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Koo BK, Joo SK, Kim D, Lee S, Bae JM, Park JH, Kim JH, Chang MS, Kim W. Development and Validation of a Scoring System, Based on Genetic and Clinical Factors, to Determine Risk of Steatohepatitis in Asian Patients with Nonalcoholic Fatty Liver Disease. Clin Gastroenterol Hepatol 2020; 18:2592-2599.e10. [PMID: 32062042 DOI: 10.1016/j.cgh.2020.02.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 01/28/2020] [Accepted: 02/07/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS There are no biomarkers of nonalcoholic steatohepatitis (NASH) that are ready for routine clinical use. We investigated whether an analysis of PNPLA3 and TM6SF2 genotypes (rs738409 and rs58542926) can be used to identify patients with nonalcoholic fatty liver disease (NAFLD), with and without diabetes, who also have NASH. METHODS We collected data from the Boramae registry in Korea on 453 patients with biopsy-proven NAFLD with sufficient clinical data for calculating scores. Patients enrolled from February 2014 through March 2016 were assigned to cohort 1 (n = 302; discovery cohort) and patients enrolled thereafter were assigned to cohort 2 (n = 151; validation cohort). DNA samples were obtained from all participants and analyzed for the PNPLA3 rs738409 C>G, TM6SF2 rs58542926 C>T, SREBF2 rs133291 C>T, MBOAT7-TMC4 rs641738 C>T, and HSD17B13 rs72613567 adenine insertion (A-INS) polymorphisms. We used multivariable logistic regression analyses with stepwise backward selection to build a model to determine patients' risk for NASH (NASH PT) using the genotype and clinical data from cohort 1 and tested its accuracy in cohort 2. We used the receiver operating characteristic (ROC) curve to compare the diagnostic performances of the NASH PT and the NASH scoring systems. RESULTS We developed a NASH PT scoring system based on PNPLA3 and TM6SF2 genotypes, diabetes status, insulin resistance, and levels of aspartate aminotransferase and high-sensitivity C-reactive protein. NASH PT scores identified patients with NASH with an area under the ROC (AUROC) of 0.859 (95% CI, 0.817-0.901) in cohort 1. In cohort 2, NASH PT scores identified patients with NASH with an AUROC of 0.787 (95% CI, 0.715-0.860), which was significantly higher than the AUROC of the NASH score (AUROC, 0.729; 95% CI, 0.647-0.812; P = .007). The AUROC of the NASH PT score for detecting NASH in patients with NAFLD with diabetes was 0.835 (95% CI, 0.776-0.895) and in patients without diabetes was 0.809 (95% CI, 0.757-0.861). The negative predictive value of the NASH PT score <-0.785 for NASH in patients with NAFLD with diabetes reached 0.905. CONCLUSIONS We developed a scoring system, based on polymorphisms in PNPLA3 and TM6SF2 and clinical factors that identifies patients with NAFLD, with or without diabetes, who have NASH, with an AUROC value of 0.787. This system might help clinicians better identify NAFLD patients at risk for NASH.
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Engel C, Ahadova A, Seppälä TT, Aretz S, Bigirwamungu-Bargeman M, Bläker H, Bucksch K, Büttner R, de Vos Tot Nederveen Cappel WT, Endris V, Holinski-Feder E, Holzapfel S, Hüneburg R, Jacobs MAJM, Koornstra JJ, Langers AM, Lepistö A, Morak M, Möslein G, Peltomäki P, Pylvänäinen K, Rahner N, Renkonen-Sinisalo L, Schulmann K, Steinke-Lange V, Stenzinger A, Strassburg CP, van de Meeberg PC, van Kouwen M, van Leerdam M, Vangala DB, Vecht J, Verhulst ML, von Knebel Doeberitz M, Weitz J, Zachariae S, Loeffler M, Mecklin JP, Kloor M, Vasen HF. Associations of Pathogenic Variants in MLH1, MSH2, and MSH6 With Risk of Colorectal Adenomas and Tumors and With Somatic Mutations in Patients With Lynch Syndrome. Gastroenterology 2020; 158:1326-1333. [PMID: 31926173 DOI: 10.1053/j.gastro.2019.12.032] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 12/05/2019] [Accepted: 12/24/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND & AIMS Lynch syndrome is caused by variants in DNA mismatch repair (MMR) genes and associated with an increased risk of colorectal cancer (CRC). In patients with Lynch syndrome, CRCs can develop via different pathways. We studied associations between Lynch syndrome-associated variants in MMR genes and risks of adenoma and CRC and somatic mutations in APC and CTNNB1 in tumors in an international cohort of patients. METHODS We combined clinical and molecular data from 3 studies. We obtained clinical data from 2747 patients with Lynch syndrome associated with variants in MLH1, MSH2, or MSH6 from Germany, the Netherlands, and Finland who received at least 2 surveillance colonoscopies and were followed for a median time of 7.8 years for development of adenomas or CRC. We performed DNA sequence analyses of 48 colorectal tumors (from 16 patients with mutations in MLH1, 29 patients with mutations in MSH2, and 3 with mutations in MSH6) for somatic mutations in APC and CTNNB1. RESULTS Risk of advanced adenoma in 10 years was 17.8% in patients with pathogenic variants in MSH2 vs 7.7% in MLH1 (P < .001). Higher proportions of patients with pathogenic variants in MLH1 or MSH2 developed CRC in 10 years (11.3% and 11.4%) than patients with pathogenic variants in MSH6 (4.7%) (P = .001 and P = .003 for MLH1 and MSH2 vs MSH6, respectively). Somatic mutations in APC were found in 75% of tumors from patients with pathogenic variants in MSH2 vs 11% in MLH1 (P = .015). Somatic mutations in CTNNB1 were found in 50% of tumors from patients with pathogenic variants in MLH1 vs 7% in MSH2 (P = .002). None of the 3 tumors with pathogenic variants in MSH6 had a mutation in CTNNB1, but all had mutations in APC. CONCLUSIONS In an analysis of clinical and DNA sequence data from patients with Lynch syndrome from 3 countries, we associated pathogenic variants in MMR genes with risk of adenoma and CRC, and somatic mutations in APC and CTNNB1 in colorectal tumors. If these findings are confirmed, surveillance guidelines might be adjusted based on MMR gene variants.
