1
|
Purrington KS, Raychaudhuri S, Simon MS, Clark J, Ratliff V, Dyson G, Craig DB, Boerner JL, Beebe-Dimmer JL, Schwartz AG. Heritable Susceptibility to Breast Cancer among African-American Women in the Detroit Research on Cancer Survivors Study. Cancer Epidemiol Biomarkers Prev 2020; 29:2369-2375. [PMID: 32868316 DOI: 10.1158/1055-9965.epi-20-0564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/16/2020] [Accepted: 08/26/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND African-American women have high rates of breast cancer associated with hereditary features. However, no studies have reported the prevalence of inherited variation across all genes known to be breast cancer risk factors among African-American patients with breast cancer not selected for high-risk characteristics. METHODS We evaluated 182 African-American women diagnosed with invasive breast cancer in metropolitan Detroit via targeted capture and multiplex sequencing of 13 well-established breast cancer risk genes and five suggested breast cancer risk genes. RESULTS We identified 24 pathogenic variants in 23 women [12.6%; 95% confidence interval (CI), 8.2%-18.4%] and five genes (BRCA2, BRCA1, ATM, RAD50, CDH1). BRCA1 and BRCA2 accounted for 58.3% of all pathogenic variants. An additional six pathogenic variants were found in suggested breast cancer risk genes (MSH6, MUTYH, NF1, BRIP1). CONCLUSIONS The prevalence of germline pathogenic variants is relatively high among African-American patients with breast cancer unselected for high-risk characteristics across a broad spectrum of genes. IMPACT This study helps to define the genomic landscape of breast cancer susceptibility in African-American women who could benefit from enhanced surveillance and screening.
Collapse
Affiliation(s)
- Kristen S Purrington
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan. .,Population Studies and Disparities Research Program, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | | | - Michael S Simon
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan.,Population Studies and Disparities Research Program, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Julie Clark
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan.,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Valerie Ratliff
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
| | - Gregory Dyson
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan.,Population Studies and Disparities Research Program, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan.,Bioinformatics & Biostatistics Core, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Douglas B Craig
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan.,Bioinformatics & Biostatistics Core, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Julie L Boerner
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan.,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Jennifer L Beebe-Dimmer
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan.,Population Studies and Disparities Research Program, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Ann G Schwartz
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan.,Population Studies and Disparities Research Program, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| |
Collapse
|
2
|
Watza D, Lusk CM, Dyson G, Purrington KS, Chen K, Wenzlaff AS, Ratliff V, Neslund-Dudas C, Bepler G, Schwartz AG. Prognostic modeling of the immune-centric transcriptome reveals interleukin signaling candidates contributing to differential patient outcomes. Carcinogenesis 2019; 39:1447-1454. [PMID: 30202894 DOI: 10.1093/carcin/bgy119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/04/2018] [Indexed: 12/28/2022] Open
Abstract
Immunotherapy is a promising advancement in the treatment of non-small-cell lung carcinoma (NSCLC), although much of how lung tumors interact with the immune system in the natural course of disease remains unknown. We investigated the impact of the expression of immune-centric genes and pathways in tumors on patient survival to reveal novel candidates for immunotherapeutic research. Tumor transcriptomes and detailed clinical characteristics were obtained from patients with NSCLC who were participants of either the Inflammation, Health and Lung Epidemiology (INHALE) (discovery, N = 280) or The Cancer Genome Atlas (TCGA) Lung (replication, N = 1026) studies. Expressions of 2253 genes derived from 48 major immune pathways were assessed for association with patient prognosis using a multivariable Cox model and pathway effects were assessed with an in-house implementation of the Gene Set Enrichment Analysis (GSEA) algorithm. Prognosis-guided gene and pathway analysis of immune-centric expression in tumors revealed significant survival enrichments across both cohorts. The 'Interleukin Signaling' pathway, containing 430 genes, was found to be statistically and significantly enriched with prognostic signal in both the INHALE (P = 0.008) and TCGA (P = 0.039) datasets. Subsequent leading-edge analysis identified a subset of genes (N = 23) shared between both cohorts, driving the pathway enrichment. Cumulative expression of this leading-edge gene signature was a strong predictor of patient survival [discovery: hazard ratio (HR) = 1.59, P = 3.0 × 10-8; replication: HR = 1.29, P = 7.4 × 10-7]. These data demonstrate the impact of immune-centric expression on patient outcomes in NSCLC. Furthermore, prognostic gene effects were localized to discrete immune pathways, of which Interleukin Signaling had the greatest impact on overall survival and the subset of genes driving these effects have promise for future therapeutic intervention.
