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Trejo-Villegas OA, Heijink IH, Ávila-Moreno F. Preclinical evidence in the assembly of mammalian SWI/SNF complexes: Epigenetic insights and clinical perspectives in human lung disease therapy. Mol Ther 2024:S1525-0016(24)00409-X. [PMID: 38910326 DOI: 10.1016/j.ymthe.2024.06.026] [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: 12/11/2023] [Revised: 04/18/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024] Open
Abstract
The SWI/SNF complex, also known as the BRG1/BRM-associated factor (BAF) complex, represents a critical regulator of chromatin remodeling mechanisms in mammals. It is alternatively referred to as mSWI/SNF and has been suggested to be imbalanced in human disease compared with human health. Three types of BAF assemblies associated with it have been described, including (1) canonical BAF (cBAF), (2) polybromo-associated BAF (PBAF), and (3) non-canonical BAF (ncBAF) complexes. Each of these BAF assemblies plays a role, either functional or dysfunctional, in governing gene expression patterns, cellular processes, epigenetic mechanisms, and biological processes. Recent evidence increasingly links the dysregulation of mSWI/SNF complexes to various human non-malignant lung chronic disorders and lung malignant diseases. This review aims to provide a comprehensive general state-of-the-art and a profound examination of the current understanding of mSWI/SNF assembly processes, as well as the structural and functional organization of mSWI/SNF complexes and their subunits. In addition, it explores their intricate functional connections with potentially dysregulated transcription factors, placing particular emphasis on molecular and cellular pathogenic processes in lung diseases. These processes are reflected in human epigenome aberrations that impact clinical and therapeutic levels, suggesting novel perspectives on the diagnosis and molecular therapies for human respiratory diseases.
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Affiliation(s)
- Octavio A Trejo-Villegas
- Lung Diseases and Functional Epigenomics Laboratory (LUDIFE), Biomedicine Research Unit (UBIMED), Facultad de Estudios Superiores-Iztacala (FES-Iztacala), Universidad Nacional Autónoma de México (UNAM), Avenida de los Barrios #1, Colonia Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Estado de México, México
| | - Irene H Heijink
- Departments of Pathology & Medical Biology and Pulmonology, GRIAC Research Institute, University Medical Center Groningen, University of Groningen, 9713 Groningen, the Netherlands
| | - Federico Ávila-Moreno
- Lung Diseases and Functional Epigenomics Laboratory (LUDIFE), Biomedicine Research Unit (UBIMED), Facultad de Estudios Superiores-Iztacala (FES-Iztacala), Universidad Nacional Autónoma de México (UNAM), Avenida de los Barrios #1, Colonia Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Estado de México, México; Research Unit, Instituto Nacional de Enfermedades Respiratorias (INER), Ismael Cosío Villegas, 14080, Ciudad de México, México; Research Tower, Subdirección de Investigación Básica, Instituto Nacional de Cancerología (INCan), 14080, Ciudad de México, México.
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2
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Wei B, Zhao J, Li J, Feng J, Sun M, Wang Z, Shi C, Yang K, Qin Y, Zhang J, Ma J, Dong H. Pathogenic germline variants in BRCA1 and TP53 increase lung cancer risk in Chinese. Cancer Med 2023; 12:21219-21228. [PMID: 37930190 PMCID: PMC10726856 DOI: 10.1002/cam4.6692] [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: 06/07/2023] [Revised: 10/07/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023] Open
Abstract
BACKGROUD Multiple studies have identified pathogenic germline variants in cancer susceptibility genes (CSGs) in Chinese lung cancer patients; however, accurate assessment of these variants' contributions to cancer predisposition is always hampered by the absence of data on the prevalence of these variants in the general population. It is necessary to conduct a large-scale case-control study to identify CSGs that significantly increase the risk of lung cancer. MATERIALS AND METHODS We performed targeted sequencing of a CSGs panel in 1117 lung cancer patients and 16,327 controls from the general Chinese population. RESULTS In comparison to controls, lung cancer patients had a considerably higher prevalence of pathogenic and likely pathogenic (P/LP) variations. Among lung cancer patients, 72% of P/LP variants carriers did not have a family cancer history, who would be ignored if germline testing was only provided for patients meeting family history-based criteria. Furthermore, compared to individuals with late-onset lung cancer, patients with early-onset lung cancer had a considerably higher prevalence of P/LP variations. With odds ratios (ORs) ranging from 4-fold (BRCA1: OR, 4.193; 95%CI, 1.382-10.768) to 29-fold (TP53: OR, 29.281; 95%CI, 1.523-1705.506), P/LP variants in the BRCA1 and TP53 genes were discovered to be strongly related to increased lung cancer risk. Additionally, with ORs ranging from 7.322-fold to infinity, we discovered 23 variations previously categorized as non-P/LP variants were highly enriched in lung cancer patients. CONCLUSION Our findings indicated that P/LP variants in BRCA1 and TP53 conferred increased risk of lung cancer in Chinese.
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Affiliation(s)
- Bing Wei
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Jiadong Zhao
- Nanjing Shenyou Institute of Genome ResearchNanjingJiangsuChina
| | - Jun Li
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Junnan Feng
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Manman Sun
- Nanjing Shenyou Institute of Genome ResearchNanjingJiangsuChina
| | - Zhizhong Wang
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Chao Shi
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Ke Yang
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Yue Qin
- Nanjing Shenyou Institute of Genome ResearchNanjingJiangsuChina
| | - Jing Zhang
- Nanjing Shenyou Institute of Genome ResearchNanjingJiangsuChina
| | - Jie Ma
- Department of Molecular Pathology, Henan Key Laboratory of Molecular PathologyThe Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhouHenanChina
| | - Hui Dong
- Department of Gastroenterology, Shanghai Key Laboratory of Pancreatic DiseasesShanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
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Fanale D, Corsini LR, Pedone E, Randazzo U, Fiorino A, Di Piazza M, Brando C, Magrin L, Contino S, Piraino P, Bazan Russo TD, Cipolla C, Russo A, Bazan V. Potential agnostic role of BRCA alterations in patients with several solid tumors: One for all, all for one? Crit Rev Oncol Hematol 2023; 190:104086. [PMID: 37536445 DOI: 10.1016/j.critrevonc.2023.104086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/27/2023] [Accepted: 07/30/2023] [Indexed: 08/05/2023] Open
Abstract
Germline BRCA1/2 alterations in the Homologous Recombination (HR) pathway are considered as main susceptibility biomarkers to Hereditary Breast and Ovarian Cancers (HBOC). The modern molecular biology technologies allowed to characterize germline and somatic BRCA1/2 alterations in several malignancies, broadening the landscape of BRCA1/2-alterated tumors. In the last years, BRCA genetic testing, beyond the preventive value, also assumed a predictive and prognostic significance for patient management. The approval of molecules with agnostic indication is leading to a new clinical model, defined "mutational". Among these drugs, the Poly (ADP)-Ribose Polymerase inhibitors (PARPi) for BRCA1/2-deficient tumors were widely studied leading to increasing therapeutic implications. In this Review we provided an overview of the main clinical studies describing the association between BRCA-mutated tumors and PARPi response, focusing on the controversial evidence about the potential agnostic indication based on BRCA1/2 alterations in several solid tumors.
