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Xiao J, Hao LW, Wang J, Yu XS, You JY, Li ZJ, Mao HD, Meng XY, Feng JX. Comprehensive characterization of the genetic landscape of familial Hirschsprung's disease. World J Pediatr 2023; 19:644-651. [PMID: 36857021 PMCID: PMC10258170 DOI: 10.1007/s12519-023-00686-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/09/2023] [Indexed: 03/02/2023]
Abstract
BACKGROUND Hirschsprung's disease (HSCR) is one of the most common congenital digestive tract malformations and can cause stubborn constipation or gastrointestinal obstruction after birth, causing great physical and mental pain to patients and their families. Studies have shown that more than 20 genes are involved in HSCR, and most cases of HSCR are sporadic. However, the overall rate of familial recurrence in 4331 cases of HSCR is about 7.6%. Furthermore, familial HSCR patients show incomplete dominance. We still do not know the penetrance and genetic characteristics of these known risk genes due to the rarity of HSCR families. METHODS To find published references, we used the title/abstract terms "Hirschsprung" and "familial" in the PubMed database and the MeSH terms "Hirschsprung" and "familial" in Web of Science. Finally, we summarized 129 HSCR families over the last 40 years. RESULTS The male-to-female ratio and the percentage of short segment-HSCR in familial HSCR are much lower than in sporadic HSCR. The primary gene factors in the syndromic families are ret proto-oncogene (RET) and endothelin B receptor gene (EDNRB). Most families show incomplete dominance and are relevant to RET, and the RET mutation has 56% penetrance in familial HSCR. When one of the parents is a RET mutation carrier in an HSCR family, the offspring's recurrence risk is 28%, and the incidence of the offspring does not depend on whether the parent suffers from HSCR. CONCLUSION Our findings will help HSCR patients obtain better genetic counseling, calculate the risk of recurrence, and provide new insights for future pedigree studies.
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Affiliation(s)
- Jun Xiao
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, 430030, China
| | - Lu-Wen Hao
- Department of Radiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Jing Wang
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, 430030, China
| | - Xiao-Si Yu
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, 430030, China
| | - Jing-Yi You
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, 430030, China
| | - Ze-Jian Li
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, 430030, China
| | - Han-Dan Mao
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, 430030, China
| | - Xin-Yao Meng
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.
- Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, 430030, China.
| | - Jie-Xiong Feng
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.
- Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, 430030, China.
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Whole genome sequencing reveals epistasis effects within RET for Hirschsprung disease. Sci Rep 2022; 12:20423. [PMID: 36443333 PMCID: PMC9705416 DOI: 10.1038/s41598-022-24077-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/09/2022] [Indexed: 11/29/2022] Open
Abstract
Common variants in RET and NRG1 have been associated with Hirschsprung disease (HSCR), a congenital disorder characterised by incomplete innervation of distal gut, in East Asian (EA) populations. However, the allelic effects so far identified do not fully explain its heritability, suggesting the presence of epistasis, where effect of one genetic variant differs depending on other (modifier) variants. Few instances of epistasis have been documented in complex diseases due to modelling complexity and data challenges. We proposed four epistasis models to comprehensively capture epistasis for HSCR between and within RET and NRG1 loci using whole genome sequencing (WGS) data in EA samples. 65 variants within the Topologically Associating Domain (TAD) of RET demonstrated significant epistasis with the lead enhancer variant (RET+3; rs2435357). These epistatic variants formed two linkage disequilibrium (LD) clusters represented by rs2506026 and rs2506028 that differed in minor allele frequency and the best-supported epistatic model. Intriguingly, rs2506028 is in high LD with one cis-regulatory variant (rs2506030) highlighted previously, suggesting that detected epistasis might be mediated through synergistic effects on transcription regulation of RET. Our findings demonstrated the advantages of WGS data for detecting epistasis, and support the presence of interactive effects of regulatory variants in RET for HSCR.
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Circ-ITCH overexpression promoted cell proliferation and migration in Hirschsprung disease through miR-146b-5p/RET axis. Pediatr Res 2022; 92:1008-1016. [PMID: 35091706 DOI: 10.1038/s41390-021-01860-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 11/09/2022]
Abstract
BACKGROUND Hirschsprung disease (HSCR) is a congenital intestinal disease caused by the abnormal proliferation and migration of enteric nerve cells (ENCC). Research suggested critical roles for circular RNA (circRNA) itchy E3 ubiquitin protein ligase (ITCH) in gastrointestinal malignancies progression. However, the function of circ-ITCH in HSCR remains poorly defined. METHODS The related genes expression in 30 HSCR patients and 30 controls without HSCR were detected using qRT-PCR. Cell proliferation was assessed by CCK-8 assay and EdU assay. Cell migration was detected with wound-healing assay and transwell assay. The interactions among circ-ITCH, miR-146b-5p, and RET were confirmed by Dual luciferase reporter assay. RESULTS Circ-ITCH and RET expressions were downregulated in HSCR patients and cells, while the miR-146b-5p expression was upregulated. Circ-ITCH overexpression facilitated cell proliferation, migration, and activated MAPK pathway, which were reversed by circRNA-ITCH knockdown. Circ-ITCH negatively regulated miR-146b-5p expression. MiR-146b-5p overexpression abolished the promoting effects of circ-ITCH overexpression on cell proliferation and migration. MiR-146b-5p inhibited RET expression. RET overexpression eliminated the inhibitory effects of miR-146b-5p overexpression on cell proliferation and migration. CONCLUSION Circ-ITCH overexpression facilitated cell proliferation and migration in HSCR by regulating miR-146b-5p/RET/MAPK axis. IMPACT The expressions of Circ-ITCH and RET were markedly reduced in HSCR, while miR-146b-5p expression was increased in HSCR. Circ-ITCH overexpression enhanced the proliferative and migratory abilities of SH-SY5Y and 293T cells. Circ-ITCH negatively regulated miR-146b-5p expression.