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Affiliation(s)
- Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.
| | - Aysel Ahadova
- Department of Applied Tumour Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cooperation Unit Applied Tumour Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Toni T Seppälä
- Department of Surgery, Helsinki University Central Hospital, Helsinki, Finland; University of Helsinki, Helsinki, Finland; Johns Hopkins University, Surgical Oncology, Baltimore, Maryland
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, Bonn, Germany; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | | | - Hendrik Bläker
- Institute of Pathology, University Hospital Leipzig, Leipzig, Germany
| | - Karolin Bucksch
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | | | | | - Volker Endris
- Department of General Pathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany; Center of Medical Genetics, Munich, Germany
| | - Stefanie Holzapfel
- Institute of Human Genetics, University of Bonn, Bonn, Germany; National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany
| | - Robert Hüneburg
- National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany; Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Maarten A J M Jacobs
- Department of Gastroenterology & Hepatology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Jan J Koornstra
- Department of Gastroenterology & Hepatology, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexandra M Langers
- Department of Gastroenterology & Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Anna Lepistö
- Department of Surgery, Helsinki University Central Hospital, Helsinki, Finland; Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland
| | - Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany; Center of Medical Genetics, Munich, Germany
| | - Gabriela Möslein
- Center for Hereditary Tumors, HELIOS Klinikum Wuppertal, University Witten-Herdecke, Wuppertal, Germany
| | - Päivi Peltomäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Kirsi Pylvänäinen
- Department of Education and Science, Central Finland Hospital District, Jyväskylä, Finland
| | - Nils Rahner
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Laura Renkonen-Sinisalo
- Department of Surgery, Helsinki University Central Hospital, Helsinki, Finland; Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland
| | - Karsten Schulmann
- Department of Hematology and Oncology, Klinikum Hochsauerland, Meschede, Germany; MVZ Arnsberg, Medical Practice for Hematology and Oncology, Arnsberg, Germany
| | - Verena Steinke-Lange
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany; Center of Medical Genetics, Munich, Germany
| | - Albrecht Stenzinger
- Department of General Pathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christian P Strassburg
- National Center for Hereditary Tumor Syndromes, University Hospital Bonn, Bonn, Germany; Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Paul C van de Meeberg
- Department of Gastroenterology & Hepatology, Slingeland Hospital, Doetinchem, The Netherlands
| | - Mariette van Kouwen
- Department of Gastroenterology & Hepatology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Monique van Leerdam
- Department of Gastroenterology & Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Deepak B Vangala
- Department of Medicine, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Juda Vecht
- Department of Gastroenterology & Hepatology, Isala Zwolle, Zwolle, The Netherlands
| | - Marie-Louise Verhulst
- Department of Gastroenterology & Hepatology, Maxima Medical Centre, Eindhoven, The Netherlands
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumour Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cooperation Unit Applied Tumour Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jürgen Weitz
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital Carl Gustav Carus of the Technical University Dresden, Dresden, Germany
| | - Silke Zachariae
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Jukka-Pekka Mecklin
- Department of Surgery, Central Finland Central Hospital, Jyväskylä, Finland; Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Matthias Kloor
- Department of Applied Tumour Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cooperation Unit Applied Tumour Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hans F Vasen
- Department of Gastroenterology & Hepatology, Leiden University Medical Center, Leiden, The Netherlands
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Salem MMI, Amin AMS, Ashour AF, Ibrahim MMES, Abo-Ismail MK. Genetic parameters and principal components analysis of breeding value for birth and weaning weight in Egyptian buffalo. Anim Biosci 2020; 34:12-19. [PMID: 32054164 PMCID: PMC7888494 DOI: 10.5713/ajas.19.0651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/21/2019] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE The objectives of the current study were to study the main environmental factors affecting birth weight (BW) and weaning weight (WW), estimate variance components, genetic parameters and genetic trend and to evaluate the variability and relationships among breeding value of BW and WW using principal components analysis (PCA). METHODS A total of 16,370 records were collected from 8,271 buffalo calves. Genetic parameters and breeding values were estimated using a bivariate animal model which includes direct, maternal and permanent maternal effects. These estimates were standardized and used in PCA. RESULTS The direct heritability estimates were 0.06 and 0.41 for BW and WW, respectively whereas direct maternal heritability values were 0.03 and 0.14, respectively. Proportions of variance due to permanent environmental effects of dam were 0.455 and 0.280 for BW and WW respectively. The genetic correlation between BW and WWs was weak approaching zero, but the maternal correlation was 0.26. The first two principal components (PC1 and PC2) were estimated utilizing the standardized breeding values according to Kaiser method. The total variance explained by the first two PCs was 71.17% in which 45.91% and 25.25% were explained by PC1 and PC2, respectively. The direct breeding values of BW were related to PC2 but those of WW and maternal breeding values of BW and WWs were associated with PC1. CONCLUSION The results of genetic parameters and PCA indicate that BW and WWs were not genetically correlated and improving growth traits of Egyptian buffaloes could be achieved using WW without any adverse effect by BW.