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Affiliation(s)
- Daniele Fanale
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Lidia Rita Corsini
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Erika Pedone
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Ugo Randazzo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Alessia Fiorino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Marianna Di Piazza
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Chiara Brando
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Luigi Magrin
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Silvia Contino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Paola Piraino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Tancredi Didier Bazan Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Calogero Cipolla
- Division of General and Oncological Surgery, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy.
| | - Viviana Bazan
- Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
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Xu J, Xu W, Choi J, Brhane Y, Christiani DC, Kothari J, McKay J, Field JK, Davies MPA, Liu G, Amos CI, Hung RJ, Briollais L. Large-scale whole exome sequencing studies identify two genes,CTSL and APOE, associated with lung cancer. PLoS Genet 2023; 19:e1010902. [PMID: 37738239 PMCID: PMC10516417 DOI: 10.1371/journal.pgen.1010902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 08/07/2023] [Indexed: 09/24/2023] Open
Abstract
Common genetic variants associated with lung cancer have been well studied in the past decade. However, only 12.3% heritability has been explained by these variants. In this study, we investigate the contribution of rare variants (RVs) (minor allele frequency <0.01) to lung cancer through two large whole exome sequencing case-control studies. We first performed gene-based association tests using a novel Bayes Factor statistic in the International Lung Cancer Consortium, the discovery study (European, 1042 cases vs. 881 controls). The top genes identified are further assessed in the UK Biobank (European, 630 cases vs. 172 864 controls), the replication study. After controlling for the false discovery rate, we found two genes, CTSL and APOE, significantly associated with lung cancer in both studies. Single variant tests in UK Biobank identified 4 RVs (3 missense variants) in CTSL and 2 RVs (1 missense variant) in APOE stongly associated with lung cancer (OR between 2.0 and 139.0). The role of these genetic variants in the regulation of CTSL or APOE expression remains unclear. If such a role is established, this could have important therapeutic implications for lung cancer patients.
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Affiliation(s)
- Jingxiong Xu
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Wei Xu
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yonathan Brhane
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - David C. Christiani
- T. H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Jui Kothari
- Department of Environmental Health, T. H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - James McKay
- International Agency for Research on Cancer, Lyon, France
| | - John K. Field
- Department of Molecular and Clinical Cancer Medicine, The University of Liverpool, Liverpool, United Kingdom
| | - Michael P. A. Davies
- Department of Molecular and Clinical Cancer Medicine, The University of Liverpool, Liverpool, United Kingdom
| | - Geoffrey Liu
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Christopher I. Amos
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States of America
| | - Rayjean J. Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Laurent Briollais
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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Ralli S, Jones SJ, Leach S, Lynch HT, Brooks-Wilson AR. Gene and pathway based burden analyses in familial lymphoid cancer cases: Rare variants in immune pathway genes. PLoS One 2023; 18:e0287602. [PMID: 37379307 DOI: 10.1371/journal.pone.0287602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 06/08/2023] [Indexed: 06/30/2023] Open
Abstract
Genome-wide association studies have revealed common genetic variants with small effect sizes associated with diverse lymphoid cancers. Family studies have uncovered rare variants with high effect sizes. However, these variants explain only a portion of the heritability of these cancers. Some of the missing heritability may be attributable to rare variants with small effect sizes. We aim to identify rare germline variants associated with familial lymphoid cancers using exome sequencing. One case per family was selected from 39 lymphoid cancer families based on early onset of disease or rarity of subtype. Control data was from Non-Finnish Europeans in gnomAD exomes (N = 56,885) or ExAC (N = 33,370). Gene and pathway-based burden tests for rare variants were performed using TRAPD. Five putatively pathogenic germline variants were found in four genes: INTU, PEX7, EHHADH, and ASXL1. Pathway-based association tests identified the innate and adaptive immune systems, peroxisomal pathway and olfactory receptor pathway as associated with lymphoid cancers in familial cases. Our results suggest that rare inherited defects in the genes involved in immune system and peroxisomal pathway may predispose individuals to lymphoid cancers.
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Affiliation(s)
- Sneha Ralli
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Samantha J Jones
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Stephen Leach
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Henry T Lynch
- Hereditary Cancer Center, Creighton University, Omaha, Nebraska, United States of America
| | - Angela R Brooks-Wilson
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
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Li Z, Wei X, Zhu Y. The prognostic value of DAAM2 in lower grade glioma, liver cancer, and breast cancer. Clin Transl Oncol 2023:10.1007/s12094-023-03111-x. [PMID: 36790676 DOI: 10.1007/s12094-023-03111-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 01/31/2023] [Indexed: 02/16/2023]
Abstract
PURPOSE Dishevelled-associated activator of morphogenesis 2 (DAAM2) is a formin protein and has a potential role in the tumor metastasis. The prognostic value of DAAM2 in pan-cancer is investigated in this study. METHODS TCGA and GTEx database were downloaded to perform bioinformatics analysis and ROC curves. Then we explored protein-protein interaction and GO-KEGG enrichment to figure out the protein pathways associated with DAAM2 and studied DAAM2-related immune infiltration and methylation. Fifteen pairs of BRCA clinical samples were enrolled to determine the expression and distribution of DAAM2 in BRCA sections by immunohistochemistry. Finally, BRCA cells were transfected with siRNA targeting DAAM2 and subsequently subject to cell proliferation, migration, and invasion assays. RESULTS DAAM2 was closely related to the diagnosis and clinical characteristics of lower grade glioma (LGG), liver hepatocellular carcinoma (LIHC), and breast cancer (BRCA). Survival curve analysis demonstrated DAAM2 served as a potential prognostic indicator of LGG and LIHC (P = 0.0029 and P = 0.025, respectively). DAAM2 was mainly participated in signaling pathways mediating cytoskeleton regulation and tumor development. The correlation of DAAM2 with tumor-infiltrating immune cells (TIICs) and methylation levels was conducive to the prediction of novel biomarkers of pan-carcinoma. DAAM2 was highly expressed in BRCA tissues than that in paracancerous tissues. The proliferation, invasion, and migration of BRCA cells were inhibited by DAAM2 siRNA. CONCLUSION DAAM2 had a specific value in foretelling the prognosis of LGG, LIHC, and BRCA. High expression level of DAAM2 has longer survival rates in LGG and LIHC. The knockdown of DAAM2 retards the proliferation, invasion, and migration of BRCA cells. This study provides a novel sight of DAAM2 into the exploration of a potential biomarker in pan-cancer.
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Affiliation(s)
- Zeying Li
- The First Clinical Medical College, Nanjing Medical University, Nanjing, 211166, China
| | - Xiao Wei
- The First Clinical Medical College, Nanjing Medical University, Nanjing, 211166, China
| | - Yichao Zhu
- Department of Physiology, Nanjing Medical University, Nanjing, 211166, China.
