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Xiao X, Yang H, Wan X, Wang Z. Effects of dietary supplementation of vitamin A on the tibia quality of goslings. Anim Biosci 2024; 37:1603-1613. [PMID: 38665078 PMCID: PMC11366536 DOI: 10.5713/ab.23.0445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/20/2024] [Indexed: 09/03/2024] Open
Abstract
OBJECTIVE This study was conducted to evaluate the effect of dietary supplementation of vitamin A (VA) on the tibial growth, calcium (Ca) and phosphorus (P) metabolism, VA, and vitamin D (VD) deposition, and associated gene expression in goslings. METHODS A total of 180 healthy, 1-day-old male goslings were randomly divided into 3 treatment groups (0, 9,000, and 15,000 IU VA/kg), with 6 replicates containing 10 goslings each. They were weighed and sampled on days 14, 28, 42, 56, and 70. RESULTS No addition of VA reduced VA content in the serum and liver of goslings, and supplementation of 15,000 IU/kg VA increased VA content from day 14 (p<0.05). The trend of VA concentration in the serum and liver was in line with the relative mRNA expression of retinoic acid receptor β in the jejunal mucosa. In both no addition of VA and supplementation of 15,000 IU/kg VA reduced 25-hydroxycholecalciferol (25-OH-VD3) content in the serum and VD content in the liver (p<0.05). From day 28, no addition of VA or supplementation of 15,000 IU/kg VA had a negative effect on tibia length, strength, and Ca, P, and ash content in goslings (p<0.05). Tibia P content was lower in the supplementation of 15,000 IU/kg VA group than in the no addition of VA group (p<0.05). No addition of VA or supplementation of 15,000 IU/kg VA had the most effect on early serum parathyroid hormone (PTH) levels in goslings (p<0.05). The effect of no addition of VA on the bone Gla protein (BGP) content of goslings started from day 14 (p<0.05). The relative mRNA expression of bone Gla-protein (BGLAP) and bone morphogenetic protein 4 (BMP4) in the liver and jejunal mucosa was decreased by either no addition of VA or supplementation of 15,000 IU/kg VA (p<0.05). CONCLUSION Both no addition of VA and supplementation of 15,000 IU/kg VA affected the mineralization process of the bone, and ultimately reduced tibial quality.
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Affiliation(s)
- Xia Xiao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
- Jiangsu Coastal Area Institute of Agricultural Science, Yancheng, Jiangsu 224002, China
| | - Haiming Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiaoli Wan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Zhiyue Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China
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Kramer M, Goodwin S, Wappel R, Borio M, Offit K, Feldman DR, Stadler ZK, McCombie WR. Exploring the genetic and epigenetic underpinnings of early-onset cancers: Variant prioritization for long read whole genome sequencing from family cancer pedigrees. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601096. [PMID: 39005350 PMCID: PMC11244929 DOI: 10.1101/2024.06.27.601096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Despite significant advances in our understanding of genetic cancer susceptibility, known inherited cancer predisposition syndromes explain at most 20% of early-onset cancers. As early-onset cancer prevalence continues to increase, the need to assess previously inaccessible areas of the human genome, harnessing a trio or quad family-based architecture for variant filtration, may reveal further insights into cancer susceptibility. To assess a broader spectrum of variation than can be ascertained by multi-gene panel sequencing, or even whole genome sequencing with short reads, we employed long read whole genome sequencing using an Oxford Nanopore Technology (ONT) PromethION of 3 families containing an early-onset cancer proband using a trio or quad family architecture. Analysis included 2 early-onset colorectal cancer family trios and one quad consisting of two siblings with testicular cancer, all with unaffected parents. Structural variants (SVs), epigenetic profiles and single nucleotide variants (SNVs) were determined for each individual, and a filtering strategy was employed to refine and prioritize candidate variants based on the family architecture. The family architecture enabled us to focus on inapposite variants while filtering variants shared with the unaffected parents, significantly decreasing background variation that can hamper identification of potentially disease causing differences. Candidate d e novo and compound heterozygous variants were identified in this way. Gene expression, in matched neoplastic and pre-neoplastic lesions, was assessed for one trio. Our study demonstrates the feasibility of a streamlined analysis of genomic variants from long read ONT whole genome sequencing and a way to prioritize key variants for further evaluation of pathogenicity, while revealing what may be missing from panel based analyses.
