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Sather CL, Yang P, Zhang C, Fitzgibbon MP, Fournier M, Toloza E, Tandon A, Schabath M, Yoder S, Nair VS. Protocol optimization of a targeted sequencing panel for genomic profiling of bronchoalveolar lavage fluid in lung cancer. Cancer Med 2023; 12:17632-17637. [PMID: 37587851 PMCID: PMC10524020 DOI: 10.1002/cam4.6380] [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: 06/15/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 08/18/2023] Open
Abstract
INTRODUCTION We investigated a commercially available sequencing panel to study the effect of sequencing depth, variant calling strategy, and targeted sequencing region on identifying tumor-derived variants in cell-free bronchoalveolar lavage (cfBAL) DNA compared with plasma cfDNA. METHODS Sequencing was performed at low or high coverage using two filtering algorithms to identify tumor variants on two panels targeting 77 and 197 genes respectively. RESULTS One hundred and four sequencing files from 40 matched DNA samples of cfBAL, plasma, germline leukocytes, and archival tumor specimens in 10 patients with early-stage lung cancer were analyzed. By low-coverage sequencing, tumor-derived cfBAL variants were detected in 5/10 patients (50%) compared with 2/10 (20%) for plasma. High-coverage sequencing did not affect the number of tumor-derived variants detected in either biospecimen type. Accounting for germline mutations eliminated false-positive plasma calls regardless of coverage (0/10 patients with tumor-derived variants identified) and increased the number of cfBAL calls (5/10 patients with tumor-derived variants identified). These results were not affected by the number of targeted genes.
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Affiliation(s)
| | - Pamela Yang
- Shared ResourcesFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Chaomei Zhang
- Tissue and Molecular Genomics CoresH. Lee Moffitt Cancer Center & Research InstituteTampaFloridaUSA
| | | | - Michelle Fournier
- Tissue and Molecular Genomics CoresH. Lee Moffitt Cancer Center & Research InstituteTampaFloridaUSA
| | - Eric Toloza
- Department of Thoracic OncologyH. Lee Moffitt Cancer Center & Research InstituteTampaFloridaUSA
| | - Amit Tandon
- Department of Thoracic OncologyH. Lee Moffitt Cancer Center & Research InstituteTampaFloridaUSA
- Present address:
Advent HealthWesley ChapelFloridaUSA
| | - Matthew Schabath
- Department of Thoracic OncologyH. Lee Moffitt Cancer Center & Research InstituteTampaFloridaUSA
- Department of Cancer EpidemiologyH. Lee Moffitt Cancer Center & Research InstituteTampaFloridaUSA
| | - Sean Yoder
- Tissue and Molecular Genomics CoresH. Lee Moffitt Cancer Center & Research InstituteTampaFloridaUSA
| | - Viswam S. Nair
- Division of Pulmonary, Critical Care & Sleep MedicineUniversity of WashingtonSeattleWashingtonUSA
- Clinical Research DivisionFred Hutchinson Cancer CenterSeattleWashingtonUSA
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Peterson J, Nodarse CL, Hernandez PV, Rani A, Huo Z, Meng L, Yoder S, Cole J, Foster TC, Fillingim R, Cruz-Almeida Y. Biological Aging In Those With Chronic Pain; The Role Of Fatigue. The Journal of Pain 2023. [DOI: 10.1016/j.jpain.2023.02.209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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Saller J, White D, Hough B, Yoder S, Whiting J, Chen DT, Magliocco A, Coppola D. An miRNA Signature Predicts Grading of Pancreatic Neuroendocrine Neoplasms. Cancer Genomics Proteomics 2023; 20:154-164. [PMID: 36870693 PMCID: PMC9989673 DOI: 10.21873/cgp.20370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND/AIM Grading pancreatic neuroendocrine neoplasms (PNENs) via mitotic rate and Ki-67 index score is complicated by interobserver variability. Differentially expressed miRNAs (DEMs) are useful for predicting tumour progression and may be useful for grading. PATIENTS AND METHODS Twelve PNENs were selected. Four patients had grade (G) 1 pancreatic neuroendocrine tumours (PNETs); 4 had G2 PNETs; and 4 had G3 PNENs (2 PNETs and 2 pancreatic neuroendocrine carcinomas). Samples were profiled using the miRNA NanoString Assay. RESULTS There were 6 statistically significant DEMs between different grades of PNENs. MiR1285-5p was the sole miRNA differentially expressed (p=0.03) between G1 and G2 PNETs. Six statistically significant DEMs (miR135a-5p, miR200a-3p, miR3151-5p, miR-345-5p, miR548d-5p and miR9-5p) (p<0.05) were identified between G1 PNETs and G3 PNENs. Finally, 5 DEMs (miR155-5p, miR15b-5p, miR222-3p, miR548d-5p and miR9-5p) (p<0.05) were identified between G2 PNETs and G3 PNENs. CONCLUSION The identified miRNA candidates are concordant with their patterns of dysregulation in other tumour types. The reliability of these DEMs as discriminators of PNEN grades support further investigations using larger patient populations.
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Affiliation(s)
- James Saller
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, U.S.A
| | - Daley White
- Department of Biomedical Library, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, U.S.A
| | - Brooke Hough
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, U.S.A
| | - Sean Yoder
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, U.S.A
| | - Junmin Whiting
- Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, U.S.A
| | - Dung-Tsa Chen
- Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, U.S.A
| | | | - Domenico Coppola
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, U.S.A.; .,Department of Pathology Florida Digestive Health Specialists, Lakewood Ranch, FL, U.S.A
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Bejanyan N, Kim J, Yu X, Cubitt C, Segura CM, Nguyen J, Kroeger J, Yoder S, Zhang C, Bhatnagar B, Choi J, Conejo-Garcia J, Anasetti C. Donor γδ T Cells Influence Immune Escape and Relapse of Acute Myeloid Leukemia (AML) after Allogeneic Hematopoietic Cell Transplantation (HCT). Transplant Cell Ther 2023. [DOI: 10.1016/s2666-6367(23)00623-1] [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: 02/07/2023]
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Peterson JA, Strath LJ, Nodarse CL, Rani A, Huo Z, Meng L, Yoder S, Cole JH, Foster TC, Fillingim RB, Cruz-Almeida Y. Epigenetic Aging Mediates the Association between Pain Impact and Brain Aging in Middle to Older Age Individuals with Knee Pain. Epigenetics 2022; 17:2178-2187. [PMID: 35950599 PMCID: PMC9665126 DOI: 10.1080/15592294.2022.2111752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/05/2022] [Indexed: 02/01/2023] Open
Abstract
Chronic musculoskeletal pain is a health burden that may accelerate the aging process. Accelerated brain aging and epigenetic aging have separately been observed in those with chronic pain. However, it is unknown whether these biological markers of aging are associated with each other in those with chronic pain. We aimed to explore the association of epigenetic aging and brain aging in middle-to-older age individuals with varying degrees of knee pain. Participants (57.91 ± 8.04 y) with low impact knee pain (n = 95), high impact knee pain (n = 53), and pain-free controls (n = 26) completed self-reported pain, a blood draw, and an MRI scan. We used an epigenetic clock previously associated with knee pain (DNAmGrimAge), the subsequent difference of predicted epigenetic and brain age from chronological age (DNAmGrimAge-Difference and Brain-PAD, respectively). There was a significant main effect for pain impact group (F (2,167) = 3.847, P = 0.023, r o t a t i o n a l e n e r g y = 1 / 2 I ω 2 = 0.038, ANCOVA) on Brain-PAD and DNAmGrimAge-difference (F (2,167) = 6.800, P = 0.001, I = m k 2 = 0.075, ANCOVA) after controlling for covariates. DNAmGrimAge-Difference and Brain-PAD were modestly correlated (r =0.198; P =0.010). Exploratory analysis revealed that DNAmGrimAge-difference mediated GCPS pain impact, GCPS pain severity, and pain-related disability scores on Brain-PAD. Based upon the current study findings, we suggest that pain could be a driver for accelerated brain aging via epigenome interactions.
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Affiliation(s)
- Jessica A. Peterson
- Pain Research & Intervention Center of Excellence (PRICE), University of Florida, Gainesville, FL, USA
- Department of Community Dentistry and Behavioral Science, University of Florida, Gainesville, FL, USA
| | - Larissa J. Strath
- Pain Research & Intervention Center of Excellence (PRICE), University of Florida, Gainesville, FL, USA
- Department of Community Dentistry and Behavioral Science, University of Florida, Gainesville, FL, USA
| | - Chavier Laffitte Nodarse
- Pain Research & Intervention Center of Excellence (PRICE), University of Florida, Gainesville, FL, USA
- Department of Community Dentistry and Behavioral Science, University of Florida, Gainesville, FL, USA
| | - Asha Rani
- Department of Neuroscience, McKnight Brain Institute, Gainesville, Florida, USA
| | - Zhiguang Huo
- Department of Biostatistics, University of Florida, Gainesville, Florida, USA
| | - Lingsong Meng
- Department of Biostatistics, University of Florida, Gainesville, Florida, USA
| | - Sean Yoder
- Molecular Genomics Core Facility, Moffit Cancer Center, Tampa, FL, USA
| | - James H. Cole
- Centre for Medical Image Computing, Department of Computer Science, University College London, London, England
- Dementia Research Centre, Queen Square Institute of Neurology, University College London, London, England
| | - Thomas C. Foster
- Genetics and Genomics Program, University of Florida, Gainesville, FL, USA
| | - Roger B. Fillingim
- Pain Research & Intervention Center of Excellence (PRICE), University of Florida, Gainesville, FL, USA
- Department of Community Dentistry and Behavioral Science, University of Florida, Gainesville, FL, USA
| | - Yenisel Cruz-Almeida
- Pain Research & Intervention Center of Excellence (PRICE), University of Florida, Gainesville, FL, USA
- Department of Community Dentistry and Behavioral Science, University of Florida, Gainesville, FL, USA
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6
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Song X, Chang S, Seminario-Vidal L, de Mingo Pulido A, Tordesillas L, Song X, Reed RA, Harkins A, Whiddon S, Nguyen JV, Segura CM, Zhang C, Yoder S, Sayegh Z, Zhao Y, Messina JL, Harro CM, Zhang X, Conejo-Garcia JR, Berglund A, Sokol L, Zhang J, Rodriguez PC, Mulé JJ, Futreal AP, Tsai KY, Chen PL. Genomic and Single-Cell Landscape Reveals Novel Drivers and Therapeutic Vulnerabilities of Transformed Cutaneous T-cell Lymphoma. Cancer Discov 2022; 12:1294-1313. [PMID: 35247891 PMCID: PMC9148441 DOI: 10.1158/2159-8290.cd-21-1207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/02/2021] [Revised: 01/10/2022] [Accepted: 02/11/2022] [Indexed: 11/16/2022]
Abstract
ABSTRACT Cutaneous T-cell lymphoma (CTCL) is a rare cancer of skin-homing T cells. A subgroup of patients develops large cell transformation with rapid progression to an aggressive lymphoma. Here, we investigated the transformed CTCL (tCTCL) tumor ecosystem using integrative multiomics spanning whole-exome sequencing (WES), single-cell RNA sequencing, and immune profiling in a unique cohort of 56 patients. WES of 70 skin biopsies showed high tumor mutation burden, UV signatures that are prognostic for survival, exome-based driver events, and most recurrently mutated pathways in tCTCL. Single-cell profiling of 16 tCTCL skin biopsies identified a core oncogenic program with metabolic reprogramming toward oxidative phosphorylation (OXPHOS), cellular plasticity, upregulation of MYC and E2F activities, and downregulation of MHC I suggestive of immune escape. Pharmacologic perturbation using OXPHOS and MYC inhibitors demonstrated potent antitumor activities, whereas immune profiling provided in situ evidence of intercellular communications between malignant T cells expressing macrophage migration inhibitory factor and macrophages and B cells expressing CD74. SIGNIFICANCE Our study contributes a key resource to the community with the largest collection of tCTCL biopsies that are difficult to obtain. The multiomics data herein provide the first comprehensive compendium of genomic alterations in tCTCL and identify potential prognostic signatures and novel therapeutic targets for an incurable T-cell lymphoma. This article is highlighted in the In This Issue feature, p. 1171.