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7
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Murciano-Goroff YR, Schram AM, Rosen EY, Won H, Gong Y, Noronha AM, Janjigian YY, Stadler ZK, Chang JC, Yang SR, Mandelker D, Offit K, Berger MF, Donoghue MTA, Bandlamudi C, Drilon A. Reversion mutations in germline BRCA1/2-mutant tumors reveal a BRCA-mediated phenotype in non-canonical histologies. Nat Commun 2022; 13:7182. [PMID: 36418296 PMCID: PMC9684575 DOI: 10.1038/s41467-022-34109-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/12/2022] [Indexed: 11/25/2022] Open
Abstract
The association between loss of BRCA1/2 and a homologous recombination deficiency phenotype is lineage dependent. In BRCA-associated cancers such as breast, ovarian, pancreas and prostate, this phenotype confers sensitivity to PARP inhibitors and platinum-therapies. Somatic reversion mutations restoring BRCA1/2 function mediate resistance, and have exclusively been reported in BRCA-associated tumors. In this study, we analyze matched tumor and normal sequencing from 31,927 patients and identify 846 (2.7%) patients with germline BRCA1/2 variants across 43 different cancer types, including 11 with somatic reversion mutations. While nine are in BRCA-associated tumors, we find two reversion mutations in non-BRCA-associated histologies, namely lung and esophagogastric adenocarcinomas. Both were detected following platinum therapy. Whole exome sequencing confirms the homologous recombination deficiency phenotype of these tumors. While reversion mutations arise in all BRCA-associated cancer types, here we show that reversion mutations arising post-platinum in non-BRCA associated histologies, while rare, may indicate BRCA1/2 mediated tumorigenesis.
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Affiliation(s)
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Ezra Y Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, 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
| | - Helen Won
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- LOXO Oncology at Lilly, Stamford, CT, USA
| | - Yixiao Gong
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anne Marie Noronha
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Jason C Chang
- Weill Cornell Medical College, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Soo-Ryum Yang
- Weill Cornell Medical College, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Michael F Berger
- Weill Cornell Medical College, 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
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark T A Donoghue
- 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
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical College, New York, NY, USA.
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Sang J, Zhang T, Kim J, Li M, Pesatori AC, Consonni D, Song L, Liu J, Zhao W, Hoang PH, Campbell DS, Feng J, D'Arcy ME, Synnott N, Chen Y, Wu Z, Zhu B, Yang XR, Brown KM, Choi J, Shi J, Landi MT. Rare germline deleterious variants increase susceptibility for lung cancer. Hum Mol Genet 2022; 31:3558-3565. [PMID: 35717579 PMCID: PMC9558843 DOI: 10.1093/hmg/ddac123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 01/10/2023] Open
Abstract
Although multiple common susceptibility loci for lung cancer (LC) have been identified by genome-wide association studies, they can explain only a small portion of heritability. The etiological contribution of rare deleterious variants (RDVs) to LC risk is not fully characterized and may account for part of the missing heritability. Here, we sequenced the whole exomes of 2777 participants from the Environment and Genetics in Lung cancer Etiology study, a homogenous population including 1461 LC cases and 1316 controls. In single-variant analyses, we identified a new RDV, rs77187983 [EHBP1, odds ratio (OR) = 3.13, 95% confidence interval (CI) = 1.34-7.30, P = 0.008] and replicated two previously reported RDVs, rs11571833 (BRCA2, OR = 2.18; 95% CI = 1.25-3.81, P = 0.006) and rs752672077 (MPZL2, OR = 3.70, 95% CI = 1.04-13.15, P = 0.044). In gene-based analyses, we confirmed BRCA2 (P = 0.007) and ATM (P = 0.014) associations with LC risk and identified TRIB3 (P = 0.009), involved in maintaining genome stability and DNA repair, as a new candidate susceptibility gene. Furthermore, cases were enriched with RDVs in homologous recombination repair [carrier frequency (CF) = 22.9% versus 19.5%, P = 0.017] and Fanconi anemia (CF = 12.5% versus 10.2%, P = 0.036) pathways. Our results were not significant after multiple testing corrections but were enriched in cases versus controls from large scale public biobank resources, including The Cancer Genome Atlas, FinnGen and UK Biobank. Our study identifies novel candidate genes and highlights the importance of RDVs in DNA repair-related genes for LC susceptibility. These findings improve our understanding of LC heritability and may contribute to the development of risk stratification and prevention strategies.
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Affiliation(s)
- Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mengying Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Angela C Pesatori
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Dario Consonni
- Epidemiology Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Lei Song
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Jia Liu
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Phuc H Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - James Feng
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Monica E D'Arcy
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Naoise Synnott
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yingxi Chen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zeni Wu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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9
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Wang C, Dai J, Qin N, Fan J, Ma H, Chen C, An M, Zhang J, Yan C, Gu Y, Xie Y, He Y, Jiang Y, Zhu M, Song C, Jiang T, Liu J, Zhou J, Wang N, Hua T, Liang S, Wang L, Xu J, Yin R, Chen L, Xu L, Jin G, Lin D, Hu Z, Shen H. Analyses of rare predisposing variants of lung cancer in 6,004 whole genomes in Chinese. Cancer Cell 2022; 40:1223-1239.e6. [PMID: 36113475 DOI: 10.1016/j.ccell.2022.08.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/08/2022] [Accepted: 08/15/2022] [Indexed: 12/24/2022]
Abstract
We present the largest whole-genome sequencing (WGS) study of non-small cell lung cancer (NSCLC) to date among 6,004 individuals of Chinese ancestry, coupled with 23,049 individuals genotyped by SNP array. We construct a high-quality haplotype reference panel for imputation and identify 20 common and low-frequency loci (minor allele frequency [MAF] ≥ 0.5%), including five loci that have never been reported before. For rare loss-of-function (LoF) variants (MAF < 0.5%), we identify BRCA2 and 18 other cancer predisposition genes that affect 5.29% of individuals with NSCLC, and 98.91% (181 of 183) of LoF variants have not been linked previously to NSCLC risk. Promoter variants of BRCA2 also have a substantial effect on NSCLC risk, and their prevalence is comparable with BRCA2 LoF variants. The associations are validated in an independent case-control study including 4,410 individuals and a prospective cohort study including 23,826 individuals. Our findings not only provide a high-quality reference panel for future array-based association studies but depict the whole picture of rare pathogenic variants for NSCLC.
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Affiliation(s)
- Cheng Wang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Juncheng Dai
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Na Qin
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Jingyi Fan
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Hongxia Ma
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine (Suzhou Centre), Gusu School, Nanjing Medical University, Suzhou 215002, Jiangsu, China; Research Units of Cohort Study on Cardiovascular Diseases and Cancers, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Congcong Chen
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Mingxing An
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Jing Zhang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Caiwang Yan
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Yayun Gu
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Yuan Xie
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Yuanlin He
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Yue Jiang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Meng Zhu
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Ci Song
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Tao Jiang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Jia Liu
- Department of Health Promotion & Chronic Non-Communicable Disease Control, Wuxi Center for Disease Control and Prevention, Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi 214145, Jiangsu, China
| | - Jun Zhou
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Nanxi Wang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Tingting Hua
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Shuang Liang
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Lu Wang
- Department of Health Promotion & Chronic Non-Communicable Disease Control, Wuxi Center for Disease Control and Prevention, Affiliated Wuxi Center for Disease Control and Prevention of Nanjing Medical University, Wuxi 214145, Jiangsu, China
| | - Jing Xu
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Rong Yin
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Department of Thoracic Surgery Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210029, Jiangsu, China
| | - Liang Chen
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu, China
| | - Lin Xu
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Department of Thoracic Surgery Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210029, Jiangsu, China
| | - Guangfu Jin
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhibin Hu
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine (Suzhou Centre), Gusu School, Nanjing Medical University, Suzhou 215002, Jiangsu, China.
| | - Hongbing Shen
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China; State Key Laboratory of Reproductive Medicine (Suzhou Centre), Gusu School, Nanjing Medical University, Suzhou 215002, Jiangsu, China; Research Units of Cohort Study on Cardiovascular Diseases and Cancers, Chinese Academy of Medical Sciences, Beijing 100730, China.
