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Benfica LF, Brito LF, do Bem RD, de Oliveira LF, Mulim HA, Braga LG, Cyrillo JNSG, Bonilha SFM, Mercadante MEZ. Detection and characterization of copy number variation in three differentially-selected Nellore cattle populations. Front Genet 2024; 15:1377130. [PMID: 38694873 PMCID: PMC11061390 DOI: 10.3389/fgene.2024.1377130] [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: 01/26/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024] Open
Abstract
Introduction: Nellore cattle (Bos taurus indicus) is the main beef cattle breed raised in Brazil. This breed is well adapted to tropical conditions and, more recently, has experienced intensive genetic selection for multiple performance traits. Over the past 43 years, an experimental breeding program has been developed in the Institute of Animal Science (IZ, Sertaozinho, SP, Brazil), which resulted in three differentially-selected lines known as Nellore Control (NeC), Nellore Selection (NeS), and Nellore Traditional (NeT). The primary goal of this selection experiment was to determine the response to selection for yearling weight (YW) and residual feed intake (RFI) on Nellore cattle. The main objectives of this study were to: 1) identify copy number variation (CNVs) in Nellore cattle from three selection lines; 2) identify and characterize CNV regions (CNVR) on these three lines; and 3) perform functional enrichment analyses of the CNVR identified. Results: A total of 14,914 unique CNVs and 1,884 CNVRs were identified when considering all lines as a single population. The CNVRs were non-uniformly distributed across the chromosomes of the three selection lines included in the study. The NeT line had the highest number of CNVRs (n = 1,493), followed by the NeS (n = 823) and NeC (n = 482) lines. The CNVRs covered 23,449,890 bp (0.94%), 40,175,556 bp (1.61%), and 63,212,273 bp (2.54%) of the genome of the NeC, NeS, and NeT lines, respectively. Two CNVRs were commonly identified between the three lines, and six, two, and four exclusive regions were identified for NeC, NeS, and NeT, respectively. All the exclusive regions overlap with important genes, such as SMARCD3, SLC15A1, and MAPK1. Key biological processes associated with the candidate genes were identified, including pathways related to growth and metabolism. Conclusion: This study revealed large variability in CNVs and CNVRs across three Nellore lines differentially selected for YW and RFI. Gene annotation and gene ontology analyses of the exclusive CNVRs to each line revealed specific genes and biological processes involved in the expression of growth and feed efficiency traits. These findings contribute to the understanding of the genetic mechanisms underlying the phenotypic differences among the three Nellore selection lines.
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Affiliation(s)
- Lorena F. Benfica
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, São Paulo, Brazil
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Ricardo D. do Bem
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, São Paulo, Brazil
| | | | - Henrique A. Mulim
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Larissa G. Braga
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, São Paulo, Brazil
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | | | - Sarah F. M. Bonilha
- Beef Cattle Research Center, Institute of Animal Science, Sertaozinho, São Paulo, Brazil
| | - Maria Eugenia Z. Mercadante
- Department of Animal Science, Faculty of Agricultural and Veterinary Sciences, Sao Paulo State University, Jaboticabal, São Paulo, Brazil
- Beef Cattle Research Center, Institute of Animal Science, Sertaozinho, São Paulo, Brazil
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2
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Lan C, Liu Y, Wu X, Wang B, Xin S, He Q, Zhong W, Liu Z. Susceptibility of ECE1 polymorphisms to Hirschsprung's disease in southern Chinese children. Front Pediatr 2022; 10:1056938. [PMID: 36619519 PMCID: PMC9813666 DOI: 10.3389/fped.2022.1056938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Hirschsprung's disease (HSCR) is currently considered to be a congenital gastrointestinal malformation caused mainly by genetic factors. Endothelin Converting Enzyme-1 (ECE1) has been reported to be associated with HSCR. However, the relationship between ECE1 single nucleotide polymorphism (SNP) rs169884 and HSCR in the southern Chinese population remains unknown. METHODS 1,470 HSCR patients and 1,473 controls from a southern Chinese population were recruited. The intronic SNP rs169884 in ECE1 was genotyped in all samples. We tested the association between rs169884 and HSCR under various genetic models. We also evaluated the effect of rs169884 on HSCR subtypes, including short-segment HSCR (S-HSCR), long-segment HSCR (L-HSCR) and total colonic aganglionosis (TCA). External epigenetic data were integrated to investigate the potential biological function of rs169884. RESULTS Chromatin states data from derived neuron cells or fetal colon tissue revealed that rs169884 might control ECE1 expression through regulating its enhancer function. We did not find a significant association between rs169884 and HSCR. For HSCR subtypes, although no significant associations were detected between rs169884 and S-HSCR (OR = 1.00, 95% CI: 0.89∼1.12, Padj = 0.77) or TCA (OR = 1.00, 95% CI: 0.72∼1.38, Padj = 0.94), we found that rs169884 could increase the risk of L-HSCR (OR = 1.23, 95% CI 1.02∼1.45, Padj = 0.024). CONCLUSION These results suggested that rs169884 might play a regulatory role for ECE1 expression and increase susceptibility of L-HSCR in southern Chinese children.
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Affiliation(s)
- Chaoting Lan
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yanqing Liu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiao Wu
- Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, China
| | - Bingtong Wang
- Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, China
| | | | - Qiuming He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wei Zhong
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zipeng Liu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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3
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Identification of Copy Number Alterations from Next-Generation Sequencing Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:55-74. [DOI: 10.1007/978-3-030-91836-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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4
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Zhong J, Liu J, Zheng Y, Xie X, He Q, Zhong W, Wu Q. miR-938 rs2505901 T>C polymorphism increases Hirschsprung disease risk: a case-control study of Chinese children. Per Med 2021; 18:551-558. [PMID: 34761964 DOI: 10.2217/pme-2021-0001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To explore the association between miR-938 rs2505901 T>C polymorphism and Hirschsprung disease (HSCR) risk in Chinese children. Materials & Methods: We conducted a case-control study in a Chinese population with 1381 cases and 1457 controls. The associated correlation strengths were assessed by adjusted odds ratios (AORs) and 95% CIs. Results: The results revealed that the rs2505901 TC and rs2505901 TC/CC genotype were related to an increased HSCR risk compared to the risk contributed by the rs2505901 TT genotype. A stratification analysis showed that the rs2505901 TC/CC genotype promoted the progression of HSCR more significantly in patients with the short-segment HSCR subtype. Conclusion: Our study indicated that miR-938 rs2505901 T>C polymorphism is significantly associated with HSCR risk in Chinese children. This result needs to be confirmed with well-designed studies.
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Affiliation(s)
- Jun Zhong
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women & Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Jiabin Liu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women & Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Yi Zheng
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women & Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Xiaoli Xie
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women & Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Qiuming He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women & Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Wei Zhong
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women & Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Qiang Wu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women & Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
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5
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Birkhoff JC, Brouwer RWW, Kolovos P, Korporaal AL, Bermejo-Santos A, Boltsis I, Nowosad K, van den Hout MCGN, Grosveld FG, van IJcken WFJ, Huylebroeck D, Conidi A. Targeted chromatin conformation analysis identifies novel distal neural enhancers of ZEB2 in pluripotent stem cell differentiation. Hum Mol Genet 2021; 29:2535-2550. [PMID: 32628253 PMCID: PMC7471508 DOI: 10.1093/hmg/ddaa141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/25/2022] Open
Abstract
The transcription factor zinc finger E-box binding protein 2 (ZEB2) controls embryonic and adult cell fate decisions and cellular maturation in many stem/progenitor cell types. Defects in these processes in specific cell types underlie several aspects of Mowat–Wilson syndrome (MOWS), which is caused by ZEB2 haplo-insufficiency. Human ZEB2, like mouse Zeb2, is located on chromosome 2 downstream of a ±3.5 Mb-long gene-desert, lacking any protein-coding gene. Using temporal targeted chromatin capture (T2C), we show major chromatin structural changes based on mapping in-cis proximities between the ZEB2 promoter and this gene desert during neural differentiation of human-induced pluripotent stem cells, including at early neuroprogenitor cell (NPC)/rosette state, where ZEB2 mRNA levels increase significantly. Combining T2C with histone-3 acetylation mapping, we identified three novel candidate enhancers about 500 kb upstream of the ZEB2 transcription start site. Functional luciferase-based assays in heterologous cells and NPCs reveal co-operation between these three enhancers. This study is the first to document in-cis Regulatory Elements located in ZEB2’s gene desert. The results further show the usability of T2C for future studies of ZEB2 REs in differentiation and maturation of multiple cell types and the molecular characterization of newly identified MOWS patients that lack mutations in ZEB2 protein-coding exons.
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Affiliation(s)
- Judith C Birkhoff
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Rutger W W Brouwer
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands.,Center for Biomics, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis 68100, Greece
| | - Anne L Korporaal
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Ana Bermejo-Santos
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Ilias Boltsis
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Karol Nowosad
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands.,Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin 20-093, Poland
| | - Mirjam C G N van den Hout
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands.,Center for Biomics, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Wilfred F J van IJcken
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands.,Center for Biomics, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven B-3000, Belgium
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, CN 3015, The Netherlands
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6
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Kuil LE, MacKenzie KC, Tang CS, Windster JD, Le TL, Karim A, de Graaf BM, van der Helm R, van Bever Y, Sloots CEJ, Meeussen C, Tibboel D, de Klein A, Wijnen RMH, Amiel J, Lyonnet S, Garcia-Barcelo MM, Tam PKH, Alves MM, Brooks AS, Hofstra RMW, Brosens E. Size matters: Large copy number losses in Hirschsprung disease patients reveal genes involved in enteric nervous system development. PLoS Genet 2021; 17:e1009698. [PMID: 34358225 PMCID: PMC8372947 DOI: 10.1371/journal.pgen.1009698] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 08/18/2021] [Accepted: 07/06/2021] [Indexed: 12/24/2022] Open
Abstract
Hirschsprung disease (HSCR) is a complex genetic disease characterized by absence of ganglia in the intestine. HSCR etiology can be explained by a unique combination of genetic alterations: rare coding variants, predisposing haplotypes and Copy Number Variation (CNV). Approximately 18% of patients have additional anatomical malformations or neurological symptoms (HSCR-AAM). Pinpointing the responsible culprits within a CNV is challenging as often many genes are affected. Therefore, we selected candidate genes based on gene enrichment strategies using mouse enteric nervous system transcriptomes and constraint metrics. Next, we used a zebrafish model to investigate whether loss of these genes affects enteric neuron development in vivo. This study included three groups of patients, two groups without coding variants in disease associated genes: HSCR-AAM and HSCR patients without associated anomalies (HSCR-isolated). The third group consisted of all HSCR patients in which a confirmed pathogenic rare coding variant was identified. We compared these patient groups to unaffected controls. Predisposing haplotypes were determined, confirming that every HSCR subgroup had increased contributions of predisposing haplotypes, but their contribution was highest in isolated HSCR patients without RET coding variants. CNV profiling proved that specifically HSCR-AAM patients had larger Copy Number (CN) losses. Gene enrichment strategies using mouse enteric nervous system transcriptomes and constraint metrics were used to determine plausible candidate genes located within CN losses. Validation in zebrafish using CRISPR/Cas9 targeting confirmed the contribution of UFD1L, TBX2, SLC8A1, and MAPK8 to ENS development. In addition, we revealed epistasis between reduced Ret and Gnl1 expression and between reduced Ret and Tubb5 expression in vivo. Rare large CN losses—often de novo—contribute to HSCR in HSCR-AAM patients. We proved the involvement of six genes in enteric nervous system development and Hirschsprung disease. Hirschsprung disease is a congenital disorder characterized by the absence of intestinal neurons in the distal part of the intestine. It is a complex genetic disorder in which multiple variations in our genome combined, result in disease. One of these variations are Copy Number Variations (CNVs): large segments of our genome that are duplicated or deleted. Patients often have Hirschsprung disease without other symptoms. However, a proportion of patients has additional associated anatomical malformations and neurological symptoms. We found that CNVs, present in patients with associated anomalies, are more often larger compared to unaffected controls or Hirschsprung patients without other symptoms. Furthermore, Copy Number (CN) losses are enriched for constrained coding regions (CCR; genes usually not impacted by genomic alterations in unaffected controls) of which the expression is higher in the developing intestinal neurons compared to the intestine. We modelled loss of these candidate genes in zebrafish by disrupting the zebrafish orthologues by genome editing. For several genes this resulted in changes in intestinal neuron development, reminiscent of HSCR observed in patients. The results presented here highlight the importance of Copy Number profiling, zebrafish validation and evaluating all CCR expressed in developing intestinal neurons during diagnostic evaluation.
