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Stopsack KH, Su XA, Vaselkiv JB, Graff RE, Ebot EM, Pettersson A, Lis RT, Fiorentino M, Loda M, Penney KL, Lotan TL, Mucci LA. Transcriptomes of Prostate Cancer with TMPRSS2:ERG and Other ETS Fusions. Mol Cancer Res 2023; 21:14-23. [PMID: 36125519 PMCID: PMC9812892 DOI: 10.1158/1541-7786.mcr-22-0446] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/30/2022] [Accepted: 09/15/2022] [Indexed: 02/03/2023]
Abstract
The most common somatic event in primary prostate cancer is a fusion between the androgen-related TMPRSS2 gene and the ERG oncogene. Tumors with these fusions, which occur early in carcinogenesis, have a distinctive etiology. A smaller subset of other tumors harbor fusions between TMPRSS2 and members of the ETS transcription factor family other than ERG. To assess the genomic similarity of tumors with non-ERG ETS fusions and those with fusions involving ERG, this study derived a transcriptomic signature of non-ERG ETS fusions and assessed this signature and ERG-related gene expression in 1,050 men with primary prostate cancer from three independent population-based and hospital-based studies. Although non-ERG ETS fusions involving ETV1, ETV4, ETV5, or FLI1 were individually rare, they jointly accounted for one in seven prostate tumors. Genes differentially regulated between non-ERG ETS tumors and tumors without ETS fusions showed similar differential expression when ERG tumors and tumors without ETS fusions were compared (differences explained: R2 = 69-77%), including ETS-related androgen receptor (AR) target genes. Differences appeared to result from similarities among ETS tumors rather than similarities among non-ETS tumors. Gene sets associated with ERG fusions were consistent with gene sets associated with non-ERG ETS fusions, including fatty acid and amino acid metabolism, an observation that was robust across cohorts. IMPLICATIONS Considering ETS fusions jointly may be useful for etiologic studies on prostate cancer, given that the transcriptome is profoundly impacted by ERG and non-ERG ETS fusions in a largely similar fashion, most notably genes regulating metabolic pathways.
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Affiliation(s)
- Konrad H. Stopsack
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Xiaofeng A. Su
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA
| | - J. Bailey Vaselkiv
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Rebecca E. Graff
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA., Division of Research, Kaiser Permanente Northern California, Oakland, CA, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Ericka M. Ebot
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Andreas Pettersson
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Rosina T. Lis
- Department of Pathology and Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA
| | - Michelangelo Fiorentino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, Pathology Unit, Addarii Institute, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Massimo Loda
- Department of Pathology, Weill Cornell Medical College, New York, NY
| | - Kathryn L. Penney
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Tamara L. Lotan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Lorelei A. Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
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Zhou CD, Pettersson A, Plym A, Tyekucheva S, Penney KL, Sesso HD, Kantoff PW, Mucci LA, Stopsack KH. Differences in Prostate Cancer Transcriptomes by Age at Diagnosis: Are Primary Tumors from Older Men Inherently Different? Cancer Prev Res (Phila) 2022; 15:815-825. [PMID: 36125434 PMCID: PMC9722523 DOI: 10.1158/1940-6207.capr-22-0212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/03/2022] [Accepted: 09/01/2022] [Indexed: 01/31/2023]
Abstract
Older age at diagnosis is consistently associated with worse clinical outcomes in prostate cancer. We sought to characterize gene expression profiles of prostate tumor tissue by age at diagnosis. We conducted a discovery analysis in The Cancer Genome Atlas prostate cancer dataset (n = 320; 29% of men >65 years at diagnosis), using linear regressions of age at diagnosis and mRNA expression and adjusting for TMPRSS2:ERG fusion status and race. This analysis identified 13 age-related candidate genes at FDR < 0.1, six of which were also found in an analysis additionally adjusted for Gleason score. We then validated the 13 age-related genes in a transcriptome study nested in the Health Professionals Follow-up Study and Physicians' Health Study (n = 374; 53% of men >65 years). Gene expression differences by age in the 13 candidate genes were directionally consistent, and age at diagnosis was weakly associated with the 13-gene score. However, the age-related genes were not consistently associated with risk of metastases and prostate cancer-specific death. Collectively, these findings argue against tumor genomic differences as a main explanation for age-related differences in prostate cancer prognosis. PREVENTION RELEVANCE Older age at diagnosis is consistently associated with worse clinical outcomes in prostate cancer. This study with independent discovery and validation sets and long-term follow-up suggests that prevention of lethal prostate cancer should focus on implementing appropriate screening, staging, and treatment among older men without expecting fundamentally different tumor biology.