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Ovejero D, Garcia-Giralt N, Martínez-Gil N, Rabionet R, Balcells S, Grinberg D, Pérez-Jurado LA, Nogués X, Etxebarria-Forondad I. Clinical description and genetic analysis of a novel familial skeletal dysplasia characterized by high bone mass and lucent bone lesions. Bone 2022; 161:116450. [PMID: 35623613 DOI: 10.1016/j.bone.2022.116450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/12/2022] [Accepted: 05/21/2022] [Indexed: 11/02/2022]
Abstract
High bone mass (HBM) disorders are a clinically and genetically heterogeneous subgroup of rare skeletal dysplasias. Here we present a case of a previously unreported familial skeletal dysplasia characterized by HBM and lucent bone lesions that we aimed to clinically characterize and genetically investigate. For phenotyping, we reviewed past clinical records and imaging tests, and performed physical examination (PE), bone densitometry, and mineral panels in affected individuals, including a male proband, his son and daughter, in addition to unaffected controls, including the proband's wife and brother. Affected individuals also underwent impact microindentation (IMI). In an effort to elucidate the disorder's molecular etiology, whole exome sequencing (WES) was performed in all individuals to filter for rare variants present only in affected ones. The cases displayed a unique skeletal phenotype with a mix of sclerotic features and lucent bone lesions, and high IMI values. Bone mineral density was very elevated in the proband and his daughter. The proband's daughter also exhibited idiopathic scoliosis (IS), in addition to mild thrombocytopenia and mild structural thyroid abnormalities, which were the only extra-skeletal abnormalities identified. WES analysis yielded 5 rare putative pathogenic variants in affected members in genes that are associated with bone metabolism including: SEM4AD, TBX18, PTCH1, PTK7, and ADGRE5. The PTK7 variant appeared as possibly implicated in the development of IS while the TBX18 and SEMA4D variants stood out as the strongest candidates for the lucent bone lesions and HBM, respectively, given their high predicted pathogenicity and putative role in bone biology. Variant functionality should be addressed in the future to assess their implication in skeletal metabolism as it is the first time that mutations in TBX18 and SEMA4D have been associated to bone developmental lesions and mineral metabolism in a clinical setting.
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Affiliation(s)
- Diana Ovejero
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain.
| | - Natalia Garcia-Giralt
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
| | - Núria Martínez-Gil
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Raquel Rabionet
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, CIBERER, IBUB, IRSJD, Barcelona, Spain
| | | | - Xavier Nogués
- Musculoskeletal Research Group, IMIM (Hospital del Mar Medical Research Institute), Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), ISCIII, Barcelona, Spain
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Nada D, Julien C, Papillon-Cavanagh S, Majewski J, Elbakry M, Elremaly W, Samuels ME, Moreau A. Identification of FAT3 as a new candidate gene for adolescent idiopathic scoliosis. Sci Rep 2022; 12:12298. [PMID: 35853984 PMCID: PMC9296578 DOI: 10.1038/s41598-022-16620-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022] Open
Abstract
In an effort to identify rare alleles associated with adolescent idiopathic scoliosis (AIS) whole-exome sequencing was performed on a discovery cohort of 73 unrelated patients and 70 age-and sex matched controls, all of French-Canadian ancestry. A collapsing gene burden test was performed to analyze rare protein-altering variants using case–control statistics. Since no single gene achieved statistical significance, targeted exon sequencing was performed for 24 genes with the smallest p values, in an independent replication cohort of unrelated severely affected females with AIS and sex-matched controls (N = 96 each). An excess of rare, potentially protein-altering variants was noted in one particular gene, FAT3, although it did not achieve statistical significance. Independently, we sequenced the exomes of all members of a rare multiplex family of three affected sisters and unaffected parents. All three sisters were compound heterozygous for two rare protein-altering variants in FAT3. The parents were single heterozygotes for each variant. The two variants in the family were also present in our discovery cohort. A second validation step was done, using another independent replication cohort of 258 unrelated AIS patients having reach their skeletal maturity and 143 healthy controls to genotype nine FAT3 gene variants, including the two variants previously identified in the multiplex family: p.L517S (rs139595720) and p.L4544F (rs187159256). Interestingly, two FAT3 variants, rs139595720 (genotype A/G) and rs80293525 (genotype C/T), were enriched in severe scoliosis cases (4.5% and 2.7% respectively) compared to milder cases (1.4% and 0.7%) and healthy controls (1.6% and 0.8%). Our results implicate FAT3 as a new candidate gene in the etiology of AIS.
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Affiliation(s)
- Dina Nada
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, (room 2.17.027), 3175 Chemin de la Côte-Ste-Catherine, Montreal, QC, H3T 1C5, Canada.,Pharmacology and Biochemistry Department, Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - Cédric Julien
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, (room 2.17.027), 3175 Chemin de la Côte-Ste-Catherine, Montreal, QC, H3T 1C5, Canada.,Injury Repair Recovery Program, McGill University Health Center Research Institute, Montreal, QC, Canada
| | | | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Mohamed Elbakry
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, (room 2.17.027), 3175 Chemin de la Côte-Ste-Catherine, Montreal, QC, H3T 1C5, Canada.,Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, Egypt
| | - Wesam Elremaly
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, (room 2.17.027), 3175 Chemin de la Côte-Ste-Catherine, Montreal, QC, H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Mark E Samuels
- Sainte-Justine University Hospital Research Center, Montreal, QC, Canada.,Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Alain Moreau
- Viscogliosi Laboratory in Molecular Genetics of Musculoskeletal Diseases, Sainte-Justine University Hospital Research Center, (room 2.17.027), 3175 Chemin de la Côte-Ste-Catherine, Montreal, QC, H3T 1C5, Canada. .,Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada. .,Department of Stomatology, Faculty of Dentistry, Université de Montréal, Montreal, QC, Canada.
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Abstract
The enteric nervous system (ENS) is the largest division of the peripheral nervous system and closely resembles components and functions of the central nervous system. Although the central role of the ENS in congenital enteric neuropathic disorders, including Hirschsprung disease and inflammatory and functional bowel diseases, is well acknowledged, its role in systemic diseases is less understood. Evidence of a disordered ENS has accumulated in neurodegenerative diseases ranging from amyotrophic lateral sclerosis, Alzheimer disease and multiple sclerosis to Parkinson disease as well as neurodevelopmental disorders such as autism. The ENS is a key modulator of gut barrier function and a regulator of enteric homeostasis. A 'leaky gut' represents the gateway for bacterial and toxin translocation that might initiate downstream processes. Data indicate that changes in the gut microbiome acting in concert with the individual genetic background can modify the ENS, central nervous system and the immune system, impair barrier function, and contribute to various disorders such as irritable bowel syndrome, inflammatory bowel disease or neurodegeneration. Here, we summarize the current knowledge on the role of the ENS in gastrointestinal and systemic diseases, highlighting its interaction with various key players involved in shaping the phenotypes. Finally, current flaws and pitfalls related to ENS research in addition to future perspectives are also addressed.
