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Islam SA, Díaz-Gay M, Wu Y, Barnes M, Vangara R, Bergstrom EN, He Y, Vella M, Wang J, Teague JW, Clapham P, Moody S, Senkin S, Li YR, Riva L, Zhang T, Gruber AJ, Steele CD, Otlu B, Khandekar A, Abbasi A, Humphreys L, Syulyukina N, Brady SW, Alexandrov BS, Pillay N, Zhang J, Adams DJ, Martincorena I, Wedge DC, Landi MT, Brennan P, Stratton MR, Rozen SG, Alexandrov LB. Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor. CELL GENOMICS 2022; 2:None. [PMID: 36388765 PMCID: PMC9646490 DOI: 10.1016/j.xgen.2022.100179] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 04/10/2022] [Accepted: 08/31/2022] [Indexed: 12/09/2022]
Abstract
Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for de novo extraction of mutational signatures, and benchmark it against another 13 bioinformatics tools by using 34 scenarios encompassing 2,500 simulated signatures found in 60,000 synthetic genomes and 20,000 synthetic exomes. For simulations with 5% noise, reflecting high-quality datasets, SigProfilerExtractor outperforms other approaches by elucidating between 20% and 50% more true-positive signatures while yielding 5-fold less false-positive signatures. Applying SigProfilerExtractor to 4,643 whole-genome- and 19,184 whole-exome-sequenced cancers reveals four novel signatures. Two of the signatures are confirmed in independent cohorts, and one of these signatures is associated with tobacco smoking. In summary, this report provides a reference tool for analysis of mutational signatures, a comprehensive benchmarking of bioinformatics tools for extracting signatures, and several novel mutational signatures, including one putatively attributed to direct tobacco smoking mutagenesis in bladder tissues.
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Affiliation(s)
- S.M. Ashiqul Islam
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Yang Wu
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke NUS Medical School, Singapore 169857, Singapore
| | - Mark Barnes
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Yudou He
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Mike Vella
- NVIDIA Corporation, 2788 San Tomas Expressway, Santa Clara, CA 95051, USA
| | - Jingwei Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Jon W. Teague
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Peter Clapham
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sergey Senkin
- Genetic Epidemiology Group, International Agency for Research on Cancer, Cedex 08, 69372 Lyon, France
| | - Yun Rose Li
- Departments of Radiation Oncology and Cancer Genetics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Laura Riva
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Andreas J. Gruber
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
- Department of Biology, University of Konstanz, Universitaetsstrasse 10, D-78464 Konstanz, Germany
| | - Christopher D. Steele
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
| | - Burçak Otlu
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Ammal Abbasi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
| | - Laura Humphreys
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | | | - Samuel W. Brady
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Boian S. Alexandrov
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nischalan Pillay
- Research Department of Pathology, Cancer Institute, University College London, London WC1E 6BT, UK
- Department of Cellular and Molecular Pathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex HA7 4LP, UK
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - David J. Adams
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - David C. Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester M20 4GJ, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, Cedex 08, 69372 Lyon, France
| | - Michael R. Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Steven G. Rozen
- Centre for Computational Biology and Programme in Cancer & Stem Cell Biology, Duke NUS Medical School, Singapore 169857, Singapore
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA 92037, USA
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2
