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Jiagge E, Jin DX, Newberg JY, Perea-Chamblee T, Pekala KR, Fong C, Waters M, Ma D, Dei-Adomakoh Y, Erb G, Arora KS, Maund SL, Njiraini N, Ntekim A, Kim S, Bai X, Thomas M, van Eeden R, Hegde P, Jee J, Chakravarty D, Schultz N, Berger MF, Frampton GM, Sokol ES, Carrot-Zhang J. Tumor sequencing of African ancestry reveals differences in clinically relevant alterations across common cancers. Cancer Cell 2023; 41:1963-1971.e3. [PMID: 37890492 PMCID: PMC11097212 DOI: 10.1016/j.ccell.2023.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 08/02/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023]
Abstract
Cancer genomes from patients with African (AFR) ancestry have been poorly studied in clinical research. We leverage two large genomic cohorts to investigate the relationship between genomic alterations and AFR ancestry in six common cancers. Cross-cancer type associations, such as an enrichment of MYC amplification with AFR ancestry in lung, breast, and prostate cancers, and depletion of BRAF alterations are observed in colorectal and pancreatic cancers. There are differences in actionable alterations, such as depletion of KRAS G12C and EGFR L858R, and enrichment of ROS1 fusion with AFR ancestry in lung cancers. Interestingly, in lung cancer, KRAS mutations are less common in both smokers and non-smokers with AFR ancestry, whereas the association of TP53 mutations with AFR ancestry is only seen in smokers, suggesting an ancestry-environment interaction that modifies driver rates. Our study highlights the need to increase representation of patients with AFR ancestry in drug development and biomarker discovery.
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Affiliation(s)
- Evelyn Jiagge
- Hematology/Oncology Division, Department of Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Dexter X. Jin
- Cancer Genomics Research, Foundation Medicine, Inc., Cambridge, MA, USA
| | - Justin Y. Newberg
- Cancer Genomics Research, Foundation Medicine, Inc., Cambridge, MA, USA
| | - Tomin Perea-Chamblee
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kelly R. Pekala
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher Fong
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michele Waters
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Ma
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Gilles Erb
- Global Product Development Medical Affairs – Oncology, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Kanika S. Arora
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer, New York, NY, USA
| | - Sophia L. Maund
- Computational Sciences, Genentech, Inc., South San Francisco, CA, USA
| | - Njoki Njiraini
- Department of Oncology, Kenyatta University Teaching Research and Referral Hospital, Nairobi, Kenya
| | - Atara Ntekim
- Department of Radiation Oncology, University of Ibadan, Ibadan, Nigeria
| | - Susie Kim
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xuechun Bai
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marlene Thomas
- Global Product Development Medical Affairs – Oncology, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Ronwyn van Eeden
- Department of Medical Oncology, Chris Hani Academic Baragwanath Hospital, Johannesburg, South Africa
| | - Priti Hegde
- Cancer Genomics Research, Foundation Medicine, Inc., Cambridge, MA, USA
| | - Justin Jee
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F. Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Ethan S. Sokol
- Cancer Genomics Research, Foundation Medicine, Inc., Cambridge, MA, USA
| | - Jian Carrot-Zhang
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinial Genetics, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Tang W, Zhang F, Byun JS, Dorsey TH, Yfantis HG, Ajao A, Liu H, Pichardo MS, Pichardo CM, Harris AR, Yang XR, Figueroa JD, Sayed S, Makokha FW, Ambs S. Population-specific Mutation Patterns in Breast Tumors from African American, European American, and Kenyan Patients. CANCER RESEARCH COMMUNICATIONS 2023; 3:2244-2255. [PMID: 37902422 PMCID: PMC10629394 DOI: 10.1158/2767-9764.crc-23-0165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 08/31/2023] [Accepted: 10/24/2023] [Indexed: 10/31/2023]
Abstract
Women of African descent have the highest breast cancer mortality in the United States and are more likely than women from other population groups to develop an aggressive disease. It remains uncertain to what extent breast cancer in Africa is reminiscent of breast cancer in African American or European American patients. Here, we performed whole-exome sequencing of genomic DNA from 191 breast tumor and non-cancerous adjacent tissue pairs obtained from 97 African American, 69 European American, 2 Asian American, and 23 Kenyan patients. Our analysis of the sequencing data revealed an elevated tumor mutational burden in both Kenyan and African American patients, when compared with European American patients. TP53 mutations were most prevalent, particularly in African American patients, followed by PIK3CA mutations, which showed similar frequencies in European American, African American, and the Kenyan patients. Mutations targeting TBX3 were confined to European Americans and those targeting the FBXW7 tumor suppressor to African American patients whereas mutations in the ARID1A gene that are known to confer resistance to endocrine therapy were distinctively enriched among Kenyan patients. A Kyoto Encyclopedia of Genes and Genomes pathway analysis could link FBXW7 mutations to an increased mitochondrial oxidative phosphorylation capacity in tumors carrying these mutations. Finally, Catalogue of Somatic Mutations in Cancer (COSMIC) mutational signatures in tumors correlated with the occurrence of driver mutations, immune cell profiles, and neighborhood deprivation with associations ranging from being mostly modest to occasionally robust. To conclude, we found mutational profiles that were different between these patient groups. The differences concentrated among genes with low mutation frequencies in breast cancer. SIGNIFICANCE The study describes differences in tumor mutational profiles between African American, European American, and Kenyan breast cancer patients. It also investigates how these profiles may relate to the tumor immune environment and the neighborhood environment in which the patients had residence. Finally, it describes an overrepresentation of ARID1A gene mutations in breast tumors of the Kenyan patients.