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Planar cell polarity (PCP) proteins support spermatogenesis through cytoskeletal organization in the testis. Semin Cell Dev Biol 2021; 121:99-113. [PMID: 34059418 DOI: 10.1016/j.semcdb.2021.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 12/26/2022]
Abstract
Few reports are found in the literature regarding the role of planar cell polarity (PCP) in supporting spermatogenesis in the testis. Yet morphological studies reported decades earlier have illustrated the directional alignment of polarized developing spermatids, most notably step 17-19 spermatids in stage V-early VIII tubules in the testis, across the plane of the epithelium in seminiferous tubules of adult rats. Such morphological features have unequivocally demonstrated the presence of PCP in developing spermatids, analogous to the PCP noted in hair cells of the cochlea in mammals. Emerging evidence in recent years has shown that Sertoli and germ cells express numerous PCP proteins, mostly notably, the core PCP proteins, PCP effectors and PCP signaling proteins. In this review, we discuss recent findings in the field regarding the two core PCP protein complexes, namely the Van Gogh-like 2 (Vangl2)/Prickle (Pk) complex and the Frizzled (Fzd)/Dishevelled (Dvl) complex. These findings have illustrated that these PCP proteins exert their regulatory role to support spermatogenesis through changes in the organization of actin and microtubule (MT) cytoskeletons in Sertoli cells. For instance, these PCP proteins confer PCP to developing spermatids. As such, developing haploid spermatids can be aligned and orderly packed within the limited space of the seminiferous tubules in the testes for the production of sperm via spermatogenesis. Thus, each adult male in the mouse, rat or human can produce an upward of 30, 50 or 300 million spermatozoa on a daily basis, respectively, throughout the adulthood. We also highlight critical areas of research that deserve attention in future studies. We also provide a hypothetical model by which PCP proteins support spermatogenesis based on recent studies in the testis. It is conceivable that the hypothetical model shown here will be updated as more data become available in future years, but this information can serve as the framework by investigators to unravel the role of PCP in spermatogenesis.
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Villalba-Benito L, Torroglosa A, Luzón-Toro B, Fernández RM, Moya-Jiménez MJ, Antiñolo G, Borrego S. ChIP-Seq-Based Approach in Mouse Enteric Precursor Cells Reveals New Potential Genes with a Role in Enteric Nervous System Development and Hirschsprung Disease. Int J Mol Sci 2020; 21:ijms21239061. [PMID: 33260622 PMCID: PMC7730166 DOI: 10.3390/ijms21239061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 01/11/2023] Open
Abstract
Hirschsprung disease (HSCR) is a neurocristopathy characterized by intestinal aganglionosis which is attributed to a failure in neural crest cell (NCC) development during the embryonic stage. The colonization of the intestine by NCCs is a process finely controlled by a wide and complex gene regulatory system. Several genes have been associated with HSCR, but many aspects still remain poorly understood. The present study is focused on deciphering the PAX6 interaction network during enteric nervous system (ENS) formation. A combined experimental and computational approach was performed to identify PAX6 direct targets, as well as gene networks shared among such targets as potential susceptibility factors for HSCR. As a result, genes related to PAX6 either directly (RABGGTB and BRD3) or indirectly (TGFB1, HRAS, and GRB2) were identified as putative genes associated with HSCR. Interestingly, GRB2 is involved in the RET/GDNF/GFRA1 signaling pathway, one of the main pathways implicated in the disease. Our findings represent a new contribution to advance in the knowledge of the genetic basis of HSCR. The investigation of the role of these genes could help to elucidate their implication in HSCR onset.
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Affiliation(s)
- Leticia Villalba-Benito
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (L.V.-B.); (A.T.); (B.L.-T.); (R.M.F.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Ana Torroglosa
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (L.V.-B.); (A.T.); (B.L.-T.); (R.M.F.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Berta Luzón-Toro
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (L.V.-B.); (A.T.); (B.L.-T.); (R.M.F.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Raquel María Fernández
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (L.V.-B.); (A.T.); (B.L.-T.); (R.M.F.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - María José Moya-Jiménez
- Department of Pediatric Surgery, University Hospital Virgen del Rocío, 41013 Seville, Spain;
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (L.V.-B.); (A.T.); (B.L.-T.); (R.M.F.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (L.V.-B.); (A.T.); (B.L.-T.); (R.M.F.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
- Correspondence:
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Mederer T, Schmitteckert S, Volz J, Martínez C, Röth R, Thumberger T, Eckstein V, Scheuerer J, Thöni C, Lasitschka F, Carstensen L, Günther P, Holland-Cunz S, Hofstra R, Brosens E, Rosenfeld JA, Schaaf CP, Schriemer D, Ceccherini I, Rusmini M, Tilghman J, Luzón-Toro B, Torroglosa A, Borrego S, Sze-man Tang C, Garcia-Barceló M, Tam P, Paramasivam N, Bewerunge-Hudler M, De La Torre C, Gretz N, Rappold GA, Romero P, Niesler B. A complementary study approach unravels novel players in the pathoetiology of Hirschsprung disease. PLoS Genet 2020; 16:e1009106. [PMID: 33151932 PMCID: PMC7643938 DOI: 10.1371/journal.pgen.1009106] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/08/2020] [Indexed: 11/24/2022] Open
Abstract
Hirschsprung disease (HSCR, OMIM 142623) involves congenital intestinal obstruction caused by dysfunction of neural crest cells and their progeny during enteric nervous system (ENS) development. HSCR is a multifactorial disorder; pathogenetic variants accounting for disease phenotype are identified only in a minority of cases, and the identification of novel disease-relevant genes remains challenging. In order to identify and to validate a potential disease-causing relevance of novel HSCR candidate genes, we established a complementary study approach, combining whole exome sequencing (WES) with transcriptome analysis of murine embryonic ENS-related tissues, literature and database searches, in silico network analyses, and functional readouts using candidate gene-specific genome-edited cell clones. WES datasets of two patients with HSCR and their non-affected parents were analysed, and four novel HSCR candidate genes could be identified: ATP7A, SREBF1, ABCD1 and PIAS2. Further rare variants in these genes were identified in additional HSCR patients, suggesting disease relevance. Transcriptomics revealed that these genes are expressed in embryonic and fetal gastrointestinal tissues. Knockout of these genes in neuronal cells demonstrated impaired cell differentiation, proliferation and/or survival. Our approach identified and validated candidate HSCR genes and provided further insight into the underlying pathomechanisms of HSCR.
