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Tjader NP, Beer AJ, Ramroop J, Tai MC, Ping J, Gandhi T, Dauch C, Neuhausen SL, Ziv E, Sotelo N, Ghanekar S, Meadows O, Paredes M, Gillespie JL, Aeilts AM, Hampel H, Zheng W, Jia G, Hu Q, Wei L, Liu S, Ambrosone CB, Palmer JR, Carpten JD, Yao S, Stevens P, Ho WK, Pan JW, Fadda P, Huo D, Teo SH, McElroy JP, Toland AE. Association of ESR1 Germline Variants with TP53 Somatic Variants in Breast Tumors in a Genome-wide Study. CANCER RESEARCH COMMUNICATIONS 2024; 4:1597-1608. [PMID: 38836758 PMCID: PMC11210444 DOI: 10.1158/2767-9764.crc-24-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/16/2024] [Accepted: 05/21/2024] [Indexed: 06/06/2024]
Abstract
In breast tumors, somatic mutation frequencies in TP53 and PIK3CA vary by tumor subtype and ancestry. Emerging data suggest tumor mutation status is associated with germline variants and genetic ancestry. We aimed to identify germline variants that are associated with somatic TP53 or PIK3CA mutation status in breast tumors. A genome-wide association study was conducted in 2,850 women of European ancestry with breast cancer using TP53 and PIK3CA mutation status (positive or negative) as well as specific functional categories [e.g., TP53 gain-of-function (GOF) and loss-of-function, PIK3CA activating] as phenotypes. Germline variants showing evidence of association were selected for validation analyses and tested in multiple independent datasets. Discovery association analyses found five variants associated with TP53 mutation status with P values <1 × 10-6 and 33 variants with P values <1 × 10-5. Forty-four variants were associated with PIK3CA mutation status with P values <1 × 10-5. In validation analyses, only variants at the ESR1 locus were associated with TP53 mutation status after multiple comparisons corrections. Combined analyses in European and Malaysian populations found ESR1 locus variants rs9383938 and rs9479090 associated with the presence of TP53 mutations overall (P values 2 × 10-11 and 4.6 × 10-10, respectively). rs9383938 also showed association with TP53 GOF mutations (P value 6.1 × 10-7). rs9479090 showed suggestive evidence (P value 0.02) for association with TP53 mutation status in African ancestry populations. No other variants were significantly associated with TP53 or PIK3CA mutation status. Larger studies are needed to confirm these findings and determine if additional variants contribute to ancestry-specific differences in mutation frequency. SIGNIFICANCE Emerging data show ancestry-specific differences in TP53 and PIK3CA mutation frequency in breast tumors suggesting that germline variants may influence somatic mutational processes. This study identified variants near ESR1 associated with TP53 mutation status and identified additional loci with suggestive association which may provide biological insight into observed differences.
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Affiliation(s)
- Nijole P. Tjader
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Abigail J. Beer
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Johnny Ramroop
- The City College of New York, City University of New York, New York, New York
| | - Mei-Chee Tai
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Jie Ping
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Tanish Gandhi
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, Ohio
- The Ohio State University Medical School, Columbus, Ohio
| | - Cara Dauch
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio
- The Ohio State University Wexner Medical Center, Clinical Trials Office, Columbus, Ohio
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Elad Ziv
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Medicine, University of California, San Francisco, San Francisco, California
- Institute for Human Genetics, University of California San Francisco, San Francisco, California
| | - Nereida Sotelo
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Shreya Ghanekar
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Owen Meadows
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, Ohio
| | - Monica Paredes
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, Ohio
| | | | - Amber M. Aeilts
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, Ohio
| | - Heather Hampel
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Guochong Jia
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Lei Wei
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Christine B. Ambrosone
- Department of Cancer Control and Prevention, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Julie R. Palmer
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - John D. Carpten
- City of Hope Comprehensive Cancer Center, Duarte, California
- Department of Integrative Translational Sciences, City of Hope, Duarte, California
| | - Song Yao
- Department of Cancer Control and Prevention, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Patrick Stevens
- Bioinformatics Shared Resource, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Weang-Kee Ho
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- School of Mathematical Sciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
| | - Jia Wern Pan
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Paolo Fadda
- Genomics Shared Resource, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois
| | - Soo-Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- Faculty of Medicine, University Malaya Cancer Research Institute, University of Malaya, Kuala Lumpur, Malaysia
| | - Joseph Paul McElroy
- Department of Biomedical Informatics, The Ohio State University Center for Biostatistics, Columbus, Ohio
| | - Amanda E. Toland
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, Ohio
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Summey RM, Gornstein E, Decker B, Dougherty KC, Rader JS, Hopp E. Landscape of potential germline pathogenic variants in select cancer susceptibility genes in patients with adult-type ovarian granulosa cell tumors. Cancer Med 2024; 13:e7340. [PMID: 38898688 PMCID: PMC11187164 DOI: 10.1002/cam4.7340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 05/14/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
OBJECTIVE The objective of this study was to assess the frequency of potential germline pathogenic variants that may contribute to risk of development of adult granulosa cell tumors (AGCT) given the paucity of germline testing guidelines for these patients. METHODS This was a retrospective cross-sectional study analyzing comprehensive genomic profiling (CGP) results of AGCT with the FOXL2 p.C134W mutation submitted to Foundation Medicine between 2012 and 2022. Cases with a potential germline pathogenic variant were identified by filtering single nucleotide variants and short indels by variant allele frequency (VAF) and presence in ClinVar for select cancer susceptibility genes. Odds ratios for AGCT risk were calculated compared to a healthy population. RESULTS Prior to analysis, 595 patients were screened and 516 with a somatic FOXL2 p.C134W mutation were included. Potential germline pathogenic variants in a DNA repair-related gene (ATM, BRCA1, BRCA2, CHEK2, PALB2, PMS2, RAD51C, or RAD51D) were found in 6.6% of FOXL2-mutated AGCT. Potential germline pathogenic CHEK2 variants were found in 3.5% (18/516) of AGCT patients, a rate that was 2.8-fold higher than Genome Aggregation Database non-cancer subjects (95% CI 1.8-4.6, p < 0.001). The founder variants p.I157T (38.9%, 7/18) and p.T367fs*15 (c.1100delC; 27.8%, 5/18) were most commonly observed. CHEK2 VAF indicated frequent loss of the wildtype copy of the gene. CONCLUSIONS These results support ongoing utilization of genomic tumor profiling and confirmatory germline testing for potential germline pathogenic variants. Further prospective investigation into the biology of germline variants in this population is warranted.
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Affiliation(s)
- Rebekah M. Summey
- Division of Gynecologic Oncology, Department of Obstetrics and GynecologyMedical College of WisconsinMilwaukeeWisconsinUSA
| | | | | | | | - Janet S. Rader
- Division of Gynecologic Oncology, Department of Obstetrics and GynecologyMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Elizabeth Hopp
- Division of Gynecologic Oncology, Department of Obstetrics and GynecologyMedical College of WisconsinMilwaukeeWisconsinUSA
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Li M, Zhang Y, Zhou P, Miao Y, Li S, Jiang L. Mutational analysis of pulmonary large cell neuroendocrine carcinoma: APC gene mutations identify a good prognostic factor. Lung Cancer 2024; 192:107825. [PMID: 38795461 DOI: 10.1016/j.lungcan.2024.107825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 04/11/2024] [Accepted: 05/13/2024] [Indexed: 05/28/2024]
Abstract
Pulmonary large cell neuroendocrine carcinoma (LCNEC) is a highly aggressive neoplasm with biological heterogeneity. Mutations in multiple genes have been identified in LCNEC. However, associations between gene alterations, histopathological characteristics, and prognosis remain ambiguous. Here, we investigated the clinicopathologic, immunohistochemical, and genomic characteristics of 19 patients with LCNEC and 9 patients with atypical carcinoid (AC). We revealed high mutation frequencies of TP53 (89.5 %), RB1 (42.1 %), APC (31.6 %), and MCL1 (31.6 %) in LCNEC, while genetic alterations were rarely found in AC. APC alterations mainly occurred to the exon 16 and were only identified in LCNEC with wild-type RB1. The 19 LCNEC were further subgrouped into APC wild-type (LCNEC-APCMT, 6/19) and APC-mutated (LCNEC-APCWT, 13/19) subgroups. In comparison with LCNEC-APCWT, LCNEC-APCMT displayed lower TMB (median: 12.64 vs 4.20, P = 0.045), and relatively mild cytologic atypia. In addition, LCNEC-APCMT distinguished itself from AC and LCNEC-APCWT by obviously downregulated expression of neuroendocrine markers (CD56 and Syn, P < 0.01) and significantly altered expression of genes downstream of APC (β-catenin migrating into the cytoplasm and nucleus, P < 0.001; c-Myc upregulating, P = 0.005). The OS of LCNEC-APCMT was numerically intermediate between AC and LCNEC-APCWT. We first proposed that APC alterations were common in LCNEC with wild-type RB1 and that LCNEC-APCMT was associated with lower TMB and better OS in comparison with LCNEC-APCWT.
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Affiliation(s)
- Mengqian Li
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China.
| | - Ying Zhang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China.
| | - Ping Zhou
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China.
| | - Yuqing Miao
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China.
| | - Shuang Li
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China.
| | - Lili Jiang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China.