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Affiliation(s)
- Charlie D. Zhou
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Andreas Pettersson
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Anna Plym
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden,Department of Urology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Svitlana Tyekucheva
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kathryn L. Penney
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Howard D. Sesso
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Division of Preventative Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Philip W. Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Convergent Therapeutics Inc., Cambridge, MA, USA
| | - Lorelei A. Mucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Konrad H. Stopsack
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Oku Y, Madia F, Lau P, Paparella M, McGovern T, Luijten M, Jacobs MN. Analyses of Transcriptomics Cell Signalling for Pre-Screening Applications in the Integrated Approach for Testing and Assessment of Non-Genotoxic Carcinogens. Int J Mol Sci 2022; 23:ijms232112718. [PMID: 36361516 PMCID: PMC9659232 DOI: 10.3390/ijms232112718] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 12/03/2022] Open
Abstract
With recent rapid advancement of methodological tools, mechanistic understanding of biological processes leading to carcinogenesis is expanding. New approach methodologies such as transcriptomics can inform on non-genotoxic mechanisms of chemical carcinogens and can be developed for regulatory applications. The Organisation for the Economic Cooperation and Development (OECD) expert group developing an Integrated Approach to the Testing and Assessment (IATA) of Non-Genotoxic Carcinogens (NGTxC) is reviewing the possible assays to be integrated therein. In this context, we review the application of transcriptomics approaches suitable for pre-screening gene expression changes associated with phenotypic alterations that underlie the carcinogenic processes for subsequent prioritisation of downstream test methods appropriate to specific key events of non-genotoxic carcinogenesis. Using case studies, we evaluate the potential of gene expression analyses especially in relation to breast cancer, to identify the most relevant approaches that could be utilised as (pre-) screening tools, for example Gene Set Enrichment Analysis (GSEA). We also consider how to address the challenges to integrate gene panels and transcriptomic assays into the IATA, highlighting the pivotal omics markers identified for assay measurement in the IATA key events of inflammation, immune response, mitogenic signalling and cell injury.
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Affiliation(s)
- Yusuke Oku
- The Organisation for Economic Cooperation and Development (OECD), 2 Rue Andre Pascal, 75016 Paris, France
- Correspondence: (Y.O.); (M.N.J.)
| | - Federica Madia
- European Commission, Joint Research Centre (JRC), Via Enrico Fermi, 2749, 21027 Ispra, Italy
| | - Pierre Lau
- Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Martin Paparella
- Institute of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020 Innbruck, Austria
| | - Timothy McGovern
- US Food and Drug Administration (FDA), 10903 New Hampshire Avenue, Silver Spring, MD 20901, USA
| | - Mirjam Luijten
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, Bilthoven, 3721 MA Utrecht, The Netherlands
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazard (CRCE), Public Health England (PHE), Chilton OX11 0RQ, Oxfordshire, UK
- Correspondence: (Y.O.); (M.N.J.)
