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Metwally M, Bayoumi A, Khan A, Adams LA, Aller R, García-Monzón C, Arias-Loste MT, Bugianesi E, Miele L, Anna A, Latchoumanin O, Han S, Alenizi S, Sharkawy RE, Elattar A, Gallego-Durán R, Fischer J, Berg T, Liddle C, Romero-Gomez M, George J, Eslam M. Copy number variation and expression of exportin-4 associates with severity of fibrosis in metabolic associated fatty liver disease. EBioMedicine 2021; 70:103521. [PMID: 34388518 PMCID: PMC8365315 DOI: 10.1016/j.ebiom.2021.103521] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 01/11/2023] Open
Abstract
Background Liver fibrosis risk is a heritable trait, the outcome of which is the net deposition of extracellular matrix by hepatic stellate cell-derived myofibroblasts. Whereas nucleotide sequence variations have been extensively studied in liver fibrosis, the role of copy number variations (CNV) in which genes exist in abnormal numbers of copies (mostly due to duplication or deletion) has had limited exploration. Methods The impact of the XPO4 CNV on histological liver damage was examined in a cohort comprised 646 Caucasian patients with biopsy-proven MAFLD and 170 healthy controls. XPO4 expression was modulated and function was examined in human and animal models. Findings Here we demonstrate in a cohort of 816 subjects, 646 with biopsy-proven metabolic associated liver disease (MAFLD) and 170 controls, that duplication in the exportin 4 (XPO4) CNV is associated with the severity of liver fibrosis. Functionally, this occurs via reduced expression of hepatic XPO4 that maintains sustained activation of SMAD3/SMAD4 and promotes TGF-β1-mediated HSC activation and fibrosis. This effect was mediated through termination of nuclear SMAD3 signalling. XPO4 demonstrated preferential binding to SMAD3 compared to other SMADs and led to reduced SMAD3-mediated responses as shown by attenuation of TGFβ1 induced SMAD transcriptional activity, reductions in the recruitment of SMAD3 to target gene promoters following TGF-β1, as well as attenuation of SMAD3 phosphorylation and disturbed SMAD3/SMAD4 complex formation. Interpretation We conclude that a CNV in XPO4 is a critical mediator of fibrosis severity and can be exploited as a therapeutic target for liver fibrosis. Funding ME and JG are supported by the Robert W. Storr Bequest to the Sydney Medical Foundation, University of Sydney; a National Health and Medical Research Council of Australia (NHMRC) Program Grant (APP1053206) and Project and ideas grants (APP2001692, APP1107178 and APP1108422). AB is supported by an Australian Government Research Training Program (RTP) scholarship. EB is supported by Horizon 2020 under grant 634413 for the project EPoS.
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Affiliation(s)
- Mayada Metwally
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Ali Bayoumi
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Anis Khan
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Leon A Adams
- Medical School, Sir Charles Gairdner Hospital Unit, University of Western Australia, Nedlands, WA, Australia
| | - Rocio Aller
- Center of Investigation of Endocrinology and Nutrition, School of Medicine, and Unit of Investigation, Hospital Clinico Universitario de Valladolid, Valladolid, Spain
| | - Carmelo García-Monzón
- Liver Research Unit, Instituto de Investigacion Sanitaria Princesa, University Hospital Santa Cristina, CIBERehd, Madrid, Spain
| | - María Teresa Arias-Loste
- Gastroenterology and Hepatology Department, Marqués de Valdecilla University Hospital, 39008 Santander, Spain
| | - Elisabetta Bugianesi
- Division of Gastroenterology, Department of Medical Science, University of Turin, Turin, Italy
| | - Luca Miele
- Department of Internal Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Alisi Anna
- Research Unit of Molecular Genetics of Complex Phenotypes, IRCCS "Bambino Gesù" Children's Hospital, Rome, Italy
| | - Olivier Latchoumanin
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Shuanglin Han
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Shafi Alenizi
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Rasha El Sharkawy
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Afaf Elattar
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Rocio Gallego-Durán
- Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, Sevilla, Spain
| | - Janett Fischer
- Section of Hepatology, Clinic for Gastroenterology and Rheumatology, University Clinic Leipzig, Leipzig, Germany
| | - Thomas Berg
- Section of Hepatology, Clinic for Gastroenterology and Rheumatology, University Clinic Leipzig, Leipzig, Germany
| | - Christopher Liddle
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Manuel Romero-Gomez
- Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, Sevilla, Spain
| | - Jacob George
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia.
| | - Mohammed Eslam
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia.