Collapse
Affiliation(s)
- Donovan Watza
- Department of Oncology, Wayne State University, Detroit, MI, USA.,Barbara Ann Karmanos Cancer Institute, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Christine M Lusk
- Department of Oncology, Wayne State University, Detroit, MI, USA.,Barbara Ann Karmanos Cancer Institute, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Gregory Dyson
- Department of Oncology, Wayne State University, Detroit, MI, USA.,Barbara Ann Karmanos Cancer Institute, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Kristen S Purrington
- Department of Oncology, Wayne State University, Detroit, MI, USA.,Barbara Ann Karmanos Cancer Institute, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Kang Chen
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA.,Department of Biochemistry Microbiology and Immunology, Wayne State University, Detroit, MI, USA.,Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University.,Mucosal Immunology Studies Team, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Detroit, MI, USA
| | - Angela S Wenzlaff
- Department of Oncology, Wayne State University, Detroit, MI, USA.,Barbara Ann Karmanos Cancer Institute, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Valerie Ratliff
- Department of Oncology, Wayne State University, Detroit, MI, USA.,Barbara Ann Karmanos Cancer Institute, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Christine Neslund-Dudas
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA.,Henry Ford Cancer Institute, Henry Ford Health System, Detroit, MI, USA
| | - Gerold Bepler
- Department of Oncology, Wayne State University, Detroit, MI, USA.,Barbara Ann Karmanos Cancer Institute, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Ann G Schwartz
- Department of Oncology, Wayne State University, Detroit, MI, USA.,Barbara Ann Karmanos Cancer Institute, School of Medicine, Wayne State University, Detroit, MI, USA
| |
Collapse
|
3
|
Lusk CM, Watza D, Dyson G, Craig D, Ratliff V, Wenzlaff AS, Lonardo F, Bollig-Fischer A, Bepler G, Purrington K, Gadgeel S, Schwartz AG. Profiling the Mutational Landscape in Known Driver Genes and Novel Genes in African American Non-Small Cell Lung Cancer Patients. Clin Cancer Res 2019; 25:4300-4308. [PMID: 30979741 DOI: 10.1158/1078-0432.ccr-18-2439] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 12/07/2018] [Accepted: 04/05/2019] [Indexed: 12/26/2022]
Abstract
PURPOSE Identifying novel driver genes and mutations in African American non-small cell lung cancer (NSCLC) cases can inform targeted therapy and improve outcomes for this traditionally underrepresented population. EXPERIMENTAL DESIGN Tumor DNA, RNA, and germline DNA were collected from African American NSCLC patients who participated in research conducted at the Karmanos Cancer Institute (KCI) in Detroit, Michigan. Known mutations were ascertained through the Sequenom LungCarta panel of 214 mutations in 26 genes, RET/ROS1 fusions, amplification of FGFR1, and expression of ALK. Paired tumor and normal DNA was whole-exome sequenced for a subset of cases without known driver mutations. RESULTS Of the 193 tumors tested, 77 known driver mutations were identified in 66 patients (34.2%). Sixty-seven of the 127 patients without a known driver mutation were sequenced. In 54 of these patients, 50 nonsynonymous mutations were predicted to have damaging effects among the 26 panel genes, 47 of which are not found in The Cancer Genome Atlas NSCLC white or African American samples. Analyzing the whole-exome sequence data using MutSig2CV identified a total of 88 genes significantly mutated at FDR q < 0.1. Only 5 of these genes were previously reported as oncogenic. CONCLUSIONS These findings suggest that broader mutation profiling including both known and novel driver genes in African Americans with NSCLC will identify additional mutations that may be useful in treatment decision-making.
Collapse
Affiliation(s)
- Christine M Lusk
- Karmanos Cancer Institute, Detroit, Michigan.,Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Donovan Watza
- Karmanos Cancer Institute, Detroit, Michigan.,Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Greg Dyson
- Karmanos Cancer Institute, Detroit, Michigan.,Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Douglas Craig
- Karmanos Cancer Institute, Detroit, Michigan.,Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Valerie Ratliff
- Karmanos Cancer Institute, Detroit, Michigan.,Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Angela S Wenzlaff
- Karmanos Cancer Institute, Detroit, Michigan.,Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Fulvio Lonardo
- Karmanos Cancer Institute, Detroit, Michigan.,Department of Pathology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Aliccia Bollig-Fischer
- Karmanos Cancer Institute, Detroit, Michigan.,Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Gerold Bepler
- Karmanos Cancer Institute, Detroit, Michigan.,Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Kristen Purrington
- Karmanos Cancer Institute, Detroit, Michigan.,Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Shirish Gadgeel
- Karmanos Cancer Institute, Detroit, Michigan.,Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan.,Currently at the Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Ann G Schwartz
- Karmanos Cancer Institute, Detroit, Michigan. .,Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan
| |
Collapse
|