1
|
Wang CY, Li MY, Li SY, Wei XG, Yuan ZW, Tang XB, Bai YZ. Spatial transcriptomics reveals gene interactions and signaling pathway dynamics in rat embryos with anorectal malformation. Cell Biol Toxicol 2024; 40:34. [PMID: 38769159 PMCID: PMC11106128 DOI: 10.1007/s10565-024-09878-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 05/15/2024] [Indexed: 05/22/2024]
Abstract
Anorectal malformation (ARM) is a prevalent early pregnancy digestive tract anomaly. The intricate anatomy of the embryonic cloaca region makes it challenging for traditional high-throughput sequencing methods to capture location-specific information. Spatial transcriptomics was used to sequence libraries of frozen sections from embryonic rats at gestational days (GD) 14 to 16, covering both normal and ARM cases. Bioinformatics analyses and predictions were performed using methods such as WGCNA, GSEA, and PROGENy. Immunofluorescence staining was used to verify gene expression levels. Gene expression data was obtained with anatomical annotations of clusters, focusing on the cloaca region's location-specific traits. WGCNA revealed gene modules linked to normal and ARM cloacal anatomy development, with cooperation between modules on GD14 and GD15. Differential gene expression profiles and functional enrichment were presented. Notably, protein levels of Pcsk9, Hmgb2, and Sod1 were found to be downregulated in the GD15 ARM hindgut. The PROGENy algorithm predicted the activity and interplay of common signaling pathways in embryonic sections, highlighting their synergistic and complementary effects. A competing endogenous RNA (ceRNA) regulatory network was constructed from whole transcriptome data. Spatial transcriptomics provided location-specific cloaca region gene expression. Diverse bioinformatics analyses deepened our understanding of ARM's molecular interactions, guiding future research and providing insights into gene regulation in ARM development.
Collapse
Affiliation(s)
- Chen-Yi Wang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Sanhao Street No. 36, Shenyang, 110004, Liaoning, China
| | - Mu-Yu Li
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Sanhao Street No. 36, Shenyang, 110004, Liaoning, China
| | - Si-Ying Li
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Sanhao Street No. 36, Shenyang, 110004, Liaoning, China
| | - Xiao-Gao Wei
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Sanhao Street No. 36, Shenyang, 110004, Liaoning, China
| | - Zheng-Wei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiao-Bing Tang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Sanhao Street No. 36, Shenyang, 110004, Liaoning, China
| | - Yu-Zuo Bai
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Sanhao Street No. 36, Shenyang, 110004, Liaoning, China.
| |
Collapse
|
2
|
Molecular Mechanisms Contributing to the Etiology of Congenital Diaphragmatic Hernia: A Review and Novel Cases. J Pediatr 2022; 246:251-265.e2. [PMID: 35314152 DOI: 10.1016/j.jpeds.2022.03.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 03/01/2022] [Accepted: 03/15/2022] [Indexed: 12/25/2022]
|
3
|
Birth defect co-occurrence patterns in the Texas Birth Defects Registry. Pediatr Res 2022; 91:1278-1285. [PMID: 34193968 PMCID: PMC8716666 DOI: 10.1038/s41390-021-01629-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 02/01/2023]
Abstract
BACKGROUND The population-level landscape of co-occurring birth defects among infants without a syndromic diagnosis is not well understood. METHODS We analyzed data from 40,771 infants with two or more major birth defects in the Texas Birth Defects Registry (TBDR; 1999-2014). We calculated adjusted observed-to-expected (O/E) ratios for all two, three, four, and five-way combinations of 138 major defects. RESULTS Among 530 patterns with the highest adjusted O/E ratios (top 5% of 10,595 patterns), 66% included only defects co-occurring within one organ system and 28% were suggestive of known patterns (e.g., midline developmental defects). Of the remaining patterns, the combination of defects with the highest O/E ratio (193.8) encompassed the diaphragm, spine, spleen, and heart defects. Fourteen patterns involved heart and spine defects with or without rib defects. Ten additional patterns primarily involved two hallmark components of VACTERL association (specifically, vertebral defects, anal atresia, cardiac defects, renal, or limb defects, but not tracheoesophageal fistula). CONCLUSIONS Our analyses provide a description of the birth defect co-occurrence patterns in a multi-ethnic, population-based sample, and revealed several patterns of interest. This work complements prior work that has suggested etiologic connections between select defects (e.g., diaphragmatic hernia and heart and spleen anomalies; heart and spine defects). IMPACT In this large-scale, population-based study of birth defect co-occurrence patterns, we found several birth defect combinations of potential interest that warrant further investigation: congenital diaphragmatic hernia, heart, spine, and spleen defects and scimitar syndrome with vertebral defects. The majority of patterns of co-occurring defects observed more frequently than expected involved multiple defects within the same system and combinations suggestive of known associations. Nearly all of the top patterns (beyond the same system and those suggestive of known associations) involved organ systems that are components of the VACTERL association, with heart, spine, and rib defect patterns being the most common.