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Whole Exome Sequencing of Biliary Tubulopapillary Neoplasms Reveals Common Mutations in Chromatin Remodeling Genes. Cancers (Basel) 2021; 13:cancers13112742. [PMID: 34205964 PMCID: PMC8198366 DOI: 10.3390/cancers13112742] [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: 04/06/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Intraductal tubulopapillary neoplasms (ITPN) have recently been described as rare precursor lesions of pancreatic ductal adenocarcinoma and cholangiocarcinoma. Despite a high number of associated invasive adenocarcinomas at the time of diagnosis, patients with ITPN tend to have a much better clinical outcome than those with classical pancreato-biliary adenocarcinoma. Furthermore, rare molecular studies of ITPN show an unexpected lack of hotspot mutations in common driver genes of pancreato-biliary adenocarcinoma, including KRAS. This article reports the first large comprehensive and comparative molecular study of pancreato-biliary ITPN. In the absence of KRAS mutations, we found a high genetic heterogeneity with enrichment in core signaling pathways, including putative actionable genomic targets in one-third of the cases. Whereas, pancreatic ITPN demonstrates a highly distinct genetic profile, differing from classical pancreatic carcinogenesis, biliary ITPN and classical cholangiocarcinoma share common alterations in key genes of the chromatin remodeling pathway, and therefore, appear more closely related than pancreatic ITPN and classical pancreatic ductal adenocarcinoma PDAC. Abstract The molecular carcinogenesis of intraductal tubulopapillary neoplasms (ITPN), recently described as rare neoplasms in the pancreato-biliary tract with a favorable prognosis despite a high incidence of associated pancreato-biliary adenocarcinoma, is still poorly understood. To identify driver genes, chromosomal gains and losses, mutational signatures, key signaling pathways, and potential therapeutic targets, the molecular profile of 11 biliary and 6 pancreatic ITPNs, associated with invasive adenocarcinoma in 14/17 cases, are studied by whole exome sequencing (WES). The WES of 17 ITPNs reveals common copy number variants (CNVs) broadly distributed across the genome, with recurrent chromosomal deletions primarily in 1p36 and 9p21 affecting the tumor suppressors CHD5 and CDKN2A, respectively, and gains in 1q affecting the prominent oncogene AKT3. The identified somatic nucleotide variants (SNVs) involve few core signaling pathways despite high genetic heterogeneity with diverse mutational spectra: Chromatin remodeling, the cell cycle, and DNA damage/repair. An OncoKB search identifies putative actionable genomic targets in 35% of the cases (6/17), including recurrent missense mutations of the FGFR2 gene in biliary ITPNs (2/11, 18%). Our results show that somatic SNV in classical cancer genes, typically associated with pancreato-biliary carcinogenesis, were absent (KRAS, IDH1/2, GNAS, and others) to rare (TP53 and SMAD4, 6%, respectively) in ITPNs. Mutational signature pattern analysis reveals a predominance of an age-related pattern. Our findings highlight that biliary ITPN and classical cholangiocarcinoma display commonalities, in particular mutations in genes of the chromatin remodeling pathway, and appear, therefore, more closely related than pancreatic ITPN and classical pancreatic ductal adenocarcinoma.
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Xie K, Tian Y, Yuan X. A Density Peak-Based Method to Detect Copy Number Variations From Next-Generation Sequencing Data. Front Genet 2021; 11:632311. [PMID: 33519925 PMCID: PMC7838601 DOI: 10.3389/fgene.2020.632311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/21/2020] [Indexed: 11/29/2022] Open
Abstract
Copy number variation (CNV) is a common type of structural variations in human genome and confers biological meanings to human complex diseases. Detection of CNVs is an important step for a systematic analysis of CNVs in medical research of complex diseases. The recent development of next-generation sequencing (NGS) platforms provides unprecedented opportunities for the detection of CNVs at a base-level resolution. However, due to the intrinsic characteristics behind NGS data, accurate detection of CNVs is still a challenging task. In this article, we propose a new density peak-based method, called dpCNV, for the detection of CNVs from NGS data. The algorithm of dpCNV is designed based on density peak clustering algorithm. It extracts two features, i.e., local density and minimum distance, from sequencing read depth (RD) profile and generates a two-dimensional data. Based on the generated data, a two-dimensional null distribution is constructed to test the significance of each genome bin and then the significant genome bins are declared as CNVs. We test the performance of the dpCNV method on a number of simulated datasets and make comparison with several existing methods. The experimental results demonstrate that our proposed method outperforms others in terms of sensitivity and F1-score. We further apply it to a set of real sequencing samples and the results demonstrate the validity of dpCNV. Therefore, we expect that dpCNV can be used as a supplementary to existing methods and may become a routine tool in the field of genome mutation analysis.