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Lawler T, Parlato L, Warren Andersen S. The histological and molecular characteristics of early-onset colorectal cancer: a systematic review and meta-analysis. Front Oncol 2024; 14:1349572. [PMID: 38737895 PMCID: PMC11082351 DOI: 10.3389/fonc.2024.1349572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
Background Early-onset colorectal cancer (CRC), defined as diagnosis before age 50, has increased in recent decades. Although more often diagnosed at advanced stage, associations with other histological and molecular markers that impact prognosis and treatment remain to be clarified. We conducted a systematic review and meta-analysis concerning the prevalence of prognostic and predictive tumor markers for early- vs. late-onset CRC, including oncogene mutations, microsatellite instability (MSI), and emerging markers including immune cells and the consensus molecular subtypes. Methods We systematically searched PubMed for original research articles published between April 2013-January 2024. Included studies compared the prevalence of tumor markers in early- vs. late-onset CRC. A meta-analysis was completed and summary odds ratios (ORs) with 95% confidence intervals (CIs) were obtained from a random effects model via inverse variance weighting. A sensitivity analysis was completed to restrict the meta-analysis to studies that excluded individuals with Lynch syndrome, a hereditary condition that influences the distribution of tumor markers for early-onset CRC. Results In total, 149 articles were identified. Tumors from early-onset CRC are less likely to include mutations in KRAS (OR, 95% CI: 0.91, 0.85-0.98), BRAF (0.63, 0.51-0.78), APC (0.70, 0.58-0.84), and NRAS (0.88, 0.78-1.00) but more likely to include mutations in PTEN (1.68, 1.04-2.73) and TP53 (1.34, 1.24-1.45). After limiting to studies that excluded Lynch syndrome, the associations between early-onset CRC and BRAF (0.77, 0.64-0.92) and APC mutation (0.81, 0.67-0.97) were attenuated, while an inverse association with PIK3CA mutation was also observed (0.88, 0.78-0.99). Early-onset tumors are less likely to develop along the CpG Island Methylator Phenotype pathway (0.24, 0.10-0.57), but more likely to possess adverse histological features including high tumor grade (1.20, 1.15-1.25), and mucinous (1.22, 1.16-1.27) or signet ring histology (2.32, 2.08-2.57). A positive association with MSI status (1.31, 1.11-1.56) was also identified. Associations with immune markers and the consensus molecular subtypes are inconsistent. Discussion A lower prevalence of mutations in KRAS and BRAF is consistent with extended survival and superior response to targeted therapies for metastatic disease. Conversely, early-onset CRC is associated with aggressive histological subtypes and TP53 and PTEN mutations, which may serve as therapeutic targets.
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Affiliation(s)
- Thomas Lawler
- School of Medicine and Public Health, Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Lisa Parlato
- School of Medicine and Public Health, Department of Population Health Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Shaneda Warren Andersen
- School of Medicine and Public Health, Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, United States
- School of Medicine and Public Health, Department of Population Health Sciences, University of Wisconsin-Madison, Madison, WI, United States
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Tapia-Valladares C, Valenzuela G, González E, Maureira I, Toro J, Freire M, Sepúlveda-Hermosilla G, Ampuero D, Blanco A, Gallegos I, Morales F, Erices JI, Barajas O, Ahumada M, Contreras HR, González J, Armisén R, Marcelain K. Distinct Driver Pathway Enrichments and a High Prevalence of TSC2 Mutations in Right Colon Cancer in Chile: A Preliminary Comparative Analysis. Int J Mol Sci 2024; 25:4695. [PMID: 38731914 PMCID: PMC11083322 DOI: 10.3390/ijms25094695] [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: 02/09/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 05/13/2024] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer deaths globally. While ethnic differences in driver gene mutations have been documented, the South American population remains understudied at the genomic level, despite facing a rising burden of CRC. We analyzed tumors of 40 Chilean CRC patients (Chp) using next-generation sequencing and compared them to data from mainly Caucasian cohorts (TCGA and MSK-IMPACT). We identified 388 mutations in 96 out of 135 genes, with TP53 (45%), KRAS (30%), PIK3CA (22.5%), ATM (20%), and POLE (20%) being the most frequently mutated. TSC2 mutations were associated with right colon cancer (44.44% in RCRC vs. 6.45% in LCRC, p-value = 0.016), and overall frequency was higher compared to TCGA (p-value = 1.847 × 10-5) and MSK-IMPACT cohorts (p-value = 3.062 × 10-2). Limited sample size restricts definitive conclusions, but our data suggest potential differences in driver mutations for Chilean patients, being that the RTK-RAS oncogenic pathway is less affected and the PI3K pathway is more altered in Chp compared to TCGA (45% vs. 25.56%, respectively). The prevalence of actionable pathways and driver mutations can guide therapeutic choices, but can also impact treatment effectiveness. Thus, these findings warrant further investigation in larger Chilean cohorts to confirm these initial observations. Understanding population-specific driver mutations can guide the development of precision medicine programs for CRC patients.
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Affiliation(s)
- Camilo Tapia-Valladares
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - Guillermo Valenzuela
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - Evelin González
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610507, Chile
| | - Ignacio Maureira
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
- Departamento de Tecnología Médica, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - Jessica Toro
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
- Centro para la Prevención y Control del Cáncer, CECAN, Universidad de Chile, Santiago 8380000, Chile
| | - Matías Freire
- CORFO Center of Excellence in Precision Medicine, Pfizer Chile, Santiago 8380000, Chile
| | | | - Diego Ampuero
- CORFO Center of Excellence in Precision Medicine, Pfizer Chile, Santiago 8380000, Chile
| | - Alejandro Blanco
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610507, Chile
| | - Iván Gallegos
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
- Centro para la Prevención y Control del Cáncer, CECAN, Universidad de Chile, Santiago 8380000, Chile
- Departamento de Patología, Hospital Clínico de la Universidad de Chile, Santiago 8380453, Chile
| | - Fernanda Morales
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - José I. Erices
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - Olga Barajas
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
- Centro para la Prevención y Control del Cáncer, CECAN, Universidad de Chile, Santiago 8380000, Chile
- Departamento de Medicina Interna, Hospital Clínico de la Universidad de Chile, Santiago 8380453, Chile
| | - Mónica Ahumada
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
- Centro para la Prevención y Control del Cáncer, CECAN, Universidad de Chile, Santiago 8380000, Chile
- Departamento de Medicina Interna, Hospital Clínico de la Universidad de Chile, Santiago 8380453, Chile
| | - Héctor R. Contreras
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
- Centro para la Prevención y Control del Cáncer, CECAN, Universidad de Chile, Santiago 8380000, Chile
| | - Jaime González
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - Ricardo Armisén
- Centro de Genética y Genómica, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 7610507, Chile
| | - Katherine Marcelain
- Departamento de Oncología Básico Clínico, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
- Centro para la Prevención y Control del Cáncer, CECAN, Universidad de Chile, Santiago 8380000, Chile
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Matejcic M, Teer JK, Hoehn HJ, Diaz DB, Shankar K, Gong J, Nguyen NT, Lorona N, Coppola D, Fulmer C, Saglam O, Jiang K, Cress D, Muñoz-Antonia T, Flores I, Gordian E, Oliveras Torres JA, Felder SI, Sanchez JA, Fleming J, Siegel EM, Freedman JA, Dutil J, Stern MC, Fridley BL, Figueiredo JC, Schmit SL. Spectrum of somatic mutational features of colorectal tumors in ancestrally diverse populations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.11.24303880. [PMID: 38558992 PMCID: PMC10980113 DOI: 10.1101/2024.03.11.24303880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Ancestrally diverse and admixed populations, including the Hispanic/Latino/a/x/e community, are underrepresented in cancer genetic and genomic studies. Leveraging the Latino Colorectal Cancer Consortium, we analyzed whole exome sequencing data on tumor/normal pairs from 718 individuals with colorectal cancer (128 Latino, 469 non-Latino) to map somatic mutational features by ethnicity and genetic ancestry. Global proportions of African, East Asian, European, and Native American ancestries were estimated using ADMIXTURE. Associations between global genetic ancestry and somatic mutational features across genes were examined using logistic regression. TP53 , APC , and KRAS were the most recurrently mutated genes. Compared to non-Latino individuals, tumors from Latino individuals had fewer KRAS (OR=0.64, 95%CI=0.41-0.97, p=0.037) and PIK3CA mutations (OR=0.55, 95%CI=0.31-0.98, p=0.043). Genetic ancestry was associated with presence of somatic mutations in 39 genes (FDR-adjusted LRT p<0.05). Among these genes, a 10% increase in African ancestry was associated with significantly higher odds of mutation in KNCN (OR=1.34, 95%CI=1.09-1.66, p=5.74×10 -3 ) and TMEM184B (OR=1.53, 95%CI=1.10-2.12, p=0.011). Among RMGs, we found evidence of association between genetic ancestry and mutation status in CDC27 (LRT p=0.0084) and between SMAD2 mutation status and AFR ancestry (OR=1.14, 95%CI=1.00-1.30, p=0.046). Ancestry was not associated with tumor mutational burden. Individuals with above-average Native American ancestry had a lower frequency of microsatellite instable (MSI-H) vs microsatellite stable tumors (OR=0.45, 95%CI=0.21-0.99, p=0.048). Our findings provide new knowledge about the relationship between ancestral haplotypes and somatic mutational profiles that may be useful in developing precision medicine approaches and provide additional insight into genomic contributions to cancer disparities. Significance Our data in ancestrally diverse populations adds essential information to characterize mutational features in the colorectal cancer genome. These results will help enhance equity in the development of precision medicine strategies.
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Booker BD, Markt SC, Schumacher FR, Rose J, Cooper G, Selfridge JE, Koroukian SM. Variation in KRAS/NRAS/BRAF-Mutation Status by Age, Sex, and Race/Ethnicity Among a Large Cohort of Patients with Metastatic Colorectal Cancer (mCRC). J Gastrointest Cancer 2024; 55:237-246. [PMID: 37355486 DOI: 10.1007/s12029-023-00954-z] [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] [Accepted: 06/18/2023] [Indexed: 06/26/2023]
Abstract
BACKGROUND Racial/ethnic disparities in metastatic colorectal cancer (mCRC) survival are well documented as is the impact that tumor mutation of KRAS and BRAF has on prognosis. It has been suggested that frequency differences of KRAS- and BRAF-mutated tumors may partially explain this disparity. Demographic differences in mutation frequency are not well established nor whether mutation and microsatellite instability (MSI) differentially impact survival among groups. METHODS Using data for 11,117 patients diagnosed with de-novo mCRC from an electronic health record-derived database we estimated adjusted odds ratios (aOR) to characterize the association between demographics and MSI and KRAS/NRAS/BRAF-mutation status. Stratified Cox models were used to identify differences in overall survival (OS), adjusting for treatment and demographics. RESULTS Being female, compared to male, (aORKRAS:1.33 (1.23-1.44); aORBRAF:1.84 (1.56-2.16)), and non-Hispanic Black race (NHB), compared to non-Hispanic White (NHW) (aORKRAS:1.62 (1.42-1.85); aORBRAF: 0.55 (0.38-0.77)) were associated with KRAS- or BRAF-mutant tumors. MSI prevalence was similar across race/ethnicity but higher in women. BRAF-mutant tumors were associated with poorer prognosis overall, especially among non-white patients. Among patients who had KRAS/NRAS/BRAF-WT tumors we observed no difference in OS by race or MSI. Among patients with KRAS-mutant tumors, Hispanic patients had more favorable prognosis adjusted hazards ratio (aHR) = 0.76 (0.65-0.89)) than their NHW counterparts. Among those with BRAF-mutant tumors, NHB patients had poorer prognosis than NHW patients (aHR:1.78 (1.08-2.93)). CONCLUSION MSI and frequency of KRAS and BRAF mutations differed by demographics. Racial/ethnic disparities in OS differed by mutation. Future studies should explore biological and/or social determinants underlying these differences.