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Affiliation(s)
- Wei Tang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
- Data Science & Artificial Intelligence, R&D, AstraZeneca, Gaithersburg, Maryland
| | - Flora Zhang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
- Colgate University, Hamilton, New York
| | - Jung S. Byun
- Division of Intramural Research, National Institute of Minority Health and Health Disparities, NIH, Bethesda, Maryland
| | - Tiffany H. Dorsey
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Harris G. Yfantis
- Department of Pathology, University of Maryland Medical Center and Veterans Affairs, Maryland Care System, Baltimore, Maryland
| | - Anuoluwapo Ajao
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Huaitian Liu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Margaret S. Pichardo
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
- Department of Surgery, Hospital of the University of Pennsylvania, Penn Medicine, Philadelphia, Pennsylvania
| | - Catherine M. Pichardo
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
- Division of Cancer Control and Population Sciences, NCI, NIH, Rockville, Maryland
| | - Alexandra R. Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, Rockville, Maryland
| | - Xiaohong R. Yang
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, Rockville, Maryland
| | - Jonine D. Figueroa
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, Rockville, Maryland
| | | | | | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
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3
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Feng J, Lan Y, Liu F, Yuan Y, Ge J, Wei S, Luo H, Li J, Luo T, Bian X. Combination of genomic instability score and TP53 status for prognosis prediction in lung adenocarcinoma. NPJ Precis Oncol 2023; 7:110. [PMID: 37907595 PMCID: PMC10618567 DOI: 10.1038/s41698-023-00465-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 10/13/2023] [Indexed: 11/02/2023] Open
Abstract
The genomic instability (GI) /homologous recombination deficiency (HRD) score, calculated as the sum of the events of loss of heterozygosity (LOH), large-scale state transition (LST) and telomere allele imbalance (TAI), is used to guide the choice of treatment in several cancers, but its relationship with genomic features, clinicopathological characteristics and prognosis in lung cancer is poorly understood, which could lead to population bias in prospective studies. We retrospectively analyzed 1011 lung cancer patients whose tumor samples were successfully profiled by high-throughput sequencing panel including GI/HRD score. Alterations of many cancer suppressor genes were associated with higher GI/HRD scores, biallelic inactivation of TP53 was correlated with a high GI/HRD score. A combination of two gene alterations exhibited a higher GI/HRD scores than single gene alterations. The GI/HRD score was associated with advanced stages in lung adenocarcinoma but not in lung squamous cell carcinoma. Furthermore, patients with higher GI/HRD scores had significantly shorter overall survival and progression-free survival than patients with lower GI/HRD scores. Finally, patients with a combination of a higher GI/HRD scores and TP53 alteration exhibited an extremely poor prognosis compared with patients with a lower GI/HRD scores and wild-type TP53 (overall survival, training cohort, hazard ratio (HR) = 8.56, P < 0.001; validation cohort, HR = 6.47, P < 0.001; progression-free survival, HR = 4.76, P < 0.001). Our study revealed the prognostic value of the GI/HRD score in lung adenocarcinoma, but not for all lung cancer. Moreover, the combination of the GI/HRD score and TP53 status could be a promising strategy to predict the prognosis of patients with lung adenocarcinoma.
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Affiliation(s)
- Juan Feng
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Yang Lan
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Feng Liu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Ye Yuan
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Jia Ge
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Sen Wei
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China
| | - Hu Luo
- Department of Respiratory and Critical Care Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Jianjun Li
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Tao Luo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China.
| | - Xiuwu Bian
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University) and Key Laboratory of Tumor Immunopathology, Ministry of Education of China, 400038, Chongqing, China.
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Li P, Kane K, Wolf FM, Berry AB, Gadgeel S, Pilling A. Race-Associated Genomic Correlates of Therapeutic Response in African American Patients With Non-Small-Cell Lung Cancer. JCO Precis Oncol 2023; 7:e2300155. [PMID: 37625101 DOI: 10.1200/po.23.00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/12/2023] [Accepted: 07/17/2023] [Indexed: 08/27/2023] Open
Abstract
PURPOSE African American individuals are disproportionately affected by lung cancer in terms of incidence and mortality. In oncogene-driven non-small-cell lung cancer (NSCLC), emerging evidence indicates that underlying molecular heterogeneity, which can be affected by ancestry, contributes to variable drug sensitivity and therapeutic responses. The purpose of this study was to evaluate race-associated differences in reported treatment decisions, therapeutic outcomes, and molecular features in KRAS- and EGFR-mutant NSCLC. MATERIALS AND METHODS This is a retrospective study using real-world clinical-genomic data from health systems in the United States to evaluate race-associated outcomes in advanced-stage KRAS- or EGFR-driven NSCLC. Our overall objectives were to evaluate race-associated therapeutic outcomes and to describe molecular features in non-Hispanic Black (NHB) and non-Hispanic White (NHW) patients with NSCLC. RESULTS A total of 723 NSCLC patients with KRAS and 315 patients with EGFR oncogenic mutations were evaluated. In KRAS-mutant patients, variable outcomes were observed in NHB and NHW patients on the basis of receiving chemotherapy alone or in combination with immune checkpoint inhibitors. NHB patients received treatment at significantly lower rates compared with NHW patients. In the EGFR-mutant cohort, NHB and NHW patients received EGFR-targeted agents at similar rates, and overall survival was not significantly different. Race-associated differences in molecular features included a higher frequency of TP53 comutation in KRAS-mutant NHB patients and higher prevalence of EGFR G719S subtype in NHB patients. CONCLUSION In a real-world cohort of patients with NSCLC, we identified race-associated differences in therapeutic outcomes and described molecular characteristics in NHB and NHW patients with NSCLC. To proactively identify patients most likely to respond to systemic therapies, a more comprehensive approach is needed to help guide therapy selection in individualized patient populations.