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Affiliation(s)
- Kun Xie
- The School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Ye Tian
- The School of Computer Science and Technology, Xidian University, Xi'an, China.,Xi'an Key Laboratory of Computational Bioinformatics, The School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Xiguo Yuan
- The School of Computer Science and Technology, Xidian University, Xi'an, China.,Xi'an Key Laboratory of Computational Bioinformatics, The School of Computer Science and Technology, Xidian University, Xi'an, China
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4
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Gad AA, Balenga N. The Emerging Role of Adhesion GPCRs in Cancer. ACS Pharmacol Transl Sci 2020; 3:29-42. [PMID: 32259086 DOI: 10.1021/acsptsci.9b00093] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Indexed: 02/08/2023]
Abstract
Aberrant expression, function, and mutation of G protein-coupled receptors (GPCRs) and their signaling partners, G proteins, have been well documented in many forms of cancer. These cell surface receptors and their endogenous ligands are implicated in all aspects of cancer including proliferation, angiogenesis, invasion, and metastasis. Adhesion GPCRs (aGPCRs) form the second largest family of GPCRs, most of which are orphan receptors with unknown physiological functions. This is mainly due to our limited insight into their structure, natural ligands, signaling pathways, and tissue expression profiles. Nevertheless, recent studies show that aGPCRs play important roles in cell adhesion to the extracellular matrix and cell-cell communication, processes that are dysregulated in cancer. Emerging evidence suggests that aGPCRs are implicated in migration, proliferation, and survival of tumor cells. We here review the role of aGPCRs in the five most common types of cancer (lung, breast, colorectal, prostate, and gastric) and emphasize the importance of further translational studies in this field.
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Affiliation(s)
- Abanoub A Gad
- Graduate Program in Life Sciences, University of Maryland, Baltimore, Maryland 20201, United States.,Division of General & Oncologic Surgery, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland 20201, United States
| | - Nariman Balenga
- Division of General & Oncologic Surgery, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland 20201, United States.,Molecular and Structural Biology program at University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, Maryland 20201, United States
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5
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Sun J, Kranzler HR, Gelernter J, Bi J. A genome-wide association study of cocaine use disorder accounting for phenotypic heterogeneity and gene–environment interaction. J Psychiatry Neurosci 2020; 45:34-44. [PMID: 31490055 PMCID: PMC6919916 DOI: 10.1503/jpn.180098] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Phenotypic heterogeneity and complicated gene–environment interplay in etiology are among the primary factors that hinder the identification of genetic variants associated with cocaine use disorder. METHODS To detect novel genetic variants associated with cocaine use disorder, we derived disease traits with reduced phenotypic heterogeneity using cluster analysis of a study sample (n = 9965). We then used these traits in genome-wide association tests, performed separately for 2070 African Americans and 1570 European Americans, using a new mixed model that accounted for the moderating effects of 5 childhood environmental factors. We used an independent sample (918 African Americans, 1382 European Americans) for replication. RESULTS The cluster analysis yielded 5 cocaine use disorder subtypes, of which subtypes 4 (n = 3258) and 5 (n = 1916) comprised heavy cocaine users, had high heritability estimates (h2 = 0.66 and 0.64, respectively) and were used in association tests. Seven of the 13 identified genetic loci in the discovery phase were available in the replication sample. In African Americans, rs114492924 (discovery p = 1.23 × E−8), a single nucleotide polymorphism in LINC01411, was replicated in the replication sample (p = 3.63 × E−3). In a meta-analysis that combined the discovery and replication results, 3 loci in African Americans were significant genome-wide: rs10188036 in TRAK2 (p = 2.95 × E−8), del-1:15511771 in TMEM51 (p = 9.11 × E−10) and rs149843442 near LPHN2 (p = 3.50 × E−8). LIMITATIONS Lack of data prevented us from replicating 6 of the 13 identified loci. CONCLUSION Our results demonstrate the importance of considering phenotypic heterogeneity and gene–environment interplay in detecting genetic variations that contribute to cocaine use disorder, because new genetic loci have been identified using our novel analytic method.