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10
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Long E, Patel H, Byun J, Amos CI, Choi J. Functional studies of lung cancer GWAS beyond association. Hum Mol Genet 2022; 31:R22-R36. [PMID: 35776125 DOI: 10.1093/hmg/ddac140] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/01/2022] [Accepted: 06/16/2022] [Indexed: 11/14/2022] Open
Abstract
Fourteen years after the first genome-wide association study (GWAS) of lung cancer was published, approximately forty-five genomic loci have now been significantly associated with lung cancer risk. While functional characterization was performed for several of these loci, a comprehensive summary of current molecular understanding of lung cancer risk has been lacking. Further, many novel computational and experimental tools now became available to accelerate the functional assessment of disease-associated variants, moving beyond locus-by-locus approaches. In this review, we first highlight the heterogeneity of lung cancer GWAS findings across histological subtypes, ancestries, and smoking status, which poses unique challenges to follow-up studies. We then summarize the published lung cancer post-GWAS studies for each risk-associated locus to assess the current understanding of biological mechanisms beyond the initial statistical association. We further summarize strategies for GWAS functional follow-up studies considering cutting-edge functional genomics tools and providing a catalog of available resources relevant to lung cancer. Overall, we aim to highlight the importance of integrating computational and experimental approaches to draw biological insights from the lung cancer GWAS results beyond association.
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Affiliation(s)
- Erping Long
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Harsh Patel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 77030, USA.,Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 77030, USA.,Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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11
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Liu J, Zhao Z, Wei S, Li B, Zhao Z. Genomic features of Chinese small cell lung cancer. BMC Med Genomics 2022; 15:117. [PMID: 35596192 PMCID: PMC9123817 DOI: 10.1186/s12920-022-01255-3] [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] [Received: 11/09/2021] [Accepted: 04/22/2022] [Indexed: 11/12/2022] Open
Abstract
Background Small cell lung cancer (SCLC) is an aggressive disease with poor survival. Although molecular and clinical characteristics have been established for SCLC in western patients, limited investigation has been performed for Chinese SCLC patients. Objective In this study, we investigated the genomic features of Chinese SCLC patients. Methods A total of 75 SCLC patients were enrolled. Genomic alterations in 618 selected genes were analyzed by targeted next-generation sequencing. Results Here, we showed that TP53 (77.30%) and RB1 (30.70%) were the most prevalent genes alterations, followed by KMT2D, ALK, LRP1B, EGFR, NOTCH3, AR, CREBBP, ROS1, and BRCA2. And the most common genetic alterations were enriched in the cell cycle signaling pathway (84.00%) of Chinese SCLC patients. DNA damage repair (DDR) pathway analysis showed that the most frequently enriched DDR pathways were fanconi anaemia (FA, 29.41%) and homology recombination (HR, 21.57%). Notably, 9.33% SCLC patients in our cohort had pathogenic or likely pathogenic germline gene variants. Compared with the U Cologne cohort, a higher prevalence in EGFR, AR, BRCA2, TSC1, ATXN3, MET, MSH2, ERBB3 and FOXA1 were found in our cohort; while compared to the data from the Johns Hopkins cohort, a higher mutated frequency in TP53, KMT2D, ALK, and EGFR were found in our cohort. Moreover, a significant association was found between high tumor mutation burden (TMB) and mutations involved in TP53, CREBBP, EPHA3, KMT2D, ALK and RB1. Approximately 33.33% of patients with SCLC harbored at least one actionable alteration annotated by OncoKB, of which one patient had alterations of level 1; seventeen patients had level 3; fifteen patients possessed level 4. Conclusion Our data might provide an insightful meaning in targeted therapy for Chinese SCLC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01255-3.
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Affiliation(s)
- Jun Liu
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of South China University of Technology, Guangzhou, 510000, China
| | - Zhuxiang Zhao
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of South China University of Technology, Guangzhou, 510000, China
| | - Shuquan Wei
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of South China University of Technology, Guangzhou, 510000, China
| | - Binkai Li
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of South China University of Technology, Guangzhou, 510000, China
| | - Ziwen Zhao
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of South China University of Technology, Guangzhou, 510000, China.
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12
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Sánchez-Ares M, Cameselle-García S, Abdulkader-Nallib I, Rodríguez-Carnero G, Beiras-Sarasquete C, Puñal-Rodríguez JA, Cameselle-Teijeiro JM. Susceptibility Genes and Chromosomal Regions Associated With Non-Syndromic Familial Non-Medullary Thyroid Carcinoma: Some Pathogenetic and Diagnostic Keys. Front Endocrinol (Lausanne) 2022; 13:829103. [PMID: 35295987 PMCID: PMC8918666 DOI: 10.3389/fendo.2022.829103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 02/07/2022] [Indexed: 12/05/2022] Open
Abstract
Thyroid cancer is the malignant tumor that is increasing most rapidly in the world, mainly at the expense of sporadic papillary thyroid carcinoma. The somatic alterations involved in the pathogenesis of sporadic follicular cell derived tumors are well recognized, while the predisposing alterations implicated in hereditary follicular tumors are less well known. Since the genetic background of syndromic familial non-medullary carcinoma has been well established, here we review the pathogenesis of non-syndromic familial non-medullary carcinoma emphasizing those aspects that may be useful in clinical and pathological diagnosis. Non-syndromic familial non-medullary carcinoma has a complex and heterogeneous genetic basis involving several genes and loci with a monogenic or polygenic inheritance model. Most cases are papillary thyroid carcinoma (classic and follicular variant), usually accompanied by benign thyroid nodules (follicular thyroid adenoma and/or multinodular goiter). The possible diagnostic and prognostic usefulness of the changes in the expression and/or translocation of various proteins secondary to several mutations reported in this setting requires further confirmation. Given that non-syndromic familial non-medullary carcinoma and sporadic non-medullary thyroid carcinoma share the same morphology and somatic mutations, the same targeted therapies could be used at present, if necessary, until more specific targeted treatments become available.