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Mian Y, Wang L, Keikhosravi A, Guo K, Misteli T, Arda HE, Finn EH. Cell type- and transcription-independent spatial proximity between enhancers and promoters. Mol Biol Cell 2024; 35:ar96. [PMID: 38717453 PMCID: PMC11244156 DOI: 10.1091/mbc.e24-02-0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/12/2024] [Accepted: 04/29/2024] [Indexed: 06/07/2024] Open
Abstract
Cell type-specific enhancers are critically important for lineage specification. The mechanisms that determine cell-type specificity of enhancer activity, however, are not fully understood. Most current models for how enhancers function invoke physical proximity between enhancer elements and their target genes. Here, we use an imaging-based approach to examine the spatial relationship of cell type-specific enhancers and their target genes with single-cell resolution. Using high-throughput microscopy, we measure the spatial distance from target promoters to their cell type-specific active and inactive enhancers in individual pancreatic cells derived from distinct lineages. We find increased proximity of all promoter-enhancer pairs relative to non-enhancer pairs separated by similar genomic distances. Strikingly, spatial proximity between enhancers and target genes was unrelated to tissue-specific enhancer activity. Furthermore, promoter-enhancer proximity did not correlate with the expression status of target genes. Our results suggest that promoter-enhancer pairs exist in a distinctive chromatin environment but that genome folding is not a universal driver of cell-type specificity in enhancer function.
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Affiliation(s)
- Yasmine Mian
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Li Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Adib Keikhosravi
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Konnie Guo
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - H. Efsun Arda
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Elizabeth H. Finn
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104
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Wang Q, Ma J, Gong Y, Zhu L, Tang H, Ye X, Su G, Huang F, Tan S, Zuo X, Gao Y, Yang P. Sex-specific circulating unconventional neutrophils determine immunological outcome of auto-inflammatory Behçet's uveitis. Cell Discov 2024; 10:47. [PMID: 38704363 PMCID: PMC11069589 DOI: 10.1038/s41421-024-00671-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/21/2024] [Indexed: 05/06/2024] Open
Abstract
Neutrophils are the most abundant immune cells that first respond to insults in circulation. Although associative evidence suggests that differences in neutrophils may be linked to the sex-specific vulnerability of inflammatory diseases, mechanistic links remain elusive. Here, we identified extensive sex-specific heterogeneity in neutrophil composition under normal and auto-inflammatory conditions at single-cell resolution. Using a combination of single-cell RNA sequencing analysis, neutrophil-specific genetic knockouts and transfer experiments, we discovered dysregulation of two unconventional (interferon-α responsive and T cell regulatory) neutrophil subsets leading to male-biased incidence, severity and poor prognosis of auto-inflammatory Behçet's uveitis. Genome-wide association study (GWAS) and exosome study revealed that male-specific negative effects of both genetic factors and circulating exosomes on unconventional neutrophil subsets contributed to male-specific vulnerability to disease. Collectively, our findings identify sex-specifically distinct neutrophil subsets and highlight unconventional neutrophil subsets as sex-specific therapeutic targets to limit inflammatory diseases.
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Affiliation(s)
- Qingfeng Wang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Junfeng Ma
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University, Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Yuxing Gong
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Lifu Zhu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University, Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Huanyu Tang
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University, Chongqing, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Xingsheng Ye
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guannan Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Fanfan Huang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shiyao Tan
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xianbo Zuo
- China-Japan Friendship Hospital, Beijing, China, and No. 1 Hospital, Anhui Medical University, Anhui, China
| | - Yuan Gao
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University, Chongqing, China.
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China.
- Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi, China.