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Affiliation(s)
- Jiangwen Sun
- From the Department of Computer Science and Engineering, University of Connecticut, School of Engineering, Storrs, CT (Sun, Bi); the University of Pennsylvania Perelman School of Medicine, Department of Psychiatry, Center for Studies of Addiction and Corporal Michael Crescenz VAMC, Philadelphia, PA (Kranzler); and the Yale University School of Medicine, Department of Psychiatry, Division of Human Genetics and Departments of Genetics and Neurobiology; and VA CT Healthcare Center, New Haven, CT (Gelernter)
| | - Henry R. Kranzler
- From the Department of Computer Science and Engineering, University of Connecticut, School of Engineering, Storrs, CT (Sun, Bi); the University of Pennsylvania Perelman School of Medicine, Department of Psychiatry, Center for Studies of Addiction and Corporal Michael Crescenz VAMC, Philadelphia, PA (Kranzler); and the Yale University School of Medicine, Department of Psychiatry, Division of Human Genetics and Departments of Genetics and Neurobiology; and VA CT Healthcare Center, New Haven, CT (Gelernter)
| | - Joel Gelernter
- From the Department of Computer Science and Engineering, University of Connecticut, School of Engineering, Storrs, CT (Sun, Bi); the University of Pennsylvania Perelman School of Medicine, Department of Psychiatry, Center for Studies of Addiction and Corporal Michael Crescenz VAMC, Philadelphia, PA (Kranzler); and the Yale University School of Medicine, Department of Psychiatry, Division of Human Genetics and Departments of Genetics and Neurobiology; and VA CT Healthcare Center, New Haven, CT (Gelernter)
| | - Jinbo Bi
- From the Department of Computer Science and Engineering, University of Connecticut, School of Engineering, Storrs, CT (Sun, Bi); the University of Pennsylvania Perelman School of Medicine, Department of Psychiatry, Center for Studies of Addiction and Corporal Michael Crescenz VAMC, Philadelphia, PA (Kranzler); and the Yale University School of Medicine, Department of Psychiatry, Division of Human Genetics and Departments of Genetics and Neurobiology; and VA CT Healthcare Center, New Haven, CT (Gelernter)
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6
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Huang B, Zhong N, Cao H, Yu G. A curated target gene pool assisting disease prediction and patient-specific biomarker selection for lung squamous cell carcinoma. Oncol Lett 2018; 16:5140-5146. [PMID: 30197682 PMCID: PMC6126348 DOI: 10.3892/ol.2018.9241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 06/13/2018] [Indexed: 12/11/2022] Open
Abstract
There have been hundreds of genes demonstrated to be associated with lung squamous cell carcinoma (LSCC), presenting various degrees of association with this disease. In the present study, gene vectors were investigated as genetic biomarkers for the diagnosis and personalized treatment of LSCC. A LSCC genetic database (LSCC_GD) was developed through literature-associated data analysis, where 260 LSCC target genes were curated. Subsequently, numerous associations between these genes and LSCC were studied. Following this, a sparse representation-based variable selection (SRVS) was employed for gene selection from two LSCC gene expression datasets, followed by a case/control classification. Results were compared using analysis of variance (ANOVA)-based gene selection approaches. Using SRVS, a gene vector was selected from each dataset, resulting in significantly higher classification accuracy (CR), compared with randomly selected genes (For datasets GSE18842 and GSE1987, CR=100 and 100% and permutation P=5.0×10−4 and 1.8×10−3, respectively). The SRVS method outperformed ANOVA in terms of the classification ratio. The results indicated that, for a given dataset, there may be a gene vector from the 260 curated LSCC genes that possesses significant prediction power. SRVS is effective in identifying the optimum gene subset target for personalized treatment.
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Affiliation(s)
- Bin Huang
- Department of Cardiothoracic Surgery, Affiliated Jiangyin Hospital of Southeast University, Jiangyin, Jiangsu 214400, P.R. China
| | - Ning Zhong
- Department of Cardiothoracic Surgery, The First People's Hospital of Kunshan, Kunshan, Jiangsu 215300, P.R. China
| | - Hongbao Cao
- Department of Genomics Research, R&D Solutions, Elsevier Inc., Rockville, MD 20852, USA.,Unit on Statistical Genomics, National Institute of Mental Health/National Institute of Health, Bethesda, MD 20892, USA
| | - Guiping Yu
- Department of Cardiothoracic Surgery, The Affiliated Jiangyin Hospital of Southeast University Medical College, Jiangyin, Jiangsu 214400, P.R. China
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7
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Khalilipour N, Baranova A, Jebelli A, Heravi-Moussavi A, Bruskin S, Abbaszadegan MR. Familial Esophageal Squamous Cell Carcinoma with damaging rare/germline mutations in KCNJ12/KCNJ18 and GPRIN2 genes. Cancer Genet 2017; 221:46-52. [PMID: 29405996 DOI: 10.1016/j.cancergen.2017.11.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 11/12/2017] [Accepted: 11/28/2017] [Indexed: 02/07/2023]
Abstract
In Iran, esophageal cancer is the fourth common cancers in women and sixth common cancers in men. Here we evaluated the importance of familial risk factors and the role of genetic predisposition in Esophageal Squamous Cell Carcinoma (ESCC) using Whole-Exome Sequencing (WES). Germline damaging mutations were identified in WES data from 9 probands of 9 unrelated ESCC pedigrees. Mutations were confirmed with Sanger sequencing and evaluated amplification-refractory mutation system-Polymerase Chain Reaction (ARMS-PCR) in 50 non-related ethnically matched samples and in complete genomics database. Sixteen candidate variants were detected in ESCC 9 probands. Four of these 16 variants were rare damaging mutations including novel mutations in KCNJ12/KCNJ18, and GPRIN2 genes. This WES study in Iranian patients with ESCC, provides insight into the identification of novel germline mutations in familial ESCC. Our data suggest an association between specific mutations and increased risk of ESCC.