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Affiliation(s)
- María Sánchez-Ares
- Department of Pathology, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Galician Healthcare Service (SERGAS), Santiago de Compostela, Spain
| | - Soledad Cameselle-García
- Department of Medical Oncology, University Hospital Complex of Ourense, Galician Healthcare Service (SERGAS), Ourense, Spain
| | - Ihab Abdulkader-Nallib
- Department of Pathology, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Galician Healthcare Service (SERGAS), Santiago de Compostela, Spain
- School of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Gemma Rodríguez-Carnero
- Department of Endocrinology and Nutrition, Clinical University Hospital of Santiago de Compostela, Galician Healthcare Service (SERGAS), Santiago de Compostela, Spain
| | - Carolina Beiras-Sarasquete
- Department of Surgery, Clinical University Hospital of Santiago de Compostela, Galician Healthcare Service (SERGAS), Santiago de Compostela, Spain
| | - José Antonio Puñal-Rodríguez
- School of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
- Department of Surgery, Clinical University Hospital of Santiago de Compostela, Galician Healthcare Service (SERGAS), Santiago de Compostela, Spain
| | - José Manuel Cameselle-Teijeiro
- Department of Pathology, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Galician Healthcare Service (SERGAS), Santiago de Compostela, Spain
- School of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
- *Correspondence: José Manuel Cameselle-Teijeiro,
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13
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Abstract
Almost 25 years have passed since a mutation of a formin gene, DIAPH1, was identified as being responsible for a human inherited disorder: a form of sensorineural hearing loss. Since then, our knowledge of the links between formins and disease has deepened considerably. Mutations of DIAPH1 and six other formin genes (DAAM2, DIAPH2, DIAPH3, FMN2, INF2 and FHOD3) have been identified as the genetic cause of a variety of inherited human disorders, including intellectual disability, renal disease, peripheral neuropathy, thrombocytopenia, primary ovarian insufficiency, hearing loss and cardiomyopathy. In addition, alterations in formin genes have been associated with a variety of pathological conditions, including developmental defects affecting the heart, nervous system and kidney, aging-related diseases, and cancer. This review summarizes the most recent discoveries about the involvement of formin alterations in monogenic disorders and other human pathological conditions, especially cancer, with which they have been associated. In vitro results and experiments in modified animal models are discussed. Finally, we outline the directions for future research in this field.
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Affiliation(s)
| | - Miguel A. Alonso
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, 28049 Madrid, Spain;
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14
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Zhou L, Li SH, Wu Y, Xin L. Establishment of a prognostic model of four genes in gastric cancer based on multiple data sets. Cancer Med 2021; 10:3309-3322. [PMID: 33934516 PMCID: PMC8124107 DOI: 10.1002/cam4.3654] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 01/22/2023] Open
Abstract
Gastric cancer (GC) is a kind of malignancy with a high mortality and recurrence. An effective prediction model based on ideal biomarkers to assess prognosis could benefit patients for optimization of treatment. Bioinformatics has played an increasingly important role in the study of cancer diseases. Therefore, this study started with bioinformatics to establish a reliable prognostic model of gastric cancer. The gene expression data and clinical data of GC tissues and normal tissues were obtained from the Gene Expression Omnibus (GEO), Genotype‐Tissue Expression (GTEx), and The Cancer Genome Atlas (TCGA) profile database. We finally identified a four gene signature and constructed a prognostic model. The results of internal and external validation showed that the model is highly reliable. In addition, we also constructed a nomogram based on the model, which was verified by a calibration curve to show its predicted accuracy. Comprehensive analysis indicated that the four genes in the model are related to the occurrence and development of tumors, perhaps they are potential targets for tumor treatment. Generally, this prognostic model can bring potential benefits to patients with gastric cancer.
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Affiliation(s)
- Liqiang Zhou
- Department of General Surgery, Nanchang University, The Second Affiliated Hospital of Nanchang University, NanChang, JiangXi, 330006, China
| | - Shi H Li
- Department of General Surgery, Nanchang University, The Second Affiliated Hospital of Nanchang University, NanChang, JiangXi, 330006, China
| | - You Wu
- Department of General Surgery, Nanchang University, The Second Affiliated Hospital of Nanchang University, NanChang, JiangXi, 330006, China
| | - Lin Xin
- Department of General Surgery, Nanchang University, The Second Affiliated Hospital of Nanchang University, NanChang, JiangXi, 330006, China
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15
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Reckamp KL, Behrendt CE, Slavin TP, Gray SW, Castillo DK, Koczywas M, Cristea MC, Babski KM, Stearns D, Marcum CA, Rodriguez YP, Hass AJ, Vecchio MM, Mora P, Cervantes AE, Sand SR, Mejia RM, Tsou TC, Salgia R, Weitzel JN. Germline mutations and age at onset of lung adenocarcinoma. Cancer 2021; 127:2801-2806. [PMID: 33858029 DOI: 10.1002/cncr.33573] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/12/2021] [Accepted: 02/12/2021] [Indexed: 01/07/2023]
Abstract
BACKGROUND To identify additional at-risk groups for lung cancer screening, which targets persons with a long history of smoking and thereby misses younger or nonsmoking cases, the authors evaluated germline pathogenic variants (PVs) in patients with lung adenocarcinoma for an association with an accelerated onset. METHODS The authors assembled a retrospective cohort (1999-2018) of oncogenetic clinic patients with lung adenocarcinoma. Eligibility required a family history of cancer, data on smoking, and a germline biospecimen to screen via a multigene panel. Germline PVs (TP53/EGFR, BRCA2, other Fanconi anemia [FA] pathway genes, and non-FA DNA repair genes) were interrogated for associations with the age at diagnosis via an accelerated failure time model. RESULTS Subjects (n = 187; age, 28-89 years; female, 72.7%; Hispanic, 11.8%) included smokers (minimum of 5 pack-years; n = 65) and nonsmokers (lighter ever smokers [n = 18] and never smokers [n = 104]). Overall, 26.7% of the subjects carried 1 to 2 germline PVs: TP53 (n = 5), EGFR (n = 2), BRCA2 (n = 6), another FA gene (n = 11), or another DNA repair gene (n = 28). After adjustment for smoking, sex, and ethnicity, the diagnosis of lung adenocarcinoma was accelerated 12.2 years (95% confidence interval [CI], 2.5-20.6 years) by BRCA2 PVs, 9.0 years (95% CI, 0.5-16.5 years) by TP53/EGFR PVs, and 6.1 years (95% CI, -1.0 to 12.6 years) by PVs in other FA genes. PVs in other DNA repair genes showed no association. Germline associations did not vary by smoking. CONCLUSIONS Among lung adenocarcinoma cases, germline PVs (TP53, EGFR, BRCA2, and possibly other FA genes) may be associated with an earlier onset. With further study, the criteria for lung cancer screening may need to include carriers of high-risk PVs, and findings could influence precision therapy and reduce lung cancer mortality by earlier stage diagnosis.