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Bhargava A, Khedkar K. Chronic Constipation Unmasking as Hirschsprung Disease in a Preadolescent: Delayed Presentation or Delayed Diagnosis? Cureus 2024; 16:e60315. [PMID: 38883048 PMCID: PMC11177269 DOI: 10.7759/cureus.60315] [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: 04/07/2024] [Accepted: 05/14/2024] [Indexed: 06/18/2024] Open
Abstract
Hirschsprung disease, a rare genetic disorder affecting the enteric nervous system, is characterized by the absence of ganglion cells in the myenteric plexus. Typically identified in neonates due to the failure to pass meconium, diagnosis beyond the first year of life is considered delayed. Common clinical manifestations in children with late-onset Hirschsprung disease include abdominal distension, abdominal pain, vomiting, fever, and abnormal bowel sounds. Sigmoid volvulus, though uncommon, can complicate Hirschsprung disease, potentially leading to misdiagnosis and severe complications such as intestinal perforation, hemorrhage, sepsis, and even mortality. Non-surgical interventions such as antibiotic therapy, intestinal decompression, and fluid resuscitation are preferred initial treatments to stabilize the patient. This case involves a 9-year-old boy who has presented with abdominal distension since birth and a lengthy history of irregular bowel habits. The diagnosis of Hirschsprung disease was confirmed at our institution, and the patient underwent a two-stage repair procedure, which was completed without any intraoperative or postoperative complications. The patient experienced an uneventful recovery, was discharged with stable vital signs, and regained normal bowel function. This case highlights the challenges of delayed diagnosis at nine years and underscores the importance of prompt management.
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Affiliation(s)
- Abhilasha Bhargava
- General Surgery, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Kiran Khedkar
- Pediatric Surgery, All India Institute of Medical Sciences, Nagpur, IND
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Gu CC, Matter A, Turner A, Aggarwal P, Yang W, Sun X, Hunt SC, Lewis CE, Arnett DK, Anson B, Kattman S, Broeckel U. Transcriptional Variabilities in Human hiPSC-derived Cardiomyocytes: All Genes Are Not Equal and Their Robustness May Foretell Donor's Disease Susceptibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.584138. [PMID: 38659937 PMCID: PMC11042381 DOI: 10.1101/2024.04.18.584138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Human induced pluripotent stem cells (hiPSCs) are frequently used to study disease-associated variations. We characterized transcriptional variability from a hiPSC-derived cardiomyocyte (hiPSC-CM) study of left ventricular hypertrophy (LVH) using donor samples from the HyperGEN study. Multiple hiPSC-CM differentiations over reprogramming events (iPSC generation) across 7 donors were used to assess variabilities from reprogramming, differentiation, and donor LVH status. Variability arising from pathological alterations was assessed using a cardiac stimulant applied to the hiPSC-CMs to trigger hypertrophic responses. We found that for most genes (73.3%~85.5%), technical variability was smaller than biological variability. Further, we identified and characterized lists of "noise" genes showing greater technical variability and "signal" genes showing greater biological variability. Together, they support a "genetic robustness" hypothesis of disease-modeling whereby cellular response to relevant stimuli in hiPSC-derived somatic cells from diseased donors tends to show more transcriptional variability. Our findings suggest that hiPSC-CMs can provide a valid model for cardiac hypertrophy and distinguish between technical and disease-relevant transcriptional changes.
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Friedman MJ, Wagner T, Lee H, Rosenfeld MG, Oh S. Enhancer-promoter specificity in gene transcription: molecular mechanisms and disease associations. Exp Mol Med 2024; 56:772-787. [PMID: 38658702 PMCID: PMC11058250 DOI: 10.1038/s12276-024-01233-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 04/26/2024] Open
Abstract
Although often located at a distance from their target gene promoters, enhancers are the primary genomic determinants of temporal and spatial transcriptional specificity in metazoans. Since the discovery of the first enhancer element in simian virus 40, there has been substantial interest in unraveling the mechanism(s) by which enhancers communicate with their partner promoters to ensure proper gene expression. These research efforts have benefited considerably from the application of increasingly sophisticated sequencing- and imaging-based approaches in conjunction with innovative (epi)genome-editing technologies; however, despite various proposed models, the principles of enhancer-promoter interaction have still not been fully elucidated. In this review, we provide an overview of recent progress in the eukaryotic gene transcription field pertaining to enhancer-promoter specificity. A better understanding of the mechanistic basis of lineage- and context-dependent enhancer-promoter engagement, along with the continued identification of functional enhancers, will provide key insights into the spatiotemporal control of gene expression that can reveal therapeutic opportunities for a range of enhancer-related diseases.