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Affiliation(s)
- Narjes Khalilipour
- Medical Genetics Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ancha Baranova
- Research Center for Medical Genetics RAMS, Moscow, Russia
| | - Amir Jebelli
- Stem Cell and Regenerative Medicine Research Department, Iranian Academic Center for Education, Culture and Research (ACECR), Mashhad Branch, Mashhad, Iran
| | | | - Sergey Bruskin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Mohammad Reza Abbaszadegan
- Medical Genetics Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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8
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Fujisawa T, Filippakopoulos P. Functions of bromodomain-containing proteins and their roles in homeostasis and cancer. Nat Rev Mol Cell Biol 2017; 18:246-262. [PMID: 28053347 DOI: 10.1038/nrm.2016.143] [Citation(s) in RCA: 372] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bromodomains (BRDs) are evolutionarily conserved protein-protein interaction modules that are found in a wide range of proteins with diverse catalytic and scaffolding functions and are present in most tissues. BRDs selectively recognize and bind to acetylated Lys residues - particularly in histones - and thereby have important roles in the regulation of gene expression. BRD-containing proteins are frequently dysregulated in cancer, they participate in gene fusions that generate diverse, frequently oncogenic proteins, and many cancer-causing mutations have been mapped to the BRDs themselves. Importantly, BRDs can be targeted by small-molecule inhibitors, which has stimulated many translational research projects that seek to attenuate the aberrant functions of BRD-containing proteins in disease.
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Affiliation(s)
- Takao Fujisawa
- Ludwig Institute for Cancer Research, Old Road Campus Research Building, Roosevelt Drive, Oxford
| | - Panagis Filippakopoulos
- Ludwig Institute for Cancer Research, Old Road Campus Research Building, Roosevelt Drive, Oxford.,Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
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9
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Chan WH, Mohamad MS, Deris S, Zaki N, Kasim S, Omatu S, Corchado JM, Al Ashwal H. Identification of informative genes and pathways using an improved penalized support vector machine with a weighting scheme. Comput Biol Med 2016; 77:102-15. [PMID: 27522238 DOI: 10.1016/j.compbiomed.2016.08.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 08/03/2016] [Accepted: 08/03/2016] [Indexed: 01/03/2023]
Abstract
Incorporation of pathway knowledge into microarray analysis has brought better biological interpretation of the analysis outcome. However, most pathway data are manually curated without specific biological context. Non-informative genes could be included when the pathway data is used for analysis of context specific data like cancer microarray data. Therefore, efficient identification of informative genes is inevitable. Embedded methods like penalized classifiers have been used for microarray analysis due to their embedded gene selection. This paper proposes an improved penalized support vector machine with absolute t-test weighting scheme to identify informative genes and pathways. Experiments are done on four microarray data sets. The results are compared with previous methods using 10-fold cross validation in terms of accuracy, sensitivity, specificity and F-score. Our method shows consistent improvement over the previous methods and biological validation has been done to elucidate the relation of the selected genes and pathway with the phenotype under study.
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Affiliation(s)
- Weng Howe Chan
- Artificial Intelligence and Bioinformatics Research Group, Faculty of Computing, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Mohd Saberi Mohamad
- Artificial Intelligence and Bioinformatics Research Group, Faculty of Computing, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia.
