defense | Uniformed Services University of the Health Sciences (Uniformed Services University)
- 1092856, 1117044, 2008781, and 1186505 Department of Health | National Health and Medical Research Council (NHMRC)
- 1092856, 1117044 and 2008781 Department of Health | National Health and Medical Research Council (NHMRC)
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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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5
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Blas PE, Rodriguez ESR, Williams HL, Levin MK, Bell JSK, Pierobon M, Barrett AS, Petricoin EF, O'Shaughnessy JA. Targeting HER2/HER3 co-mutations in metastatic breast cancer: Case reports of exceptional responders to trastuzumab and pertuzumab therapy. Cancer Rep (Hoboken) 2024; 7:e1954. [PMID: 38441358 PMCID: PMC10913072 DOI: 10.1002/cnr2.1954] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/13/2023] [Accepted: 12/04/2023] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Overexpression of HER2 plays an important role in cancer progression and is the target of multiple therapies in HER2-positive breast cancer. Recent studies have also highlighted the presence of activating mutations in HER2, and HER3 that are predicted to enhance HER2 downstream pathway activation in a HER2-dependent manner. METHODS In this report, we present two exceptional responses in hormone receptor-positive, HER2-nonamplified, HER2/HER3 co-mutated metastatic breast cancer patients who were treated with the anti-HER2-directed monoclonal antibodies, trastuzumab and pertuzumab. RESULTS Both patients acheived exceptional responses to treatment, suggesting that combined trastuzumab, pertuzumab, and endocrine therapy could be a highly effective therapy for these patients and our observations could help prioritize trastuzumab deruxtecan as an early therapeutic choice for patients whose cancers have activating mutations in HER2.
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Affiliation(s)
- Page E. Blas
- Clinical Oncology Research CoordinationBaylor Scott and White Research InstituteDallasTexasUSA
| | | | - Heather L. Williams
- Clinical Oncology Research CoordinationBaylor Scott and White Research InstituteDallasTexasUSA
| | - Maren K. Levin
- Clinical Oncology Research CoordinationBaylor Scott and White Research InstituteDallasTexasUSA
| | - Joshua S. K. Bell
- Department of Translational ScienceTempus Labs Inc.ChicagoIllinoisUSA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular MedicineGeorge Mason UniversityManassasVirginiaUSA
| | | | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular MedicineGeorge Mason UniversityManassasVirginiaUSA
| | - Joyce A. O'Shaughnessy
- Breast Cancer Research ProgramBaylor University Medical Center, Texas Oncology, US OncologyDallasTexasUSA
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6
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Delgado-Coka LA, Horowitz M, Torrente-Goncalves M, Roa-Peña L, Leiton CV, Hasan M, Babu S, Fassler D, Oentoro J, Karen Bai JD, Petricoin EF, Matrisian LM, Blais EM, Marchenko N, Allard FD, Jiang W, Larson B, Hendifar A, Chen C, Abousamra S, Samaras D, Kurc T, Saltz J, Escobar-Hoyos LF, Shroyer K. Keratin 17 modulates the immune topography of pancreatic cancer. Res Sq 2024:rs.3.rs-3886691. [PMID: 38464123 PMCID: PMC10925455 DOI: 10.21203/rs.3.rs-3886691/v1] [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] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Background The immune microenvironment impacts tumor growth, invasion, metastasis, and patient survival and may provide opportunities for therapeutic intervention in pancreatic ductal adenocarcinoma (PDAC). Although never studied as a potential modulator of the immune response in most cancers, Keratin 17 (K17), a biomarker of the most aggressive (basal) molecular subtype of PDAC, is intimately involved in the histogenesis of the immune response in psoriasis, basal cell carcinoma, and cervical squamous cell carcinoma. Thus, we hypothesized that K17 expression could also impact the immune cell response in PDAC, and that uncovering this relationship could provide insight to guide the development of immunotherapeutic opportunities to extend patient survival. Methods Multiplex immunohistochemistry (mIHC) and automated image analysis based on novel computational imaging technology were used to decipher the abundance and spatial distribution of T cells, macrophages, and tumor cells, relative to K17 expression in 235 PDACs. Results K17 expression had profound effects on the exclusion of intratumoral CD8 + T cells and was also associated with decreased numbers of peritumoral CD8 + T cells, CD16 + macrophages, and CD163 + macrophages (p < 0.0001). The differences in the intratumor and peritumoral CD8 + T cell abundance were not impacted by neoadjuvant therapy, tumor stage, grade, lymph node status, histologic subtype, nor KRAS, p53, SMAD4, or CDKN2A mutations. Conclusions Thus, K17 expression correlates with major differences in the immune microenvironment that are independent of any tested clinicopathologic or tumor intrinsic variables, suggesting that targeting K17-mediated immune effects on the immune system could restore the innate immunologic response to PDAC and might provide novel opportunities to restore immunotherapeutic approaches for this most deadly form of cancer.
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7
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Albain KS, Yau C, Petricoin EF, Wolf DM, Lang JE, Chien AJ, Haddad T, Forero-Torres A, Wallace AM, Kaplan H, Pusztai L, Euhus D, Nanda R, Elias AD, Clark AS, Godellas C, Boughey JC, Isaacs C, Tripathy D, Lu J, Yung RL, Gallagher RI, Wulfkuhle JD, Brown-Swigart L, Krings G, Chen YY, Potter DA, Stringer-Reasor E, Blair S, Asare SM, Wilson A, Hirst GL, Singhrao R, Buxton M, Clennell JL, Sanil A, Berry S, Asare AL, Matthews JB, DeMichele AM, Hylton NM, Melisko M, Perlmutter J, Rugo HS, Symmans WF, van’t Veer LJ, Yee D, Berry DA, Esserman LJ. Neoadjuvant Trebananib plus Paclitaxel-based Chemotherapy for Stage II/III Breast Cancer in the Adaptively Randomized I-SPY2 Trial-Efficacy and Biomarker Discovery. Clin Cancer Res 2024; 30:729-740. [PMID: 38109213 PMCID: PMC10956403 DOI: 10.1158/1078-0432.ccr-22-2256] [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: 10/28/2022] [Revised: 10/11/2023] [Accepted: 12/13/2023] [Indexed: 12/20/2023]
Abstract
PURPOSE The neutralizing peptibody trebananib prevents angiopoietin-1 and angiopoietin-2 from binding with Tie2 receptors, inhibiting angiogenesis and proliferation. Trebananib was combined with paclitaxel±trastuzumab in the I-SPY2 breast cancer trial. PATIENTS AND METHODS I-SPY2, a phase II neoadjuvant trial, adaptively randomizes patients with high-risk, early-stage breast cancer to one of several experimental therapies or control based on receptor subtypes as defined by hormone receptor (HR) and HER2 status and MammaPrint risk (MP1, MP2). The primary endpoint is pathologic complete response (pCR). A therapy "graduates" if/when it achieves 85% Bayesian probability of success in a phase III trial within a given subtype. Patients received weekly paclitaxel (plus trastuzumab if HER2-positive) without (control) or with weekly intravenous trebananib, followed by doxorubicin/cyclophosphamide and surgery. Pathway-specific biomarkers were assessed for response prediction. RESULTS There were 134 participants randomized to trebananib and 133 to control. Although trebananib did not graduate in any signature [phase III probabilities: Hazard ratio (HR)-negative (78%), HR-negative/HER2-positive (74%), HR-negative/HER2-negative (77%), and MP2 (79%)], it demonstrated high probability of superior pCR rates over control (92%-99%) among these subtypes. Trebananib improved 3-year event-free survival (HR 0.67), with no significant increase in adverse events. Activation levels of the Tie2 receptor and downstream signaling partners predicted trebananib response in HER2-positive disease; high expression of a CD8 T-cell gene signature predicted response in HR-negative/HER2-negative disease. CONCLUSIONS The angiopoietin (Ang)/Tie2 axis inhibitor trebananib combined with standard neoadjuvant therapy increased estimated pCR rates across HR-negative and MP2 subtypes, with probabilities of superiority >90%. Further study of Ang/Tie2 receptor axis inhibitors in validated, biomarker-predicted sensitive subtypes is warranted.
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Affiliation(s)
- Kathy S. Albain
- Loyola University Chicago Stritch School of Medicine, Chicago, IL
| | - Christina Yau
- University of California San Francisco, San Francisco, CA
| | | | - Denise M. Wolf
- University of California San Francisco, San Francisco, CA
| | | | - A. Jo Chien
- University of California San Francisco, San Francisco, CA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Debu Tripathy
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Janice Lu
- University of Southern California, Los Angeles, CA
| | | | | | | | | | - Gregor Krings
- University of California San Francisco, San Francisco, CA
| | - Yunn Yi Chen
- University of California San Francisco, San Francisco, CA
| | | | | | - Sarah Blair
- University of California San Diego, La Jolla, CA
| | - Smita M. Asare
- Quantum Leap Healthcare Collaborative, San Francisco, CA
| | - Amy Wilson
- Quantum Leap Healthcare Collaborative, San Francisco, CA
| | | | - Ruby Singhrao
- University of California San Francisco, San Francisco, CA
| | | | | | | | | | - Adam L. Asare
- Quantum Leap Healthcare Collaborative, San Francisco, CA
| | | | | | - Nola M. Hylton
- University of California San Francisco, San Francisco, CA
| | | | | | - Hope S. Rugo
- University of California San Francisco, San Francisco, CA
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8
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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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9
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Schaefer A, Hodge RG, Zhang H, Hobbs GA, Dilly J, Huynh M, Goodwin CM, Zhang F, Diehl JN, Pierobon M, Baldelli E, Javaid S, Guthrie K, Rashid NU, Petricoin EF, Cox AD, Hahn WC, Aguirre AJ, Bass AJ, Der CJ. RHOA L57V drives the development of diffuse gastric cancer through IGF1R-PAK1-YAP1 signaling. Sci Signal 2023; 16:eadg5289. [PMID: 38113333 PMCID: PMC10791543 DOI: 10.1126/scisignal.adg5289] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 11/03/2023] [Indexed: 12/21/2023]
Abstract
Cancer-associated mutations in the guanosine triphosphatase (GTPase) RHOA are found at different locations from the mutational hotspots in the structurally and biochemically related RAS. Tyr42-to-Cys (Y42C) and Leu57-to-Val (L57V) substitutions are the two most prevalent RHOA mutations in diffuse gastric cancer (DGC). RHOAY42C exhibits a gain-of-function phenotype and is an oncogenic driver in DGC. Here, we determined how RHOAL57V promotes DGC growth. In mouse gastric organoids with deletion of Cdh1, which encodes the cell adhesion protein E-cadherin, the expression of RHOAL57V, but not of wild-type RHOA, induced an abnormal morphology similar to that of patient-derived DGC organoids. RHOAL57V also exhibited a gain-of-function phenotype and promoted F-actin stress fiber formation and cell migration. RHOAL57V retained interaction with effectors but exhibited impaired RHOA-intrinsic and GAP-catalyzed GTP hydrolysis, which favored formation of the active GTP-bound state. Introduction of missense mutations at KRAS residues analogous to Tyr42 and Leu57 in RHOA did not activate KRAS oncogenic potential, indicating distinct functional effects in otherwise highly related GTPases. Both RHOA mutants stimulated the transcriptional co-activator YAP1 through actin dynamics to promote DGC progression; however, RHOAL57V additionally did so by activating the kinases IGF1R and PAK1, distinct from the FAK-mediated mechanism induced by RHOAY42C. Our results reveal that RHOAL57V and RHOAY42C drive the development of DGC through distinct biochemical and signaling mechanisms.
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Affiliation(s)
- Antje Schaefer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Richard G. Hodge
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Haisheng Zhang
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - G. Aaron Hobbs
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Julien Dilly
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Minh Huynh
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Craig M. Goodwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Feifei Zhang
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - J. Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Sehrish Javaid
- Program in Oral and Craniofacial Biomedicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karson Guthrie
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Naim U. Rashid
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Adrienne D. Cox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Program in Oral and Craniofacial Biomedicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William C. Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Andrew J. Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Adam J. Bass
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Herbert Irving Comprehensive Cancer Center at Columbia University, New York, NY 10032, USA
| | - Channing J. Der
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Program in Oral and Craniofacial Biomedicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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10
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Gallagher RI, Wulfkuhle J, Wolf DM, Brown-Swigart L, Yau C, O'Grady N, Basu A, Lu R, Campbell MJ, Magbanua MJ, Coppé JP, Asare SM, Sit L, Matthews JB, Perlmutter J, Hylton N, Liu MC, Symmans WF, Rugo HS, Isaacs C, DeMichele AM, Yee D, Pohlmann PR, Hirst GL, Esserman LJ, van 't Veer LJ, Petricoin EF. Protein signaling and drug target activation signatures to guide therapy prioritization: Therapeutic resistance and sensitivity in the I-SPY 2 Trial. Cell Rep Med 2023; 4:101312. [PMID: 38086377 PMCID: PMC10772394 DOI: 10.1016/j.xcrm.2023.101312] [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: 12/07/2022] [Revised: 07/03/2023] [Accepted: 11/14/2023] [Indexed: 12/22/2023]
Abstract
Molecular subtyping of breast cancer is based mostly on HR/HER2 and gene expression-based immune, DNA repair deficiency, and luminal signatures. We extend this description via functional protein pathway activation mapping using pre-treatment, quantitative expression data from 139 proteins/phosphoproteins from 736 patients across 8 treatment arms of the I-SPY 2 Trial (ClinicalTrials.gov: NCT01042379). We identify predictive fit-for-purpose, mechanism-of-action-based signatures and individual predictive protein biomarker candidates by evaluating associations with pathologic complete response. Elevated levels of cyclin D1, estrogen receptor alpha, and androgen receptor S650 associate with non-response and are biomarkers for global resistance. We uncover protein/phosphoprotein-based signatures that can be utilized both for molecularly rationalized therapeutic selection and for response prediction. We introduce a dichotomous HER2 activation response predictive signature for stratifying triple-negative breast cancer patients to either HER2 or immune checkpoint therapy response as a model for how protein activation signatures provide a different lens to view the molecular landscape of breast cancer and synergize with transcriptomic-defined signatures.
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Affiliation(s)
- Rosa I Gallagher
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA.
| | - Julia Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA.
| | - Denise M Wolf
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lamorna Brown-Swigart
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christina Yau
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nicholas O'Grady
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amrita Basu
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ruixiao Lu
- Quantum Leap Healthcare Collaborative, San Francisco, CA 94118, USA
| | - Michael J Campbell
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mark J Magbanua
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jean-Philippe Coppé
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Smita M Asare
- Quantum Leap Healthcare Collaborative, San Francisco, CA 94118, USA
| | - Laura Sit
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey B Matthews
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Nola Hylton
- Department of Radiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Minetta C Liu
- Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - W Fraser Symmans
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hope S Rugo
- Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA
| | - Angela M DeMichele
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Douglas Yee
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paula R Pohlmann
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gillian L Hirst
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laura J Esserman
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laura J van 't Veer
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA.
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Corder ML, Petricoin EF, Li Y, Cleland TP, DeCandia AL, Alonso Aguirre A, Pukazhenthi BS. Metabolomic profiling implicates mitochondrial and immune dysfunction in disease syndromes of the critically endangered black rhinoceros (Diceros bicornis). Sci Rep 2023; 13:15464. [PMID: 37726331 PMCID: PMC10509206 DOI: 10.1038/s41598-023-41508-4] [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: 05/04/2023] [Accepted: 08/28/2023] [Indexed: 09/21/2023] Open
Abstract
The critically endangered black rhinoceros (Diceros bicornis; black rhino) experiences extinction threats from poaching in-situ. The ex-situ population, which serves as a genetic reservoir against impending extinction threats, experiences its own threats to survival related to several disease syndromes not typically observed among their wild counterparts. We performed an untargeted metabolomic analysis of serum from 30 ex-situ housed black rhinos (Eastern black rhino, EBR, n = 14 animals; Southern black rhino, SBR, n = 16 animals) and analyzed differences in metabolite profiles between subspecies, sex, and health status (healthy n = 13 vs. diseased n = 14). Of the 636 metabolites detected, several were differentially (fold change > 1.5; p < 0.05) expressed between EBR vs. SBR (40 metabolites), female vs. male (36 metabolites), and healthy vs. diseased (22 metabolites). Results suggest dysregulation of propanoate, amino acid metabolism, and bile acid biosynthesis in the subspecies and sex comparisons. Assessment of healthy versus diseased rhinos indicates involvement of arachidonic acid metabolism, bile acid biosynthesis, and the pentose phosphate pathway in animals exhibiting inflammatory disease syndromes. This study represents the first systematic characterization of the circulating serum metabolome in the black rhinoceros. Findings further implicate mitochondrial and immune dysfunction as key contributors for the diverse disease syndromes reported in ex-situ managed black rhinos.
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Affiliation(s)
- Molly L Corder
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, 22630, USA
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, 20900, USA
- Department of Environmental Sciences and Policy, George Mason University, Fairfax, Virginia, 22030, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, 20900, USA
| | - Yue Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | | | - Alexandra L DeCandia
- Department of Biology, Georgetown University, Washington, DC, 20057, USA
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Conservation Genomics, Washington, DC, 20008, USA
| | - A Alonso Aguirre
- Department of Fish, Wildlife, and Conservation Biology, Warner College of Natural Resources, Colorado State University, Fort Collins, 80523, USA
| | - Budhan S Pukazhenthi
- Smithsonian's National Zoo and Conservation Biology Institute, Center for Species Survival, Front Royal, 22630, USA.