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Affiliation(s)
- Benjamin D Booker
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Robbins E210, Cleveland, OH, 44106-4945, USA.
| | - Sarah C Markt
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Robbins E210, Cleveland, OH, 44106-4945, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Robbins E210, Cleveland, OH, 44106-4945, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Johnie Rose
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Robbins E210, Cleveland, OH, 44106-4945, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- University Hospitals, Cleveland, OH, USA
| | - Greg Cooper
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Robbins E210, Cleveland, OH, 44106-4945, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- University Hospitals, Cleveland, OH, USA
| | - J Eva Selfridge
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- University Hospitals, Cleveland, OH, USA
| | - Siran M Koroukian
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Robbins E210, Cleveland, OH, 44106-4945, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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Gupta S, May FP, Kupfer SS, Murphy CC. Birth Cohort Colorectal Cancer (CRC): Implications for Research and Practice. Clin Gastroenterol Hepatol 2024; 22:455-469.e7. [PMID: 38081492 DOI: 10.1016/j.cgh.2023.11.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/21/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
Abstract
Colorectal cancer (CRC) epidemiology is changing due to a birth cohort effect, first recognized by increasing incidence of early onset CRC (EOCRC, age <50 years). In this paper, we define "birth cohort CRC" as the observed phenomenon, among individuals born 1960 and later, of increasing CRC risk across successive birth cohorts, rising EOCRC incidence, increasing incidence among individuals aged 50 to 54 years, and flattening of prior decreasing incidence among individuals aged 55 to 74 years. We demonstrate birth cohort CRC is associated with unique features, including increasing rectal cancer (greater than colon) and distant (greater than local) stage CRC diagnosis, and increasing EOCRC across all racial/ethnic groups. We review potential risk factors, etiologies, and mechanisms for birth cohort CRC, using EOCRC as a starting point and describing importance of viewing these through the lens of birth cohort. We also outline implications of birth cohort CRC for epidemiologic and translational research, as well as current clinical practice. We postulate that recognition of birth cohort CRC as an entity-including and extending beyond rising EOCRC-can advance understanding of risk factors, etiologies, and mechanisms, and address the public health consequences of changing CRC epidemiology.
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Affiliation(s)
- Samir Gupta
- Section of Gastroenterology, Jennifer Moreno San Diego VA Medical Center, San Diego, California; Division of Gastroenterology, Department of Medicine, and Moores Cancer Center, University of California, La Jolla, California.
| | - Folasade P May
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California; Greater Los Angeles Veterans Affairs Healthcare System, Los Angeles, California; UCLA Kaiser Permanente Center for Health Equity, Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California
| | - Sonia S Kupfer
- Section of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Caitlin C Murphy
- Department of Health Promotion & Behavioral Sciences, University of Texas Health Science Center at Houston (UTHealth Houston) School of Public Health, Houston, Texas
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9
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Innocenti F, Mu W, Qu X, Ou FS, Kabbarah O, Blanke CD, Venook AP, Lenz HJ, Rashid NU. DNA Mutational Profiling in Patients With Colorectal Cancer Treated With Standard of Care Reveals Differences in Outcome and Racial Distribution of Mutations. J Clin Oncol 2024; 42:399-409. [PMID: 37992266 PMCID: PMC10824387 DOI: 10.1200/jco.23.00825] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 09/02/2023] [Accepted: 09/25/2023] [Indexed: 11/24/2023] Open
Abstract
PURPOSE CALGB (Alliance)/SWOG 80405 was a randomized phase III trial that in first-line patients with metastatic colorectal cancer (mCRC) treated with bevacizumab or cetuximab with chemotherapy. We aimed to discover novel mutated genes associated with prognosis and differential response to therapy with the biologics. METHODS Primary tumor DNA from 548 patients was sequenced using FoundationOne. The effect of mutated genes and mutations on overall survival (OS) was tested adjusting for microsatellite instability status, BRAF V600E, all RAS mutations, arm, sex, and age. RESULTS The median number (lower-upper quartile) of mutated genes was 5 (3-7), 5 (3-6) in microsatellite stable and 12.5 (4.5-32) in microsatellite instability-high tumors. Mutated KRAS and APC were more frequent in Black (53% and 85%) than White (27% and 65%, respectively) patients while BRAF V600E was less frequent in Black (5%) than White (14%) patients. The median OS in patients with BRAF non-V600E (2.2% of patients) was 31.9 months (95% CI, 15.1 to not applicable [NA]) similar to that of BRAF wild-type (WT) patients (31.2 months [95% CI, 29.0 to 33.9]). Mutated LRP1B (10.7% of patients) was associated with improved OS compared with WT LRP1B (hazard ratio, 0.57 [95% CI, 0.40 to 0.80]). RNF43 (5.6% of patients) interacted with treatment arms as, in the cetuximab arm, patients with mutated RNF43 had a median OS of 11.5 (95% CI, 10.8 to NA) months compared with 30.1 (95% CI, 24.9 to 35.3) months in patients with WT RNF43, whereas in the bevacizumab arm, patients with mutated RNF43 had a median OS of 25.0 (95% CI, 14.2 to NA) months compared with 31.3 (95% CI, 29.0 to 34.3) months in patients with WT RNF43. CONCLUSION These results can provide new tools to predict patient outcome and improve therapeutic decisions and trial participation in patient minorities. The molecular alterations identified in this study may direct biomarker-driven studies.
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Affiliation(s)
- Federico Innocenti
- Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Wancen Mu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Xueping Qu
- Alliance Statistics and Data Center, Mayo Clinic, Rochester, MN
| | | | | | | | - Alan P. Venook
- University of California at San Francisco, San Francisco, CA
| | - Heinz-Josef Lenz
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Naim U. Rashid
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
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10
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Stebbing J, Schlechter BL. Genes and Race in Colon Cancer. J Clin Oncol 2024; 42:369-372. [PMID: 38060992 DOI: 10.1200/jco.23.02094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 01/31/2024] Open
Affiliation(s)
- Justin Stebbing
- Department of Life Sciences, Anglia Ruskin University, Cambridge, United Kingdom
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11
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Lawler T, Parlato L, Warren Andersen S. Racial disparities in colorectal cancer clinicopathological and molecular tumor characteristics: a systematic review. Cancer Causes Control 2024; 35:223-239. [PMID: 37688643 PMCID: PMC11090693 DOI: 10.1007/s10552-023-01783-y] [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: 03/21/2023] [Accepted: 08/21/2023] [Indexed: 09/11/2023]
Abstract
PURPOSE African Americans have the highest colorectal cancer (CRC) mortality of all racial groups in the USA, which may relate to differences in healthcare access or advanced stage at diagnosis. Recent evidence indicates that differences in tumor characteristics may also underlie disparities in mortality. To highlight recent findings and areas for investigation, we completed the first systematic review of racial disparities in CRC tumor prognostic markers, including clinicopathological markers, microsatellite instability (MSI), oncogene mutations, and novel markers, including cancer stem cells and immune markers. METHODS Relevant studies were identified via PubMed, limited to original research published within the last 10 years. Ninety-six articles were identified that compared the prevalence of mortality-related CRC tumor characteristics in African Americans (or other African ancestry populations) to White cases. RESULTS Tumors from African ancestry cases are approximately 10% more likely to contain mutations in KRAS, which confer elevated mortality and resistance to epidermal growth factor receptor inhibition. Conversely, African Americans have approximately 50% lower odds for BRAF-mutant tumors, which occur less frequently but have similar effects on mortality and therapeutic resistance. There is less consistent evidence supporting disparities in mutations for other oncogenes, including PIK3CA, TP53, APC, NRAS, HER2, and PTEN, although higher rates of PIK3CA mutations and lower prevalence of MSI status for African ancestry cases are supported by recent evidence. Although emerging evidence suggests that immune markers reflecting anti-tumor immunity in the tumor microenvironment may be lower for African American cases, there is insufficient evidence to evaluate disparities in other novel markers, cancer stem cells, microRNAs, and the consensus molecular subtypes. CONCLUSION Higher rates of KRAS-mutant tumors in in African Americans may contribute to disparities in CRC mortality. Additional work is required to understand whether emerging markers, including immune cells, underlie the elevated CRC mortality observed for African Americans.
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Affiliation(s)
- Thomas Lawler
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Lisa Parlato
- School of Medicine and Public Health, Department of Population Health Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Shaneda Warren Andersen
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA.
- School of Medicine and Public Health, Department of Population Health Sciences, University of Wisconsin-Madison, Madison, WI, USA.
- University of Wisconsin-Madison, Suite 1007B, WARF, 610 Walnut Street, Madison, WI, 53726, USA.
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12
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Saberi F, Youssef O, Kokkola A, Khodadoostan M, Puolakkainen P, Salehi R, Knuutila S. The frequency of NRAS mutation in stool samples of Iranian colorectal cancers compared to Finnish patients. JOURNAL OF RESEARCH IN MEDICAL SCIENCES : THE OFFICIAL JOURNAL OF ISFAHAN UNIVERSITY OF MEDICAL SCIENCES 2024; 29:4. [PMID: 38524743 PMCID: PMC10956560 DOI: 10.4103/jrms.jrms_208_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/25/2023] [Accepted: 10/18/2023] [Indexed: 03/26/2024]
Abstract
Background Stools from colorectal cancer patients are noninvasive samples that could be used to compare the frequency of hotspot mutations between two different ethnic cohorts. Materials and Methods We collected stool samples from the Iranian cohort (52 patients and 49 controls) and the Finnish cohort (40 patients and 14 controls). Following stool DNA extraction, we used the AmpliSeq Colon and Lung Cancer panel to prepare DNA libraries before sequencing. Results The Iranian cohort exhibited 35 hotspot mutations in the BRAF, ERBB4, FBXW7, FGFR1, FGFR3, KRAS, MAP2K, MET, NRAS, PIK3C, SMAD4, and TP53 genes. In the Finnish cohort, 13 hotspot mutations were found in the AKT1, APC, KIT, KRAS, SMO, STK11, and TP53 genes. Mutations in NRAS and FGFR3 were observed only in the Iranian cohort, while APC mutations were exclusive for the Finnish cohort. Conclusion Genes involved in MAPK and PI3K-MAPK pathways showed a higher frequency of mutations in Iranian patients which may have therapeutic implications.