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Affiliation(s)
- Mohamed Mahmoud Ibrahim Salem
- Department of Animal and Fish Production, Faculty of Agriculture, University of Alexandria, Alexandria, 21545, Egypt
| | - Amin Mohamed Said Amin
- Animal Production Research Institute, Agricultural Research Center, Dooki, Giza, 12619, Egypt
| | - Ayman Fouad Ashour
- Animal Production Research Institute, Agricultural Research Center, Dooki, Giza, 12619, Egypt
| | | | - Mohammed Kotb Abo-Ismail
- Animal science Department, College of Agriculture, Food and Environmental Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
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Stanich PP, Pearlman R, Hinton A, Gutierrez S, LaDuca H, Hampel H, Jasperson K. Prevalence of Germline Mutations in Polyposis and Colorectal Cancer-Associated Genes in Patients With Multiple Colorectal Polyps. Clin Gastroenterol Hepatol 2019; 17:2008-2015.e3. [PMID: 30557735 DOI: 10.1016/j.cgh.2018.12.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 11/18/2018] [Accepted: 12/07/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Guidelines recommend genetic testing of patients with 10 or more cumulative adenomatous polyps. However, little is known about the utility of these tests-especially for older patients. We aimed to determine the prevalence of pathogenic mutations in patients with multiple colorectal polyps, stratified by age. METHODS We performed a cross-sectional study of patients with 10 or more colorectal polyps who underwent multigene panel testing (MGPT) from March 2012 through December 2016 (n = 3789). Demographic, clinical and family history data were obtained from test requisition forms and accompanying clinic notes, pedigrees, and pathology reports. Subjects were stratified based on reported polyp histology. Primary outcomes of interest were gene mutations associated with adenomatous polyposis, hamartomatous polyposis, and non-polyposis colorectal cancer syndromes. RESULTS Based on MGPT, the prevalence of mutations in adenomatous polyposis genes decreased with increasing age in all polyp count groups in the adenoma cohort (P < .001 for 10-19, 20-99, and 100 or more polyps). The prevalence of mutations in all genes of interest also decreased with increasing age but remained above 5% in all age and polyp cohorts. Increased age at testing was associated with a significantly lower risk of a mutation in any gene of interest with multivariate analysis. In the hamartoma cohort, the prevalence of mutations in hamartomatous polyposis genes was high regardless of polyp count (40% with 10-19 polyps, 72.1% with 20-99 polyps, and 50% with 100 or more polyps). CONCLUSION Our findings support continued genetic testing of patients with 10 or more polyps including adenomas and/or hamartomas. MGPT that includes analysis of polyposis and non-polyposis colorectal cancer genes should be considered for these patients given the high proportion with mutations (above 5%) in all age groups.
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Affiliation(s)
- Peter P Stanich
- Division of Gastroenterology, Hepatology and Nutrition, Ohio State University Wexner Medical Center, Columbus, Ohio.