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12
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Pierobon M, Petricoin EF. Functional proteomic analysis, a missing piece for understanding clonal evolution and cooperation in the tissue microecology. Expert Rev Mol Diagn 2023; 23:1057-1059. [PMID: 37902050 DOI: 10.1080/14737159.2023.2277371] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/20/2023] [Indexed: 10/31/2023]
Affiliation(s)
- Mariaelena Pierobon
- School of Systems Biology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Emanuel F Petricoin
- School of Systems Biology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
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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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Bui TBV, Wolf DM, Moore K, Harris IS, Phadatare P, Yau C, Swigart LAB, Esserman LJ, Coppe JP, Wulfkuhle J, Petricoin EF, Campbell M, Selfors LM, Dillon DA, Overmoyer B, Lynce F, Van ’t Veer L, Rosenbluth J. Abstract PD5-02: PD5-02 An Organoid Model System to Study Resistance Mechanisms, Predictive Biomarkers, and New Strategies to Overcome Therapeutic Resistance in Early-Stage Triple-Negative Breast Cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-pd5-02] [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: 03/06/2023]
Abstract
Abstract
Background: While new treatments and improved subtyping schemas are anticipated to improve treatment response in triple-negative breast cancer (TNBC) patients, therapeutic resistance remains a significant challenge. Moreover, there is an urgent need for additional research model systems to study resistance and residual disease in breast cancer, including aggressive subtypes of breast cancer. Organoid culture is a promising technology used for growing breast cancer cells with high efficiency; however, the extent to which treatment resistance can be modeled using this system is unknown. This research used patient-derived organoid cultures in the context of computational analyses of large molecular and clinical datasets to study resistance mechanisms, biomarkers, and alternative treatment strategies to overcome drug resistance in early-stage TNBC. Methods: Organoid cultures were derived from breast tumor samples (taken from lumpectomy, mastectomy, or core biopsy samples), digested to the organoid level using collagenase, and grown in three dimensional cultures using a basement membrane extract and a fully-defined organoid medium (Dekkers et al. Nat Protoc 2021). An evaluation of all available I-SPY2 biomarker data (Wolf et al. Cancer Cell 2022) was performed focusing on genes, proteins, and pathways associated with resistance. These were then used to study whether resistance biomarkers identified in patient tumors are also present in organoids propagated from breast cancer post-treatment residual disease. To this end, bulk RNA sequencing data of organoids were normalized and merged with the TCGA dataset (Hoadley et al. Cell 2018) to enable analysis in a larger context, and immunofluorescence staining of organoids was performed. A high-throughput 386 anti-cancer drug compound screen and subsequent synergy testing with the most promising compounds were performed to identify and predict alternative treatment strategies. Additional assays to explore kinome activity in this organoid model are in progress. Results: A TNBC organoid biobank was established (n=31), which was enriched for inflammatory breast cancer (IBC; n=15), an aggressive form of breast cancer. Most organoids were derived from residual disease after neoadjuvant therapy. Bulk RNA sequencing analysis performed on 10 TNBC organoids revealed 3 subsets that were characterized predominantly by either normal-like/luminal androgen receptor or basal-like features or expressed distinct gene expression profiles, with IBC cases present in all 3 subsets. Intriguingly, the IBC organoids were characterized by higher expression of a number of immune-related signatures, despite an absence of clear immune cells in culture. A residual disease IBC/TNBC organoid resistant to chemotherapy was used to perform the 386-drug compound screen. The organoid model showed resistance to veliparib-cisplatin, consistent with the expression of gene/protein biomarkers predictive of drug resistance found in I-SPY2 (low PARPi7 levels and high pFOXO1 and pMEK1/2 expression). In addition, the screen identified multiple classes of inhibitors as promising synergistic/additive candidates for overcoming resistance to cisplatin. Conclusion: In this proof-of-principle study, we demonstrated the utility of matching I-SPY2 resistance biomarkers and signatures to residual disease tumor organoid cultures. We show that tumor organoid cultures modeling drug resistance states are a useful complement to existing research models of breast cancer and can be used for compound testing. We have developed a pipeline to propagate residual tumors from patients enrolled in I-SPY2 into organoid cultures to create a broader platform for preclinical drug testing informed by tumor biology with the ultimate goal of enabling faster, more successful translational studies and increased treatment options for resistant disease.
Citation Format: Tam Binh V. Bui, Denise M. Wolf, Kaitlin Moore, Isaac S. Harris, Pravin Phadatare, Christina Yau, Lamorna A. Brown Swigart, Laura J. Esserman, Jean-Philippe Coppe, Julia Wulfkuhle, Emanuel F. Petricoin, Michael Campbell, Laura M. Selfors, Deborah A. Dillon, Beth Overmoyer, Filipa Lynce, Laura Van ’t Veer, Jennifer Rosenbluth. PD5-02 An Organoid Model System to Study Resistance Mechanisms, Predictive Biomarkers, and New Strategies to Overcome Therapeutic Resistance in Early-Stage Triple-Negative Breast Cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD5-02.
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Affiliation(s)
- Tam Binh V. Bui
- 1University of California, San Francisco, Utrecht University
| | | | | | | | | | - Christina Yau
- 6University of California, San Francisco and Buck Institute for Research on Aging, Novato, California
| | | | | | | | | | | | | | | | - Deborah A. Dillon
- 14Brigham and Women’s Hospital, Breast Oncology Program, Susan F. Smith Center for Women’s Cancers, Dana-Farber Brigham Cancer Center; Harvard Medical School
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Weinberg K, Pierobon M, Blais E, Davis J, O’Shaughnessy J, Petricoin EF. Abstract P4-07-51: Impact of the Theralink CLIA protein/phosphoprotein assay on treatment selection in routine clinical practice: a prospective observational study in advanced breast cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p4-07-51] [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: 03/06/2023]
Abstract
Abstract
Background: The Theralink Reverse Phase Protein Array-based (RPPA) CLIA assay is a novel molecular assay developed to assist physicians in therapy selection for patients diagnosed with advanced/recurrent breast cancer. The assay was specifically designed to quantitatively measure protein activation/phosphorylation of 32 FDA-approved and Phase III drug targets and pathway-linked downstream substrates, providing functional information on actionable oncogenic drivers in individual tumors. Given the recent commercialization of the Theralink assay (TLA), knowledge gaps exist regarding its use in routine clinical practice and the impact of the test on clinical decision-making in real world practice. The primary objective of this analysis was to assess how the TLA has been integrated in therapy selection for breast cancer patients with a focus on understanding its target population, the rationale for patient selection by the treating physician, and the utilization of the molecule information generated by the assay as part of the therapeutic decision-making process. Findings from this study will help optimize patient selection and maximize the clinical impact of the test as a tool for advancing precision oncology. Methods: We prospectively collected data from 124 women with advanced breast cancer whose tumors were profiled using the Breast Cancer TLA from February, 2021 to May, 2022. All patients were confirmed as actively managed for advanced/recurrent breast cancer. Eight μm FFPE sections (n=5) from a recently collected tissue biopsy were used to isolate tumor epithelia via Laser Capture Microdissection and to generate RPPA-based molecular profiles. Clinical management and therapy selection information for 68 patients was gathered via surveys completed by treating physicians. Results: Median age of the 124 participants was 53 years (range 26-82) and 111 (89.5%) patients had stage IV disease. The cohort included 66 hormone receptors positive (of which 5 were HER2+), 51 triple negative, and 7 HR-/HER2+ breast cancers. The TLA yielded molecular information for all specimens and profiles were generated on average in 11 days. One or more targets were highly activated (highly actionable) in 91 patients (73.4%) and moderately activated (partially actionable) in 29 patents; only 4 patients had no actionable target (3.2%). Previous treatment information was available for 118 (95.2%) patients. The TLA was requested to assist with the selection of first-line treatment in 36 patients (of which 24 had previously received neoadjuvant treatment), second-line treatment in 35 patients and third- or subsequential-lines of treatment in 47 patients. Clinicians provided feedback on the use of the assay for 68 patients included in the study. The survey revealed that the TLA impacted treatment selection in 50 (73.5%) cases and was used to either expand options beyond standard of care (30 cases), refine/re-prioritize available treatments (11 cases), narrow treatment from a plethora of options (2 cases) or a combination of the three (7 cases). When TLA data were used for treatment selection, physicians defined the assay highly and moderately beneficial for patient management in 15 and 27 cases, respectively. Conclusion: Our study suggests the TLA yields useful information for selecting treatment for breast cancer patients with advanced/recurrent disease. In this prospective analysis, the assay identified actionable targets in more than 90% of patients, which is significantly higher than what has previously been reported for genomic profiling alone. Overall, physicians found the information yielded by the assay useful for selecting treatment. The inclusion of the TLA in oncology may offer important insights for advancing precision medicine for breast cancer patients.
Citation Format: Kris Weinberg, Mariaelena Pierobon, Edik Blais, Justin Davis, Joyce O’Shaughnessy, Emanuel F. Petricoin. Impact of the Theralink CLIA protein/phosphoprotein assay on treatment selection in routine clinical practice: a prospective observational study in advanced breast cancer. [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-07-51.
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Affiliation(s)
| | | | | | | | - Joyce O’Shaughnessy
- 5Baylor University Medical Center, Texas Oncology, US Oncology, Dallas, TX, USA
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Wulfkuhle J, Blas P, Williams H, Mueller C, Gallagher RI, Pierobon M, O’Shaughnessy J, Petricoin EF. Abstract PD5-08: PD5-08 Drug target activation mapping of matched triple negative primary and axillary lymph node metastases identifies and links the ER-AR-GR steroid hormone receptor axis with downstream AKT activation. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-pd5-08] [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: 03/06/2023]
Abstract
Abstract
Title: Drug target activation mapping of matched triple negative primary and axillary LN metastases identifies and links the ER-AR-GR steroid hormone receptor axis with downstream AKT activation Background: Triple negative breast cancer (TNBC) is comprised of heterogeneous subtypes that arise from various molecular alterations that result in TNBC having the poorest overall prognosis. There is growing interest in more sensitive ways to measure estrogen receptor (ER) and HER2 levels in the ER “negative” and HER2 “low/negative” settings, as there are patients with TNBC whose tumors are actually ER and/or HER2 “expressing/active”, and who may benefit from ER- and/or HER2-targeted therapies. Given the limitations of IHC in reliably quantitating ER and HER2 in low (0-1+) expressing tumors, we utilized highly sensitive reverse phase protein array (RPPA) to quantitate expression of these therapeutic targets along with downstream signaling activation mapping in a unique pilot set of patient-matched primary (P) and axillary lymph node (LN) metastases obtained synchronously. The quantitative expression of steroid hormone receptor expression/activation (ER, glucocorticoid receptor (GR), androgen receptor (AR)) along with their signaling architecture and dynamics were analyzed. Methods: A 12 P-LN paired tumor set was chosen for analysis (N=24). Manual macrodissection was used to enrich for tumor epithelium prior to RPPA analysis that quantitatively measured 155 proteins/phosphoprotein drug targets in key signaling pathways known to be involved in steroid hormone receptor biology and tumorigenesis. Statistical analysis using paired sample t-testing or Wilcoxon rank testing was performed (p< 0.05 uncorrected). Results: Protein pathway activation mapping and unsupervised clustering analysis revealed a subset of TNBCs from 3 of the 12 (25%) patients (N=4: 1 LN and 1 P, and one patient-matched LN and P) that was characterized by high relative levels of total ER. Interestingly, these same tumors also had amongst the highest relative levels of both total AR and activated (phosphorylated) GR compared to the rest of the 20 tumor samples. Downstream signaling analysis found significant (p< 0.05) activation/phosphorylation of AKT (S473 and/or T308) associated with the ER-AR-GR/steroid hormone activated/”high” TNBC signature compared to the 20 tumors that were steroid hormone “low”. Conclusions: Functional protein pathway activation mapping of a unique study set of synchronously obtained TNBC primary and LN metastasis revealed a steroid hormone receptor expression/activation signature of co-incidentally activated/expressed ER, GR and AR, that was also characterized by increased AKT activation (p< 0.05). This steroid hormone receptor “activated” signature was not observed to be significantly differentially expressed in LN compared to P tissues in cohort or matched pair analysis, suggesting that this signature may be present as an intrinsic event in the P, and not acquired in LN metastases. Recent data from stage I-III TNBC patients treated in the neoadjuvant setting with an AKT inhibitor1 revealed that responding TNBC patients had pre-treatment tumor biopsies that were enriched for both high AR expression and high phosphoAKT (S473 and/or T308) levels. If these observations that a subset of TNBCs are steroid hormone receptor “activated” despite being ER “negative” are confirmed in larger study sets, we hypothesize that this subgroup, identified by RPPA analysis of both P and LN metastases, could be potentially sensitive to AKT inhibition in combination with agents that target steroid hormone receptors. 1Shi Z, et al. Functional Mapping of AKT Signaling and Biomarkers of Response from the FAIRLANE Trial of Neoadjuvant Ipatasertib plus Paclitaxel for Triple-Negative Breast Cancer. Clin Cancer Res. 2022 Mar 1;28(5):993-1003
Citation Format: Julia Wulfkuhle, Page Blas, Heather Williams, Claudius Mueller, Rosa I. Gallagher, Mariaelena Pierobon, Joyce O’Shaughnessy, Emanuel F. Petricoin. PD5-08 Drug target activation mapping of matched triple negative primary and axillary lymph node metastases identifies and links the ER-AR-GR steroid hormone receptor axis with downstream AKT activation [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD5-08.
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Affiliation(s)
| | - Page Blas
- 2Baylor Scott and White Research Institute
| | | | | | | | | | - Joyce O’Shaughnessy
- 7Baylor University Medical Center, Texas Oncology, US Oncology, Dallas, TX, USA
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Wolf DM, Yau C, Wulfkuhle J, Gallagher RI, Swigart LAB, Hirst GL, Coppe JP, Magbanua MJM, Sayaman R, Investigators ISPY, Sit L, Hylton NM, DeMichele A, Berry DA, Pusztai L, Yee D, Esserman LJ, Petricoin EF, Van ’t Veer L. Abstract PD5-04: PD5-04 Characterizing the HER2-/Immune-/DNA repair (DRD-) response predictive breast cancer subtype: the hunt for new protein targets in a high-needs population with low response to all I-SPY2 agents. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-pd5-04] [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: 03/06/2023]
Abstract
Abstract
Background: In previous work we leveraged the I-SPY2 trial to create treatment response predictive subtypes (RPS) incorporating tumor biology beyond clinical HR/HER2, to better predict drug responses in an expanded treatment landscape that includes platinum agents, dual HER2-targeting regimens and immunotherapy [1]. We showed that best performing schemas incorporate Immune, DRD and HER2/Luminal phenotypes, and that treatment allocation based on these would increase the overall pCR rate to 63% from 51% using HR/HER2-based treatment selection. The RPS schema has been selected for prospective evaluation in I-SPY2. Using the RPS, one would prioritize platinum-based therapy for HER2-/Immune-/DRD+, immunotherapy for HER2-/Immune+, and dual-anti-HER2 for HER2+ that are not luminal. HER2+/Luminal patients have low response rates to dual-anti-HER2 therapy but may respond better to anti-AKT. However, there is still a considerable ‘biomarker-negative’ group of resistant cancers (HER2-/Immune-/DRD-) with very low pCR rates to all tested agents, that require a new therapeutic approach. Here we characterize the protein signaling architecture of these tumors to identify new target candidates. Methods: 987 I-SPY 2 patients from 10 arms of the trial were considered for this analysis. All have gene expression, pCR and RPS; 944 have distant recurrence free survival (DRFS) data; and 736 have reverse phase protein array (RPPA) data from laser capture microdissected tumor epithelium. These data – known collectively as the I-SPY2-990 mRNA/RPPA Data Resource - were recently made public on NCBI’s Gene Expression Omnibus [GEO: GSE196096]. We focus on HER2-/Immune-/DRD- tumors, applying Wilcoxon and t-tests to identify phosphoproteins that differ between HR+HER2-/Immune-/DRD- and other HR+HER2- tumors; and between TN/Immune-/DRD- and other TNs. The Benjamini-Hochberg (BH) method is used to adjust p-values for multiple hypothesis testing. In addition, the Kaplan-Meier method is used to estimate DRFS. Results: 201/736 I-SPY 2 patients with RPPA data are classified HER2-/Immune-/DRD- (HR+HER2-: n=138; TN: n=63). Of these, 8.5% (17/201) achieved pCR. Non-responding HER2-/Immune-DRD- had worse outcomes than responders (~75% vs. ~95% DRFS at 5 years). 60/139 phospho-proteins differ significantly between HR+HER2-/Immune-/DRD- and other HR+HER2- tumors (n=122). These tumors are relatively ‘cold’, in that 90% (54/60) of the phosphoprotein activities characterizing this group are at lower levels than in the overall HR+HER2- population; including immune (e.g. pPDL1, pJAK/STAT) and proliferation (e.g., Ki67, CyclinB1, pAURK) endpoints. Phosphoproteins showing higher levels in this subset include ERBB2 (BH p=1.7E-06), Cyclin D1 (BH p=1.4E-05), pAR (BH p=1.4E-05), and ER (BH p=3E-04). Within the TN subset, only 3/139 phospho-proteins differed significantly between TN/Immune-/DRD- and other TN tumors (n=189). These were all immune-related (pPDL1, pSTAT1, and HLA DR), with lower expression in the TN/Immune-/DRD- group. Conclusion: HR+HER2- and TN patients who are Immune-Low and DRD-Low have very low pCR rates to all tested therapeutics in I-SPY2 including standard chemotherapy, platinum, and immunotherapy. Senolytics (possibly targeting Cyclin D1), HER2low agents, and AR modulators may overcome resistance in HR+HER2-/Immune-/DRD-, whereas an immune activator beyond checkpoint inhibition is suggested for TN/Immune-/DRD- patients. [1] Wolf et. al., Redefining Breast Cancer Subtypes to Guide Treatment Prioritization and Maximize Response: Predictive Biomarkers across 10 Cancer Therapies. Cancer Cell 2022
Citation Format: Denise M. Wolf, Christina Yau, Julia Wulfkuhle, Rosa I. Gallagher, Lamorna A. Brown Swigart, Gillian L. Hirst, Jean-Philippe Coppe, Mark Jesus M. Magbanua, Rosalyn Sayaman, I-SPY2 Investigators, Laura Sit, Nola M. Hylton, Angela DeMichele, Donald A. Berry, Lajos Pusztai, Douglas Yee, Laura J. Esserman, Emanuel F. Petricoin, Laura Van ’t Veer. PD5-04 Characterizing the HER2-/Immune-/DNA repair (DRD-) response predictive breast cancer subtype: the hunt for new protein targets in a high-needs population with low response to all I-SPY2 agents [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD5-04.