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Affiliation(s)
- Pin Li
- Department of Public Health Sciences, Henry Ford Health System, Henry Ford Cancer Institute, Detroit, MI
| | | | | | | | - Shirish Gadgeel
- Department of Internal Medicine, Henry Ford Health System, Henry Ford Cancer Institute, Detroit, MI
| | - Amanda Pilling
- Department of Internal Medicine, Henry Ford Health System, Henry Ford Cancer Institute, Detroit, MI
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Li L, Gu Y, Zhang M, Shi X, Li Z, Xu X, Sun T, Dong Y, Xue C, Zhu X, Lv R, Jiao K, Ji X, Wang LJ, Zhang Y, Liang Z, Jin Y, Yin R, Wu M, Liang H. HRD effects on first-line adjuvant chemotherapy and PARPi maintenance therapy in Chinese ovarian cancer patients. NPJ Precis Oncol 2023; 7:51. [PMID: 37258600 DOI: 10.1038/s41698-023-00402-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/15/2023] [Indexed: 06/02/2023] Open
Abstract
Homologous recombination deficiency (HRD) testing has been approved by FDA for selecting epithelial ovarian cancer (EOC) patients who may benefit from the first-line poly (ADP-ribose) polymerase inhibitor (PARPi) maintenance therapy. However, the effects of HRD on the clinical outcomes of first-line chemotherapy and first-line PARPi maintenance therapy have not been rigorously evaluated in Chinese EOC patients. Here, we developed an HRD assay and applied it to two large retrospectively collected Chinese EOC patient cohorts. In the first-line adjuvant chemotherapy cohort (FACT, N = 380), HRD status significantly improved PFS (median, 15.6 months vs. 9.4 months; HR, 0.688; 95% CI, 0.526-0.899; P = 0.003) and OS (median, 89.5 months vs. 60.9 months; HR, 0.636; 95% CI, 0.423-0.955; P = 0.008). In the first-line PARPi maintenance therapy cohort (FPMT, N = 83), HRD status significantly improved PFS (median, NA vs. 12 months; HR, 0.438; 95% CI, 0.201-0.957; P = 0.033) and OS (median, NA vs. NA months; HR, 0.12; 95% CI, 0.029-0.505; P = 0.001). Our results demonstrate that HRD status is a significant predictor for PFS and OS in both first-line chemotherapy and first-line PARPi maintenance therapy, providing strong real-world evidence for conducting genetic testing and improving clinical recommendations for Chinese EOC patients.
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Affiliation(s)
- Lei Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China
| | - Yu Gu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China
| | - Mengpei Zhang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xiaohua Shi
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhe Li
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Xinyun Xu
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Tianqi Sun
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Yu Dong
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Chao Xue
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Xiaoru Zhu
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Ran Lv
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Kai Jiao
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Xuwo Ji
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Li-Juan Wang
- Department of Gynecological Oncology, Sun Yat-Sen Memorial Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Yang Zhang
- Precision Scientific (Beijing) Co., Ltd., Beijing, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Ying Jin
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China.
| | - Rutie Yin
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.
| | - Ming Wu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- National Clinical Research Center for Obstetric & Gynecologic Diseases, Beijing, China.
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Boyd AE, Grizzard PJ, Hylton Rorie K, Lima S. Lipidomic Profiling Reveals Biological Differences between Tumors of Self-Identified African Americans and Non-Hispanic Whites with Cancer. Cancers (Basel) 2023; 15:2238. [PMID: 37190166 PMCID: PMC10136787 DOI: 10.3390/cancers15082238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/27/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
In the US, the incidence and mortality of many cancers are disproportionately higher in African Americans (AA). Yet, AA remain poorly represented in molecular studies investigating the roles that biological factors might play in the development, progression, and outcomes of many cancers. Given that sphingolipids, key components of mammalian cellular membranes, have well-established roles in the etiology of cancer progression, malignancy, and responses to therapy, we conducted a robust mass spectrometry analysis of sphingolipids in normal adjacent uninvolved tissues and tumors of self-identified AA and non-Hispanic White (NHW) males with cancers of the lung, colon, liver, and head and neck and of self-identified AA and NHW females with endometrial cancer. In these cancers, AA have worse outcomes than NHW. The goal of our study was to identify biological candidates to be evaluated in future preclinical studies targeting race-specific alterations in the cancers of AA. We have identified that various sphingolipids are altered in race-specific patterns, but more importantly, the ratios of 24- to 16-carbon fatty acyl chain-length ceramides and glucosylceramides are higher in the tumors of AA. As there is evidence that ceramides with 24-carbon fatty acid chain length promote cellular survival and proliferation, whereas 16-carbon chain length promote apoptosis, these results provide important support for future studies tailored to evaluate the potential roles these differences may play in the outcomes of AA with cancer.
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Affiliation(s)
- April E. Boyd
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Pamela J. Grizzard
- Tissue and Data Acquisition and Analysis Core, Virginia Commonwealth University, Richmond, VA 23298, USA
| | | | - Santiago Lima
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA
- Massey Cancer Center, Richmond, VA 23298, USA
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Telisnor G, DeRemer DL, Frimpong E, Agyare E, Allen J, Ricks-Santi L, Han B, George T, Rogers SC. Review of genetic and pharmacogenetic differences in cytotoxic and targeted therapies for pancreatic cancer in African Americans. J Natl Med Assoc 2023; 115:164-174. [PMID: 36801148 PMCID: PMC10639003 DOI: 10.1016/j.jnma.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/16/2022] [Accepted: 01/24/2023] [Indexed: 02/19/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is currently the third leading cause of cancer mortality and the incidence is projected to increase by 2030. Despite recent advances in its treatment, African Americans have a 50-60% higher incidence and 30% higher mortality rate when compared to European Americans possibly resulting from differences in socioeconomic status, access to healthcare, and genetics. Genetics plays a role in cancer predisposition, response to cancer therapeutics (pharmacogenetics), and in tumor behavior, making some genes targets for oncologic therapeutics. We hypothesize that the germline genetic differences in predisposition, drug response, and targeted therapies also impact PDAC disparities. To demonstrate the impact of genetics and pharmacogenetics on PDAC disparities, a review of the literature was performed using PubMed with variations of the following keywords: pharmacogenetics, pancreatic cancer, race, ethnicity, African, Black, toxicity, and the FDA-approved drug names: Fluoropyrimidines, Topoisomerase inhibitors, Gemcitabine, Nab-Paclitaxel, Platinum agents, Pembrolizumab, PARP-inhibitors, and NTRK fusion inhibitors. Our findings suggest that the genetic profiles of African Americans may contribute to disparities related to FDA approved chemotherapeutic response for patients with PDAC. We recommend a strong focus on improving genetic testing and participation in biobank sample donations for African Americans. In this way, we can improve our current understanding of genes that influence drug response for patients with PDAC.