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Affiliation(s)
- Xiaofei Song
- Department of Genomic Medicine, The UT MD Anderson Cancer Center, Houston, TX, USA
| | - Shiun Chang
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Lucia Seminario-Vidal
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Alvaro de Mingo Pulido
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Leticia Tordesillas
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The UT MD Anderson Cancer Center, Houston, TX, USA
| | - Rhianna A. Reed
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Andrea Harkins
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Shannen Whiddon
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jonathan V. Nguyen
- Advanced Analytical and Digital Laboratory, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Carlos Moran Segura
- Advanced Analytical and Digital Laboratory, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Chaomei Zhang
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Sean Yoder
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Zena Sayegh
- Tissue Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Yun Zhao
- Department of Biopharma Services, Admera Health, Holmdel, NJ, USA
| | - Jane L. Messina
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Carly M. Harro
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Xiaohui Zhang
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - José R. Conejo-Garcia
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Anders Berglund
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Lubomir Sokol
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The UT MD Anderson Cancer Center, Houston, TX, USA
| | - Paulo C. Rodriguez
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - James J. Mulé
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Andrew P. Futreal
- Department of Genomic Medicine, The UT MD Anderson Cancer Center, Houston, TX, USA
| | - Kenneth Y. Tsai
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Pei-Ling Chen
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Department of Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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7
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Cruz-Almeida Y, Johnson A, Meng L, Sinha P, Rani A, Yoder S, Huo Z, Foster TC, Fillingim RB. Epigenetic age predictors in community-dwelling adults with high impact knee pain. Mol Pain 2022; 18:17448069221118004. [PMID: 35968561 PMCID: PMC9380216 DOI: 10.1177/17448069221118004] [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] [Indexed: 11/20/2022] Open
Abstract
Gerontological research reveals considerable interindividual variability in aging
phenotypes, and emerging evidence suggests that high impact chronic pain may be
associated with various accelerated biological aging processes. In particular,
epigenetic aging is a robust predictor of health-span and disability compared to
chronological age alone. The current study aimed to determine whether several
epigenetic aging biomarkers were associated with high impact chronic pain in
middle to older age adults (44–78 years old). Participants (n =
213) underwent a blood draw, demographic, psychosocial, pain and functional
assessments. We estimated five epigenetic clocks and calculated the difference
between epigenetic age and chronological age, which has been previously reported
to predict overall mortality risk, as well as included additional derived
variables of epigenetic age previously associated with pain. There were
significant differences across Pain Impact groups in three out of the five
epigenetic clocks examined (DNAmAge, DNAmPhenoAge and DNAmGrimAge), indicating
that pain-related disability during the past 6 months was associated with
markers of epigenetic aging. Only DNAmPhenoAge and DNAmGrimAge were associated
with higher knee pain intensity during the past 48 h. Finally, pain
catastrophizing, depressive symptomatology and more neuropathic pain symptoms
were significantly associated with an older epigenome in only one of the five
epigenetic clocks (i.e. DNAmGrimAge) after correcting for multiple comparisons
(corrected p’s < 0.05). Given the scant literature in
relation to epigenetic aging and the complex experience of pain, additional
research is needed to understand whether epigenetic aging may help identify
people with chronic pain at greater risk of functional decline and poorer health
outcomes.
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Affiliation(s)
- Yenisel Cruz-Almeida
- Pain Research & Intervention Center of Excellence, 3463University of Florida, Gainesville, FL, USA.,Institute on Aging, 3463University of Florida, Gainesville, FL, USA.,Center for Cognitive Aging & Memory, McKnight Brain Foundation, 3463University of Florida, Gainesville, FL, USA.,Department of Community Dentistry & Behavioral Science, College of Dentistry, 3463University of Florida, Gainesville, FL, USA.,Department of Neuroscience, College of Medicine, 3463University of Florida, Gainesville, FL, USA
| | - Alisa Johnson
- Pain Research & Intervention Center of Excellence, 3463University of Florida, Gainesville, FL, USA.,Institute on Aging, 3463University of Florida, Gainesville, FL, USA.,Department of Community Dentistry & Behavioral Science, College of Dentistry, 3463University of Florida, Gainesville, FL, USA
| | - Lingsong Meng
- Department of Biostatistics, College of Public Health & Health Professions and College of Medicine, 3463University of Florida, Gainesville, FL, USA
| | - Puja Sinha
- Department of Neuroscience, College of Medicine, 3463University of Florida, Gainesville, FL, USA
| | - Asha Rani
- Department of Neuroscience, College of Medicine, 3463University of Florida, Gainesville, FL, USA
| | - Sean Yoder
- 25301Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Zhiguang Huo
- Department of Biostatistics, College of Public Health & Health Professions and College of Medicine, 3463University of Florida, Gainesville, FL, USA
| | - Thomas C Foster
- Institute on Aging, 3463University of Florida, Gainesville, FL, USA.,Center for Cognitive Aging & Memory, McKnight Brain Foundation, 3463University of Florida, Gainesville, FL, USA.,Department of Neuroscience, College of Medicine, 3463University of Florida, Gainesville, FL, USA.,Age-Related Memory Loss Program, McKnight Brain Foundation, 3463University of Florida, Gainesville, FL, USA
| | - Roger B Fillingim
- Pain Research & Intervention Center of Excellence, 3463University of Florida, Gainesville, FL, USA.,Institute on Aging, 3463University of Florida, Gainesville, FL, USA.,Department of Community Dentistry & Behavioral Science, College of Dentistry, 3463University of Florida, Gainesville, FL, USA
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Dash S, Cen L, Yoder S, Mesa T, Smith A, Zhang C, Teer J, Armaiz-Pena G, Monteiro A. Abstract 736: HOXA5 induction by norepinephrine in precursor cells of ovarian cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-736] [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
Chronic stress induced by repetitive activation of the sympathetic nervous system leads to rapid release of catecholamines like norepinephrine (NE). Several studies have shown that increased levels of NE can contribute to tumor progression by promoting tumor growth, migration and invasion of ovarian cancer cells. However, the role of NE in tumor initiation remains mostly unknown. The purpose of this study was to explore the acute and chronic effects of NE on immortalized normal fallopian tube and ovarian cell lines presumed to be the origin of epithelial ovarian cancers. Normal immortalized ovarian (iOSE11) and fallopian tube (iFTE283) surface epithelial cells were treated with 10µM NE for 15 min, 1h and 4h followed by whole-transcriptome RNA-Seq. 234 and 313 differentially expressed genes were identified at 1h and 4h time points in iFTE283 cells respectively; while 53 and 34 differentially expressed genes were identified at 1h and 4h time points in iOSE11 cells. Gene ontology analysis using Panther Statistical Overrepresentation Test was performed on these differentially expressed genes. Panther Protein Class analysis revealed ‘transcription factor' to be the most significantly overrepresented at both 1h and 4h time-points. Promoter enrichment analysis using oPOSSUM database identified transcription factor HOXA5 to be consistently enriched at both time points in both cell lines. Time course studies performed by qPCR and luciferase promoter assays for HOXA5 transcription factor in normal cells (iOSE11, iFTE283), partially transformed cells (iOSE11-p53R175H, iFTE283-p53R175H, iFTE282-p53R175H and iOSE4-cMyc) and cancer cells (OvCAR8, SkoV3) revealed that HOXA5 induction by NE occurred only in normal immortalized cells and partially transformed p53R175H overexpressing cells, but not in cancer cells. In contrast, chronic exposure to NE for 4 months followed by HOXA5 time course study by qPCR revealed attenuation of HOXA5 induction in normal as well as p53R175H overexpressing cells. Additionally, long term NE treatment lead to increased proliferation and colony forming capacity in iFTE283, iFTE283-p53R175H and iFTE282-p53R175H cells. p53R175H overexpressing iFTE283 cells also showed slight increase in chromosomal instability, as measured by karyotype, after 4 months of treatment with NE. These observations suggest that HOXA5 plays a central role in regulating the early response to NE in normal as well as p53R175H overexpressing ovarian epithelial and fallopian tube cells, but this induction is attenuated in cancer cells as well as in normal and partially transformed cells that are exposed to long term NE treatment. We will further assess the induction of HOXA5 by NE through promoter bashing experiments.
Citation Format: Sweta Dash, Ling Cen, Sean Yoder, Tania Mesa, Andrew Smith, Chaomei Zhang, Jamie Teer, Guillermo Armaiz-Pena, Alvaro Monteiro. HOXA5 induction by norepinephrine in precursor cells of ovarian cancer [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 736.
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Affiliation(s)
- Sweta Dash
- 1H. Lee Moffitt Cancer Center, Tampa, FL
| | - Ling Cen
- 1H. Lee Moffitt Cancer Center, Tampa, FL
| | - Sean Yoder
- 1H. Lee Moffitt Cancer Center, Tampa, FL
| | - Tania Mesa
- 1H. Lee Moffitt Cancer Center, Tampa, FL
| | | | | | - Jamie Teer
- 1H. Lee Moffitt Cancer Center, Tampa, FL
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Moore C, Monforte H, Teer JK, Zhang Y, Yoder S, Brohl AS, Reed DR. TRIM28 congenital predisposition to Wilms' tumor: novel mutations and presentation in a sibling pair. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a004796. [PMID: 32699065 PMCID: PMC7476416 DOI: 10.1101/mcs.a004796] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 04/23/2020] [Indexed: 12/12/2022] Open
Abstract
Wilms’ tumor is the most common renal malignancy in children. In addition to staging, molecular risk stratification, such as loss of heterozygosity (LOH) in Chromosomes 1 and 16, is being increasingly used. Although genetic predisposition syndromes have been well-characterized in some Wilms’ tumors, recent sequencing and biology efforts are expanding the classification of this malignancy. Here we present a case of siblings with remarkably similar presentations of bilateral Wilms’ tumor at ∼12 mo of age. Thorough exam after the younger sibling was diagnosed did not reveal any signs to suggest one of the known Wilms’ predisposition syndromes. Both were treated with standard therapies with good response and long-term sustained complete remission of 53 and 97 mo, respectively. Whole-exome sequencing was performed on a tumor sample from each patient and matched blood from one, revealing a shared truncation mutation of TRIM28 in all three samples with heterozygosity in the germline sample. TRIM28 loss has been recently implicated in early-stage Wilms’ tumors with epithelioid morphology. These siblings expand the phenotype for presentation with multifocal disease with retained excellent response to standard therapy.