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Affiliation(s)
| | - Christina Yau
- 2University of California, San Francisco and Buck Institute for Research on Aging, Novato, California
| | | | | | | | | | | | | | | | | | - Laura Sit
- 11University of California, San Francisco
| | | | | | | | | | - Douglas Yee
- 16Masonic Cancer Center, University of Minnesota, Minnesota
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Petricoin EF, Corgiat BA, O’Shaughnessy J, LoRusso P, Weinberg K, Davis J, Gawryletz C. Abstract HER2-17: HER2-17 Novel Quantitative HER2 Assay for Determining Dynamic HER2 Expression in the HER2 IHC 0 “Ultra-Low” Setting: Implications for Precision Therapy in HER2- Breast Cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-her2-17] [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: 03/06/2023]
Abstract
Abstract
Background: The HER2 antibody drug conjugate (ADC) fam-trastuzumab deruxtecan-nxki (T-DXd) significantly improves outcomes over standard chemotherapy in pts with HER2-LOW (IHC 1+ and IHC 2+ FISH-) metastatic breast cancer (MBC). Data from the DAISY (NCT04132960) trial in pts with HER2 IHC 0 or “ultra low” MBC revealed median progression-free survival (PFS) of 4.2 mos vs 6.7 mos in HER2-LOW and 11.1 mos in HER2 3+ pts (Diéras V, et al. Cancer Res. 2022;82(4_Suppl):PD8-02). There is an urgent need to develop methods to accurately discern HER2 LOW expression versus HER2 IHC 0/ultra-low expression so appropriate pts may receive T-DXd. We have developed a quantitative HER2 assay using reverse phase protein array (RPPA) technology with laser capture microdissection (LCM) enrichment of tumor epithelium that measures HER2 expression over a 65-fold dynamic range in HER2 IHC 0 to 3+ breast cancers. In I-SPY 1 and 2 trials we found that RPPA-assessed quantitative HER2 and activated/phosphorylated HER2 expression predicted for pathologic complete response in pts with HER2 IHC 0, HER2-LOW and HER2 3+ disease with various HER2 and other targeted agents. We then developed and validated the first CLIA/CAP-accredited quantitative HER2 protein expression and activation assay, and now explore quantitative HER2 expression in HER2 IHC 0/ultra low disease. Given the recent approval of sacituzumab govitecan-hziy in TNBC and the results of the TROPiCS-02 (NCT03901339), we also evaluated quantitative RPPA-based TROP-2 expression levels in HER2 IHC 0 breast cancer. Methods: LCM-enriched tumor epithelium was obtained from freshly cut FFPE core needle and resected breast cancer samples from 175 pts with pathology-determined HER2 IHC 0 status (N=68 ER+ and N=107 ER-). Quantitative HER2 output is generated as a relative intensity unit (RU) that is interpolated to an internal calibrator curve and a population referent comprised of known HER2+ (IHC 3+ and 2+/FISH+), HER2-LOW and HER2 IHC 0/ultra-low tumors to generate population-based cut-points as a referent. RPPA-based quantitative HER2 expression are reported as one of four levels of expression across the HER2 dynamic range observed: “non/extremely low”, “modest“, “moderate”, and “high”. Quantitative TROP2 protein expression levels were also measured for each case by the RPPA assay on the same lysate using the same adjectival determinants of relative expression as HER2. Results: For the HER2 IHC 0 ER+ cohort, we observed HER2 protein expression over a 25-fold dynamic range and that 57% (N=39) had HER2 non/extremely low, 37% (N=25) modest, and 4 (6%) moderate/high HER2 expression by RPPA. For the HER2 IHC 0 ER- cohort, we observed HER2 protein expression over a 15-fold dynamic range and that 71% (N=76) had non/extremely low, and 31% (N=29%) modest HER2 expression. We observed TROP-2 protein expression over a 35-fold dynamic range across all tumors measured, and it was found to be at least modestly expressed in 95% (37/39) ER+ and 95% (72/76) ER- of the IHC 0/ultra-low tumors that were also found to be HER2 non/extremely low by RPPA. Conclusions: LCM-RPPA quantitative assessment of HER2 expression showed that nearly 40% of ER+ IHC 0 and 30% of ER- IHC 0 “ultra-low” breast cancers actually had modest to moderate HER2 expression. Interestingly, this frequency approximates the response rate of 30% seen with T-DXd in HER2 IHC 0 pts in the DAISY trial. Quantitatively measured TROP2 is at least modestly expressed in the vast majority of RPPA-assessed HER2 IHC 0 cancers regardless of ER status, making a TROP2-directed ADC an attractive therapeutic option for these pts. If validated in larger studies, LCM-RPPA-based HER2 expression could provide a better understanding of the potential for therapeutic efficacy with T-DXd in patients with HER2 IHC “ultra-low” disease, and may better define true ultra-low HER2 expression in HER2 IHC 0 tumor biopsies at baseline and refine the lower limit of the HER2-LOW designation.
Citation Format: Emanuel F. Petricoin, Brian A. Corgiat, Joyce O’Shaughnessy, Patricia LoRusso, Kris Weinberg, Justin Davis, Chelsea Gawryletz. HER2-17 Novel Quantitative HER2 Assay for Determining Dynamic HER2 Expression in the HER2 IHC 0 “Ultra-Low” Setting: Implications for Precision Therapy in HER2- Breast Cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr HER2-17.
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Affiliation(s)
| | | | - Joyce O’Shaughnessy
- 3Baylor University Medical Center, Texas Oncology, US Oncology, Dallas, TX, USA
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Hilley S, Dunetz R, Blais E, Pierobon M, Petricoin EF, Baldelli E. Abstract P5-03-12: DNA repair genes are more frequently mutated in non-white populations of metastatic breast cancer (MBC) patients. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p5-03-12] [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: 03/06/2023]
Abstract
Abstract
Background: Although improvements in detection, therapeutic development and molecular profiling have decreased MBC mortality over the last twenty years, clinical outcomes are not being equally realized among all patients. Representation and enrollment into clinical trials are often not reflective of the general MBC population in terms of race and ethnicity, with Black and Hispanic patients being largely and often underrepresented. Not only does this imbalance translate into overall access to novel agents, but the lack of understanding of therapeutic efficacy in minority populations and tumor-based molecular differences reduce the use of truly personalized treatments for these groups. There is an opportunity to improve clinical outcomes for all patients with MBC, starting with a better understanding of the degree of any potential differences in underlying tumor molecular biology between racial groups. Methods: We utilized data from two cohorts of patients whose tumors underwent molecular profiling to examine differences in the frequency of genetic mutations across racial groups with MBC. The first cohort included 856 MBCs whose genomic profiles were retrieved from the AACR Genomics Evidence Neoplasia Information Exchange (GENIE) publicly available database. The second cohort included a separate set of 91 patients with MBC from an ongoing precision medicine program sponsored by the Side-Out Foundation (SOF). While the GENIE data were collected at 19 large academic cancer centers, the SOF data are derived from patients treated in the community setting. We compared the relative distributions of age and reported ethnicity between datasets, and compared the 20 most frequently mutated genes in each racial group across datasets. The analysis across races included 73 genes that were examined for differences in mutation frequency using Fisher’s Exact test and Pearson Chi-Square test (p< 0.05 uncorrected). Results: Although the GENIE set was significantly larger, race distribution was not statistically significant across the two populations. The combined populations included 831 white patients (88.4%), 43 Black patients (4.6%), 30 Asian patients (3.2%), and 35 Hispanic patients (3.7%). The age of initial (59.61) and metastatic (61.19) diagnosis was older in the SOF population compared to the GENIE population (48.81, 53.14; p < 0.001). Hispanic patients (46.92) were diagnosed with MBC at a younger age compared to White patients (53.78; p < 0.001). Of the 73 genes analyzed, 11 genes were found less frequently mutated in whites compared to non-whites including, NTRK1, SDHA, MSH6, TCF3, FANCC, GNAS, COP1, RECQL4, WRN, BCL6, and U2AF1. When the same 73 genes were examined for differences across racial groups, alterations of 22 genes reached statistical significance. The gene(s) with the largest difference compared to white patients were RECQL4 in black patients (13.95% vs 5.29%; p = 0.019), WRN in Asian patients (16.63% vs 2.53%; p < 0.001), and RECQL4 and ERBB2 in Hispanic patients (16.13% vs 5.29%; p = 0.019, p = 0.020). Of the 22 genes that were more frequently altered in the non-white population, 6 have roles in DNA repair including RECQL4, WRN, ERCC2, BLM, MSH6, FANCC. 4/22 are receptor tyrosine kinases (RTKs), including NTRK2, RET, ERBB3, and ERBB2, and 3/22 have roles in immune function, including BCL6, CIITA, and TLR4. Conclusion: Analysis of genomic alterations derived from 2 independent real-world molecular profiling-based cohorts identified in non-whites MBC patients a set of candidate “actionable” genes involved in DNA damage repair, RTK expression, and immune function. Although these results require further validation, considering the relatively small samples sizes of the non-white populations, these findings may provide actionable targets for non-white patients with MBC that could be utilized in future trials.
Citation Format: Sydney Hilley, Rick Dunetz, Edik Blais, Mariaelena Pierobon, Emanuel F. Petricoin, Elisa Baldelli. DNA repair genes are more frequently mutated in non-white populations of metastatic breast cancer (MBC) patients [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-03-12.
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Abu-Khalaf MM, Alex Hodge K, Hatzis C, Baldelli E, El Gazzah E, Valdes F, Sikov WM, Mita MM, Denduluri N, Murphy R, Zelterman D, Liotta L, Dunetz B, Dunetz R, Petricoin EF, Pierobon M. AKT/mTOR signaling modulates resistance to endocrine therapy and CDK4/6 inhibition in metastatic breast cancers. NPJ Precis Oncol 2023; 7:18. [PMID: 36797347 PMCID: PMC9935518 DOI: 10.1038/s41698-023-00360-5] [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: 11/07/2022] [Accepted: 02/07/2023] [Indexed: 02/18/2023] Open
Abstract
Endocrine therapy (ET) in combination with CDK4/6 inhibition is routinely used as first-line treatment for HR+/HER2- metastatic breast cancer (MBC) patients. However, 30-40% of patients quickly develop disease progression. In this open-label multicenter clinical trial, we utilized a hypothesis-driven protein/phosphoprotein-based approach to identify predictive markers of response to ET plus CDK4/6 inhibition in pre-treatment tissue biopsies. Pathway-centered signaling profiles were generated from microdissected tumor epithelia and surrounding stroma/immune cells using the reverse phase protein microarray. Phosphorylation levels of the CDK4/6 downstream substrates Rb (S780) and FoxM1 (T600) were higher in patients with progressive disease (PD) compared to responders (p = 0.02). Systemic PI3K/AKT/mTOR activation in tumor epithelia and stroma/immune cells was detected in patients with PD. This activation was not explained by underpinning genomic alterations alone. As the number of FDA-approved targeted compounds increases, functional protein-based signaling analyses may become a critical component of response prediction and treatment selection for MBC patients.
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Affiliation(s)
- Maysa M. Abu-Khalaf
- grid.415231.00000 0004 0577 7855Sidney Kimmel Cancer Center at Thomas Jefferson University, Philadelphia, PA USA
| | - K. Alex Hodge
- grid.22448.380000 0004 1936 8032School of Systems Biology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, VA USA
| | | | - Elisa Baldelli
- grid.22448.380000 0004 1936 8032School of Systems Biology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, VA USA
| | - Emna El Gazzah
- grid.22448.380000 0004 1936 8032School of Systems Biology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, VA USA
| | - Frances Valdes
- grid.419791.30000 0000 9902 6374Sylvester Comprehensive Cancer Center (UM SCCC), University of Miami, Miami, FL USA
| | - William M. Sikov
- grid.241223.4Women and Infants Hospital of Rhode Island, Providence, RI USA
| | - Monica M. Mita
- grid.50956.3f0000 0001 2152 9905Cedars-Sinai Medical Center, Los Angeles, CA USA
| | - Neelima Denduluri
- grid.492966.60000 0004 0481 8256Virginia Cancer Specialists, Fairfax, VA USA
| | - Rita Murphy
- grid.415231.00000 0004 0577 7855Sidney Kimmel Cancer Center at Thomas Jefferson University, Philadelphia, PA USA
| | | | - Lance Liotta
- grid.22448.380000 0004 1936 8032School of Systems Biology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, VA USA
| | | | - Rick Dunetz
- grid.490989.5Side Out Foundation, Fairfax, VA USA
| | - Emanuel F. Petricoin
- grid.22448.380000 0004 1936 8032School of Systems Biology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, VA USA
| | - Mariaelena Pierobon
- School of Systems Biology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, VA, USA.
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Goodwin CM, Waters AM, Klomp JE, Javaid S, Bryant KL, Stalnecker CA, Drizyte-Miller K, Papke B, Yang R, Amparo AM, Ozkan-Dagliyan I, Baldelli E, Calvert V, Pierobon M, Sorrentino JA, Beelen AP, Bublitz N, Lüthen M, Wood KC, Petricoin EF, Sers C, McRee AJ, Cox AD, Der CJ. Combination Therapies with CDK4/6 Inhibitors to Treat KRAS-Mutant Pancreatic Cancer. Cancer Res 2023; 83:141-157. [PMID: 36346366 PMCID: PMC9812941 DOI: 10.1158/0008-5472.can-22-0391] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/08/2022] [Accepted: 10/28/2022] [Indexed: 11/09/2022]
Abstract
Mutational loss of CDKN2A (encoding p16INK4A) tumor-suppressor function is a key genetic step that complements activation of KRAS in promoting the development and malignant growth of pancreatic ductal adenocarcinoma (PDAC). However, pharmacologic restoration of p16INK4A function with inhibitors of CDK4 and CDK6 (CDK4/6) has shown limited clinical efficacy in PDAC. Here, we found that concurrent treatment with both a CDK4/6 inhibitor (CDK4/6i) and an ERK-MAPK inhibitor (ERKi) synergistically suppresses the growth of PDAC cell lines and organoids by cooperatively blocking CDK4/6i-induced compensatory upregulation of ERK, PI3K, antiapoptotic signaling, and MYC expression. On the basis of these findings, a Phase I clinical trial was initiated to evaluate the ERKi ulixertinib in combination with the CDK4/6i palbociclib in patients with advanced PDAC (NCT03454035). As inhibition of other proteins might also counter CDK4/6i-mediated signaling changes to increase cellular CDK4/6i sensitivity, a CRISPR-Cas9 loss-of-function screen was conducted that revealed a spectrum of functionally diverse genes whose loss enhanced CDK4/6i growth inhibitory activity. These genes were enriched around diverse signaling nodes, including cell-cycle regulatory proteins centered on CDK2 activation, PI3K-AKT-mTOR signaling, SRC family kinases, HDAC proteins, autophagy-activating pathways, chromosome regulation and maintenance, and DNA damage and repair pathways. Novel therapeutic combinations were validated using siRNA and small-molecule inhibitor-based approaches. In addition, genes whose loss imparts a survival advantage were identified (e.g., RB1, PTEN, FBXW7), suggesting possible resistance mechanisms to CDK4/6 inhibition. In summary, this study has identified novel combinations with CDK4/6i that may have clinical benefit to patients with PDAC. SIGNIFICANCE CRISPR-Cas9 screening and protein activity mapping reveal combinations that increase potency of CDK4/6 inhibitors and overcome drug-induced compensations in pancreatic cancer.
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Affiliation(s)
- Craig M. Goodwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Andrew M. Waters
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jennifer E. Klomp
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Sehrish Javaid
- Program in Oral and Craniofacial Biomedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kirsten L. Bryant
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Pharmacology, George Mason University, Fairfax, Virginia
| | - Clint A. Stalnecker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kristina Drizyte-Miller
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Bjoern Papke
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Berlin Institute of Health (BIH), Anna-Louise-Karsch-Str. 2, 10178 Berlin, Germany
| | - Runying Yang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Amber M. Amparo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, Virginia
| | - Valerie Calvert
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, Virginia
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, Virginia
| | | | | | - Natalie Bublitz
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Berlin Institute of Health (BIH), Anna-Louise-Karsch-Str. 2, 10178 Berlin, Germany
| | - Mareen Lüthen
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Berlin Institute of Health (BIH), Anna-Louise-Karsch-Str. 2, 10178 Berlin, Germany
| | - Kris C. Wood
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Fairfax, Virginia
| | - Christine Sers
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, 10117 Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Berlin Institute of Health (BIH), Anna-Louise-Karsch-Str. 2, 10178 Berlin, Germany
| | - Autumn J. McRee
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Adrienne D. Cox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Pharmacology, George Mason University, Fairfax, Virginia.,Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Channing J. Der
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Pharmacology, George Mason University, Fairfax, Virginia
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Pandya PH, Jannu AJ, Bijangi-Vishehsaraei K, Dobrota E, Bailey BJ, Barghi F, Shannon HE, Riyahi N, Damayanti NP, Young C, Malko R, Justice R, Albright E, Sandusky GE, Wurtz LD, Collier CD, Marshall MS, Gallagher RI, Wulfkuhle JD, Petricoin EF, Coy K, Trowbridge M, Sinn AL, Renbarger JL, Ferguson MJ, Huang K, Zhang J, Saadatzadeh MR, Pollok KE. Integrative Multi-OMICs Identifies Therapeutic Response Biomarkers and Confirms Fidelity of Clinically Annotated, Serially Passaged Patient-Derived Xenografts Established from Primary and Metastatic Pediatric and AYA Solid Tumors. Cancers (Basel) 2022; 15:259. [PMID: 36612255 PMCID: PMC9818438 DOI: 10.3390/cancers15010259] [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: 11/04/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/04/2023] Open
Abstract
Establishment of clinically annotated, molecularly characterized, patient-derived xenografts (PDXs) from treatment-naïve and pretreated patients provides a platform to test precision genomics-guided therapies. An integrated multi-OMICS pipeline was developed to identify cancer-associated pathways and evaluate stability of molecular signatures in a panel of pediatric and AYA PDXs following serial passaging in mice. Original solid tumor samples and their corresponding PDXs were evaluated by whole-genome sequencing, RNA-seq, immunoblotting, pathway enrichment analyses, and the drug−gene interaction database to identify as well as cross-validate actionable targets in patients with sarcomas or Wilms tumors. While some divergence between original tumor and the respective PDX was evident, majority of alterations were not functionally impactful, and oncogenic pathway activation was maintained following serial passaging. CDK4/6 and BETs were prioritized as biomarkers of therapeutic response in osteosarcoma PDXs with pertinent molecular signatures. Inhibition of CDK4/6 or BETs decreased osteosarcoma PDX growth (two-way ANOVA, p < 0.05) confirming mechanistic involvement in growth. Linking patient treatment history with molecular and efficacy data in PDX will provide a strong rationale for targeted therapy and improve our understanding of which therapy is most beneficial in patients at diagnosis and in those already exposed to therapy.