Collapse
|
4
|
Friedmacher F, Rolle U, Puri P. Genetically Modified Mouse Models of Congenital Diaphragmatic Hernia: Opportunities and Limitations for Studying Altered Lung Development. Front Pediatr 2022; 10:867307. [PMID: 35633948 PMCID: PMC9136148 DOI: 10.3389/fped.2022.867307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/18/2022] [Indexed: 11/21/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a relatively common and life-threatening birth defect, characterized by an abnormal opening in the primordial diaphragm that interferes with normal lung development. As a result, CDH is accompanied by immature and hypoplastic lungs, being the leading cause of morbidity and mortality in patients with this condition. In recent decades, various animal models have contributed novel insights into the pathogenic mechanisms underlying CDH and associated pulmonary hypoplasia. In particular, the generation of genetically modified mouse models, which show both diaphragm and lung abnormalities, has resulted in the discovery of multiple genes and signaling pathways involved in the pathogenesis of CDH. This article aims to offer an up-to-date overview on CDH-implicated transcription factors, molecules regulating cell migration and signal transduction as well as components contributing to the formation of extracellular matrix, whilst also discussing the significance of these genetic models for studying altered lung development with regard to the human situation.
Collapse
Affiliation(s)
- Florian Friedmacher
- Department of Pediatric Surgery, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Udo Rolle
- Department of Pediatric Surgery, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Prem Puri
- Beacon Hospital, University College Dublin, Dublin, Ireland.,Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| |
Collapse
|
5
|
Cannata G, Caporilli C, Grassi F, Perrone S, Esposito S. Management of Congenital Diaphragmatic Hernia (CDH): Role of Molecular Genetics. Int J Mol Sci 2021; 22:ijms22126353. [PMID: 34198563 PMCID: PMC8231903 DOI: 10.3390/ijms22126353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 12/11/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a relatively common major life-threatening birth defect that results in significant mortality and morbidity depending primarily on lung hypoplasia, persistent pulmonary hypertension, and cardiac dysfunction. Despite its clinical relevance, CDH multifactorial etiology is still not completely understood. We reviewed current knowledge on normal diaphragm development and summarized genetic mutations and related pathways as well as cellular mechanisms involved in CDH. Our literature analysis showed that the discovery of harmful de novo variants in the fetus could constitute an important tool for the medical team during pregnancy, counselling, and childbirth. A better insight into the mechanisms regulating diaphragm development and genetic causes leading to CDH appeared essential to the development of new therapeutic strategies and evidence-based genetic counselling to parents. Integrated sequencing, development, and bioinformatics strategies could direct future functional studies on CDH; could be applied to cohorts and consortia for CDH and other birth defects; and could pave the way for potential therapies by providing molecular targets for drug discovery.
Collapse
Affiliation(s)
- Giulia Cannata
- Pediatric Clinic, Pietro Barilla Children’s Hospital, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.C.); (C.C.); (F.G.)
| | - Chiara Caporilli
- Pediatric Clinic, Pietro Barilla Children’s Hospital, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.C.); (C.C.); (F.G.)
| | - Federica Grassi
- Pediatric Clinic, Pietro Barilla Children’s Hospital, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.C.); (C.C.); (F.G.)
| | - Serafina Perrone
- Neonatology Unit, Pietro Barilla Children’s Hospital, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy;
| | - Susanna Esposito
- Pediatric Clinic, Pietro Barilla Children’s Hospital, University of Parma, Via Gramsci 14, 43126 Parma, Italy; (G.C.); (C.C.); (F.G.)