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Affiliation(s)
- Colin Moore
- Adolescent and Young Adult Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA.,Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA.,Center for Cancer and Blood Disorders, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA
| | - Hector Monforte
- Department of Anatomic Pathology, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Yonghong Zhang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Sean Yoder
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Andrew S Brohl
- Sarcoma Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Damon R Reed
- Adolescent and Young Adult Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA.,Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA.,Sarcoma Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA.,Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
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10
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Sadeghi M, Ordway B, Rafiei I, Borad P, Fang B, Koomen JL, Zhang C, Yoder S, Johnson J, Damaghi M. Integrative Analysis of Breast Cancer Cells Reveals an Epithelial-Mesenchymal Transition Role in Adaptation to Acidic Microenvironment. Front Oncol 2020; 10:304. [PMID: 32211331 PMCID: PMC7076123 DOI: 10.3389/fonc.2020.00304] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 02/20/2020] [Indexed: 01/06/2023] Open
Abstract
Early ducts of breast tumors are unequivocally acidic. High rates of glycolysis combined with poor perfusion lead to a congestion of acidic metabolites in the tumor microenvironment, and pre-malignant cells must adapt to this acidosis to thrive. Adaptation to acidosis selects cancer cells that can thrive in harsh conditions and are capable of outgrowing the normal or non-adapted neighbors. This selection is usually accompanied by phenotypic change. Epithelial mesenchymal transition (EMT) is one of the most important switches correlated to malignant tumor cell phenotype and has been shown to be induced by tumor acidosis. New evidence shows that the EMT switch is not a binary system and occurs on a spectrum of transition states. During confirmation of the EMT phenotype, our results demonstrated a partial EMT phenotype in our acid-adapted cell population. Using RNA sequencing and network analysis we found 10 dysregulated network motifs in acid-adapted breast cancer cells playing a role in EMT. Our further integrative analysis of RNA sequencing and SILAC proteomics resulted in recognition of S100B and S100A6 proteins at both the RNA and protein level. Higher expression of S100B and S100A6 was validated in vitro by Immunocytochemistry. We further validated our finding both in vitro and in patients' samples by IHC analysis of Tissue Microarray (TMA). Correlation analysis of S100A6 and LAMP2b as marker of acidosis in each patient from Moffitt TMA approved the acid related role of S100A6 in breast cancer patients. Also, DCIS patients with higher expression of S100A6 showed lower survival compared to lower expression. We propose essential roles of acid adaptation in cancer cells EMT process through S100 proteins such as S100A6 that can be used as therapeutic strategy targeting both acid-adapted and malignant phenotypes.
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Affiliation(s)
- Mehdi Sadeghi
- Department of Cell and Molecular Biology, Faculty of Science, Semnan University, Semnan, Iran
| | - Bryce Ordway
- Department of Cancer Physiology, Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Ilyia Rafiei
- Department of Cell and Molecular Biology, Faculty of Science, Semnan University, Semnan, Iran
| | - Punit Borad
- Department of Cancer Physiology, Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Bin Fang
- Proteomics Core, Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - John L Koomen
- Proteomics Core, Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Chaomei Zhang
- Molecular Biology Core, Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Sean Yoder
- Molecular Biology Core, Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Joseph Johnson
- Microscopy Core, Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Mehdi Damaghi
- Department of Cancer Physiology, Moffitt Cancer Center and Research Institute, Tampa, FL, United States.,Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
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11
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Dutil J, Teer JK, Golubeva V, Yoder S, Tong WL, Arroyo N, Karam R, Echenique M, Matta JL, Monteiro AN. Germline variants in cancer genes in high-risk non-BRCA patients from Puerto Rico. Sci Rep 2019; 9:17769. [PMID: 31780696 PMCID: PMC6882826 DOI: 10.1038/s41598-019-54170-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 02/13/2019] [Accepted: 11/05/2019] [Indexed: 12/30/2022] Open
Abstract
Inherited pathogenic variants in genes that confer moderate to high risk of breast cancer may explain up to 50% of familial breast cancer. This study aimed at identifying inherited pathogenic variants in breast cancer cases from Puerto Rico that were not linked to BRCA1 or BRCA2. Forty-eight breast cancer patients that met the clinical criteria for BRCA testing but had received a negative BRCA1/2 result were recruited. Fifty-three genes previously implicated in hereditary cancer predisposition were captured using the BROCA Agilent cancer risk panel followed by massively parallel sequencing. Missense variants of uncertain clinical significance in CHEK2 were evaluated using an in vitro kinase assays to determine their impact on function. Pathogenic variants were identified in CHEK2, MUTYH, and RAD51B in four breast cancer patients, which represented 8.3% of the cohort. We identified three rare missense variants of uncertain significance in CHEK2 and two variants (p.Pro484Leu and p.Glu239Lys) showed markedly decreased kinase activity in vitro comparable to a known pathogenic variant. Interestingly, the local ancestry at the RAD51B locus in the carrier of p.Arg47* was predicted to be of African origin. In this cohort, 12.5% of the BRCA-negative breast cancer patients were found to carry a known pathogenic variant or a variant affecting protein activity. This study reveals an unmet clinical need of genetic testing that could benefit a significant proportion of at-risk Latinas. It also highlights the complexity of Hispanic populations as pathogenic factors may originate from any of the ancestral populations that make up their genetic backgrounds.
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Affiliation(s)
- Julie Dutil
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, PR, USA.
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Volha Golubeva
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Sean Yoder
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Wei Lue Tong
- University of South Florida Morsani College of Medicine, Tampa, FL, USA
| | - Nelly Arroyo
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, PR, USA
| | | | - Miguel Echenique
- Auxilio Cancer Center, Auxilio Mutuo Hospital, San Juan, PR, USA
| | - Jaime L Matta
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, PR, USA
| | - Alvaro N Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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12
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Stewart PA, Welsh EA, Slebos RJC, Fang B, Izumi V, Chambers M, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Fellows KM, Francis JM, Saller JJ, Mesa T, Zhang C, Yoder S, DeNicola GM, Beg AA, Boyle TA, Teer JK, Ann Chen Y, Koomen JM, Eschrich SA, Haura EB. Proteogenomic landscape of squamous cell lung cancer. Nat Commun 2019; 10:3578. [PMID: 31395880 PMCID: PMC6687710 DOI: 10.1038/s41467-019-11452-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [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: 08/10/2018] [Accepted: 07/08/2019] [Indexed: 12/18/2022] Open
Abstract
How genomic and transcriptomic alterations affect the functional proteome in lung cancer is not fully understood. Here, we integrate DNA copy number, somatic mutations, RNA-sequencing, and expression proteomics in a cohort of 108 squamous cell lung cancer (SCC) patients. We identify three proteomic subtypes, two of which (Inflamed, Redox) comprise 87% of tumors. The Inflamed subtype is enriched with neutrophils, B-cells, and monocytes and expresses more PD-1. Redox tumours are enriched for oxidation-reduction and glutathione pathways and harbor more NFE2L2/KEAP1 alterations and copy gain in the 3q2 locus. Proteomic subtypes are not associated with patient survival. However, B-cell-rich tertiary lymph node structures, more common in Inflamed, are associated with better survival. We identify metabolic vulnerabilities (TP63, PSAT1, and TFRC) in Redox. Our work provides a powerful resource for lung SCC biology and suggests therapeutic opportunities based on redox metabolism and immune cell infiltrates. Squamous cell lung cancer has dismal prognosis due to the dearth of effective treatments. Here, the authors perform an integrated proteogenomic analysis of the disease, revealing three proteomics-based subtypes and suggesting potential therapeutic opportunities.
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Affiliation(s)
- Paul A Stewart
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.,Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Eric A Welsh
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Robbert J C Slebos
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Bin Fang
- Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Victoria Izumi
- Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Matthew Chambers
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Guolin Zhang
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Ling Cen
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Fredrik Pettersson
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Yonghong Zhang
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Zhihua Chen
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Chia-Ho Cheng
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Ram Thapa
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Zachary Thompson
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Katherine M Fellows
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Jewel M Francis
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - James J Saller
- Department of Anatomical Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Tania Mesa
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Chaomei Zhang
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Sean Yoder
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Gina M DeNicola
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Amer A Beg
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Theresa A Boyle
- Department of Anatomical Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Yian Ann Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - John M Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Steven A Eschrich
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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13
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Ramello MC, Benzaïd I, Kuenzi BM, Lienlaf-Moreno M, Kandell WM, Santiago DN, Pabón-Saldaña M, Darville L, Fang B, Rix U, Yoder S, Berglund A, Koomen JM, Haura EB, Abate-Daga D. An immunoproteomic approach to characterize the CAR interactome and signalosome. Sci Signal 2019; 12:12/568/eaap9777. [PMID: 30755478 DOI: 10.1126/scisignal.aap9777] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Adoptive transfer of T cells that express a chimeric antigen receptor (CAR) is an approved immunotherapy that may be curative for some hematological cancers. To better understand the therapeutic mechanism of action, we systematically analyzed CAR signaling in human primary T cells by mass spectrometry. When we compared the interactomes and the signaling pathways activated by distinct CAR-T cells that shared the same antigen-binding domain but differed in their intracellular domains and their in vivo antitumor efficacy, we found that only second-generation CARs induced the expression of a constitutively phosphorylated form of CD3ζ that resembled the endogenous species. This phenomenon was independent of the choice of costimulatory domains, or the hinge/transmembrane region. Rather, it was dependent on the size of the intracellular domains. Moreover, the second-generation design was also associated with stronger phosphorylation of downstream secondary messengers, as evidenced by global phosphoproteome analysis. These results suggest that second-generation CARs can activate additional sources of CD3ζ signaling, and this may contribute to more intense signaling and superior antitumor efficacy that they display compared to third-generation CARs. Moreover, our results provide a deeper understanding of how CARs interact physically and/or functionally with endogenous T cell molecules, which will inform the development of novel optimized immune receptors.
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Affiliation(s)
- Maria C Ramello
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Ismahène Benzaïd
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Brent M Kuenzi
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.,Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL 33620, USA
| | - Maritza Lienlaf-Moreno
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Wendy M Kandell
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.,Cancer Biology Ph.D. Program, University of South Florida, Tampa, FL 33620, USA
| | - Daniel N Santiago
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.,Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Mibel Pabón-Saldaña
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.,Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Lancia Darville
- Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Bin Fang
- Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Sean Yoder
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Anders Berglund
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - John M Koomen
- Proteomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.,Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Daniel Abate-Daga
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA. .,Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.,Department of Oncological Sciences, University of South Florida, Tampa, FL 33612, USA
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14
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Hill KS, Roberts ER, Wang X, Marin E, Park TD, Son S, Ren Y, Fang B, Yoder S, Kim S, Wan L, Sarnaik AA, Koomen JM, Messina JL, Teer JK, Kim Y, Wu J, Chalfant CE, Kim M. PTPN11 Plays Oncogenic Roles and Is a Therapeutic Target for BRAF Wild-Type Melanomas. Mol Cancer Res 2018; 17:583-593. [PMID: 30355677 DOI: 10.1158/1541-7786.mcr-18-0777] [Citation(s) in RCA: 27] [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: 07/24/2018] [Revised: 09/06/2018] [Accepted: 10/15/2018] [Indexed: 02/07/2023]
Abstract
Melanoma is one of the most highly mutated cancer types. To identify functional drivers of melanoma, we searched for cross-species conserved mutations utilizing a mouse melanoma model driven by loss of PTEN and CDKN2A, and identified mutations in Kras, Erbb3, and Ptpn11. PTPN11 encodes the SHP2 protein tyrosine phosphatase that activates the RAS/RAF/MAPK pathway. Although PTPN11 is an oncogene in leukemia, lung, and breast cancers, its roles in melanoma are not clear. In this study, we found that PTPN11 is frequently activated in human melanoma specimens and cell lines and is required for full RAS/RAF/MAPK signaling activation in BRAF wild-type (either NRAS mutant or wild-type) melanoma cells. PTPN11 played oncogenic roles in melanoma by driving anchorage-independent colony formation and tumor growth. In Pten- and Cdkn2a-null mice, tet-inducible and melanocyte-specific PTPN11E76K expression significantly enhanced melanoma tumorigenesis. Melanoma cells derived from this mouse model showed doxycycline-dependent tumor growth in nude mice. Silencing PTPN11E76K expression by doxycycline withdrawal caused regression of established tumors by induction of apoptosis and senescence, and suppression of proliferation. Moreover, the PTPN11 inhibitor (SHP099) also caused regression of NRASQ61K -mutant melanoma. Using a quantitative tyrosine phosphoproteomics approach, we identified GSK3α/β as one of the key substrates that were differentially tyrosine-phosphorylated in these experiments modulating PTPN11. This study demonstrates that PTPN11 plays oncogenic roles in melanoma and regulates RAS and GSK3β signaling pathways. IMPLICATIONS: This study identifies PTPN11 as an oncogenic driver and a novel and actionable therapeutic target for BRAF wild-type melanoma.