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Affiliation(s)
- Guettchina Telisnor
- College of Pharmacy, CaRE(2) Health Equity Center, University of Florida, Gainesville, FL, USA
| | - David L DeRemer
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Esther Frimpong
- Department of Pharmaceutical Sciences, College of Pharmacy, Florida Agricultural and Mechanical University, Tallahassee, FL, USA
| | - Edward Agyare
- Department of Pharmaceutical Sciences, College of Pharmacy, Florida Agricultural and Mechanical University, Tallahassee, FL, USA
| | - John Allen
- College of Pharmacy, CaRE(2) Health Equity Center, University of Florida, Gainesville, FL, USA
| | - Luisel Ricks-Santi
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Bo Han
- Department of Surgery, College of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Thomas George
- Division of Hematology and Oncology, College of Medicine, University of Florida, 600 SW Archer Road, PO BOX 100278, Gainesville, FL 32610- 0278, USA
| | - Sherise C Rogers
- Division of Hematology and Oncology, College of Medicine, University of Florida, 600 SW Archer Road, PO BOX 100278, Gainesville, FL 32610- 0278, USA.
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8
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Belleau P, Deschênes A, Chambwe N, Tuveson DA, Krasnitz A. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 2023; 83:49-58. [PMID: 36351074 PMCID: PMC9811156 DOI: 10.1158/0008-5472.can-22-0682] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 09/23/2022] [Accepted: 11/02/2022] [Indexed: 11/10/2022]
Abstract
Genetic ancestry-oriented cancer research requires the ability to perform accurate and robust genetic ancestry inference from existing cancer-derived data, including whole-exome sequencing, transcriptome sequencing, and targeted gene panels, very often in the absence of matching cancer-free genomic data. Here we examined the feasibility and accuracy of computational inference of genetic ancestry relying exclusively on cancer-derived data. A data synthesis framework was developed to optimize and assess the performance of the ancestry inference for any given input cancer-derived molecular profile. In its core procedure, the ancestral background of the profiled patient is replaced with one of any number of individuals with known ancestry. The data synthesis framework is applicable to multiple profiling platforms, making it possible to assess the performance of inference specifically for a given molecular profile and separately for each continental-level ancestry; this ability extends to all ancestries, including those without statistically sufficient representation in the existing cancer data. The inference procedure was demonstrated to be accurate and robust in a wide range of sequencing depths. Testing of the approach in four representative cancer types and across three molecular profiling modalities showed that continental-level ancestry of patients can be inferred with high accuracy, as quantified by its agreement with the gold standard of deriving ancestry from matching cancer-free molecular data. This study demonstrates that vast amounts of existing cancer-derived molecular data are potentially amenable to ancestry-oriented studies of the disease without requiring matching cancer-free genomes or patient self-reported ancestry. SIGNIFICANCE The development of a computational approach that enables accurate and robust ancestry inference from cancer-derived molecular profiles without matching cancer-free data provides a valuable methodology for genetic ancestry-oriented cancer research.
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Affiliation(s)
- Pascal Belleau
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Astrid Deschênes
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Nyasha Chambwe
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, New York
| | - David A. Tuveson
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Alexander Krasnitz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
- Cancer Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
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9
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James BA, Williams JL, Nemesure B. A systematic review of genetic ancestry as a risk factor for incidence of non-small cell lung cancer in the US. Front Genet 2023; 14:1141058. [PMID: 37082203 PMCID: PMC10110850 DOI: 10.3389/fgene.2023.1141058] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/14/2023] [Indexed: 04/22/2023] Open
Abstract
Background: Non-Small Cell Lung Cancer (NSCLC), the leading cause of cancer-related death in the United States, is the most diagnosed form of lung cancer. While lung cancer incidence has steadily declined over the last decade, disparities in incidence and mortality rates persist among African American (AA), Caucasian American (CA), and Hispanic American (HA) populations. Researchers continue to explore how genetic ancestry may influence differential outcomes in lung cancer risk and development. The purpose of this evaluation is to highlight experimental research that investigates the differential impact of genetic mutations and ancestry on NSCLC incidence. Methods: This systematic review was conducted using PubMed and Google Scholar search engines. The following key search terms were used to select articles published between 2011 and 2022: "African/European/Latin American Ancestry NSCLC"; "Racial Disparities NSCLC"; "Genetic Mutations NSCLC"; "NSCLC Biomarkers"; "African Americans/Hispanic Americans/Caucasian Americans NSCLC incidence." Systematic reviews, meta-analyses, and studies outside of the US were excluded. A total of 195 articles were initially identified and after excluding 156 which did not meet eligibility criteria, 38 were included in this investigation. Results: Studies included in this analysis focused on racial/ethnic disparities in the following common genetic mutations observed in NSCLC: KRAS, EGFR, TP53, PIK3CA, ALK Translocations, ROS-1 Rearrangements, STK11, MET, and BRAF. Results across studies varied with respect to absolute differential expression. No significant differences in frequencies of specific genetic mutational profiles were noted between racial/ethnic groups. However, for HAs, lower mutational frequencies in KRAS and STK11 genes were observed. In genetic ancestry level analyses, multiple studies suggest that African ancestry is associated with a higher frequency of EGFR mutations. Conversely, Latin ancestry is associated with TP53 mutations. At the genomic level, several novel predisposing variants associated with African ancestry and increased risk of NSCLC were discovered. Family history among all racial/ethnic groups was also considered a risk factor for NSCLC. Conclusion: Results from racially and ethnically diverse studies can elucidate driving factors that may increase susceptibility and subsequent lung cancer risk across different racial/ethnic groups. Identification of biomarkers that can be used as diagnostic, prognostic, and therapeutic tools may help improve lung cancer survival among high-risk populations.