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Affiliation(s)
- Farideh Saberi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Omar Youssef
- Department of Pathology, University of Helsinki, Helsinki, Finland, Europe
- Department of Clinical and Chemical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Finland, Europe
| | - Arto Kokkola
- The HUCH Gastrointestinal Clinic, University Central Hospital of Helsinki, Helsinki, Finland, Europe
| | - Mahsa Khodadoostan
- Department of Gastroenterology and Hepatology, Alzahra Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Pauli Puolakkainen
- The HUCH Gastrointestinal Clinic, University Central Hospital of Helsinki, Helsinki, Finland, Europe
| | - Rasoul Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Diseases, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sakari Knuutila
- Department of Pathology, University of Helsinki, Helsinki, Finland, Europe
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13
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Tjader NP, Beer AJ, Ramroop J, Tai MC, Ping J, Gandhi T, Dauch C, Neuhausen SL, Ziv E, Sotelo N, Ghanekar S, Meadows O, Paredes M, Gillespie J, Aeilts A, Hampel H, Zheng W, Jia G, Hu Q, Wei L, Liu S, Ambrosone CB, Palmer JR, Carpten JD, Yao S, Stevens P, Ho WK, Pan JW, Fadda P, Huo D, Teo SH, McElroy JP, Toland AE. Association of ESR1 germline variants with TP53 somatic variants in breast tumors in a genome-wide study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.06.23299442. [PMID: 38106140 PMCID: PMC10723566 DOI: 10.1101/2023.12.06.23299442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Background In breast tumors, somatic mutation frequencies in TP53 and PIK3CA vary by tumor subtype and ancestry. HER2 positive and triple negative breast cancers (TNBC) have a higher frequency of TP53 somatic mutations than other subtypes. PIK3CA mutations are more frequently observed in hormone receptor positive tumors. Emerging data suggest tumor mutation status is associated with germline variants and genetic ancestry. We aimed to identify germline variants that are associated with somatic TP53 or PIK3CA mutation status in breast tumors. Methods A genome-wide association study was conducted using breast cancer mutation status of TP53 and PIK3CA and functional mutation categories including TP53 gain of function (GOF) and loss of function mutations and PIK3CA activating/hotspot mutations. The discovery analysis consisted of 2850 European ancestry women from three datasets. Germline variants showing evidence of association with somatic mutations were selected for validation analyses based on predicted function, allele frequency, and proximity to known cancer genes or risk loci. Candidate variants were assessed for association with mutation status in a multi-ancestry validation study, a Malaysian study, and a study of African American/Black women with TNBC. Results The discovery Germline x Mutation (GxM) association study found five variants associated with one or more TP53 phenotypes with P values <1×10-6, 33 variants associated with one or more TP53 phenotypes with P values <1×10-5, and 44 variants associated with one or more PIK3CA phenotypes with P values <1×10-5. In the multi-ancestry and Malaysian validation studies, germline ESR1 locus variant, rs9383938, was associated with the presence of TP53 mutations overall (P values 6.8×10-5 and 9.8×10-8, respectively) and TP53 GOF mutations (P value 8.4×10-6). Multiple variants showed suggestive evidence of association with PIK3CA mutation status in the validation studies, but none were significant after correction for multiple comparisons. Conclusions We found evidence that germline variants were associated with TP53 and PIK3CA mutation status in breast cancers. Variants near the estrogen receptor alpha gene, ESR1, were significantly associated with overall TP53 mutations and GOF mutations. Larger multi-ancestry studies are needed to confirm these findings and determine if these variants contribute to ancestry-specific differences in mutation frequency.
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Affiliation(s)
- Nijole P. Tjader
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Abigail J. Beer
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Johnny Ramroop
- The City College of New York, City University of New York, New York, NY, USA
| | - Mei-Chee Tai
- Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
| | - Jie Ping
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, TN 37203
| | - Tanish Gandhi
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- The Ohio State University Medical School, Columbus, OH, 43210, USA
| | - Cara Dauch
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- The Ohio State University Wexner Medical Center, Clinical Trials Office, Columbus, OH 43210, USA
| | - Susan L. Neuhausen
- Beckman Research Institute of City of Hope, Department of Population Sciences, Duarte, CA, USA
| | - Elad Ziv
- University of California, Helen Diller Family Comprehensive Cancer Center, San Francisco, San Francisco, CA, USA
- University of California, Department of Medicine, San Francisco, San Francisco, CA, USA
- University of California San Francisco, Institute for Human Genetics, San Francisco, CA, USA
| | - Nereida Sotelo
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Shreya Ghanekar
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Owen Meadows
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Monica Paredes
- Biomedical Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Jessica Gillespie
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Amber Aeilts
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Heather Hampel
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, TN 37203
| | - Guochong Jia
- Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Nashville, TN 37203
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Lei Wei
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Christine B. Ambrosone
- Department of Cancer Control and Prevention, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Julie R. Palmer
- Slone Epidemiology Center at Boston University, Boston, MA, USA
| | - John D. Carpten
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Department of Integrative Translational Sciences, City of Hope, Duarte, CA
| | - Song Yao
- Department of Cancer Control and Prevention, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Patrick Stevens
- The Ohio State University Comprehensive Cancer Center, Bioinformatics Shared Resource, Columbus, OH, USA
| | - Weang-Kee Ho
- Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
- School of Mathematical Sciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor 43500, Malaysia
| | - Jia Wern Pan
- Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
| | - Paolo Fadda
- The Ohio State University Comprehensive Cancer Center, Genomics Shared Resource, Columbus, OH, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Soo-Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor 47500, Malaysia
- Faculty of Medicine, University Malaya Cancer Research Institute, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Joseph Paul McElroy
- The Ohio State University Center for Biostatistics, Department of Biomedical Informatics, Columbus, OH, USA
| | - Amanda Ewart Toland
- Department of Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, OH, 43210, USA
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14
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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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15
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Abate M, Walch H, Arora K, Vanderbilt CM, Fei T, Drebin H, Shimada S, Maio A, Kemel Y, Stadler ZK, Schmeltz J, Sihag S, Ku GY, Gu P, Tang L, Vardhana S, Berger MF, Brennan MF, Schultz ND, Strong VE. Unique Genomic Alterations and Microbial Profiles Identified in Patients With Gastric Cancer of African, European, and Asian Ancestry: A Novel Path for Precision Oncology. Ann Surg 2023; 278:506-518. [PMID: 37436885 PMCID: PMC10527605 DOI: 10.1097/sla.0000000000005970] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
OBJECTIVE Here, we characterize differences in the genetic and microbial profiles of GC in patients of African (AFR), European, and Asian ancestry. BACKGROUND Gastric cancer (GC) is a heterogeneous disease with clinicopathologic variations due to a complex interplay of environmental and biological factors, which may affect disparities in oncologic outcomes.. METHODS We identified 1042 patients with GC with next-generation sequencing data from an institutional Integrated Mutation Profiling of Actionable Cancer Targets assay and the Cancer Genomic Atlas group. Genetic ancestry was inferred from markers captured by the Integrated Mutation Profiling of Actionable Cancer Targets and the Cancer Genomic Atlas whole exome sequencing panels. Tumor microbial profiles were inferred from sequencing data using a validated microbiome bioinformatics pipeline. Genomic alterations and microbial profiles were compared among patients with GC of different ancestries. RESULTS We assessed 8023 genomic alterations. The most frequently altered genes were TP53 , ARID1A , KRAS , ERBB2 , and CDH1 . Patients of AFR ancestry had a significantly higher rate of CCNE1 alterations and a lower rate of KRAS alterations ( P < 0.05), and patients of East Asian ancestry had a significantly lower rate of PI3K pathway alterations ( P < 0.05) compared with other ancestries. Microbial diversity and enrichment did not differ significantly across ancestry groups ( P > 0.05). CONCLUSIONS Distinct patterns of genomic alterations and variations in microbial profiles were identified in patients with GC of AFR, European, and Asian ancestry. Our findings of variation in the prevalence of clinically actionable tumor alterations among ancestry groups suggest that precision medicine can mitigate oncologic disparities.