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Ma TM, Romero T, Nickols NG, Rettig MB, Garraway IP, Roach M, Michalski JM, Pisansky TM, Lee WR, Jones CU, Rosenthal SA, Wang C, Hartman H, Nguyen PL, Feng FY, Boutros PC, Saigal C, Chamie K, Jackson WC, Morgan TM, Mehra R, Salami SS, Vince R, Schaeffer EM, Mahal BA, Dess RT, Steinberg ML, Elashoff D, Sandler HM, Spratt DE, Kishan AU. Comparison of Response to Definitive Radiotherapy for Localized Prostate Cancer in Black and White Men: A Meta-analysis. JAMA Netw Open 2021; 4:e2139769. [PMID: 34964855 PMCID: PMC8717118 DOI: 10.1001/jamanetworkopen.2021.39769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
IMPORTANCE Black men have a 2-fold increased risk of dying from prostate cancer compared with White men. However, race-specific differences in response to initial treatment remain unknown. OBJECTIVE To compare overall and treatment-specific outcomes of Black and White men with localized prostate cancer receiving definitive radiotherapy (RT). DATA SOURCES A systematic search was performed of relevant published randomized clinical trials conducted by the NRG Oncology/Radiation Therapy Oncology Group between January 1, 1990, and December 31, 2010. This meta-analysis was performed from July 1, 2019, to July 1, 2021. STUDY SELECTION Randomized clinical trials of definitive RT for patients with localized prostate cancer comprising a substantial number of Black men (self-identified race) enrolled that reported on treatment-specific and overall outcomes. DATA EXTRACTION AND SYNTHESIS Individual patient data were obtained from 7 NRG Oncology/Radiation Therapy Oncology Group randomized clinical trials evaluating definitive RT with or without short- or long-term androgen deprivation therapy. Unadjusted Fine-Gray competing risk models, with death as a competing risk, were developed to evaluate the cumulative incidences of end points. Cox proportional hazards models were used to evaluate differences in all-cause mortality and the composite outcome of distant metastasis (DM) or death. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline was followed. MAIN OUTCOMES AND MEASURES Subdistribution hazard ratios (sHRs) of biochemical recurrence (BCR), DM, and prostate cancer-specific mortality (PCSM). RESULTS A total of 8814 patients (1630 [18.5%] Black and 7184 [81.5%] White) were included; mean (SD) age was 69.1 (6.8) years. Median follow-up was 10.6 (IQR, 8.0-17.8) years for surviving patients. At enrollment, Black men were more likely to have high-risk disease features. However, even without adjustment, Black men were less likely to experience BCR (sHR, 0.88; 95% CI, 0.58-0.91), DM (sHR, 0.72; 95% CI, 0.58-0.91), or PCSM (sHR, 0.72; 95% CI, 0.54-0.97). No significant differences in all-cause mortality were identified (HR, 0.99; 95% CI, 0.92-1.07). Upon adjustment, Black race remained significantly associated with improved BCR (adjusted sHR, 0.79; 95% CI, 0.72-0.88; P < .001), DM (adjusted sHR, 0.69; 95% CI, 0.55-0.87; P = .002), and PCSM (adjusted sHR, 0.68; 95% CI, 0.50-0.93; P = .01). CONCLUSIONS AND RELEVANCE The findings of this meta-analysis suggest that Black men enrolled in randomized clinical trials present with more aggressive disease but have better BCR, DM, and PCSM with definitive RT compared with White men, suggesting that other determinants of outcome, such as access to care, are important factors of achieving racial equity.
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Affiliation(s)
- Ting Martin Ma
- Department of Radiation Oncology, University of California, Los Angeles (UCLA)
| | | | - Nicholas G. Nickols
- Department of Radiation Oncology, University of California, Los Angeles (UCLA)
- Department of Radiation Oncology, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, California
| | - Matthew B. Rettig
- Division of Hematology and Oncology, David Geffen School of Medicine, UCLA
- Division of Hematology and Oncology, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, California
| | - Isla P. Garraway
- Department of Urology, UCLA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, UCLA
- Division of Urology, Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, California
| | - Mack Roach
- Department of Radiation Oncology, Helen Diller Comprehensive Cancer Center, University of California, San Francisco
| | - Jeff M. Michalski
- Washington University School of Medicine in St Louis, St Louis, Missouri
| | | | - W. Robert Lee
- Department of Radiation Oncology, Duke University School of Medicine, Durham, North Carolina
| | | | - Seth A. Rosenthal
- Sutter Medical Group and Sutter Cancer Centers, Roseville, California
| | - Chenyang Wang
- Department of Radiation Oncology, Division of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston
| | - Holly Hartman
- Department of Radiation Oncology, University of Michigan, Ann Arbor
| | - Paul L. Nguyen
- Department of Radiation Oncology, Brigham and Women’s Hospital/Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Felix Y. Feng
- Department of Radiation Oncology, Helen Diller Comprehensive Cancer Center, University of California, San Francisco
| | - Paul C. Boutros
- Department of Urology, UCLA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, UCLA
- Department of Human Genetics, UCLA
| | | | | | | | - Todd M. Morgan
- Department of Urology, University of Michigan, Ann Arbor
| | - Rohit Mehra
- Department of Pathology, University of Michigan, Ann Arbor
| | | | - Randy Vince
- Department of Urology, University of Michigan, Ann Arbor
| | - Edward M. Schaeffer
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Brandon A. Mahal
- Department of Radiation Oncology, Brigham and Women’s Hospital/Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Robert T. Dess
- Department of Radiation Oncology, University of Michigan, Ann Arbor