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Affiliation(s)
- Meyer J Friedman
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tobias Wagner
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Haram Lee
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea
| | - Michael G Rosenfeld
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Soohwan Oh
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea.
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Gunadi, Amadeus VC, Utami FDT, Halim FV, Novebri NA, Hanggoro RA, Lestari AN, Iskandar K, Dwihantoro A, Purnomo E. Aberrant SOX10 and RET expressions in patients with Hirschsprung disease. BMC Pediatr 2024; 24:189. [PMID: 38493096 PMCID: PMC10943800 DOI: 10.1186/s12887-024-04682-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 03/01/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND HSCR is a complex genetic disorder characterized by the absence of ganglion cells in the intestine, leading to a functional obstruction. It is due to a disruption of complex signaling pathways within the gene regulatory network (GRN) during the development of the enteric nervous system (ENS), including SRY-Box Transcription Factor 10 (SOX10) and REarranged during Transfection (RET). This study evaluated the expressions of SOX10 and RET in HSCR patients in Indonesia. METHODS Total RNA of 19 HSCR ganglionic and aganglionic colons and 16 control colons were analyzed using quantitative real-time polymerase chain reaction for SOX10 and RET with GAPDH as the reference gene. Livak's method (2-ΔΔCT) was used to determine the expression levels of SOX10 and RET. RESULTS Most patients were males (68.4%), in the short aganglionosis segment (78.9%), and had undergone transanal endorectal pull-through (36.6%). There were significant upregulated SOX10 expressions in both ganglionic (2.84-fold) and aganglionic (3.72-fold) colon of HSCR patients compared to controls' colon (ΔCT 5.21 ± 2.04 vs. 6.71 ± 1.90; p = 0.032; and ΔCT 4.82 ± 1.59 vs. 6.71 ± 1.90; p = 0.003; respectively). Interestingly, the RET expressions were significantly downregulated in both ganglionic (11.71-fold) and aganglionic (29.96-fold) colon of HSCR patients compared to controls' colon (ΔCT 12.54 ± 2.21 vs. 8.99 ± 3.13; p = 0.0004; and ΔCT 13.90 ± 2.64 vs. 8.99 ± 3.13; p = 0.0001; respectively). CONCLUSIONS Our study shows aberrant SOX10 and RET expressions in HSCR patients, implying the critical role of SOX10 and RET in the pathogenesis of HSCR, particularly in the Indonesian population. Our study further confirms the involvement of SOX10-RET within the GNR during the ENS development.
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Affiliation(s)
- Gunadi
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Jl. Kesehatan No. 1, Yogyakarta, 55281, Indonesia.
| | - Verrell Christopher Amadeus
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Jl. Kesehatan No. 1, Yogyakarta, 55281, Indonesia
| | - Fadila Dyah Trie Utami
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Jl. Kesehatan No. 1, Yogyakarta, 55281, Indonesia
| | - Fiqih Vidiantoro Halim
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Jl. Kesehatan No. 1, Yogyakarta, 55281, Indonesia
| | - Nabilah Anisa Novebri
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Jl. Kesehatan No. 1, Yogyakarta, 55281, Indonesia
| | - Rahaditya Alrasyidi Hanggoro
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Jl. Kesehatan No. 1, Yogyakarta, 55281, Indonesia
| | - Avinindita Nura Lestari
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group/Translational Research Unit, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Jl. Kesehatan No. 1, Yogyakarta, 55281, Indonesia
| | - Kristy Iskandar
- Department of Child Health/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, 55291, Indonesia
| | - Andi Dwihantoro
- Pediatric Surgery Division, Department of Surgery, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, 55281, Indonesia
| | - Eko Purnomo
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, 55281, Indonesia
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Gunamalai L, Singh P, Berg B, Shi L, Sanchez E, Smith A, Breton G, Bedford MT, Balciunas D, Kapoor A. Functional characterization of QT interval associated SCN5A enhancer variants identify combined additive effects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584440. [PMID: 38559211 PMCID: PMC10979898 DOI: 10.1101/2024.03.11.584440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Several empirical and theoretical studies suggest presence of multiple enhancers per gene that collectively regulate gene expression, and that common sequence variation impacting on the activities of these enhancers is a major source of inter-individual variability in gene expression. However, for vast majority of genes, enhancers and the underlying regulatory variation remains unknown. Even for the genes with well-characterized enhancers, the nature of the combined effects from multiple enhancers and their variants, when known, on gene expression regulation remains unexplored. Here, we have evaluated the combined effects from five SCN5A enhancers and their regulatory variants that are known to collectively correlate