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Affiliation(s)
- Kristen S Hill
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Evan R Roberts
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Xue Wang
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Ellen Marin
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Taeeun D Park
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Sorany Son
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Yuan Ren
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Bin Fang
- Department of Proteomics, Moffitt Cancer Center, Tampa, Florida
| | - Sean Yoder
- Molecular Genomics Core, Moffitt Cancer Center, Tampa, Florida
| | - Sungjune Kim
- Department of Immunology, Moffitt Cancer Center, Tampa, Florida.,Department of Radiology, Moffitt Cancer Center, Tampa, Florida
| | - Lixin Wan
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Amod A Sarnaik
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida
| | - John M Koomen
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida.,Department of Proteomics, Moffitt Cancer Center, Tampa, Florida
| | - Jane L Messina
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida.,Department of Pathology, Moffitt Cancer Center, Tampa, Florida
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida
| | - Youngchul Kim
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida
| | - Jie Wu
- Peggy and Charles Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Charles E Chalfant
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida.,Department of Research Service, James A. Haley Veterans Hospital, Tampa, Florida
| | - Minjung Kim
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida. .,Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida.,Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida
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15
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Kim Y, Hoehn HJ, Chen Y, Barnard ME, Bloomer A, Yoder S, Coppola D, Schmit SL. Abstract 4217: Prognostic gene expression signatures of immune responses in the colon cancer microenvironment. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4217] [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
Colorectal cancer remains the 2nd leading cause of cancer deaths in the United States. This suggests that traditional prognostic factors are not optimally refined for predicting survival outcomes and guiding therapeutic decisions for some patients. Mounting evidence supports that quantifying the strength and diversity of host immune responses in the tumor microenvironment may improve prognostication and clinical decision-making; however, standard pathological assessment of T cell infiltration is time-consuming and difficult to standardize for clinical utility. The goal of this study was to develop a molecular classifier associated with CRC prognosis based on the expression of 770 immune-related genes measured on the Nanostring (NS) nCounter PanCancer Immune Profiling Panel. This panel includes markers of immune cell types, common cancer antigens, and diverse categories of immune responses (e.g. T cell function, cytokines). We also aimed to assess the validity of combining gene expression data derived from different tissue types (FFPE, fresh frozen) and mRNA profiling platforms (NS, Rosetta/Merck human RSTA Custom Affymetrix 2.0 microarray). FFPE (N=24) and fresh frozen tumor tissues (N=28) from 50 primary stage II colon cancers from the Moffitt Cancer Center Total Cancer Care cohort were profiled using the NS platform, and microarray data were generated on frozen tissues from all patients. Geometric mean-normalized NS data of FFPE and frozen tumor tissues were merged by the ComBat algorithm that adjusted for different RNA source types. 634 (87%) genes in the NS dataset had expression values that positively correlated with those of the microarray data. A 2-way hierarchical cluster analysis of these genes in NS data revealed two clusters of patients with non-overlapping overall survival (OS) curves, but no statistically significant difference due mainly to a lack of events (Log-rank P=0.12; 5-year OS probability=91.3% vs 74.1% for cluster 1 (N=23) and cluster 2 (N=27)). To examine cross-platform predictability of the 2 clusters, a 5-gene classifier was trained on NS data using penalized logistic regression. Applying this classifier to microarray data on the same patient set (N=49) significantly discriminated the clusters (AUC=0.8, P<0.01). Functional annotation of the 5 genes (CD27, CD37, ITGAL, KLRG1 and LAG3) revealed enrichment for T cell receptor signaling, hematopoietic cell lineage, and natural killer cell mediated cytotoxicity (FDR P<0.001). This pilot study provides early evidence that an immune gene expression panel may capture the prognostic value of intratumoral host immune responses. It also supports the feasibility of combining different RNA sources and expression platforms. Expanded future studies that pool across sample types and publicly-available expression datasets are needed to validate the 9-gene classifier from this study and examine its broader prognostic impact.
Citation Format: Youngchul Kim, Hannah J. Hoehn, Yunyun Chen, Mollie E. Barnard, Amanda Bloomer, Sean Yoder, Domenico Coppola, Stephanie L. Schmit. Prognostic gene expression signatures of immune responses in the colon cancer microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4217.
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16
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Teer JK, Yoder S, Gjyshi A, Nicosia SV, Zhang C, Monteiro ANA. Mutational heterogeneity in non-serous ovarian cancers. Sci Rep 2017. [PMID: 28852190 DOI: 10.1038/s41598-017-10432-9]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Epithelial ovarian cancer is a leading cause of death in gynecological cancers. While several systematic studies have revealed the mutation landscape of serous epithelial ovarian cancer, other non-serous subtypes of the disease have not been explored as extensively. Here we conduct exome sequencing of nine non-serous epithelial ovarian tumors (six endometrioid and three mucinous) and their corresponding normal DNA as well as a tumor-only granulosa cell sample. We integrated the exome data with targeted gene sequencing for 1,321 genes selected for their involvement in cancer from additional 28 non-serous ovarian tumors and compared our results to TCGA ovarian serous cystadenocarcinoma and uterine corpus endometrial carcinomas. Prevalence of TP53 mutations in non-serous was much lower than in serous epithelial OC, whereas the prevalence of PIK3CA, PIK3R1, PTEN, CTNNB1, ARID1A, and KRAS was higher. We confirmed the high prevalence of FOXL2 and KRAS mutations in granulosa cell tumors and in mucinous tumors, respectively. We also identified POLE proofreading domain mutations in three endometrioid ovarian tumors. These results highlight mutational differences between serous and non-serous ovarian cancers, and further distinguish different non-serous subtypes.
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Affiliation(s)
- Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Sean Yoder
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Anxhela Gjyshi
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.,University of South Florida Cancer Biology PhD Program, Tampa, FL, 33612, USA
| | - Santo V Nicosia
- Department of Pathology and Cell Biology, USF Morsani School of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Chaomei Zhang
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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17
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Teer JK, Yoder S, Gjyshi A, Nicosia SV, Zhang C, Monteiro ANA. Mutational heterogeneity in non-serous ovarian cancers. Sci Rep 2017; 7:9728. [PMID: 28852190 PMCID: PMC5574976 DOI: 10.1038/s41598-017-10432-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [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: 11/01/2016] [Accepted: 08/09/2017] [Indexed: 12/30/2022] Open
Abstract
Epithelial ovarian cancer is a leading cause of death in gynecological cancers. While several systematic studies have revealed the mutation landscape of serous epithelial ovarian cancer, other non-serous subtypes of the disease have not been explored as extensively. Here we conduct exome sequencing of nine non-serous epithelial ovarian tumors (six endometrioid and three mucinous) and their corresponding normal DNA as well as a tumor-only granulosa cell sample. We integrated the exome data with targeted gene sequencing for 1,321 genes selected for their involvement in cancer from additional 28 non-serous ovarian tumors and compared our results to TCGA ovarian serous cystadenocarcinoma and uterine corpus endometrial carcinomas. Prevalence of TP53 mutations in non-serous was much lower than in serous epithelial OC, whereas the prevalence of PIK3CA, PIK3R1, PTEN, CTNNB1, ARID1A, and KRAS was higher. We confirmed the high prevalence of FOXL2 and KRAS mutations in granulosa cell tumors and in mucinous tumors, respectively. We also identified POLE proofreading domain mutations in three endometrioid ovarian tumors. These results highlight mutational differences between serous and non-serous ovarian cancers, and further distinguish different non-serous subtypes.
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Affiliation(s)
- Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Sean Yoder
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Anxhela Gjyshi
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.,University of South Florida Cancer Biology PhD Program, Tampa, FL, 33612, USA
| | - Santo V Nicosia
- Department of Pathology and Cell Biology, USF Morsani School of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Chaomei Zhang
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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Stewart P, Slebos R, Welsh E, Cen L, Zhang Y, Chen Z, Cheng CH, Pettersson F, Berglund A, Zhang G, Fang B, Izumi V, Yoder S, Fellows K, Chen Y, Teer J, Eschrich S, Koomen J, Haura E. Proteogenomic Landscape of Squamous Cell Lung Cancer. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.06.037] [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: 11/28/2022]
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Pettersson F, Stewart PA, Slebos RJ, Welsh EA, Cen L, Zhang Y, Chen Z, Cheng CH, Zhang G, Fang B, Izumi V, Yoder S, Fellows K, Chen YA, Teer JK, Eschrich S, Koomen JM, Berglund A, Haura EB. Abstract 1565: OnPLS-based integrative proteogenomics analysis of lung squamous cell cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1565] [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
Introduction: Multivariate projection methods such as PCA and PLS has been widely applied for analysis of biological and chemical data. OnPLS is a recent extension to these methods suitable for integrative analysis of omics data. With OnPLS it is possible to compare multiple omics datasets to identify joint variation and variation locally unique for each of the studied datasets. OnPLS is a new approach for truly integrative analysis of omics data to be contrasted to commonly applied approaches limiting analysis to 1) comparing findings from individually analyzed blocks of data 2) pairwise comparison of individual probes.
Experimental: A Java based implementation of OnPLS was used for the statistical modeling. 116 lung squamous cell cancer samples were characterized using gene expression profiling and global proteomics. The OnPLS model was applied to jointly model variation between mRNA and protein expression. Enrichment analysis of factor loadings was performed using the Enrichr tools to identify biological mechanisms explained by the different joint and unique components of the OnPLS model.
Results: Using a cross-validation procedure the model with the highest predictive ability was calculated having two joint components and one locally unique component for each of the proteomics and gene expression datasets. The model explained 21.9% of the variation in the expression data and 26.1% of the variation in the proteomics data. The first joint component captures the highest degree of common variation between mRNA and protein activity. From the mRNA data, this component is related to immune infiltrates, especially monocytes and B-cells, whereas this component is related to extracellular matrix activity from the protein data. This suggests covariance of mRNA immune-related gene expression and extracellular matrix-related protein expression. As expected, local variation specific to the protein measurements involved regulation of protein activation and processing. mRNA-specific variation is related to keratinization, a key process in squamous cell cancer.
Conclusion: OnPLS offers an interesting approach for integrative analysis of omics data. Applying this approach to proteo-genomics data of lung squamous cell cancers suggest similar patterns of activity is represented in protein and gene expression data, however the biological processes associated with this activity may be distinct.