- Correspondence: ; Tel.: +39-0521-7047
| |
Collapse
|
6
|
Boycott KM, Campeau PM, Howley HE, Pavlidis P, Rogic S, Oriel C, Berman JN, Hamilton RM, Hicks GG, Lipshitz HD, Masson JY, Shoubridge EA, Junker A, Leroux MR, McMaster CR, Michaud JL, Turvey SE, Dyment D, Innes AM, van Karnebeek CD, Lehman A, Cohn RD, MacDonald IM, Rachubinski RA, Frosk P, Vandersteen A, Wozniak RW, Pena IA, Wen XY, Lacaze-Masmonteil T, Rankin C, Hieter P. The Canadian Rare Diseases Models and Mechanisms (RDMM) Network: Connecting Understudied Genes to Model Organisms. Am J Hum Genet 2020; 106:143-152. [PMID: 32032513 DOI: 10.1016/j.ajhg.2020.01.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/10/2020] [Indexed: 01/14/2023] Open
Abstract
Advances in genomics have transformed our ability to identify the genetic causes of rare diseases (RDs), yet we have a limited understanding of the mechanistic roles of most genes in health and disease. When a novel RD gene is first discovered, there is minimal insight into its biological function, the pathogenic mechanisms of disease-causing variants, and how therapy might be approached. To address this gap, the Canadian Rare Diseases Models and Mechanisms (RDMM) Network was established to connect clinicians discovering new disease genes with Canadian scientists able to study equivalent genes and pathways in model organisms (MOs). The Network is built around a registry of more than 500 Canadian MO scientists, representing expertise for over 7,500 human genes. RDMM uses a committee process to identify and evaluate clinician-MO scientist collaborations and approve 25,000 Canadian dollars in catalyst funding. To date, we have made 85 clinician-MO scientist connections and funded 105 projects. These collaborations help confirm variant pathogenicity and unravel the molecular mechanisms of RD, and also test novel therapies and lead to long-term collaborations. To expand the impact and reach of this model, we made the RDMM Registry open-source, portable, and customizable, and we freely share our committee structures and processes. We are currently working with emerging networks in Europe, Australia, and Japan to link international RDMM networks and registries and enable matches across borders. We will continue to create meaningful collaborations, generate knowledge, and advance RD research locally and globally for the benefit of patients and families living with RD.
Collapse
Affiliation(s)
- Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada.
| | - Philippe M Campeau
- Centre de Recherche du CHU Ste-Justine, Department of Pediatrics, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Heather E Howley
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sanja Rogic
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Christine Oriel
- Maternal Infant Child and Youth Research Network (MICYRN), Vancouver, BC V5Z 4H4, Canada
| | - Jason N Berman
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Robert M Hamilton
- Labatt Family Heart Centre and Translational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Geoffrey G Hicks
- Regenerative Medicine Program, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P5, Canada; Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P5, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jean-Yves Masson
- Oncology Division, CHU de Québec-Université Laval, Laval University Cancer Research Center, Quebec City, QC, G1R 3S3, Canada
| | - Eric A Shoubridge
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Anne Junker
- Department of Pediatrics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Michel R Leroux
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | | | - Jaques L Michaud
- Centre de Recherche du CHU Ste-Justine, Department of Pediatrics, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Stuart E Turvey
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - David Dyment
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Alberta Children's Hospital, Calgary, AB T2N 4N1, Canada
| | - Clara D van Karnebeek
- Department of Human Genetics, Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada; Department of Pediatrics, Amsterdam University Medical Centres, Amsterdam, the Netherlands; Department of Clinical Genetics, Amsterdam University Medical Centres, Amsterdam, the Netherlands
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Ronald D Cohn
- Genetics and Genome Biology Program, SickKids Research Institute, Department of Paediatrics and Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Ian M MacDonald
- Department of Ophthalmology and Visual Sciences, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R7, Canada
| | - Richard A Rachubinski
- Genetics and Genome Biology Program, SickKids Research Institute, Department of Paediatrics and Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Patrick Frosk
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
| | - Anthony Vandersteen
- Department of Pediatrics, Maritime Medical Genetics Service, Dalhousie University, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Richard W Wozniak
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Izabella A Pena
- CHEO Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Xiao-Yan Wen
- Zebrafish Centre for Advanced Drug Discovery, Keenan Research Centre for Biomedical Science, St Michael's Hospital, Unity Health Toronto, Department of Medicine, University of Toronto, Toronto, ON M5B 1T8
| | - Thierry Lacaze-Masmonteil
- Maternal Infant Child and Youth Research Network (MICYRN), Vancouver, BC V5Z 4H4, Canada; Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Catharine Rankin
- Department of Psychology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| |
Collapse
|
7
|
Abstract
Congenital diaphragmatic hernia (CDH) is a common birth defect that is associated with significant morbidity and mortality, especially when associated with additional congenital anomalies. Both environmental and genetic factors are thought to contribute to CDH. The genetic contributions to CDH are highly heterogeneous and incompletely defined. No one genetic cause accounts for more than 1-2% of CDH cases. In this review, we summarize the known genetic causes of CDH from chromosomal anomalies to individual genes. Both de novo and inherited variants contribute to CDH. Genes causing CDH are increasingly identified from animal models and from genomic strategies including exome and genome sequencing in humans. CDH genes are often transcription factors, genes involved in cell migration or the components of extracellular matrix. We provide clinical genetic testing strategies in the clinical evaluation that can identify a genetic cause in up to ∼30% of patients with non-isolated CDH and can be useful to refine prognosis, identify associated medical and neurodevelopmental issues to address, and inform family planning options.