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Affiliation(s)
- Laura E. Kuil
- Department of Clinical Genetics, Erasmus MC–Sophia Children’s Hospital, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Katherine C. MacKenzie
- Department of Clinical Genetics, Erasmus MC–Sophia Children’s Hospital, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Clara S. Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Li Dak-Sum Research Centre, The University of Hong Kong–Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong, China
| | - Jonathan D. Windster
- Department of Clinical Genetics, Erasmus MC–Sophia Children’s Hospital, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Paediatric Surgery, Erasmus MC–Sophia Children’s Hospital, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Thuy Linh Le
- Laboratory of embryology and genetics of malformations, Institut Imagine Université de Paris INSERM UMR1163 Necker Enfants malades University Hospital, Paris, France
| | - Anwarul Karim
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Bianca M. de Graaf
- Department of Clinical Genetics, Erasmus MC–Sophia Children’s Hospital, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Robert van der Helm
- Department of Clinical Genetics, Erasmus MC–Sophia Children’s Hospital, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Yolande van Bever
- Department of Clinical Genetics, Erasmus MC–Sophia Children’s Hospital, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Cornelius E. J. Sloots
- Department of Paediatric Surgery, Erasmus MC–Sophia Children’s Hospital, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Conny Meeussen
- Department of Paediatric Surgery, Erasmus MC–Sophia Children’s Hospital, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Dick Tibboel
- Department of Paediatric Surgery, Erasmus MC–Sophia Children’s Hospital, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC–Sophia Children’s Hospital, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - René M. H. Wijnen
- Department of Paediatric Surgery, Erasmus MC–Sophia Children’s Hospital, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jeanne Amiel
- Laboratory of embryology and genetics of malformations, Institut Imagine Université de Paris INSERM UMR1163 Necker Enfants malades University Hospital, Paris, France
| | - Stanislas Lyonnet
- Laboratory of embryology and genetics of malformations, Institut Imagine Université de Paris INSERM UMR1163 Necker Enfants malades University Hospital, Paris, France
| | | | - Paul K. H. Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Li Dak-Sum Research Centre, The University of Hong Kong–Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong, China
| | - Maria M. Alves
- Department of Clinical Genetics, Erasmus MC–Sophia Children’s Hospital, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Alice S. Brooks
- Department of Clinical Genetics, Erasmus MC–Sophia Children’s Hospital, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Robert M. W. Hofstra
- Department of Clinical Genetics, Erasmus MC–Sophia Children’s Hospital, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Stem Cells and Regenerative Medicine, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC–Sophia Children’s Hospital, University Medical Center Rotterdam, Rotterdam, The Netherlands
- * E-mail:
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7
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Karim A, Tang CSM, Tam PKH. The Emerging Genetic Landscape of Hirschsprung Disease and Its Potential Clinical Applications. Front Pediatr 2021; 9:638093. [PMID: 34422713 PMCID: PMC8374333 DOI: 10.3389/fped.2021.638093] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 07/02/2021] [Indexed: 12/25/2022] Open
Abstract
Hirschsprung disease (HSCR) is the leading cause of neonatal functional intestinal obstruction. It is a rare congenital disease with an incidence of one in 3,500-5,000 live births. HSCR is characterized by the absence of enteric ganglia in the distal colon, plausibly due to genetic defects perturbing the normal migration, proliferation, differentiation, and/or survival of the enteric neural crest cells as well as impaired interaction with the enteric progenitor cell niche. Early linkage analyses in Mendelian and syndromic forms of HSCR uncovered variants with large effects in major HSCR genes including RET, EDNRB, and their interacting partners in the same biological pathways. With the advances in genome-wide genotyping and next-generation sequencing technologies, there has been a remarkable progress in understanding of the genetic basis of HSCR in the past few years, with common and rare variants with small to moderate effects being uncovered. The discovery of new HSCR genes such as neuregulin and BACE2 as well as the deeper understanding of the roles and mechanisms of known HSCR genes provided solid evidence that many HSCR cases are in the form of complex polygenic/oligogenic disorder where rare variants act in the sensitized background of HSCR-associated common variants. This review summarizes the roadmap of genetic discoveries of HSCR from the earlier family-based linkage analyses to the recent population-based genome-wide analyses coupled with functional genomics, and how these discoveries facilitated our understanding of the genetic architecture of this complex disease and provide the foundation of clinical translation for precision and stratified medicine.
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Affiliation(s)
- Anwarul Karim
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Clara Sze-Man Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Li Dak-Sum Research Center, The University of Hong Kong—Karolinska Institute Collaboration in Regenerative Medicine, Hong Kong, China
| | - Paul Kwong-Hang Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Li Dak-Sum Research Center, The University of Hong Kong—Karolinska Institute Collaboration in Regenerative Medicine, Hong Kong, China
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8
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Bahrami R, Shajari A, Aflatoonian M, Noorishadkam M, Akbarian-Bafghi MJ, Morovati-Sharifabad M, Heiranizadeh N, Neamatzadeh H. Association of REarranged during Transfection (RET) c.73 + 9277T > C and c.135G > a Polymorphisms with Susceptibility to Hirschsprung Disease: A Systematic Review and Meta-Analysis. Fetal Pediatr Pathol 2020; 39:476-490. [PMID: 31590591 DOI: 10.1080/15513815.2019.1672225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Background: Previous studies have suggested a close association between REarranged during Transfection (RET) c.73 + 9277T > C and c.135G > A polymorphisms and Hirschsprung disease (HSCR) susceptibility. The results are inconsistent and contradictory. Thus, we performed a meta-analysis to evaluate the association of RET c.73 + 9277T > C and c.135G > A polymorphisms with risk of HSCR.Methods: The eligible literatures were searched by PubMed, Google Scholar, EMBASE, and CNKI up to August 5 2019.Results: A total of 20 studies including 10 studies with 1136 cases and 2420 controls on c.73 + 9277T > C and 10 studies with 917 cases and 1159 controls on c.135G > A were selected. Pooled ORs revealed that c.73 + 9277T > C and c.135G > A polymorphisms were significantly associated with an increased risk of HSCR. Moreover, stratified analysis revealed that c.73 + 9277T > C and c.135G > A polymorphisms were associated with HSCR risk in Asian, Caucasian and Chinese populations.Conclusions: This meta-analysis result indicated that the RET c.73 + 9277T > C and c.135G > A polymorphisms were associated with susceptibility to HSCR.
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Affiliation(s)
- Reza Bahrami
- Neonatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Shajari
- Department of Pediatrics, Yazd Branch, Islamic Azad University, Yazd, Iran
| | - Majid Aflatoonian
- Department of Pediatrics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mahmood Noorishadkam
- Department of Pediatrics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | | | - Naeimeh Heiranizadeh
- Department of Surgery, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Hossein Neamatzadeh
- Department of Medical Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Mother and Newborn Health Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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9
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Rao J, Peng L, Liang X, Jiang H, Geng C, Zhao X, Liu X, Fan G, Chen F, Mu F. Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms. BMC Bioinformatics 2020; 21:518. [PMID: 33176676 PMCID: PMC7659224 DOI: 10.1186/s12859-020-03859-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 11/03/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND DNBSEQ™ platforms are new massively parallel sequencing (MPS) platforms that use DNA nanoball technology. Use of data generated from DNBSEQ™ platforms to detect single nucleotide variants (SNVs) and small insertions and deletions (indels) has proven to be quite effective, while the feasibility of copy number variants (CNVs) detection is unclear. RESULTS Here, we first benchmarked different CNV detection tools based on Illumina whole-genome sequencing (WGS) data of NA12878 and then assessed these tools in CNV detection based on DNBSEQ™ sequencing data from the same sample. When the same tool was used, the CNVs detected based on DNBSEQ™ and Illumina data were similar in quantity, length and distribution, while great differences existed within results from different tools and even based on data from a single platform. We further estimated the CNV detection power based on available CNV benchmarks of NA12878 and found similar precision and sensitivity between the DNBSEQ™ and Illumina platforms. We also found higher precision of CNVs shorter than 1 kbp based on DNBSEQ™ platforms than those based on Illumina platforms by using Pindel, DELLY and LUMPY. We carefully compared these two available benchmarks and found a large proportion of specific CNVs between them. Thus, we constructed a more complete CNV benchmark of NA12878 containing 3512 CNV regions. CONCLUSIONS We assessed and benchmarked CNV detections based on WGS with DNBSEQ™ platforms and provide guidelines for future studies.
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Affiliation(s)
- Junhua Rao
- MGI, BGI-Shenzhen, Shenzhen, 518083, China
| | | | | | - Hui Jiang
- MGI, BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Xia Zhao
- MGI, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, 518083, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, Shandong, China.,IGDB-BGI Joint Center for Omics, BGI-Shenzhen, Shenzhen, 518083, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, Shandong, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Fang Chen
- MGI, BGI-Shenzhen, Shenzhen, 518083, China. .,BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Feng Mu
- MGI, BGI-Shenzhen, Shenzhen, 518083, China. .,MGI-Wuhan, BGI-Shenzhen, Wuhan, 430074, China.
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10
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Ma X, Sun J, Zhu S, Du Z, Li D, Li W, Li Z, Tian Y, Kang X, Sun G. MiRNAs and mRNAs Analysis during Abdominal Preadipocyte Differentiation in Chickens. Animals (Basel) 2020; 10:ani10030468. [PMID: 32168898 PMCID: PMC7143929 DOI: 10.3390/ani10030468] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/02/2020] [Accepted: 03/07/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary We sequenced the miRNAs and mRNAs of preabdominal fat cells and differentiated adipocytes, and target genes of miRNA combined with mRNA transcriptome data jointly. We found that the MAPK signal pathway, insulin signal pathway, fatty acid metabolism, ECM( extracellular matrix)–receptor interaction, and other signal pathways were involved in the differentiation of preabdominal fat cells. In addition, we found that some miRNAs–mRNAs combinations were strongly related to the differentiation of fat cells (miR-214−ACSBG2, NFKB2, CAMK2A, ACLY, CCND3, PLK3, ITGB2; miR-148a-5p−ROCK2; miR-10a-5p−ELOVL5; miR-146b-5p−LAMA4; miR-6615-5p−FLNB; miR-1774−COL6A1). Our findings provide important resources for the study of adipocyte differentiation. Abstract The excessive deposition of abdominal fat has become an important factor in restricting the production efficiency of chickens, so reducing abdominal fat deposition is important for improving growth rate. It has been proven that miRNAs play an important role in regulating many physiological processes of organisms. In this study, we constructed a model of adipogenesis by isolating preadipocytes (Ab-Pre) derived from abdominal adipose tissue and differentiated adipocytes (Ab-Ad) in vitro. Deep sequencing of miRNAs and mRNAs expressed in Ab-Pre and Ab-Ad groups was conducted to explore the effect of miRNAs and mRNAs on fat deposition. We identified 80 differentially expressed miRNAs (DEMs) candidates, 58 of which were up-regulated and 22 down-regulated. Furthermore, six miRNAs and six mRNAs were verified by qRT-PCR, and the results showed that the expression of the DEMs and differentially expressed genes (DEGs) in the two groups was consistent with our sequencing results. When target genes of miRNA were combined with mRNA transcriptome data, a total of 891 intersection genes were obtained, we predicted the signal pathways of cross genes enrichment to the MAPK signal pathway, insulin signal pathway, fatty acid metabolism, and ECM–receptor interaction. Meanwhile, we constructed miRNA and negatively correlated mRNA target networks, including 12 miRNA–mRNAs pairs, which showed a strong association with the abdominal adipocyte differentiation (miR-214−ACSBG2, NFKB2, CAMK2A, ACLY, CCND3, PLK3, ITGB2; miR-148a-5p−ROCK2; miR-10a-5p−ELOVL5; miR-146b-5p−LAMA4; miR-6615-5p−FLNB; miR-1774−COL6A1). Overall, these findings provide a background for further research on lipid metabolism. Thus, we can better understand the molecular genetic mechanism of chicken abdominal fat deposition.