with SCN5A cardiac expression and underlie QT interval association in the general population. Using small deletions centered at the regulatory variants in episomal reporter assays in a mouse cardiomyocyte cell line we demonstrate that the variants and their flanking sequences play critical role in individual enhancer activities, likely being a transcription factor (TF) binding site. By performing oligonucleotide-based pulldown assays on predicted TFs we identify the TFs likely driving allele-specific enhancer activities. Using all 32 possible allelic synthetic constructs in reporter assays, representing the five biallelic enhancers in tandem in their genomic order, we demonstrate combined additive effects on overall enhancer activities. Using transient enhancer assays in developing zebrafish embryos we demonstrate the four out the five enhancer elements act as enhancers in vivo . Together, these studies extend the previous findings to uncover the TFs driving the enhancer activities of QT interval associated SCN5A regulatory variants, reveal the additive effects from allelic combinations of these regulatory variants, and prove their potential to act as enhancers in vivo .
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Wang Q, Pu S, Xiang B, Chen J. A novel structural variant of RET causes familial Hirschsprung's disease via nonsense-mediated mRNA decay. Genes Dis 2024; 11:7-10. [PMID: 37588200 PMCID: PMC10425783 DOI: 10.1016/j.gendis.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/05/2023] [Indexed: 08/18/2023] Open
Affiliation(s)
- Qi Wang
- Department of Pediatric Surgery and Laboratory of Pediatric Surgery, Rare Diseases Center, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Siyu Pu
- Department of Pediatric Surgery and Laboratory of Pediatric Surgery, Rare Diseases Center, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Bo Xiang
- Department of Pediatric Surgery and Laboratory of Pediatric Surgery, Rare Diseases Center, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jing Chen
- Department of Pediatric Surgery and Laboratory of Pediatric Surgery, Rare Diseases Center, Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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Kanai SM, Clouthier DE. Endothelin signaling in development. Development 2023; 150:dev201786. [PMID: 38078652 PMCID: PMC10753589 DOI: 10.1242/dev.201786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Since the discovery of endothelin 1 (EDN1) in 1988, the role of endothelin ligands and their receptors in the regulation of blood pressure in normal and disease states has been extensively studied. However, endothelin signaling also plays crucial roles in the development of neural crest cell-derived tissues. Mechanisms of endothelin action during neural crest cell maturation have been deciphered using a variety of in vivo and in vitro approaches, with these studies elucidating the basis of human syndromes involving developmental differences resulting from altered endothelin signaling. In this Review, we describe the endothelin pathway and its functions during the development of neural crest-derived tissues. We also summarize how dysregulated endothelin signaling causes developmental differences and how this knowledge may lead to potential treatments for individuals with gene variants in the endothelin pathway.
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Affiliation(s)
- Stanley M. Kanai
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - David E. Clouthier
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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Hollingsworth EW, Liu TA, Jacinto SH, Chen CX, Alcantara JA, Kvon EZ. Rapid and Quantitative Functional Interrogation of Human Enhancer Variant Activity in Live Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.10.570890. [PMID: 38105996 PMCID: PMC10723448 DOI: 10.1101/2023.12.10.570890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Functional analysis of non-coding variants associated with human congenital disorders remains challenging due to the lack of efficient in vivo models. Here we introduce dual-enSERT, a robust Cas9-based two-color fluorescent reporter system which enables rapid, quantitative comparison of enhancer allele activities in live mice of any genetic background. We use this new technology to examine and measure the gain- and loss-of-function effects of enhancer variants linked to limb polydactyly, autism, and craniofacial malformation. By combining dual-enSERT with single-cell transcriptomics, we characterize variant enhancer alleles at cellular resolution, thereby implicating candidate molecular pathways in pathogenic enhancer misregulation. We further show that independent, polydactyly-linked enhancer variants lead to ectopic expression in the same cell populations, indicating shared genetic mechanisms underlying non-coding variant pathogenesis. Finally, we streamline dual-enSERT for analysis in F0 animals by placing both reporters on the same transgene separated by a synthetic insulator. Dual-enSERT allows researchers to go from identifying candidate enhancer variants to analysis of comparative enhancer activity in live embryos in under two weeks.