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Affiliation(s)
- Miseker Abate
- Department of Surgery, Memorial Sloan Kettering Cancer Center (MSK), New York, NY
- Human Oncology and Pathogenesis Program, MSK
- Department of Surgery, Weill Cornell Medicine
| | - Henry Walch
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, MSK
| | - Kanika Arora
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, MSK
| | | | - Teng Fei
- Department of Epidemiology and Biostatistics, MSK
| | - Harrison Drebin
- Department of Surgery, Memorial Sloan Kettering Cancer Center (MSK), New York, NY
- Human Oncology and Pathogenesis Program, MSK
| | - Shoji Shimada
- Department of Surgery, Memorial Sloan Kettering Cancer Center (MSK), New York, NY
- Human Oncology and Pathogenesis Program, MSK
| | - Anna Maio
- Niehaus Center of Inherited Cancer Genomics, MSK
| | - Yelena Kemel
- Niehaus Center of Inherited Cancer Genomics, MSK
| | - Zsofia K. Stadler
- Niehaus Center of Inherited Cancer Genomics, MSK
- Department of Medicine, MSK
- Department of Medicine, Weill Cornell Medicine
| | | | - Smita Sihag
- Department of Surgery, Memorial Sloan Kettering Cancer Center (MSK), New York, NY
- Department of Surgery, Weill Cornell Medicine
| | - Geoffrey Y. Ku
- Department of Medicine, MSK
- Department of Medicine, Weill Cornell Medicine
| | | | - Laura Tang
- Department of Pathology and Laboratory Medicine, MSK
- Department of Pathology and Laboratory Medicine, WCM
| | - Santosha Vardhana
- Human Oncology and Pathogenesis Program, MSK
- Department of Medicine, MSK
- Department of Medicine, Weill Cornell Medicine
| | - Michael F. Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, MSK
- Department of Pathology and Laboratory Medicine, MSK
- Department of Pathology and Laboratory Medicine, WCM
| | - Murray F. Brennan
- Department of Surgery, Memorial Sloan Kettering Cancer Center (MSK), New York, NY
- Department of Surgery, Weill Cornell Medicine
| | | | - Vivian E. Strong
- Department of Surgery, Memorial Sloan Kettering Cancer Center (MSK), New York, NY
- Department of Surgery, Weill Cornell Medicine
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Seagle HM, Keller SR, Tavtigian SV, Horton C, Holowatyj AN. Clinical Multigene Panel Testing Identifies Racial and Ethnic Differences in Germline Pathogenic Variants Among Patients With Early-Onset Colorectal Cancer. J Clin Oncol 2023; 41:4279-4289. [PMID: 37319387 PMCID: PMC10852379 DOI: 10.1200/jco.22.02378] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/03/2023] [Accepted: 03/06/2023] [Indexed: 06/17/2023] Open
Abstract
PURPOSE The early-onset colorectal cancer (EOCRC) burden differs across racial/ethnic groups, yet the role of germline genetic predisposition in EOCRC disparities remains uncharacterized. We defined the prevalence and spectrum of inherited colorectal cancer (CRC) susceptibility gene variations among patients with EOCRC by race and ethnicity. PATIENTS AND METHODS We included individuals diagnosed with a first primary CRC between age 15 and 49 years who identified as Ashkenazi Jewish, Asian, Black, Hispanic, or White and underwent germline genetic testing of 14 CRC susceptibility genes performed by a clinical testing laboratory. Variant comparisons by racial and ethnic groups were evaluated using chi-square tests and multivariable logistic regression adjusted for sex, age, CRC site, and number of primary colorectal tumors. RESULTS Among 3,980 patients with EOCRC, a total of 530 germline pathogenic or likely pathogenic variants were identified in 485 individuals (12.2%). By race/ethnicity, 12.7% of Ashkenazim patients, 9.5% of Asian patients, 10.3% of Black patients, 14.0% of Hispanic patients, and 12.4% of White patients carried a germline variant. The prevalence of Lynch syndrome (P = .037), as well as APC, CHEK2, MLH1, monoallelic MUTYH, and PTEN variants, varied by race/ethnicity among patients with EOCRC (all P < .026). Ashkenazim and Hispanic patients had significantly higher odds of presenting with a pathogenic APC variant, which included p.I1307K (odds ratio [OR], 2.67; 95% CI, 1.30 to 5.49; P = .007) and MLH1 variant (OR, 8.69; 95% CI, 2.68 to 28.20; P = .0003), respectively, versus White patients in adjusted models. CONCLUSION Germline genetic features differed by race/ethnicity in young patients with CRC, suggesting that current multigene panel tests may not be representative of EOCRC risk in diverse populations. Further study is needed to optimize genes selected for genetic testing in EOCRC via ancestry-specific gene and variant discovery to yield equitable clinical benefits for all patients and to mitigate inequities in disease burden.
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Affiliation(s)
- Hannah M. Seagle
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt University School of Medicine, Nashville, TN
| | - Samantha R. Keller
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt University School of Medicine, Nashville, TN
| | - Sean V. Tavtigian
- Department of Oncological Sciences, University of Utah, Salt Lake City, UT
| | - Carolyn Horton
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA
| | - Andreana N. Holowatyj
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt University School of Medicine, Nashville, TN
- Department of Population Health Sciences, University of Utah, Salt Lake City, UT
- Vanderbilt-Ingram Cancer Center, Nashville, TN
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17
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Martinez-Perez D, Viñal D, Peña-Lopez J, Jimenez-Bou D, Ruiz-Gutierrez I, Martinez-Recio S, Alameda-Guijarro M, Rueda-Lara A, Martin-Montalvo G, Ghanem I, Custodio AB, Trilla-Fuertes L, Gamez-Pozo A, Barbachano A, Rodriguez-Cobos J, Bustamante-Madrid P, Fernandez-Barral A, Burgos A, Prieto-Nieto MI, Pastrian LG, González-Sancho JM, Muñoz A, Feliu J, Rodríguez-Salas N. Clinico-Pathological Features, Outcomes and Impacts of COVID-19 Pandemic on Patients with Early-Onset Colorectal Cancer: A Single-Institution Experience. Cancers (Basel) 2023; 15:4242. [PMID: 37686518 PMCID: PMC10487095 DOI: 10.3390/cancers15174242] [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: 06/05/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND The rising incidence of colorectal cancer (CRC) among young patients is alarming. We aim to characterize the clinico-pathological features and outcomes of patients with early-onset CRC (EOCRC), as well as the impacts of COVID-19 pandemic. METHODS We included all patients with pathologically confirmed diagnoses of CRC at Hospital Universitario La Paz from October 2016 to December 2021. The EOCRC cut-off age was 50 years old. RESULTS A total of 1475 patients diagnosed with CRC were included, eighty (5.4%) of whom had EOCRC. Significant differences were found between EOCRC and later-onset patients regarding T, N stage and metastatic presentation at diagnosis; perineural invasion; tumor budding; high-grade tumors; and signet ring cell histology, with all issues having higher prevalence in the early-onset group. More EOCRC patients had the RAS/ BRAF wild type. Chemotherapy was administered more frequently to patients with EOCRC. In the metastatic setting, the EOCRC group presented a significantly longer median OS. Regarding the COVID-19 pandemic, more patients with COVID-19 were diagnosed with metastatic disease (61%) in the year after the lockdown (14 March 2020) than in the pre-pandemic EOCRC group (29%). CONCLUSIONS EOCRC is diagnosed at a more advanced stage and with worse survival features in localized patients. More patients with EOCRC were diagnosed with metastatic disease in the year after the COVID-19 pandemic lockdown. The long-term consequences of COVID-19 are yet to be determined.
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Affiliation(s)
- Daniel Martinez-Perez
- Department of Medical Oncology, Central University Hospital of Asturias, 33011 Oviedo, Spain; (D.M.-P.); (J.F.); (N.R.-S.)
| | - David Viñal
- Department of Medical Oncology, Hospital Universitario La Paz, 28046 Madrid, Spain; (J.P.-L.); (D.J.-B.); (I.R.-G.); (M.A.-G.); (A.R.-L.); (G.M.-M.); (I.G.); (A.B.C.)
| | - Jesús Peña-Lopez
- Department of Medical Oncology, Hospital Universitario La Paz, 28046 Madrid, Spain; (J.P.-L.); (D.J.-B.); (I.R.-G.); (M.A.-G.); (A.R.-L.); (G.M.-M.); (I.G.); (A.B.C.)
| | - Diego Jimenez-Bou
- Department of Medical Oncology, Hospital Universitario La Paz, 28046 Madrid, Spain; (J.P.-L.); (D.J.-B.); (I.R.-G.); (M.A.-G.); (A.R.-L.); (G.M.-M.); (I.G.); (A.B.C.)
| | - Iciar Ruiz-Gutierrez
- Department of Medical Oncology, Hospital Universitario La Paz, 28046 Madrid, Spain; (J.P.-L.); (D.J.-B.); (I.R.-G.); (M.A.-G.); (A.R.-L.); (G.M.-M.); (I.G.); (A.B.C.)
| | - Sergio Martinez-Recio
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain;
| | - María Alameda-Guijarro
- Department of Medical Oncology, Hospital Universitario La Paz, 28046 Madrid, Spain; (J.P.-L.); (D.J.-B.); (I.R.-G.); (M.A.-G.); (A.R.-L.); (G.M.-M.); (I.G.); (A.B.C.)
| | - Antonio Rueda-Lara
- Department of Medical Oncology, Hospital Universitario La Paz, 28046 Madrid, Spain; (J.P.-L.); (D.J.-B.); (I.R.-G.); (M.A.-G.); (A.R.-L.); (G.M.-M.); (I.G.); (A.B.C.)
| | - Gema Martin-Montalvo
- Department of Medical Oncology, Hospital Universitario La Paz, 28046 Madrid, Spain; (J.P.-L.); (D.J.-B.); (I.R.-G.); (M.A.-G.); (A.R.-L.); (G.M.-M.); (I.G.); (A.B.C.)
| | - Ismael Ghanem
- Department of Medical Oncology, Hospital Universitario La Paz, 28046 Madrid, Spain; (J.P.-L.); (D.J.-B.); (I.R.-G.); (M.A.-G.); (A.R.-L.); (G.M.-M.); (I.G.); (A.B.C.)
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz (IdiPAZ), 28046 Madrid, Spain; (A.B.); (J.R.-C.); (P.B.-M.); (A.F.-B.); (M.I.P.-N.); (J.M.G.-S.); (A.M.)
| | - Ana Belén Custodio
- Department of Medical Oncology, Hospital Universitario La Paz, 28046 Madrid, Spain; (J.P.-L.); (D.J.-B.); (I.R.-G.); (M.A.-G.); (A.R.-L.); (G.M.-M.); (I.G.); (A.B.C.)
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz (IdiPAZ), 28046 Madrid, Spain; (A.B.); (J.R.-C.); (P.B.-M.); (A.F.-B.); (M.I.P.-N.); (J.M.G.-S.); (A.M.)
| | - Lucia Trilla-Fuertes
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain; (L.T.-F.); (A.G.-P.)
| | - Angelo Gamez-Pozo
- Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz-IdiPAZ, 28046 Madrid, Spain; (L.T.-F.); (A.G.-P.)
| | - Antonio Barbachano
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz (IdiPAZ), 28046 Madrid, Spain; (A.B.); (J.R.-C.); (P.B.-M.); (A.F.-B.); (M.I.P.-N.); (J.M.G.-S.); (A.M.)
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain;
| | - Javier Rodriguez-Cobos
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz (IdiPAZ), 28046 Madrid, Spain; (A.B.); (J.R.-C.); (P.B.-M.); (A.F.-B.); (M.I.P.-N.); (J.M.G.-S.); (A.M.)
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain;
| | - Pilar Bustamante-Madrid
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz (IdiPAZ), 28046 Madrid, Spain; (A.B.); (J.R.-C.); (P.B.-M.); (A.F.-B.); (M.I.P.-N.); (J.M.G.-S.); (A.M.)
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain;
| | - Asuncion Fernandez-Barral
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz (IdiPAZ), 28046 Madrid, Spain; (A.B.); (J.R.-C.); (P.B.-M.); (A.F.-B.); (M.I.P.-N.); (J.M.G.-S.); (A.M.)
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain;
| | - Aurora Burgos
- Department of Gastroenterology, Hospital Universitario La Paz, 28046 Madrid, Spain;
| | - Maria Isabel Prieto-Nieto
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz (IdiPAZ), 28046 Madrid, Spain; (A.B.); (J.R.-C.); (P.B.-M.); (A.F.-B.); (M.I.P.-N.); (J.M.G.-S.); (A.M.)