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Ayuso P, García-Martín E, Cornejo-García JA, Agúndez JAG, Ladero JM. Genetic Variants of Alcohol Metabolizing Enzymes and Alcohol-Related Liver Cirrhosis Risk. J Pers Med 2021; 11:jpm11050409. [PMID: 34068303 PMCID: PMC8153263 DOI: 10.3390/jpm11050409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/30/2021] [Accepted: 05/09/2021] [Indexed: 11/25/2022] Open
Abstract
Alcohol-related liver disease (ARLD) is a major public health issue caused by excessive alcohol consumption. ARLD encompasses a wide range of chronic liver lesions, alcohol-related liver cirrhosis being the most severe and harmful state. Variations in the genes encoding the enzymes, which play an active role in ethanol metabolism, might influence alcohol exposure and hence be considered as risk factors of developing cirrhosis. We conducted a case-control study in which 164 alcohol-related liver cirrhosis patients and 272 healthy controls were genotyped for the following functional single nucleotide variations (SNVs): ADH1B gene, rs1229984, rs1041969, rs6413413, and rs2066702; ADH1C gene, rs35385902, rs283413, rs34195308, rs1693482, and rs35719513; CYP2E1 gene, rs3813867. Furthermore, copy number variations (CNVs) for ADH1A, ADH1B, ADH1C, and CYP2E1 genes were analyzed. A significant protective association with the risk of developing alcohol-related liver cirrhosis was observed between the mutant alleles of SNVs ADH1B rs1229984 (Pc value = 0.037) and ADH1C rs283413 (Pc value = 0.037). We identified CNVs in all genes studied, ADH1A gene deletions being more common in alcohol-related liver cirrhosis patients than in control subjects, although the association lost statistical significance after multivariate analyses. Our findings support that susceptibility to alcohol-related liver cirrhosis is related to variations in alcohol metabolism genes.
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Affiliation(s)
- Pedro Ayuso
- ARADyAL, Instituto de Salud Carlos III, University Institute of Molecular Pathology Biomarkers, UEx, 10003 Cáceres, Spain; (E.G.-M.); (J.A.G.A.)
- Correspondence:
| | - Elena García-Martín
- ARADyAL, Instituto de Salud Carlos III, University Institute of Molecular Pathology Biomarkers, UEx, 10003 Cáceres, Spain; (E.G.-M.); (J.A.G.A.)
| | - José A. Cornejo-García
- ARADyAL, Instituto de Salud Carlos III Research Laboratory, IBIMA, Regional University Hospital of Málaga, UMA, 29010 Málaga, Spain;
| | - José A. G. Agúndez
- ARADyAL, Instituto de Salud Carlos III, University Institute of Molecular Pathology Biomarkers, UEx, 10003 Cáceres, Spain; (E.G.-M.); (J.A.G.A.)