| | - Safaai Deris
- Faculty of Creative Technology & Heritage, Universiti Malaysia Kelantan, Locked Bag 01, Bachok, 16300 Kota Bharu, Kelantan, Malaysia
| | - Nazar Zaki
- College of Information Technology, United Arab Emirate University, Al Ain 15551, United Arab Emirates
| | - Shahreen Kasim
- Faculty of Computer Science and Information Technology, Universiti Tun Hussein Onn Malaysia, 86400 Batu Pahat, Malaysia
| | - Sigeru Omatu
- Department of Electronics, Information and Communication Engineering, Osaka Institute of Technology, Osaka 535-8585, Japan
| | - Juan Manuel Corchado
- Biomedical Research Institute of Salamanca/BISITE Research Group, University of Salamanca, Salamanca, Spain
| | - Hany Al Ashwal
- College of Information Technology, United Arab Emirate University, Al Ain 15551, United Arab Emirates
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10
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Liu Y, An S, Ward R, Yang Y, Guo XX, Li W, Xu TR. G protein-coupled receptors as promising cancer targets. Cancer Lett 2016; 376:226-39. [PMID: 27000991 DOI: 10.1016/j.canlet.2016.03.031] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/14/2016] [Accepted: 03/14/2016] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) regulate an array of fundamental biological processes, such as growth, metabolism and homeostasis. Specifically, GPCRs are involved in cancer initiation and progression. However, compared with the involvement of the epidermal growth factor receptor in cancer, that of GPCRs have been largely ignored. Recent findings have implicated many GPCRs in tumorigenesis, tumor progression, invasion and metastasis. Moreover, GPCRs contribute to the establishment and maintenance of a microenvironment which is permissive for tumor formation and growth, including effects upon surrounding blood vessels, signaling molecules and the extracellular matrix. Thus, GPCRs are considered to be among the most useful drug targets against many solid cancers. Development of selective ligands targeting GPCRs may provide novel and effective treatment strategies against cancer and some anticancer compounds are now in clinical trials. Here, we focus on tumor related GPCRs, such as G protein-coupled receptor 30, the lysophosphatidic acid receptor, angiotensin receptors 1 and 2, the sphingosine 1-phosphate receptors and gastrin releasing peptide receptor. We also summarize their tissue distributions, activation and roles in tumorigenesis and discuss the potential use of GPCR agonists and antagonists in cancer therapy.
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Affiliation(s)
- Ying Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Su An
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Richard Ward
- Molecular Pharmacology Group, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Yang Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Xiao-Xi Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Wei Li
- Kidney Cancer Research, Diagnosis and Translational Technology Center of Yunnan Province, Department of Urology, The People's Hospital of Yunnan Province, Kunming, Yunnan 650032, China.
| | - Tian-Rui Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
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11
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Lung Cancer Genomics in the Era of Accelerated Targeted Drug Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 890:1-23. [PMID: 26703796 DOI: 10.1007/978-3-319-24932-2_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Lung cancer is the leading cause of cancer-related deaths in the United States and the 5-year overall survival outlook for a patient has not improved in several decades. Recently, however, molecular and genomic profiling of the lung tumors has revealed recurring somatic mutations. As a result the therapeutic landscape of lung cancer is undergoing a paradigm shift from a purely histology-based understanding of the disease to subtype distinctions based on tumor genetics, which has launched cancer-specific, mechanism-based targeted therapies with clear benefit to patients. While targeted therapy advancements are being made at an ever increasing rate, a new challenge in the form of drug resistance has also emerged. This review summarizes the current literature for these issues.
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12
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Jeon MS, Song SH, Yun J, Kang JY, Kim HP, Han SW, Kim TY. Aberrant Epigenetic Modifications of LPHN2 Function as a Potential Cisplatin-Specific Biomarker for Human Gastrointestinal Cancer. Cancer Res Treat 2015; 48:676-86. [PMID: 26511811 PMCID: PMC4843720 DOI: 10.4143/crt.2015.153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/01/2015] [Indexed: 12/22/2022] Open
Abstract
Purpose Epigenetic alterations of specific genes have recently been identified as diagnostic biomarkers for human cancers. However, there are currently no standardized epigenetic biomarkers for drug sensitivity in human gastrointestinal cancer. Therefore, the aim of this study is to identify a novel epigenetic biomarker in gastrointestinal cancer. Materials and Methods Using bisulfite sequencing and pyrosequencing analysis, DNA methylation patterns of gastric, colon primary tissues and their cancer cells were analyzed, and histone modifications were analyzed using chromatin immunoprecipitation assay. In addition, cancer cells were exposed to cisplatin and treated with a DNA methyltransferase inhibitor. Results We report that in human gastric and colon cancers, latrophilin 2 (LPHN2) is silenced by epigenetic modifications, including CpG island methylation and aberrant histone modifications. We also confirmed that LPHN2 was silenced by DNA hypermethylation in primary gastric and colon tumor tissues compared to their normal counterparts. Interestingly, we found that cancer cells with methylated LPHN2 showed higher sensitivity to cisplatin. Also, 5-aza- 2′-deoxycytidine combined with cisplatin decreased the cytotoxicity of cisplatin in cancer cells with methylated LPHN2. In addition, LPHN2 knockdown in cancer cells with high LPHN2 expression sensitized these cells to the anti-proliferative effects of cisplatin. Conclusion In human gastrointestinal cancer, we found that LPHN2 is regulated by epigenetic modifications, and that cancer cells with lower LPHN2 expression show higher sensitivity to cisplatin. Therefore, the methylation status of LPHN2 is a potential novel epigenetic biomarker for cisplatin treatment in human gastric and colon cancers.
