1
|
Ntowe KW, Lee MS, Plichta JK. Clinical genetics in breast cancer. J Surg Oncol 2024; 130:16-22. [PMID: 38557982 PMCID: PMC11246818 DOI: 10.1002/jso.27630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024]
Abstract
As genetic testing becomes increasingly more accessible and more applicable with a broader range of clinical implications, it may also become more challenging for breast cancer providers to remain up-to-date. This review outlines some of the current clinical guidelines and recent literature surrounding germline genetic testing, as well as genomic testing, in the screening, prevention, diagnosis, and treatment of breast cancer, while identifying potential areas of further research.
Collapse
Affiliation(s)
- Koumani W. Ntowe
- Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | - Michael S. Lee
- Department of Surgery, Duke University Medical Center, Durham, North Carolina
| | - Jennifer K. Plichta
- Department of Surgery, Duke University Medical Center, Durham, North Carolina
- Duke Cancer Institute, Duke University, Durham, North Carolina
- Department of Population Health Sciences, Duke University Medical Center, Durham, North Carolina
| |
Collapse
|
2
|
Gao Y, Sharma T, Cui Y. Addressing the Challenge of Biomedical Data Inequality: An Artificial Intelligence Perspective. Annu Rev Biomed Data Sci 2023; 6:153-171. [PMID: 37104653 PMCID: PMC10529864 DOI: 10.1146/annurev-biodatasci-020722-020704] [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] [Indexed: 04/29/2023]
Abstract
Artificial intelligence (AI) and other data-driven technologies hold great promise to transform healthcare and confer the predictive power essential to precision medicine. However, the existing biomedical data, which are a vital resource and foundation for developing medical AI models, do not reflect the diversity of the human population. The low representation in biomedical data has become a significant health risk for non-European populations, and the growing application of AI opens a new pathway for this health risk to manifest and amplify. Here we review the current status of biomedical data inequality and present a conceptual framework for understanding its impacts on machine learning. We also discuss the recent advances in algorithmic interventions for mitigating health disparities arising from biomedical data inequality. Finally, we briefly discuss the newly identified disparity in data quality among ethnic groups and its potential impacts on machine learning.
Collapse
Affiliation(s)
- Yan Gao
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA;
| | - Teena Sharma
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA;
| | - Yan Cui
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA;
| |
Collapse
|
3
|
Desai AP, Kosari F, Disselhorst M, Yin J, Agahi A, Peikert T, Udell J, Johnson SH, Smadbeck J, Murphy S, Karagouga G, McCune A, Schaefer-Klein J, Borad MJ, Cheville J, Vasmatzis G, Baas P, Mansfield A. Dynamics and survival associations of T cell receptor clusters in patients with pleural mesothelioma treated with immunotherapy. J Immunother Cancer 2023; 11:e006035. [PMID: 37279993 PMCID: PMC10255162 DOI: 10.1136/jitc-2022-006035] [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: 04/26/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) are now a first-line treatment option for patients with pleural mesothelioma with the recent approval of ipilimumab and nivolumab. Mesothelioma has a low tumor mutation burden and no robust predictors of survival with ICI. Since ICIs enable adaptive antitumor immune responses, we investigated T-cell receptor (TCR) associations with survival in participants from two clinical trials treated with ICI. METHODS We included patients with pleural mesothelioma who were treated with nivolumab (NivoMes, NCT02497508) or nivolumab and ipilimumab (INITIATE, NCT03048474) after first-line therapy. TCR sequencing was performed with the ImmunoSEQ assay in 49 and 39 pretreatment and post-treatment patient peripheral blood mononuclear cell (PBMC) samples. These data were integrated with TCR sequences found in bulk RNAseq data by TRUST4 program in 45 and 35 pretreatment and post-treatment tumor biopsy samples and TCR sequences from over 600 healthy controls. The TCR sequences were clustered into groups of shared antigen specificity using GIANA. Associations of TCR clusters with overall survival were determined by cox proportional hazard analysis. RESULTS We identified 4.2 million and 12 thousand complementarity-determining region 3 (CDR3) sequences from PBMCs and tumors, respectively, in patients treated with ICI. These CDR3 sequences were integrated with 2.1 million publically available CDR3 sequences from healthy controls and clustered. ICI-enhanced T-cell infiltration and expanded T cell diversity in tumors. Cases with TCR clones in the top tertile in the pretreatment tissue or in circulation had significantly better survival than the bottom two tertiles (p<0.04). Furthermore, a high number of shared TCR clones between pretreatment tissue and in circulation was associated with improved survival (p=0.01). To potentially select antitumor clusters, we filtered for clusters that were (1) not found in healthy controls, (2) recurrent in multiple patients with mesothelioma, and (3) more prevalent in post-treatment than pretreatment samples. The detection of two-specific TCR clusters provided significant survival benefit compared with detection of 1 cluster (HR<0.001, p=0.026) or the detection of no TCR clusters (HR=0.10, p=0.002). These two clusters were not found in bulk tissue RNA-seq data and have not been reported in public CDR3 databases. CONCLUSIONS We identified two unique TCR clusters that were associated with survival on treatment with ICI in patients with pleural mesothelioma. These clusters may enable approaches for antigen discovery and inform future targets for design of adoptive T cell therapies.