| | | | | | - Howard M. Sandler
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Daniel E. Spratt
- Department of Radiation Oncology, University Hospitals Seidman Cancer Center, Cleveland Medical Center, Cleveland, Ohio
| | - Amar U. Kishan
- Department of Radiation Oncology, University of California, Los Angeles (UCLA)
- Department of Urology, UCLA
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Yamoah K, Asamoah FA, Abrahams AOD, Awasthi S, Mensah JE, Dhillon J, Mahal BA, Gueye SM, Jalloh M, Farahani SJ, Lal P, Rebbeck TR, Yarney J. Prostate tumors of native men from West Africa show biologically distinct pathways-A comparative genomic study. Prostate 2021; 81:1402-1410. [PMID: 34529278 PMCID: PMC8563425 DOI: 10.1002/pros.24238] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 08/02/2021] [Accepted: 08/30/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND Native African men (NAM) experience a disproportionate burden of prostate cancer (PCa) and have higher mortality rates compared to European American men (EAM). While socioeconomic status has been implicated as a driver of this disparity, little is known about the genomic mechanisms and distinct biological pathways that are associated with PCa of native men of African origin. METHODS To understand biological factors that contribute to this disparity we utilized a total of 406 multi-institutional localized PCa samples, collected by Men of African Descent and Carcinoma of the Prostate biospecimen network and Moffitt Cancer Center/University of Pennsylvania Health science system. We performed comparative genomics and immunohistochemistry to identify the biomarkers that are highly enriched in NAM from west Africa and compared them with African American Men (AAM) and EAM. Quantified messenger RNA expression and Median H scores based on immune reactivity of staining cells, were compared using Mann Whitney test. For gene expression analysis, p values were further adjusted for multiple comparisons using false discovery rates. RESULTS Immunohistochemical analysis on selected biomarkers showed a consistent association between ETS related gene (ERG) status and race with 83% of NAM exhibiting tumors that lacked TMPRSS2-ERG translocation (ERGnegative ) as compared to AAM (71%) and EAM (52%). A higher proportion of NAM (29%) were also found to be double negative (ERGnegative and PTENLoss ) as compared to AAM (6%) and EAM (7%). NAM tumors had significantly higher immunoreactivity (H-score) for PSMA, and EZH2, whereas they have lower H-score for PTEN, MYC, AR, RB and Racemase, (all p < .05). Comparative genomics revealed that NAM had significant transcriptomic variability in AR-activity score. In pathways enrichment analysis NAM tumors exhibited the enrichment of proinflammatory pathways including cytokine, interleukins, inflammatory response, and nuclear factor kappa B signaling. CONCLUSIONS Prostate tumors in NAM are genomically distinct and are characterized by the dysregulation of several biomarkers. Furthermore, these tumors are also highly enriched for the major proinflammatory pathways. These distinct biological features may have implications for diagnosis and response to targeted therapy among Black men, globally.
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Affiliation(s)
- Kosj Yamoah
- Department of Radiation Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Francis A. Asamoah
- National Center for Radiotherapy, Oncology and Nuclear Medicine, Korle Bu Teaching Hospital Accra, Ghana, West Africa
| | - Afua O. D. Abrahams
- Department of Pathology, University of Ghana Medical School, Korle bu Teaching Hospital, Ghana, West Africa
| | - Shivanshu Awasthi
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - James E. Mensah
- Department of Surgery, University of Ghana Medical School, Korle bu Teaching Hospital, Ghana, West Africa
| | - Jasreman Dhillon
- Department of Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Brandon A. Mahal
- Department of Radiation Oncology, University of Miami, Miami, FL, USA
| | | | | | | | - Priti Lal
- Department of Pathology, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy R. Rebbeck
- Dana Farber Cancer Institute and Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Joel Yarney
- National Center for Radiotherapy, Oncology and Nuclear Medicine, Korle Bu Teaching Hospital Accra, Ghana, West Africa
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Abraham-Miranda J, Awasthi S, Yamoah K. Immunologic disparities in prostate cancer between American men of African and European descent. Crit Rev Oncol Hematol 2021; 164:103426. [PMID: 34273500 DOI: 10.1016/j.critrevonc.2021.103426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/18/2020] [Accepted: 07/12/2021] [Indexed: 11/27/2022] Open
Abstract
Health disparities between American men of African and European descent (AA and EA, respectively) can be attributed to multiple factors, including disparities in socioeconomic status, access to healthcare, lifestyle, ancestry, and molecular aberrations. Numerous clinical trials and research studies are being performed to identify new and better therapeutic approaches to detect and treat prostate cancer. Of potential concern is the fact that the majority of the patients enrolled on these trials are EA. This disproportionate enrollment of EA could have implications when disease management recommendations are proposed without regard to the existing disparities in prostate cancer between races. With increasing advancements in immunotherapies, the immunological disparities between men of diverse ethnicities will need to be fully explored to develop novel and effective therapeutic approaches for prostate cancer patients globally. To help address this need, this review fully describes inequalities in prostate cancer at the immunological level between AA and EA.