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Affiliation(s)
- Pankita H. Pandya
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Asha Jacob Jannu
- Department of Biostatistics & Health Data Science Indiana, University School of Medicine, Indianapolis, IN 46202, USA
| | - Khadijeh Bijangi-Vishehsaraei
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Erika Dobrota
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Barbara J. Bailey
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Farinaz Barghi
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Harlan E. Shannon
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Niknam Riyahi
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Nur P. Damayanti
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Courtney Young
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rada Malko
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ryli Justice
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Eric Albright
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - George E. Sandusky
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - L. Daniel Wurtz
- Department of Orthopedics Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Christopher D. Collier
- Department of Orthopedics Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Mark S. Marshall
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rosa I. Gallagher
- Center for Applied Proteomics and Molecular Medicine, Institute for Biomedical Innovation, George Mason University, Manassas, VA 20110, USA
| | - Julia D. Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, Institute for Biomedical Innovation, George Mason University, Manassas, VA 20110, USA
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, Institute for Biomedical Innovation, George Mason University, Manassas, VA 20110, USA
| | - Kathy Coy
- Preclinical Modeling and Therapeutics Core, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Melissa Trowbridge
- Preclinical Modeling and Therapeutics Core, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Anthony L. Sinn
- Preclinical Modeling and Therapeutics Core, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jamie L. Renbarger
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Michael J. Ferguson
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kun Huang
- Department of Biostatistics & Health Data Science Indiana, University School of Medicine, Indianapolis, IN 46202, USA
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - M. Reza Saadatzadeh
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Karen E. Pollok
- Department of Pediatrics, Hematology/Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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23
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Lang JE, Forero-Torres A, Yee D, Yau C, Wolf D, Park J, Parker BA, Chien AJ, Wallace AM, Murthy R, Albain KS, Ellis ED, Beckwith H, Haley BB, Elias AD, Boughey JC, Yung RL, Isaacs C, Clark AS, Han HS, Nanda R, Khan QJ, Edmiston KK, Stringer-Reasor E, Price E, Joe B, Liu MC, Brown-Swigart L, Petricoin EF, Wulfkuhle JD, Buxton M, Clennell JL, Sanil A, Berry S, Asare SM, Wilson A, Hirst GL, Singhrao R, Asare AL, Matthews JB, Melisko M, Perlmutter J, Rugo HS, Symmans WF, van 't Veer LJ, Hylton NM, DeMichele AM, Berry DA, Esserman LJ. Safety and efficacy of HSP90 inhibitor ganetespib for neoadjuvant treatment of stage II/III breast cancer. NPJ Breast Cancer 2022; 8:128. [PMID: 36456573 PMCID: PMC9715670 DOI: 10.1038/s41523-022-00493-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/10/2022] [Indexed: 12/03/2022] Open
Abstract
HSP90 inhibitors destabilize oncoproteins associated with cell cycle, angiogenesis, RAS-MAPK activity, histone modification, kinases and growth factors. We evaluated the HSP90-inhibitor ganetespib in combination with standard chemotherapy in patients with high-risk early-stage breast cancer. I-SPY2 is a multicenter, phase II adaptively randomized neoadjuvant (NAC) clinical trial enrolling patients with stage II-III breast cancer with tumors 2.5 cm or larger on the basis of hormone receptors (HR), HER2 and Mammaprint status. Multiple novel investigational agents plus standard chemotherapy are evaluated in parallel for the primary endpoint of pathologic complete response (pCR). Patients with HER2-negative breast cancer were eligible for randomization to ganetespib from October 2014 to October 2015. Of 233 women included in the final analysis, 140 were randomized to the standard NAC control; 93 were randomized to receive 150 mg/m2 ganetespib every 3 weeks with weekly paclitaxel over 12 weeks, followed by AC. Arms were balanced for hormone receptor status (51-52% HR-positive). Ganetespib did not graduate in any of the biomarker signatures studied before reaching maximum enrollment. Final estimated pCR rates were 26% vs. 18% HER2-negative, 38% vs. 22% HR-negative/HER2-negative, and 15% vs. 14% HR-positive/HER2-negative for ganetespib vs control, respectively. The predicted probability of success in phase 3 testing was 47% HER2-negative, 72% HR-negative/HER2-negative, and 19% HR-positive/HER2-negative. Ganetespib added to standard therapy is unlikely to yield substantially higher pCR rates in HER2-negative breast cancer compared to standard NAC, and neither HSP90 pathway nor replicative stress expression markers predicted response. HSP90 inhibitors remain of limited clinical interest in breast cancer, potentially in other clinical settings such as HER2-positive disease or in combination with anti-PD1 neoadjuvant chemotherapy in triple negative breast cancer.Trial registration: www.clinicaltrials.gov/ct2/show/NCT01042379.
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Affiliation(s)
- Julie E Lang
- University of Southern California, Los Angeles, USA.
| | | | | | - Christina Yau
- University of California San Francisco, San Francisco, USA
| | - Denise Wolf
- University of California San Francisco, San Francisco, USA
| | - John Park
- University of California San Francisco, San Francisco, USA
| | | | - A Jo Chien
- University of California San Francisco, San Francisco, USA
| | - Anne M Wallace
- University of California San Francisco, San Francisco, USA
| | - Rashmi Murthy
- University of Texas MD Anderson Cancer Center, Houston, USA
| | - Kathy S Albain
- Loyola University Chicago Stritch School of Medicine, Maywood, USA
| | | | | | | | | | | | | | | | - Amy S Clark
- University of Pennsylvania, Philadelphia, USA
| | | | | | | | | | | | - Elissa Price
- University of California San Francisco, San Francisco, USA
| | - Bonnie Joe
- University of California San Francisco, San Francisco, USA
| | | | | | | | | | | | | | | | | | - Smita M Asare
- Quantum Leap Healthcare Collaborative, San Francisco, USA
| | - Amy Wilson
- Quantum Leap Healthcare Collaborative, San Francisco, USA
| | | | - Ruby Singhrao
- University of California San Francisco, San Francisco, USA
| | - Adam L Asare
- Quantum Leap Healthcare Collaborative, San Francisco, USA
| | | | | | | | - Hope S Rugo
- University of California San Francisco, San Francisco, USA
| | | | | | - Nola M Hylton
- University of California San Francisco, San Francisco, USA
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24
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Le Roux Ö, Pershing NLK, Kaltenbrun E, Newman NJ, Everitt JI, Baldelli E, Pierobon M, Petricoin EF, Counter CM. Genetically manipulating endogenous Kras levels and oncogenic mutations in vivo influences tissue patterning of murine tumorigenesis. eLife 2022; 11:75715. [PMID: 36069770 PMCID: PMC9451540 DOI: 10.7554/elife.75715] [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: 11/20/2021] [Accepted: 08/02/2022] [Indexed: 12/04/2022] Open
Abstract
Despite multiple possible oncogenic mutations in the proto-oncogene KRAS, unique subsets of these mutations are detected in different cancer types. As KRAS mutations occur early, if not being the initiating event, these mutational biases are ostensibly a product of how normal cells respond to the encoded oncoprotein. Oncogenic mutations can impact not only the level of active oncoprotein, but also engagement with proteins. To attempt to separate these two effects, we generated four novel Cre-inducible (LSL) Kras alleles in mice with the biochemically distinct G12D or Q61R mutations and encoded by native (nat) rare or common (com) codons to produce low or high protein levels. While there were similarities, each allele also induced a distinct transcriptional response shortly after activation in vivo. At one end of the spectrum, activating the KrasLSL-natG12D allele induced transcriptional hallmarks suggestive of an expansion of multipotent cells, while at the other end, activating the KrasLSL-comQ61R allele led to hallmarks of hyperproliferation and oncogenic stress. Evidence suggests that these changes may be a product of signaling differences due to increased protein expression as well as the specific mutation. To determine the impact of these distinct responses on RAS mutational patterning in vivo, all four alleles were globally activated, revealing that hematolymphopoietic lesions were permissive to the level of active oncoprotein, squamous tumors were permissive to the G12D mutant, while carcinomas were permissive to both these features. We suggest that different KRAS mutations impart unique signaling properties that are preferentially capable of inducing tumor initiation in a distinct cell-specific manner.
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Affiliation(s)
- Özgün Le Roux
- Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, United States
| | - Nicole L K Pershing
- Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, United States
| | - Erin Kaltenbrun
- Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, United States
| | - Nicole J Newman
- Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, United States
| | - Jeffrey I Everitt
- Department of Pathology, Duke University Medical Center, Durham, United States
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason University, Manassas, United States
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason University, Manassas, United States
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason University, Manassas, United States
| | - Christopher M Counter
- Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, United States
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25
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Baldelli E, Mandarano M, Bellezza G, Petricoin EF, Pierobon M. Analysis of neuroendocrine clones in NSCLCs using an immuno-guided laser-capture microdissection-based approach. Cell Rep Methods 2022; 2:100271. [PMID: 36046628 PMCID: PMC9421534 DOI: 10.1016/j.crmeth.2022.100271] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/03/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022]
Abstract
Clonal evolution and lineage plasticity are key contributors to tumor heterogeneity and response to treatment in cancer. However, capturing signal transduction events in coexisting clones remains challenging from a technical perspective. In this study, we developed and tested a signal-transduction-based workflow to isolate and profile coexisting clones within a complex cellular system like non-small cell lung cancers (NSCLCs). Cooccurring clones were isolated under immunohistochemical guidance using laser-capture microdissection, and cell signaling activation portraits were measured using the reverse-phase protein microarray. To increase the translational potential of this work and capture druggable vulnerabilities within different clones, we measured expression/activation of a panel of key drug targets and downstream substrates of FDA-approved or investigational agents. We isolated intermixed clones, including poorly represented ones (<5% of cells), within the tumor microecology and identified molecular characteristics uniquely attributable to cancer cells that undergo lineage plasticity and neuroendocrine transdifferentiation in NSCLCs.
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Affiliation(s)
- Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Martina Mandarano
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
- Department of Medicine and Surgery, Section of Anatomic Pathology and Histology, University of Perugia, Perugia, Italy
| | - Guido Bellezza
- Department of Medicine and Surgery, Section of Anatomic Pathology and Histology, University of Perugia, Perugia, Italy
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
- School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
- School of Systems Biology, George Mason University, Manassas, VA, USA
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26
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Huynh MV, Hobbs GA, Schaefer A, Pierobon M, Carey LM, Diehl JN, DeLiberty JM, Thurman RD, Cooke AR, Goodwin CM, Cook JH, Lin L, Waters AM, Rashid NU, Petricoin EF, Campbell SL, Haigis KM, Simeone DM, Lyssiotis CA, Cox AD, Der CJ. Functional and biological heterogeneity of KRAS Q61 mutations. Sci Signal 2022; 15:eabn2694. [PMID: 35944066 PMCID: PMC9534304 DOI: 10.1126/scisignal.abn2694] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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] [Indexed: 12/28/2022]
Abstract
Missense mutations at the three hotspots in the guanosine triphosphatase (GTPase) RAS-Gly12, Gly13, and Gln61 (commonly known as G12, G13, and Q61, respectively)-occur differentially among the three RAS isoforms. Q61 mutations in KRAS are infrequent and differ markedly in occurrence. Q61H is the predominant mutant (at 57%), followed by Q61R/L/K (collectively 40%), and Q61P and Q61E are the rarest (2 and 1%, respectively). Probability analysis suggested that mutational susceptibility to different DNA base changes cannot account for this distribution. Therefore, we investigated whether these frequencies might be explained by differences in the biochemical, structural, and biological properties of KRASQ61 mutants. Expression of KRASQ61 mutants in NIH 3T3 fibroblasts and RIE-1 epithelial cells caused various alterations in morphology, growth transformation, effector signaling, and metabolism. The relatively rare KRASQ61E mutant stimulated actin stress fiber formation, a phenotype distinct from that of KRASQ61H/R/L/P, which disrupted actin cytoskeletal organization. The crystal structure of KRASQ61E was unexpectedly similar to that of wild-type KRAS, a potential basis for its weak oncogenicity. KRASQ61H/L/R-mutant pancreatic ductal adenocarcinoma (PDAC) cell lines exhibited KRAS-dependent growth and, as observed with KRASG12-mutant PDAC, were susceptible to concurrent inhibition of ERK-MAPK signaling and of autophagy. Our results uncover phenotypic heterogeneity among KRASQ61 mutants and support the potential utility of therapeutic strategies that target KRASQ61 mutant-specific signaling and cellular output.
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Affiliation(s)
- Minh V. Huynh
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - G. Aaron Hobbs
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Antje Schaefer
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine,
George Mason University, Manassas, VA 20110, USA
| | - Leiah M. Carey
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J. Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jonathan M. DeLiberty
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan D. Thurman
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adelaide R. Cooke
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Craig M. Goodwin
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joshua H. Cook
- Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, MA 02215, USA
- Department of Medicine, Brigham & Women's
Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical
School, Boston, MA 02115, USA
| | - Lin Lin
- Department of Molecular and Integrative Physiology,
University of Michigan Health System, Ann Arbor, MI 48109, USA
| | - Andrew M. Waters
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Naim U. Rashid
- Department of Biostatistics, University of North Carolina
at Chapel Hill, NC 27955, USA
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine,
George Mason University, Manassas, VA 20110, USA
| | - Sharon L. Campbell
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kevin M. Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, MA 02215, USA
- Department of Medicine, Brigham & Women's
Hospital, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute, Cambridge, MA 02142, USA
- Harvard Digestive Disease Center, Harvard Medical School,
Boston, MA 02115, USA
| | - Diane M. Simeone
- Perlmutter Cancer Center, New York University, New York,
NY10016, USA
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative Physiology,
University of Michigan Health System, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of
Gastroenterology, University of Michigan, Ann Arbor, MI 48198, USA
- University of Michigan Comprehensive Cancer Center, Ann
Arbor, MI 48109, USA
| | - Adrienne D. Cox
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Radiation Oncology, University of North
Carolina at Chapel Hill, Chapel Hill, NC 2799, USA
| | - Channing J. Der
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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27
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Wolf DM, Yau C, Wulfkuhle J, Brown-Swigart L, Gallagher RI, Lee PRE, Zhu Z, Magbanua MJ, Sayaman R, O'Grady N, Basu A, Delson A, Coppé JP, Lu R, Braun J, Asare SM, Sit L, Matthews JB, Perlmutter J, Hylton N, Liu MC, Pohlmann P, Symmans WF, Rugo HS, Isaacs C, DeMichele AM, Yee D, Berry DA, Pusztai L, Petricoin EF, Hirst GL, Esserman LJ, van 't Veer LJ. Redefining breast cancer subtypes to guide treatment prioritization and maximize response: Predictive biomarkers across 10 cancer therapies. Cancer Cell 2022; 40:609-623.e6. [PMID: 35623341 PMCID: PMC9426306 DOI: 10.1016/j.ccell.2022.05.005] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [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: 11/11/2021] [Revised: 02/16/2022] [Accepted: 05/06/2022] [Indexed: 12/26/2022]
Abstract
Using pre-treatment gene expression, protein/phosphoprotein, and clinical data from the I-SPY2 neoadjuvant platform trial (NCT01042379), we create alternative breast cancer subtypes incorporating tumor biology beyond clinical hormone receptor (HR) and human epidermal growth factor receptor-2 (HER2) status to better predict drug responses. We assess the predictive performance of mechanism-of-action biomarkers from ∼990 patients treated with 10 regimens targeting diverse biology. We explore >11 subtyping schemas and identify treatment-subtype pairs maximizing the pathologic complete response (pCR) rate over the population. The best performing schemas incorporate Immune, DNA repair, and HER2/Luminal phenotypes. Subsequent treatment allocation increases the overall pCR rate to 63% from 51% using HR/HER2-based treatment selection. pCR gains from reclassification and improved patient selection are highest in HR+ subsets (>15%). As new treatments are introduced, the subtyping schema determines the minimum response needed to show efficacy. This data platform provides an unprecedented resource and supports the usage of response-based subtypes to guide future treatment prioritization.
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Affiliation(s)
- Denise M Wolf
- Department of Laboratory Medicine, University of California, San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA.
| | - Christina Yau
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Julia Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Lamorna Brown-Swigart
- Department of Laboratory Medicine, University of California, San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA
| | - Rosa I Gallagher
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Pei Rong Evelyn Lee
- Department of Laboratory Medicine, University of California, San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA
| | - Zelos Zhu
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mark J Magbanua
- Department of Laboratory Medicine, University of California, San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA
| | - Rosalyn Sayaman
- Department of Laboratory Medicine, University of California, San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA
| | - Nicholas O'Grady
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amrita Basu
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amy Delson
- Breast Science Advocacy Core, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jean Philippe Coppé
- Department of Laboratory Medicine, University of California, San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA
| | - Ruixiao Lu
- Quantum Leap Healthcare Collaborative, San Francisco, CA 94118, USA
| | - Jerome Braun
- Quantum Leap Healthcare Collaborative, San Francisco, CA 94118, USA
| | - Smita M Asare
- Quantum Leap Healthcare Collaborative, San Francisco, CA 94118, USA
| | - Laura Sit
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey B Matthews
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Nola Hylton
- Department of Radiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Minetta C Liu
- Department of Surgery, Mayo Clinic, Rochester, MN 55905, USA
| | - Paula Pohlmann
- MedStar Georgetown University Hospital, Georgetown University, Washington, DC 20057, USA
| | - W Fraser Symmans
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hope S Rugo
- Division of Hematology/Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA
| | - Angela M DeMichele
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Douglas Yee
- Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Lajos Pusztai
- Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Gillian L Hirst
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laura J Esserman
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Laura J van 't Veer
- Department of Laboratory Medicine, University of California, San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA.
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28
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Gnawali GR, Okumura K, Perez K, Gallagher R, Wulfkuhle J, Petricoin EF, Padi SKR, Bearss J, He Z, Wang W, Kraft AS. Synthesis of 2-oxoquinoline derivatives as dual pim and mTORC protein kinase inhibitors. Med Chem Res 2022; 31:1154-1175. [DOI: 10.1007/s00044-022-02904-z] [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: 10/18/2022]
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29
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Javaid S, Schaefer A, Goodwin CM, Nguyen VV, Massey FL, Pierobon M, Gambrell-Sanders D, Waters AM, Lambert KN, Diehl JN, Hobbs GA, Wood KC, Petricoin EF, Der CJ, Cox AD. Concurrent Inhibition of ERK and Farnesyltransferase Suppresses the Growth of HRAS Mutant Head and Neck Squamous Cell Carcinoma. Mol Cancer Ther 2022; 21:762-774. [PMID: 35247914 DOI: 10.1158/1535-7163.mct-21-0142] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 08/16/2021] [Accepted: 02/22/2022] [Indexed: 12/24/2022]
Abstract
Human papilloma virus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) is a common cancer worldwide with an unmet need for more effective, less toxic treatments. Currently, both the disease and the treatment of HNSCC cause significant mortality and morbidity. Targeted therapies hold new promise for patients with HPV-negative status whose tumors harbor oncogenic HRAS mutations. Recent promising clinical results have renewed interest in the development of farnesyltransferase inhibitors (FTIs) as a therapeutic strategy for HRAS-mutant cancers. With the advent of clinical evaluation of the FTI tipifarnib for the treatment of HRAS-mutant HNSCC, we investigated the activity of tipifarnib and inhibitors of HRAS effector signaling in HRAS-mutant HNSCC cell lines. First, we validated that HRAS is a cancer driver in HRAS-mutant HNSCC lines. Second, we showed that treatment with the FTI tipifarnib largely phenocopied HRAS silencing, supporting HRAS as a key target of FTI antitumor activity. Third, we performed reverse-phase protein array analyses to profile FTI treatment-induced changes in global signaling, and conducted CRISPR/Cas9 genetic loss-of-function screens to identify previously unreported genes and pathways that modulate sensitivity to tipifarnib. Fourth, we determined that concurrent inhibition of HRAS effector signaling (ERK, PI3K, mTORC1) increased sensitivity to tipifarnib treatment, in part by overcoming tipifarnib-induced compensatory signaling. We also determined that ERK inhibition could block tipifarnib-induced epithelial-to-mesenchymal transition, providing a potential basis for the effectiveness of this combination. Our results support future investigations of these and other combination treatments for HRAS mutant HNSCC.