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11
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Wang Y, Jiang Q, Chakravarti A, Cai H, Xu Z, Wu W, Gu B, Li L, Cai W. MicroRNA-4516-mediated regulation of MAPK10 relies on 3' UTR cis-acting variants and contributes to the altered risk of Hirschsprung disease. J Med Genet 2020; 57:634-642. [PMID: 32066630 DOI: 10.1136/jmedgenet-2019-106615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/18/2019] [Accepted: 01/18/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Hirschsprung disease (HSCR) is a life-threatening congenital disorder in which the enteric nervous system is completely missing from the distal gut. Recent studies have shown that miR-4516 markedly inhibits cell migration, and as one of its potential targets, MAPK10 functions as a modifier for developing HSCR. We thus aimed to evaluate the role of miR-4516 and MAPK10 in HSCR and how they contribute to the pathogenesis of HSCR. METHODS We examined 13 genetic variants using the MassArray system in a case-control study (n=1015). We further investigated miR-4516-mediated regulation of MAPK10 in HSCR cases and human neural cells, the effects of cis-acting elements in MAPK10 on miR-4516-mediated modulation and cell migration process. RESULTS Three positive 3' UTR variants in MAPK10 were associated with altered HSCR susceptibility. We also showed that miR-4516 directly regulates MAPK10 expression, and this regulatory mechanism is significantly affected by the 3' UTR cis-acting elements of MAPK10. In addition, knock-down of MAPK10 rescued the effect of miR-4516 on the migration of human neural cells. CONCLUSION Our findings indicate a key role of miR-4516 and its direct target MAPK10 in HSCR risk, and highlight the general importance of cis- and posttranscriptional modulation for 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 .,Department of Pediatric Gastroenterology, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Qian Jiang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, China
| | - Aravinda Chakravarti
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, New York, USA
| | - Hao Cai
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Department of Pediatric Gastroenterology, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China
| | - Ze Xu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Department of Pediatric Gastroenterology, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China
| | - Wenjie Wu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Department of Pediatric Gastroenterology, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, China
| | - Beilin Gu
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Long Li
- Department of General Surgery, Capital Institute of Pediatrics Affiliated Children's Hospital, Beijing, China
| | - Wei Cai
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China .,Department of Pediatric Gastroenterology, Shanghai Institute for Pediatric Research, Shanghai, China
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12
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Lantieri F, Gimelli S, Viaggi C, Stathaki E, Malacarne M, Santamaria G, Grossi A, Mosconi M, Sloan-Béna F, Prato AP, Coviello D, Ceccherini I. Copy number variations in candidate genomic regions confirm genetic heterogeneity and parental bias in Hirschsprung disease. Orphanet J Rare Dis 2019; 14:270. [PMID: 31767031 PMCID: PMC6878652 DOI: 10.1186/s13023-019-1205-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 09/13/2019] [Indexed: 11/26/2022] Open
Abstract
Background Hirschsprung Disease (HSCR) is a congenital defect of the intestinal innervations characterized by complex inheritance. Many susceptibility genes including RET, the major HSCR gene, and several linked regions and associated loci have been shown to contribute to disease pathogenesis. Nonetheless, a proportion of patients still remains unexplained. Copy Number Variations (CNVs) have already been involved in HSCR, and for this reason we performed Comparative Genomic Hybridization (CGH), using a custom array with high density probes. Results A total of 20 HSCR candidate regions/genes was tested in 55 sporadic patients and four patients with already known chromosomal aberrations. Among 83 calls, 12 variants were experimentally validated, three of which involving the HSCR crucial genes SEMA3A/3D, NRG1, and PHOX2B. Conversely RET involvement in HSCR does not seem to rely on the presence of CNVs while, interestingly, several gains and losses did co-occur with another RET defect, thus confirming that more than one predisposing event is necessary for HSCR to develop. New loci were also shown to be involved, such as ALDH1A2, already found to play a major role in the enteric nervous system. Finally, all the inherited CNVs were of maternal origin. Conclusions Our results confirm a wide genetic heterogeneity in HSCR occurrence and support a role of candidate genes in expression regulation and cell signaling, thus contributing to depict further the molecular complexity of the genomic regions involved in the Enteric Nervous System development. The observed maternal transmission bias for HSCR associated CNVs supports the hypothesis that in females these variants might be more tolerated, requiring additional alterations to develop HSCR disease.
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Affiliation(s)
- Francesca Lantieri
- Dipartimento di Scienze della Salute, sezione di Biostatistica, Universita' degli Studi di Genova, 16132, Genoa, Italy
| | - Stefania Gimelli
- Department of Medical Genetic and Laboratories, University Hospitals of Geneva, Geneva, Switzerland
| | - Chiara Viaggi
- S.C. Laboratorio Genetica Umana, Ospedali Galliera, Genoa, Italy
| | - Elissavet Stathaki
- Department of Medical Genetic and Laboratories, University Hospitals of Geneva, Geneva, Switzerland
| | - Michela Malacarne
- S.C. Laboratorio Genetica Umana, Ospedali Galliera, Genoa, Italy.,Present address: U.O.C. Laboratorio di Genetica Umana, IRCCS Istituto Giannina Gaslini, Genoa, 16148, Italy
| | - Giuseppe Santamaria
- U.O.C. Genetica Medica, IRCCS, Istituto Giannina Gaslini, 16148, Genoa, Italy
| | - Alice Grossi
- U.O.C. Genetica Medica, IRCCS, Istituto Giannina Gaslini, 16148, Genoa, Italy
| | - Manuela Mosconi
- UOC Chirurgia Pediatrica, Istituto Giannina Gaslini, 16148, Genoa, Italy
| | - Frédérique Sloan-Béna
- Department of Medical Genetic and Laboratories, University Hospitals of Geneva, Geneva, Switzerland
| | - Alessio Pini Prato
- UOC Chirurgia Pediatrica, Istituto Giannina Gaslini, 16148, Genoa, Italy.,Present address: Children Hospital, AON SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Domenico Coviello
- S.C. Laboratorio Genetica Umana, Ospedali Galliera, Genoa, Italy.,Present address: U.O.C. Laboratorio di Genetica Umana, IRCCS Istituto Giannina Gaslini, Genoa, 16148, Italy
| | - Isabella Ceccherini
- U.O.C. Genetica Medica, IRCCS, Istituto Giannina Gaslini, 16148, Genoa, Italy.
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13
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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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14
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Null mutation of the endothelin receptor type B gene causes embryonic death in the GK rat. PLoS One 2019; 14:e0217132. [PMID: 31170185 PMCID: PMC6553694 DOI: 10.1371/journal.pone.0217132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 05/06/2019] [Indexed: 12/28/2022] Open
Abstract
The Hirschsprung disease (HSCR) is an inherited disease that is controlled by multiple genes and has a complicated genetic mechanism. HSCR patients suffer from various extents of constipation due to dysplasia of the enteric nervous system (ENS), which can be so severe as to cause complete intestinal obstruction. Many genes have been identified as playing causative roles in ENS dysplasia and HSCR, among them the endothelin receptor type B gene (Ednrb) has been identified to play an important role. Mutation of Ednrb causes a series of symptoms that include deafness, pigmentary abnormalities, and aganglionosis. In our previous studies of three rat models carrying the same spotting lethal (sl) mutation on Ednrb, the haplotype of a region on chromosome (Chr) 2 was found to be responsible for the differing severities of the HSCR-like symptoms. To confirm that the haplotype of the responsible region on Chr 2 modifies the severity of aganglionosis caused by Ednrb mutation and to recreate a rat model with severe symptoms, we selected the GK inbred strain, whose haplotype in the responsible region on Chr 2 resembles that of the rat strain in which severe symptoms accompany the Ednrbsl mutation. An Ednrb mutation was introduced into the GK rat by crossing with F344-Ednrbsl and by genome editing. The null mutation of Ednrb was found to cause embryonic death in F2 progeny possessing the GK haplotype in the responsible region on Chr 2. The results of this study are unexpected, and they provide new clues and animal models that promise to contribute to studies on the genetic regulatory network in the development of ENS and on embryogenesis.
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15
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Porokuokka LL, Virtanen HT, Lindén J, Sidorova Y, Danilova T, Lindahl M, Saarma M, Andressoo JO. Gfra1 Underexpression Causes Hirschsprung's Disease and Associated Enterocolitis in Mice. Cell Mol Gastroenterol Hepatol 2018; 7:655-678. [PMID: 30594740 PMCID: PMC6444303 DOI: 10.1016/j.jcmgh.2018.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 12/19/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS RET, the receptor for the glial cell line-derived neurotrophic factor (GDNF) family ligands, is the most frequently mutated gene in congenital aganglionic megacolon or Hirschsprung's disease (HSCR). The leading cause of mortality in HSCR is HSCR-associated enterocolitis (HAEC), which is characterized by altered mucin composition, mucin retention, bacterial adhesion to enterocytes, and epithelial damage, although the order of these events is obscure. In mice, loss of GDNF signaling leads to a severely underdeveloped enteric nervous system and neonatally fatal kidney agenesis, thereby precluding the use of these mice for modeling postnatal HSCR and HAEC. Our aim was to generate a postnatally viable mouse model for HSCR/HAEC and analyze HAEC etiology. METHODS GDNF family receptor alpha-1 (GFRa1) hypomorphic mice were generated by placing a selectable marker gene in the sixth intron of the Gfra1 locus using gene targeting in mouse embryonic stem cells. RESULTS We report that 70%-80% reduction in GDNF co-receptor GFRa1 expression levels in mice results in HSCR and HAEC, leading to death within the first 25 postnatal days. These mice mirror the disease progression and histopathologic findings in children with untreated HSCR/HAEC. CONCLUSIONS In GFRa1 hypomorphic mice, HAEC proceeds from goblet cell dysplasia, with abnormal mucin production and retention, to epithelial damage. Microbial enterocyte adherence and tissue invasion are late events and therefore unlikely to be the primary cause of HAEC. These results suggest that goblet cells may be a potential target for preventative treatment and that reduced expression of GFRa1 may contribute to HSCR susceptibility.
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Affiliation(s)
| | - Heikki T Virtanen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jere Lindén
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Yulia Sidorova
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Tatiana Danilova
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Maria Lindahl
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Mart Saarma
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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16
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Theofanopoulou C, Gastaldon S, O’Rourke T, Samuels BD, Messner A, Martins PT, Delogu F, Alamri S, Boeckx C. Self-domestication in Homo sapiens: Insights from comparative genomics. PLoS One 2017; 12:e0185306. [PMID: 29045412 PMCID: PMC5646786 DOI: 10.1371/journal.pone.0185306] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/11/2017] [Indexed: 02/07/2023] Open
Abstract
This study identifies and analyzes statistically significant overlaps between selective sweep screens in anatomically modern humans and several domesticated species. The results obtained suggest that (paleo-)genomic data can be exploited to complement the fossil record and support the idea of self-domestication in Homo sapiens, a process that likely intensified as our species populated its niche. Our analysis lends support to attempts to capture the "domestication syndrome" in terms of alterations to certain signaling pathways and cell lineages, such as the neural crest.
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Affiliation(s)
- Constantina Theofanopoulou
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute for Complex Systems, Barcelona, Spain
| | - Simone Gastaldon
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
- School of Psychology, University of Padova, Padova, Italy
| | - Thomas O’Rourke
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
| | - Bridget D. Samuels
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, United States of America
| | - Angela Messner
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
| | | | - Francesco Delogu
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Saleh Alamri
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
| | - Cedric Boeckx
- Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain
- Universitat de Barcelona Institute for Complex Systems, Barcelona, Spain
- ICREA, Barcelona, Spain
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17
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Bahrami A, Joodi M, Moetamani-Ahmadi M, Maftouh M, Hassanian SM, Ferns GA, Avan A. Genetic Background of Hirschsprung Disease: A Bridge Between Basic Science and Clinical Application. J Cell Biochem 2017; 119:28-33. [PMID: 28543993 DOI: 10.1002/jcb.26149] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/18/2017] [Indexed: 01/04/2023]
Abstract
Hirschsprung's disease (HSCR) is a congenital disorder, defined by partial or complete loss of the neuronal ganglion cells in the intestinal tract, which is caused by the failure of neural crest cells to migrate completely during intestinal development during fetal life. HSCR has a multifactorial etiology, and genetic factors play a key role in its pathogenesis; these include mutations within several gene loci. These have been identified by screening candidate genes, or by conducting genome wide association (GWAS) studies. However, only a small portion of them have been proposed as major genetic risk factors for the HSCR. In this review, we focus on those genes that have been identified as either low penetrant or high penetrant variants that determine the risk of Hirschsprung's disease. J. Cell. Biochem. 119: 28-33, 2018. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Afsane Bahrami
- Department of Modern Sciences and Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Marjan Joodi
- Department of Pediatric Surgery, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Sarvar Children's Hospital, Endoscopic and Minimally Invasive Surgery Research Center, Mashhad, Iran
| | - Mehrdad Moetamani-Ahmadi
- Department of Modern Sciences and Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Iran
| | - Mina Maftouh
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Division of Medical Education, Brighton and Sussex Medical School, Falmer, Brighton, Sussex BN1 9PH, United Kingdom
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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18
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Zare F, Dow M, Monteleone N, Hosny A, Nabavi S. An evaluation of copy number variation detection tools for cancer using whole exome sequencing data. BMC Bioinformatics 2017; 18:286. [PMID: 28569140 PMCID: PMC5452530 DOI: 10.1186/s12859-017-1705-x] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/22/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Recently copy number variation (CNV) has gained considerable interest as a type of genomic/genetic variation that plays an important role in disease susceptibility. Advances in sequencing technology have created an opportunity for detecting CNVs more accurately. Recently whole exome sequencing (WES) has become primary strategy for sequencing patient samples and study their genomics aberrations. However, compared to whole genome sequencing, WES introduces more biases and noise that make CNV detection very challenging. Additionally, tumors' complexity makes the detection of cancer specific CNVs even more difficult. Although many CNV detection tools have been developed since introducing NGS data, there are few tools for somatic CNV detection for WES data in cancer. RESULTS In this study, we evaluated the performance of the most recent and commonly used CNV detection tools for WES data in cancer to address their limitations and provide guidelines for developing new ones. We focused on the tools that have been designed or have the ability to detect cancer somatic aberrations. We compared the performance of the tools in terms of sensitivity and false discovery rate (FDR) using real data and simulated data. Comparative analysis of the results of the tools showed that there is a low consensus among the tools in calling CNVs. Using real data, tools show moderate sensitivity (~50% - ~80%), fair specificity (~70% - ~94%) and poor FDRs (~27% - ~60%). Also, using simulated data we observed that increasing the coverage more than 10× in exonic regions does not improve the detection power of the tools significantly. CONCLUSIONS The limited performance of the current CNV detection tools for WES data in cancer indicates the need for developing more efficient and precise CNV detection methods. Due to the complexity of tumors and high level of noise and biases in WES data, employing advanced novel segmentation, normalization and de-noising techniques that are designed specifically for cancer data is necessary. Also, CNV detection development suffers from the lack of a gold standard for performance evaluation. Finally, developing tools with user-friendly user interfaces and visualization features can enhance CNV studies for a broader range of users.