Collapse
Affiliation(s)
- Aakash P Desai
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Farhad Kosari
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Maria Disselhorst
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jun Yin
- Quantitative Health Sciences, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Alireza Agahi
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Tobias Peikert
- Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Julia Udell
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Sarah H Johnson
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - James Smadbeck
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Stephen Murphy
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Giannoula Karagouga
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Alexa McCune
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Janet Schaefer-Klein
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Mitesh J Borad
- Hematology/Medical Oncology, Mayo Clinic, Phoenix, Arizona, USA
| | - John Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - George Vasmatzis
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Paul Baas
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Aaron Mansfield
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
4
|
Lei B, Jiang X, Saxena A. TCGA Expression Analyses of 10 Carcinoma Types Reveal Clinically Significant Racial Differences. Cancers (Basel) 2023; 15:2695. [PMID: 37345032 DOI: 10.3390/cancers15102695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 06/23/2023] Open
Abstract
Epidemiological studies reveal disparities in cancer incidence and outcome rates between racial groups in the United States. In our study, we investigated molecular differences between racial groups in 10 carcinoma types. We used publicly available data from The Cancer Genome Atlas to identify patterns of differential gene expression in tumor samples obtained from 4112 White, Black/African American, and Asian patients. We identified race-dependent expression of numerous genes whose mRNA transcript levels were significantly correlated with patients' survival. Only a small subset of these genes was differentially expressed in multiple carcinomas, including genes involved in cell cycle progression such as CCNB1, CCNE1, CCNE2, and FOXM1. In contrast, most other genes, such as transcriptional factor ETS1 and apoptotic gene BAK1, were differentially expressed and clinically significant only in specific cancer types. Our analyses also revealed race-dependent, cancer-specific regulation of biological pathways. Importantly, homology-directed repair and ERBB4-mediated nuclear signaling were both upregulated in Black samples compared to White samples in four carcinoma types. This large-scale pan-cancer study refines our understanding of the cancer health disparity and can help inform the use of novel biomarkers in clinical settings and the future development of precision therapies.
Collapse
Affiliation(s)
- Brian Lei
- Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
- Biology Department, Brooklyn College, New York, NY 11210, USA
| | - Xinyin Jiang
- Department of Health and Nutrition Sciences, Brooklyn College, New York, NY 11210, USA
- Biology and Biochemistry Programs, CUNY Graduate Center, New York, NY 10016, USA
| | - Anjana Saxena
- Biology Department, Brooklyn College, New York, NY 11210, USA
- Biology and Biochemistry Programs, CUNY Graduate Center, New York, NY 10016, USA
| |
Collapse
|
5
|
Mitr R, Pollack JR. RE: Lower Exome Sequencing Coverage of Ancestrally African Patients in the Cancer Genome Atlas. J Natl Cancer Inst 2022; 114:1728. [PMID: 35801943 PMCID: PMC9745426 DOI: 10.1093/jnci/djac132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/28/2022] [Indexed: 01/11/2023] Open
Affiliation(s)
- Rhea Mitr
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan R Pollack
- Correspondence to: Jonathan R. Pollack, MD, PhD, Department of Pathology, Stanford University School of Medicine, 269 Campus Dr, CCSR-3245A, Stanford, CA, USA (e-mail: )
| |
Collapse
|