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Affiliation(s)
- Mi-Seong Jeon
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | - Sang-Hyun Song
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Jiyeon Yun
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | - Jee-Youn Kang
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
| | - Hwang-Phill Kim
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Sae-Won Han
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Tae-You Kim
- Cancer Research Institute, Seoul National University, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea.,Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
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13
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Sultana A, Nakaya N, Dong L, Abu-Asab M, Qian H, Tomarev SI. Deletion of olfactomedin 2 induces changes in the AMPA receptor complex and impairs visual, olfactory, and motor functions in mice. Exp Neurol 2014; 261:802-11. [PMID: 25218043 DOI: 10.1016/j.expneurol.2014.09.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/21/2014] [Accepted: 09/02/2014] [Indexed: 12/19/2022]
Abstract
Olfactomedin 2 (Olfm2) is a secretory glycoprotein belonging to the family of olfactomedin domain-containing proteins. A previous study has shown that a mutation in OLFM2 is associated with primary open angle glaucoma in Japanese patients. In the present study, we generated Olfm2 deficient mice by replacing the Olfm2 gene with the LacZ gene. The loss of Olfm2 resulted in no gross abnormalities. However, Olfm2 null mice showed reduced exploration, locomotion, olfactory sensitivity, abnormal motor coordination, and anxiety related behavior. The pattern of the Olfm2 gene expression was studied in the brain and eye using β-galactosidase staining. In the brain, Olfm2 was mainly expressed in the olfactory bulb, cortex, piriform cortex, olfactory trabeculae, and inferior and superior colliculus. In the eye expression was detected mainly in retinal ganglion cells. In Olfm2 null mice, the amplitude of the first negative wave in the visual evoked potential test was significantly reduced as compared with wild-type littermates. Olfm2, similar to Olfm1, interacted with the GluR2 subunit of the AMPAR complexes and Olfm2 co-segregated with the AMPA receptor subunit GluR2 and other synaptic proteins in the synaptosomal membrane fraction upon biochemical fractionation of the adult mice cortex and retina. Immunoprecipitation from the synaptosomal membrane fraction of the Olfm2 null mouse brain cortex using the GluR2 antibody showed reduced levels of several components of the AMPAR complex in the immunoprecipitates including Olfm1, PSD95 and CNIH2. These results suggest that heterodimers of Olfm1 and Olfm2 interact with AMPAR more efficiently than Olfm2 homodimers and that Olfm2 plays a role in the organization of the AMPA receptor complexes.
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Affiliation(s)
- Afia Sultana
- Section on Retinal Ganglion Cell Biology, Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Naoki Nakaya
- Section on Retinal Ganglion Cell Biology, Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Lijin Dong
- Genetic Engineering Facility, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Mones Abu-Asab
- Histopathology Core Facility, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Haohua Qian
- Visual Function Core, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Stanislav I Tomarev
- Section on Retinal Ganglion Cell Biology, Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Targeting the phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) pathway: an emerging treatment strategy for squamous cell lung carcinoma. Cancer Treat Rev 2014; 40:980-9. [PMID: 25037117 DOI: 10.1016/j.ctrv.2014.06.006] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 05/29/2014] [Accepted: 06/08/2014] [Indexed: 01/19/2023]
Abstract
Squamous cell lung carcinoma accounts for approximately 30% of all non-small cell lung cancers (NSCLCs). Despite progress in the understanding of the biology of cancer, cytotoxic chemotherapy remains the standard of care for patients with squamous cell lung carcinoma, but the prognosis is generally poor. The phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) pathway is one of the most commonly activated signaling pathways in cancer, leading to cell proliferation, survival, and differentiation. It has therefore become a major focus of clinical research. Various alterations in the PI3K/AKT/mTOR pathway have been identified in squamous cell lung carcinoma and a number of agents targeting these alterations are in clinical development for use as single agents and in combination with other targeted and conventional treatments. These include pan-PI3K inhibitors, isoform-specific PI3K inhibitors, AKT inhibitors, mTOR inhibitors, and dual PI3K/mTOR inhibitors. These agents have demonstrated antitumor activity in preclinical models of NSCLC and preliminary clinical evidence is also available for some agents. This review will discuss the role of the PI3K/AKT/mTOR pathway in cancer and how the discovery of genetic alterations in this pathway in patients with squamous cell lung carcinoma can inform the development of targeted therapies for this disease. An overview of ongoing clinical trials investigating PI3K/AKT/mTOR pathway inhibitors in squamous cell lung carcinoma will also be included.