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Affiliation(s)
- Fatima Zare
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA
| | - Michelle Dow
- Biomedical Informatics Department, University of California San Diego, San Diego, CA, USA
| | - Nicholas Monteleone
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA
| | - Abdelrahman Hosny
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA
| | - Sheida Nabavi
- Computer Science and Engineering Department and Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
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19
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Partial microduplication in the histone acetyltransferase complex member KANSL1 is associated with congenital heart defects in 22q11.2 microdeletion syndrome patients. Sci Rep 2017; 7:1795. [PMID: 28496102 PMCID: PMC5431949 DOI: 10.1038/s41598-017-01896-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/06/2017] [Indexed: 12/16/2022] Open
Abstract
22q11.2 microdeletion syndrome (22q11.2DS) is the most common microdeletion disorder in humans, with an incidence of 1/4000 live births. It is caused by a heterozygous deletion of 1.5–3 Mb on chromosome region 22q11.2. Patients with the deletion present features that include neuropsychiatric problems, craniofacial abnormalities and cardiovascular malformations. However, the phenotype is highly variable and the factors related to the clinical heterogeneity are not fully understood. About 65% of patients with 22q11.2DS have congenital heart defects (CHD). The main goal of this study was to identify common CNVs in 22q11.2DS patients that could be associated with the incomplete penetrance of CHD. Analysis of genomic DNA from 253 patients with 22q11.2DS using array technology showed an association between a microduplication located in region 17q21.31 and CHD (p-value = 0.023, OR = 2.75, 95% CI = 1.17–7.03). This region includes the first three exons of KANSL1 gene. Bioinformatic analysis showed that KANSL1 and CRKL, a gene in the commonly deleted region of 22q11.2DS, are part of the same regulatory module in a miRNA-mRNA network. These results show that a KANSL1 microduplication, in combination with the 22q11.2 deletion, is associated with increased risk of CHD in these patients, suggesting that KANSL1 plays a role as a modifier gene in 22q11.2DS patients.
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20
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Baxter AL, Vivian JL, Hagelstrom RT, Hossain W, Golden WL, Wassman ER, Vanzo RJ, Butler MG. A Novel Partial Duplication of ZEB2 and Review of ZEB2 Involvement in Mowat-Wilson Syndrome. Mol Syndromol 2017; 8:211-218. [PMID: 28690488 DOI: 10.1159/000473693] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2017] [Indexed: 12/14/2022] Open
Abstract
Mowat-Wilson syndrome is a rare genetic condition characterized by intellectual disability, structural anomalies, and dysmorphic features. It is caused by haploinsufficiency of the ZEB2 gene in chromosome 2q22.3. Over 180 distinct mutations in ZEB2 have been reported, including nonsense and missense point mutations, deletions, and large chromosomal rearrangements. We report on a 14-year-old female with a clinical diagnosis of Mowat-Wilson syndrome. Chromosomal microarray identified a novel de novo 69-kb duplication containing exons 1 and 2 of the ZEB2 gene. Sequence analysis identified no other variants in this gene. This is the first report of a partial duplication of the ZEB2 gene resulting in Mowat-Wilson syndrome.
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Affiliation(s)
| | | | - R Tanner Hagelstrom
- Department of Human Genetics Laboratory, University of Nebraska Medical Center, Omaha, NE, USA
| | - Waheeda Hossain
- Department of Psychiatry and Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS
| | | | | | | | - Merlin G Butler
- Department of Psychiatry and Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS
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21
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Lantieri F, Malacarne M, Gimelli S, Santamaria G, Coviello D, Ceccherini I. Custom Array Comparative Genomic Hybridization: the Importance of DNA Quality, an Expert Eye, and Variant Validation. Int J Mol Sci 2017; 18:E609. [PMID: 28287439 PMCID: PMC5372625 DOI: 10.3390/ijms18030609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/01/2017] [Accepted: 03/07/2017] [Indexed: 12/16/2022] Open
Abstract
The presence of false positive and false negative results in the Array Comparative Genomic Hybridization (aCGH) design is poorly addressed in literature reports. We took advantage of a custom aCGH recently carried out to analyze its design performance, the use of several Agilent aberrations detection algorithms, and the presence of false results. Our study provides a confirmation that the high density design does not generate more noise than standard designs and, might reach a good resolution. We noticed a not negligible presence of false negative and false positive results in the imbalances call performed by the Agilent software. The Aberration Detection Method 2 (ADM-2) algorithm with a threshold of 6 performed quite well, and the array design proved to be reliable, provided that some additional filters are applied, such as considering only intervals with average absolute log₂ratio above 0.3. We also propose an additional filter that takes into account the proportion of probes with log₂ratio exceeding suggestive values for gain or loss. In addition, the quality of samples was confirmed to be a crucial parameter. Finally, this work raises the importance of evaluating the samples profiles by eye and the necessity of validating the imbalances detected.
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Affiliation(s)
- Francesca Lantieri
- Dipartimento di Scienzedella Salute, Sezione di Biostatistica, Università degli Studi di Genova, Via Pastore 1, 16132 Genoa, Italy.
| | - Michela Malacarne
- Struttura Complessa Laboratorio Genetica Umana, E.O. Ospedali Galliera, Via Volta 6, 16128 Genoa, Italy.
| | - Stefania Gimelli
- Department of Medical Genetic and Laboratories, University Hospitals of Geneva, Bâtiment de Base 8C-3-840.3, 4 Rue Gabrielle-Perret-Gentil, 1211 Geneva 14, Switzerland.
| | - Giuseppe Santamaria
- UOC Genetica Medica, Istituto Giannina Gaslini, L. go G. Gaslini 5, 16148 Genoa, Italy.
| | - Domenico Coviello
- Struttura Complessa Laboratorio Genetica Umana, E.O. Ospedali Galliera, Via Volta 6, 16128 Genoa, Italy.
| | - Isabella Ceccherini
- UOC Genetica Medica, Istituto Giannina Gaslini, L. go G. Gaslini 5, 16148 Genoa, Italy.
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22
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Gui H, Schriemer D, Cheng WW, Chauhan RK, Antiňolo G, Berrios C, Bleda M, Brooks AS, Brouwer RWW, Burns AJ, Cherny SS, Dopazo J, Eggen BJL, Griseri P, Jalloh B, Le TL, Lui VCH, Luzón-Toro B, Matera I, Ngan ESW, Pelet A, Ruiz-Ferrer M, Sham PC, Shepherd IT, So MT, Sribudiani Y, Tang CSM, van den Hout MCGN, van der Linde HC, van Ham TJ, van IJcken WFJ, Verheij JBGM, Amiel J, Borrego S, Ceccherini I, Chakravarti A, Lyonnet S, Tam PKH, Garcia-Barceló MM, Hofstra RMW. Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes. Genome Biol 2017; 18:48. [PMID: 28274275 PMCID: PMC5343413 DOI: 10.1186/s13059-017-1174-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/17/2017] [Indexed: 12/17/2022] Open
Abstract
Background Hirschsprung disease (HSCR), which is congenital obstruction of the bowel, results from a failure of enteric nervous system (ENS) progenitors to migrate, proliferate, differentiate, or survive within the distal intestine. Previous studies that have searched for genes underlying HSCR have focused on ENS-related pathways and genes not fitting the current knowledge have thus often been ignored. We identify and validate novel HSCR genes using whole exome sequencing (WES), burden tests, in silico prediction, unbiased in vivo analyses of the mutated genes in zebrafish, and expression analyses in zebrafish, mouse, and human. Results We performed de novo mutation (DNM) screening on 24 HSCR trios. We identify 28 DNMs in 21 different genes. Eight of the DNMs we identified occur in RET, the main HSCR gene, and the remaining 20 DNMs reside in genes not reported in the ENS. Knockdown of all 12 genes with missense or loss-of-function DNMs showed that the orthologs of four genes (DENND3, NCLN, NUP98, and TBATA) are indispensable for ENS development in zebrafish, and these results were confirmed by CRISPR knockout. These genes are also expressed in human and mouse gut and/or ENS progenitors. Importantly, the encoded proteins are linked to neuronal processes shared by the central nervous system and the ENS. Conclusions Our data open new fields of investigation into HSCR pathology and provide novel insights into the development of the ENS. Moreover, the study demonstrates that functional analyses of genes carrying DNMs are warranted to delineate the full genetic architecture of rare complex diseases. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1174-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongsheng Gui
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.,Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Duco Schriemer
- Department of Neuroscience, section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - William W Cheng
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.,Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands
| | - Rajendra K Chauhan
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands
| | - Guillermo Antiňolo
- 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
| | - Courtney Berrios
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Marta Bleda
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain.,Department of Medicine, School of Clinical Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands
| | - Rutger W W Brouwer
- Erasmus Center for Biomics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Alan J Burns
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands.,Stem Cells and Regenerative Medicine, Birth Defects Research Centre, UCL Institute of Child Health, London, UK
| | - Stacey S Cherny
- Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Joaquin Dopazo
- 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
| | - Bart J L Eggen
- Department of Neuroscience, section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Binta Jalloh
- Department of Biology, Emory University, Atlanta, USA
| | - Thuy-Linh Le
- Laboratory of embryology and genetics of human malformations, INSERM UMR 1163, Institut Imagine, Paris, France.,Department of Genetics, Paris Descartes-Sorbonne Paris Cité University, Hôpital Necker-Enfants Malades (APHP), Paris, France
| | - Vincent C H Lui
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - 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
| | - Ivana Matera
- UOC Genetica Medica, Istituto Gaslini, Genoa, Italy
| | - Elly S W Ngan
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Anna Pelet
- Laboratory of embryology and genetics of human malformations, INSERM UMR 1163, Institut Imagine, Paris, France.,Department of Genetics, Paris Descartes-Sorbonne Paris Cité University, Hôpital Necker-Enfants Malades (APHP), Paris, France
| | - Macarena Ruiz-Ferrer
- 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
| | - Pak C Sham
- Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | | | - Man-Ting So
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Yunia Sribudiani
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands.,Department of Biochemistry and Molecular Biology, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Clara S M Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | | | - Herma C van der Linde
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands
| | - Tjakko J van Ham
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands
| | | | - Joke B G M Verheij
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jeanne Amiel
- Laboratory of embryology and genetics of human malformations, INSERM UMR 1163, Institut Imagine, Paris, France.,Department of Genetics, Paris Descartes-Sorbonne Paris Cité University, Hôpital Necker-Enfants Malades (APHP), 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
| | | | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Stanislas Lyonnet
- Laboratory of embryology and genetics of human malformations, INSERM UMR 1163, Institut Imagine, Paris, France.,Department of Genetics, Paris Descartes-Sorbonne Paris Cité University, Hôpital Necker-Enfants Malades (APHP), Paris, France
| | - Paul K H Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Maria-Mercè Garcia-Barceló
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.
| | - Robert M W Hofstra
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands. .,Stem Cells and Regenerative Medicine, Birth Defects Research Centre, UCL Institute of Child Health, London, UK.
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23
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Yang D, Yang J, Li S, Jiang M, Cao G, Yang L, Zhang X, Zhou Y, Li K, Tang ST. Effects of RET, NRG1 and NRG3 Polymorphisms in a Chinese Population with Hirschsprung Disease. Sci Rep 2017; 7:43222. [PMID: 28256518 PMCID: PMC5335705 DOI: 10.1038/srep43222] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/20/2017] [Indexed: 12/12/2022] Open
Abstract
The RET proto-oncogene was identified as a major locus involved in Hirschsprung disease (HSCR). A genome-wide association study (GWAS) and whole exome sequencing identified NRG1 and NRG3 as additional HSCR susceptibility loci. We investigated the effects of RET (rs2506030 and rs2435357), NRG1 (rs2439302, rs16879552 and rs7835688) and NRG3 (rs10748842, rs10883866 and rs6584400) polymorphisms in a Chinese population with HSCR. We assessed single nucleotide polymorphisms (SNPs) in the RET, NRG1 and NRG3 genes in a cohort of 362 sporadic HSCR patients and 1,448 normal controls using a TaqMan genotyping assay. Significant associations were found between HSCR risk and rs2506030, rs2435357, rs2439302 and rs7835688 (odds ratio [OR] 1.64, P = 1.72E-06; 2.97, P = 5.15E-33; 1.84, P = 9.36E-11; and 1.93, P = 1.88E-12, respectively). Two locus analyses of SNPs indicated increased disease risks of HSCR between NRG1 rs2439302 and RET rs2435357 or rs2506030. RET rs2506030 (GG genotype) and rs2435357 (TT genotype), in combination with NRG1 rs2439302 (GG genotype), were strongly associated with the highest risk of HSCR (OR = 56.53, P = 4.50E-07) compared with the two loci or a single SNP of either RET or NRG1. Our results support the association between genetic variation of RET and NRG1 and susceptibility to HSCR in the Chinese population.