Citation Format: Fredrik Pettersson, Paul A. Stewart, Robbert J. Slebos, Eric A. Welsh, Ling Cen, Yonghong Zhang, Zhihua Chen, Chia-Ho Cheng, Guolin Zhang, Bin Fang, Victoria Izumi, Sean Yoder, Katherine Fellows, Y Ann Chen, Jamie K. Teer, Steven Eschrich, John M. Koomen, Anders Berglund, Eric B. Haura. OnPLS-based integrative proteogenomics analysis of lung squamous cell cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1565. doi:10.1158/1538-7445.AM2017-1565
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Affiliation(s)
| | | | | | | | - Ling Cen
- Moffitt Cancer Center, Tampa, FL
| | | | | | | | | | - Bin Fang
- Moffitt Cancer Center, Tampa, FL
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20
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Stewart PA, Slebos RJ, Welsh EA, Cen L, Zhang Y, Chen Z, Cheng CH, Pettersson F, Berglund A, Zhang G, Fang B, Izumi V, Yoder S, Fellows K, Chen A, Teer JK, Eschrich SA, Koomen JM, Haura EB. Abstract 205: Underlying mechanisms of genome-proteome discordance in squamous cell lung cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-205] [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
Introduction: Genomic analyses have yielded a tremendous amount of data on the genetic changes in lung cancers, but translating these experiments into actionable information benefitting lung squamous cell carcinoma (SQLC) patients has proven more difficult. Studies by the NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC), our group, and others have demonstrated that gene and protein expression show only moderate correlation, demonstrating limitations in explaining phenotypic changes from genomics alone. These findings indicate a clear need for integrative proteogenomics to better understand tumor biology, especially in a complex disease like SQLC.
Experimental: We have assembled a comprehensive proteogenomic dataset including DNA copy number (Affymetrix CytoScan HD Assay), targeted exome sequencing (Agilent Comprehensive Cancer Panel), RNA-sequencing (Illumina NextSeq), and shotgun proteomics (Q Exactive LC-MS/MS) on 116 surgically resected SQLC tumor samples with extensive clinical and follow up data.
Results: We have identified 6584 high confidence proteins from preliminary proteomic analysis. After quality control filtering, we utilized 5562 gene-protein pairs for further analysis. Clustering of patient RNA expression in this patient cohort has been unable to fully reproduce the molecular classification previously published for SQLC. Furthermore, proteomic results indicate yet another potential classification strategy selecting patient subgroups that differ at protein level. We observed a 0.29 median Spearman’s correlation of 5562 gene-protein pairs. There were 2781 highly correlated gene-protein pairs (greater than median) and 2781 poorly correlated gene-protein pairs (less than median) including 773 anti-correlated gene-protein pairs (less than 0). We hypothesized that poorly correlated gene-protein pairs could be functionally related in a pathway-dependent manner. Enrichment analysis of poorly correlated proteins identified pathways related to mRNA processing, growth factor signaling (EGFR, FGFR), and nonsense-mediated decay (NMD). Interestingly, there were 9 frequently mutated SQLC genes in the low correlation gene-protein pairs but only 3 in the highly correlated pairs. We found three distinct patient subgroups by clustering poorly correlated proteins. Analysis of these subgroups showed differentially expressed pathways related to mRNA processing, ubiquitination, and NMD.
Conclusion: Differential modulation of the proteome outside of genomic regulation may suggest important regulatory mechanisms in cancer and give new insights into treating SQLC. Analysis of poorly correlated gene-protein pairs suggests certain pathways are dysregulated in cancer, and ongoing DNA analysis and future analyses involving miRNAs, RNA-binding proteins, and the ubiquitin proteome system will help elucidate our preliminary findings.
Citation Format: Paul A. Stewart, Robbert J. Slebos, Eric A. Welsh, Ling Cen, Yonghong Zhang, Zhihua Chen, Chia-Ho Cheng, Fredrik Pettersson, Anders Berglund, Guolin Zhang, Bin Fang, Victoria Izumi, Sean Yoder, Katherine Fellows, Ann Chen, Jamie K. Teer, Steven A. Eschrich, John M. Koomen, Eric B. Haura. Underlying mechanisms of genome-proteome discordance in squamous cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 205. doi:10.1158/1538-7445.AM2017-205
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Affiliation(s)
| | | | | | - Ling Cen
- Moffitt Cancer Center, Tampa, FL
| | | | | | | | | | | | | | - Bin Fang
- Moffitt Cancer Center, Tampa, FL
| | | | | | | | - Ann Chen
- Moffitt Cancer Center, Tampa, FL
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Hoggard TM, Henderson-Jackson E, Bui MM, Caracciolo J, Teer JK, Yoder S, Binitie O, Gonzalez RJ, Brohl AS, Reed DR. Myoepithelial carcinoma with RB1 mutation: remarkable chemosensitivity to carcinoma of unknown origin therapy. BMC Cancer 2017; 17:250. [PMID: 28390395 PMCID: PMC5385017 DOI: 10.1186/s12885-017-3249-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/31/2017] [Indexed: 12/30/2022] Open
Abstract
Background Myoepithelial carcinoma of soft tissue is a rare, malignant neoplasm that is morphologically and immunophenotypically similar to its counterpart in salivary gland. It demonstrates myoepithelial differentiation, possessing both epithelial and myogenic characteristics. Thought to be chemotherapy insensitive, the optimal treatment regimen of this tumor has yet to be established and only a select few cases in the literature discuss treatment efficacy in detail. Case presentation Here we present a case of a young adult with metastatic myoepithelial carcinoma with an initial excellent response to systemic therapy utilizing carboplatin and paclitaxel with continued complete response after 3 years. The patient also underwent complete surgical excision and received adjuvant radiation to the primary site of disease. Exome sequencing revealed an inactivating mutation in RB1 which we believe to be the first such mutation to be reported in this cancer type. Conclusions Given increasing evidence suggesting RB1 loss is associated with responsiveness to conventional chemotherapies, particularly platinum-based regimens, we hypothesize that this genetic feature predisposed chemosensitivity in our patient’s tumor.
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Affiliation(s)
- Timothy M Hoggard
- University of South Florida Morsani College of Medicine, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA
| | - Evita Henderson-Jackson
- Department of Anatomic Pathology, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA.,Sarcoma Department, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA
| | - Marilyn M Bui
- Department of Anatomic Pathology, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA.,Sarcoma Department, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA
| | - Jamie Caracciolo
- Department of Diagnostic Imaging, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA
| | - Sean Yoder
- Molecular Genomics Core Facility, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA
| | - Odion Binitie
- Sarcoma Department, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA.,Adolescent and Young Adult Program; H. Lee Moffitt Cancer Center and Research Institute, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA
| | | | - Andrew S Brohl
- Sarcoma Department, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA
| | - Damon R Reed
- Sarcoma Department, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA. .,Chemical Biology and Molecular Medicine Program, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA. .,Adolescent and Young Adult Program; H. Lee Moffitt Cancer Center and Research Institute, 12901 Bruce B Downs Blvd., Tampa, FL, 33612, USA.
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22
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Teer J, Yoder S, Gjyshi A, Zhang C, Monteiro A. Abstract B11: Mutational heterogeneity in non-serous ovarian cancers. Clin Cancer Res 2016. [DOI: 10.1158/1557-3265.ovca15-b11] [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 mutational landscape of non-serous ovarian carcinomas is underexplored despite their substantial contribution to ovarian cancer morbidity and mortality. In this study we report whole exome sequencing analysis of 10 non-serous ovarian tumors and matched normal samples. We also report targeted gene sequencing results of an additional 28 non-serous tumor samples targeting 1,321 genes selected for their involvement in cancer.
Methods: Whole exome capture was performed using Roche NimbleGen SeqCap EZ, followed by sequencing of captured libraries using an Illumina HiScan platform. Target gene capture was performed using SureSelect custom designs, using GAIIx sequencing technology. Sequences from both experimental procedures were aligned to the human genome using the Burrows-Wheeler Aligner and the Genome Analysis ToolKit was used for insertion/deletion realignment, quality score calibration, and variant identification. Mutations were detected with MuTect or Strelka (whole exome) or GATK (target gene).
Results: We annotated 32,965 somatic mutations (829-15,737 per tumor) for an overall rate of mutation 12.2 per Mb. Interestingly, a BRCA2 frameshift mutation was observed in mucinous tumors; although inherited BRCA mutations have not been previously observed in mucinous histology. TP53 mutations were much less common than observed in high-grade serous ovarian cancers. PTEN stood out as a gene containing truncating mutations in many samples. We confirmed FOXL2 importance in granulosa, KRAS in mucinous histology and identified POLE mutations in endometrioid ovarian samples. Finally, we report comparative analysis of our results to The Cancer Genome Atlas (TCGA) database.
Conclusion: In summary, we report that non-serous ovarian tumors are mutationally distinct from serous ovarian tumors, having a mutational profile more similar to non-serous endometrial cancers.
Citation Format: Jaime Teer, Sean Yoder, Anxhela Gjyshi, Chaomei Zhang, Alvaro Monteiro. Mutational heterogeneity in non-serous ovarian cancers. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr B11.
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Affiliation(s)
- Jaime Teer
- 1Bioinformatics and Biostatistics Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL,
| | - Sean Yoder
- 2Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL,
| | - Anxhela Gjyshi
- 3University of South Florida Cancer Biology PhD Program, Tampa, FL,
| | - Chaomei Zhang
- 2Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL,
| | - Alvaro Monteiro
- 4Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
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Bot A, Kochenderfer J, Mardiros A, Perez A, Navale L, Chang R, Wei-Shen Y, Yoder S, Xiao-Chi J, Rosenberg SA, Go WY, Wiezorek JS, Roberts M, Chang DD. Biomarker analysis of patients treated with anti-CD19 chimeric antigen receptor (CAR) T cells. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.3028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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24
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Beatty M, Han Y, McDaniel J, Mailloux A, Painter J, Bronk C, Yoder S, Beg A, Yu XZ, Fu J, Engelman R, Liu C, Rajadhyaksha A, Epling-Burnette P. Cereblon, a molecular target of lenalidomide (IMiDs), negatively regulates T cell activation (IRM7P.715). The Journal of Immunology 2015. [DOI: 10.4049/jimmunol.194.supp.61.16] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Thalidomide analogs classified as immunomodulatory drugs (IMiDs) are rapidly emerging T-cell stimulants for the treatment of cancer. Cereblon, an E3-Ub ligase receptor with no known immune regulatory function, is the first identified target of IMiDs. The drug is hypothesized to have antagonistic properties by interfering with substrate recruitment to the thalidomide-binding domain in cereblon, and agonistic activity through an exposed ring that may recruit new proteins to the Ub complex. To explore this further at the molecular level, we studied immune regulation in cereblon deficient mice (crbn-/-), which exhibited an expanded white blood cell and neutrophil compartment, and higher numbers of peripheral and splenic lymphocytes. Mature crbn-/- T cells were capable of proliferation and IL-2 production following CD3 ligation in the absence of CD28 co-ligation. This positively associates with proximal phosphorylation events including pZap70, pAKT, pro-survival Bcl-XL and Bcl-2 protein expression, and corresponds with decreased pro-apoptotic proteins Bim, Bad, and Bax. Consistent with this data in a lethal graft-versus-host (GVHD) model, MHC-class I mismatched T cells from crbn-/- mice showed shortened post-transplant survival, greater weight-loss, and higher IFN-γ compared to transplanted wild-type T-cells. These data suggest that native targets of cereblon restrain the activation threshold of T-cells and that IMiD-associated blockade of cereblon leads to T-cell potentiation.