| | - Rachel Pearlman
- Division of Human Genetics; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Alice Hinton
- Division of Gastroenterology, Hepatology and Nutrition, Ohio State University Wexner Medical Center, Columbus, Ohio; Division of Biostatistics, Ohio State University, Columbus, Ohio
| | | | | | - Heather Hampel
- Division of Human Genetics; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
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Bouvet D, Bodo S, Munier A, Guillerm E, Bertrand R, Colas C, Duval A, Coulet F, Muleris M. Methylation Tolerance-Based Functional Assay to Assess Variants of Unknown Significance in the MLH1 and MSH2 Genes and Identify Patients With Lynch Syndrome. Gastroenterology 2019; 157:421-431. [PMID: 30998989 DOI: 10.1053/j.gastro.2019.03.071] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/07/2019] [Accepted: 03/29/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Approximately 75% of patients with suspected Lynch syndrome carry variants in MLH1 or MSH2, proteins encoded by these genes are required for DNA mismatch repair (MMR). However, 30% of these are variants of unknown significance (VUS). A assay that measures cell response to the cytotoxic effects of a methylating agent can determine the effects of VUS in MMR genes and identify patients with constitutional MMR-deficiency syndrome. We adapted this method to test the effects of VUS in MLH1 and MSH2 genes found in patients with suspected Lynch syndrome. METHODS We transiently expressed MLH1 or MSH2 variants in MLH1- or MSH2-null human colorectal cancer cell lines (HCT116 or LoVo), respectively. The MMR process causes death of cells with methylation-damaged DNA bases, so we measured proportions of cells that undergo death following exposure to the methylating agent; cells that escaped its toxicity were considered to have variants that affect function of the gene product. Using this assay, we analyzed 88 variants (mainly missense variants), comprising a validation set of 40 previously classified variants (19 in MLH1 and 21 in MSH2) and a prospective set of 48 VUS (25 in MLH1 and 23 in MSH2). Prediction scores were calculated for all VUS according to the recommendations of the American College of Medical Genetics and Genomics, based on clinical, somatic, in silico, population, and functional data. RESULTS The assay correctly classified 39 of 40 variants in the validation set. The assay identified 12 VUS that did alter function of the gene product and 28 VUS that did not; the remaining 8 VUS had intermediate effects on MMR capacity and could not be classified. Comparison of assay results with prediction scores confirmed the ability of the assay to discriminate VUS that affected the function of the gene products from those that did not. CONCLUSIONS Using an assay that measures the ability of the cells to undergo death following DNA damage induction by a methylating agent, we were able to assess whether variants in MLH1 and MSH2 cause defects in DNA MMR. This assay might be used to help assessing the pathogenicity of VUS in MLH1 and MSH2 found in patients with suspected Lynch syndrome.
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Affiliation(s)
- Delphine Bouvet
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, Paris, France; Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Sahra Bodo
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, Paris, France; Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Annie Munier
- Sorbonne Université, Inserm, Centre de recherche Saint-Antoine, UMS30-LUMIC, Plateforme de Cytométrie en Flux CISA, site Saint-Antoine, Paris, France
| | - Erell Guillerm
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, Paris, France; Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Genetics Department, AP-HP, Hôpital Universitaire Pitié-Salpétrière, Paris, France
| | - Romane Bertrand
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, Paris, France; Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France
| | - Chrystelle Colas
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, Paris, France; Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Institut Curie, Paris Sciences Lettres Research University, Department of Genetics, Paris, France
| | - Alex Duval
- Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Biochimie, biologie moléculaire, Paris, France
| | - Florence Coulet
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, Paris, France; Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France; Genetics Department, AP-HP, Hôpital Universitaire Pitié-Salpétrière, Paris, France
| | - Martine Muleris
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, Paris, France; Equipe labellisée par la Ligue Nationale contre le Cancer, Paris, France.
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Brant SR, Okou DT, Simpson CL, Cutler DJ, Haritunians T, Bradfield JP, Chopra P, Prince J, Begum F, Kumar A, Huang C, Venkateswaran S, Datta LW, Wei Z, Thomas K, Herrinton LJ, Klapproth JMA, Quiros AJ, Seminerio J, Liu Z, Alexander JS, Baldassano RN, Dudley-Brown S, Cross RK, Dassopoulos T, Denson LA, Dhere TA, Dryden GW, Hanson JS, Hou JK, Hussain SZ, Hyams JS, Isaacs KL, Kader H, Kappelman MD, Katz J, Kellermayer R, Kirschner BS, Kuemmerle JF, Kwon JH, Lazarev M, Li E, Mack D, Mannon P, Moulton DE, Newberry RD, Osuntokun BO, Patel AS, Saeed SA, Targan SR, Valentine JF, Wang MH, Zonca M, Rioux JD, Duerr RH, Silverberg MS, Cho JH, Hakonarson H, Zwick ME, McGovern DP, Kugathasan S. Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease. Gastroenterology 2017; 152:206-217.e2. [PMID: 27693347 PMCID: PMC5164948 DOI: 10.1053/j.gastro.2016.09.032] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/14/2016] [Accepted: 09/17/2016] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS The inflammatory bowel diseases (IBD) ulcerative colitis (UC) and Crohn's disease (CD) cause significant morbidity and are increasing in prevalence among all populations, including African Americans. More than 200 susceptibility loci have been identified in populations of predominantly European ancestry, but few loci have been associated with IBD in other ethnicities. METHODS We performed 2 high-density, genome-wide scans comprising 2345 cases of African Americans with IBD (1646 with CD, 583 with UC, and 116 inflammatory bowel disease unclassified) and 5002 individuals without IBD (controls, identified from the Health Retirement Study and Kaiser Permanente database). Single-nucleotide polymorphisms (SNPs) associated at P < 5.0 × 10-8 in meta-analysis with a nominal evidence (P < .05) in each scan were considered to have genome-wide significance. RESULTS We detected SNPs at HLA-DRB1, and African-specific SNPs at ZNF649 and LSAMP, with associations of genome-wide significance for UC. We detected SNPs at USP25 with associations of genome-wide significance for IBD. No associations of genome-wide significance were detected for CD. In addition, 9 genes previously associated with IBD contained SNPs with significant evidence for replication (P < 1.6 × 10-6): ADCY3, CXCR6, HLA-DRB1 to HLA-DQA1 (genome-wide significance on conditioning), IL12B,PTGER4, and TNC for IBD; IL23R, PTGER4, and SNX20 (in strong linkage disequilibrium with NOD2) for CD; and KCNQ2 (near TNFRSF6B) for UC. Several of these genes, such as TNC (near TNFSF15), CXCR6, and genes associated with IBD at the HLA locus, contained SNPs with unique association patterns with African-specific alleles. CONCLUSIONS We performed a genome-wide association study of African Americans with IBD and identified loci associated with UC in only this population; we also replicated IBD, CD, and UC loci identified in European populations. The detection of variants associated with IBD risk in only people of African descent demonstrates the importance of studying the genetics of IBD and other complex diseases in populations beyond those of European ancestry.