- Department of Surgery, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Laura Guerra Pastrian
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain;
- Department of Pathology, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - José Manuel González-Sancho
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz (IdiPAZ), 28046 Madrid, Spain; (A.B.); (J.R.-C.); (P.B.-M.); (A.F.-B.); (M.I.P.-N.); (J.M.G.-S.); (A.M.)
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain;
| | - Alberto Muñoz
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz (IdiPAZ), 28046 Madrid, Spain; (A.B.); (J.R.-C.); (P.B.-M.); (A.F.-B.); (M.I.P.-N.); (J.M.G.-S.); (A.M.)
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain;
| | - Jaime Feliu
- Department of Medical Oncology, Central University Hospital of Asturias, 33011 Oviedo, Spain; (D.M.-P.); (J.F.); (N.R.-S.)
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz (IdiPAZ), 28046 Madrid, Spain; (A.B.); (J.R.-C.); (P.B.-M.); (A.F.-B.); (M.I.P.-N.); (J.M.G.-S.); (A.M.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain;
- Catedra UAM-AMGEN, 28046 Madrid, Spain
| | - Nuria Rodríguez-Salas
- Department of Medical Oncology, Central University Hospital of Asturias, 33011 Oviedo, Spain; (D.M.-P.); (J.F.); (N.R.-S.)
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz (IdiPAZ), 28046 Madrid, Spain; (A.B.); (J.R.-C.); (P.B.-M.); (A.F.-B.); (M.I.P.-N.); (J.M.G.-S.); (A.M.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain;
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18
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Isaic A, Motofelea AC, Costachescu D, Pop GN, Totolici B, Popovici D, Diaconescu RG. What Is the Comparative Efficacy of Surgical, Endoscopic, Transanal Resection, and Radiotherapy Modalities in the Treatment of Rectal Cancer? Healthcare (Basel) 2023; 11:2347. [PMID: 37628544 PMCID: PMC10454130 DOI: 10.3390/healthcare11162347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Rectal cancer is a significant healthcare burden, and effective treatment is crucial. This research aims to compare the effectiveness of surgical and endoscopic resection, transanal resection, and radiotherapy. METHODS A literature analysis was conducted in order to identify relevant studies, by comparing the different surgical approaches and variables affecting treatment decisions. The findings were analyzed and synthesized to provide a comprehensive overview. RESULTS Surgical treatment, particularly TME (total mesorectal excision), proved consistent efficacy in achieving complete tumor resection and improving long-term survival. Endoscopic treatment and transanal resection techniques were promising for early-stage tumors but were associated with higher local recurrence rates. Radiotherapy, especially in combination with chemotherapy, played a crucial role in locally advanced cases, improving local control and reducing recurrence risk. Patient data, tumor characteristics, and healthcare system factors were identified as important factors in treatment modality selection. CONCLUSION Surgical treatment, specifically TME, remains the recommended standard approach for rectal cancer, providing excellent oncological outcomes. Endoscopic treatment and transanal resection techniques can be considered for selected early-stage cases, while radiotherapy is beneficial for locally advanced tumors. Treatment decisions should be personalized based on patient and tumor characteristics, considering the available resources and expertise within the healthcare system.
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Affiliation(s)
- Alexandru Isaic
- IInd Surgery Clinic, Timisoara Emergency County Hospital, 300723 Timisoara, Romania;
- Department X of General Surgery, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Alexandru Cătălin Motofelea
- Department of Internal Medicine, Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
| | - Dan Costachescu
- Department of Orthopedics-Traumatology, Urology, Radiology, and Medical Imaging, “Victor Babes” University of Medicine and Pharmacy Timisoara, Eftimie Murgu Square 2, 300041 Timisoara, Romania;
- Department of Oncology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Gheorghe Nicusor Pop
- Center for Modeling Biological Systems and Data Analysis, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Bogdan Totolici
- 1st Clinic of General Surgery, Arad County Emergency Clinical Hospital, 310158 Arad, Romania;
- Department of General Surgery, Faculty of Medicine, “Victor Babes” Western University of Arad, 310025 Arad, Romania
| | - Dorel Popovici
- Department of Oncology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
| | - Razvan Gheorghe Diaconescu
- OncoHelp Hospital, 300239 Timisoara, Romania;
- Department of Surgery, Faculty of Medicine, “Victor Babes” Western University of Arad, 310025 Arad, Romania
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19
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Sivakumar S, Moore JA, Montesion M, Sharaf R, Lin DI, Colón CI, Fleishmann Z, Ebot EM, Newberg JY, Mills JM, Hegde PS, Pan Q, Dowlati A, Frampton GM, Sage J, Lovly CM. Integrative Analysis of a Large Real-World Cohort of Small Cell Lung Cancer Identifies Distinct Genetic Subtypes and Insights into Histologic Transformation. Cancer Discov 2023; 13:1572-1591. [PMID: 37062002 PMCID: PMC10326603 DOI: 10.1158/2159-8290.cd-22-0620] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 03/08/2023] [Accepted: 04/06/2023] [Indexed: 04/17/2023]
Abstract
Small cell lung cancer (SCLC) is a recalcitrant neuroendocrine carcinoma with dismal survival outcomes. A major barrier in the field has been the relative paucity of human tumors studied. Here we provide an integrated analysis of 3,600 "real-world" SCLC cases. This large cohort allowed us to identify new recurrent alterations and genetic subtypes, including STK11-mutant tumors (1.7%) and TP53/RB1 wild-type tumors (5.5%), as well as rare cases that were human papillomavirus-positive. In our cohort, gene amplifications on 4q12 are associated with increased overall survival, whereas CCNE1 amplification is associated with decreased overall survival. We also identify more frequent alterations in the PTEN pathway in brain metastases. Finally, profiling cases of SCLC containing oncogenic drivers typically associated with NSCLC demonstrates that SCLC transformation may occur across multiple distinct molecular cohorts of NSCLC. These novel and unsuspected genetic features of SCLC may help personalize treatment approaches for this fatal form of cancer. SIGNIFICANCE Minimal changes in therapy and survival outcomes have occurred in SCLC for the past four decades. The identification of new genetic subtypes and novel recurrent mutations as well as an improved understanding of the mechanisms of transformation to SCLC from NSCLC may guide the development of personalized therapies for subsets of patients with SCLC. This article is highlighted in the In This Issue feature, p. 1501.
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Affiliation(s)
| | - Jay A Moore
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | | | - Radwa Sharaf
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | | | - Caterina I Colón
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California
| | | | | | | | | | | | - Quintin Pan
- University Hospitals Seidman Cancer Center and Case Western Reserve University, Cleveland, Ohio
| | - Afshin Dowlati
- University Hospitals Seidman Cancer Center and Case Western Reserve University, Cleveland, Ohio
| | | | - Julien Sage
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California
| | - Christine M Lovly
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
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20
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Manirakiza F, Rutaganda E, Yamada H, Iwashita Y, Rugwizangoga B, Seminega B, Dusabejambo V, Ntakirutimana G, Ruhangaza D, Uwineza A, Shinmura K, Sugimura H. Clinicopathological Characteristics and Mutational Landscape of APC, HOXB13, and KRAS among Rwandan Patients with Colorectal Cancer. Curr Issues Mol Biol 2023; 45:4359-4374. [PMID: 37232746 DOI: 10.3390/cimb45050277] [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: 03/27/2023] [Revised: 04/24/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023] Open
Abstract
Cancer research in Rwanda is estimated to be less than 1% of the total African cancer research output with limited research on colorectal cancer (CRC). Rwandan patients with CRC are young, with more females being affected than males, and most patients present with advanced disease. Considering the paucity of oncological genetic studies in this population, we investigated the mutational status of CRC tissues, focusing on the Adenomatous polyposis coli (APC), Kirsten rat sarcoma (KRAS), and Homeobox B13 (HOXB13) genes. Our aim was to determine whether there were any differences between Rwandan patients and other populations. To do so, we performed Sanger sequencing of the DNA extracted from formalin-fixed paraffin-embedded adenocarcinoma samples from 54 patients (mean age: 60 years). Most tumors were located in the rectum (83.3%), and 92.6% of the tumors were low-grade. Most patients (70.4%) reported never smoking, and 61.1% of patients had consumed alcohol. We identified 27 variants of APC, including 3 novel mutations (c.4310_4319delAAACACCTCC, c.4463_4470delinsA, and c.4506_4507delT). All three novel mutations are classified as deleterious by MutationTaster2021. We found four synonymous variants (c.330C>A, c.366C>T, c.513T>C, and c.735G>A) of HOXB13. For KRAS, we found six variants (Asp173, Gly13Asp, Gly12Ala, Gly12Asp, Gly12Val, and Gln61His), the last four of which are pathogenic. In conclusion, here we contribute new genetic variation data and provide clinicopathological information pertinent to CRC in Rwanda.