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Affiliation(s)
- Matthew Beatty
- 1Immunology, Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Ying Han
- 1Immunology, Moffitt Cancer Center & Research Institute, Tampa, FL
- 2Immunology, Tianjin Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jessica McDaniel
- 1Immunology, Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Adam Mailloux
- 1Immunology, Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Jeffrey Painter
- 1Immunology, Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Chrystina Bronk
- 1Immunology, Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Sean Yoder
- 3Molecular Genomics Core Facility, Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Amer Beg
- 1Immunology, Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Xue-Zhong Yu
- 4Microbiology and Immunology, Medical University of South Carolina, Charleston, SC
| | - Jianing Fu
- 4Microbiology and Immunology, Medical University of South Carolina, Charleston, SC
| | - Robert Engelman
- 5Comparative Medicine, University of South Florida, Tampa, FL
| | - Chen Liu
- 6Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL
| | - Anjali Rajadhyaksha
- 7Pediatric Neurology, Pediatrics, Brain and Mind Research Institute, Weill Cornell Med. Col., New York, NY
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25
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Pidala J, Bloom GC, Eschrich S, Sarwal M, Enkemann S, Betts BC, Beato F, Yoder S, Anasetti C. Tolerance associated gene expression following allogeneic hematopoietic cell transplantation. PLoS One 2015; 10:e0117001. [PMID: 25774806 PMCID: PMC4361657 DOI: 10.1371/journal.pone.0117001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 11/07/2014] [Indexed: 12/25/2022] Open
Abstract
Biologic markers of immune tolerance may facilitate tailoring of immune suppression duration after allogeneic hematopoietic cell transplantation (HCT). In a cross-sectional study, peripheral blood samples were obtained from tolerant (n = 15, median 38.5 months post-HCT) and non-tolerant (n = 17, median 39.5 post-HCT) HCT recipients and healthy control subjects (n = 10) for analysis of immune cell subsets and differential gene expression. There were no significant differences in immune subsets across groups. We identified 281 probe sets unique to the tolerant (TOL) group and 122 for non-tolerant (non-TOL). These were enriched for process networks including NK cell cytotoxicity, antigen presentation, lymphocyte proliferation, and cell cycle and apoptosis. Differential gene expression was enriched for CD56, CD66, and CD14 human lineage-specific gene expression. Differential expression of 20 probe sets between groups was sufficient to develop a classifier with > 90% accuracy, correctly classifying 14/15 TOL cases and 15/17 non-TOL cases. These data suggest that differential gene expression can be utilized to accurately classify tolerant patients following HCT. Prospective investigation of immune tolerance biologic markers is warranted.
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Affiliation(s)
- Joseph Pidala
- Blood and Marrow Transplantation, Moffitt Cancer Center, Tampa, FL, United States of America
- * E-mail:
| | - Gregory C. Bloom
- Bioinformatics, Moffitt Cancer Center, Tampa, FL, United States of America
| | - Steven Eschrich
- Bioinformatics, Moffitt Cancer Center, Tampa, FL, United States of America
| | - Minnie Sarwal
- Department of Surgery, UCSF School of Medicine, San Francisco, CA, United States of America
| | - Steve Enkemann
- Molecular Genomics, Moffitt Cancer Center, Tampa, FL, United States of America
| | - Brian C. Betts
- Blood and Marrow Transplantation, Moffitt Cancer Center, Tampa, FL, United States of America
| | - Francisca Beato
- Blood and Marrow Transplantation, Moffitt Cancer Center, Tampa, FL, United States of America
| | - Sean Yoder
- Molecular Genomics, Moffitt Cancer Center, Tampa, FL, United States of America
| | - Claudio Anasetti
- Blood and Marrow Transplantation, Moffitt Cancer Center, Tampa, FL, United States of America
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26
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McGraw KL, Zhang LM, Rollison DE, Basiorka AA, Fulp W, Rawal B, Jerez A, Billingsley DL, Lin HY, Kurtin SE, Yoder S, Zhang Y, Guinta K, Mallo M, Solé F, Calasanz MJ, Cervera J, Such E, González T, Nevill TJ, Haferlach T, Smith AE, Kulasekararaj A, Mufti G, Karsan A, Maciejewski JP, Sokol L, Epling-Burnette PK, Wei S, List AF. The relationship of TP53 R72P polymorphism to disease outcome and TP53 mutation in myelodysplastic syndromes. Blood Cancer J 2015; 5:e291. [PMID: 25768405 PMCID: PMC4382654 DOI: 10.1038/bcj.2015.11] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 12/23/2014] [Accepted: 01/13/2015] [Indexed: 01/22/2023] Open
Abstract
Nonsynonymous TP53 exon 4 single-nucleotide polymorphism (SNP), R72P, is linked to cancer and mutagen susceptibility. R72P associations with specific cancer risk, particularly hematological malignancies, have been conflicting. Myelodysplastic syndrome (MDS) with chromosome 5q deletion is characterized by erythroid hypoplasia arising from lineage-specific p53 accumulation resulting from ribosomal insufficiency. We hypothesized that apoptotically diminished R72P C-allele may influence predisposition to del(5q) MDS. Bone marrow and blood DNA was sequenced from 705 MDS cases (333 del(5q), 372 non-del(5q)) and 157 controls. Genotype distribution did not significantly differ between del(5q) cases (12.6% CC, 38.1% CG, 49.2% GG), non-del(5q) cases (9.7% CC, 44.6% CG, 45.7% GG) and controls (7.6% CC, 37.6% CG, 54.8% GG) (P=0.13). Allele frequency did not differ between non-del(5q) and del(5q) cases (P=0.91) but trended towards increased C-allele frequency comparing non-del(5q) (P=0.08) and del(5q) (P=0.10) cases with controls. Median lenalidomide response duration increased proportionate to C-allele dosage in del(5q) patients (2.2 (CC), 1.3 (CG) and 0.89 years (GG)). Furthermore, C-allele homozygosity in del(5q) was associated with prolonged overall and progression-free survival and non-terminal interstitial deletions that excluded 5q34, whereas G-allele homozygozity was associated with inferior outcome and terminal deletions involving 5q34 (P=0.05). These findings comprise the largest MDS R72P SNP analysis.
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Affiliation(s)
- K L McGraw
- Hematology Department, H Lee Moffitt Cancer Center, Tampa, FL, USA
| | - L M Zhang
- Molecular Genomics Core Lab, H Lee Moffitt Cancer Center, Tampa, FL, USA
| | - D E Rollison
- Cancer Epidemiology, H Lee Moffitt Cancer Center, Tampa, FL, USA
| | - A A Basiorka
- 1] Hematology Department, H Lee Moffitt Cancer Center, Tampa, FL, USA [2] Cancer Biology PhD Program, University of South Florida, Tampa, FL, USA
| | - W Fulp
- Biostatistics and Bioinformatics Department, H Lee Moffitt Cancer Center, Tampa, FL, USA
| | - B Rawal
- Mayo Clinic, Biostatistics-Division of Health Sciences Research, Jacksonville, FL, USA
| | - A Jerez
- Cleveland Clinic, Taussig Cancer Institute, Cleveland, OH, USA
| | | | - H-Y Lin
- Biostatistics and Bioinformatics Department, H Lee Moffitt Cancer Center, Tampa, FL, USA
| | | | - S Yoder
- Molecular Genomics Core Lab, H Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Y Zhang
- Biostatistics and Bioinformatics Department, H Lee Moffitt Cancer Center, Tampa, FL, USA
| | - K Guinta
- Cleveland Clinic, Taussig Cancer Institute, Cleveland, OH, USA
| | - M Mallo
- Institut de Recerca Contra la Leucèmia Josep Carreras (IJC) Badalona, Barcelona, Spain
| | - F Solé
- Institut de Recerca Contra la Leucèmia Josep Carreras (IJC) Badalona, Barcelona, Spain
| | - M J Calasanz
- Hematology Department, Hospital Universitario La Fe, Valencia, Spain
| | - J Cervera
- Hematology Department, Hospital Universitario La Fe, Valencia, Spain
| | - E Such
- Hematology Department, Hospital Universitario La Fe, Valencia, Spain
| | - T González
- Genomics Medicine Public Foundation, Hospital Clinico Universitario, Santiago de Compostela, Spain
| | - T J Nevill
- British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | - A E Smith
- King's College London, King's College Hospital, London, UK
| | | | - G Mufti
- King's College London, King's College Hospital, London, UK
| | - A Karsan
- British Columbia Cancer Agency, Vancouver, BC, Canada
| | - J P Maciejewski
- Cleveland Clinic, Taussig Cancer Institute, Cleveland, OH, USA
| | - L Sokol
- Hematology Department, H Lee Moffitt Cancer Center, Tampa, FL, USA
| | | | - S Wei
- Immunology Department, H Lee Moffitt Cancer Center, Tampa, FL, USA
| | - A F List
- Hematology Department, H Lee Moffitt Cancer Center, Tampa, FL, USA
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Bronk CC, Yoder S, Hopewell EL, Yang S, Celis E, Yu XZ, Beg AA. NF-κB is crucial in proximal T-cell signaling for calcium influx and NFAT activation. Eur J Immunol 2014; 44:3741-6. [PMID: 25251667 DOI: 10.1002/eji.201444904] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/12/2014] [Accepted: 09/19/2014] [Indexed: 12/30/2022]
Abstract
In the accepted model of T-cell activation, parallel signal-transduction pathways activate the transcription factors NF-κB, NFAT, and AP-1 to drive clonal expansion of T cells in response to Ag. Genome-wide transcriptional profiling following Ag-induced CD8(+) T-cell activation in C57BL/6 mouse T cells revealed that genes regulated by NFAT were also reduced in the absence of NF-κB p50 and cRel subunits. Importantly, p50(-/-) cRel(-/-) CD8(+) T cells had significantly diminished NFAT and AP-1 activation compared with WT or PKCθ(-/-) CD8(+) T cells. Attenuated NFAT activation after TCR engagement was associated with reduced calcium influx, PLCγ and Zap70 activation. Interestingly, pharmacological bypass of PLCγ-regulated pathways largely rescued p50(-/-) cRel(-/-) T-cell proliferative defects. These results indicate a crucial and unexpected requirement for NF-κB p50 and cRel subunits in proximal TCR signaling and calcium responses. They further suggest that key defects in T cells in the absence of NF-κB pathway components may be due to impaired proximal T-cell signaling.