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Affiliation(s)
- Julieta Abraham-Miranda
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Shivanshu Awasthi
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Kosj Yamoah
- Department of Radiation Oncology, 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.
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7
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Yamoah K, Lal P, Awasthi S, Naghavi AO, Rounbehler RJ, Gerke T, Berglund AE, Pow-Sang JM, Schaeffer EM, Dhillon J, Park JY, Rebbeck TR. TMPRSS2-ERG fusion impacts anterior tumor location in men with prostate cancer. Prostate 2021; 81:109-117. [PMID: 33141952 PMCID: PMC7810127 DOI: 10.1002/pros.24086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/16/2020] [Accepted: 10/23/2020] [Indexed: 11/06/2022]
Abstract
BACKGROUND In prostate cancer (PCa), lack of androgen receptor (AR) regulated TMPRSS2-ETS-related gene (ERG) gene fusion (ERGnegative ) status has been associated with African American race; however, the implications of ERG status for the location of dominant tumors within the prostate remains understudied. METHODS An African American-enriched multiinstitutional cohort of 726 PCa patients consisting of both African American men (AAM; n = 254) and European American men (EAM; n = 472) was used in the analyses. Methods of categorical analysis were used. Messenger RNA (mRNA) expression differences between anterior and posterior tumor lesions were analyzed using Wilcoxon rank-sum tests with multiple comparison corrections. RESULTS Anti-ERG immunohistochemistry staining showed that the association between ERG status and anterior tumors is independent of race and is consistently robust for both AAM (ERGnegative 81.4% vs. ERGpositive 18.6%; p = .005) and EAM (ERGnegative 60.4% vs. ERGpositive 39.6%; p < .001). In a multivariable model, anterior tumors were more likely to be IHC-ERGnegative (odds ratio [OR]: 3.20; 95% confidence interval [CI]: 2.14-4.78; p < .001). IHC-ERGnegative were also more likely to have high-grade tumors (OR: 1.73; 95% CI: 1.06-2.82; p = .02). In the exploratory genomic analysis, mRNA expression of location-dependent genes is highly influenced by ERG status and African American race. However, tumor location did not impact the expression of AR or the major canonical AR-target genes (KLK3, AMACR, and MYC). CONCLUSIONS ERGnegative tumor status is the strongest predictor of anterior prostate tumors, regardless of race. Furthermore, AR expression and canonical AR signaling do not impact tumor location.
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Affiliation(s)
- Kosj Yamoah
- H Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Priti Lal
- The Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | | | | | | | - Travis Gerke
- H Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | | | | | | | | | - Jong Y. Park
- H Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Timothy R. Rebbeck
- Dana Farber Cancer Institute and Harvard TH Chan School of Public Health, Boston, MA
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Berglund AE, Putney RM, Creed JH, Aden-Buie G, Gerke TA, Rounbehler RJ. Accessible Pipeline for Translational Research Using TCGA: Examples of Relating Gene Mechanism to Disease-Specific Outcomes. Methods Mol Biol 2021; 2194:127-142. [PMID: 32926365 DOI: 10.1007/978-1-0716-0849-4_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bioinformatic scientists are often asked to do widespread analyses of publicly available datasets in order to identify genetic alterations in cancer for genes of interest; therefore, we sought to create a set of tools to conduct common statistical analyses of The Cancer Genome Atlas (TCGA) data. These tools have been developed in response to requests from our collaborators to ask questions, validate findings, and better understand the function of their gene of interest. We describe here what data we have used, how to obtain it, and what figures we have found useful.