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Affiliation(s)
- Tanja Mederer
- Department of Human Molecular Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefanie Schmitteckert
- Department of Human Molecular Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Julia Volz
- Department of Human Molecular Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Cristina Martínez
- Department of Human Molecular Genetics, Heidelberg University Hospital, Heidelberg, Germany
- Lleida Institute for Biomedical Research Dr. Pifarré Foundation (IRBLleida), Lleida, Spain
| | - Ralph Röth
- Department of Human Molecular Genetics, Heidelberg University Hospital, Heidelberg, Germany
- nCounter Core Facility, Department of Human Molecular Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | - Jutta Scheuerer
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Cornelia Thöni
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Lasitschka
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Leonie Carstensen
- Pediatric Surgery Division, Heidelberg University Hospital, Heidelberg, Germany
| | - Patrick Günther
- Pediatric Surgery Division, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Robert Hofstra
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Baylor Genetics Laboratories, Houston, Texas, United States of America
| | - Christian P. Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Baylor Genetics Laboratories, Houston, Texas, United States of America
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Duco Schriemer
- Department of Neuroscience, University Medical Center, Groningen, The Netherlands
| | - Isabella Ceccherini
- UOSD Genetica e Genomica delle Malattie Rare, IRCCS, Instituto Giannina Gaslini, Genova, Italy
| | - Marta Rusmini
- UOSD Genetica e Genomica delle Malattie Rare, IRCCS, Instituto Giannina Gaslini, Genova, Italy
| | - Joseph Tilghman
- Center for Human Genetics and Genomics, New York University School of Medicine, United States of America
| | - Berta Luzón-Toro
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Ana Torroglosa
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Clara Sze-man Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Mercè Garcia-Barceló
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Paul Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Nagarajan Paramasivam
- Division of Theoretical Bioinformatics, German Cancer Research Center, Heidelberg, Germany
| | | | | | - Norbert Gretz
- Center of Medical Research, Medical Faculty Mannheim, Mannheim, Germany
| | - Gudrun A. Rappold
- Department of Human Molecular Genetics, Heidelberg University Hospital, Heidelberg, Germany
- Interdisciplinary Center for Neurosciences, University of Heidelberg, Heidelberg, Germany
| | - Philipp Romero
- Pediatric Surgery Division, Heidelberg University Hospital, Heidelberg, Germany
| | - Beate Niesler
- Department of Human Molecular Genetics, Heidelberg University Hospital, Heidelberg, Germany
- nCounter Core Facility, Department of Human Molecular Genetics, Heidelberg University Hospital, Heidelberg, Germany
- Interdisciplinary Center for Neurosciences, University of Heidelberg, Heidelberg, Germany
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10
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Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease. Genome Res 2020; 30:1618-1632. [PMID: 32948616 PMCID: PMC7605255 DOI: 10.1101/gr.264473.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/14/2020] [Indexed: 12/16/2022]
Abstract
It is widely recognized that noncoding genetic variants play important roles in many human diseases, but there are multiple challenges that hinder the identification of functional disease-associated noncoding variants. The number of noncoding variants can be many times that of coding variants; many of them are not functional but in linkage disequilibrium with the functional ones; different variants can have epistatic effects; different variants can affect the same genes or pathways in different individuals; and some variants are related to each other not by affecting the same gene but by affecting the binding of the same upstream regulator. To overcome these difficulties, we propose a novel analysis framework that considers convergent impacts of different genetic variants on protein binding, which provides multiscale information about disease-associated perturbations of regulatory elements, genes, and pathways. Applying it to our whole-genome sequencing data of 918 short-segment Hirschsprung disease patients and matched controls, we identify various novel genes not detected by standard single-variant and region-based tests, functionally centering on neural crest migration and development. Our framework also identifies upstream regulators whose binding is influenced by the noncoding variants. Using human neural crest cells, we confirm cell stage-specific regulatory roles of three top novel regulatory elements on our list, respectively in the RET, RASGEF1A, and PIK3C2B loci. In the PIK3C2B regulatory element, we further show that a noncoding variant found only in the patients affects the binding of the gliogenesis regulator NFIA, with a corresponding up-regulation of multiple genes in the same topologically associating domain.
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11
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Niu WB, Bai MR, Song HL, Lu YJ, Wu WJ, Gong YM, Yu XX, Wei ZL, Yu WW, Gu BL, Cai W, Chu X. Association of Variants in PLD1, 3p24.1, and 10q11.21 Regions With Hirschsprung's Disease in Han Chinese Population. Front Genet 2020; 11:738. [PMID: 32765588 PMCID: PMC7381268 DOI: 10.3389/fgene.2020.00738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 06/19/2020] [Indexed: 01/31/2023] Open
Abstract
Background and Aims: Hirschsprung's disease (HSCR) is a rare genetically heterogeneous congenital disorder. A recent study based on whole genome sequencing demonstrated that common variants at four novel loci, which contained two intronic variants on CASQ2 and PLD1, and intergenic variants located between SLC4A7 and EOMES at 3p24.1, and between LINC01518 and LOC283028 at 10q11.21, were associated with HSCR susceptibility. To validate these associations with HSCR susceptibility, we performed a case-control study in a Han Chinese sample set. Methods: We selected four previously identified single nucleotide polymorphisms (SNPs) for replication, along with tag SNPs to cover the four associated regions. In total, 61 SNPs were genotyped in 420 HSCR patients and 1,665 healthy controls from the Han Chinese population. Results: None of the 14 tag SNPs in the CASQ2 gene region, including the previously associated rs9428225, showed an association with HSCR. Among the 24 tag SNPs from the SLC4A7-EOMES region at 3p24.1, rs2642925 [odds ratio (OR) = 1.41, 95% confidence interval (95% CI) = 1.10-1.79; P Additive = 0.007] and the previously associated SNP rs9851320 showed a suggestive association (OR = 1.22, 95% CI = 1.01-1.47; P Additive = 0.042). A non-synonymous SNP, rs2287579, in PLD1 showed a suggestive association with HSCR susceptibility (OR = 1.71, 95% CI = 1.18-2.46; P Additive = 0.004). Additionally, the previously associated PLD1 SNP rs12632766 showed a suggestive significance (OR = 1.20, 95% CI = 1.01-1.42, P Additive = 0.038). In the LINC01518-LOC283028 region at 10q11.21, three SNPs meet the study-wide significance threshold. Rs17153309 was the most associated SNP (OR = 1.60, 95% CI = 1.34-1.90; P Additive = 1.13 × 10-7). The previously associated SNP rs1414027 also showed significant association (OR = 1.43, 95% CI = 1.20-1.70, P Additive = 3.92 × 10-5). Two associated SNPs at 10q11.21 (rs1414027 and rs624804) were expression quantitative trait loci in digestive tract tissues from GTEx databases. Conclusions: Our results confirmed that variants of the LINC01518-LOC283028 region were associated with HSCR in the Han Chinese population. Additionally, the susceptibility of SNPs in the LINC01518-LOC283028 region were associated with the expression levels of nearby genes. These results provide new insight into the pathogenesis of HSCR.