| | - José María Ladero
- Service of Gastroenterology (Liver Unit), Hospital Clínico San Carlos, Universidad Complutense Medical School, 28040 Madrid, Spain;
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Brick LA, Keller MC, Knopik VS, McGeary JE, Palmer RH. Shared additive genetic variation for alcohol dependence among subjects of African and European ancestry. Addict Biol 2019; 24:132-144. [PMID: 29178570 DOI: 10.1111/adb.12578] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 09/05/2017] [Accepted: 10/15/2017] [Indexed: 02/01/2023]
Abstract
Alcohol dependence (AD) affects individuals from all racial/ethnic groups, and previous research suggests that there is considerable variation in AD risk between and among various ancestrally defined groups in the United States. Although the reasons for these differences are likely due in part to contributions of complex sociocultural factors, limited research has attempted to examine whether similar genetic variation plays a role across ancestral groups. Using a pooled sample of individuals of African and European ancestry (AA/EA) obtained through data shared within the Database for Genotypes and Phenotypes, we estimated the extent to which additive genetic similarity for AD between AA and EAs using common single nucleotide polymorphisms overlapped across the two populations. AD was represented as a factor score by using Diagnostic and Statistical Manual dependence criteria, and genetic data were imputed by using the 1000 Genomes Reference Panel. Analyses revealed a significant single nucleotide polymorphism-based heritability of 17 percent (SE = 5) in EAs and 24 percent (SE = 15) in AAs. Further, a significant genetic correlation of 0.77 (SE = 0.46) suggests that the allelic architecture influencing the AD factor for EAs and AAs is largely similar across the two populations. Analyses indicated that investigating the genetic underpinnings of alcohol dependence in different ethnic groups may serve to highlight core etiological factors common to both groups and unique etiological factors specific to each ethnic group.
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Affiliation(s)
- Leslie A. Brick
- Division of Behavioral Genetics, Department of Psychiatry; Rhode Island Hospital; Providence RI USA
- Department of Psychiatry and Human Behavior, Alpert Medical School; Brown University; Providence RI USA
| | - Matthew C. Keller
- Institute for Behavior Genetics, Department of Psychology and Neuroscience; University of Colorado at Boulder; Boulder CO USA
| | - Valerie S. Knopik
- Division of Behavioral Genetics, Department of Psychiatry; Rhode Island Hospital; Providence RI USA
- Department of Psychiatry and Human Behavior, Alpert Medical School; Brown University; Providence RI USA
| | - John E. McGeary
- Division of Behavioral Genetics, Department of Psychiatry; Rhode Island Hospital; Providence RI USA
- Department of Psychiatry and Human Behavior, Alpert Medical School; Brown University; Providence RI USA
- Providence Veterans Affairs Medical Center; Providence RI USA
| | - Rohan H.C. Palmer
- Behavior Genetics of Addiction Laboratory, Department of Psychology; Emory University; Atlanta GA USA
- Division of Behavioral Genetics, Department of Psychiatry; Rhode Island Hospital; Providence RI USA
- Department of Psychiatry and Human Behavior, Alpert Medical School; Brown University; Providence RI USA
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Rodríguez-López J, Flórez G, Blanco V, Pereiro C, Fernández JM, Fariñas E, Estévez V, Gómez-Trigo J, Gurriarán X, Calvo R, Sáiz P, Vázquez FL, Arrojo M, Costas J. Genome wide analysis of rare copy number variations in alcohol abuse or dependence. J Psychiatr Res 2018; 103:212-218. [PMID: 29890507 DOI: 10.1016/j.jpsychires.2018.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/30/2018] [Accepted: 06/01/2018] [Indexed: 11/18/2022]
Abstract
Genetics plays an important role in alcohol abuse/dependence. Its heritability has been estimated as 45-65%. Rare copy number variations (CNVs) have been confirmed as relevant genetic factors in other neuropsychiatric disorders, such as autism spectrum disorders, schizophrenia, epilepsy, or Tourette syndrome. In the present study, we analyzed the role of rare CNVs affecting exons of coding genes in a sample from Northwest Spain genotyped using the Illumina Infinium PsychArray Beadchip. After rigorous genotyping quality control procedure, 712 patients with alcohol abuse or dependence and 804 controls were used for CNV detection. CNV calling was performed using PennCNV and cnvPartition, and analyses were restricted to CNVs of at least 100 kb and including at least 10 single nucleotide polymorphisms. Logistic regression was used to test for the effect of CNV as well as number of genes affected by CNVs on case/control status, after adjustment for demographic and experimental covariates. We have found an excess of deletions (p = 0.008) and genes affected by deletions (p = 0.017) in cases. This effect was restricted to the 14.8% of affected genes that are intolerant to loss-of-function mutations (gene count p = 0.009). The importance of this subset of genes is emerging in other psychiatric disorders of neurodevelopmental origin, suggesting that disturbance in neurodevelopment mediated by genetic alterations may be a risk factor for alcohol use disorder.