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Affiliation(s)
- Dehua Yang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jun Yang
- Department of Pediatric Surgery, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430015, China
| | - Shuai Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Meng Jiang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Guoqing Cao
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Li Yang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xi Zhang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ying Zhou
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Kang Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shao-Tao Tang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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24
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Copy number variation of bovine MAPK10 modulates the transcriptional activity and affects growth traits. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.09.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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25
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A Novel Zebrafish ret Heterozygous Model of Hirschsprung Disease Identifies a Functional Role for mapk10 as a Modifier of Enteric Nervous System Phenotype Severity. PLoS Genet 2016; 12:e1006439. [PMID: 27902697 PMCID: PMC5130169 DOI: 10.1371/journal.pgen.1006439] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/21/2016] [Indexed: 11/19/2022] Open
Abstract
Hirschsprung disease (HSCR) is characterized by absence of enteric neurons from the distal colon and severe intestinal dysmotility. To understand the pathophysiology and genetics of HSCR we developed a unique zebrafish model that allows combined genetic, developmental and in vivo physiological studies. We show that ret mutant zebrafish exhibit cellular, physiological and genetic features of HSCR, including absence of intestinal neurons, reduced peristalsis, and varying phenotype expressivity in the heterozygous state. We perform live imaging experiments using a UAS-GAL4 binary genetic system to drive fluorescent protein expression in ENS progenitors. We demonstrate that ENS progenitors migrate at reduced speed in ret heterozygous embryos, without changes in proliferation or survival, establishing this as a principal pathogenic mechanism for distal aganglionosis. We show, using live imaging of actual intestinal movements, that intestinal motility is severely compromised in ret mutants, and partially impaired in ret heterozygous larvae, and establish a clear correlation between neuron position and organised intestinal motility. We exploited the partially penetrant ret heterozygous phenotype as a sensitised background to test the influence of a candidate modifier gene. We generated mapk10 loss-of-function mutants, which show reduced numbers of enteric neurons. Significantly, we show that introduction of mapk10 mutations into ret heterozygotes enhanced the ENS deficit, supporting MAPK10 as a HSCR susceptibility locus. Our studies demonstrate that ret heterozygous zebrafish is a sensitized model, with many significant advantages over existing murine models, to explore the pathophysiology and complex genetics of HSCR. Hirschsprung Disease (HSCR) is a common congenital intestinal motility disorder diagnosed at birth by absence of enteric neurons in the distal gut, leading to intestinal obstruction that requires life-saving surgery. HSCR exhibits complex inheritance patterns and its genetic basis is not fully understood. Although well studied by human geneticists, and modelled using mouse, significant questions remain about the cellular and genetic causes of the disease and the relationship between neuron loss and defective intestinal motility. Here we use accessible, transparent zebrafish to address these outstanding questions. We establish that ret mutant zebrafish display key features of HSCR, including absence of intestinal neurons, reduced gut motility and varying phenotype expressivity. Using live imaging, possible in zebrafish but not in mouse, we demonstrate that decreased migration speed of enteric neuron progenitors colonising the gut is the principal defect leading to neuron deficits. By direct examination of gut motility in zebrafish larvae, we establish a clear correlation between neurons and motility patterns. Finally, we show that mapk10 mutations worsen the enteric neuron deficit of ret mutants, indicating that mutations in MAPK10 may increase susceptibility to HSCR. We show many benefits of modelling human genetic diseases in zebrafish and advance our understanding of HSCR.
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26
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Bae JS, Koh I, Cheong HS, Seo JM, Kim DY, Oh JT, Kim HY, Jung K, Sul JH, Park WY, Kim JH, Shin HD. A genome-wide association analysis of chromosomal aberrations and Hirschsprung disease. Transl Res 2016; 177:31-40.e6. [PMID: 27370899 DOI: 10.1016/j.trsl.2016.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 05/12/2016] [Accepted: 06/06/2016] [Indexed: 12/12/2022]
Abstract
Hirschsprung disease (HSCR) is a neurocristopathy characterized by the absence of intramural ganglion cells along variable lengths of the gastrointestinal tract. Although the RET proto-oncogene is considered to be the main risk factor for HSCR, only about 30% of the HSCR cases can be explained by variations in previously known genes including RET. Recently, copy number variation (CNV) and loss of heterozygosity (LOH) have emerged as new ways to understand human genomic variation. The goal of this present study is to identify new HSCR genetic factors related to CNV in Korean patients. In the genome-wide genotyping, using Illumina's HumanOmni1-Quad BeadChip (1,140,419 markers), of 123 HSCR patients and 432 unaffected subjects (total n = 555), a total of 8,188 CNVs (1 kb ∼ 1 mb) were identified by CNVpartition. As a result, 16 CNV regions and 13 LOH regions were identified as associated with HSCR (minimum P = 0.0005). Two top CNV regions (deletions at chr6:32675155-32680480 and chr22:20733495-21607293) were successfully validated by additional real-time quantitative polymerase chain reaction analysis. In addition, 2 CNV regions (6p21.32 and 22q11.21) and 2 LOH regions (3p22.2 and 14q23.3) were discovered to be unique to the HSCR patients group. Regarding the large-scale chromosomal aberrations (>1 mb), 11 large aberrations in the HSCR patients group were identified, which suggests that they may be a risk factor for HSCR. Although further replication in a larger cohort is needed, our findings may contribute to the understanding of the etiology of HSCR.
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Affiliation(s)
- Joon Seol Bae
- Laboratory of Translational Genomics, Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - InSong Koh
- Department of Physiology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Republic of Korea
| | - Jeong-Meen Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Dae-Yeon Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jung-Tak Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyun-Young Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Kyuwhan Jung
- Department of Surgery, Jeju National University Hospital, Aran 13gil 15, Jeju, Republic of Korea
| | - Jae Hoon Sul
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Calif, USA; Semel Center for Informatics and Personalized Genomics, University of California, Los Angeles, Calif, USA
| | - Woong-Yang Park
- Laboratory of Translational Genomics, Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea.
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea; Department of Life Science, Sogang University, Seoul, Republic of Korea.
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27
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Regulators of gene expression in Enteric Neural Crest Cells are putative Hirschsprung disease genes. Dev Biol 2016; 416:255-265. [DOI: 10.1016/j.ydbio.2016.06.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 05/17/2016] [Accepted: 06/02/2016] [Indexed: 11/21/2022]
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28
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Bondurand N, Southard-Smith EM. Mouse models of Hirschsprung disease and other developmental disorders of the enteric nervous system: Old and new players. Dev Biol 2016; 417:139-57. [PMID: 27370713 DOI: 10.1016/j.ydbio.2016.06.042] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/27/2016] [Accepted: 06/27/2016] [Indexed: 12/18/2022]
Abstract
Hirschsprung disease (HSCR, intestinal aganglionosis) is a multigenic disorder with variable penetrance and severity that has a general population incidence of 1/5000 live births. Studies using animal models have contributed to our understanding of the developmental origins of HSCR and the genetic complexity of this disease. This review summarizes recent progress in understanding control of enteric nervous system (ENS) development through analyses in mouse models. An overview of signaling pathways that have long been known to control the migration, proliferation and differentiation of enteric neural progenitors into and along the developing gut is provided as a framework for the latest information on factors that influence enteric ganglia formation and maintenance. Newly identified genes and additional factors beyond discrete genes that contribute to ENS pathology including regulatory sequences, miRNAs and environmental factors are also introduced. Finally, because HSCR has become a paradigm for complex oligogenic diseases with non-Mendelian inheritance, the importance of gene interactions, modifier genes, and initial studies on genetic background effects are outlined.
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Affiliation(s)
- Nadege Bondurand
- INSERM, U955, Equipe 6, F-94000 Creteil, France; Universite Paris-Est, UPEC, F-94000 Creteil, France.
| | - E Michelle Southard-Smith
- Vanderbilt University Medical Center, Department of Medicine, 2215 Garland Ave, Nashville, TN 37232, USA.
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29
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Lopez-Anido C, Sun G, Koenning M, Srinivasan R, Hung HA, Emery B, Keles S, Svaren J. Differential Sox10 genomic occupancy in myelinating glia. Glia 2015; 63:1897-1914. [PMID: 25974668 PMCID: PMC4644515 DOI: 10.1002/glia.22855] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/22/2015] [Indexed: 11/11/2022]
Abstract
Myelin is formed by specialized myelinating glia: oligodendrocytes and Schwann cells in the central and peripheral nervous systems, respectively. While there are distinct developmental aspects and regulatory pathways in these two cell types, myelination in both systems requires the transcriptional activator Sox10. Sox10 interacts with cell type-specific transcription factors at some loci to induce myelin gene expression, but it is largely unknown how Sox10 transcriptional networks globally compare between oligodendrocytes and Schwann cells. We used in vivo ChIP-Seq analysis of spinal cord and peripheral nerve (sciatic nerve) to identify unique and shared Sox10 binding sites and assess their correlation with active enhancers and transcriptional profiles in oligodendrocytes and Schwann cells. Sox10 binding sites overlap with active enhancers and critical cell type-specific regulators of myelination, such as Olig2 and Myrf in oligodendrocytes, and Egr2/Krox20 in Schwann cells. Sox10 sites also associate with genes critical for myelination in both oligodendrocytes and Schwann cells and are found within super-enhancers previously defined in brain. In Schwann cells, Sox10 sites contain binding motifs of putative partners in the Sp/Klf, Tead, and nuclear receptor protein families. Specifically, siRNA analysis of nuclear receptors Nr2f1 and Nr2f2 revealed downregulation of myelin genes Mbp and Ndrg1 in primary Schwann cells. Our analysis highlights different mechanisms that establish cell type-specific genomic occupancy of Sox10, which reflects the unique characteristics of oligodendrocyte and Schwann cell differentiation. GLIA 2015;63:1897-1914.
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Affiliation(s)
- Camila Lopez-Anido
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Comparative Biomedical Sciences Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Guannan Sun
- Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Matthias Koenning
- Department of Anatomy and Neuroscience and the Centre for Neuroscience Research, University of Melbourne, Melbourne, Australia
| | - Rajini Srinivasan
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Holly A. Hung
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ben Emery
- Department of Anatomy and Neuroscience and the Centre for Neuroscience Research, University of Melbourne, Melbourne, Australia
| | - Sunduz Keles
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - John Svaren
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53705, USA
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30
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Wang J, Du H, Mou YR, Niu JY, Zhang WT, Yang HC, Li AW. Abundance and significance of neuroligin-1 and glutamate in Hirschsprung’s disease. World J Gastroenterol 2015; 21:7172-7180. [PMID: 26109803 PMCID: PMC4476878 DOI: 10.3748/wjg.v21.i23.7172] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/20/2015] [Accepted: 04/09/2015] [Indexed: 02/07/2023] Open
Abstract
AIM: To investigate the abundance and potential diagnostic significance of neuroligin-1 and glutamate (Glu) in Hirschsprung’s disease (HSCR).
METHODS: Ninety children with HSCR and 50 children without HSCR matched for similar nutritional status, age and basal metabolic index were studied. The expression and localization of neuroligin-1 and Glu were assessed using double-labeling immunofluorescence staining of longitudinal muscles with adherent myenteric plexus from the surgically excised colon of children with HSCR. Western blot analysis, quantitative real-time PCR (qRT-PCR) and immunohistochemistry were performed to evaluate the abundance of neuroligin-1 and Glu in different HSCR-affected segments (ganglionic, transitional, and aganglionic segments). Enzyme-linked immunosorbent assay (ELISA) was used to detect and compare serum Glu levels in the long-segment HSCR, short-segment HSCR and non-HSCR samples.
RESULTS: Neuroligin-1 and Glu were co-expressed highest to lowest in the ganglionic, transitional and aganglionic segments based on Western blot (neuroligin-1: 0.177 ± 0.008 vs 0.101 ± 0.006, 0.177 ± 0.008 vs 0.035 ± 0.005, and 0.101 ± 0.006 vs 0.035 ± 0.005, P < 0.005; Glu: 0.198 ± 0.006 vs 0.115 ± 0.008, 0.198 ± 0.006 vs 0.040 ± 0.003, and 0.115 ± 0.008 vs 0.040 ± 0.003, P < 0.005) and qRT-PCR (neuroligin-1: 9.58 × 10-5± 9.94 × 10-6vs 2.49 × 10-5± 1.38 × 10-6, 9.58 × 10-5± 9.94 × 10-6vs 7.17 × 10-6 ± 1.12 × 10-6, and 2.49 × 10-5± 1.38 × 10-6vs 7.17 × 10-6± 1.12 × 10-6, P < 0.005). Serum Glu level was the highest to lowest in the non-HSCR, short-type HSCR and long-type HSCR samples based on ELISA (in nmol/μL, 0.93 ± 0.31 vs 0.57 ± 0.25, 0.93 ± 0.31 vs 0.23 ± 0.16, and 0.57 ± 0.25 vs 0.23 ± 0.16, P < 0.005).