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Affiliation(s)
- Wei-Bo Niu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute of Pediatric Research, Shanghai, China
| | - Mei-Rong Bai
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute of Pediatric Research, Shanghai, China
| | - Huan-Lei Song
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute of Pediatric Research, Shanghai, China
| | - Yan-Jiao Lu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute of Pediatric Research, Shanghai, China
| | - Wen-Jie Wu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute of Pediatric Research, Shanghai, China
| | - Yi-Ming Gong
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute of Pediatric Research, Shanghai, China
| | - Xian-Xian Yu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute of Pediatric Research, Shanghai, China
| | - Zhi-Liang Wei
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute of Pediatric Research, Shanghai, China
| | - Wen-Wen Yu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute of Pediatric Research, Shanghai, China
| | - Bei-Lin Gu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute of Pediatric Research, Shanghai, China
| | - Wei Cai
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute of Pediatric Research, Shanghai, China
| | - Xun Chu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute of Pediatric Research, Shanghai, China
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12
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Torroglosa A, Villalba-Benito L, Fernández RM, Luzón-Toro B, Moya-Jiménez MJ, Antiñolo G, Borrego S. Identification of New Potential LncRNA Biomarkers in Hirschsprung Disease. Int J Mol Sci 2020; 21:ijms21155534. [PMID: 32748823 PMCID: PMC7432910 DOI: 10.3390/ijms21155534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
Hirschsprung disease (HSCR) is a neurocristopathy defined by intestinal aganglionosis due to alterations during the development of the Enteric Nervous System (ENS). A wide spectrum of molecules involved in different signaling pathways and mechanisms have been described in HSCR onset. Among them, epigenetic mechanisms are gaining increasing relevance. In an effort to better understand the epigenetic basis of HSCR, we have performed an analysis for the identification of long non-coding RNAs (lncRNAs) by qRT-PCR in enteric precursor cells (EPCs) from controls and HSCR patients. We aimed to test the presence of a set lncRNAs among 84 lncRNAs in human EPCs, which were previously related with crucial cellular processes for ENS development, as well as to identify the possible differences between HSCR patients and controls. As a result, we have determined a set of lncRNAs with positive expression in human EPCs that were screened for mutations using the exome data from our cohort of HSCR patients to identify possible variants related to this pathology. Interestingly, we identified three lncRNAs with different levels of their transcripts (SOCS2-AS, MEG3 and NEAT1) between HSCR patients and controls. We propose such lncRNAs as possible regulatory elements implicated in the onset of HSCR as well as potential biomarkers of this pathology.
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Affiliation(s)
- Ana Torroglosa
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Leticia Villalba-Benito
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Raquel María Fernández
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Berta Luzón-Toro
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - María José Moya-Jiménez
- Department of Pediatric Surgery, University Hospital Virgen del Rocío, 41013 Seville, Spain;
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain; (A.T.); (L.V.-B.); (R.M.F.); (B.L.-T.); (G.A.)
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
- Correspondence:
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13
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Choi YJ, Ohn JH, Kim N, Kim W, Park K, Won S, Sael L, Shin CM, Lee SM, Lee S, An HJ, Jang DM, Han BW, Lee HS, Kang SJ, Kim JS, Lee DH. Family-based exome sequencing combined with linkage analyses identifies rare susceptibility variants of MUC4 for gastric cancer. PLoS One 2020; 15:e0236197. [PMID: 32701958 PMCID: PMC7377420 DOI: 10.1371/journal.pone.0236197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/30/2020] [Indexed: 12/24/2022] Open
Abstract
Genome-wide association studies of gastric cancer (GC) cases have revealed common gastric cancer susceptibility loci with low effect size. We investigated rare variants with high effect size via whole-exome sequencing (WES) of subjects with familial clustering of gastric cancer. WES of DNAs from the blood of 19 gastric cancer patients and 36 unaffected family members from 14 families with two or more gastric cancer patients were tested. Linkage analysis combined with association tests were performed using Pedigree Variant Annotation, Analysis, and Search Tool (pVAAST) software. Based on the logarithm of odds (LOD) and permutation-based composite likelihood ratio test (CLRT) from pVAAST, MUC4 was identified as a predisposing gene (LOD P-value = 1.9×10-5; permutation-based P-value of CLRT ≤ 9.9×10-9). In a larger cohort consisting of 597 GC patients and 9,759 healthy controls genotyped with SNP array, we discovered common variants in MUC4 regions (rs148735556, rs11717039, and rs547775645) significantly associated with GC supporting the association of MUC4 with gastric cancer. And the MUC4 variants were found in higher frequency in The Cancer Genome Atlas Study (TCGA) germline samples of patients with multiple cancer types. Immunohistochemistry indicated that MUC4 was downregulated in the noncancerous gastric mucosa of subjects with MUC4 germline missense variants, suggesting that loss of the protective function of MUC4 predisposes an individual to gastric cancer. Rare variants in MUC4 can be novel gastric cancer susceptibility loci in Koreans possessing the familial clustering of gastric cancer.
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Affiliation(s)
- Yoon Jin Choi
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jung Hun Ohn
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Nayoung Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
- * E-mail:
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Kyungtaek Park
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea
| | - Sungho Won
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea
- Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Lee Sael
- Department of Artificial Intelligence and Data Science, Ajou University, Seoul, South Korea
| | - Cheol Min Shin
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Sun Min Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Sejoon Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, South Korea
| | - Dong Man Jang
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Byung Woo Han
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Hye Seung Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Seung Joo Kang
- Department of Internal Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, South Korea
| | - Joo Sung Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Department of Internal Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, South Korea
| | - Dong Ho Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
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14
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miR-618 rs2682818 C>A polymorphism decreases Hirschsprung disease risk in Chinese children. Biosci Rep 2020; 40:223573. [PMID: 32364585 PMCID: PMC7214396 DOI: 10.1042/bsr20193989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/27/2020] [Accepted: 04/30/2020] [Indexed: 12/02/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenous non-coding small RNAs that play an important role in the development of many malignant tumors. In addition, recent studies have reported that single nucleotide polymorphisms (SNPs) located in the miRNA functional region was inextricably linked to tumor susceptibility. In the present study, we investigated the susceptibility between miR-618 rs2682818 C>A and Hirschsprung disease (HSCR) in the Southern Chinese population (1470 patients and 1473 controls). Odds ratios (ORs) and 95% confidence intervals (CIs) were used for estimating the strength of interrelation between them. We found that the CA/AA genotypes of miR-618 rs2682818 were associated with a decreased risk of HSCR when compared with the CC genotype (OR = 0.84, 95% CI = 0.72–0.99, P=0.032). Based on the stratified analysis of HSCR subtypes, the rs2682818 CA/AA genotypes were able to significantly lessen the risk of HSCR compared with CC genotype in patients with long-segment HSCR (adjusted OR = 0.70, 95% CI = 0.52–0.93, P=0.013). In conclusion, our results indicated that the miR-618 rs2682818 C>A polymorphism was associated with a reduced risk of HSCR in Chinese children, especially in patients with long-segment HSCR (L-HSCR) subtype.