Collapse
Affiliation(s)
- Lan Yu
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Rebecca R. Hernan
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
8
|
Camilleri M, Sandler RS, Peery AF. Etiopathogenetic Mechanisms in Diverticular Disease of the Colon. Cell Mol Gastroenterol Hepatol 2019; 9:15-32. [PMID: 31351939 PMCID: PMC6881605 DOI: 10.1016/j.jcmgh.2019.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 02/08/2023]
Abstract
This article reviews epidemiological evidence of heritability and putative mechanisms in diverticular disease, with greatest attention to 3 recent studies of genetic associations with diverticular disease based on genome-wide or whole-genome sequencing studies in large patient cohorts. We provide an analysis of the biological plausibility of the significant associations with gene variants reported and highlight the relevance of ANO1, CPI-17 (aka PPP1R14A), COLQ6, COL6A1, CALCB or CALCA, COL6A1, ARHGAP15, and S100A10 to colonic neuromuscular function and tissue properties that may result in altered compliance and predispose to the development of diverticular disease. Such studies also identify candidate genes for future studies.
Collapse
Affiliation(s)
- Michael Camilleri
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Robert S Sandler
- Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Anne F Peery
- Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
| |
Collapse
|
9
|
Sakurai K, Shioda K, Eguchi A, Watanabe M, Miyaso H, Mori C, Shioda T. DNA methylome of human neonatal umbilical cord: Enrichment of differentially methylated regions compared to umbilical cord blood DNA at transcription factor genes involved in body patterning and effects of maternal folate deficiency or children's sex. PLoS One 2019; 14:e0214307. [PMID: 31063509 PMCID: PMC6504184 DOI: 10.1371/journal.pone.0214307] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 03/11/2019] [Indexed: 11/18/2022] Open
Abstract
The DOHaD (developmental origins of health and disease) hypothesis claims that fetal malnutrition or exposure to environmental pollutants may affect their lifelong health. Epigenetic changes may play significant roles in DOHaD; however, access to human fetuses for research has ethical and technical hurdles. Umbilical cord blood (CB) has been commonly used as an epigenetic surrogate of fetuses, but it does not provide direct evidence of fetal exposure to pollutants. Here, we propose umbilical cord tissue (UC), which accumulates substances delivered to fetuses during gestation, as an alternative surrogate for epigenetic studies on fetuses. To explore the feasibility to examine UC epigenome by deep sequencing, we determined CpG methylation profiles of human postnatal UC by reduced representation bisulfite sequencing. Principal component analysis clearly separated the DNA methylomes of UC and CB pairs isolated from the same newborn (n = 10). Although all UC chromosomes were modestly hypomethylated compared to CB chromosomes, GO analysis revealed strong enrichment of differentially methylated regions (DMRs) at promoter-associated CpG islands in the HOX gene clusters and other genes encoding transcription factors involved in determination of the body pattern. DNA methylomes of UC autosomes were largely comparable between males and females. Deficiency of folate during pregnancy has been suggested to affect fetal DNA methylation to cause congenital anomalies. Whereas DNA methylome of UC was not significantly affected by early-gestational (12 weeks) low levels of maternal plasma folate (< 8 ng/ml, n = 10) compared to controls (>19 ng/mL, n = 10), two specific loci of LTR12C endogenous retroviruses in chromosome 12 were significantly hypermethylated in the low-folate group. Our study suggests that UC is useful as an alternative surrogate for studying environmental effects on DNA methylation in human fetuses, compensating CB by providing additional information about epigenetic regulation of genes involved in developmental body patterning and endogenous retroviruses.