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Affiliation(s)
- Anders E Berglund
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
| | - Ryan M Putney
- Department of Bioinformatics and Biostatistics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Jordan H Creed
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Garrick Aden-Buie
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Travis A Gerke
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Robert J Rounbehler
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
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Stopsack KH, Huang Y, Tyekucheva S, Gerke TA, Bango C, Elfandy H, Bowden M, Penney KL, Roberts TM, Parmigiani G, Kantoff PW, Mucci LA, Loda M. Multiplex Immunofluorescence in Formalin-Fixed Paraffin-Embedded Tumor Tissue to Identify Single-Cell-Level PI3K Pathway Activation. Clin Cancer Res 2020; 26:5903-5913. [PMID: 32913135 DOI: 10.1158/1078-0432.ccr-20-2000] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/11/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE Identifying cancers with high PI3K pathway activity is critical for treatment selection and eligibility into clinical trials of PI3K inhibitors. Assessments of tumor signaling pathway activity need to consider intratumoral heterogeneity and multiple regulatory nodes. EXPERIMENTAL DESIGN We established a novel, mechanistically informed approach to assessing tumor signaling pathways by quantifying single-cell-level multiplex immunofluorescence using custom algorithms. In a proof-of-concept study, we stained archival formalin-fixed, paraffin-embedded (FFPE) tissue from patients with primary prostate cancer in two prospective cohort studies, the Health Professionals Follow-up Study and the Physicians' Health Study. PTEN, stathmin, and phospho-S6 were quantified on 14 tissue microarrays as indicators of PI3K activation to derive cell-level PI3K scores. RESULTS In 1,001 men, 988,254 tumor cells were assessed (median, 743 per tumor; interquartile range, 290-1,377). PI3K scores were higher in tumors with PTEN loss scored by a pathologist, higher Gleason grade, and a new, validated bulk PI3K transcriptional signature. Unsupervised machine-learning approaches resulted in similar clustering. Within-tumor heterogeneity in cell-level PI3K scores was high. During long-term follow-up (median, 15.3 years), rates of progression to metastases and death from prostate cancer were twice as high in the highest quartile of PI3K activation compared with the lowest quartile (hazard ratio, 2.04; 95% confidence interval, 1.13-3.68). CONCLUSIONS Our novel pathway-focused approach to quantifying single-cell-level immunofluorescence in FFPE tissue identifies prostate tumors with PI3K pathway activation that are more aggressive and may respond to pathway inhibitors.
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Affiliation(s)
- Konrad H Stopsack
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Ying Huang
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Svitlana Tyekucheva
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Travis A Gerke
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Clyde Bango
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Habiba Elfandy
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Michaela Bowden
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Kathryn L Penney
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Thomas M Roberts
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Giovanni Parmigiani
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Philip W Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Massimo Loda
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. .,Department of Pathology, Weill Cornell Medical College, New York, New York.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,New York Genome Center, New York, New York
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10
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Abstract
PURPOSE Most prostate cancer in African American men lacks the ETS (E26 transforming specific) family fusion event (ETS-). We aimed to establish clinically relevant biomarkers in African American men by studying ETS dependent gene expression patterns to identified race specific genes predictive of outcomes. MATERIALS AND METHODS Two multicenter cohorts of a total of 1,427 men were used for the discovery and validation (635 and 792 men, respectively) of race specific predictive biomarkers. We used false discovery rate adjusted q values to identify race and ETS dependent genes which were differentially expressed in African American men who experienced biochemical recurrence within 5 years. Principal component modeling along with survival analysis was done to assess the accuracy of the gene panel in predicting recurrence. RESULTS We identified 3,047 genes which were differentially expressed based on ETS status. Of these genes 362 were differentially expressed in a race specific manner (false discovery rate 0.025 or less). A total of 81 genes were race specific and over expressed in African American men who experienced biochemical recurrence. The final gene panel included APOD, BCL6, EMP1, MYADM, SRGN and TIMP3. These genes were associated with 5-year biochemical recurrence (HR 1.97, 95% CI 1.27-3.06, p = 0.002) and they improved the predictive accuracy of clinicopathological variables only in African American men (60-month time dependent AUC 0.72). CONCLUSIONS In an effort to elucidate biological features associated with prostate cancer aggressiveness in African American men we identified ETS dependent biomarkers predicting early onset biochemical recurrence only in African American men. Thus, these ETS dependent biomarkers representing ideal candidates for biomarkers of aggressive disease in this patient population.
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