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Affiliation(s)
- Sehrish Javaid
- Program in Oral and Craniofacial Biomedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Antje Schaefer
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Craig M Goodwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Victoria V Nguyen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Frances L Massey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, Institute for Advanced Biomedical Research, George Mason University, Manassas, Virginia
| | | | - Andrew M Waters
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kathryn N Lambert
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - J Nathaniel Diehl
- Curriculum in Genetics & Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - G Aaron Hobbs
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kris C Wood
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, Institute for Advanced Biomedical Research, George Mason University, Manassas, Virginia
| | - Channing J Der
- Program in Oral and Craniofacial Biomedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Adrienne D Cox
- Program in Oral and Craniofacial Biomedicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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30
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Hetrick B, Chilin LD, He S, Dabbagh D, Alem F, Narayanan A, Luchini A, Li T, Liu X, Copeland J, Pak A, Cunningham T, Liotta L, Petricoin EF, Andalibi A, Wu Y. Development of a hybrid alphavirus-SARS-CoV-2 pseudovirion for rapid quantification of neutralization antibodies and antiviral drugs. Cell Rep Methods 2022; 2:100181. [PMID: 35229082 PMCID: PMC8866097 DOI: 10.1016/j.crmeth.2022.100181] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/24/2021] [Accepted: 02/17/2022] [Indexed: 11/16/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S)-pseudotyped viruses are commonly used for quantifying antiviral drugs and neutralizing antibodies. Here, we describe the development of a hybrid alphavirus-SARS-CoV-2 (Ha-CoV-2) pseudovirion, which is a non-replicating SARS-CoV-2 virus-like particle composed of viral structural proteins (S, M, N, and E) and an RNA genome derived from a fast-expressing alphaviral vector. We validated Ha-CoV-2 for rapid quantification of neutralization antibodies, antiviral drugs, and viral variants. In addition, as a proof of concept, we used Ha-CoV-2 to quantify the neutralizing antibodies from an infected and vaccinated individual and found that the one-dose vaccination with Moderna mRNA-1273 greatly increased the anti-serum titer by approximately 6-fold. The post-vaccination serum can neutralize all nine variants tested. These results demonstrate that Ha-CoV-2 can be used as a robust platform for the rapid quantification of neutralizing antibodies against SARS-CoV-2 and its emerging variants.
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Affiliation(s)
- Brian Hetrick
- Center for Infectious Disease Research, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Linda D Chilin
- Center for Infectious Disease Research, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Sijia He
- Center for Infectious Disease Research, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Deemah Dabbagh
- Center for Infectious Disease Research, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Farhang Alem
- Center for Infectious Disease Research, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Aarthi Narayanan
- Center for Infectious Disease Research, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Alessandra Luchini
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Tuanjie Li
- Department of Pathology, Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Xuefeng Liu
- Department of Pathology, Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC 20057, USA
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Joshua Copeland
- TruGenomix, Inc., 155 Gibbs Street, Room 559, Rockville, MD 20850, USA
| | - Angela Pak
- TruGenomix, Inc., 155 Gibbs Street, Room 559, Rockville, MD 20850, USA
| | - Tshaka Cunningham
- TruGenomix, Inc., 155 Gibbs Street, Room 559, Rockville, MD 20850, USA
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Ali Andalibi
- Center for Infectious Disease Research, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - Yuntao Wu
- Center for Infectious Disease Research, School of Systems Biology, George Mason University, Manassas, VA 20110, USA
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31
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Shi Z, Wulfkuhle J, Nowicka M, Gallagher RI, Saura C, Nuciforo PG, Calvo I, Andersen J, Passos-Coelho JL, Gil-Gil MJ, Bermejo B, Pratt DA, Ciruelos EM, Villagrasa P, Wongchenko MJ, Petricoin EF, Oliveira M, Isakoff SJ. Functional Mapping of AKT Signaling and Biomarkers of Response from the FAIRLANE Trial of Neoadjuvant Ipatasertib plus Paclitaxel for Triple-Negative Breast Cancer. Clin Cancer Res 2022; 28:993-1003. [PMID: 34907082 PMCID: PMC9377742 DOI: 10.1158/1078-0432.ccr-21-2498] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/27/2021] [Accepted: 12/09/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE Despite extensive genomic and transcriptomic profiling, it remains unknown how signaling pathways are differentially activated and how tumors are differentially sensitized to certain perturbations. Here, we aim to characterize AKT signaling activity and its association with other genomic or IHC-based PI3K/AKT pathway biomarkers as well as the clinical activity of ipatasertib (AKT inhibitor) in the FAIRLANE trial. EXPERIMENTAL DESIGN In FAIRLANE, 151 patients with early triple-negative breast cancer (TNBC) were randomized 1:1 to receive paclitaxel with ipatasertib or placebo for 12 weeks prior to surgery. Adding ipatasertib did not increase pathologic complete response rate and numerically improved overall response rate by MRI. We used reverse-phase protein microarrays (RPPA) to examine the total level and/or phosphorylation states of over 100 proteins in various signaling or cell processes including PI3K/AKT and mTOR signaling. One hundred and twenty-five baseline and 127 on-treatment samples were evaluable by RPPA, with 110 paired samples at both time points. RESULTS Tumors with genomic/protein alterations in PIK3CA/AKT1/PTEN were associated with higher levels of AKT phosphorylation. In addition, phosphorylated AKT (pAKT) levels exhibited a significant association with enriched clinical benefit of ipatasertib, and identified patients who received benefit in the absence of PIK3CA/AKT1/PTEN alterations. Ipatasertib treatment led to a downregulation of AKT/mTORC1 signaling, which was more pronounced among the tumors with PIK3CA/AKT1/PTEN alterations or among the responders to the treatment. CONCLUSIONS We showed that the high baseline pAKT levels are associated with the alterations of PI3K/AKT pathway components and enriched benefit of ipatasertib in TNBC.
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Affiliation(s)
- Zhen Shi
- Department of Oncology Biomarker, Genentech Inc., South San Francisco, California
| | - Julia Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | | | - Rosa I. Gallagher
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | - Cristina Saura
- Medical Oncology Department, Vall d’Hebron University Hospital, Barcelona, Spain
- Breast Cancer Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
- SOLTI Breast Cancer Research Group, Barcelona, Spain
| | - Paolo G. Nuciforo
- Molecular Oncology Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Isabel Calvo
- Breast Cancer Unit, Centro Integral Oncologico Clara Campal (CIOCC), Madrid, Spain
| | - Jay Andersen
- Medical Oncology/Hematology, Compass Oncology, Tigard, Oregon
| | | | - Miguel J. Gil-Gil
- SOLTI Breast Cancer Research Group, Barcelona, Spain
- Medical Oncology Service, Institut Català d’Oncologia, L’Hospitalet, Barcelona, Spain
- Institut d'Investigació Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
| | - Begoña Bermejo
- Hospital Clinico Universitario de Valencia, Valencia, Spain
| | - Debra A. Pratt
- Texas Oncology Cancer Center, US Oncology, Austin, Texas
| | - Eva M. Ciruelos
- SOLTI Breast Cancer Research Group, Barcelona, Spain
- Medical Oncology Department, University Hospital 12 de Octubre, Madrid, Spain
| | | | | | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | - Mafalda Oliveira
- Medical Oncology Department, Vall d’Hebron University Hospital, Barcelona, Spain
- Breast Cancer Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
- SOLTI Breast Cancer Research Group, Barcelona, Spain
| | - Steven J. Isakoff
- Division of Hematology/Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
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32
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Stalnecker CA, Grover KR, Edwards AC, Coleman MF, Yang R, DeLiberty JM, Papke B, Goodwin CM, Pierobon M, Petricoin EF, Gautam P, Wennerberg K, Cox AD, Der CJ, Hursting SD, Bryant KL. Concurrent Inhibition of IGF1R and ERK Increases Pancreatic Cancer Sensitivity to Autophagy Inhibitors. Cancer Res 2022; 82:586-598. [PMID: 34921013 PMCID: PMC8886214 DOI: 10.1158/0008-5472.can-21-1443] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 05/11/2021] [Revised: 11/11/2021] [Accepted: 12/14/2021] [Indexed: 01/18/2023]
Abstract
The aggressive nature of pancreatic ductal adenocarcinoma (PDAC) mandates the development of improved therapies. As KRAS mutations are found in 95% of PDAC and are critical for tumor maintenance, one promising strategy involves exploiting KRAS-dependent metabolic perturbations. The macrometabolic process of autophagy is upregulated in KRAS-mutant PDAC, and PDAC growth is reliant on autophagy. However, inhibition of autophagy as monotherapy using the lysosomal inhibitor hydroxychloroquine (HCQ) has shown limited clinical efficacy. To identify strategies that can improve PDAC sensitivity to HCQ, we applied a CRISPR-Cas9 loss-of-function screen and found that a top sensitizer was the receptor tyrosine kinase (RTK) insulin-like growth factor 1 receptor (IGF1R). Additionally, reverse phase protein array pathway activation mapping profiled the signaling pathways altered by chloroquine (CQ) treatment. Activating phosphorylation of RTKs, including IGF1R, was a common compensatory increase in response to CQ. Inhibition of IGF1R increased autophagic flux and sensitivity to CQ-mediated growth suppression both in vitro and in vivo. Cotargeting both IGF1R and pathways that antagonize autophagy, such as ERK-MAPK axis, was strongly synergistic. IGF1R and ERK inhibition converged on suppression of glycolysis, leading to enhanced dependence on autophagy. Accordingly, concurrent inhibition of IGF1R, ERK, and autophagy induced cytotoxicity in PDAC cell lines and decreased viability in human PDAC organoids. In conclusion, targeting IGF1R together with ERK enhances the effectiveness of autophagy inhibitors in PDAC. SIGNIFICANCE Compensatory upregulation of IGF1R and ERK-MAPK signaling limits the efficacy of autophagy inhibitors chloroquine and hydroxychloroquine, and their concurrent inhibition synergistically increases autophagy dependence and chloroquine sensitivity in pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Clint A. Stalnecker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kajal R. Grover
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - A. Cole Edwards
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michael F. Coleman
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Runying Yang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jonathan M. DeLiberty
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Björn Papke
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Craig M. Goodwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | - Prson Gautam
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Krister Wennerberg
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Adrienne D. Cox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Channing J. Der
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Stephen D. Hursting
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kirsten L. Bryant
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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33
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Naeem A, Harish V, Coste S, Parasido EM, Choudhry MU, Kromer LF, Ihemelandu C, Petricoin EF, Pierobon M, Noon MS, Yenugonda VM, Avantaggiati M, Kupfer GM, Fricke S, Rodriguez O, Albanese C. Regulation of Chemosensitivity in Human Medulloblastoma Cells by p53 and the PI3 Kinase Signaling Pathway. Mol Cancer Res 2022; 20:114-126. [PMID: 34635507 PMCID: PMC8738155 DOI: 10.1158/1541-7786.mcr-21-0277] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 04/18/2021] [Revised: 07/06/2021] [Accepted: 10/04/2021] [Indexed: 01/07/2023]
Abstract
In medulloblastoma, p53 expression has been associated with chemoresistance and radiation resistance and with poor long-term outcomes in the p53-mutated sonic hedgehog, MYC-p53, and p53-positive medulloblastoma subgroups. We previously established a direct role for p53 in supporting drug resistance in medulloblastoma cells with high basal protein expression levels (D556 and DAOY). We now show that p53 genetic suppression in medulloblastoma cells with low basal p53 protein expression levels (D283 and UW228) significantly reduced drug responsiveness, suggesting opposing roles for low p53 protein expression levels. Mechanistically, the enhanced cell death by p53 knockdown in high-p53 cells was associated with an induction of mTOR/PI3K signaling. Both mTOR inhibition and p110α/PIK3CA induction confirmed these findings, which abrogated or accentuated the enhanced chemosensitivity response in D556 cells respectively while converse was seen in D283 cells. Co-treatment with G-actin-sequestering peptide, thymosin β4 (Tβ4), induced p-AKTS473 in both p53-high and p53-low cells, enhancing chemosensitivity in D556 cells while enhancing chemoresistance in D283 and UW228 cells. IMPLICATIONS: Collectively, we identified an unexpected role for the PI3K signaling in enhancing cell death in medulloblastoma cells with high basal p53 expression. These studies indicate that levels of p53 immunopositivity may serve as a diagnostic marker of chemotherapy resistance and for defining therapeutic targeting.
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Affiliation(s)
- Aisha Naeem
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC.,Health Research Governance Department, Ministry of Public Health, Doha, Qatar
| | - Varsha Harish
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Sophie Coste
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Erika M. Parasido
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Muhammad Umer Choudhry
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Lawrence F. Kromer
- Department of Neuroscience, Georgetown University Medical Center, Washington, DC
| | - Chukuemeka Ihemelandu
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Emanuel F. Petricoin
- George Mason University, Center for Applied Proteomics and Molecular Medicine, Manassas, Virginia
| | - Mariaelena Pierobon
- George Mason University, Center for Applied Proteomics and Molecular Medicine, Manassas, Virginia
| | | | | | - Maria Avantaggiati
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | - Gary M. Kupfer
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC.,Department of Pediatrics, Georgetown University Medical Center, Washington, DC
| | - Stanley Fricke
- Department of Radiology, Georgetown University Medical Center, Washington, DC.,Center for Translational Imaging, Georgetown University Medical Center, Washington, DC
| | - Olga Rodriguez
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC.,Center for Translational Imaging, Georgetown University Medical Center, Washington, DC
| | - Chris Albanese
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC.,Department of Radiology, Georgetown University Medical Center, Washington, DC.,Center for Translational Imaging, Georgetown University Medical Center, Washington, DC.,Corresponding Author: Chris Albanese, Department of OncologyGeorgetown University Medical Center, Lombardi Cancer Center, NRB W417, Washington, DC 20007. Phone: 202-687-3305; E-mail:
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34
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Alem F, Olanrewaju AA, Omole S, Hobbs HE, Ahsan N, Matulis G, Brantner CA, Zhou W, Petricoin EF, Liotta LA, Caputi M, Bavari S, Wu Y, Kashanchi F, Hakami RM. Exosomes originating from infection with the cytoplasmic single-stranded RNA virus Rift Valley fever virus (RVFV) protect recipient cells by inducing RIG-I mediated IFN-B response that leads to activation of autophagy. Cell Biosci 2021; 11:220. [PMID: 34953502 PMCID: PMC8710069 DOI: 10.1186/s13578-021-00732-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 09/27/2021] [Accepted: 12/12/2021] [Indexed: 12/12/2022] Open
Abstract
Background Although multiple studies have demonstrated a role for exosomes during virus infections, our understanding of the mechanisms by which exosome exchange regulates immune response during viral infections and affects viral pathogenesis is still in its infancy. In particular, very little is known for cytoplasmic single-stranded RNA viruses such as SARS-CoV-2 and Rift Valley fever virus (RVFV). We have used RVFV infection as a model for cytoplasmic single-stranded RNA viruses to address this gap in knowledge. RVFV is a highly pathogenic agent that causes RVF, a zoonotic disease for which no effective therapeutic or approved human vaccine exist. Results We show here that exosomes released from cells infected with RVFV (designated as EXi-RVFV) serve a protective role for the host and provide a mechanistic model for these effects. Our results show that treatment of both naïve immune cells (U937 monocytes) and naïve non-immune cells (HSAECs) with EXi-RVFV induces a strong RIG-I dependent activation of IFN-B. We also demonstrate that this strong anti-viral response leads to activation of autophagy in treated cells and correlates with resistance to subsequent viral infection. Since we have shown that viral RNA genome is associated with EXi-RVFV, RIG-I activation might be mediated by the presence of packaged viral RNA sequences. Conclusions Using RVFV infection as a model for cytoplasmic single-stranded RNA viruses, our results show a novel mechanism of host protection by exosomes released from infected cells (EXi) whereby the EXi activate RIG-I to induce IFN-dependent activation of autophagy in naïve recipient cells including monocytes. Because monocytes serve as reservoirs for RVFV replication, this EXi-RVFV-induced activation of autophagy in monocytes may work to slow down or halt viral dissemination in the infected organism. These findings offer novel mechanistic insights that may aid in future development of effective vaccines or therapeutics, and that may be applicable for a better molecular understanding of how exosome release regulates innate immune response to other cytoplasmic single-stranded RNA viruses. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-021-00732-z.
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Affiliation(s)
- Farhang Alem
- School of Systems Biology, George Mason University, Manassas, VA, USA.,Center for Infectious Disease Research (Formerly, National Center for Biodefense and Infectious Diseases), George Mason University, Manassas, VA, USA
| | - Adeyemi A Olanrewaju
- School of Systems Biology, George Mason University, Manassas, VA, USA.,Center for Infectious Disease Research (Formerly, National Center for Biodefense and Infectious Diseases), George Mason University, Manassas, VA, USA
| | - Samson Omole
- School of Systems Biology, George Mason University, Manassas, VA, USA.,Center for Infectious Disease Research (Formerly, National Center for Biodefense and Infectious Diseases), George Mason University, Manassas, VA, USA
| | - Heather E Hobbs
- School of Systems Biology, George Mason University, Manassas, VA, USA.,Center for Infectious Disease Research (Formerly, National Center for Biodefense and Infectious Diseases), George Mason University, Manassas, VA, USA
| | - Noor Ahsan
- School of Systems Biology, George Mason University, Manassas, VA, USA.,Center for Infectious Disease Research (Formerly, National Center for Biodefense and Infectious Diseases), George Mason University, Manassas, VA, USA.,Lentigen Technology, Inc., Gaithersburg, MD, USA
| | - Graham Matulis
- School of Systems Biology, George Mason University, Manassas, VA, USA.,Center for Infectious Disease Research (Formerly, National Center for Biodefense and Infectious Diseases), George Mason University, Manassas, VA, USA
| | - Christine A Brantner
- Nanofabrication and Imaging Center, George Washington University, Washington, DC, USA
| | - Weidong Zhou
- School of Systems Biology, George Mason University, Manassas, VA, USA.,Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Emanuel F Petricoin
- School of Systems Biology, George Mason University, Manassas, VA, USA.,Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Lance A Liotta
- School of Systems Biology, George Mason University, Manassas, VA, USA.,Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Massimo Caputi
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | | | - Yuntao Wu
- School of Systems Biology, George Mason University, Manassas, VA, USA.,Center for Infectious Disease Research (Formerly, National Center for Biodefense and Infectious Diseases), George Mason University, Manassas, VA, USA
| | - Fatah Kashanchi
- School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Ramin M Hakami
- School of Systems Biology, George Mason University, Manassas, VA, USA. .,Center for Infectious Disease Research (Formerly, National Center for Biodefense and Infectious Diseases), George Mason University, Manassas, VA, USA.