Collapse
Affiliation(s)
- Kenichi Sakurai
- Department of Nutrition and Metabolic Medicine, Center for Preventive Medical Sciences, Chiba University, Chiba, Japan
| | - Keiko Shioda
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States of America
| | - Akifumi Eguchi
- Department of Nutrition and Metabolic Medicine, Center for Preventive Medical Sciences, Chiba University, Chiba, Japan
| | - Masahiro Watanabe
- Department of Sustainable Health Science, Center for Preventive Medical Sciences, Chiba University, Chiba, Japan
| | - Hidenori Miyaso
- Department of Sustainable Health Science, Center for Preventive Medical Sciences, Chiba University, Chiba, Japan
| | - Chisato Mori
- Department of Sustainable Health Science, Center for Preventive Medical Sciences, Chiba University, Chiba, Japan
- Department of Bioenvironmental Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- * E-mail: (CM); (TS)
| | - Toshi Shioda
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States of America
- * E-mail: (CM); (TS)
| |
Collapse
|
10
|
Schafmayer C, Harrison JW, Buch S, Lange C, Reichert MC, Hofer P, Cossais F, Kupcinskas J, von Schönfels W, Schniewind B, Kruis W, Tepel J, Zobel M, Rosendahl J, Jacobi T, Walther-Berends A, Schroeder M, Vogel I, Sergeev P, Boedeker H, Hinrichsen H, Volk A, Erk JU, Burmeister G, Hendricks A, Hinz S, Wolff S, Böttner M, Wood AR, Tyrrell J, Beaumont RN, Langheinrich M, Kucharzik T, Brezina S, Huber-Schönauer U, Pietsch L, Noack LS, Brosch M, Herrmann A, Thangapandi RV, Schimming HW, Zeissig S, Palm S, Focke G, Andreasson A, Schmidt PT, Weitz J, Krawczak M, Völzke H, Leeb G, Michl P, Lieb W, Grützmann R, Franke A, Lammert F, Becker T, Kupcinskas L, D'Amato M, Wedel T, Datz C, Gsur A, Weedon MN, Hampe J. Genome-wide association analysis of diverticular disease points towards neuromuscular, connective tissue and epithelial pathomechanisms. Gut 2019; 68:854-865. [PMID: 30661054 DOI: 10.1136/gutjnl-2018-317619] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/03/2019] [Accepted: 01/05/2019] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Diverticular disease is a common complex disorder characterised by mucosal outpouchings of the colonic wall that manifests through complications such as diverticulitis, perforation and bleeding. We report the to date largest genome-wide association study (GWAS) to identify genetic risk factors for diverticular disease. DESIGN Discovery GWAS analysis was performed on UK Biobank imputed genotypes using 31 964 cases and 419 135 controls of European descent. Associations were replicated in a European sample of 3893 cases and 2829 diverticula-free controls and evaluated for risk contribution to diverticulitis and uncomplicated diverticulosis. Transcripts at top 20 replicating loci were analysed by real-time quatitative PCR in preparations of the mucosal, submucosal and muscular layer of colon. The localisation of expressed protein at selected loci was investigated by immunohistochemistry. RESULTS We discovered 48 risk loci, of which 12 are novel, with genome-wide significance and consistent OR in the replication sample. Nominal replication (p<0.05) was observed for 27 loci, and additional 8 in meta-analysis with a population-based cohort. The most significant novel risk variant rs9960286 is located near CTAGE1 with a p value of 2.3×10-10 and 0.002 (ORallelic=1.14 (95% CI 1.05 to 1.24)) in the replication analysis. Four loci showed stronger effects for diverticulitis, PHGR1 (OR 1.32, 95% CI 1.12 to 1.56), FAM155A-2 (OR 1.21, 95% CI 1.04 to 1.42), CALCB (OR 1.17, 95% CI 1.03 to 1.33) and S100A10 (OR 1.17, 95% CI 1.03 to 1.33). CONCLUSION In silico analyses point to diverticulosis primarily as a disorder of intestinal neuromuscular function and of impaired connective fibre support, while an additional diverticulitis risk might be conferred by epithelial dysfunction.