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Affiliation(s)
- Karen L Reckamp
- City of Hope Comprehensive Cancer Center, Duarte, California
| | | | - Thomas P Slavin
- City of Hope Comprehensive Cancer Center, Duarte, California
| | - Stacy W Gray
- City of Hope Comprehensive Cancer Center, Duarte, California
| | | | | | | | | | | | | | | | | | | | - Pamela Mora
- Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru
| | | | - Sharon R Sand
- City of Hope Comprehensive Cancer Center, Duarte, California
| | - Rosa M Mejia
- City of Hope Comprehensive Cancer Center, Duarte, California
| | - Terrence C Tsou
- City of Hope Comprehensive Cancer Center, Duarte, California
| | - Ravi Salgia
- City of Hope Comprehensive Cancer Center, Duarte, California
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16
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Liu Y, Xia J, McKay J, Tsavachidis S, Xiao X, Spitz MR, Cheng C, Byun J, Hong W, Li Y, Zhu D, Song Z, Rosenberg SM, Scheurer ME, Kheradmand F, Pikielny CW, Lusk CM, Schwartz AG, Wistuba II, Cho MH, Silverman EK, Bailey-Wilson J, Pinney SM, Anderson M, Kupert E, Gaba C, Mandal D, You M, de Andrade M, Yang P, Liloglou T, Davies MPA, Lissowska J, Swiatkowska B, Zaridze D, Mukeria A, Janout V, Holcatova I, Mates D, Stojsic J, Scelo G, Brennan P, Liu G, Field JK, Hung RJ, Christiani DC, Amos CI. Rare deleterious germline variants and risk of lung cancer. NPJ Precis Oncol 2021; 5:12. [PMID: 33594163 PMCID: PMC7887261 DOI: 10.1038/s41698-021-00146-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 12/11/2020] [Indexed: 01/19/2023] Open
Abstract
Recent studies suggest that rare variants exhibit stronger effect sizes and might play a crucial role in the etiology of lung cancers (LC). Whole exome plus targeted sequencing of germline DNA was performed on 1045 LC cases and 885 controls in the discovery set. To unveil the inherited causal variants, we focused on rare and predicted deleterious variants and small indels enriched in cases or controls. Promising candidates were further validated in a series of 26,803 LCs and 555,107 controls. During discovery, we identified 25 rare deleterious variants associated with LC susceptibility, including 13 reported in ClinVar. Of the five validated candidates, we discovered two pathogenic variants in known LC susceptibility loci, ATM p.V2716A (Odds Ratio [OR] 19.55, 95%CI 5.04-75.6) and MPZL2 p.I24M frameshift deletion (OR 3.88, 95%CI 1.71-8.8); and three in novel LC susceptibility genes, POMC c.*28delT at 3' UTR (OR 4.33, 95%CI 2.03-9.24), STAU2 p.N364M frameshift deletion (OR 4.48, 95%CI 1.73-11.55), and MLNR p.Q334V frameshift deletion (OR 2.69, 95%CI 1.33-5.43). The potential cancer-promoting role of selected candidate genes and variants was further supported by endogenous DNA damage assays. Our analyses led to the identification of new rare deleterious variants with LC susceptibility. However, in-depth mechanistic studies are still needed to evaluate the pathogenic effects of these specific alleles.
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Grants
- R01 CA060691 NCI NIH HHS
- U19 CA203654 NCI NIH HHS
- R01 CA084354 NCI NIH HHS
- R01 HL110883 NHLBI NIH HHS
- U01 CA076293 NCI NIH HHS
- R01 CA080127 NCI NIH HHS
- R01 CA141769 NCI NIH HHS
- P30 ES006096 NIEHS NIH HHS
- P50 CA090578 NCI NIH HHS
- P30 CA022453 NCI NIH HHS
- S10 RR024574 NCRR NIH HHS
- HHSN261201300011C NCI NIH HHS
- R01 CA134682 NCI NIH HHS
- R01 CA134433 NCI NIH HHS
- R01 HL113264 NHLBI NIH HHS
- R01 HL082487 NHLBI NIH HHS
- R01 CA250905 NCI NIH HHS
- U19 CA148127 NCI NIH HHS
- P20 GM103534 NIGMS NIH HHS
- R01 CA092824 NCI NIH HHS
- R01 CA087895 NCI NIH HHS
- U01 HL089897 NHLBI NIH HHS
- K07 CA181480 NCI NIH HHS
- HHSN268201100011I NHLBI NIH HHS
- HHSN268201100011C NHLBI NIH HHS
- R01 CA127219 NCI NIH HHS
- R01 CA074386 NCI NIH HHS
- P30 CA023108 NCI NIH HHS
- U01 HL089856 NHLBI NIH HHS
- P30 ES030285 NIEHS NIH HHS
- P30 CA125123 NCI NIH HHS
- DP1 AG072751 NIA NIH HHS
- U01 CA243483 NCI NIH HHS
- HHSN268200782096C NHLBI NIH HHS
- HHSN268201200007C NHLBI NIH HHS
- N01HG65404 NHGRI NIH HHS
- R35 GM122598 NIGMS NIH HHS
- U01 CA209414 NCI NIH HHS
- R03 CA077118 NCI NIH HHS
- 001 World Health Organization
- DP1 CA174424 NCI NIH HHS
- This work was supported by grants from the National Institutes of Health (R01CA127219, R01CA141769, R01CA060691, R01CA87895, R01CA80127, R01CA84354, R01CA134682, R01CA134433, R01CA074386, R01CA092824, R01CA250905, R01HL113264, R01HL082487, R01HL110883, R03CA77118, P20GM103534, P30CA125123, P30CA023108, P30CA022453, P30ES006096, P50CA090578, U01CA243483, U01HL089856, U01HL089897, U01CA76293, U19CA148127, U01CA209414, K07CA181480, N01-HG-65404, HHSN268200782096C, HHSN261201300011I, HHSN268201100011, HHSN268201 200007C, DP1-CA174424, DP1-AG072751, CA125123, RR024574, Intramural Research Program of the National Human Genome Research Institute (JEB-W), and Herrick Foundation. Dr. Amos is an Established Research Scholar of the Cancer Prevention Research Institute of Texas (RR170048). We also want to acknowledge the Cytometry and Cell Sorting Core support by the Cancer Prevention and Research Institute of Texas Core Facility (RP180672). At Toronto, the study is supported by The Canadian Cancer Society Research Institute (# 020214) to R. H., Ontario Institute for Cancer Research to R. H, and the Alan Brown Chair to G. L. and Lusi Wong Programs at the Princess Margaret Hospital Foundation. The Liverpool Lung Project is supported by Roy Castle Lung Cancer Foundation.
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Affiliation(s)
- Yanhong Liu
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jun Xia
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - James McKay
- International Agency for Research on Cancer, Lyon, France
| | - Spiridon Tsavachidis
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Xiangjun Xiao
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Margaret R Spitz
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Chao Cheng
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Jinyoung Byun
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Wei Hong
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Yafang Li
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Dakai Zhu
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Zhuoyi Song
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Michael E Scheurer
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Farrah Kheradmand
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA
| | - Claudio W Pikielny
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
| | - Christine M Lusk
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Ann G Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Susan M Pinney
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Elena Kupert
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Colette Gaba
- The University of Toledo College of Medicine, Toledo, OH, USA
| | - Diptasri Mandal
- Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Ming You
- Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Ping Yang
- Mayo Clinic College of Medicine, Scottsdale, AZ, USA
| | - Triantafillos Liloglou
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Michael P A Davies
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Jolanta Lissowska
- M. Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Beata Swiatkowska
- Nofer Institute of Occupational Medicine, Department of Environmental Epidemiology, Lodz, Poland
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Anush Mukeria
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Vladimir Janout
- Faculty of Health Sciences, Palacky University, Olomouc, Czech Republic
| | - Ivana Holcatova
- Institute of Public Health and Preventive Medicine, Charles University, 2nd Faculty of Medicine, Prague, Czech Republic
| | - Dana Mates
- National Institute of Public Health, Bucharest, Romania
| | - Jelena Stojsic
- Department of Thoracopulmonary Pathology, Service of Pathology, Clinical Center of Serbia, Belgrade, Serbia
| | | | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Geoffrey Liu
- Princess Margaret Cancer Center, Toronto, ON, Canada
| | - John K Field
- Roy Castle Lung Cancer Research Programme, The University of Liverpool, Department of Molecular and Clinical Cancer Medicine, Liverpool, UK
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | | | - Christopher I Amos
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.