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Affiliation(s)
- Felix Manirakiza
- Department of Pathology, College of Medicine and Health Sciences, University of Rwanda, Kigali P.O. Box 3286, Rwanda
- Department of Pathology, University Teaching Hospital of Kigali, Kigali P.O. Box 655, Rwanda
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Shizuoka 431-3192, Japan
| | - Eric Rutaganda
- Department of Internal Medicine, University Teaching Hospital of Kigali, Kigali P.O. Box 655, Rwanda
| | - Hidetaka Yamada
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Shizuoka 431-3192, Japan
| | - Yuji Iwashita
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Shizuoka 431-3192, Japan
| | - Belson Rugwizangoga
- Department of Pathology, College of Medicine and Health Sciences, University of Rwanda, Kigali P.O. Box 3286, Rwanda
- Department of Pathology, University Teaching Hospital of Kigali, Kigali P.O. Box 655, Rwanda
| | - Benoit Seminega
- Department of Internal Medicine, University Teaching Hospital of Kigali, Kigali P.O. Box 655, Rwanda
| | - Vincent Dusabejambo
- Department of Internal Medicine, University Teaching Hospital of Kigali, Kigali P.O. Box 655, Rwanda
| | - Gervais Ntakirutimana
- Department of Pathology, University Teaching Hospital of Kigali, Kigali P.O. Box 655, Rwanda
| | | | - Annette Uwineza
- Department of Pathology, University Teaching Hospital of Kigali, Kigali P.O. Box 655, Rwanda
- Department of Biochemistry, Molecular Biology and Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali P.O. Box 3286, Rwanda
| | - Kazuya Shinmura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Shizuoka 431-3192, Japan
| | - Haruhiko Sugimura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Shizuoka 431-3192, Japan
- Sasaki Institute Sasaki Foundation, 2-2 Kanda Surugadai, Chiyoda-Ku, Tokyo 101-0062, Japan
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KRAS, NRAS, BRAF, HER2 and MSI Status in a Large Consecutive Series of Colorectal Carcinomas. Int J Mol Sci 2023; 24:ijms24054868. [PMID: 36902296 PMCID: PMC10003572 DOI: 10.3390/ijms24054868] [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: 01/28/2023] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
This study aimed to analyze clinical and regional factors influencing the distribution of actionable genetic alterations in a large consecutive series of colorectal carcinomas (CRCs). KRAS, NRAS and BRAF mutations, HER2 amplification and overexpression, and microsatellite instability (MSI) were tested in 8355 CRC samples. KRAS mutations were detected in 4137/8355 (49.5%) CRCs, with 3913 belonging to 10 common substitutions affecting codons 12/13/61/146, 174 being represented by 21 rare hot-spot variants, and 35 located outside the "hot" codons. KRAS Q61K substitution, which leads to the aberrant splicing of the gene, was accompanied by the second function-rescuing mutation in all 19 tumors analyzed. NRAS mutations were detected in 389/8355 (4.7%) CRCs (379 hot-spot and 10 non-hot-spot substitutions). BRAF mutations were identified in 556/8355 (6.7%) CRCs (codon 600: 510; codons 594-596: 38; codons 597-602: 8). The frequency of HER2 activation and MSI was 99/8008 (1.2%) and 432/8355 (5.2%), respectively. Some of the above events demonstrated differences in distribution according to patients' age and gender. In contrast to other genetic alterations, BRAF mutation frequencies were subject to geographic variation, with a relatively low incidence in areas with an apparently warmer climate (83/1726 (4.8%) in Southern Russia and North Caucasus vs. 473/6629 (7.1%) in other regions of Russia, p = 0.0007). The simultaneous presence of two drug targets, BRAF mutation and MSI, was observed in 117/8355 cases (1.4%). Combined alterations of two driver genes were detected in 28/8355 (0.3%) tumors (KRAS/NRAS: 8; KRAS/BRAF: 4; KRAS/HER2: 12; NRAS/HER2: 4). This study demonstrates that a substantial portion of RAS alterations is represented by atypical mutations, KRAS Q61K substitution is always accompanied by the second gene-rescuing mutation, BRAF mutation frequency is a subject to geographical variations, and a small fraction of CRCs has simultaneous alterations in more than one driver gene.
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22
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Holowatyj AN, Wen W, Gibbs T, Seagle HM, Keller SR, Edwards DRV, Washington MK, Eng C, Perea J, Zheng W, Guo X. Racial/Ethnic and Sex Differences in Somatic Cancer Gene Mutations among Patients with Early-Onset Colorectal Cancer. Cancer Discov 2023; 13:570-579. [PMID: 36520636 PMCID: PMC10436779 DOI: 10.1158/2159-8290.cd-22-0764] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/07/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Molecular features underlying colorectal cancer disparities remain uncharacterized. Here, we investigated somatic mutation patterns by race/ethnicity and sex among 5,856 non-Hispanic white (NHW), 535 non-Hispanic Black (NHB), and 512 Asian/Pacific Islander (API) patients with colorectal cancer (2,016 early-onset colorectal cancer patients: sequencing age <50 years). NHB patients with early-onset nonhypermutated colorectal cancer, but not API patients, had higher adjusted tumor mutation rates than NHW patients. There were significant differences for LRP1B, FLT4, FBXW7, RNF43, ATRX, APC, and PIK3CA mutation frequencies in early-onset nonhypermutated colorectal cancers between racial/ethnic groups. Heterogeneities by race/ethnicity were observed for the effect of APC, FLT4, and FAT1 between early-onset and late-onset nonhypermutated colorectal cancer. By sex, heterogeneity was observed for the effect of EP300, BRAF, WRN, KRAS, AXIN2, and SMAD2. Males and females with nonhypermutated colorectal cancer had different trends in EP300 mutations by age group. These findings define genomic patterns of early-onset nonhypermutated colorectal cancer by race/ethnicity and sex, which yields novel biological clues into early-onset colorectal cancer disparities. SIGNIFICANCE NHBs, but not APIs, with early-onset nonhypermutated colorectal cancer had higher adjusted tumor mutation rates versus NHWs. Differences for FLT4, FBXW7, RNF43, LRP1B, APC, PIK3CA, and ATRX mutation rates between racial/ethnic groups and EP300, KRAS, AXIN2, WRN, BRAF, and LRP1B mutation rates by sex were observed in tumors of young patients. See related commentary by Shen et al., p. 530 . This article is highlighted in the In This Issue feature, p. 517.
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Affiliation(s)
- Andreana N. Holowatyj
- Department of Medicine, Microbiology and Immunology
- Vanderbilt-Ingram Cancer Center, Nashville, TN
- Vanderbilt University School of Medicine, Nashville, TN
| | - Wanqing Wen
- Department of Medicine, Microbiology and Immunology
| | | | - Hannah M. Seagle
- Department of Medicine, Microbiology and Immunology
- Vanderbilt University School of Medicine, Nashville, TN
| | - Samantha R. Keller
- Department of Medicine, Microbiology and Immunology
- Vanderbilt University School of Medicine, Nashville, TN
| | - Digna R. Velez Edwards
- Department of Obstetrics and Gynecology; Vanderbilt University Medical Center, Nashville, TN
| | - Mary K. Washington
- Department of Pathology, Microbiology and Immunology
- Vanderbilt-Ingram Cancer Center, Nashville, TN
| | - Cathy Eng
- Department of Medicine, Microbiology and Immunology
- Vanderbilt-Ingram Cancer Center, Nashville, TN
| | - Jose Perea
- Molecular Medicine Unit, Department of Medicine, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
- Department of Surgery, “Vithas Arturo Soria” University Hospital and School of Medicine, European University of Madrid, Madrid, Spain
| | - Wei Zheng
- Department of Medicine, Microbiology and Immunology
- Vanderbilt-Ingram Cancer Center, Nashville, TN
| | - Xingyi Guo
- Department of Medicine, Microbiology and Immunology
- Vanderbilt-Ingram Cancer Center, Nashville, TN
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23
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Jardim DL, Murugesan K, Elvin JA, Huang RSP, Kurzrock R. PD-L1 gene amplification and focality: relationship with protein expression. J Immunother Cancer 2023; 11:jitc-2022-006311. [PMID: 36849197 PMCID: PMC9972417 DOI: 10.1136/jitc-2022-006311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2023] [Indexed: 03/01/2023] Open
Abstract
PD-L1 (CD274) amplification occurs in a small subset of malignancies and may predict anti-PD-1/PD-L1 immunotherapy responsiveness. We hypothesized that both copy number (CN) and focality of cancer-related PD-L1 amplifications impact protein expression, and, thus, analyzed solid tumors that underwent comprehensive genomic profiling between March 2016 and February 2022 at Foundation Medicine. PD-L1 CN alterations were detected using a comparative genomic hybridization-like method. PD-L1 CN changes were correlated with PD-L1 protein expression (DAKO 22C3 antibody) by immunohistochemistry (IHC). Overall, 60,793 samples were analyzed (most frequent histologies: lung adenocarcinoma (20%), colon adenocarcinoma (12%), lung squamous carcinoma (8%)). Using a definition of CD274 CN ≥ specimen ploidy +4 (6 copies), 1.21% of tumors (738/60,793) were PD-L1 amplified. Focality category distribution was as follows: <0.1 mB (n=18 (2.4%)), ≥0.1 to <4 mB (n=230 (31.1%)), ≥4 to <20 mB (n=310 (42%)), ≥20mB (n=180 (24.4%)). Lower levels of PD-L1 amplification (below specimen ploidy +4) were more frequently non-focal amplifications compared to higher levels. In addition, more focal amplification (<0.1 mB) correlated with higher PD-L1 IHC expression. Median tumor proportion score (TPS) for samples with PD-L1 amplification (ploidy ≥+4) according to focality were 87.5% (<0.1 mB), 80% (≥0.1 to <4 mB), 40% (≥4 to <20 mB), 1% (≥20mB). In specimens with PD-L1 ploidy less than +4, but highly focal (<0.1 mB), the 75th percentile of PD-L1 expression by TPS was 80%. Conversely, non-focal (≥20 mB) PD-L1 amplification (ploidy ≥+4) can present high PD-L1 expression (TPS≥50%), albeit infrequently (0.09% of our cohort). In conclusion, PD-L1 expression measured by IHC is influenced by PD-L1 amplification level and focality. Further correlation between amplification, focality, protein expression and therapeutic outcome for PD-L1 and other targetable genes warrants exploration.
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Affiliation(s)
| | - Karthikeyan Murugesan
- Cancer Genomics Research, Foundation Medicine Inc, Cambridge, Massachusetts, USA,Foundation Medicine Inc, Cambridge, Massachusetts, USA
| | | | | | - Razelle Kurzrock
- Department of Medicine, WIN Consortium for Personalized Cancer Therapy, La Jolla, San Diego, USA,Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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24
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Arora K, Tran TN, Kemel Y, Mehine M, Liu YL, Nandakumar S, Smith SA, Brannon AR, Ostrovnaya I, Stopsack KH, Razavi P, Safonov A, Rizvi HA, Hellmann MD, Vijai J, Reynolds TC, Fagin JA, Carrot-Zhang J, Offit K, Solit DB, Ladanyi M, Schultz N, Zehir A, Brown CL, Stadler ZK, Chakravarty D, Bandlamudi C, Berger MF. Genetic Ancestry Correlates with Somatic Differences in a Real-World Clinical Cancer Sequencing Cohort. Cancer Discov 2022; 12:2552-2565. [PMID: 36048199 PMCID: PMC9633436 DOI: 10.1158/2159-8290.cd-22-0312] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/12/2022] [Accepted: 08/29/2022] [Indexed: 01/12/2023]
Abstract
Accurate ancestry inference is critical for identifying genetic contributors of cancer disparities among populations. Although methods to infer genetic ancestry have historically relied upon genome-wide markers, the adaptation to targeted clinical sequencing panels presents an opportunity to incorporate ancestry inference into routine diagnostic workflows. We show that global ancestral contributions and admixture of continental populations can be quantitatively inferred using markers captured by the MSK-IMPACT clinical panel. In a pan-cancer cohort of 45,157 patients, we observed differences by ancestry in the frequency of somatic alterations, recapitulating known associations and revealing novel associations. Despite the comparable overall prevalence of driver alterations by ancestry group, the proportion of patients with clinically actionable alterations was lower for African (30%) compared with European (33%) ancestry. Although this result is largely explained by population-specific cancer subtype differences, it reveals an inequity in the degree to which different populations are served by existing precision oncology interventions. SIGNIFICANCE We performed a comprehensive analysis of ancestral associations with somatic mutations in a real-world pan-cancer cohort, including >5,000 non-European individuals. Using an FDA-authorized tumor sequencing panel and an FDA-recognized oncology knowledge base, we detected differences in the prevalence of clinically actionable alterations, potentially contributing to health care disparities affecting underrepresented populations. This article is highlighted in the In This Issue feature, p. 2483.