CONCLUSION: Neuroligin-1 and Glu may represent new markers of ganglion cells, whose expression may correlate with the pathogenesis, diagnosis, differential diagnosis or classification of HSCR.
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Zhang Z, Jiang Q, Li Q, Cheng W, Qiao G, Xiao P, Gan L, Su L, Miao C, Li L. Genotyping analysis of 3 RET polymorphisms demonstrates low somatic mutation rate in Chinese Hirschsprung disease patients. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:5528-5534. [PMID: 26191260 PMCID: PMC4503131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/13/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Genetic mosaicism has been reported for both coding and non-coding sequences in the RET gene in Hirschsprung disease (HSCR) patients. This study aimed to investigate somatic mutation rate in Chinese population by comparing both homozygous genotype percentage and risk allele frequency of 3 RET single nucleotide polymorphisms (SNPs) among blood and colon samples. METHODS DNA was extracted from 59 HSCR blood samples, 59 control blood samples and 76 fresh frozen colon tissue samples (grouped into ganglionic, transitional and aganglionic level). Genotype status of rs2435357 and rs2506030 was examined by competitive allele specific hydrolysis probes (Taqman) PCR technology, and rs2506004 was examined by Sanger sequencing. Homozygous genotype percentage and risk allele frequency were calculated for each type of sample and compared by chi-square test. P<0.05 was regarded as being statistically significant. RESULTS Colon tissue DNA samples showed similar frequency of SNPs as that of the blood DNA samples in HSCR patients, both of which are significantly higher than the control blood group (rs2435357 TT genotype: 71.2%, 74.7% versus 22.0% in HSCR blood, HSCR colon and control blood DNA respectively, P=0.000; rs2506004 AA genotype: 72.4%, 83.1% versus 25.5%, P=0.000; rs2506030 GG genotype: 79.7%, 77.2% versus 54.2%, P=0.000 and 0.004). With respect to DNA extracted from ganglionic, transitional and aganglionic levels, no statistically significant difference was demonstrated in those 3 regions (rs2435357: P=0.897; rs2506004: P=0.740; rs2506030: P=0.901). CONCLUSION Our data does not support the notion that high frequency of somatic changes as an underlying etiology of Chinese HSCR population.
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Affiliation(s)
- Zhen Zhang
- Department of Pediatric Surgery, Capital Institute of PediatricsBeijing, China
| | - Qian Jiang
- Department of Medical Genetics, Capital Institute of PediatricsBeijing, China
| | - Qi Li
- Department of Pediatric Surgery, Capital Institute of PediatricsBeijing, China
| | - Wei Cheng
- Department of Surgery, Beijing United Family HospitalChina
- Department of Paediatrics and Surgery, Faculty of Medicine, Nursing and Health Sciences, Monash UniversityVictoria, Australia
| | - Guoliang Qiao
- Department of Pediatric Surgery, Capital Institute of PediatricsBeijing, China
| | - Ping Xiao
- Department of Pathology, Capital Institute of Pediatrics Affiliated Children’s HospitalBeijing, China
| | - Liang Gan
- Department of Pediatric Surgery, Capital Institute of PediatricsBeijing, China
| | - Lin Su
- Anhui Medical UniversityHefei, China
| | - Chunyue Miao
- Peking University Capital Institute of Pediatrics Teaching HospitalBeijing, China
| | - Long Li
- Department of Pediatric Surgery, Capital Institute of PediatricsBeijing, China
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Huang J, Dang R, Torigoe D, Lei C, Lan X, Chen H, Sasaki N, Wang J, Agui T. Identification of genetic loci affecting the severity of symptoms of Hirschsprung disease in rats carrying Ednrbsl mutations by quantitative trait locus analysis. PLoS One 2015; 10:e0122068. [PMID: 25790447 PMCID: PMC4366197 DOI: 10.1371/journal.pone.0122068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 02/12/2015] [Indexed: 01/17/2023] Open
Abstract
Hirschsprung’s disease (HSCR) is a congenital disease in neonates characterized by the absence of the enteric ganglia in a variable length of the distal colon. This disease results from multiple genetic interactions that modulate the ability of enteric neural crest cells to populate developing gut. We previously reported that three rat strains with different backgrounds (susceptible AGH-Ednrbsl/sl, resistant F344-Ednrbsl/sl, and LEH-Ednrbsl/sl) but the same null mutation of Ednrb show varying severity degrees of aganglionosis. This finding suggests that strain-specific genetic factors affect the severity of HSCR. Consistent with this finding, a quantitative trait locus (QTL) for the severity of HSCR on chromosome (Chr) 2 was identified using an F2 intercross between AGH and F344 strains. In the present study, we performed QTL analysis using an F2 intercross between the susceptible AGH and resistant LEH strains to identify the modifier/resistant loci for HSCR in Ednrb-deficient rats. A significant locus affecting the severity of HSCR was also detected within the Chr 2 region. These findings strongly suggest that a modifier gene of aganglionosis exists on Chr 2. In addition, two potentially causative SNPs (or mutations) were detected upstream of a known HSCR susceptibility gene, Gdnf. These SNPs were possibly responsible for the varied length of gut affected by aganglionosis.
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Affiliation(s)
- Jieping Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruihua Dang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail: (RD); (CL)
| | - Daisuke Torigoe
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail: (RD); (CL)
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Nobuya Sasaki
- Laboratory of Laboratory Animal Science and Medicine, School of Veterinary Medicine, Kitasato University, Aomori, Japan
| | - Jinxi Wang
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Takashi Agui
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
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Musser MA, Correa H, Southard-Smith EM. Enteric neuron imbalance and proximal dysmotility in ganglionated intestine of the Sox10Dom/+ Hirschsprung mouse model. Cell Mol Gastroenterol Hepatol 2015; 1:87-101. [PMID: 25844395 PMCID: PMC4380251 DOI: 10.1016/j.jcmgh.2014.08.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 08/05/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS In Hirschsprung disease (HSCR), neural crest-derived progenitors (NCPs) fail to completely colonize the intestine so that the enteric nervous system (ENS) is absent from distal bowel. Despite removal of the aganglionic region, many HSCR patients suffer from residual intestinal dysmotility. To test the hypothesis that inappropriate lineage segregation of NCPs in proximal ganglionated regions of the bowel could contribute to such postoperative disease, we investigated neural crest (NC)-derived lineages and motility in ganglionated, postnatal intestine of the Sox10Dom/+ HSCR mouse model. METHODS Cre-mediated fate-mapping was applied to evaluate relative proportions of NC-derived cell types. Motility assays were performed to assess gastric emptying and small intestine motility while colonic inflammation was assessed by histopathology for Sox10Dom/+ mutants relative to wildtype controls. RESULTS Sox10Dom/+ mice showed regional alterations in neuron and glia proportions as well as Calretinin+ and nNOS+ neuronal subtypes. In the colon, imbalance of enteric NC derivatives correlated with the extent of aganglionosis. All Sox10Dom/+ mice exhibited reduced small intestinal transit at 4-weeks of age, and at 6-weeks, Sox10Dom/+ males had increased gastric emptying rates. Sox10Dom/+ mice surviving to 6-weeks of age had little or no colonic inflammation when compared to wildtype littermates, suggesting that these changes in GI motility are neurally mediated. CONCLUSIONS The Sox10Dom mutation disrupts the balance of NC-derived lineages and affects GI motility in the proximal, ganglionated intestine of adult animals. This is the first report identifying alterations in enteric neuronal classes in Sox10Dom/+ mutants, which suggests a previously unrecognized role for Sox10 in neuronal subtype specification.
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Affiliation(s)
- Melissa A. Musser
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Hernan Correa
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - E. Michelle Southard-Smith
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
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Analysis of genome-wide copy number variations in Chinese indigenous and western pig breeds by 60 K SNP genotyping arrays. PLoS One 2014; 9:e106780. [PMID: 25198154 PMCID: PMC4157799 DOI: 10.1371/journal.pone.0106780] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 08/07/2014] [Indexed: 12/28/2022] Open
Abstract
Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs.
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Kawai H, Satomi K, Morishita Y, Murata Y, Sugano M, Nakano N, Noguchi M. Developmental markers of ganglion cells in the enteric nervous system and their application for evaluation of Hirschsprung disease. Pathol Int 2014; 64:432-42. [DOI: 10.1111/pin.12191] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 07/08/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Hitomi Kawai
- Department of Pathology; Tsukuba University Hospital; University of Tsukuba; Tsukuba Japan
| | - Kaishi Satomi
- Department of Diagnostic Pathology; Faculty of Medicine; University of Tsukuba; Tsukuba Japan
| | - Yukio Morishita
- Department of Diagnostic Pathology; Tokyo Medical University Ibaraki Medical Center; Ami Japan
| | - Yoshihiko Murata
- Department of Diagnostic Pathology; Graduate School of Comprehensive Human Sciences; University of Tsukuba; Tsukuba Japan
| | - Masato Sugano
- Department of Diagnostic Pathology; Faculty of Medicine; University of Tsukuba; Tsukuba Japan
| | - Noriyuki Nakano
- Department of Diagnostic Pathology; Graduate School of Comprehensive Human Sciences; University of Tsukuba; Tsukuba Japan
| | - Masayuki Noguchi
- Department of Diagnostic Pathology; Faculty of Medicine; University of Tsukuba; Tsukuba Japan
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Warburton D, Ronemus M, Kline J, Jobanputra V, Williams I, Anyane-Yeboa K, Chung W, Yu L, Wong N, Awad D, Yu CY, Leotta A, Kendall J, Yamrom B, Lee YH, Wigler M, Levy D. The contribution of de novo and rare inherited copy number changes to congenital heart disease in an unselected sample of children with conotruncal defects or hypoplastic left heart disease. Hum Genet 2014; 133:11-27. [PMID: 23979609 PMCID: PMC3880624 DOI: 10.1007/s00439-013-1353-9] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 07/21/2013] [Indexed: 12/25/2022]
Abstract
Congenital heart disease (CHD) is the most common congenital malformation, with evidence of a strong genetic component. We analyzed data from 223 consecutively ascertained families, each consisting of at least one child affected by a conotruncal defect (CNT) or hypoplastic left heart disease (HLHS) and both parents. The NimbleGen HD2-2.1 comparative genomic hybridization platform was used to identify de novo and rare inherited copy number variants (CNVs). Excluding 10 cases with 22q11.2 DiGeorge deletions, we validated de novo CNVs in 8 % of 148 probands with CNTs, 12.7 % of 71 probands with HLHS and none in 4 probands with both. Only 2 % of control families showed a de novo CNV. We also identified a group of ultra-rare inherited CNVs that occurred de novo in our sample, contained a candidate gene for CHD, recurred in our sample or were present in an affected sibling. We confirmed the contribution to CHD of copy number changes in genes such as GATA4 and NODAL and identified several genes in novel recurrent CNVs that may point to novel CHD candidate loci. We also found CNVs previously associated with highly variable phenotypes and reduced penetrance, such as dup 1q21.1, dup 16p13.11, dup 15q11.2-13, dup 22q11.2, and del 2q23.1. We found that the presence of extra-cardiac anomalies was not related to the frequency of CNVs, and that there was no significant difference in CNV frequency or specificity between the probands with CNT and HLHS. In agreement with other series, we identified likely causal CNVs in 5.6 % of our total sample, half of which were de novo.
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Affiliation(s)
- Dorothy Warburton
- Departments of Pediatrics and Genetics and Development, Columbia University, New York, NY, USA,
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Cooper DN, Krawczak M, Polychronakos C, Tyler-Smith C, Kehrer-Sawatzki H. Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum Genet 2013; 132:1077-130. [PMID: 23820649 PMCID: PMC3778950 DOI: 10.1007/s00439-013-1331-2] [Citation(s) in RCA: 423] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/15/2013] [Indexed: 02/06/2023]
Abstract
Some individuals with a particular disease-causing mutation or genotype fail to express most if not all features of the disease in question, a phenomenon that is known as 'reduced (or incomplete) penetrance'. Reduced penetrance is not uncommon; indeed, there are many known examples of 'disease-causing mutations' that fail to cause disease in at least a proportion of the individuals who carry them. Reduced penetrance may therefore explain not only why genetic diseases are occasionally transmitted through unaffected parents, but also why healthy individuals can harbour quite large numbers of potentially disadvantageous variants in their genomes without suffering any obvious ill effects. Reduced penetrance can be a function of the specific mutation(s) involved or of allele dosage. It may also result from differential allelic expression, copy number variation or the modulating influence of additional genetic variants in cis or in trans. The penetrance of some pathogenic genotypes is known to be age- and/or sex-dependent. Variable penetrance may also reflect the action of unlinked modifier genes, epigenetic changes or environmental factors. At least in some cases, complete penetrance appears to require the presence of one or more genetic variants at other loci. In this review, we summarize the evidence for reduced penetrance being a widespread phenomenon in human genetics and explore some of the molecular mechanisms that may help to explain this enigmatic characteristic of human inherited disease.