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15
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Ge X, Jiang L. [Research progress of thyroid transcription factor-1 as molecular marker in lung carcinoma]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2014; 17:491-5. [PMID: 24949691 PMCID: PMC6000104 DOI: 10.3779/j.issn.1009-3419.2014.06.10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
肺癌是全球癌症相关死亡的主要病因之一。多数的肺癌患者确诊时已处于晚期,中位生存期为1年左右,5年生存率不足16%,预后极差。近年来的研究热点主要集中于涉及致癌过程中新的生物因子的潜在作用。最近研究表明,甲状腺转录因子(thyroid transcription factor-1, TTF-1)是肺癌的一种特异性的谱系生存癌基因。在肿瘤进展过程中,TTF-1的生物学活性和临床功能表现出相反的作用。在此,本文总结了TTF-1在肺癌的发生、发展、诊断及预后方面的作用,以期为TTF-1作为肺癌新型生物标记物的作用提供见解。
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Affiliation(s)
- Xiaoxiao Ge
- Department of Pulmonary, Shanghai Chest Hospital , Shanghai Jiaotong University, Shanghai 200030, China
| | - Liyan Jiang
- Department of Pulmonary, Shanghai Chest Hospital , Shanghai Jiaotong University, Shanghai 200030, China
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Renieri A, Mencarelli MA, Cetta F, Baldassarri M, Mari F, Furini S, Piu P, Ariani F, Dragani TA, Frullanti E. Oligogenic germline mutations identified in early non-smokers lung adenocarcinoma patients. Lung Cancer 2014; 85:168-74. [PMID: 24954872 DOI: 10.1016/j.lungcan.2014.05.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/28/2014] [Indexed: 01/15/2023]
Abstract
OBJECTIVES A polygenic model is commonly assumed for the predisposition to common cancers. With respect to lung cancer, Genome Wide Association Studies (GWAS) have identified three loci at 15q25, 5p15.33, and 6p21. However, the relative risks associated with alleles at these loci are low; in addition, the data are limited to smokers, and have not been quite reproducible. MATERIALS AND METHODS In order to investigate genetic susceptibility we have adopted an entirely novel patient selection strategy. First, we have selected for adenocarcinoma (ADCA) histology only; second, we have selected non-smokers; third we have selected patients who developed ADCA of lung before the age of 60 and who had an older unaffected sib: we have identified 31 such sib-pairs. Among them, we selected two patients with very early age at disease onset (37- and 49-years old), and having a healthy sibling available for genome comparison older than at least 7 years. RESULTS On germline DNA samples of four subjects of two such pairs we have carried out whole exome sequencing. Truncating mutations were detected in 8 'cancer genes' in one affected, and in 5 cancer genes in the other affected subject: but none in the two healthy sibs (p=0.0026). Some of these mutant genes (such as BAG6, SPEN and WISP3) are recognized as major cancer players in lung tumors; others have been previously identified in other human cancers (JAK2, TCEB3C, NELFE, TAF1B, EBLN2), in mouse models (GON4L, NOP58, and RBMX) or in genome-wide association studies (KIAA2018, ZNF311). CONCLUSIONS This study identifies for the first time in non-smokers with lung adenocarcinoma specific sets of germline mutations that, together, may predispose to this tumor.
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Affiliation(s)
- Alessandra Renieri
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy; Medical Genetics, University of Siena, Siena, Italy; Istituto Toscano Tumori, Florence, Italy.
| | | | | | - Margherita Baldassarri
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy; Medical Genetics, University of Siena, Siena, Italy
| | - Francesca Mari
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy; Medical Genetics, University of Siena, Siena, Italy
| | - Simone Furini
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Pietro Piu
- Department of Medicine, Surgery & Neuroscience, University of Siena, Siena, Italy
| | | | | | - Elisa Frullanti
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy.
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