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Affiliation(s)
- Julio Rodríguez-López
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Galicia, Spain
| | - Gerardo Flórez
- Unidade de Conductas Adictivas, Servizo de Psiquiatría, Complexo Hospitalario Universitario de Ourense (CHUO), Servizo Galego de Saúde (SERGAS), Ourense, Galicia, Spain
| | - Vanessa Blanco
- Departament of Evolutionary and Educational Psychology, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - César Pereiro
- Unidade Asistencial de Drogodependencias (ACLAD), A Coruña, Galicia, Spain
| | | | - Emilio Fariñas
- Unidade Municipal de Atención a Drogodependientes (UMAD), Santiago de Compostela, Galicia, Spain
| | - Valentín Estévez
- Unidade de Conductas Adictivas, Servizo de Psiquiatría, Complexo Hospitalario Universitario de Ourense (CHUO), Servizo Galego de Saúde (SERGAS), Ourense, Galicia, Spain
| | - Jesús Gómez-Trigo
- Unidade de Conductas Adictivas, Servizo de Psiquiatría, Complexo Hospitalario Universitario de Ourense (CHUO), Servizo Galego de Saúde (SERGAS), Ourense, Galicia, Spain; Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Galicia, Spain
| | - Xaquín Gurriarán
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Galicia, Spain
| | - Raquel Calvo
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Galicia, Spain
| | - Pilar Sáiz
- Department of Psychiatry, Universidad de Oviedo, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Servicio de Salud del Principado de Asturias (SESPA), Oviedo, Spain
| | - Fernando Lino Vázquez
- Departament of Clinical Psychology and Psychobiology, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Manuel Arrojo
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Galicia, Spain; Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Galicia, Spain
| | - Javier Costas
- Instituto de Investigación Sanitaria (IDIS) de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Galicia, Spain.
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Abstract
OBJECTIVE Proteins involving absorption, distribution, metabolism, and excretion (ADME) play a critical role in drug pharmacokinetics. The type and frequency of genetic variation in the ADME genes differ among populations. The aim of this study was to systematically investigate common and rare ADME coding variation in diverse ethnic populations by exome sequencing. MATERIALS AND METHODS Data derived from commercial exome capture arrays and next-generation sequencing were used to characterize coding variation in 298 ADME genes in 251 Northeast Asians and 1181 individuals from the 1000 Genomes Project. RESULTS Approximately 75% of the ADME coding sequence was captured at high quality across the joint samples harboring more than 8000 variants, with 49% of individuals carrying at least one 'knockout' allele. ADME genes carried 50% more nonsynonymous variation than non-ADME genes (P=8.2×10) and showed significantly greater levels of population differentiation (P=7.6×10). Out of the 2135 variants identified that were predicted to be deleterious, 633 were not on commercially available ADME or general-purpose genotyping arrays. Forty deleterious variants within important ADME genes, with frequencies of at least 2% in at least one population, were identified as candidates for future pharmacogenetic studies. CONCLUSION Exome sequencing was effective in accurately genotyping most ADME variants important for pharmacogenetic research, in addition to identifying rare or potentially de novo coding variants that may be clinically meaningful. Furthermore, as a class, ADME genes are more variable and less sensitive to purifying selection than non-ADME genes.