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Affiliation(s)
- David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, 24105 Kiel, Germany
| | | | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
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Masson AL, Talseth-Palmer BA, Evans TJ, Grice DM, Duesing K, Hannan GN, Scott RJ. Copy number variation in hereditary non-polyposis colorectal cancer. Genes (Basel) 2013; 4:536-55. [PMID: 24705261 PMCID: PMC3927572 DOI: 10.3390/genes4040536] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/02/2013] [Accepted: 09/11/2013] [Indexed: 12/12/2022] Open
Abstract
Hereditary non-polyposis colorectal cancer (HNPCC) is the commonest form of inherited colorectal cancer (CRC) predisposition and by definition describes families which conform to the Amsterdam Criteria or reiterations thereof. In ~50% of patients adhering to the Amsterdam criteria germline variants are identified in one of four DNA Mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2. Loss of function of any one of these genes results in a failure to repair DNA errors occurring during replication which can be most easily observed as DNA microsatellite instability (MSI)—a hallmark feature of this disease. The remaining 50% of patients without a genetic diagnosis of disease may harbour more cryptic changes within or adjacent to MLH1, MSH2, MSH6 or PMS2 or elsewhere in the genome. We used a high density cytogenetic array to screen for deletions or duplications in a series of patients, all of whom adhered to the Amsterdam/Bethesda criteria, to determine if genomic re-arrangements could account for a proportion of patients that had been shown not to harbour causative mutations as assessed by standard diagnostic techniques. The study has revealed some associations between copy number variants (CNVs) and HNPCC mutation negative cases and further highlights difficulties associated with CNV analysis.
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Affiliation(s)
- Amy L. Masson
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, 2305, Australia; E-Mails: (A.L.M.); (B.A.T.-P.); (T.-J.E.); (D.M.G.)
- School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, 2308, Australia
| | - Bente A. Talseth-Palmer
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, 2305, Australia; E-Mails: (A.L.M.); (B.A.T.-P.); (T.-J.E.); (D.M.G.)
- School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, 2308, Australia
| | - Tiffany-Jane Evans
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, 2305, Australia; E-Mails: (A.L.M.); (B.A.T.-P.); (T.-J.E.); (D.M.G.)
- School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, 2308, Australia
| | - Desma M. Grice
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, 2305, Australia; E-Mails: (A.L.M.); (B.A.T.-P.); (T.-J.E.); (D.M.G.)
- CSIRO Preventative Health Flagship and Division of Animal, Food and Health Sciences, North Ryde, New South Wales, 2113, Australia; E-Mails: (K.D.); (G.N.H.)
| | - Konsta Duesing
- CSIRO Preventative Health Flagship and Division of Animal, Food and Health Sciences, North Ryde, New South Wales, 2113, Australia; E-Mails: (K.D.); (G.N.H.)
| | - Garry N. Hannan
- CSIRO Preventative Health Flagship and Division of Animal, Food and Health Sciences, North Ryde, New South Wales, 2113, Australia; E-Mails: (K.D.); (G.N.H.)
| | - Rodney J. Scott
- Information Based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, New South Wales, 2305, Australia; E-Mails: (A.L.M.); (B.A.T.-P.); (T.-J.E.); (D.M.G.)
- School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, 2308, Australia
- Division of Molecular Medicine, Hunter Area Pathology Service, John Hunter Hospital, Newcastle, New South Wales, 2305, Australia
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +61-2-4921-4974; Fax: +61-2-4921-4253
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Gao H, Chen D, Liu X, Wu M, Mi J, Wang W. Polymorphisms and expression of the WNT8A gene in Hirschsprung's disease. Int J Mol Med 2013; 32:647-52. [PMID: 23836442 DOI: 10.3892/ijmm.2013.1433] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 07/01/2013] [Indexed: 12/22/2022] Open
Abstract
Hirschsprung's disease (HSCR) is a congenital disorder characterized by an absence of intrinsic ganglion cells in the nerves forming the plexus of the lower intestine. The WNT signaling pathway is considered to play an important role in embryonic development. In the present study, we analyzed 2 polymorphisms of the WNT8A gene (rs78301778 and rs6596422) to determine their association with the risk and development of HSCR. Allele frequencies and genotype distributions were analyzed by sequence analysis in patients with HSCR and normal controls. Using real-time PCR, western blot analysis and immunohistochemistry, we detected the mRNA and protein expression of WNT8A in patients with HSCR. The data indicated that the differences in genotype distributions and allele frequencies of rs78301778 and rs6596422 between various clinical classifications were statistically significant. The analysis of the mRNA and protein expression of WNT8A revealed that the expression of WNT8A was increased in the stenotic colon segments compared with the normal colon segments. In conclusion, the data presented in this study suggest that the WNT8A gene is involved in the susceptibility to HSCR, and plays an important role in the occurrence and development of HSCR. These findings warrant further investigation.
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Affiliation(s)
- Hong Gao
- Laboratory of Pediatric Congenital Malformation, Ministry of Public Health, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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Methylation analysis of EDNRB in human colon tissues of Hirschsprung's disease. Pediatr Surg Int 2013; 29:683-8. [PMID: 23579558 DOI: 10.1007/s00383-013-3308-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/03/2013] [Indexed: 01/05/2023]
Abstract
PURPOSE Hirschsprung's disease (HSCR) is characterized by absence of the enteric nervous system in a variable portion of the distal gut. The endothelin receptor type B (EDNRB) gene has been localized to the chromosome 13q22 region and encodes a G-protein coupled receptor, is generally accepted as a crucial gene for HSCR. This study is to identify the epigenetic changes of EDNRB in the pathogenesis of HSCR. METHODS We investigated the expression levels of EDNRB in 58 HSCR patients and 25 unrelated controls, using reverse transcriptase polymerase chain reaction (RT-PCR) and western blot assay. Moreover, using the methylation-specific polymerase chain reaction, we examined the methylation status of the promoter region of EDNRB. RESULTS Aberrant high expression level of EDNRB was detected in HSCR patients compared with the control group (P = 0.023). Besides, western blot assay confirmed the up-regulation of EDNRB in the post transcription level in the aganglionosis segment of HSCR patients. Furthermore, there was a significantly lower ratio of methylation level of EDNRB in HSCR. CONCLUSIONS Our study demonstrates that epigenetic inactivation of the EDNRB gene may play a role in the development of HSCR.
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Tian M, Wang Y, Gu X, Feng C, Fang S, Hu X, Li N. Copy number variants in locally raised Chinese chicken genomes determined using array comparative genomic hybridization. BMC Genomics 2013; 14:262. [PMID: 23594354 PMCID: PMC3637819 DOI: 10.1186/1471-2164-14-262] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 04/15/2013] [Indexed: 11/10/2022] Open
Abstract
Background Copy number variants contribute to genetic variation in birds. Analyses of copy number variants in chicken breeds had focused primarily on those from commercial varieties with nothing known about the occurrence and diversity of copy number variants in locally raised Chinese chicken breeds. To address this deficiency, we characterized copy number variants in 11 chicken breeds and compared the variation among these breeds. Results We presented a detailed analysis of the copy number variants in locally raised Chinese chicken breeds identified using a customized comparative genomic hybridization array. We identified 833 copy number variants contained within 308 copy number variant regions. The median and mean sizes of the copy number variant regions were 14.6 kb and 35.1 kb, respectively. Of the copy number variant regions, 138 (45%) involved gain of DNA, 159 (52%) involved loss of DNA, and 11 (3%) involved both gain and loss of DNA. Principal component analysis and agglomerative hierarchical clustering revealed the close relatedness of the four locally raised chicken breeds, Shek-Ki, Langshan, Qingyuan partridge, and Wenchang. Biological process enrichment analysis of the copy number variant regions confirmed the greater variation among the four aforementioned varieties than among the seven other breeds studied. Conclusion Our description of the distribution of the copy number variants and comparison of the differences among the copy number variant regions of the 11 chicken breeds supplemented the information available concerning the copy number variants of other Chinese chicken breeds. In addition to its relevance for functional analysis, our results provided the first insight into how chicken breeds can be clustered on the basis of their genomic copy number variation.
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Talseth-Palmer BA, Holliday EG, Evans TJ, McEvoy M, Attia J, Grice DM, Masson AL, Meldrum C, Spigelman A, Scott RJ. Continuing difficulties in interpreting CNV data: lessons from a genome-wide CNV association study of Australian HNPCC/lynch syndrome patients. BMC Med Genomics 2013; 6:10. [PMID: 23531357 PMCID: PMC3626775 DOI: 10.1186/1755-8794-6-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 03/18/2013] [Indexed: 01/13/2023] Open
Abstract
Background Hereditary non-polyposis colorectal cancer (HNPCC)/Lynch syndrome (LS) is a cancer syndrome characterised by early-onset epithelial cancers, especially colorectal cancer (CRC) and endometrial cancer. The aim of the current study was to use SNP-array technology to identify genomic aberrations which could contribute to the increased risk of cancer in HNPCC/LS patients. Methods Individuals diagnosed with HNPCC/LS (100) and healthy controls (384) were genotyped using the Illumina Human610-Quad SNP-arrays. Copy number variation (CNV) calling and association analyses were performed using Nexus software, with significant results validated using QuantiSNP. TaqMan Copy-Number assays were used for verification of CNVs showing significant association with HNPCC/LS identified by both software programs. Results We detected copy number (CN) gains associated with HNPCC/LS status on chromosome 7q11.21 (28% cases and 0% controls, Nexus; p = 3.60E-20 and QuantiSNP; p < 1.00E-16) and 16p11.2 (46% in cases, while a CN loss was observed in 23% of controls, Nexus; p = 4.93E-21 and QuantiSNP; p = 5.00E-06) via in silico analyses. TaqMan Copy-Number assay was used for validation of CNVs showing significant association with HNPCC/LS. In addition, CNV burden (total CNV length, average CNV length and number of observed CNV events) was significantly greater in cases compared to controls. Conclusion A greater CNV burden was identified in HNPCC/LS cases compared to controls supporting the notion of higher genomic instability in these patients. One intergenic locus on chromosome 7q11.21 is possibly associated with HNPCC/LS and deserves further investigation. The results from this study highlight the complexities of fluorescent based CNV analyses. The inefficiency of both CNV detection methods to reproducibly detect observed CNVs demonstrates the need for sequence data to be considered alongside intensity data to avoid false positive results.
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Affiliation(s)
- Bente A Talseth-Palmer
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW, Australia.
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Obermayr F, Hotta R, Enomoto H, Young HM. Development and developmental disorders of the enteric nervous system. Nat Rev Gastroenterol Hepatol 2013; 10:43-57. [PMID: 23229326 DOI: 10.1038/nrgastro.2012.234] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The enteric nervous system (ENS) arises from neural crest-derived cells that migrate into and along the gut, leading to the formation of a complex network of neurons and glial cells that regulates motility, secretion and blood flow. This Review summarizes the progress made in the past 5 years in our understanding of ENS development, including the migratory pathways of neural crest-derived cells as they colonize the gut. The importance of interactions between neural crest-derived cells, between signalling pathways and between developmental processes (such as proliferation and migration) in ensuring the correct development of the ENS is also presented. The signalling pathways involved in ENS development that were determined using animal models are also described, as is the evidence for the involvement of the genes encoding these molecules in Hirschsprung disease-the best characterized paediatric enteric neuropathy. Finally, the aetiology and treatment of Hirschsprung disease in the clinic and the potential involvement of defects in ENS development in other paediatric motility disorders are outlined.
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Affiliation(s)
- Florian Obermayr
- Department of Pediatric Surgery, University Children's Hospital, University of Tübingen, Hoppe-Seyler Straße 3, Tübingen 72076, Germany
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Abstract
Total colonic aganglionosis (TCA) is a relatively uncommon form of Hirschsprung disease (HSCR), occurring in approximately 2%-13% of cases. It can probably be classified as TCA (defined as aganglionosis extending from the anus to at least the ileocecal valve, but not >50 cm proximal to the ileocecal valve) and total colonic and small bowel aganglionosis, which may involve a very long segment of aganglionosis. It is not yet clear whether TCA merely represents a long form of HSCR or a different expression of the disease. There are many differences between TCA and other forms of HSCR, which require explanation if its ubiquitous clinical features are to be understood. Clinically, TCA appears to represent a different spectrum of disease in terms of presentation and difficulties that may be experienced in diagnosis, suggesting a different pathophysiology from the more common forms of HSCR. There is also some evidence suggesting that instead of being purely congenital, it may represent certain different pathophysiologic mechanisms. This study, in addition to reviewing current understanding and differences between TCA and the more frequently encountered rectosigmoid (or short-segment) expression, correlates them with what is currently known about the genetic and molecular biological background. Moreover, it reviews current outcomes to find consensus on management.
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Affiliation(s)
- Samuel W Moore
- Division of Paediatric Surgery, University of Stellenbosch, Tygerberg, South Africa.