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Affiliation(s)
- Steven R. Brant
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns
Hopkins University School of Medicine, Baltimore, MD, 21231, USA,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health,
Baltimore, MD, 21205, USA
| | - David T. Okou
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Claire L. Simpson
- Department of Genetics, Genomics and Informatics, University of Tennessee
Health Science Center, Memphis, TN, 38163, USA,Computational and Statistical Genomics Branch, National Human Genome
Research Institute, National Institutes of Health, Baltimore, MD 21224, USA
| | - David J. Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta,
GA, 30322, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Jonathan P. Bradfield
- Center for Applied Genomics, Abramson Research Center, The Children's
Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta,
GA, 30322, USA
| | - Jarod Prince
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Ferdouse Begum
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health,
Baltimore, MD, 21205, USA
| | - Archana Kumar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Chengrui Huang
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health,
Baltimore, MD, 21205, USA
| | - Suresh Venkateswaran
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Lisa W. Datta
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns
Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Zhi Wei
- Center for Applied Genomics, Abramson Research Center, The Children's
Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kelly Thomas
- Center for Applied Genomics, Abramson Research Center, The Children's
Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | | | | | - Antonio J. Quiros
- Department of Pediatrics, MUSC Pediatric Center for Inflammatory Bowel
Disorders, Summerville, SC, 29485, USA
| | - Jenifer Seminerio
- Department of Gastroenterology, MUSC Digestive Disease Center, Charleston,
SC, 29486, USA
| | - Zhenqiu Liu
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Jonathan S. Alexander
- Department of Molecular and Cellular Physiology, Louisiana State University
Health Sciences Center, Shreveport, LA, 71130, USA
| | - Robert N. Baldassano
- Department of Pediatrics, Children's Hospital of Philadelphia,
Philadelphia, PA, 19104, USA
| | - Sharon Dudley-Brown
- Department of Medicine, Johns Hopkins University Schools of Medicine &
Nursing, Baltimore, MD, 21287, USA
| | - Raymond K. Cross
- Department of Medicine, University of Maryland School of Medicine,
Baltimore, MD, 21201, USA
| | | | - Lee A. Denson
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati
Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Tanvi A. Dhere
- Department of Medicine, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Gerald W. Dryden
- Department of Medicine, University of Louisville, Louisville, KY, 40202,
USA
| | - John S. Hanson
- Charlotte Gastroenterology and Hepatology, Charlotte, NC, 28207, USA
| | - Jason K. Hou
- Department of Medicine, Baylor College of Medicine; VA HSR&D Center for
Innovations in Quality Effectiveness and Safety; Michael E. DeBakey VA Medical Center,
Houston, TX, 77030, USA
| | - Sunny Z. Hussain
- Department of Pediatrics, Willis-Knighton Physician Network, Shreveport,
LA, 71118, USA
| | | | - Kim L. Isaacs
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel
Hill, NC, 27514, USA
| | - Howard Kader
- Department of Pediatrics, University of Maryland School of Medicine,
Baltimore, MD, 21201, USA
| | - Michael D. Kappelman
- Department of Pediatrics, University of North Carolina at Chapel Hill,
Chapel Hill, NC, 27514, USA
| | - Jeffry Katz
- Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas
Children's Hospital, Houston, TX, 77030, USA
| | - Barbara S. Kirschner
- Department of Pediatrics, University of Chicago Comer Children's
Hospital, Chicago, IL, 60637, USA
| | - John F. Kuemmerle
- Medicine and Physiology and Biophysics, Medical College of Virginia Campus
of Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - John H. Kwon
- Department of Internal Medicine, University of Texas Southwestern Medical
Center, Dallas, TX, 75390, USA
| | - Mark Lazarev
- Department of Medicine, Johns Hopkins University School of Medicine,
Baltimore, MD, 21205, USA
| | - Ellen Li
- Department of Medicine, Stony Brook University School of Medicine, Stony
Brook, NY, 11794, USA
| | - David Mack
- Department of Pediatrics, University of Ottawa and Children’s
Hospital of Eastern Ontario, Ottawa, Ontario, K1H 8L1, Canada
| | - Peter Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham,
AL, 35294, USA
| | | | - Rodney D. Newberry