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35
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Klomp JE, Lee YS, Goodwin CM, Papke B, Klomp JA, Waters AM, Stalnecker CA, DeLiberty JM, Drizyte-Miller K, Yang R, Diehl JN, Yin HH, Pierobon M, Baldelli E, Ryan MB, Li S, Peterson J, Smith AR, Neal JT, McCormick AK, Kuo CJ, Counter CM, Petricoin EF, Cox AD, Bryant KL, Der CJ. CHK1 protects oncogenic KRAS-expressing cells from DNA damage and is a target for pancreatic cancer treatment. Cell Rep 2021; 37:110060. [PMID: 34852220 PMCID: PMC8665414 DOI: 10.1016/j.celrep.2021.110060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 04/07/2021] [Revised: 09/09/2021] [Accepted: 11/03/2021] [Indexed: 12/17/2022] Open
Abstract
We apply genetic screens to delineate modulators of KRAS mutant pancreatic ductal adenocarcinoma (PDAC) sensitivity to ERK inhibitor treatment, and we identify components of the ATR-CHK1 DNA damage repair (DDR) pathway. Pharmacologic inhibition of CHK1 alone causes apoptotic growth suppression of both PDAC cell lines and organoids, which correlates with loss of MYC expression. CHK1 inhibition also activates ERK and AMPK and increases autophagy, providing a mechanistic basis for increased efficacy of concurrent CHK1 and ERK inhibition and/or autophagy inhibition with chloroquine. To assess how CHK1 inhibition-induced ERK activation promotes PDAC survival, we perform a CRISPR-Cas9 loss-of-function screen targeting direct/indirect ERK substrates and identify RIF1. A key component of non-homologous end joining repair, RIF1 suppression sensitizes PDAC cells to CHK1 inhibition-mediated apoptotic growth suppression. Furthermore, ERK inhibition alone decreases RIF1 expression and phenocopies RIF1 depletion. We conclude that concurrent DDR suppression enhances the efficacy of ERK and/or autophagy inhibitors in KRAS mutant PDAC.
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Affiliation(s)
- Jennifer E Klomp
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ye S Lee
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Craig M Goodwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Björn Papke
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeff A Klomp
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Andrew M Waters
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Clint A Stalnecker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jonathan M DeLiberty
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kristina Drizyte-Miller
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Runying Yang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hongwei H Yin
- Departments of Cancer and Cell Biology, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Meagan B Ryan
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Siqi Li
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC
| | - Jackson Peterson
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC
| | - Amber R Smith
- Department of Medicine, Stanford University, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James T Neal
- Department of Medicine, Stanford University, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aaron K McCormick
- Department of Medicine, Stanford University, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Calvin J Kuo
- Department of Medicine, Stanford University, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christopher M Counter
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA 20110, USA
| | - Adrienne D Cox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kirsten L Bryant
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Channing J Der
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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36
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Clark AS, Yau C, Wolf DM, Petricoin EF, van 't Veer LJ, Yee D, Moulder SL, Wallace AM, Chien AJ, Isaacs C, Boughey JC, Albain KS, Kemmer K, Haley BB, Han HS, Forero-Torres A, Elias A, Lang JE, Ellis ED, Yung R, Tripathy D, Nanda R, Wulfkuhle JD, Brown-Swigart L, Gallagher RI, Helsten T, Roesch E, Ewing CA, Alvarado M, Crane EP, Buxton M, Clennell JL, Paoloni M, Asare SM, Wilson A, Hirst GL, Singhrao R, Steeg K, Asare A, Matthews JB, Berry S, Sanil A, Melisko M, Perlmutter J, Rugo HS, Schwab RB, Symmans WF, Hylton NM, Berry DA, Esserman LJ, DeMichele AM. Neoadjuvant T-DM1/pertuzumab and paclitaxel/trastuzumab/pertuzumab for HER2 + breast cancer in the adaptively randomized I-SPY2 trial. Nat Commun 2021; 12:6428. [PMID: 34741023 PMCID: PMC8571284 DOI: 10.1038/s41467-021-26019-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/10/2021] [Indexed: 12/02/2022] Open
Abstract
HER2-targeted therapy dramatically improves outcomes in early breast cancer. Here we report the results of two HER2-targeted combinations in the neoadjuvant I-SPY2 phase 2 adaptive platform trial for early breast cancer at high risk of recurrence: ado-trastuzumab emtansine plus pertuzumab (T-DM1/P) and paclitaxel, trastuzumab and pertuzumab (THP). Eligible women have >2.5 cm clinical stage II/III HER2+ breast cancer, adaptively randomized to T-DM1/P, THP, or a common control arm of paclitaxel/trastuzumab (TH), followed by doxorubicin/cyclophosphamide, then surgery. Both T-DM1/P and THP arms 'graduate' in all subtypes: predicted pCR rates are 63%, 72% and 33% for T-DM1/P (n = 52), THP (n = 45) and TH (n = 31) respectively. Toxicity burden is similar between arms. Degree of HER2 pathway signaling and phosphorylation in pretreatment biopsy specimens are associated with response to both T-DM1/P and THP and can further identify highly responsive HER2+ tumors to HER2-directed therapy. This may help identify patients who can safely de-escalate cytotoxic chemotherapy without compromising excellent outcome.
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Affiliation(s)
- Amy S Clark
- University of Pennsylvania, Philadelphia, PA, USA.
| | - Christina Yau
- University of California San Francisco, San Francisco, CA, USA
| | - Denise M Wolf
- University of California San Francisco, San Francisco, CA, USA
| | | | | | - Douglas Yee
- University of Minnesota, Minneapolis, MN, USA
| | | | | | - A Jo Chien
- University of California San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | - Hyo S Han
- Moffitt Cancer Center, Tampa, FL, USA
| | | | | | - Julie E Lang
- University of Southern California, Los Angeles, CA, USA
| | | | | | | | | | | | | | | | | | - Erin Roesch
- University of California San Diego, San Diego, CA, USA
| | - Cheryl A Ewing
- University of California San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | - Smita M Asare
- University of California San Francisco, San Francisco, CA, USA
| | - Amy Wilson
- University of California San Francisco, San Francisco, CA, USA
| | - Gillian L Hirst
- University of California San Francisco, San Francisco, CA, USA
| | - Ruby Singhrao
- University of California San Francisco, San Francisco, CA, USA
| | - Katherine Steeg
- University of California San Francisco, San Francisco, CA, USA
| | - Adam Asare
- University of California San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | - Hope S Rugo
- University of California San Francisco, San Francisco, CA, USA
| | | | | | - Nola M Hylton
- University of California San Francisco, San Francisco, CA, USA
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37
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Diehl JN, Klomp JE, Snare KR, Hibshman PS, Blake DR, Kaiser ZD, Gilbert TSK, Baldelli E, Pierobon M, Papke B, Yang R, Hodge RG, Rashid NU, Petricoin EF, Herring LE, Graves LM, Cox AD, Der CJ. The KRAS-regulated kinome identifies WEE1 and ERK coinhibition as a potential therapeutic strategy in KRAS-mutant pancreatic cancer. J Biol Chem 2021; 297:101335. [PMID: 34688654 PMCID: PMC8591367 DOI: 10.1016/j.jbc.2021.101335] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 04/27/2021] [Revised: 09/24/2021] [Accepted: 10/19/2021] [Indexed: 02/07/2023] Open
Abstract
Oncogenic KRAS drives cancer growth by activating diverse signaling networks, not all of which have been fully delineated. We set out to establish a system-wide profile of the KRAS-regulated kinase signaling network (kinome) in KRAS-mutant pancreatic ductal adenocarcinoma (PDAC). We knocked down KRAS expression in a panel of six cell lines and then applied multiplexed inhibitor bead/MS to monitor changes in kinase activity and/or expression. We hypothesized that depletion of KRAS would result in downregulation of kinases required for KRAS-mediated transformation and in upregulation of other kinases that could potentially compensate for the deleterious consequences of the loss of KRAS. We identified 15 upregulated and 13 downregulated kinases in common across the panel of cell lines. In agreement with our hypothesis, all 15 of the upregulated kinases have established roles as cancer drivers (e.g., SRC, TGF-β1, ILK), and pharmacological inhibition of one of these upregulated kinases, DDR1, suppressed PDAC growth. Interestingly, 11 of the 13 downregulated kinases have established driver roles in cell cycle progression, particularly in mitosis (e.g., WEE1, Aurora A, PLK1). Consistent with a crucial role for the downregulated kinases in promoting KRAS-driven proliferation, we found that pharmacological inhibition of WEE1 also suppressed PDAC growth. The unexpected paradoxical activation of ERK upon WEE1 inhibition led us to inhibit both WEE1 and ERK concurrently, which caused further potent growth suppression and enhanced apoptotic death compared with WEE1 inhibition alone. We conclude that system-wide delineation of the KRAS-regulated kinome can identify potential therapeutic targets for KRAS-mutant pancreatic cancer.
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Affiliation(s)
- J Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jennifer E Klomp
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kayla R Snare
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Priya S Hibshman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Devon R Blake
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Zane D Kaiser
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Thomas S K Gilbert
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Björn Papke
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Runying Yang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Richard G Hodge
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Naim U Rashid
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Laura E Herring
- Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lee M Graves
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Adrienne D Cox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Channing J Der
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Cell Biology and Physiology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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38
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Baldelli E, Hodge KA, Bellezza G, Shah NJ, Gambara G, Sidoni A, Mandarano M, Ruhunusiri C, Dunetz B, Abu-Khalaf M, Wulfkuhle J, Gallagher RI, Liotta L, de Bono J, Mehra N, Riisnaes R, Ravaggi A, Odicino F, Sereni MI, Blackburn M, Zupa A, Improta G, Demsko P, Crino' L, Ludovini V, Giaccone G, Petricoin EF, Pierobon M. PD-L1 quantification across tumor types using the reverse phase protein microarray: implications for precision medicine. J Immunother Cancer 2021; 9:jitc-2020-002179. [PMID: 34620701 PMCID: PMC8499669 DOI: 10.1136/jitc-2020-002179] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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] [Accepted: 09/20/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Anti-programmed cell death protein 1 and programmed cell death ligand 1 (PD-L1) agents are broadly used in first-line and second-line treatment across different tumor types. While immunohistochemistry-based assays are routinely used to assess PD-L1 expression, their clinical utility remains controversial due to the partial predictive value and lack of standardized cut-offs across antibody clones. Using a high throughput immunoassay, the reverse phase protein microarray (RPPA), coupled with a fluorescence-based detection system, this study compared the performance of six anti-PD-L1 antibody clones on 666 tumor samples. METHODS PD-L1 expression was measured using five antibody clones (22C3, 28-8, CAL10, E1L3N and SP142) and the therapeutic antibody atezolizumab on 222 lung, 71 ovarian, 52 prostate and 267 breast cancers, and 54 metastatic lesions. To capture clinically relevant variables, our cohort included frozen and formalin-fixed paraffin-embedded samples, surgical specimens and core needle biopsies. Pure tumor epithelia were isolated using laser capture microdissection from 602 samples. Correlation coefficients were calculated to assess concordance between antibody clones. For two independent cohorts of patients with lung cancer treated with nivolumab, RPPA-based PD-L1 measurements were examined along with response to treatment. RESULTS Median-center PD-L1 dynamic ranged from 0.01 to 39.37 across antibody clones. Correlation coefficients between the six antibody clones were heterogeneous (range: -0.48 to 0.95) and below 0.50 in 61% of the comparisons. In nivolumab-treated patients, RPPA-based measurement identified a subgroup of tumors, where low PD-L1 expression equated to lack of response. CONCLUSIONS Continuous RPPA-based measurements capture a broad dynamic range of PD-L1 expression in human specimens and heterogeneous concordance levels between antibody clones. This high throughput immunoassay can potentially identify subgroups of tumors in which low expression of PD-L1 equates to lack of response to treatment.
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Affiliation(s)
- Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - K Alex Hodge
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Guido Bellezza
- Department of Experimental Medicine, Section of Anatomic Pathology and Histology, University of Perugia, Perugia, Italy
| | - Neil J Shah
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Guido Gambara
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Angelo Sidoni
- Department of Experimental Medicine, Section of Anatomic Pathology and Histology, University of Perugia, Perugia, Italy
| | - Martina Mandarano
- Department of Experimental Medicine, Section of Anatomic Pathology and Histology, University of Perugia, Perugia, Italy
| | - Chamodya Ruhunusiri
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA.,School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | | | - Maysa Abu-Khalaf
- Department of Medical Oncology, Sidney Kimmel Cancer Center at Jefferson Health, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Julia Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Rosa I Gallagher
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | | | - Niven Mehra
- The Institute of Cancer Research, London, UK
| | | | - Antonella Ravaggi
- Angelo Nocivelli Institute of Molecular Medicine, Division of Gynecologic Oncology, University of Brescia and ASST Spedali Civili di Brescia, Brescia, Italy
| | - Franco Odicino
- Angelo Nocivelli Institute of Molecular Medicine, Division of Gynecologic Oncology, University of Brescia and ASST Spedali Civili di Brescia, Brescia, Italy
| | - Maria Isabella Sereni
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA.,Angelo Nocivelli Institute of Molecular Medicine, Division of Gynecologic Oncology, University of Brescia and ASST Spedali Civili di Brescia, Brescia, Italy
| | - Matthew Blackburn
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Angela Zupa
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA.,Unita' Operativa di Anatomia Patologica, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) CROB, Rionero In Vulture, Italy
| | - Giuseppina Improta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA.,Unita' Operativa di Anatomia Patologica, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) CROB, Rionero In Vulture, Italy
| | - Perry Demsko
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Lucio Crino'
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Vienna Ludovini
- Division of Medical Oncology, S. Maria della Misericordia Hospital, Perugia, Italy
| | - Giuseppe Giaccone
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA .,School of Systems Biology, George Mason University, Manassas, Virginia, USA
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39
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Yee D, Isaacs C, Wolf DM, Yau C, Haluska P, Giridhar KV, Forero-Torres A, Jo Chien A, Wallace AM, Pusztai L, Albain KS, Ellis ED, Beckwith H, Haley BB, Elias AD, Boughey JC, Kemmer K, Yung RL, Pohlmann PR, Tripathy D, Clark AS, Han HS, Nanda R, Khan QJ, Edmiston KK, Petricoin EF, Stringer-Reasor E, Falkson CI, Majure M, Mukhtar RA, Helsten TL, Moulder SL, Robinson PA, Wulfkuhle JD, Brown-Swigart L, Buxton M, Clennell JL, Paoloni M, Sanil A, Berry S, Asare SM, Wilson A, Hirst GL, Singhrao R, Asare AL, Matthews JB, Hylton NM, DeMichele A, Melisko M, Perlmutter J, Rugo HS, Fraser Symmans W, Van't Veer LJ, Berry DA, Esserman LJ. Ganitumab and metformin plus standard neoadjuvant therapy in stage 2/3 breast cancer. NPJ Breast Cancer 2021; 7:131. [PMID: 34611148 PMCID: PMC8492731 DOI: 10.1038/s41523-021-00337-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 11/23/2020] [Accepted: 08/26/2021] [Indexed: 12/11/2022] Open
Abstract
I-SPY2 is an adaptively randomized phase 2 clinical trial evaluating novel agents in combination with standard-of-care paclitaxel followed by doxorubicin and cyclophosphamide in the neoadjuvant treatment of breast cancer. Ganitumab is a monoclonal antibody designed to bind and inhibit function of the type I insulin-like growth factor receptor (IGF-1R). Ganitumab was tested in combination with metformin and paclitaxel (PGM) followed by AC compared to standard-of-care alone. While pathologic complete response (pCR) rates were numerically higher in the PGM treatment arm for hormone receptor-negative, HER2-negative breast cancer (32% versus 21%), this small increase did not meet I-SPY's prespecified threshold for graduation. PGM was associated with increased hyperglycemia and elevated hemoglobin A1c (HbA1c), despite the use of metformin in combination with ganitumab. We evaluated several putative predictive biomarkers of ganitumab response (e.g., IGF-1 ligand score, IGF-1R signature, IGFBP5 expression, baseline HbA1c). None were specific predictors of response to PGM, although several signatures were associated with pCR in both arms. Any further development of anti-IGF-1R therapy will require better control of anti-IGF-1R drug-induced hyperglycemia and the development of more predictive biomarkers.