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Affiliation(s)
- Ethan W. Hollingsworth
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
- Medical Scientist Training Program, University of California, Irvine School of Medicine, Irvine, CA 92697, USA
| | - Taryn A. Liu
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Sandra H. Jacinto
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Cindy X. Chen
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Joshua A. Alcantara
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Evgeny Z. Kvon
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
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Lee D, Han SK, Yaacov O, Berk-Rauch H, Mathiyalagan P, Ganesh SK, Chakravarti A. Tissue-specific and tissue-agnostic effects of genome sequence variation modulating blood pressure. Cell Rep 2023; 42:113351. [PMID: 37910504 PMCID: PMC10726310 DOI: 10.1016/j.celrep.2023.113351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 09/21/2023] [Accepted: 10/11/2023] [Indexed: 11/03/2023] Open
Abstract
Genome-wide association studies (GWASs) have identified numerous variants associated with polygenic traits and diseases. However, with few exceptions, a mechanistic understanding of which variants affect which genes in which tissues to modulate trait variation is lacking. Here, we present genomic analyses to explain trait heritability of blood pressure (BP) through the genetics of transcriptional regulation using GWASs, multiomics data from different tissues, and machine learning approaches. Approximately 500,000 predicted regulatory variants across four tissues explain 33.4% of variant heritability: 2.5%, 5.3%, 7.7%, and 11.8% for kidney-, adrenal-, heart-, and artery-specific variants, respectively. Variation in the enhancers involved shows greater tissue specificity than in the genes they regulate, suggesting that gene regulatory networks perturbed by enhancer variants in a tissue relevant to a phenotype are the major source of interindividual variation in BP. Thus, our study provides an approach to scan human tissue and cell types for their physiological contribution to any trait.
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Affiliation(s)
- Dongwon Lee
- Department of Pediatrics, Division of Nephrology, Boston Children's Hospital, Boston & Harvard Medical School, Boston, MA, USA.
| | - Seong Kyu Han
- Department of Pediatrics, Division of Nephrology, Boston Children's Hospital, Boston & Harvard Medical School, Boston, MA, USA
| | - Or Yaacov
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA
| | - Hanna Berk-Rauch
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA
| | - Prabhu Mathiyalagan
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA
| | - Santhi K Ganesh
- Department of Internal Medicine & Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Aravinda Chakravarti
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA.
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14
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Chatterjee S, Fries LE, Yaacov O, Hu N, Berk-Rauch HE, Chakravarti A. RET enhancer haplotype-dependent remodeling of the human fetal gut development program. PLoS Genet 2023; 19:e1011030. [PMID: 37948459 PMCID: PMC10664930 DOI: 10.1371/journal.pgen.1011030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 11/22/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
Hirschsprung disease (HSCR) is associated with deficiency of the receptor tyrosine kinase RET, resulting in loss of cells of the enteric nervous system (ENS) during fetal gut development. The major contribution to HSCR risk is from common sequence variants in RET enhancers with additional risk from rare coding variants in many genes. Here, we demonstrate that these RET enhancer variants specifically alter the human fetal gut development program through significant decreases in gene expression of RET, members of the RET-EDNRB gene regulatory network (GRN), other HSCR genes, with an altered transcriptome of 2,382 differentially expressed genes across diverse neuronal and mesenchymal functions. A parsimonious hypothesis for these results is that beyond RET's direct effect on its GRN, it also has a major role in enteric neural crest-derived cell (ENCDC) precursor proliferation, its deficiency reducing ENCDCs with relative expansion of non-ENCDC cells. Thus, genes reducing RET proliferative activity can potentially cause HSCR. One such class is the 23 RET-dependent transcription factors enriched in early gut development. We show that their knockdown in human neuroblastoma SK-N-SH cells reduces RET and/or EDNRB gene expression, expanding the RET-EDNRB GRN. The human embryos we studied had major remodeling of the gut transcriptome but were unlikely to have had HSCR: thus, genetic or epigenetic changes in addition to those in RET are required for aganglionosis.