- Department of Internal Medicine, Washington University School of Medicine,
St. Louis, MO, 63110, USA
| | - Bankole O. Osuntokun
- Department of Pediatrics, Cook Children's Medical Center, Fort Worth,
TX, 76104, USA
| | - Ashish S. Patel
- Department of Pediatrics, University of Texas Southwestern Medical Center,
Dallas, TX, 75390, USA
| | - Shehzad A. Saeed
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati
Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Stephan R. Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | | | - Ming-Hsi Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic Florida,
Jacksonville, FL, 32224, USA
| | - Martin Zonca
- Department of Internal Medicine, Henry Ford Health System, Detroit, MI,
48202, USA
| | - John D. Rioux
- Department of Medicine, Université de Montréal and the
Montreal Heart Institute Research Center, Montreal, Quebec, H1T 1C8, Canada
| | - Richard H. Duerr
- Department of Medicine and Clinical and Translational Science Institute,
School of Medicine; and Department of Human Genetics, Graduate School of Public Health;
University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mark S. Silverberg
- Department of Medicine, Zane Cohen Centre for Digestive Diseases, Mount
Sinai Hospital, University of Toronto, Toronto, Toronto, Ontario, M5G1X5, Canada
| | - Judy H. Cho
- Medicine and Genetics, Icahn School of Medicine at Mount Sinai, Charles
Bronfman Institute for Personalized Medicine, New York, NY, 10029, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's
Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Michael E. Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta,
GA, 30322, USA
| | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia; Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia.
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7
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Daher R, Kannengiesser C, Houamel D, Lefebvre T, Bardou-Jacquet E, Ducrot N, de Kerguenec C, Jouanolle AM, Robreau AM, Oudin C, Le Gac G, Moulouel B, Loustaud-Ratti V, Bedossa P, Valla D, Gouya L, Beaumont C, Brissot P, Puy H, Karim Z, Tchernitchko D. Heterozygous Mutations in BMP6 Pro-peptide Lead to Inappropriate Hepcidin Synthesis and Moderate Iron Overload in Humans. Gastroenterology 2016; 150:672-683.e4. [PMID: 26582087 DOI: 10.1053/j.gastro.2015.10.049] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 10/14/2015] [Accepted: 10/29/2015] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Hereditary hemochromatosis is a heterogeneous group of genetic disorders characterized by parenchymal iron overload. It is caused by defective expression of liver hepcidin, the main regulator of iron homeostasis. Iron stimulates the gene encoding hepcidin (HAMP) via the bone morphogenetic protein (BMP)6 signaling to SMAD. Although several genetic factors have been found to cause late-onset hemochromatosis, many patients have unexplained signs of iron overload. We investigated BMP6 function in these individuals. METHODS We sequenced the BMP6 gene in 70 consecutive patients with a moderate increase in serum ferritin and liver iron levels who did not carry genetic variants associated with hemochromatosis. We searched for BMP6 mutations in relatives of 5 probands and in 200 healthy individuals (controls), as well as in 2 other independent cohorts of hyperferritinemia patients. We measured serum levels of hepcidin by liquid chromatography-tandem mass spectrometry and analyzed BMP6 in liver biopsy specimens from patients by immunohistochemistry. The functions of mutant and normal BMP6 were assessed in transfected cells using immunofluorescence, real-time quantitative polymerase chain reaction, and immunoblot analyses. RESULTS We identified 3 heterozygous missense mutations in BMP6 (p.Pro95Ser, p.Leu96Pro, and p.Gln113Glu) in 6 unrelated patients with unexplained iron overload (9% of our cohort). These mutations were detected in less than 1% of controls. p.Leu96Pro also was found in 2 patients from the additional cohorts. Family studies indicated dominant transmission. Serum levels of hepcidin were inappropriately low in patients. A low level of BMP6, compared with controls, was found in a biopsy specimen from 1 patient. In cell lines, the mutated residues in the BMP6 propeptide resulted in defective secretion of BMP6; reduced signaling via SMAD1, SMAD5, and SMAD8; and loss of hepcidin production. CONCLUSIONS We identified 3 heterozygous missense mutations in BMP6 in patients with unexplained iron overload. These mutations lead to loss of signaling to SMAD proteins and reduced hepcidin production. These mutations might increase susceptibility to mild-to-moderate late-onset iron overload.