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Affiliation(s)
- Kanika Arora
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thinh Ngoc. Tran
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Kemel
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Miika Mehine
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying L. Liu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Subhiksha Nandakumar
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shaleigh A Smith
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A. Rose Brannon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Konrad H. Stopsack
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anton Safonov
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hira A. Rizvi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew D. Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph Vijai
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thomas C. Reynolds
- Office of Health Equity, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James A. Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jian Carrot-Zhang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth Offit
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B. Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carol L. Brown
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Office of Health Equity, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsofia K. Stadler
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chaitanya Bandlamudi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F. Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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25
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Cheng ML, Lee JK, Kumar R, Klein H, Raskina K, Schrock AB, Michael KS, Mazor T, Cerami E, Oxnard GR, Liu D, Beltran H, Sholl LM, Nishino M, Jänne PA. Response to MEK Inhibitor Therapy in MAP2K1 ( MEK1) K57N Non-Small-Cell Lung Cancer and Genomic Landscape of MAP2K1 Mutations in Non-Small-Cell Lung Cancer. JCO Precis Oncol 2022; 6:e2200382. [PMID: 36455195 DOI: 10.1200/po.22.00382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Affiliation(s)
- Michael L Cheng
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA.,Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Present address: Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
| | | | - Rachit Kumar
- Harold Alfond Center for Cancer Care, MaineHealth, Augusta, MA
| | - Harry Klein
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Kesi S Michael
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA.,Present address: Foundation Medicine, Cambridge, MA
| | - Tali Mazor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Ethan Cerami
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | | | - David Liu
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Himisha Beltran
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Mizuki Nishino
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Department of Imaging, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Pasi A Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA.,Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
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26
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Sa JK, Kim J, Kang S, Kim SW, Song T, Shim SH, Choi MC, No JH, Song JY, Kim D, Kim YM, Kim JH, Lee JW. Somatic genomic landscape of East Asian epithelial ovarian carcinoma and its clinical implications from prospective clinical sequencing; A Korean Gynecologic Oncology Group study (KGOG 3047). Int J Cancer 2022; 151:1086-1097. [PMID: 35666535 DOI: 10.1002/ijc.34150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/27/2022] [Accepted: 05/17/2022] [Indexed: 12/24/2022]
Abstract
Through the wide adaptation of next-generation sequencing (NGS) technology within clinical practice, molecular profiling of the tumor has been the principal component of personalized treatment. In this study, we have generated a large collection of cancer genomes on East Asian epithelial ovarian carcinoma (EOC) patients and demonstrate the feasibility and utility of NGS platforms to explore the dynamic interrelations of major cancer driver alterations and their impacts on clinical prognosis and management. A total of 652 EOC patients have undergone clinical NGS panels to determine the prevalence of germline and somatic mutations. Notably, TP53 was the most frequently altered event (73%), followed by both BRCA1 and BRCA2 (22% each) and MYC (19%) through pan-EOC analysis. When analyzed based on individual histopathological levels, TP53 mutation was highly dominant in high-grade serous and mucinous histology, whereas mutations in PIK3CA and ARID1A were mostly observed in clear cell carcinoma, and KRAS, BRAF, and CDKN2A mutations were enriched in endometrioid, low-grade serous, and mucinous tumors, respectively. The network-based probabilistic model showed significant co-occurrences of TP53 with BRCA1 and ALK with BRCA2, NOTCH1, and ROS1, whereas mutual exclusivity of TP53 with KRAS and PIK3CA was evident. Furthermore, we utilized machine-learning algorithms to identify molecular correlates that conferred increased sensitivity to platinum and olaparib treatments including somatic mutations in BRCA1, ATM, and MYC. Conversely, patients with ALK mutation were considerably resistant to both treatment modalities. Collectively, our results demonstrate the clinical feasibility of prospective genetic sequencing to facilitate personalized treatment opportunities for patients with EOC.
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Affiliation(s)
- Jason K Sa
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jihye Kim
- Departments of Obstetrics and Gynecology, Chung-ang University Gwang-myeong Hospital, Gwang-myeong, Republic of Korea
| | - Sokbom Kang
- Gynecologic Cancer Branch, Research Institute and Hospital, National Cancer Center, Goyang, South Korea
| | - Sang Wun Kim
- Department of Obstetrics and Gynecology, Institute of Women's Life Medical Science, Women's Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Taejong Song
- Department of Obstetrics and Gynecology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Seung-Hyuk Shim
- Department of Obstetrics and Gynecology, Research Institute of Medical Science, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Min Chul Choi
- Comprehensive Gynecologic Cancer Center, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Jae Hong No
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jae-Yun Song
- Department of Obstetrics and Gynecology, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - Deokhoon Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Yong-Man Kim
- Department of Obstetrics and Gynecology, College of Medicine, University of Ulsan, Asan Medical Center, Seoul, Korea
| | - Jae-Hoon Kim
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jeong-Won Lee
- Departments of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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27
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Abstract
Understanding molecular features of colorectal cancer across diverse populations is an indispensable step toward reducing the pronounced disparities in this disease burden. Based on the findings that individuals of African ancestry have an observed increase in the frequency of KRAS, AOC, and PIK3CA mutations, Myer and colleagues suggest that patients of African ancestry should consider treatment and clinical trials specific to these mutations. See related article by Myer et al., p. 1282 (2).
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Affiliation(s)
- Cathy Eng
- Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Andreana N Holowatyj
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
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28
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Abdullah M, Meilany S, Trimarsanto H, Malik SG, Sukartini N, Idrus F, Nursyirwan SA, Muzellina VN, Pribadi RR, Utari AP, Maulahela H, Syam AF. Genomic profiles of Indonesian colorectal cancer patients. F1000Res 2022; 11:443. [PMID: 37125020 PMCID: PMC10133825 DOI: 10.12688/f1000research.109136.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/13/2023] [Indexed: 02/23/2023] Open
Abstract
Background: Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide and genetic mutation plays a vital role in CRC development. A previous study has suggested that genetic alterations among Indonesian patients with CRC might differ from those known in developed countries. This study aimed to describe the genomic profiles of Indonesian patients with CRC. Methods: A total of 13 patients were recruited for this study from May to July 2019. Tissue samples were collected, and genomic DNA was extracted from the samples. AmpliSeq for Illumina Cancer HotSpot Panel v2 Next-generation sequencing was used for DNA sequencing and a genome analysis toolkit was used for local realignment around the discovered variants. Results: A total of 45 genes comprising 391 single nucleotide variants (SNVs) with a depth >10 were observed. The genes with the most variants were STK11, SMAD4, EGFR, and ERBB4 and the genes with the most non-synonymous variants were SMAD4, TP53, FGFR3, CDKN2A, and STK11. Genes and SNVs in at least 90% of all samples consisted of 43 genes comprising 286 variants. Genes with the most non-synonymous SNVs were EGFR, SMO, FGFR3, TP53, STK11, CDKN2A. Genes related to the chromosomal instability pathway, such as TP53, SMAD4, KRAS, and APC, are also found in the analysis. Conclusions: Our findings showed that all patients with CRC in this study had genetic mutations in the chromosomal instability pathway. Analysis of genetic mutation of Indonesian patients with CRC might be crucial for advanced targeted therapy and for better clinical outcomes.
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Affiliation(s)
- Murdani Abdullah
- Division of Gastroenterology, Pancreatobiliary, and Digestive Endoscopy, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo National General Hospital, Jakarta, 10430, Indonesia
- Human Cancer Research Center, Indonesian Medical Education and Research Institute, Faculty of Medicine, Universitas Indonesia, Jakarta, 10430, Indonesia
| | - Sofy Meilany
- Virology and Cancer Pathobiology Research Center, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo National General Hospital, Jakarta, 10430, Indonesia
| | - Hidayat Trimarsanto
- Eijkman Institute for Molecular Biology, Ministry of Research and Technology/National Research and Innovation Agency, Jakarta, 10430, Indonesia
| | - Safarina G. Malik
- Eijkman Institute for Molecular Biology, Ministry of Research and Technology/National Research and Innovation Agency, Jakarta, 10430, Indonesia
| | - Ninik Sukartini
- Department of Clinical Pathology, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo National General Hospital, Jakarta, 10430, Indonesia
| | - Firhat Idrus
- Division of Gastroenterology, Pancreatobiliary, and Digestive Endoscopy, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo National General Hospital, Jakarta, 10430, Indonesia
| | - Saskia A. Nursyirwan
- Division of Gastroenterology, Pancreatobiliary, and Digestive Endoscopy, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo National General Hospital, Jakarta, 10430, Indonesia
| | - Virly N. Muzellina
- Division of Gastroenterology, Pancreatobiliary, and Digestive Endoscopy, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo National General Hospital, Jakarta, 10430, Indonesia
| | - Rabbinu R. Pribadi
- Division of Gastroenterology, Pancreatobiliary, and Digestive Endoscopy, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo National General Hospital, Jakarta, 10430, Indonesia
| | - Amanda P. Utari
- Division of Gastroenterology, Pancreatobiliary, and Digestive Endoscopy, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo National General Hospital, Jakarta, 10430, Indonesia
| | - Hasan Maulahela
- Division of Gastroenterology, Pancreatobiliary, and Digestive Endoscopy, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo National General Hospital, Jakarta, 10430, Indonesia
| | - Ari F. Syam
- Division of Gastroenterology, Pancreatobiliary, and Digestive Endoscopy, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo National General Hospital, Jakarta, 10430, Indonesia
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