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15
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Luzón‐Toro B, Villalba‐Benito L, Torroglosa A, Fernández RM, Antiñolo G, Borrego S. What is new about the genetic background of Hirschsprung disease? Clin Genet 2019; 97:114-124. [DOI: 10.1111/cge.13615] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Berta Luzón‐Toro
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS)University Hospital Virgen del Rocío/CSIC/University of Seville Seville Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER) Seville Spain
| | - Leticia Villalba‐Benito
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS)University Hospital Virgen del Rocío/CSIC/University of Seville Seville Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER) Seville Spain
| | - Ana Torroglosa
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS)University Hospital Virgen del Rocío/CSIC/University of Seville Seville Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER) Seville Spain
| | - Raquel M. Fernández
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS)University Hospital Virgen del Rocío/CSIC/University of Seville Seville Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER) Seville Spain
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS)University Hospital Virgen del Rocío/CSIC/University of Seville Seville Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER) Seville Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBIS)University Hospital Virgen del Rocío/CSIC/University of Seville Seville Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER) Seville Spain
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16
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Linkage analysis and whole exome sequencing reveals AHNAK2 as a novel genetic cause for autosomal recessive CMT in a Malaysian family. Neurogenetics 2019; 20:117-127. [DOI: 10.1007/s10048-019-00576-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/03/2019] [Indexed: 10/27/2022]
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17
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López SH, Avetisyan M, Wright CM, Mesbah K, Kelly RG, Moon AM, Heuckeroth RO. Loss of Tbx3 in murine neural crest reduces enteric glia and causes cleft palate, but does not influence heart development or bowel transit. Dev Biol 2018; 444 Suppl 1:S337-S351. [PMID: 30292786 DOI: 10.1016/j.ydbio.2018.09.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/23/2018] [Accepted: 09/23/2018] [Indexed: 01/12/2023]
Abstract
Transcription factors that coordinate migration, differentiation or proliferation of enteric nervous system (ENS) precursors are not well defined. To identify novel transcriptional regulators of ENS development, we performed microarray analysis at embryonic day (E) 17.5 and identified many genes that were enriched in the ENS compared to other bowel cells. We decided to investigate the T-box transcription factor Tbx3, which is prominently expressed in developing and mature ENS. Haploinsufficiency for TBX3 causes ulnar-mammary syndrome (UMS) in humans, a multi-organ system disorder. TBX3 also regulates several genes known to be important for ENS development. To test the hypothesis that Tbx3 is important for ENS development or function, we inactivated Tbx3 in all neural crest derivatives, including ENS progenitors using Wnt1-Cre and a floxed Tbx3 allele. Tbx3 fl/fl; Wnt1-Cre conditional mutant mice die shortly after birth with cleft palate and difficulty feeding. The ENS of mutants was well-organized with a normal density of enteric neurons and nerve fiber bundles, but small bowel glial cell density was reduced. Despite this, bowel motility appeared normal. Furthermore, although Tbx3 is expressed in cardiac neural crest, Tbx3 fl/fl; Wnt1-Cre mice had structurally normal hearts. Thus, loss of Tbx3 within neural crest has selective effects on Tbx3-expressing neural crest derivatives.
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Affiliation(s)
- Silvia Huerta López
- The Children's Hospital of Philadelphia Research Institute, 3615 Civic Center Blvd, Abramson Research Center - Suite # 1116I, Philadelphia, PA 19104-4318, United States
| | - Marina Avetisyan
- The Children's Hospital of Philadelphia Research Institute, 3615 Civic Center Blvd, Abramson Research Center - Suite # 1116I, Philadelphia, PA 19104-4318, United States; Department of Pediatrics, Washington University School of Medicine in St. Louis, 660 South Euclid Avenue, St. Louis, MO 63110, United States
| | - Christina M Wright
- The Children's Hospital of Philadelphia Research Institute, 3615 Civic Center Blvd, Abramson Research Center - Suite # 1116I, Philadelphia, PA 19104-4318, United States; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, United States
| | - Karim Mesbah
- Aix-Marseille Univ, CNRS, IBDM, Marseille, France
| | | | - Anne M Moon
- Weis Center for Research, Geisinger Clinic, Danville, PA, United States; Departments of Pediatrics and Human Genetics, University of Utah, Salt Lake City, United States
| | - Robert O Heuckeroth
- The Children's Hospital of Philadelphia Research Institute, 3615 Civic Center Blvd, Abramson Research Center - Suite # 1116I, Philadelphia, PA 19104-4318, United States; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104-4318, United States.
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18
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Wang Y, Yan W, Wang J, Zhou Y, Chen J, Gu B, Cai W. Common genetic variants in GAL, GAP43 and NRSN1 and interaction networks confer susceptibility to Hirschsprung disease. J Cell Mol Med 2018; 22:3377-3387. [PMID: 29654647 PMCID: PMC6010875 DOI: 10.1111/jcmm.13612] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/22/2018] [Indexed: 01/21/2023] Open
Abstract
Hirschsprung disease (HSCR) is a severe multifactorial genetic disorder. Microarray studies indicated GAL,GAP43 and NRSN1 might contribute to the altered risk in HSCR. Thus, we focused on genetic variations in GAL,GAP43 and NRSN1, and the gene‐gene interactions involved in HSCR susceptibility. We recruited a strategy combining case‐control study and MassArray system with interaction network analysis. For GAL,GAP43 and NRSN1, a total of 18 polymorphisms were assessed in 104 subjects with sporadic HSCR and 151 controls of Han Chinese origin. We found statistically significant differences between HSCR and control groups at 5 genetic variants. For each gene, the haplotypes combining all polymorphisms were the most significant. Based on SNPsyn, MDR and GeneMANIA analyses, we observed significant gene‐gene interactions among GAL,GAP43,NRSN1 and our previous identified RELN,GABRG2 and PTCH1. Our study for the first time indicates that genetic variants within GAL,GAP43 and NRSN1 and related gene‐gene interaction networks might be involved in the altered susceptibility to HSCR in the Han Chinese population, which might shed more light on HSCR pathogenesis.