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Affiliation(s)
- Raed Daher
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France
| | - Caroline Kannengiesser
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France; AP-HP, Département de Génétique, Hôpital Bichat, Paris, France
| | - Dounia Houamel
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France
| | - Thibaud Lefebvre
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France; AP-HP, Centre Français des Porphyries, Hôpital Louis Mourier, Colombes, France
| | | | - Nicolas Ducrot
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France
| | | | - Anne-Marie Jouanolle
- Department of Liver Disease and Molecular Genetics, CHU Rennes, Rennes, France; CHU Rennes, French Reference Center for Rare Iron Overload Diseases of Genetic Origin
| | - Anne-Marie Robreau
- AP-HP, Centre Français des Porphyries, Hôpital Louis Mourier, Colombes, France
| | - Claire Oudin
- AP-HP, Centre Français des Porphyries, Hôpital Louis Mourier, Colombes, France
| | - Gerald Le Gac
- INSERM U1078, Université de Brest, CHRU de Brest, Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Bretagne, Brest, France
| | - Boualem Moulouel
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France
| | | | - Pierre Bedossa
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; AP-HP, Laboratoire d'Anatomo-Pathologie, Hôpital Beaujon, Clichy, France
| | - Dominique Valla
- AP-HP, Département d'Hépatologie, Hôpital Beaujon, Clichy, France
| | - Laurent Gouya
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France; AP-HP, Centre Français des Porphyries, Hôpital Louis Mourier, Colombes, France
| | - Carole Beaumont
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France
| | - Pierre Brissot
- Department of Liver Disease and Molecular Genetics, CHU Rennes, Rennes, France
| | - Hervé Puy
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France; AP-HP, Centre Français des Porphyries, Hôpital Louis Mourier, Colombes, France
| | - Zoubida Karim
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France.
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8
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Bonora E, Bianco F, Cordeddu L, Bamshad M, Francescatto L, Dowless D, Stanghellini V, Cogliandro RF, Lindberg G, Mungan Z, Cefle K, Ozcelik T, Palanduz S, Ozturk S, Gedikbasi A, Gori A, Pippucci T, Graziano C, Volta U, Caio G, Barbara G, D'Amato M, Seri M, Katsanis N, Romeo G, De Giorgio R. Mutations in RAD21 disrupt regulation of APOB in patients with chronic intestinal pseudo-obstruction. Gastroenterology 2015; 148:771-782.e11. [PMID: 25575569 PMCID: PMC4375026 DOI: 10.1053/j.gastro.2014.12.034] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 12/03/2014] [Accepted: 12/23/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Chronic intestinal pseudo-obstruction (CIPO) is characterized by severe intestinal dysmotility that mimics a mechanical subocclusion with no evidence of gut obstruction. We searched for genetic variants associated with CIPO to increase our understanding of its pathogenesis and to identify potential biomarkers. METHODS We performed whole-exome sequencing of genomic DNA from patients with familial CIPO syndrome. Blood and lymphoblastoid cells were collected from patients and controls (individuals without CIPO); levels of messenger RNA (mRNA) and proteins were analyzed by quantitative reverse-transcription polymerase chain reaction, immunoblot, and mobility shift assays. Complementary DNAs were transfected into HEK293 cells. Expression of rad21 was suppressed in zebrafish embryos using a splice-blocking morpholino (rad21a). Gut tissues were collected and analyzed. RESULTS We identified a homozygous mutation (p.622, encodes Ala>Thr) in RAD21 in patients from a consanguineous family with CIPO. Expression of RUNX1, a target of RAD21, was reduced in cells from patients with CIPO compared with controls. In zebrafish, suppression of rad21a reduced expression of runx1; this phenotype was corrected by injection of human RAD21 mRNA, but not with the mRNA from the mutated p.622 allele. rad21a Morpholino zebrafish had delayed intestinal transit and greatly reduced numbers of enteric neurons, similar to patients with CIPO. This defect was greater in zebrafish with suppressed expression of ret and rad21, indicating their interaction in the regulation of gut neurogenesis. The promoter region of APOB bound RAD21 but not RAD21 p.622 Ala>Thr; expression of wild-type RAD21 in HEK293 cells repressed expression of APOB, compared with control vector. The gut-specific isoform of APOB (APOB48) is overexpressed in sera from patients with CIPO who carry the RAD21 mutation. APOB48 also is overexpressed in sporadic CIPO in sera and gut biopsy specimens. CONCLUSIONS Some patients with CIPO carry mutations in RAD21 that disrupt the ability of its product to regulate genes such as RUNX1 and APOB. Reduced expression of rad21 in zebrafish, and dysregulation of these target genes, disrupts intestinal transit and the development of enteric neurons.
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Affiliation(s)
- Elena Bonora
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Francesca Bianco
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | | | - Michael Bamshad
- University of Washington Center for Mendelian Genomics, Seattle, USA
| | | | - Dustin Dowless
- Center for Human Disease Modeling Duke University, Durham, USA
| | - Vincenzo Stanghellini
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Rosanna F. Cogliandro
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | | | | | - Kivanc Cefle
- Istanbul Medical Faculty, Dept. of Internal Medicine, Division of Medical Genetics
| | | | - Sukru Palanduz
- Istanbul Medical Faculty, Dept. of Internal Medicine, Division of Medical Genetics
| | - Sukru Ozturk
- Istanbul Medical Faculty, Dept. of Internal Medicine, Division of Medical Genetics
| | - Asuman Gedikbasi
- Istanbul Medical Faculty, Dept. of Internal Medicine, Division of Medical Genetics
| | - Alessandra Gori
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Tommaso Pippucci
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Claudio Graziano
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Umberto Volta
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Giacomo Caio
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Giovanni Barbara
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | | | - Marco Seri
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | | | - Giovanni Romeo
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy.
| | - Roberto De Giorgio
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy; Centro Unificato di Ricerca Biomedica Applicata, Bologna, Italy.