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10
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Perrotta F, Chino V, Allocca V, D’Agnano V, Bortolotto C, Bianco A, Corsico AG, Stella GM. Idiopathic pulmonary fibrosis and lung cancer: targeting the complexity of the pharmacological interconnection. Expert Rev Respir Med 2022; 16:1043-1055. [DOI: 10.1080/17476348.2022.2145948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Fabio Perrotta
- - Department of Translational Medical Sciences, University of Campania “L. Vanvitelli”, 80131, Napoli, Italy
- - U.O.C. Clinica Pneumologica “L. Vanvitelli”, A.O. dei Colli, Ospedale Monaldi, 80131, Napoli, Italy
| | - Vittorio Chino
- - University of Pavia Medical School, 27100 Pavia, Italy
- - Department of Medical Sciences and Infective Diseases, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo Foundation and University of Pavia Medical School, Pavia, Italy
| | - Valentino Allocca
- - Department of Translational Medical Sciences, University of Campania “L. Vanvitelli”, 80131, Napoli, Italy
- - U.O.C. Clinica Pneumologica “L. Vanvitelli”, A.O. dei Colli, Ospedale Monaldi, 80131, Napoli, Italy
| | - Vito D’Agnano
- - Department of Translational Medical Sciences, University of Campania “L. Vanvitelli”, 80131, Napoli, Italy
- - U.O.C. Clinica Pneumologica “L. Vanvitelli”, A.O. dei Colli, Ospedale Monaldi, 80131, Napoli, Italy
| | - Chandra Bortolotto
- - Dept. of Clinical-Surgical, Diagnostic and Paediatric Sciences, University of Pavia Medical School, Pavia, Italy
- - Department of Intensive Medicine, Unit of Radiology, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Andrea Bianco
- - Department of Translational Medical Sciences, University of Campania “L. Vanvitelli”, 80131, Napoli, Italy
- - U.O.C. Clinica Pneumologica “L. Vanvitelli”, A.O. dei Colli, Ospedale Monaldi, 80131, Napoli, Italy
| | - Angelo Guido Corsico
- - Department of Medical Sciences and Infective Diseases, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo Foundation and University of Pavia Medical School, Pavia, Italy
- - Dept. of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, Pavia, Italy
| | - Giulia Maria Stella
- - Department of Medical Sciences and Infective Diseases, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo Foundation and University of Pavia Medical School, Pavia, Italy
- - Dept. of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, Pavia, Italy
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11
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Steele CD, Abbasi A, Islam SMA, Bowes AL, Khandekar A, Haase K, Hames-Fathi S, Ajayi D, Verfaillie A, Dhami P, McLatchie A, Lechner M, Light N, Shlien A, Malkin D, Feber A, Proszek P, Lesluyes T, Mertens F, Flanagan AM, Tarabichi M, Van Loo P, Alexandrov LB, Pillay N. Signatures of copy number alterations in human cancer. Nature 2022; 606:984-991. [PMID: 35705804 PMCID: PMC9242861 DOI: 10.1038/s41586-022-04738-6] [Citation(s) in RCA: 146] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 04/07/2022] [Indexed: 12/15/2022]
Abstract
Gains and losses of DNA are prevalent in cancer and emerge as a consequence of inter-related processes of replication stress, mitotic errors, spindle multipolarity and breakage-fusion-bridge cycles, among others, which may lead to chromosomal instability and aneuploidy1,2. These copy number alterations contribute to cancer initiation, progression and therapeutic resistance3-5. Here we present a conceptual framework to examine the patterns of copy number alterations in human cancer that is widely applicable to diverse data types, including whole-genome sequencing, whole-exome sequencing, reduced representation bisulfite sequencing, single-cell DNA sequencing and SNP6 microarray data. Deploying this framework to 9,873 cancers representing 33 human cancer types from The Cancer Genome Atlas6 revealed a set of 21 copy number signatures that explain the copy number patterns of 97% of samples. Seventeen copy number signatures were attributed to biological phenomena of whole-genome doubling, aneuploidy, loss of heterozygosity, homologous recombination deficiency, chromothripsis and haploidization. The aetiologies of four copy number signatures remain unexplained. Some cancer types harbour amplicon signatures associated with extrachromosomal DNA, disease-specific survival and proto-oncogene gains such as MDM2. In contrast to base-scale mutational signatures, no copy number signature was associated with many known exogenous cancer risk factors. Our results synthesize the global landscape of copy number alterations in human cancer by revealing a diversity of mutational processes that give rise to these alterations.
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Affiliation(s)
- Christopher D Steele
- Research Department of Pathology, Cancer Institute, University College London, London, UK
| | - Ammal Abbasi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - S M Ashiqul Islam
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Amy L Bowes
- Research Department of Pathology, Cancer Institute, University College London, London, UK
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Kerstin Haase
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Shadi Hames-Fathi
- Research Department of Pathology, Cancer Institute, University College London, London, UK
| | - Dolapo Ajayi
- Research Department of Pathology, Cancer Institute, University College London, London, UK
| | | | - Pawan Dhami
- CRUK-UCL Cancer Institute Translational Technology Platform (Genomics), London, UK
| | - Alex McLatchie
- CRUK-UCL Cancer Institute Translational Technology Platform (Genomics), London, UK
| | - Matt Lechner
- Research Department of Oncology, UCL Cancer Institute, London, UK
| | - Nicholas Light
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Adam Shlien
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - David Malkin
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Feber
- Translational Epigenetics, Division of Molecular Pathology, Institute of Cancer Research, London, UK
- Clinical Genomics, Translational Research Laboratory, Royal Marsden NHS Trust, London, UK
| | - Paula Proszek
- Translational Epigenetics, Division of Molecular Pathology, Institute of Cancer Research, London, UK
- Clinical Genomics, Translational Research Laboratory, Royal Marsden NHS Trust, London, UK
| | - Tom Lesluyes
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden
| | - Adrienne M Flanagan
- Research Department of Pathology, Cancer Institute, University College London, London, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | - Maxime Tarabichi
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Institute for Interdisciplinary Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA.
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA.
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London, UK.
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK.
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12
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Zhu B, Joo L, Zhang T, Koka H, Lee D, Shi J, Lee P, Wang D, Wang F, Chan WC, Law SH, Tsoi YK, Tse GM, Lai SW, Wu C, Yang S, Yang Chan EY, Shan Wong SY, Wang M, Song L, Jones K, Zhu B, Hutchinson A, Hicks B, Prokunina-Olsson L, Garcia-Closas M, Chanock S, Tse LA, Yang XR. Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients. HGG ADVANCES 2022; 3:100076. [PMID: 35047861 PMCID: PMC8756551 DOI: 10.1016/j.xhgg.2021.100076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/30/2021] [Indexed: 12/24/2022] Open
Abstract
Recent genomic studies suggest that Asian breast cancer (BC) may have distinct somatic features; however, most comparisons of BC genomic features across populations did not account for differences in age, subtype, and sequencing methods. In this study, we analyzed whole-exome sequencing (WES) data to characterize somatic copy number alterations (SCNAs) and mutation profiles in 98 Hong Kong BC (HKBC) patients and compared with those from The Cancer Genome Atlas of European ancestry (TCGA-EA, N = 686), which had similar distributions of age at diagnosis and PAM50 subtypes as in HKBC. We developed a two-sample Poisson model to compare driver gene selection pressure, which reflects the effect sizes of cancer driver genes, while accounting for differences in sample size, sequencing platforms, depths, and mutation calling methods. We found that somatic mutation and SCNA profiles were overall very similar between HKBC and TCGA-EA. The selection pressure for small insertions and deletions (indels) in GATA3 (false discovery rate (FDR) corrected p < 0.01) and single-nucleotide variants (SNVs) in TP53 (nominal p = 0.02, FDR corrected p = 0.28) was lower in HKBC than in TCGA-EA. Among the 13 signatures of single-base substitutions (SBS) that are common in BC, we found a suggestively higher contribution of SBS18 and a lower contribution of SBS1 in HKBC than in TCGA-EA, while the two APOBEC-induced signatures showed similar prevalence. Our results suggest that the genomic landscape of BC was largely very similar between HKBC and TCGA-EA, despite suggestive differences in some driver genes and mutational signatures that warrant future investigations in large and diverse Asian populations.