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Affiliation(s)
- Crystina C Bronk
- Department of Immunology, Moffitt Cancer Center, Tampa, FL, USA; Department of Oncologic Sciences, University of South Florida, Tampa, FL, USA
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Buckley MA, Shen HC, Mendoza-Fandino GA, Woods NT, Gjyshi A, French J, Lawrenson K, Song H, Tyrer J, Carvalho RS, Valle A, Chen A, Yoder S, Bloom G, Tsai YY, Yang A, Hughes TR, Qu X, Cicek M, Larson M, Goode E, Fridley B, Ramus S, Chenevix-Trench G, Pharoah P, Sellers TA, Gayther S, Monteiro AN. Abstract 3285: Functional analysis of the 9p22 locus implicates the transcriptional regulation of BNC2 as a mechanism in ovarian cancer predisposition. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-3285] [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
An ovarian cancer Genome Wide Association Study (GWAS) identified 9p22.2 as a novel susceptibility locus with the most statistically significant single nucleotide polymorphisms (SNPs) located in an intergenic region near the Basonuclin 2 (BNC2) gene, which codes for a putative transcription regulator containing three pairs of zinc finger (ZF) domains. The minor alleles are protective in terms of ovarian cancer susceptibility. However, the molecular mechanisms by which these SNPs modify susceptibility remain largely unknown. The significant SNPs in the 9p22.2 locus lie in non-coding regions and therefore are hypothesized to affect the activity of regulatory elements and modify the expression of a target gene(s). In order to test this hypothesis we conducted fine mapping for the locus which delimited a ∼74kb region containing SNPs with a p-value less than 10-8. FAIRE-Seq and ChIP-Seq experiments for histone markers conducted in immortalized ovarian surface epithelial cells (IOSE) and fallopian tube epithelial cells (IFTE) were used to prioritize functional SNP candidates which overlap with regulatory elements. Luciferase assays tested the ability of these regulatory elements to activate transcription. Chromosome conformation capture (3C) experiments demonstrate a physical interaction between the BNC2 promoter and candidate regulatory elements containing risk-associated SNPs. Methylation Quantification at Trait Loci (mQTL) revealed an association between decreased methylation at the BNC2 promoter and the protective minor alleles. Expression analysis shows decreased expression of BNC2 in cancer versus normal tissue implicating tumor suppressor function of BNC2. Therefore the protective minor allele likely increases expression of BNC2 which in turn contains tumor suppressing properties that decrease ovarian cancer risk. BNC2 protein is in complex with transcriptional regulatory proteins, in particular the NURD complex components. Moreover, BNC2 acts as a transcriptional repressor in in vitro transfection assays indicating that it functions in transcriptional repression. We then used protein binding microarrays and CHIP-Seq experiments to identify its putative DNA binding motifs and its downstream target genes. Analysis of this data suggests that BNC2 functions in a regulatory transcription network that impacts on genes implicated in ovarian cancer with enrichment for genes in the TGF-beta response pathway.
Citation Format: Melissa A. Buckley, Howard C. Shen, Gustavo A. Mendoza-Fandino, Nicholas T. Woods, Anxhela Gjyshi, Juliet French, Kate Lawrenson, Honglin Song, Jonathan Tyrer, Renato S. Carvalho, Alexandra Valle, Ann Chen, Sean Yoder, Gregory Bloom, Ya-Yu Tsai, Ally Yang, Timothy R. Hughes, Xiaotao Qu, Mine Cicek, Melissa Larson, Ellen Goode, Brooke Fridley, Susan Ramus, Georgia Chenevix-Trench, Paul Pharoah, Thomas A. Sellers, Simon Gayther, Alvaro N.A. Monteiro, Ovarian Cancer Association Consortium. Functional analysis of the 9p22 locus implicates the transcriptional regulation of BNC2 as a mechanism in ovarian cancer predisposition. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3285. doi:10.1158/1538-7445.AM2014-3285
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Affiliation(s)
| | | | | | | | | | - Juliet French
- 3QIMR Berghofer Medical Research Institute, Herston, Australia
| | | | | | | | | | | | - Ann Chen
- 1Moffitt Cancer Center, Tampa, FL
| | | | | | | | - Ally Yang
- 5University of Toronto, Ontario, Canada
| | | | | | | | | | | | | | - Susan Ramus
- 2University of Southern California, Los Angeles, CA
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Padron E, Yoder S, Kunigal S, Mesa T, Teer JK, Al Ali N, Sekeres MA, Painter JS, Zhang L, Lancet J, Maciejewski JP, Epling-Burnette PK, Sotomayor E, Komrokji RS, List AF. ETV6 and signaling gene mutations are associated with secondary transformation of myelodysplastic syndromes to chronic myelomonocytic leukemia. Blood 2014; 123:3675-7. [PMID: 24904105 PMCID: PMC4047502 DOI: 10.1182/blood-2014-03-562637] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Eric Padron
- Department of Hematologic Malignancies, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FLImmunology Program, H. Lee Moffitt Cancer Center and Research Institute, and the University of South Florida, Tampa, FL
| | - Sean Yoder
- Molecular Genomics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Sateesh Kunigal
- Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, and the University of South Florida, Tampa, FL
| | - Tania Mesa
- Molecular Genomics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Jamie K Teer
- Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Najla Al Ali
- Department of Hematologic Malignancies, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Mikkael A Sekeres
- Leukemia Program and Translational Hematology and Oncology Research, Cleveland Clinic Taussig Cancer Institute, Cleveland, OH
| | - Jeffrey S Painter
- Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, and the University of South Florida, Tampa, FL
| | - Ling Zhang
- Pathology Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Jeffrey Lancet
- Department of Hematologic Malignancies, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Jaroslaw P Maciejewski
- Leukemia Program and Translational Hematology and Oncology Research, Cleveland Clinic Taussig Cancer Institute, Cleveland, OH
| | - Pearlie K Epling-Burnette
- Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, and the University of South Florida, Tampa, FLJames A Haley Veterans Administration Hospital, Tampa, FL
| | - Eduardo Sotomayor
- Department of Hematologic Malignancies, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FLImmunology Program, H. Lee Moffitt Cancer Center and Research Institute, and the University of South Florida, Tampa, FL
| | - Rami S Komrokji
- Department of Hematologic Malignancies, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Alan F List
- Department of Hematologic Malignancies, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
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Mailloux A, Zhang L, Moscinski L, Bennett J, Yang L, Yoder S, Sokol L, Loughran T, Epling-Burnette P. Pathophysiology of cytopenias in an autoimmune lymphoproliferative disease linked to bone marrow fibrosis (P3165). The Journal of Immunology 2013. [DOI: 10.4049/jimmunol.190.supp.43.44] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Large Granular Lymphocyte (LGL) leukemia is associated with unexplained cytopenias, autoimmune features, and CD57+CD8+perforin+ T-cell lympoproliferation. Like many autoimmune disorders, the pathophysiology of cytopenias in LGL leukemia is unknown. Bone marrow (BM) pathology from 24 LGL leukemia patients was retrospectively studied using H&E, reticulin, and trichrome-stained sections, and revealed that BM fibrosis was present in 21 out of 24 patients (88%). Fibrosis, a previously undefined complication, was significantly associated with splenomegaly, the presence of cytopenias, and coexistance of autoimmune diseases. LGL cell numbers in the BM, but not peripheral blood, was associated with fibrosis severity. Colony forming assays in the presence of exogenous bioartificial collagen matrix using healthy bone marrow mononuclear cells (BM-MNCs) revealed a direct inhibitory effect of collagen on progenitor growth. Consistent with microarray analysis, primary mesenchymal stromal cultures (MSCs) from LGL leukemia BM displayed heightened collagen deposition. In co-culture assays, collagen matrix produced by LGL MSCs directly inhibited healthy hematopoietic progenitor growth support. This study demonstrates that excessive collagen matrix deposition by deregulated MSCs may result from the local BM accumulation of activated CD8+ LGL leukemia T-cells. Therefore, BM fibrosis should be explored as a mechanism for secondary cytopenias associated with autoimmune diseases.
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Affiliation(s)
- Adam Mailloux
- 1Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Ling Zhang
- 2Hematopathology & Laboratory Medicine, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Lynn Moscinski
- 2Hematopathology & Laboratory Medicine, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - John Bennett
- 3Hematology Oncology Pathology, University of Rochester, Rochester, NY
| | - Lili Yang
- 4Tianjin Cancer Institute and Hostpital, Tianjin, China
| | - Sean Yoder
- 5Molecular Genomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Lubomir Sokol
- 6Malignant Hematology, Molecular Oncology and Experimental Therapeudics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | | | - Pearlie Epling-Burnette
- 1Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
- 8James A. Hailey VA Hosp., Tampa, FL
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Bradley E, Williams J, Schilling M, Coggins P, Crist C, Yoder S, Campano S. Effects of sodium lactate and acetic acid derivatives on the quality and sensory characteristics of hot-boned pork sausage patties. Meat Sci 2011; 88:145-50. [DOI: 10.1016/j.meatsci.2010.12.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 11/22/2010] [Accepted: 12/02/2010] [Indexed: 10/18/2022]
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Patel NA, Apostolatos A, Yoder S, Ghansah T, Watson JE, Cooper DR, Li P. Developmentally regulated alternative splicing of anti‐apoptotic proteins during adipogenesis. FASEB J 2011. [DOI: 10.1096/fasebj.25.1_supplement.900.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Reams RR, Agrawal D, Davis MB, Yoder S, Odedina FT, Kumar N, Higginbotham JM, Akinremi T, Suther S, Soliman KF. Microarray comparison of prostate tumor gene expression in African-American and Caucasian American males: a pilot project study. Infect Agent Cancer 2009; 4 Suppl 1:S3. [PMID: 19208208 PMCID: PMC2638462 DOI: 10.1186/1750-9378-4-s1-s3] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [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] [Indexed: 12/01/2022] Open
Abstract
African American Men are 65% more likely to develop prostate cancer and are twice as likely to die of prostate cancer, than are Caucasian American Males. The explanation for this glaring health disparity is still unknown; although a number of different plausible factors have been offered including genetic susceptibility and gene-environment interactions. We favor the hypothesis that altered gene expression plays a major role in the disparity observed in prostate cancer incidence and mortality between African American and Caucasian American Males. To discover genes or gene expression pattern(s) unique to African American or to Caucasian American Males that explain the observed prostate cancer health disparity in African American males, we conducted a micro array pilot project study that used prostate tumors with a Gleason score of 6. We compared gene expression profiling in tumors from African-American Males to prostate tumors in Caucasian American Males. A comparison of case-matched ratios revealed at least 67 statistically significant genes that met filtering criteria of at least +/- 4.0 fold change and p < 0.0001. Gene ontology terms prevalent in African American prostate tumor/normal ratios relative to Caucasian American prostate tumor/normal ratios included interleukins, progesterone signaling, Chromatin-mediated maintenance and myeloid dendritic cell proliferation. Functional in vitro assays are underway to determine roles that selected genes in these onotologies play in contributing to prostate cancer development and health disparity.
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Affiliation(s)
- R Renee Reams
- College of Pharmacy & Pharmaceutical Sciences Florida A&M University, Tallahassee, Florida, USA
| | | | - Melissa B Davis
- Institute of Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, USA
| | - Sean Yoder
- H. Lee Moffitt Cancer Center Tampa, Florida, USA
| | | | - Nagi Kumar
- H. Lee Moffitt Cancer Center Tampa, Florida, USA
| | - Joseph M Higginbotham
- College of Pharmacy & Pharmaceutical Sciences Florida A&M University, Tallahassee, Florida, USA
| | - Titilola Akinremi
- Department of Pathology, Federal Medical Center (FMC), Abeokuta, Nigeria
| | - Sandra Suther
- Institute of Public Health, Florida A&M University, Tallahassee, Florida, USA
| | - Karam Fa Soliman
- College of Pharmacy & Pharmaceutical Sciences Florida A&M University, Tallahassee, Florida, USA
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Gritsko T, Williams A, Turkson J, Kaneko S, Bowman T, Huang M, Nam S, Eweis I, Diaz N, Sullivan D, Yoder S, Enkemann S, Eschrich S, Lee JH, Beam CA, Cheng J, Minton S, Muro-Cacho CA, Jove R. Persistent activation of stat3 signaling induces survivin gene expression and confers resistance to apoptosis in human breast cancer cells. Clin Cancer Res 2006; 12:11-9. [PMID: 16397018 DOI: 10.1158/1078-0432.ccr-04-1752] [Citation(s) in RCA: 415] [Impact Index Per Article: 23.1] [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: 12/24/2022]
Abstract
PURPOSE Signal transducer and activator of transcription 3 (Stat3) protein is persistently activated in breast cancer and promotes tumor cell survival. To gain a better understanding of the role of constitutive Stat3 signaling in breast cancer progression, we evaluated the expression profile of potential Stat3-regulated genes that may confer resistance to apoptosis. EXPERIMENTAL DESIGN Stat3 signaling was blocked with antisense oligonucleotides in human MDA-MB-435s breast cancer cells and Affymetrix GeneChip microarray analysis was done. The candidate Stat3 target gene Survivin was further evaluated in molecular assays using cultured breast cancer cells and immunohistochemistry of breast tumor specimens. RESULTS Survivin, a member of the inhibitor of apoptosis protein family, was identified as a potential Stat3-regulated gene by microarray analysis. This was confirmed in Survivin gene promoter studies and chromatin immunoprecipitation assays showing that Stat3 directly binds to and regulates the Survivin promoter. Furthermore, direct inhibition of Stat3 signaling blocked the expression of Survivin protein and induced apoptosis in breast cancer cells. Direct inhibition of Survivin expression also induced apoptosis. Increased Survivin protein expression correlates significantly (P = 0.001) with elevated Stat3 activity in primary breast tumor specimens from high-risk patients who were resistant to chemotherapy treatment. CONCLUSIONS We identify Survivin as a direct downstream target gene of Stat3 in human breast cancer cells that is critical for their survival in culture. Our findings suggest that activated Stat3 signaling contributes to breast cancer progression and resistance to chemotherapy by, at least in part, inducing expression of the antiapoptotic protein, Survivin.