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9
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Gylfe AE, Kondelin J, Turunen M, Ristolainen H, Katainen R, Pitkänen E, Kaasinen E, Rantanen V, Tanskanen T, Varjosalo M, Lehtonen H, Palin K, Taipale M, Taipale J, Renkonen-Sinisalo L, Järvinen H, Böhm J, Mecklin JP, Ristimäki A, Kilpivaara O, Tuupanen S, Karhu A, Vahteristo P, Aaltonen LA. Identification of candidate oncogenes in human colorectal cancers with microsatellite instability. Gastroenterology 2013; 145:540-3.e22. [PMID: 23684749 DOI: 10.1053/j.gastro.2013.05.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 05/09/2013] [Accepted: 05/13/2013] [Indexed: 12/18/2022]
Abstract
Microsatellite instability can be found in approximately 15% of all colorectal cancers. To detect new oncogenes we sequenced the exomes of 25 colorectal tumors and respective healthy colon tissue. Potential mutation hot spots were confirmed in 15 genes; ADAR, DCAF12L2, GLT1D1, ITGA7, MAP1B, MRGPRX4, PSRC1, RANBP2, RPS6KL1, SNCAIP, TCEAL6, TUBB6, WBP5, VEGFB, and ZBTB2; these were validated in 86 tumors with microsatellite instability. ZBTB2, RANBP2, and PSRC1 also were found to contain hot spot mutations in the validation set. The form of ZBTB2 associated with colorectal cancer increased cell proliferation. The mutation hot spots might be used to develop personalized tumor profiling and therapy.
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Affiliation(s)
- Alexandra E Gylfe
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
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10
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Qu F, Zhou J, Zhou Z, Li H, Burrows E. Genetic analysis of Aralia cordata Thunb by RAPD. Afr J Tradit Complement Altern Med 2008; 6:17-22. [PMID: 20162037 PMCID: PMC2816525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In the research, genetic analysis of Aralia cordata Thunb. (Araliaceae) was conducted using randomly amplified polymorphism DNA (RAPD). 161 loci were detected with 12 RAPD primers. Percentage of Polymorphic Band (PPB) varied from 34.78% to 63.35%. All the samples were respectively collected from the eight provinces richest in Aralia cordata Thunb resources in China, including Hunan, Yunnan, Zhejiang, Sichuan, Jiangxi, Anhui, Shanxi and Gansu. The results showed that Hunan Province enjoyed the highest level of genetic differentiation and Gansu was the lowest. The total genetic diversity (H(T)) of RAPD, intraspecific genetic diversity (H(S)) and genetic diversity (D(ST)) of the various places was respectively 26.33%, 11.14%, and 49.36%. The differentiation among the species accounted for 98.76% of total genetic diversity (G(ST)). Based on the cluster results of genetic distance, the 8 samples were classified into three groups. It is concluded that Hunan Province enjoyed the highest level of genetic differentiation of Aralia cordata Thunb and Gansu was the lowest, which provides a basis for the taxonomic identification and germplasm resource research of Aralia cordata Thunb in the future.
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Affiliation(s)
- Fan Qu
- School of Medicine, Zhejiang University, 388 Yuhang Tang Road, Hangzhou, Zhejiang 310058, PR China.
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11
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Udin N, Ahmad KAK, Ahmad F, Omar E, Aziz ME, Kumar R, Abdullah JM. Molecular genetic analysis of a suprasellar immature teratoma : mutation of exon 4 p53 gene. Malays J Med Sci 2008; 15:43-46. [PMID: 22589625 PMCID: PMC3341889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2005] [Accepted: 12/30/2007] [Indexed: 05/31/2023] Open
Abstract
We described an intracranial immature teratoma in a 13 year old Malay boy who presented with history of chronic headache and blurring of vision. Physical findings revealed bilateral papilloedema but no other localizing sign. A Magnetic Resonance Imaging of the brain revealed a suprasellar well defined lobulated midline heterogenous mass which was intraoperatively described as mainly solid tumour with multiple small cystic component filled with yellowish jelly like material. Histopathological finding confirmed the case as immature teratoma. Molecular genetic analysis of p53 and p27 genes revealed substitution of nucleotide G to C at location nucleotide 12139, exon 4 of gene p53. No alteration was detected at exon 5-6 and 8 of p53 gene and exon 1 and 2 of p27 gene. This is the first case report of an intracranial immature teratoma with genetic mutation occuring in a Malay boy.
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Affiliation(s)
- Nujaimin Udin
- Corresponding Author : Dr. Nujaimin Udin, MBBCh (Cairo), M.Surg (Neuro surgery) USM, Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia., Tel: +609 7664240, Fax: +6097663370,
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