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Affiliation(s)
- Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Lijin Joo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Hela Koka
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - DongHyuk Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Priscilla Lee
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Feng Wang
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Wing-cheong Chan
- Department of Surgery, North District Hospital, Hong Kong, China
| | - Sze Hong Law
- Department of Surgery, North District Hospital, Hong Kong, China
- Department of Pathology, Yan Chai Hospital, Hong Kong, China
| | - Yee-kei Tsoi
- Department of Surgery, North District Hospital, Hong Kong, China
| | - Gary M. Tse
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Shui Wun Lai
- Department of Pathology, North District Hospital, Hong Kong, China
| | - Cherry Wu
- Department of Pathology, North District Hospital, Hong Kong, China
| | - Shuyuan Yang
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Emily Ying Yang Chan
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Samuel Yeung Shan Wong
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Mingyi Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ludmila Prokunina-Olsson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Lap Ah Tse
- Division of Occupational and Environmental Health, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaohong R. Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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13
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Hsiao YW, Lu TP. Race-Specific Genetic Profiles of Homologous Recombination Deficiency in Multiple Cancers. J Pers Med 2021; 11:1287. [PMID: 34945758 PMCID: PMC8705317 DOI: 10.3390/jpm11121287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022] Open
Abstract
Homologous recombination deficiency (HRD) has been used to predict both cancer prognosis and the response to DNA-damaging therapies in many cancer types. HRD has diverse manifestations in different cancers and even in different populations. Many screening strategies have been designed for detecting the sensitivity of a patient's HRD status to targeted therapies. However, these approaches suffer from low sensitivity, and are not specific to each cancer type and population group. Therefore, identifying race-specific and targetable HRD-related genes is of clinical importance. Here, we conducted analyses using genomic sequencing data that was generated by the Pan-Cancer Atlas. Collapsing non-synonymous variants with functional damage to HRD-related genes, we analyzed the association between these genes and race within cancer types using the optimal sequencing kernel association test (SKAT-O). We have identified race-specific mutational patterns of curated HRD-related genes across cancers. Overall, more significant mutation sites were found in ATM, BRCA2, POLE, and TOP2B in both the 'White' and 'Asian' populations, whereas PTEN, EGFG, and RIF1 mutations were observed in both the 'White' and 'African American/Black' populations. Furthermore, supported by pathogenic tendency databases and previous reports, in the 'African American/Black' population, several associations, including BLM with breast invasive carcinoma, ERCC5 with ovarian serous cystadenocarcinoma, as well as PTEN with stomach adenocarcinoma, were newly described here. Although several HRD-related genes are common across cancers, many of them were found to be specific to race. Further studies, using a larger cohort of diverse populations, are necessary to identify HRD-related genes that are specific to race, for guiding gene testing methods.
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Affiliation(s)
- Yi-Wen Hsiao
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100, Taiwan;
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100, Taiwan;
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 100, Taiwan
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14
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Zingone A, Sinha S, Ante M, Nguyen C, Daujotyte D, Bowman ED, Sinha N, Mitchell KA, Chen Q, Yan C, Loher P, Meerzaman D, Ruppin E, Ryan BM. A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients. Nat Commun 2021; 12:5605. [PMID: 34556645 PMCID: PMC8460807 DOI: 10.1038/s41467-021-25763-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 07/22/2021] [Indexed: 11/09/2022] Open
Abstract
Deciphering the post-transcriptional mechanisms (PTM) regulating gene expression is critical to understand the dynamics underlying transcriptomic regulation in cancer. Alternative polyadenylation (APA)-regulation of mRNA 3'UTR length by alternating poly(A) site usage-is a key PTM mechanism whose comprehensive analysis in cancer remains an important open challenge. Here we use a method and analysis pipeline that sequences 3'end-enriched RNA directly to overcome the saturation limitation of traditional 5'-3' based sequencing. We comprehensively map the APA landscape in lung cancer in a cohort of 98 tumor/non-involved tissues derived from European American and African American patients. We identify a global shortening of 3'UTR transcripts in lung cancer, with notable functional implications on the expression of both coding and noncoding genes. We find that APA of non-coding RNA transcripts (long non-coding RNAs and microRNAs) is a recurrent event in lung cancer and discover that the selection of alternative polyA sites is a form of non-coding RNA expression control. Our results indicate that mRNA transcripts from EAs are two times more likely than AAs to undergo APA in lung cancer. Taken together, our findings comprehensively map and identify the important functional role of alternative polyadenylation in determining transcriptomic heterogeneity in lung cancer.
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Affiliation(s)
- Adriana Zingone
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US
| | - Sanju Sinha
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, US
| | - Michael Ante
- Lexogen GmbH, Campus Vienna Biocenter 5, 1030, Vienna, Austria
- Ares Genetics GmbH, Karl-Farkas-Gasse 18, 1030, Vienna, Austria
| | - Cu Nguyen
- Computational Genomics Research, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20850, US
| | - Dalia Daujotyte
- Lexogen GmbH, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Elise D Bowman
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US
| | - Neelam Sinha
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, US
| | - Khadijah A Mitchell
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US
| | - Qingrong Chen
- Computational Genomics Research, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20850, US
| | - Chunhua Yan
- Computational Genomics Research, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20850, US
| | - Phillipe Loher
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19017, US
| | - Daoud Meerzaman
- Computational Genomics Research, Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20850, US
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, US
| | - Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, US.