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Sulovari A, Liu Z, Zhu Z, Li D. Genome-wide meta-analysis of copy number variations with alcohol dependence. THE PHARMACOGENOMICS JOURNAL 2017; 18:398-405. [PMID: 28696413 DOI: 10.1038/tpj.2017.35] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/10/2017] [Accepted: 06/07/2017] [Indexed: 12/26/2022]
Abstract
Genetic association studies and meta-analyses of alcohol dependence (AD) have reported AD-associated single nucleotide polymorphisms (SNPs). These SNPs collectively account for a small portion of estimated heritability in AD. Recent genome-wide copy number variation (CNV) studies have identified CNVs associated with AD and substance dependence, suggesting that a portion of the missing heritability is explained by CNV. We applied PennCNV and QuantiSNP CNV calling algorithms to identify consensus CNVs in five AD cohorts of European and African origins. After rigorous quality control, genome-wide meta-analyses of CNVs were carried out in 3243 well-diagnosed AD cases and 2802 controls. We identified nine CNV regions, including a deletion in chromosome 5q21.3 with a suggestive association with AD (OR=2.15 (1.41-3.29) and P=3.8 × 10-4) and eight nominally significant CNV regions. All regions were replicated with consistent effect sizes across studies and populations. Pathway and gene-drug interaction enrichment analyses based on the resulting genes indicated the mitogen-activated protein kinase signaling pathway and the recombinant insulin and hyaluronidase drugs, which were relevant to AD biology or treatment. To our knowledge, this is the first genome-wide meta-analysis of CNVs with addiction. Further investigation of the AD-associated CNV regions will provide better understanding of the AD genetic mechanism.
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Affiliation(s)
- A Sulovari
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA
| | - Z Liu
- Spine Surgery, Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Z Zhu
- Spine Surgery, Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - D Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA.,Department of Computer Science, University of Vermont, Burlington, VT, USA.,Neuroscience, Behavior, and Health Initiative, University of Vermont, Burlington, VT, USA
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Lee B, Yoon K, Lee S, Kang JM, Kim J, Shim SH, Kim HM, Song S, Naka K, Kim AK, Yang HK, Kim SJ. Homozygous deletions at 3p22, 5p14, 6q15, and 9p21 result in aberrant expression of tumor suppressor genes in gastric cancer. Genes Chromosomes Cancer 2014; 54:142-55. [PMID: 25521327 DOI: 10.1002/gcc.22226] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 10/28/2014] [Indexed: 12/27/2022] Open
Abstract
Homozygous deletion is a frequent mutational mechanism of silencing tumor suppressor genes in cancer. Therefore, homozygous deletions have been analyzed for identification of tumor suppressor genes that can be utilized as biomarkers or therapeutic targets for cancer treatment. In this study, to elucidate potential tumor suppressor genes involved in gastric cancer (GC), we analyzed the entire set of large homozygous deletions in six human GC cell lines through genome- and transcriptome-wide approaches. We identified 51 genes in homozygous deletion regions of chromosomes and confirmed the deletion frequency in tumor tissues of 219 GC patients from The Cancer Genome Atlas database. We evaluated the effect of homozygous deletions on the mRNA level and found significantly affected genes in chromosome bands 9p21, 3p22, 5p14, and 6q15. Among the genes in 9p21, we investigated the potential tumor suppressive effect of KLHL9. We demonstrated that ectopic expression of KLHL9 inhibited cell proliferation and tumor formation in KLHL9-deficient SNU-16 cell line. In addition, we observed that homozygous focal deletions generated truncated transcripts of TGFBR2, CTNNA1, and STXBP5. Ectopic expression of two kinds of TGFBR2-reverse GADL1 fusion genes suppressed TGF-β signaling, which may lead to the loss of sensitivity to TGF-β tumor suppressive activity. In conclusion, our findings suggest that novel tumor suppressor genes that are aberrantly expressed through homozygous deletions may play important roles in gastric tumorigenesis.
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Affiliation(s)
- Bona Lee
- CHA Cancer Institute, CHA University, Seongnam-si, 463-400, Republic of Korea; College of Pharmacy, Sookmyung Women's University, Seoul, 140-742, Republic of Korea
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