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17
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Lung cancer LDCT screening and mortality reduction - evidence, pitfalls and future perspectives. Nat Rev Clin Oncol 2020; 18:135-151. [PMID: 33046839 DOI: 10.1038/s41571-020-00432-6] [Citation(s) in RCA: 204] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2020] [Indexed: 12/17/2022]
Abstract
In the past decade, the introduction of molecularly targeted agents and immune-checkpoint inhibitors has led to improved survival outcomes for patients with advanced-stage lung cancer; however, this disease remains the leading cause of cancer-related mortality worldwide. Two large randomized controlled trials of low-dose CT (LDCT)-based lung cancer screening in high-risk populations - the US National Lung Screening Trial (NLST) and NELSON - have provided evidence of a statistically significant mortality reduction in patients. LDCT-based screening programmes for individuals at a high risk of lung cancer have already been implemented in the USA. Furthermore, implementation programmes are currently underway in the UK following the success of the UK Lung Cancer Screening (UKLS) trial, which included the Liverpool Health Lung Project, Manchester Lung Health Check, the Lung Screen Uptake Trial, the West London Lung Cancer Screening pilot and the Yorkshire Lung Screening trial. In this Review, we focus on the current evidence on LDCT-based lung cancer screening and discuss the clinical developments in high-risk populations worldwide; additionally, we address aspects such as cost-effectiveness. We present a framework to define the scope of future implementation research on lung cancer screening programmes referred to as Screening Planning and Implementation RAtionale for Lung cancer (SPIRAL).
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18
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Liu M, Liu X, Suo P, Gong Y, Qu B, Peng X, Xiao W, Li Y, Chen Y, Zeng Z, Lu Y, Huang T, Zhao Y, Liu M, Li L, Chen Y, Zhou Y, Liu G, Yao J, Chen S, Song L. The contribution of hereditary cancer-related germline mutations to lung cancer susceptibility. Transl Lung Cancer Res 2020; 9:646-658. [PMID: 32676327 PMCID: PMC7354149 DOI: 10.21037/tlcr-19-403] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background Germline variations may contribute to lung cancer susceptibility besides environmental factors. The influence of germline mutations on lung cancer susceptibility and their correlation with somatic mutations has not been systematically investigated. Methods In this study, germline mutations from 1,026 non-small cell lung cancer (NSCLC) patients were analyzed with a 58-gene next-generation sequencing (NGS) panel containing known hereditary cancer-related genes, and were categorized based on American College of Medical Genetics and Genomics (ACMG) guidelines in pathogenicity, and the corresponding somatic mutations were analyzed using a 605-gene NGS panel containing known cancer-related genes. Results Plausible genetic susceptibility was found in 4.7% of lung cancer patients, in which 14 patients with pathogenic mutations (P group) and 34 patients with likely-pathogenic mutations (LP group) were identified. The ratio of the first degree relatives with lung cancer history of the P groups was significantly higher than the Non-P group (P=0.009). The ratio of lung cancer patients with history of other cancers was higher in P (P=0.0007) or LP (P=0.017) group than the Non-P group. Pathogenic mutations fell most commonly in BRCA2, followed by CHEK2 and ATM. Likely-pathogenic mutations fell most commonly in NTRK1 and EXT2, followed by BRIP1 and PALB2. These genes are involved in DNA repair, cell cycle regulation and tumor suppression. By comparing the germline mutation frequency from this study with that from the whole population or East Asian population (gnomAD database), we found that the overall odds ratio (OR) for P or LP group was 17.93 and 15.86, respectively, when compared with the whole population, and was 2.88 and 3.80, respectively, when compared with the East Asian population, suggesting the germline mutations of the P and LP groups were risk factors for lung cancer. Somatic mutation analysis revealed no significant difference in tumor mutation burden (TMB) among the groups, although a trend of lower TMB in the pathogenic group was found. The SNV/INDEL mutation frequency of TP53 in the P group was significantly lower than the other two groups, and the copy number variation (CNV) mutation frequency of PIK3CA and MET was significantly higher than the Non-P group. Pathway enrichment analysis found no significant difference in aberrant pathways among the three groups. Conclusions A proportion of 4.7% of patients carrying germline variants may be potentially linked to increased susceptibility to lung cancer. Patients with pathogenic germline mutations exhibited stronger family history and higher lung cancer risk.
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Affiliation(s)
- Mengyuan Liu
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Xinyi Liu
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Peisu Suo
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Yuan Gong
- The Second Medical Center of the Chinese PLA General Hospital, Beijing 100853, China
| | - Baolin Qu
- The Second Medical Center of the Chinese PLA General Hospital, Beijing 100853, China
| | - Xiumei Peng
- The Fourth Medical Center of the Chinese PLA General Hospital, Beijing 100037, China
| | - Wenhua Xiao
- The Fourth Medical Center of the Chinese PLA General Hospital, Beijing 100037, China
| | - Yuemin Li
- The Eighth Medical Center of the Chinese PLA General Hospital, Beijing 100091, China
| | - Yan Chen
- The Fifth Medical Center of the Chinese PLA General Hospital, Beijing 100039, China
| | - Zhen Zeng
- The Fifth Medical Center of the Chinese PLA General Hospital, Beijing 100039, China
| | - Yinying Lu
- The Fifth Medical Center of the Chinese PLA General Hospital, Beijing 100039, China
| | - Tanxiao Huang
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Yingshen Zhao
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Ming Liu
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Lifeng Li
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Yaru Chen
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Yanqing Zhou
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Guifeng Liu
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Jianfei Yao
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Shifu Chen
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China
| | - Lele Song
- HaploX Biotechnology, Co., Ltd., Shenzhen 518057, China.,The Eighth Medical Center of the Chinese PLA General Hospital, Beijing 100091, China
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19
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Xu J, Xu W, Briollais L. A Bayes factor approach with informative prior for rare genetic variant analysis from next generation sequencing data. Biometrics 2020; 77:316-328. [PMID: 32277476 DOI: 10.1111/biom.13278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/15/2020] [Accepted: 04/01/2020] [Indexed: 11/28/2022]
Abstract
The discovery of rare genetic variants through next generation sequencing is a very challenging issue in the field of human genetics. We propose a novel region-based statistical approach based on a Bayes Factor (BF) to assess evidence of association between a set of rare variants (RVs) located on the same genomic region and a disease outcome in the context of case-control design. Marginal likelihoods are computed under the null and alternative hypotheses assuming a binomial distribution for the RV count in the region and a beta or mixture of Dirac and beta prior distribution for the probability of RV. We derive the theoretical null distribution of the BF under our prior setting and show that a Bayesian control of the false Discovery Rate can be obtained for genome-wide inference. Informative priors are introduced using prior evidence of association from a Kolmogorov-Smirnov test statistic. We use our simulation program, sim1000G, to generate RV data similar to the 1000 genomes sequencing project. Our simulation studies showed that the new BF statistic outperforms standard methods (SKAT, SKAT-O, Burden test) in case-control studies with moderate sample sizes and is equivalent to them under large sample size scenarios. Our real data application to a lung cancer case-control study found enrichment for RVs in known and novel cancer genes. It also suggests that using the BF with informative prior improves the overall gene discovery compared to the BF with noninformative prior.