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Affiliation(s)
- Tanya Gritsko
- Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute Department of Interdisciplinary Oncology, University of South Florida College of Medicine, Tampa, Florida, USA
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Kinder Haake S, Yoder S, Gerardo SH. Efficient gene transfer and targeted mutagenesis in Fusobacterium nucleatum. Plasmid 2005; 55:27-38. [PMID: 16115683 PMCID: PMC1592470 DOI: 10.1016/j.plasmid.2005.06.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [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: 05/09/2005] [Revised: 06/09/2005] [Accepted: 06/16/2005] [Indexed: 10/25/2022]
Abstract
Fusobacterium nucleatum is a Gram-negative anaerobe important in dental biofilm ecology and infectious diseases with significant societal impact. The lack of efficient genetic systems has hampered molecular analyses in this microorganism. We previously reported construction of a shuttle plasmid, pHS17, using the native fusobacterial plasmid pFN1 and an erythromycin resistance cassette. However, the host range of pHS17 was restricted to F. nucleatum, ATCC 10953, and the transformation efficiency was limited. This study was undertaken to improve genetic systems for molecular analysis in F. nucleatum. We identified a second F. nucleatum strain, ATCC 23726, which is transformed with improved efficiency compared to ATCC 10953. Two novel second generation pFN1-based shuttle plasmids, pHS23 and pHS30, were developed and enable transformation of ATCC 23726 at 6.2 x 10(4) and 1.5 x 10(6) transformants/mug plasmid DNA, respectively. The transformation efficiency of pHS30, which harbors a catP gene conferring resistance to chloramphenicol, was more than 1000-fold greater than that of pHS17. The improved transformation efficiency facilitated disruption of the chromosomal rnr gene using a suicide plasmid pHS19, the first demonstration of targeted mutagenesis in F. nucleatum. These results provide significant advances in the development of systems for molecular analysis in F. nucleatum.
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Affiliation(s)
- Susan Kinder Haake
- Section of Periodontics, UCLA School of Dentistry, Los Angeles, CA 90095-1668, USA.
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Paterson CL, Yoder S. SEXUALLY TRANSMITTED DISEASE RATES AND THE NEED FOR A STUDENT HEALTH CENTER AT THE SALLISH KOOTENAI TRIBAL COLLEGE IN PABLO, MONTANA. J Investig Med 2004. [DOI: 10.1097/00042871-200401001-00220] [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: 11/25/2022]
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Paterson CL, Yoder S. 220 SEXUALLY TRANSMITTED DISEASE RATES AND THE NEED FOR A STUDENT HEALTH CENTER AT THE SALLISH KOOTENAI TRIBAL COLLEGE IN PABLO, MONTANA. J Investig Med 2004. [DOI: 10.1136/jim-52-suppl1-220] [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: 11/04/2022]
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38
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Han TK, Yoder S, Cao C, Ugen KE, Dao ML. Expression of Streptococcus mutans wall-associated protein A gene in Chinese hamster ovary cells: prospect for a dental caries DNA vaccine. DNA Cell Biol 2001; 20:595-601. [PMID: 11747611 DOI: 10.1089/104454901317095016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 11/13/2022] Open
Abstract
The Streptococcus mutans strain GS-5 wall-associated protein A (Wap-A) is a precursor to the extracellular antigen A (AgA), a recognized candidate dental caries vaccine. The full-length wapA gene (wapA-E) and a C-terminal truncated version (wapA-G) encoding the AgA were cloned into the mammalian expression vector pcDNA 3.1/V5/His-TOPO. The resulting constructs were propagated in the Escherichia coli Top10. To investigate the expression of the S. mutans genes in mammalian cells, the above constructs were used to transfect Chinese hamster ovary (CHO) cells in the presence of the cationic lipid pfx-8. Transient expression of the wapA-E and wapA-G genes was observed at 24 h post-transfection, as shown by Western immunoblot analysis using a rabbit antiserum to S. mutans cell wall. Immunochemical staining of the transfected CHO cells showed expression of WapA mainly in the cells and budding vesicles, whereas AgA was found mainly in the transfected cells and extracellular medium. The expression of S. mutans proteins in CHO cells, in either vesicles or soluble form, suggested an antibody response to the above DNA constructs. Work is under way to test the efficacy of these as DNA vaccines against S. mutans.
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Affiliation(s)
- T K Han
- Department of Biology, College of Arts and Sciences, University of South Florida, Tampa, Florida 33620-5150, USA
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40
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Drake AI, Gray N, Yoder S, Pramuka M, Llewellyn M. Factors predicting return to work following mild traumatic brain injury: a discriminant analysis. J Head Trauma Rehabil 2000; 15:1103-12. [PMID: 10970931 DOI: 10.1097/00001199-200010000-00004] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Studies of mild traumatic brain injury (MTBI) suggest that most individuals recover rapidly and return to their everyday activities. However, a percentage of MTBI patients report persistent problems with cognitive, physical, and emotional symptoms. There is also evidence that some experience changes in occupational functioning following MTBI. The current study used a stepwise discriminant function analysis (DFA) to examine the role of injury severity variables, cognitive performance, and ratings of symptoms of TBI in predicting work status following MTBI. Subjects included 121 MTBI patients who were all active-duty military personnel. The stepwise DFA revealed that age and three cognitive variables (verbal memory, verbal fluency, and a speed test of planning and strategy) were predictive of work status 3-15 months following a documented MTBI, correctly classifying work status 68.8% of the time. A cross-validation DFA was conducted, with a 66.1% correct classification rate. These findings highlight the importance of cognitive impairments in identifying those at risk for occupational impairment following MTBI.
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Yoder S, Cao C, Ugen KE, Dao ML. High-level expression of a truncated wall-associated protein A from the dental cariogenic Streptococcus mutans. DNA Cell Biol 2000; 19:401-8. [PMID: 10945230 DOI: 10.1089/10445490050085898] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Streptococcus mutans plays a primary role in the formation of dental caries. Previously, in our laboratory, an S. mutans genomic library was prepared, and the wapA gene was cloned into the shuttle vector, pSA4/4B2. To generate overexpression of wapA and to facilitate efficient purification of the WapA protein for use as an immunogen, an expression vector with the strong tac promoter was used. In order to answer questions regarding the optimization of solubility and expression based on gene size or the hydrophobicity of the protein product, 12 truncated constructs of the wapA gene were prepared using PCR. The truncated products were subcloned into the pGEX-6P-1 glutathione S-transferase (GST) fusion vector and expressed in E. coli BL21. The fusion proteins were analyzed by SDS-PAGE and confirmed by analysis with anti-GST and anti-WapA antibodies. Our study suggests that abrogation of the wapA promoter is necessary for expression of this gene in this expression system. Deletion of the signal peptide and the hydrophobic C terminus of WapA increased expression compared with the full-length construct, and truncation at the protease cleavage site of the C-terminal region greatly increased the stability of the protein without a loss in reactivity with the anti-WapA antibody. Western immunoblot analysis with anti-WapA antiserum clearly showed that the majority of the epitopes of the GST-WapA fusions are located in the N-terminal region of WapA. The immunogenicity of the various WapA fusion products is being examined in mice and rats to further map the immunologically dominant regions of the protein. This method effectively increased the expression of WapA and should contribute to the further understanding of gene expression of E. coli, as well as aid in the characterization of this protein for future immunologic evaluation.
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Affiliation(s)
- S Yoder
- Department of Biology, University of South Florida, Tampa, USA
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Argueta C, Yoder S, Holtzman AE, Aronson TW, Glover N, Berlin OG, Stelma GN, Froman S, Tomasek P. Isolation and identification of nontuberculous mycobacteria from foods as possible exposure sources. J Food Prot 2000; 63:930-3. [PMID: 10914663 DOI: 10.4315/0362-028x-63.7.930] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A variety of foods collected from local supermarkets and produce stands were examined as possible sources of nontuberculous mycobacterial exposure. Food samples were combined with sterile ultrapure water and manually shaken. To remove large particles, the suspensions were filtered through a sterile strainer, centrifuged, and the supernatants were discarded. The food pellets were stored at -75 degrees C. The pellets were treated with either oxalic acid or sodium hydroxide-sodium citrate solutions to reduce contamination by nonmycobacterial organisms. Decontaminated pellets were cultured on both Middlebrook 7H10C agar and Middlebrook 7H10C agar with supplemental malachite green. Plates were observed for growth at 2 and 8 weeks. Isolates demonstrating acid-fastness were identified to species using polymerase chain reaction and restriction enzyme analysis. Nontuberculous mycobacteria (NTM) were recovered from 25 of 121 foods. Six different species of NTM were isolated, the most predominant being Mycobacterium avium.
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Affiliation(s)
- C Argueta
- Education and Research Institute, Olive View-UCLA Medical Center, Sylmar, California 91342, USA.
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Yoder S, Argueta C, Holtzman A, Aronson T, Berlin OG, Tomasek P, Glover N, Froman S, Stelma G. PCR comparison of Mycobacterium avium isolates obtained from patients and foods. Appl Environ Microbiol 1999; 65:2650-3. [PMID: 10347056 PMCID: PMC91391 DOI: 10.1128/aem.65.6.2650-2653.1999] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium avium is a cause of disseminated disease in AIDS patients. A need for a better understanding of possible sources and routes of transmission of this organism has arisen. This study utilized a PCR typing method designed to amplify DNA segments located between the insertion sequences IS1245 and IS1311 to compare levels of relatedness of M. avium isolates found in patients and foods. Twenty-five of 121 food samples yielded 29 mycobacterial isolates, of which 12 were M. avium. Twelve food and 103 clinical M. avium isolates were tested. A clinical isolate was found to be identical to a food isolate, and close relationships were found between two patient isolates and two food isolates. Relatedness between food isolates and patient isolates suggests the possibility that food is a potential source of M. avium infection. This study demonstrates a rapid, inexpensive method for typing M. avium, possibly replacing pulsed-field gel electrophoresis.
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Affiliation(s)
- S Yoder
- Education and Research Institute, Olive View-UCLA Medical Center, Sylmar, California 91342, USA.
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45
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Donatelli DD, Yoder S. Turning conflict into cooperation: an independent study (continuing education credit). Ohio Nurses Rev 1995; 70:15-7; quiz 19. [PMID: 8632883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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