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15
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Chatsirisupachai K, Lesluyes T, Paraoan L, Van Loo P, de Magalhães JP. An integrative analysis of the age-associated multi-omic landscape across cancers. Nat Commun 2021; 12:2345. [PMID: 33879792 PMCID: PMC8058097 DOI: 10.1038/s41467-021-22560-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 03/17/2021] [Indexed: 02/07/2023] Open
Abstract
Age is the most important risk factor for cancer, as cancer incidence and mortality increase with age. However, how molecular alterations in tumours differ among patients of different age remains largely unexplored. Here, using data from The Cancer Genome Atlas, we comprehensively characterise genomic, transcriptomic and epigenetic alterations in relation to patients' age across cancer types. We show that tumours from older patients present an overall increase in genomic instability, somatic copy-number alterations (SCNAs) and somatic mutations. Age-associated SCNAs and mutations are identified in several cancer-driver genes across different cancer types. The largest age-related genomic differences are found in gliomas and endometrial cancer. We identify age-related global transcriptomic changes and demonstrate that these genes are in part regulated by age-associated DNA methylation changes. This study provides a comprehensive, multi-omics view of age-associated alterations in cancer and underscores age as an important factor to consider in cancer research and clinical practice.
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Affiliation(s)
- Kasit Chatsirisupachai
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | | | - Luminita Paraoan
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | | | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK.
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16
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Carrot-Zhang J, Soca-Chafre G, Patterson N, Thorner AR, Nag A, Watson J, Genovese G, Rodriguez J, Gelbard MK, Corrales-Rodriguez L, Mitsuishi Y, Ha G, Campbell JD, Oxnard GR, Arrieta O, Cardona AF, Gusev A, Meyerson M. Genetic Ancestry Contributes to Somatic Mutations in Lung Cancers from Admixed Latin American Populations. Cancer Discov 2021; 11:591-598. [PMID: 33268447 PMCID: PMC7933062 DOI: 10.1158/2159-8290.cd-20-1165] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/26/2020] [Accepted: 11/19/2020] [Indexed: 12/24/2022]
Abstract
Inherited lung cancer risk, particularly in nonsmokers, is poorly understood. Genomic and ancestry analysis of 1,153 lung cancers from Latin America revealed striking associations between Native American ancestry and their somatic landscape, including tumor mutational burden, and specific driver mutations in EGFR, KRAS, and STK11. A local Native American ancestry risk score was more strongly correlated with EGFR mutation frequency compared with global ancestry correlation, suggesting that germline genetics (rather than environmental exposure) underlie these disparities. SIGNIFICANCE: The frequency of somatic EGFR and KRAS mutations in lung cancer varies by ethnicity, but we do not understand why. Our study suggests that the variation in EGFR and KRAS mutation frequency is associated with genetic ancestry and suggests further studies to identify germline alleles that underpin this association.See related commentary by Gomez et al., p. 534.This article is highlighted in the In This Issue feature, p. 521.
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Affiliation(s)
- Jian Carrot-Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Departments of Genetics and Medicine, Harvard Medical School, Boston, Massachusetts
| | - Giovanny Soca-Chafre
- Personalized Medicine Laboratory, Instituto Nacional de Cancerologia, México City, México
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Departments of Genetics and Medicine, Harvard Medical School, Boston, Massachusetts
| | - Aaron R Thorner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Anwesha Nag
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jacqueline Watson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Giulio Genovese
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Departments of Genetics and Medicine, Harvard Medical School, Boston, Massachusetts
| | - July Rodriguez
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia
| | - Maya K Gelbard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Luis Corrales-Rodriguez
- Medical Oncology, Hospital San Juan de Dios, San José, Costa Rica
- Centro de Investigación y Manejo del Cáncer - CIMCA, San José, Costa Rica
| | - Yoichiro Mitsuishi
- Division of Respiratory Medicine, Graduate School of Medicine, Juntendo University, Bunkyo-ku, Tokyo, Japan
| | - Gavin Ha
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Joshua D Campbell
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Geoffrey R Oxnard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Oscar Arrieta
- Personalized Medicine Laboratory, Instituto Nacional de Cancerologia, México City, México.
- Thoracic Oncology Unit, Instituto Nacional de Cancerología, México City, México
| | - Andres F Cardona
- Foundation for Clinical and Applied Cancer Research - FICMAC, Bogotá, Colombia.
- Clinical and Translational Oncology Group, Clínica del Country, Bogotá, Colombia
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Departments of Genetics and Medicine, Harvard Medical School, Boston, Massachusetts
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17
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Arauz RF, Byun JS, Tandon M, Sinha S, Kuhn S, Taylor S, Zingone A, Mitchell KA, Pine SR, Gardner K, Perez-Stable EJ, Napoles AM, Ryan BM. Whole-Exome Profiling of NSCLC Among African Americans. J Thorac Oncol 2020; 15:1880-1892. [PMID: 32931935 PMCID: PMC7704928 DOI: 10.1016/j.jtho.2020.08.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Lung cancer incidence is higher among African Americans (AAs) compared with European Americans (EAs) in the United States, especially among men. Although significant progress has been made profiling the genomic makeup of lung cancer in EAs, AAs continue to be underrepresented. Our objective was to chart the genome-wide landscape of somatic mutations in lung cancer tumors from AAs. METHODS In this study, we used the whole-exome sequencing of 82 tumor and noninvolved tissue pairs from AAs. Patients were selected from an ongoing case-control study conducted by the National Cancer Institute and the University of Maryland. RESULTS Among all samples, we identified 178 significantly mutated genes (p < 0.05), five of which passed the threshold for false discovery rate (p < 0.1). In lung adenocarcinoma (LUAD) tumors, mutation rates in STK11 (p = 0.05) and RB1 (p = 0.008) were significantly higher in AA LUAD tumors (25% and 13%, respectively) compared with The Cancer Genome Atlas EA samples (14% and 4%, respectively). In squamous cell carcinomas, mutation rates in STK11 (p = 0.002) were significantly higher among AA (8%) than EA tumors from The Cancer Genome Atlas (1%). Integrated somatic mutation data with CIBERSORT (Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts) data analysis revealed LUAD tumors from AAs carrying STK11 mutations have decreased interferon signaling. CONCLUSIONS Although a considerable degree of the somatic mutation landscape is shared between EAs and AAs, discrete differences in mutation frequency in potentially important oncogenes and tumor suppressors exist. A better understanding of the molecular basis of lung cancer in AA patients and leveraging this information to guide clinical interventions may help reduce disparities.