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Affiliation(s)
- Douglas Yee
- Masonic Cancer Center, University of Minnesota, 420 Delaware St., SE, MMC 480, Minneapolis, MN, 55455, USA.
| | - Claudine Isaacs
- Georgetown University, 3800 Reservoir Rd, NW, Washington, DC, 20007, USA
| | - Denise M Wolf
- University of California San Francisco Department of Laboratory Medicine, 2340 Sutter Street, S433, San Francisco, CA, 94115, USA
| | - Christina Yau
- University of California San Francisco Department of Laboratory Medicine, 2340 Sutter Street, S433, San Francisco, CA, 94115, USA
| | - Paul Haluska
- Mayo Clinic Rochester c/o Merck Corporation, 126 E. Lincoln Ave Rahway, New Jersey, 07065, USA
| | - Karthik V Giridhar
- Mayo Clinic Division of Medical Oncology, 200 1st St SW, Rochester, MN, 55905, USA
| | - Andres Forero-Torres
- University of Alabama at Birmingham c/o Seattle Genetics, 21823 30th Drive S.E., Bothell, WA, 98021, USA
| | - A Jo Chien
- University of California San Francisco Division of Hematology-Oncology, 550 16th Street, San Francisco, CA, 94158, USA
| | - Anne M Wallace
- University of California San Diego Department of Surgery, 3855 Health Sciences Dr, M/C 0698, La Jolla, CA, 92093, USA
| | - Lajos Pusztai
- Yale University Medical Onciology, 111 Goose Lane, Fl 2, Guilford, CT, 06437, USA
| | - Kathy S Albain
- Loyola University Chicago Stritch School of Medicine Cardinal Bernardin Cancer Center, 2160 South First Ave, Maywood, IL, 60153, USA
| | - Erin D Ellis
- Swedish Cancer Institute Medical Oncology, 1221 Madison Street, Seattle, WA, 98104, USA
| | - Heather Beckwith
- Masonic Cancer Center, University of Minnesota, 420 Delaware St., SE, MMC 480, Minneapolis, MN, 55455, USA
| | - Barbara B Haley
- UT Southwestern Medical Center Division of Hematology-Oncology, 5323 Harry Hines Blvd, Bldg E6.222D, Dallas, TX, 75390-9155, USA
| | - Anthony D Elias
- University of Colorado Anschutz Medical Center Division of Medical Oncology, 1665 Aurora Ct., Rm. 3200, MS F700, Aurora, CO, 80045, USA
| | - Judy C Boughey
- Mayo Clinic Division of Medical Oncology, 200 1st St SW, Rochester, MN, 55905, USA
| | - Kathleen Kemmer
- OHSU Knight Cancer Institute South Waterfront Center for Health and Healing, 3303 SW Bond Ave Building 1, Suite 7, Portland, OR, 97239, USA
| | - Rachel L Yung
- University of Washington Seattle Cancer Care Alliance, 825 Eastlake Ave East, Seattle, WA, 98109-1023, USA
| | - Paula R Pohlmann
- Georgetown University, 3800 Reservoir Rd, NW, Washington, DC, 20007, USA
| | - Debu Tripathy
- MD Anderson Cancer Center, 1515 Holcombe, Houston, Texas, 77030, USA
| | - Amy S Clark
- University of Pennsylvania Division of Hematology-Oncology 3 Perelman Center, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Hyo S Han
- Moffit Cancer Center, 2902 USF Magnolia Drive, Tampa, FL, 33612, USA
| | - Rita Nanda
- University of Chicago Section of Hematology/Oncology, 5841S. Maryland Avenue, MC 2115, Chicago, IL, 60437, USA
| | - Qamar J Khan
- University of Kansas Division of Oncology, 2330 Shawnee Mission Pkwy, Ste 210, Westwood, KS, 66205, USA
| | - Kristen K Edmiston
- Inova Medical Group, 3580 Joseph Siewick Dr 101, Fairfax, VA, 22033-1764, USA
| | - Emanuel F Petricoin
- George Mason University Institute for Advanced Biomedical Research, 10920 George Mason Circle Room 2008, MS1A9, Manassas, Virginia, 20110, USA
| | - Erica Stringer-Reasor
- University of Alabama at Birmingham Hematology/Oncology, 1802 Sixth Avenue South 2510, Birmingham, AL, 35294-3300, USA
| | - Carla I Falkson
- Wilmot Cancer Institute Pluta Cancer Center, 125 Red Creek Drive, Rochester, NY, 14623, USA
| | - Melanie Majure
- University of California San Francisco, 550 16th Street, 6464, San Francisco, CA, 94158, USA
| | - Rita A Mukhtar
- University of California San Francisco, 550 16th Street, 6464, San Francisco, CA, 94158, USA
| | - Teresa L Helsten
- University of California San Diego Division of Hematology-Oncology, 9400 Campus Point Dr, La Jolla, CA, 92037, USA
| | - Stacy L Moulder
- MD Anderson Cancer Center, 1515 Holcombe, Houston, Texas, 77030, USA
| | - Patricia A Robinson
- Loyola University Chicago Stritch School of Medicine Cardinal Bernardin Cancer Center, 2160 South First Ave, Maywood, IL, 60153, USA
| | - Julia D Wulfkuhle
- George Mason University Institute for Advanced Biomedical Research, 10920 George Mason Circle Room 2008, MS1A9, Manassas, Virginia, 20110, USA
| | - Lamorna Brown-Swigart
- University of California San Francisco Department of Laboratory Medicine, 2340 Sutter Street, S433, San Francisco, CA, 94115, USA
| | - Meredith Buxton
- University of California San Francisco c/o Global Coalition for Adaptive Research, 1661 Massachusetts Ave, Lexington, MA, 02420, USA
| | - Julia L Clennell
- University of California San Francisco c/o IQVIA, 135 Main St 21 floor, San Francisco, CA, 94105, USA
| | | | - Ashish Sanil
- Berry Consultants, LLC 3345 Bee Cave Rd Suite 201, Austin, TX, 78746, USA
| | - Scott Berry
- Berry Consultants, LLC 3345 Bee Cave Rd Suite 201, Austin, TX, 78746, USA
| | - Smita M Asare
- Quantum Leap Healthcare Collaborative, 3450 California St, San Francisco, CA, 94143, USA
| | - Amy Wilson
- Quantum Leap Healthcare Collaborative, 3450 California St, San Francisco, CA, 94143, USA
| | - Gillian L Hirst
- University of California San Francisco, 550 16th Street, 6464, San Francisco, CA, 94158, USA
| | - Ruby Singhrao
- University of California San Francisco, 550 16th Street, 6464, San Francisco, CA, 94158, USA
| | - Adam L Asare
- Quantum Leap Healthcare Collaborative, 3450 California St, San Francisco, CA, 94143, USA
| | - Jeffrey B Matthews
- University of California San Francisco, 550 16th Street, 6464, San Francisco, CA, 94158, USA
| | - Nola M Hylton
- University of California San Francisco, 550 16th Street, 6464, San Francisco, CA, 94158, USA
| | - Angela DeMichele
- University of Pennsylvania Division of Hematology-Oncology 3 Perelman Center, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Michelle Melisko
- University of California San Francisco, 550 16th Street, 6464, San Francisco, CA, 94158, USA
| | - Jane Perlmutter
- University of California San Francisco, 550 16th Street, 6464, San Francisco, CA, 94158, USA
| | - Hope S Rugo
- University of California San Francisco, 550 16th Street, 6464, San Francisco, CA, 94158, USA
| | - W Fraser Symmans
- MD Anderson Cancer Center, 1515 Holcombe, Houston, Texas, 77030, USA
| | - Laura J Van't Veer
- University of California San Francisco Department of Laboratory Medicine, 2340 Sutter Street, S433, San Francisco, CA, 94115, USA
| | - Donald A Berry
- Quantum Leap Healthcare Collaborative, 3450 California St, San Francisco, CA, 94143, USA
| | - Laura J Esserman
- University of California San Francisco, 550 16th Street, 6464, San Francisco, CA, 94158, USA
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40
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Magni R, Rruga F, Alsaab FM, Sharif S, Howard M, Espina V, Kim B, Lepene B, Lee G, Alayouni MA, Steinberg H, Araujo R, Kashanchi F, Riccardi F, Morreira S, Araujo A, Poli F, Jaganath D, Semitala FC, Worodria W, Andama A, Choudhary A, Honnen WJ, Petricoin EF, Cattamanchi A, Colombatti R, de Waard JH, Oberhelman R, Pinter A, Gilman RH, Liotta LA, Luchini A. Author Correction: Lipoarabinomannan antigenic epitope differences in tuberculosis disease subtypes. Sci Rep 2021; 11:19546. [PMID: 34580341 PMCID: PMC8476616 DOI: 10.1038/s41598-021-98304-1] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Ruben Magni
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Fatlum Rruga
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.,Dipartimento Di Salute Della Donna e del Bambino, Laboratorio di Oncoematologia, Università di Padova, Padova, Italy
| | - Fahad M Alsaab
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.,College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Al Ahsa, Saudi Arabia
| | - Sara Sharif
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Marissa Howard
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | | | | | - Gwenyth Lee
- Department of Global Community Health and Behavioral Sciences, Tulane University, New Orleans, LA, USA.,Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Mohamad A Alayouni
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | | | - Robyn Araujo
- Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Fatah Kashanchi
- School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Fabio Riccardi
- Aid Health and Development Onlus, Bissau, Guinea-Bissau.,University of Tor Vergata, Rome, Italy
| | | | | | - Fernando Poli
- Departamento de Tuberculosis, Instituto de Biomedicina "Dr. Jacinto Convit", Universidad Central de Venezuela, Caracas, Venezuela
| | - Devan Jaganath
- Division of Pediatric Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA.,Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Fred C Semitala
- Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda.,Infectious Diseases Research Collaboration, Kampala, Uganda
| | - William Worodria
- Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda.,Mulago National Referral Hospital, Kampala, Uganda
| | - Alfred Andama
- Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda.,Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Alok Choudhary
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - William J Honnen
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Adithya Cattamanchi
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Raffaella Colombatti
- Department of Women's and Child's Health, Azienda Ospedaliera-Università di Padova, Padova, Italy
| | - Jacobus H de Waard
- Departamento de Tuberculosis, Instituto de Biomedicina "Dr. Jacinto Convit", Universidad Central de Venezuela, Caracas, Venezuela.,One Health Research Group, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito, Ecuador
| | - Richard Oberhelman
- Department of Global Community Health and Behavioral Sciences, Tulane University, New Orleans, LA, USA
| | - Abraham Pinter
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Robert H Gilman
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.,Asociación Benéfica PRISMA, Lima, Peru.,Program in Global Disease Epidemiology and Control, Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Lance A Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Alessandra Luchini
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA.
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Baldelli E, El Gazzah E, Moran JC, Hodge KA, Manojlovic Z, Bassiouni R, Carpten JD, Ludovini V, Baglivo S, Crinò L, Bianconi F, Dong T, Loffredo J, Petricoin EF, Pierobon M. Wild-Type KRAS Allele Effects on Druggable Targets in KRAS Mutant Lung Adenocarcinomas. Genes (Basel) 2021; 12:genes12091402. [PMID: 34573384 PMCID: PMC8467269 DOI: 10.3390/genes12091402] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
KRAS mutations are one of the most common oncogenic drivers in non-small cell lung cancer (NSCLC) and in lung adenocarcinomas in particular. Development of therapeutics targeting KRAS has been incredibly challenging, prompting indirect inhibition of downstream targets such as MEK and ERK. Such inhibitors, unfortunately, come with limited clinical efficacy, and therefore the demand for developing novel therapeutic strategies remains an urgent need for these patients. Exploring the influence of wild-type (WT) KRAS on druggable targets can uncover new vulnerabilities for the treatment of KRAS mutant lung adenocarcinomas. Using commercially available KRAS mutant lung adenocarcinoma cell lines, we explored the influence of WT KRAS on signaling networks and druggable targets. Expression and/or activation of 183 signaling proteins, most of which are targets of FDA-approved drugs, were captured by reverse-phase protein microarray (RPPA). Selected findings were validated on a cohort of 23 surgical biospecimens using the RPPA. Kinase-driven signatures associated with the presence of the KRAS WT allele were detected along the MAPK and AKT/mTOR signaling pathway and alterations of cell cycle regulators. FoxM1 emerged as a potential vulnerability of tumors retaining the KRAS WT allele both in cell lines and in the clinical samples. Our findings suggest that loss of WT KRAS impacts on signaling events and druggable targets in KRAS mutant lung adenocarcinomas.
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Affiliation(s)
- Elisa Baldelli
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA 20110, USA; (E.B.); (E.E.G.); (J.C.M.); (K.A.H.); (T.D.); (J.L.); (E.F.P.)
| | - Emna El Gazzah
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA 20110, USA; (E.B.); (E.E.G.); (J.C.M.); (K.A.H.); (T.D.); (J.L.); (E.F.P.)
- School of Systems Biology, George Mason University, Manassas, VA 20110, USA
| | - John Conor Moran
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA 20110, USA; (E.B.); (E.E.G.); (J.C.M.); (K.A.H.); (T.D.); (J.L.); (E.F.P.)
| | - Kimberley A. Hodge
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA 20110, USA; (E.B.); (E.E.G.); (J.C.M.); (K.A.H.); (T.D.); (J.L.); (E.F.P.)
| | - Zarko Manojlovic
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (Z.M.); (R.B.); (J.D.C.)
| | - Rania Bassiouni
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (Z.M.); (R.B.); (J.D.C.)
| | - John D. Carpten
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; (Z.M.); (R.B.); (J.D.C.)
| | - Vienna Ludovini
- Division of Medical Oncology, S. Maria della Misericordia Hospital, 06156 Perugia, Italy; (V.L.); (S.B.)
| | - Sara Baglivo
- Division of Medical Oncology, S. Maria della Misericordia Hospital, 06156 Perugia, Italy; (V.L.); (S.B.)
| | - Lucio Crinò
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy;
| | | | - Ting Dong
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA 20110, USA; (E.B.); (E.E.G.); (J.C.M.); (K.A.H.); (T.D.); (J.L.); (E.F.P.)
| | - Jeremy Loffredo
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA 20110, USA; (E.B.); (E.E.G.); (J.C.M.); (K.A.H.); (T.D.); (J.L.); (E.F.P.)
| | - Emanuel F. Petricoin
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA 20110, USA; (E.B.); (E.E.G.); (J.C.M.); (K.A.H.); (T.D.); (J.L.); (E.F.P.)
| | - Mariaelena Pierobon
- Center for Applied Proteomics & Molecular Medicine, George Mason University, Manassas, VA 20110, USA; (E.B.); (E.E.G.); (J.C.M.); (K.A.H.); (T.D.); (J.L.); (E.F.P.)
- School of Systems Biology, George Mason University, Manassas, VA 20110, USA
- Correspondence: ; Tel.: +1-703-993-9839
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42
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Hendifar A, Blais EM, Wolpin B, Subbiah V, Collisson E, Singh I, Cannon T, Shaw K, Petricoin EF, Klempner S, Lyons E, Wang-Gillam A, Pishvaian MJ, O'Reilly EM. Retrospective Case Series Analysis of RAF Family Alterations in Pancreatic Cancer: Real-World Outcomes From Targeted and Standard Therapies. JCO Precis Oncol 2021; 5:PO.20.00494. [PMID: 34476331 PMCID: PMC8407652 DOI: 10.1200/po.20.00494] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 12/02/2020] [Revised: 06/14/2021] [Accepted: 07/23/2021] [Indexed: 12/19/2022] Open
Abstract
PURPOSE In pancreatic cancer (PC), the RAF family alterations define a rare subset of patients that may predict response to inhibition of the BRAF/MEK/ERK signaling pathway. A comprehensive understanding of the molecular and clinical characteristics of RAF-mutated PC may support future development of RAF-directed strategies. METHODS Clinical outcomes were assessed across a multi-institutional case series of 81 patients with RAF family-mutated PC. Mutational subgroups were defined on the basis of RAF alteration hotspots and therapeutic implications. RESULTS The frequency of RAF alterations in PC was 2.2% (84 of 3,781) within a prevalence cohort derived from large molecular databases where BRAF V600E (Exon 15), BRAF ΔNVTAP (Exon 11), and SND1-BRAF fusions were the most common variants. In our retrospective case series, we identified 17 of 81 (21.0%) molecular profiles with a BRAF V600/Exon 15 mutation without any confounding drivers, 25 of 81 (30.9%) with BRAF or RAF1 fusions, and 18 of 81 (22.2%) with Exon 11 mutations. The remaining 21 of 81 (25.9%) profiles had atypical RAF variants and/or multiple oncogenic drivers. Clinical benefit from BRAF/MEK/ERK inhibitors was observed in 3 of 3 subjects within the V600 subgroup (two partial responses), 4 of 6 with fusions (two partial responses), 2 of 6 with Exon 11 mutations (one partial response), and 0 of 3 with confounding drivers. Outcomes analyses also suggested a trend favoring fluorouracil-based regimens over gemcitabine/nab-paclitaxel within the fusion subgroup (P = .027). CONCLUSION Prospective evaluation of RAF-directed therapies is warranted in RAF-mutated PC; however, differential responses to targeted agents or standard regimens for each mutational subgroup should be a consideration when designing clinical trials. In KRAS wild-type PDAC, certain RAF alterations predict benefit from map-kinase targeted therapy![]()
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Affiliation(s)
| | | | - Brian Wolpin
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Vivek Subbiah
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Eric Collisson
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Isha Singh
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Kenna Shaw
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Samuel Klempner
- Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Emily Lyons
- Pancreatic Cancer Action Network, Manhattan Beach, CA
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43
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Pierobon M, Robert NJ, Northfelt DW, Jahanzeb M, Wong S, Hodge KA, Baldelli E, Aldrich J, Craig DW, Liotta LA, Avramovic S, Wojtusiak J, Alemi F, Wulfkuhle JD, Bellos A, Gallagher RI, Arguello D, Conrad A, Kemkes A, Loesch DM, Vocila L, Dunetz B, Carpten JD, Petricoin EF, Anthony SP. Multi-omic molecular profiling guide's efficacious treatment selection in refractory metastatic breast cancer: a prospective phase II clinical trial. Mol Oncol 2021; 16:104-115. [PMID: 34437759 PMCID: PMC8732340 DOI: 10.1002/1878-0261.13091] [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: 03/16/2021] [Revised: 07/30/2021] [Accepted: 08/25/2021] [Indexed: 11/22/2022] Open
Abstract
This prospective phase II clinical trial (Side Out 2) explored the clinical benefits of treatment selection informed by multi‐omic molecular profiling (MoMP) in refractory metastatic breast cancers (MBCs). Core needle biopsies were collected from 32 patients with MBC at trial enrollment. Patients had received an average of 3.94 previous lines of treatment in the metastatic setting before enrollment in this study. Samples underwent MoMP, including exome sequencing, RNA sequencing (RNA‐Seq), immunohistochemistry, and quantitative protein pathway activation mapping by Reverse Phase Protein Microarray (RPPA). Clinical benefit was assessed using the previously published growth modulation index (GMI) under the hypothesis that MoMP‐selected therapy would warrant further investigation for GMI ≥ 1.3 in ≥ 35% of the patients. Of the 32 patients enrolled, 29 received treatment based on their MoMP and 25 met the follow‐up criteria established by the trial protocol. Molecular information was delivered to the tumor board in a median time frame of 14 days (11–22 days), and targetable alterations for commercially available agents were found in 23/25 patients (92%). Of the 25 patients, 14 (56%) reached GMI ≥ 1.3. A high level of DNA topoisomerase I (TOPO1) led to the selection of irinotecan‐based treatments in 48% (12/25) of the patients. A pooled analysis suggested clinical benefit in patients with high TOPO1 expression receiving irinotecan‐based regimens (GMI ≥ 1.3 in 66.7% of cases). These results confirmed previous observations that MoMP increases the frequency of identifiable actionable alterations (92% of patients). The MoMP proposed allows the identification of biomarkers that are frequently expressed in MBCs and the evaluation of their role as predictors of response to commercially available agents. Lastly, this study confirmed the role of MoMP for informing treatment selection in refractory MBC patients: more than half of the enrolled patients reached a GMI ≥ 1.3 even after multiple lines of previous therapies for metastatic disease.