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Affiliation(s)
- Yang Wang
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Weihui Yan
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Jun Wang
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Ying Zhou
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Jie Chen
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Beilin Gu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Wei Cai
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China.,Shanghai Institute for Pediatric Research, Shanghai, China
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19
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Hirschsprung disease - integrating basic science and clinical medicine to improve outcomes. Nat Rev Gastroenterol Hepatol 2018; 15:152-167. [PMID: 29300049 DOI: 10.1038/nrgastro.2017.149] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Hirschsprung disease is defined by the absence of enteric neurons at the end of the bowel. The enteric nervous system (ENS) is the intrinsic nervous system of the bowel and regulates most aspects of bowel function. When the ENS is missing, there are no neurally mediated propulsive motility patterns, and the bowel remains contracted, causing functional obstruction. Symptoms of Hirschsprung disease include constipation, vomiting, abdominal distension and growth failure. Untreated disease usually causes death in childhood because bloodstream bacterial infections occur in the context of bowel inflammation (enterocolitis) or bowel perforation. Current treatment is surgical resection of the bowel to remove or bypass regions where the ENS is missing, but many children have problems after surgery. Although the anatomy of Hirschsprung disease is simple, many clinical features remain enigmatic, and diagnosis and management remain challenging. For example, the age of presentation and the type of symptoms that occur vary dramatically among patients, even though every affected child has missing neurons in the distal bowel at birth. In this Review, basic science discoveries are linked to clinical manifestations of Hirschsprung disease, including partial penetrance, enterocolitis and genetics. Insights into disease mechanisms that might lead to new prevention, diagnostic and treatment strategies are described.
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20
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Zhang Z, Li Q, Diao M, Liu N, Cheng W, Xiao P, Zou J, Su L, Yu K, Wu J, Li L, Jiang Q. Sporadic Hirschsprung Disease: Mutational Spectrum and Novel Candidate Genes Revealed by Next-generation Sequencing. Sci Rep 2017; 7:14796. [PMID: 29093530 PMCID: PMC5666020 DOI: 10.1038/s41598-017-14835-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 10/18/2017] [Indexed: 12/20/2022] Open
Abstract
Hirschsprung disease (HSCR) is a common cause of functional colonic obstruction in children. The currently available genetic testing is often inadequate as it mainly focuses on RET and several other genes, accounting for only 15–20% of cases. To identify novel, potentially pathogenic variants, we isolated a panel of genes from a whole-exome sequencing study and from the published mouse aganglionosis phenotypes, enteric nervous system development, and a literature review. The coding exons of 172 genes were analyzed in 83 sporadic patients using next-generation sequencing. Rare stop-gain, splice-site variants, frameshift and in-frame insertions/deletions and non-synonymous variants (conserved and predicted to be deleterious) were prioritized as the most promising variants to have an effect on HSCR and subjected to burden analysis. GeneMANIA interaction database was used to identify protein–protein interaction-based networks. In addition, 6 genes (PTPN13, PHKB, AGL, ZFHX3, LAMA1, and AP3B2) were prioritized for follow-up studies: both their time-space expression patterns in mouse and human colon showed that they are good candidates for predicting pathogenicity. The results of this study broaden the mutational spectrum of HSCR candidate genes, and they provide an insight into the relative contributions of individual genes to this highly heterogeneous disorder.
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Affiliation(s)
- Zhen Zhang
- Department of General Surgery, Capital Institute of Pediatrics, Beijing, China
| | - Qi Li
- Department of General Surgery, Capital Institute of Pediatrics, Beijing, China
| | - Mei Diao
- Department of General Surgery, Capital Institute of Pediatrics, Beijing, China
| | - Na Liu
- MyGenostics Inc, Beijing, China
| | - Wei Cheng
- Department of Surgery, Beijing United Family Hospital, Beijing, China.,Department of Paediatrics and Surgery, Faculty of Medicine, Nursing and Health Sciences, Monash University, Victoria, Australia
| | - Ping Xiao
- Department of Pathology, Capital Institute of Pediatrics Affiliated Children's Hospital, Beijing, China
| | - Jizhen Zou
- Department of Pathology, Capital Institute of Pediatrics Affiliated Children's Hospital, Beijing, China
| | - Lin Su
- Reproductive Medicine Center, Clinical College of PLA Affiliated Anhui Medical University, Hefei, China
| | - Kaihui Yu
- Department of Pathophysiology, School of Preclinical Sciences, Guangxi Medical University, Nanning, China
| | - Jian Wu
- MyGenostics Inc, Beijing, China
| | - Long Li
- Department of General Surgery, Capital Institute of Pediatrics, Beijing, China
| | - Qian Jiang
- Department of Medical Genetics, Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China.
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21
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Pan W, Yu H, Zheng B, Gao Y, Li P, Huang Q, Xie C, Ge X. Upregulation of MiR-369-3p suppresses cell migration and proliferation by targeting SOX4 in Hirschsprung's disease. J Pediatr Surg 2017; 52:1363-1370. [PMID: 28412032 DOI: 10.1016/j.jpedsurg.2017.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 01/17/2023]
Abstract
BACKGROUND Hirschsprung disease (HSCR) is a congenital digestive disease in the new born. miR-369-3p has been reported to be involved in many human diseases. However, the relationship between miR-369-3p and HSCR remains largely unknown. METHODS In this study, qRT-PCR was used to detect the relative expression of miR-369-3p in 60 HSCR bowel tissue samples and 47 matched controls. Bioinformatic analysis and dual-luciferase reporter assay were performed to evaluate the target for miR-369-3p. Cell Counting Kit-8 (CCK-8) assay, Transwell assay, wound healing assay and flow cytometry were employed to investigate the biological function of miR-369-3p in human SH-SY5Y and 293T cell lines. RESULTS We found that ganglion cell numbers were remarkably reduced while miR-369-3p was significantly upregulated in HSCR tissues compared to that in adjacent normal tissues (P<0.01). Dual-luciferase reporter assay showed that the 3'-UTR of SOX4 was a direct target to miR-369-3p. Moreover, an increased level of miR-369-3p was inversely correlated with decreased levels of SOX4 mRNA and protein (P<0.05, respectively). Dysregulation of miR-369-3p and SOX4 significantly suppressed cell proliferation and migration in SH-SY5Y and 293T cell lines in vitro (P<0.05, respectively). CONCLUSION Our study demonstrates that aberrant expression of miR-369-3p might play a crucial role in the development HSCR by regulating SOX4 expression, which may infer that it is an effective diagnostic target in the pathogenesis of HSCR, but investigation is still needed to explore the underlying mechanism.