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Affiliation(s)
- Rony F Arauz
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Jung S Byun
- Division of Intramural Research, National Institute on Minority Health and Health Disparities, Bethesda, Maryland; Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Mayank Tandon
- CCR Collaborative Bioinformatics Resource CCBR, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland; Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Sanju Sinha
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland; Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Skyler Kuhn
- CCR Collaborative Bioinformatics Resource CCBR, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland; Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Sheryse Taylor
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Adriana Zingone
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Khadijah A Mitchell
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Sharon R Pine
- Departments of Pharmacology and Medicine, Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Kevin Gardner
- National Institute of Minority Health and Health Disparities, Bethesda, Maryland; Department of Pathology and Cell Biology, Columbia University Medical Center, Columbia University, New York, New York
| | | | - Anna M Napoles
- National Institute of Minority Health and Health Disparities, Bethesda, Maryland
| | - Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.
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18
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Mukand NH, Zolekar A, Ko NY, Calip GS. Risks of Second Primary Gynecologic Cancers following Ovarian Cancer Treatment in Asian Ethnic Subgroups in the United States, 2000-2016. Cancer Epidemiol Biomarkers Prev 2020; 29:2220-2229. [PMID: 32856609 PMCID: PMC10772992 DOI: 10.1158/1055-9965.epi-20-0095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/03/2020] [Accepted: 08/04/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The differential occurrence of second primary cancers by race following ovarian cancer is poorly understood. Our objective was to determine the incidence of second primary gynecologic cancers (SPGC) following definitive therapy for ovarian cancer. Specifically, we aimed to determine differences in SPGC incidence by Asian ethnic subgroups. METHODS We identified 27,602 women ages 20 years and older and diagnosed with first primary epithelial ovarian cancer between 2000 and 2016 who received surgery and chemotherapy in 18 population-based Surveillance, Epidemiology and End Results Program registries. We compared the incidence of SPGC with expected incidence rates in the general population of women using estimated standardized incidence ratios (SIR) and 95% confidence intervals (CI). RESULTS The incidence of SPGC was lower among White women (SIR = 0.73; 95% CI, 0.59-0.89), and higher among Black (SIR = 1.80; 95% CI, 0.96-3.08) and Asian/Pacific Islander (API) women (SIR = 1.83; 95% CI, 1.07-2.93). Increased risk of vaginal cancers was observed among all women, although risk estimates were highest among API women (SIR = 26.76; 95% CI, 5.52-78.2) and were also significant for risk of uterine cancers (SIR = 2.53; 95% CI, 1.35-4.33). Among API women, only Filipinas had significantly increased incidence of SPGC overall including both uterine and vaginal cancers. CONCLUSIONS Risk of SPGC following treatment of ovarian cancer differs by race and ethnicity, with Filipina women having the highest rates of second gynecologic cancers among Asian women. IMPACT Ensuring access and adherence to surveillance may mitigate ethnic differences in the early detection and incidence of second gynecologic cancers.
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Affiliation(s)
- Nita H Mukand
- University of Illinois at Chicago, College of Pharmacy, Chicago, Illinois
- University of Illinois Cancer Center, Chicago, Illinois
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Ashwini Zolekar
- University of Illinois at Chicago, College of Pharmacy, Chicago, Illinois
| | - Naomi Y Ko
- Section of Hematology Oncology, Boston University School of Medicine, Boston, Massachusetts
| | - Gregory S Calip
- University of Illinois at Chicago, College of Pharmacy, Chicago, Illinois.
- University of Illinois Cancer Center, Chicago, Illinois
- Flatiron Health, New York, New York
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19
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Shen J, Song R, Chow WH, Zhao H. Homologous recombination repair capacity in peripheral blood lymphocytes and breast cancer risk. Carcinogenesis 2020; 41:1363-1367. [PMID: 32692853 PMCID: PMC7566366 DOI: 10.1093/carcin/bgaa081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/01/2020] [Accepted: 07/17/2020] [Indexed: 11/14/2022] Open
Abstract
Deficiency in homologous recombination repair (HRR) capacity is frequently observed in breast tumors. However, whether HRR deficiency is a tumor-specific biomarker or a risk factor for breast cancer is unknown. In this two-stage study, using a host cell reactivation assay, we assessed the relationship between HRR capacity in peripheral blood lymphocytes (PBLs) and breast cancer risk. The discovery stage included 152 breast cancer patients and 152 healthy controls matched on age and race. HRR capacity was found to be significantly lower in Black women than in White women among controls (P = 0.015) and cases (P = 0.012). Among cases, triple negative breast cancer patients had significantly lower HRR capacity than ER+/PR+ breast cancer patients (P = 0.006). In risk assessment, HRR capacity was found to be significantly lower in cases than in controls (P < 0.001), and decreased HRR capacity was associated with 1.42-fold increased risk of breast cancer (95% CI: 1.21, 2.53). In the validation stage, we assessed HRR capacity in a nested case-control study using pre-diagnostic samples. We found that decreased HRR capacity was associated with 1.21-fold increased risk of breast cancer (95% CI: 1.04, 4.58). In summary, our results demonstrate that decreased HRR capacity in PBLs is a risk factor for breast cancer.
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Affiliation(s)
- Jie Shen
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Family Medicine and Population Health, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Renduo Song
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wong-Ho Chow
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hua Zhao
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Family Medicine and Population Health, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
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20
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Henriksson R. It is not just about molecules! Optimal cancer care for the future needs more research on external factors. Acta Oncol 2020; 59:373-375. [PMID: 32048539 DOI: 10.1080/0284186x.2020.1726458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Roger Henriksson
- Department of Radiation Sciences, University of Umea, Umea, Sweden
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21
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Dart A. Cancer disparities. Nat Rev Cancer 2020; 20:141. [PMID: 31996789 DOI: 10.1038/s41568-020-0242-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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