Collapse
Affiliation(s)
- Clemens Schafmayer
- Department of Visceral and Thoracic Surgery, Kiel University, Kiel, Germany
| | | | - Stephan Buch
- Medical Department 1, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden (TU Dresden), Dresden, Germany
| | | | - Matthias C Reichert
- Department of Medicine II, Saarland University Medical Center, Saarland University, Homburg, Germany
| | - Philipp Hofer
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | | | - Juozas Kupcinskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | | | | | - Wolfgang Kruis
- Department of Internal Medicine, Gastroenterology and Pulmonology, Evangelic Hospital Köln-Kalk, Cologne, Germany
| | - Jürgen Tepel
- Department of General and Thoracic Surgery, Hospital Osnabrück, Osnabrück, Germany
| | - Myrko Zobel
- Department of Gastroenterology, Helios Hospital Weißeritztal, Freital, Germany
| | - Jonas Rosendahl
- Medical Department 1, University Hospital Halle, Martin-Luther Universität Halle-Wittenberg, Halle, Germany
| | | | | | | | - Ilka Vogel
- Department of Surgery, Community Hospital Kiel, Kiel, Germany
| | - Petr Sergeev
- Department of Internal Medicine II, Hospital Riesa, Kiel, Germany
| | - Hans Boedeker
- Department of Internal Medicine, Hospital Freiberg, Freiberg, Germany
| | | | - Andreas Volk
- Department of Visceral, Thoracic and Vascular Surgery, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Jens-Uwe Erk
- Medical Department 1, University Hospital Halle, Martin-Luther Universität Halle-Wittenberg, Halle, Germany
| | - Greta Burmeister
- Department of Visceral and Thoracic Surgery, Kiel University, Kiel, Germany
| | | | - Sebastian Hinz
- Department of Visceral and Thoracic Surgery, Kiel University, Kiel, Germany
| | - Sebastian Wolff
- Department of Internal Medicine, Gastroenterology and Pulmonology, Evangelic Hospital Köln-Kalk, Cologne, Germany
| | | | - Andrew R Wood
- University of Exeter Medical School, University of Exeter, United Kingdom, Exeter, UK
| | - Jessica Tyrrell
- University of Exeter Medical School, University of Exeter, United Kingdom, Exeter, UK
| | - Robin N Beaumont
- University of Exeter Medical School, University of Exeter, United Kingdom, Exeter, UK
| | | | | | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Ursula Huber-Schönauer
- Department of Internal Medicine, Hospital Oberndorf, Teaching Hospital of the Paracelsus Private Medical University of Salzburg, Oberndorf, Austria
| | - Leonora Pietsch
- Medical Department 1, University Hospital Halle, Martin-Luther Universität Halle-Wittenberg, Halle, Germany
| | - Laura Sophie Noack
- Medical Department 1, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Mario Brosch
- Medical Department 1, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Alexander Herrmann
- Medical Department 1, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Raghavan Veera Thangapandi
- Medical Department 1, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | | | - Sebastian Zeissig
- Medical Department 1, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Stefan Palm
- Outpatient Center for Gastroenterology, Dippoldiswalde, Germany
| | - Gerd Focke
- Outpatient Center for Gastroenterology Dresden-Blasewitz, Dresden, Germany
| | - Anna Andreasson
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.,Stress Research Institute, Stockholm University, Stockholm, Sweden
| | - Peter T Schmidt
- Department of Medicine Solna and Centre for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Juergen Weitz
- Department of Visceral, Thoracic and Vascular Surgery, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Gernot Leeb
- Department of Gastroenterology, Hospital Oberpullendorf, Oberpullendorf, Austria
| | - Patrick Michl
- Medical Department 1, University Hospital Halle, Martin-Luther Universität Halle-Wittenberg, Halle, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology & Popgen Biobank, Kiel University, Kiel, Germany
| | - Robert Grützmann
- Department of Surgery, University Hospital Erlangen, Erlangen, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Frank Lammert
- Department of Medicine II, Saarland University Medical Center, Saarland University, Homburg, Germany
| | - Thomas Becker
- Department of Visceral and Thoracic Surgery, Kiel University, Kiel, Germany
| | - Limas Kupcinskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Mauro D'Amato
- Department of Medicine Solna and Centre for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Thilo Wedel
- Institute of Anatomy, Kiel University, Kiel, Germany
| | - Christian Datz
- Department of Internal Medicine, Hospital Oberndorf, Teaching Hospital of the Paracelsus Private Medical University of Salzburg, Oberndorf, Austria
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Michael N Weedon
- University of Exeter Medical School, University of Exeter, United Kingdom, Exeter, UK
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden (TU Dresden), Dresden, Germany
| |
Collapse
|