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Affiliation(s)
- Weikang Pan
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, China
| | - Hui Yu
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, China
| | - Baijun Zheng
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, China
| | - Ya Gao
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, China.
| | - Peng Li
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, China
| | - Qiang Huang
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, China
| | - Chong Xie
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, China
| | - Xin Ge
- Department of Pediatric Surgery, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, China
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22
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Villalba-Benito L, Torroglosa A, Fernández RM, Ruíz-Ferrer M, Moya-Jiménez MJ, Antiñolo G, Borrego S. Overexpression of DNMT3b target genes during Enteric Nervous System development contribute to the onset of Hirschsprung disease. Sci Rep 2017; 7:6221. [PMID: 28740121 PMCID: PMC5524929 DOI: 10.1038/s41598-017-06539-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/09/2017] [Indexed: 12/27/2022] Open
Abstract
Hirschsprung disease (HSCR) is attributed to a failure of neural crest cells (NCCs) to migrate, proliferate, differentiate and/or survive in the bowel wall during embryonic Enteric Nervous System (ENS) development. ENS formation is the result from a specific gene expression pattern regulated by epigenetic events, such DNA methylation by the DNA methyltransferases (DNMTs), among other mechanisms. Specifically, DNMT3b de novo methyltransferase is associated with NCCs development and has been shown to be implicated in ENS formation and in HSCR. Aiming to elucidate the specific mechanism underlying the DNMT3b role in such processes, we have performed a chromatin immunoprecipitation coupled with massively parallel sequencing analysis to identify the DNMT3B target genes in enteric precursor cells (EPCs) from mice. Moreover, the expression patterns of those target genes have been analyzed in human EPCs from HSCR patients in comparison with controls. Additionally, we have carried out a search of rare variants in those genes in a HSCR series. Through this approach we found 9 genes showing a significantly different expression level in both groups. Therefore, those genes may have a role in the proper human ENS formation and a failure in their expression pattern might contribute to this pathology.
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Affiliation(s)
- Leticia Villalba-Benito
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain
| | - Ana Torroglosa
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain
| | - Raquel María Fernández
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain
| | - Macarena Ruíz-Ferrer
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain
| | - María José Moya-Jiménez
- Department of Pediatric Surgery, University Hospital Virgen del Rocío, Seville, 41013, Spain
| | - Guillermo Antiñolo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain
| | - Salud Borrego
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, 41013, Spain.
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, 41013, Spain.
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23
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Tang CSM, Gui H, Kapoor A, Kim JH, Luzón-Toro B, Pelet A, Burzynski G, Lantieri F, So MT, Berrios C, Shin HD, Fernández RM, Le TL, Verheij JBGM, Matera I, Cherny SS, Nandakumar P, Cheong HS, Antiñolo G, Amiel J, Seo JM, Kim DY, Oh JT, Lyonnet S, Borrego S, Ceccherini I, Hofstra RMW, Chakravarti A, Kim HY, Sham PC, Tam PKH, Garcia-Barceló MM. Trans-ethnic meta-analysis of genome-wide association studies for Hirschsprung disease. Hum Mol Genet 2017; 25:5265-5275. [PMID: 27702942 DOI: 10.1093/hmg/ddw333] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/28/2016] [Indexed: 02/04/2023] Open
Abstract
Hirschsprung disease (HSCR) is the most common cause of neonatal intestinal obstruction. It is characterized by the absence of ganglia in the nerve plexuses of the lower gastrointestinal tract. So far, three common disease-susceptibility variants at the RET, SEMA3 and NRG1 loci have been detected through genome-wide association studies (GWAS) in Europeans and Asians to understand its genetic etiologies. Here we present a trans-ethnic meta-analysis of 507 HSCR cases and 1191 controls, combining all published GWAS results on HSCR to fine-map these loci and narrow down the putatively causal variants to 99% credible sets. We also demonstrate that the effects of RET and NRG1 are universal across European and Asian ancestries. In contrast, we detected a European-specific association of a low-frequency variant, rs80227144, in SEMA3 [odds ratio (OR) = 5.2, P = 4.7 × 10-10]. Conditional analyses on the lead SNPs revealed a secondary association signal, corresponding to an Asian-specific, low-frequency missense variant encoding RET p.Asp489Asn (rs9282834, conditional OR = 20.3, conditional P = 4.1 × 10-14). When in trans with the RET intron 1 enhancer risk allele, rs9282834 increases the risk of HSCR from 1.1 to 26.7. Overall, our study provides further insights into the genetic architecture of HSCR and has profound implications for future study designs.
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Affiliation(s)
- Clara Sze-Man Tang
- Department of Surgery.,Centre for Genomic Sciences.,Dr Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong SAR, China
| | | | - Ashish Kapoor
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Berta Luzón-Toro
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Anna Pelet
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Grzegorz Burzynski
- Department of Clinical Genetic, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | | | - Courtney Berrios
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul 121-742, Republic of Korea.,Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Raquel M Fernández
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Thuy-Linh Le
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Joke B G M Verheij
- Department of Clinical Genetic, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ivana Matera
- UOC Genetica Medica, Istituto Giannina Gaslini, 16148 Genova, Italy
| | - Stacey S Cherny
- Centre for Genomic Sciences.,Department of Psychiatry.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Priyanka Nandakumar
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 121-742, Republic of Korea
| | - Guillermo Antiñolo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Jeong-Meen Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Republic of Korea
| | - Dae-Yeon Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Jung-Tak Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Salud Borrego
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | | | - Robert M W Hofstra
- Department of Clinical Genetic, Erasmus Medical Center, Rotterdam, The Netherlands.,Stem Cells and Regenerative Medicine, Birth Defects Research Centre UCL Institute of Child Health, London, UK
| | - Aravinda Chakravarti
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hyun-Young Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul 110-744, Republic of Korea
| | - Pak Chung Sham
- Centre for Genomic Sciences.,Department of Psychiatry.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Paul K H Tam
- Department of Surgery.,Dr Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong SAR, China
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24
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Mukawa M, Nariai T, Onda H, Yoneyama T, Aihara Y, Hirota K, Kudo T, Sumita K, Maehara T, Kawamata T, Kasuya H, Akagawa H. Exome Sequencing Identified CCER2 as a Novel Candidate Gene for Moyamoya Disease. J Stroke Cerebrovasc Dis 2017; 26:150-161. [DOI: 10.1016/j.jstrokecerebrovasdis.2016.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/01/2016] [Accepted: 09/03/2016] [Indexed: 10/20/2022] Open
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