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Affiliation(s)
| | | | | | - Mohammad Jahanzeb
- A Division of 21st Century Oncology, Florida Precision Oncology, Raton, FL, USA
| | - Shukmei Wong
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | | | | | - David W Craig
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Sanja Avramovic
- Department of Health Administration and Policy, George Mason University, Fairfax, VA, USA
| | - Janusz Wojtusiak
- Department of Health Administration and Policy, George Mason University, Fairfax, VA, USA
| | - Farrokh Alemi
- Department of Health Administration and Policy, George Mason University, Fairfax, VA, USA
| | | | | | | | | | | | | | | | - Linda Vocila
- Translational Drug Development (TD2), Scottsdale, AZ, USA
| | | | - John D Carpten
- Translational Genomics Research Institute, Phoenix, AZ, USA
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44
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Schultz CW, McCarthy GA, Nerwal T, Nevler A, DuHadaway JB, McCoy MD, Jiang W, Brown SZ, Goetz A, Jain A, Calvert VS, Vishwakarma V, Wang D, Preet R, Cassel J, Summer R, Shaghaghi H, Pommier Y, Baechler SA, Pishvaian MJ, Golan T, Yeo CJ, Petricoin EF, Prendergast GC, Salvino J, Singh PK, Dixon DA, Brody JR. The FDA-Approved Anthelmintic Pyrvinium Pamoate Inhibits Pancreatic Cancer Cells in Nutrient-Depleted Conditions by Targeting the Mitochondria. Mol Cancer Ther 2021; 20:2166-2176. [PMID: 34413127 DOI: 10.1158/1535-7163.mct-20-0652] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 02/09/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal aggressive cancer, in part due to elements of the microenvironment (hypoxia, hypoglycemia) that cause metabolic network alterations. The FDA-approved antihelminthic pyrvinium pamoate (PP) has previously been shown to cause PDAC cell death, although the mechanism has not been fully determined. We demonstrated that PP effectively inhibited PDAC cell viability with nanomolar IC50 values (9-93 nmol/L) against a panel of PDAC, patient-derived, and murine organoid cell lines. In vivo, we demonstrated that PP inhibited PDAC xenograft tumor growth with both intraperitoneal (IP; P < 0.0001) and oral administration (PO; P = 0.0023) of human-grade drug. Metabolomic and phosphoproteomic data identified that PP potently inhibited PDAC mitochondrial pathways including oxidative phosphorylation and fatty acid metabolism. As PP treatment reduced oxidative phosphorylation (P < 0.001), leading to an increase in glycolysis (P < 0.001), PP was 16.2-fold more effective in hypoglycemic conditions similar to those seen in PDAC tumors. RNA sequencing demonstrated that PP caused a decrease in mitochondrial RNA expression, an effect that was not observed with established mitochondrial inhibitors rotenone and oligomycin. Mechanistically, we determined that PP selectively bound mitochondrial G-quadruplexes and inhibited mitochondrial RNA transcription in a G-quadruplex-dependent manner. This subsequently led to a 90% reduction in mitochondrial encoded gene expression. We are preparing to evaluate the efficacy of PP in PDAC in an IRB-approved window-of-opportunity trial (IND:144822).
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Affiliation(s)
- Christopher W Schultz
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Grace A McCarthy
- Brenden-Colson Center for Pancreatic Care, Departments of Surgery and Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Teena Nerwal
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Avinoam Nevler
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | | | - Wei Jiang
- Pathology Department, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Samantha Z Brown
- Brenden-Colson Center for Pancreatic Care, Departments of Surgery and Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Austin Goetz
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Aditi Jain
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | | | - Dezhen Wang
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, Nebraska
| | | | - Joel Cassel
- Wistar Institute, Philadelphia, Pennsylvania
| | - Ross Summer
- Jane and Leonard Korman Respiratory Institute at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Hoora Shaghaghi
- Jane and Leonard Korman Respiratory Institute at Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Yves Pommier
- Developmental Therapeutics Branch, NCI Bethesda, Maryland
| | | | | | - Talia Golan
- Oncology institute, Chaim Sheba Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Charles J Yeo
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | | | | | - Pankaj K Singh
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, Nebraska
| | | | - Jonathan R Brody
- Brenden-Colson Center for Pancreatic Care, Departments of Surgery and Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon.
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Damluji AA, Wei S, Bruce SA, Haymond A, Petricoin EF, Liotta L, Maxwell GL, Moore BC, Bell R, Garofalo S, Houpt ER, Trump D, deFilippi CR. Seropositivity of COVID-19 among asymptomatic healthcare workers: A multi-site prospective cohort study from Northern Virginia, United States. ACTA ACUST UNITED AC 2021; 2:100030. [PMID: 34386793 PMCID: PMC8319689 DOI: 10.1016/j.lana.2021.100030] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/30/2021] [Accepted: 07/13/2021] [Indexed: 11/28/2022]
Abstract
Background Because of their direct patient contact, healthcare workers (HCW) face an unprecedented risk of exposure to COVID-19. The aim of this study was to examine incidence of COVID-19 disease among asymptomatic HCW and community participants in Northern Virginia during 6 months of follow-up. Methods This is a prospective cohort study that enrolled healthy HCW and residents who never had a symptomatic COVID-19 infection prior to enrolment from the community in Northern Virginia from April to November 2020. All participants were invited to enrol in study, and they were followed at 2-, and 6-months intervals. Participants were evaluated by commercial chemiluminescence SARS-CoV-2 serology assays as part of regional health system and public health surveillance program to monitor the spread of COVID-19 disease. Findings Of a total of 1,819 asymptomatic HCW enrolled, 1,473 (96%) had data at two-months interval, and 1,323 (73%) participants had data at 6-months interval. At baseline, 21 (1.15%) were found to have prior COVID-19 exposure. At two-months interval, COVID-19 rate was 2.8% and at six months follow-up, the overall incidence rate increased to 4.8%, but was as high as 7.9% among those who belong to the youngest age group (20–29 years). Seroconversion rates in HCW were comparable to the seropositive rates in the Northern Virginia community. The overall incidence of COVID-19 in the community was 4.5%, but the estimate was higher among Hispanic ethnicity (incidence rate = 15.3%) potentially reflecting different socio-economic factors among the community participants and the HCW group. Using cross-sectional logistic regression and spatio-temporal mixed effects models, significant factors that influence the transmission rate among HCW include age, race/ethnicity, resident ZIP-code, and household exposure, but not direct patient contact. Interpretation In Northern Virginia, the seropositive rate of COVID-19 disease among HCW was comparable to that in the community.
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Affiliation(s)
- Abdulla A Damluji
- The Inova Center of Outcomes Research, Inova Heart and Vascular Institute, 3300 Gallows Road, I-465, Falls Church, VA 22042, United States.,Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Siqi Wei
- Department of Statistics, George Mason University, Fairfax, VA, United States
| | - Scott A Bruce
- Department of Statistics, Texas A&M University, College Station, TX, United States
| | - Amanda Haymond
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, United States
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, United States
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, United States
| | - G Larry Maxwell
- The Inova Center of Outcomes Research, Inova Heart and Vascular Institute, 3300 Gallows Road, I-465, Falls Church, VA 22042, United States
| | - Brian C Moore
- The Inova Center of Outcomes Research, Inova Heart and Vascular Institute, 3300 Gallows Road, I-465, Falls Church, VA 22042, United States
| | - Rachel Bell
- The Inova Center of Outcomes Research, Inova Heart and Vascular Institute, 3300 Gallows Road, I-465, Falls Church, VA 22042, United States
| | - Stephanie Garofalo
- The Inova Center of Outcomes Research, Inova Heart and Vascular Institute, 3300 Gallows Road, I-465, Falls Church, VA 22042, United States
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, United States
| | - David Trump
- Virginia Department of Health, Richmond, VA, United States
| | - Christopher R deFilippi
- The Inova Center of Outcomes Research, Inova Heart and Vascular Institute, 3300 Gallows Road, I-465, Falls Church, VA 22042, United States
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46
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Baldelli E, Subramanian M, Alsubaie AM, Baglivo S, Hodge KA, Bianconi F, Ludovini V, Crino' L, Petricoin EF, Pierobon M. Abstract 1993: Off-target effects of ultra-low dose dimethyl sulfoxide on targetable signaling events in lung cancer in vitro models. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-1993] [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: The identification of targetable alterations in cancer continues to offer novel opportunities to the drug discovery process. However, pre-clinical testing often requires solubilization of these drugs in cosolvents like dimethyl sulfoxide (DMSO). Using commercially available models commonly used for in vitro drug screening and pre-clinical testing, we explored the DMSO off-target effects on functional signaling networks, drug targets, and downstream substrates.
Materials and Methods: Eight commercially available Non-Small Cell Lung Cancer (NSCLC) cell lines were incubated with three ultra-low concentrations of DMSO (0.0008%, 0.002%, and 0.004% v/v, respectively) for 5 min, as well as 1, 6 and 24 hours. Following incubation, expression and activation levels of 183 proteins were captured using Reverse Phase Protein Array (RPPA) technology, of which 134 were kinases and downstream substrates.
Results: The DMSO effect was heterogenous across cell lines and varied based on multiple factors including: concentration, exposure time, and cell line. Of the 183 proteins measured, 88% were statistically significant at the highest DMSO concentration, followed by 81% and 67% at lower concentrations. Only 28 proteins were found statistically different in more than 5 cell lines indicating heterogenous response across models. pERK 1/2 T202/Y204 emerged as the most frequently affected node along with stress-induced response and mitogenic proteins. These cell line specific DMSO-induced alterations, may modulate response to targeted agents and chemotherapeutics.
Conclusions: Ultra-low DMSO concentrations have broad and heterogenous effects on targetable signaling proteins which are model, time, and concentration dependent. As such, off-target effects need to be carefully evaluated in the design and implementation of pre-clinical drug screening and testing.
Citation Format: Elisa Baldelli, Mahalakshmi Subramanian, Abduljalil M. Alsubaie, Sara Baglivo, K A. Hodge, Fortunato Bianconi, Vienna Ludovini, Lucio Crino', Emanuel F. Petricoin, Mariaelena Pierobon. Off-target effects of ultra-low dose dimethyl sulfoxide on targetable signaling events in lung cancer in vitro models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1993.
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Affiliation(s)
| | | | | | - Sara Baglivo
- 2S. Maria della Misericordia Hospital, Perugia, Italy
| | | | | | | | - Lucio Crino'
- 5Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
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47
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El Gazzah E, Baldelli E, Ruhunsiri C, Petricoin EF, Pierobon M. Abstract 2000: Different oncogenic KRAS mutations produce distinct heterogenous outcomes in signaling pathways of isogenic mouse embryonic fibroblasts. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2000] [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: Growing evidence points towards the concept that not all RAS allelic variances are equal. Different RAS mutations produce distinct variations in signal transduction to sustain their proliferative needs accordingly. This is an especially important concept to consider as medicine shifts towards a more personalized approach. In accordance with this notion, through this study, we aim to explore the network dynamics and pinpoint disparities in signaling events associated with seven common KRAS allelic variances in non-small cell lung carcinoma.
Methods: We used Mouse Embryonic Fibroblasts (MEF) provided by the RAS initiative (https://www.cancer.gov/research/key-initiatives/ras/outreach/reference-reagents/cell-lines). MEF were engineered to selectively harbor and express either wild type KRAS (4A and 4B WT) or one of seven following mutations: 4B G12D, G12C, G12R, G12V, G13D, Q61R and Q61L. Using high throughput immunoassay, Reverse Phase Protein Microarray (RPPA), we explored broad changes in signaling dynamics across our models. Specifically, we captured expression and/or activation levels of 68 proteins and phosphoproteins including: Receptor Tyrosine Kinases, MAPK, AKT/mTOR, JNK/STAT. Data were analyzed using unsupervised hierarchical clustering analysis using the Ward methods and the Kruskal Wallis test. P values <0.05 were considered significant.
Results: Based on the unsupervised clustering analysis, Q61R and Q61L mutations showed the least activated signaling when compared to all other models. Activation of Raf was increased in cells harboring mutations of the G12 residues compared to those with mutations of the G13 and Q61 residues. Furthermore, the five G12 mutations clustered together with an overall higher active signaling compared to other cell lines. However, among the group of G12 mutants, unique signal transduction profiles were identified. We report distinct significant differences that divide the clustered G12 mutants into high versus low activation of specific signaling proteins. For example, ERK T202/Y204 (p=0.011) and S6 Ribosomal Protein S235/236 (p=0.001) phosphorylation were significantly higher in G12R compared to G12C and G12D models. On the contrary, STAT1 and STAT3 protein phosphorylation at residues Y701 and Y705 respectively were decreased in the G12R model. G12C has the lowest activation levels of p90RSK S380 (p=0.029), NF-KappaB p65 S536 (p=0.027) and P70 S6 Kinase S371 (p=0.013).
Conclusions: In alignment with other findings, we show that based on RAS mutation, individual signaling components are affected differently, producing extensive heterogeneity in signaling dynamics. Even within grouped mutations presenting an overall similar net effect on downstream signaling, each individual variant produced discrete alterations.
Citation Format: Emna El Gazzah, Elisa Baldelli, Chamodya Ruhunsiri, Emanuel F. Petricoin, Mariaelena Pierobon. Different oncogenic KRAS mutations produce distinct heterogenous outcomes in signaling pathways of isogenic mouse embryonic fibroblasts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2000.
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48
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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 UNM, 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] [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. LMD was used to investigate 3-D molecular heterogeneity in ovarian cancer tissue Diverse molecular profiles were identified from 3-D spatially separated samples Molecular heterogeneity impacts HGSOC prognostic sub-type assignment Proteomic heterogeneity analysis web portal deployed at www.lmdomics.org
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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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Haymond A, Damluji AA, Narayanan A, Mueller C, Reeder A, Alem F, Maxwell GL, Petricoin EF, Liotta L, deFilippi CR. Durability of Viral Neutralization in Asymptomatic Coronavirus Disease 2019 for at Least 60 Days. J Infect Dis 2021; 223:1677-1680. [PMID: 33718952 PMCID: PMC7989428 DOI: 10.1093/infdis/jiab140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 02/09/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023] Open
Abstract
A cohort consisting of asymptomatic healthcare workers donated temporal serum samples after infection with severe acute respiratory syndrome coronavirus 2. Analysis shows that all asymptomatic healthcare workers had neutralizing antibodies, that these antibodies persist for ≥60 days, and that anti-spike receptor-binding domain immunoglobulin G levels were correspondingly durable over the same time period.
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Affiliation(s)
- Amanda Haymond
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Abdulla A Damluji
- Inova Center of Outcomes Research, Inova Heart Vascular Institute, Falls Church, Virginia, USA
| | - Aarthi Narayanan
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, USA
| | - Claudius Mueller
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Alex Reeder
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Farhang Alem
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, USA
| | - G Larry Maxwell
- Inova Center of Outcomes Research, Inova Heart Vascular Institute, Falls Church, Virginia, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Lance Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Christopher R deFilippi
- Inova Center of Outcomes Research, Inova Heart Vascular Institute, Falls Church, Virginia, USA
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50
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Pin E, Petricoin EF, Cortes N, Bowman TG, Andersson E, Uhlén M, Nilsson P, Caswell SV. Immunoglobulin A Autoreactivity toward Brain Enriched and Apoptosis-Regulating Proteins in Saliva of Athletes after Acute Concussion and Subconcussive Impacts. J Neurotrauma 2021; 38:2373-2383. [PMID: 33858214 DOI: 10.1089/neu.2020.7375] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The diagnosis and management of concussion is hindered by its diverse clinical presentation and assessment tools reliant on subjectively experienced symptoms. The biomechanical threshold of concussion is also not well understood, and asymptomatic concussion or "subconcussive impacts" of variable magnitudes are common in contact sports. Concerns have risen because athletes returning to activity too soon have an increased risk of prolonged recovery or long-term adverse health consequences. To date, little is understood on a molecular level regarding concussion and subconcussive impacts. Recent research suggests that neuroinflammatory mechanisms may serve an important role subsequent to concussion and possibly to subconcussive impacts. These studies suggest that autoantibodies may be a valuable tool for detection of acute concussion and monitoring for changes caused by cumulative exposure to subconcussive impacts. Hence, we aimed to profile the immunoglobulin (Ig)A autoantibody repertoire in saliva by screening a unique sport-related head trauma biobank. Saliva samples (n = 167) were donated by male and female participants enrolled in either the concussion (24-48 h post-injury) or subconcussion (non-concussed participants having moderate or high cumulative subconcussive impact exposure) cohorts. Study design included discovery and verification phases. Discovery aimed to identify new candidate autoimmune targets of IgA. Verification tested whether concussion and subconcussion cohorts increased IgA reactivity and whether cohorts showed similarities. The results show a significant increase in the prevalence of IgA toward protein fragments representing 5-hydroxytryptamine receptor 1A (HTR1A), serine/arginine repetitive matrix 4 (SRRM4) and FAS (tumor necrosis factor receptor superfamily member 6) after concussion and subconcussion. These results may suggest that concussion and subconcussion induce similar physiological effects, especially in terms of immune response. Our study demonstrates that saliva is a potential biofluid for autoantibody detection in concussion and subconcussion. After rigorous confirmation in much larger independent study sets, a validated salivary autoantibody assay could provide a non-subjective quantitative means of assessing concussive and subconcussive events.
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Affiliation(s)
- Elisa Pin
- Division of Affinity Proteomics, Department of Protein Science, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, School of Kinesiology, George Mason University, Manassas, Virginia, USA.,Institute for BioHealth Innovation, and School of Kinesiology, George Mason University, Manassas, Virginia, USA
| | - Nelson Cortes
- Institute for BioHealth Innovation, and School of Kinesiology, George Mason University, Manassas, Virginia, USA.,Sports Medicine Assessment Research and Testing Laboratory, School of Kinesiology, George Mason University, Manassas, Virginia, USA
| | - Thomas G Bowman
- Department of Athletic Training, University of Lynchburg, Lynchburg, Virginia, USA
| | - Eni Andersson
- Division of Affinity Proteomics, Department of Protein Science, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Mathias Uhlén
- Division of Systems Biology, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Peter Nilsson
- Division of Affinity Proteomics, Department of Protein Science, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Shane V Caswell
- Institute for BioHealth Innovation, and School of Kinesiology, George Mason University, Manassas, Virginia, USA.,Sports Medicine Assessment Research and Testing Laboratory, School of Kinesiology, George Mason University, Manassas, Virginia, USA
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