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Affiliation(s)
- Jingxiong Xu
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Wei Xu
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Center, Toronto, Canada
| | - Laurent Briollais
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
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20
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Hsu PC, Kadlubar SA, Siegel ER, Rogers LJ, Todorova VK, Su LJ, Makhoul I. Genome-wide DNA methylation signatures to predict pathologic complete response from combined neoadjuvant chemotherapy with bevacizumab in breast cancer. PLoS One 2020; 15:e0230248. [PMID: 32298288 PMCID: PMC7162481 DOI: 10.1371/journal.pone.0230248] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/25/2020] [Indexed: 02/07/2023] Open
Abstract
TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT00203502.
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Affiliation(s)
- Ping-Ching Hsu
- Department of Environmental and Occupational Health, College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Susan A. Kadlubar
- Department of Environmental and Occupational Health, College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Eric R. Siegel
- Department of Biostatistics, Colleges of Medicine and of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Lora J. Rogers
- Department of Epidemiology, College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Valentina K. Todorova
- Department of Internal Medicine, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - L. Joseph Su
- Department of Epidemiology, College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Issam Makhoul
- Department of Internal Medicine, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
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21
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Campos C, Fragoso S, Luís R, Pinto F, Brito C, Esteves S, Pataco M, Santos S, Machado P, Vicente JB, Costa Rosa J, Cavaco BM, Moura C, Pojo M. High-Throughput Sequencing Identifies 3 Novel Susceptibility Genes for Hereditary Melanoma. Genes (Basel) 2020; 11:genes11040403. [PMID: 32276436 PMCID: PMC7230562 DOI: 10.3390/genes11040403] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 12/19/2022] Open
Abstract
Cutaneous melanoma is one of the most aggressive human cancers due to its high invasiveness. Germline mutations in high-risk melanoma susceptibility genes have been associated with development hereditary melanoma; however, most genetic culprits remain elusive. To unravel novel susceptibility genes for hereditary melanoma, we performed whole exome sequencing (WES) on eight patients with multiple primary melanomas, high number of nevi, and negative for high and intermediate-risk germline mutations. Thirteen new potentially pathogenic variants were identified after bioinformatics analysis and validation. CDH23, ARHGEF40, and BRD9 were identified as the most promising susceptibility genes in hereditary melanoma. In silico analysis of CDH23 and ARHGEF40 variants provided clues for altered protein structure and function associated with the identified mutations. Then, we also evaluated the clinical value of CDH23, ARHGEF40, and BRD9 expression in sporadic melanoma by using the TCGA dataset (n = 461). No differences were observed in BRD9 expression between melanoma and normal skin samples, nor with melanoma stage, whereas ARHGEF40 was found overexpressed, and CDH23 was downregulated and its loss was associated with worse survival. Altogether, these results reveal three novel genes with clinical relevance in hereditary and sporadic melanoma.
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Affiliation(s)
- Catarina Campos
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Sofia Fragoso
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Rafael Luís
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Filipe Pinto
- i3S-Institute for Research and Innovation in Health, University of Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | - Cheila Brito
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Susana Esteves
- Unidade de Investigação Clínica (UIC) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Margarida Pataco
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Sidónia Santos
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Patrícia Machado
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - João B. Vicente
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República (EAN), 2780-157 Oeiras, Portugal
| | - Joaninha Costa Rosa
- Serviço de Anatomia Patológica do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
- NOVA Medical School|Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria, 130, 1169-056 Lisboa, Portugal
| | - Branca M. Cavaco
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Cecília Moura
- Clínica de Risco Familiar do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
- Serviço de Dermatologia do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
| | - Marta Pojo
- Unidade de Investigação em Patobiologia Molecular (UIPM) do Instituto Português de Oncologia de Lisboa Francisco Gentil E.P.E., Rua Prof. Lima Basto, 1099-023 Lisboa, Portugal
- Correspondence: ; Tel.: +351-21-722-9800 (ext. 1794)
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22
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Sarquis M, Moraes DC, Bastos-Rodrigues L, Azevedo PG, Ramos AV, Reis FV, Dande PV, Paim I, Friedman E, De Marco L. Germline Mutations in Familial Papillary Thyroid Cancer. Endocr Pathol 2020; 31:14-20. [PMID: 32034658 DOI: 10.1007/s12022-020-09607-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Thyroid cancer, predominantly of papillary histology (PTC), is a common cancer mostly diagnosed sporadically. Hereditary PTC is encountered in ~ 5% of cases and may present at an earlier age, with greater risks of metastasis and recurrence, compared with sporadic cases. The molecular basis of hereditary PTC is unknown in most cases. In this study, the genetic basis of hereditary PTC in three Brazilian families was investigated. Whole exome sequencing (WES) was carried out for probands in each family, and validated, pathogenic/likely pathogenic sequence variants (P/LPSVs) were genotyped in additional family members to establish their putative pathogenic role. Overall, seven P/LPSVs in seven novel genes were detected: p.D283N*ANXA3, p.Y157S*NTN4, p.G172W*SERPINA1, p.G188S*FKBP10, p.R937C*PLEKHG5, p.L32Q*P2RX5, and p.Q76*SAPCD1. These results indicate that these novel genes are seemingly associated with hereditary PTC, but extension and validation in other PTC families are required.
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Affiliation(s)
- Marta Sarquis
- Department of Medicine, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Debora C Moraes
- Department of Surgery, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Luciana Bastos-Rodrigues
- Department of Nutrition, Faculdade de Enfermagem, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Pedro G Azevedo
- Department of Surgery, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Fabiana Versiani Reis
- Department of Surgery, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Paula V Dande
- Department of Surgery, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Isabela Paim
- Department of Surgery, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Eitan Friedman
- The Suzanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Chaim Sheba Medical Center, Tel-Hashomer, Israel
- The Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Luiz De Marco
- Department of Surgery, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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Sun SW, Zhou M, Chen L, Wu JH, Meng ZJ, Miao SY, Han HL, Zhu CC, Xiong XZ. Whole exome sequencing identifies a rare variant in DAAM2 as a potential candidate in idiopathic pulmonary ossification. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:327. [PMID: 31475197 DOI: 10.21037/atm.2019.06.14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background Diffuse pulmonary ossification (DPO) is a rare disease characterized by bone tissue formation in the lung. DPO can be classified into idiopathic pulmonary ossification (IPO) and secondary pulmonary ossification. Cases with no identified etiology are classified as IPO. Variants of dishevelled associated activator of morphogenesis 2 (DAAM2) have been reported to be involved in the bone-resorption of osteoclasts. Methods Whole exome sequencing (WES) was used on samples from a patient with IPO and his healthy parents. The effects of all variants were determined using functional predictors (PolyPhen-2, SIFT, FATHMM and MutationTaster); variants existing only in the patient were further screened compared with his healthy parents. Results Forty deleterious variants, including 25 single nucleotide variants (SNVs) and 15 insertions and deletions (indels), were identified by WES. Finally, DAAM2 (c.G2960T:p.R987L) was screened by pathway analysis. Conclusions We identified a novel variant of DAAM2 (c.G2960T:p.R987L) that might participate in the disease process of IPO.
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Affiliation(s)
- Sheng-Wen Sun
- Department of Respiratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Mei Zhou
- Department of Respiratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Long Chen
- Department of Respiratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jiang-Hua Wu
- Department of Respiratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zhao-Ji Meng
- Department of Respiratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shuai-Ying Miao
- Department of Respiratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hong-Li Han
- Department of Respiratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Chen-Chen Zhu
- Department of Respiratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xian-Zhi Xiong
- Department of Respiratory Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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