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Moore SW. Chromosomal and related Mendelian syndromes associated with Hirschsprung's disease. Pediatr Surg Int 2012; 28:1045-58. [PMID: 23001136 DOI: 10.1007/s00383-012-3175-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/28/2012] [Indexed: 12/12/2022]
Abstract
Hirschsprung's disease (HSCR) is a fairly frequent cause of intestinal obstruction in children. It is characterized as a sex-linked heterogonous disorder with variable severity and incomplete penetrance giving rise to a variable pattern of inheritance. Although Hirschsprung's disease occurs as an isolated phenotype in at least 70% of cases, it is not infrequently associated with a number of congenital abnormalities and associated syndromes, demonstrating a spectrum of congenital anomalies. Certain of these syndromic phenotypes have been linked to distinct genetic sites, indicating underlying genetic associations of the disease and probable gene-gene interaction, in its pathogenesis. These associations with HSCR include Down's syndrome and other chromosomal anomalies, Waardenburg syndrome and other Dominant sensorineural deafness, the Congenital Central Hypoventilation and Mowat-Wilson and other brain-related syndromes, as well as the MEN2 and other tumour associations. A number of other autosomal recessive syndromes include the Shah-Waardenburg, the Bardet-Biedl and Cartilage-hair hypoplasia, Goldberg-Shprintzen syndromes and other syndromes related to cholesterol and fat metabolism among others. The genetics of Hirschsprung's disease are highly complex with the majority of known genetic sites relating to the main susceptibility pathways (RET an EDNRB). Non-syndromic non-familial, short-segment HSCR appears to represent a non-Mendelian condition with variable expression and sex-dependent penetrance. Syndromic and familial forms, on the other hand, have complex patterns of inheritance and being reported as autosomal dominant, recessive and polygenic patterns of inheritance. The phenotypic variability and incomplete penetrance observed in Hirschsprung's disease could also be explained by the involvement of modifier genes, especially in its syndromic forms. In this review, we look at the chromosomal and Mendelian associations and their underlying signalling pathways, to obtain a better understanding of the pathogenetic mechanisms involved in developing aganglionosis of the distal bowel.
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Affiliation(s)
- S W Moore
- Division of Pediatric Surgery, Department of Surgical Sciences, Faculty of Health Sciences, University of Stellenbosch, P.O. Box 19063, Tygerberg, South Africa.
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Tang CSM, Cheng G, So MT, Yip BHK, Miao XP, Wong EHM, Ngan ESW, Lui VCH, Song YQ, Chan D, Cheung K, Yuan ZW, Lei L, Chung PHY, Liu XL, Wong KKY, Marshall CR, Scherer S, Cherny SS, Sham PC, Tam PKH, Garcia-Barceló MM. Genome-wide copy number analysis uncovers a new HSCR gene: NRG3. PLoS Genet 2012; 8:e1002687. [PMID: 22589734 PMCID: PMC3349728 DOI: 10.1371/journal.pgen.1002687] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 03/20/2012] [Indexed: 01/23/2023] Open
Abstract
Hirschsprung disease (HSCR) is a congenital disorder characterized by aganglionosis of the distal intestine. To assess the contribution of copy number variants (CNVs) to HSCR, we analysed the data generated from our previous genome-wide association study on HSCR patients, whereby we identified NRG1 as a new HSCR susceptibility locus. Analysis of 129 Chinese patients and 331 ethnically matched controls showed that HSCR patients have a greater burden of rare CNVs (p = 1.50×10−5), particularly for those encompassing genes (p = 5.00×10−6). Our study identified 246 rare-genic CNVs exclusive to patients. Among those, we detected a NRG3 deletion (p = 1.64×10−3). Subsequent follow-up (96 additional patients and 220 controls) on NRG3 revealed 9 deletions (combined p = 3.36×10−5) and 2 de novo duplications among patients and two deletions among controls. Importantly, NRG3 is a paralog of NRG1. Stratification of patients by presence/absence of HSCR–associated syndromes showed that while syndromic–HSCR patients carried significantly longer CNVs than the non-syndromic or controls (p = 1.50×10−5), non-syndromic patients were enriched in CNV number when compared to controls (p = 4.00×10−6) or the syndromic counterpart. Our results suggest a role for NRG3 in HSCR etiology and provide insights into the relative contribution of structural variants in both syndromic and non-syndromic HSCR. This would be the first genome-wide catalog of copy number variants identified in HSCR. Copy number variations (CNVs) are significant genetic risk factors in disease pathogenesis and represent an important portion of missing heritability for some human diseases, making their discovery essential for the identification of genes and risk factors for a wide range of diseases, including Hirschsprung disease (HSCR, congenital colon aganglionosis). Since the discovery of the major HSCR gene, RET, a number of rare mutations have been reported in RET and other genes involved in the development of the enteric nervous system. However, these mutations contribute to only a small proportion of the disease susceptibility. Taking advantage of the recent technical and methodological advances, we have examined the contribution of CNVs to the disease. We have found that HSCR patients are enriched with CNVs encompassing genes. In particular, we found that deletions of NRG3, a paralog of the previously identified HSCR–susceptibility gene NRG1, were associated with the HSCR phenotype.
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Affiliation(s)
- Clara Sze-Man Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Guo Cheng
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Man-Ting So
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Benjamin Hon-Kei Yip
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Xiao-Ping Miao
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Emily Hoi-Man Wong
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Elly Sau-Wai Ngan
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Vincent Chi-Hang Lui
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - You-Qiang Song
- Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Danny Chan
- Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kenneth Cheung
- Department of Orthopedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Zhen-Wei Yuan
- Department of Paediatric Surgery, Shengjing Hospital, China Medical University, Shenyang, China
| | - Liu Lei
- Department of Surgery, Shenzhen Children's Hospital, Shenzhen, China
| | - Patrick Ho-Yu Chung
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Xue-Lai Liu
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kenneth Kak-Yuen Wong
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Christian R. Marshall
- Program in Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Steve Scherer
- Program in Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- The McLaughlin Centre and the Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Stacey S. Cherny
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Genome Research Centre, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Brain and Cognitive Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Pak-Chung Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Genome Research Centre, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Brain and Cognitive Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Paul Kwong-Hang Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Maria-Mercè Garcia-Barceló
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- * E-mail:
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McKeown SJ, Stamp L, Hao MM, Young HM. Hirschsprung disease: a developmental disorder of the enteric nervous system. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 2:113-29. [PMID: 23799632 DOI: 10.1002/wdev.57] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hirschsprung disease (HSCR), which is also called congenital megacolon or intestinal aganglionosis, is characterized by an absence of enteric (intrinsic) neurons from variable lengths of the most distal bowel. Because enteric neurons are essential for propulsive intestinal motility, infants with HSCR suffer from severe constipation and have a distended abdomen. Currently the only treatment is surgical removal of the affected bowel. HSCR has an incidence of around 1:5,000 live births, with a 4:1 male:female gender bias. Most enteric neurons arise from neural crest cells that emigrate from the caudal hindbrain and then migrate caudally along the entire gut. The absence of enteric neurons from variable lengths of the bowel in HSCR results from a failure of neural crest-derived cells to colonize the affected gut regions. HSCR is therefore regarded as a neurocristopathy. HSCR is a multigenic disorder and has become a paradigm for understanding complex factorial disorders. The major HSCR susceptibility gene is RET. The penetrance of several mutations in HSCR susceptibility genes is sex-dependent. HSCR can occur as an isolated disorder or as part of syndromes; for example, Type IV Waardenburg syndrome is characterized by deafness and pigmentation defects as well as intestinal aganglionosis. Studies using animal models have shown that HSCR genes regulate multiple processes including survival, proliferation, differentiation, and migration. Research into HSCR and the development of enteric neurons is an excellent example of the cross fertilization of ideas that can occur between human molecular geneticists and researchers using animal models. WIREs Dev Biol 2013, 2:113-129. doi: 10.1002/wdev.57 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Sonja J McKeown
- Department of Anatomy & Cell Biology, University of Melbourne, Melbourne 3010, VIC, Australia
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Broders-Bondon F, Paul-Gilloteaux P, Carlier C, Radice GL, Dufour S. N-cadherin and β1-integrins cooperate during the development of the enteric nervous system. Dev Biol 2012; 364:178-91. [PMID: 22342243 DOI: 10.1016/j.ydbio.2012.02.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 01/18/2012] [Accepted: 02/02/2012] [Indexed: 12/20/2022]
Abstract
Cell adhesion controls various embryonic morphogenetic processes, including the development of the enteric nervous system (ENS). Ablation of β1-integrin (β1-/-) expression in enteric neural crest cells (ENCC) in mice leads to major alterations in the ENS structure caused by reduced migration and increased aggregation properties of ENCC during gut colonization, which gives rise to a Hirschsprung's disease-like phenotype. In the present study, we examined the role of N-cadherin in ENS development and the interplay with β1 integrins during this process. The Ht-PA-Cre mouse model was used to target gene disruption of N-cadherin and β1 integrin in migratory NCC and to produce single- and double-conditional mutants for these two types of adhesion receptors. Double mutation of N-cadherin and β1 integrin led to embryonic lethality with severe defects in ENS development. N-cadherin-null (Ncad-/-) ENCC exhibited a delayed colonization in the developing gut at E12.5, although this was to a lesser extent than in β1-/- mutants. This delay of Ncad-/- ENCC migration was recovered at later stages of development. The double Ncad-/-; β1-/- mutant ENCC failed to colonize the distal part of the gut and there was more severe aganglionosis in the proximal hindgut than in the single mutants for N-cadherin or β1-integrin. This was due to an altered speed of locomotion and directionality in the gut wall. The abnormal aggregation defect of ENCC and the disorganized ganglia network in the β1-/- mutant was not observed in the double mutant. This indicates that N-cadherin enhances the effect of the β1-integrin mutation and demonstrates cooperation between these two adhesion receptors during ENS ontogenesis. In conclusion, our data reveal that N-cadherin is not essential for ENS development but it does modulate the modes of ENCC migration and acts in concert with β1-integrin to control the proper development of the ENS.
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Abstract
Genomic and personalized medicine have become buzz phrases that pervade all fields of medicine. Rapid advances in "-omics" fields of research (chief of which are genomics, proteinomics, and epigenomics) over the last few years have allowed us to dissect the molecular signatures and functional pathways that underlie disease initiation and progression and to identify molecular profiles that help the classification of tumor subtypes and determine their natural course, prognosis, and responsiveness to therapies. Genomic medicine implements the use of traditional genetic information, as well as modern pangenomic information, with the aim of individualizing risk assessment, prevention, diagnosis, and treatment of cancers and other diseases. It is of note that personalizing medical treatment based on genetic information is not the revolution of the 21st century. Indeed, the use of genetic information, such as human leukocyte antigen-matching for solid organ transplantation or blood transfusion based on ABO blood group antigens, has been standard of care for several decades. However, in recent years rapid technical advances have allowed us to perform high-throughput, high-density molecular analyses to depict the genomic, proteinomic, and epigenomic make-up of an individual at a reasonable cost. Hence, the so-called genomic revolution is more or less the logical evolution from years of bench-based research and bench-to-bedside translational medicine.
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Affiliation(s)
- Marc Dammann
- Department of General, Visceral and Transplantation Surgery, University Hospital Essen, Essen, Germany
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Dang R, Torigoe D, Sasaki N, Agui T. QTL analysis identifies a modifier locus of aganglionosis in the rat model of Hirschsprung disease carrying Ednrb(sl) mutations. PLoS One 2011; 6:e27902. [PMID: 22132166 PMCID: PMC3222640 DOI: 10.1371/journal.pone.0027902] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 10/27/2011] [Indexed: 01/31/2023] Open
Abstract
Hirschsprung disease (HSCR) exhibits complex genetics with incomplete penetrance and variable severity thought to result as a consequence of multiple gene interactions that modulate the ability of enteric neural crest cells to populate the developing gut. As reported previously, when the same null mutation of the Ednrb gene, Ednrbsl, was introgressed into the F344 strain, almost 60% of F344-Ednrbsl/sl pups did not show any symptoms of aganglionosis, appearing healthy and normally fertile. These findings strongly suggested that the severity of HSCR was affected by strain-specific genetic factor (s). In this study, the genetic basis of such large strain differences in the severity of aganglionosis in the rat model was studied by whole-genome scanning for quantitative trait loci (QTLs) using an intercross of (AGH-Ednrbsl×F344-Ednrbsl) F1 with the varying severity of aganglionosis. Genome linkage analysis identified one significant QTL on chromosome 2 for the severity of aganglionosis. Our QTL analyses using rat models of HSCR revealed that multiple genetic factors regulated the severity of aganglionosis. Moreover, a known HSCR susceptibility gene, Gdnf, was found in QTL that suggested a novel non-coding sequence mutation in GDNF that modifies the penetrance and severity of the aganglionosis phenotype in EDNRB-deficient rats. A further identification and analysis of responsible genes located on the identified QTL could lead to the richer understanding of the genetic basis of HSCR development.
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Affiliation(s)
- Ruihua Dang
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Daisuke Torigoe
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Nobuya Sasaki
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
| | - Takashi Agui
- Laboratory of Laboratory Animal Science and Medicine, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Hokkaido, Japan
- * E-mail:
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