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Affiliation(s)
- Sumantra Chatterjee
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, United States of America
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, United States of America
| | - Lauren E. Fries
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, United States of America
| | - Or Yaacov
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, United States of America
| | - Nan Hu
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, United States of America
| | - Hanna E. Berk-Rauch
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, United States of America
| | - Aravinda Chakravarti
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, United States of America
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, United States of America
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15
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Montalva L, Cheng LS, Kapur R, Langer JC, Berrebi D, Kyrklund K, Pakarinen M, de Blaauw I, Bonnard A, Gosain A. Hirschsprung disease. Nat Rev Dis Primers 2023; 9:54. [PMID: 37828049 DOI: 10.1038/s41572-023-00465-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/12/2023] [Indexed: 10/14/2023]
Abstract
Hirschsprung disease (HSCR) is a rare congenital intestinal disease that occurs in 1 in 5,000 live births. HSCR is characterized by the absence of ganglion cells in the myenteric and submucosal plexuses of the intestine. Most patients present during the neonatal period with the first meconium passage delayed beyond 24 h, abdominal distension and vomiting. Syndromes associated with HSCR include trisomy 21, Mowat-Wilson syndrome, congenital central hypoventilation syndrome, Shah-Waardenburg syndrome and cartilage-hair hypoplasia. Multiple putative genes are involved in familial and isolated HSCR, of which the most common are the RET proto-oncogene and EDNRB. Diagnosis consists of visualization of a transition zone on contrast enema and confirmation via rectal biopsy. HSCR is typically managed by surgical removal of the aganglionic bowel and reconstruction of the intestinal tract by connecting the normally innervated bowel down to the anus while preserving normal sphincter function. Several procedures, namely Swenson, Soave and Duhamel procedures, can be undertaken and may include a laparoscopically assisted approach. Short-term and long-term comorbidities include persistent obstructive symptoms, enterocolitis and soiling. Continued research and innovation to better understand disease mechanisms holds promise for developing novel techniques for diagnosis and therapy, and improving outcomes in patients.
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Affiliation(s)
- Louise Montalva
- Department of Paediatric Surgery, Robert-Debré Children's University Hospital, Paris, France.
- Faculty of Health, Paris-Cité University, Paris, France.
- NeuroDiderot, INSERM UMR1141, Paris, France.
| | - Lily S Cheng
- Division of Paediatric Surgery, Texas Children's Hospital, Houston, TX, USA
- Division of Paediatric Surgery, University of Virginia, Charlottesville, VA, USA
| | - Raj Kapur
- Department of Pathology, Seattle Children's Hospital, Seattle, WA, USA
| | - Jacob C Langer
- Division of Paediatric Surgery, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Dominique Berrebi
- Department of Pathology, Robert-Debré and Necker Children's University Hospital, Paris, France
| | - Kristiina Kyrklund
- Department of Paediatric Surgery, Helsinki University Central Hospital, Helsinki, Finland
| | - Mikko Pakarinen
- Department of Paediatric Surgery, Helsinki University Central Hospital, Helsinki, Finland
| | - Ivo de Blaauw
- Department of Surgery, Division of Paediatric Surgery, Radboudumc-Amalia Children's Hospital, Nijmegen, Netherlands
| | - Arnaud Bonnard
- Department of Paediatric Surgery, Robert-Debré Children's University Hospital, Paris, France
- Faculty of Health, Paris-Cité University, Paris, France
- NeuroDiderot, INSERM UMR1141, Paris, France
| | - Ankush Gosain
- Department of Paediatric Surgery, Children's Hospital Colorado, Aurora, CO, USA.
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16
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Vincent E, Chatterjee S, Cannon GH, Auer D, Ross H, Chakravarti A, Goff LA. Ret deficiency decreases neural crest progenitor proliferation and restricts fate potential during enteric nervous system development. Proc Natl Acad Sci U S A 2023; 120:e2211986120. [PMID: 37585461 PMCID: PMC10451519 DOI: 10.1073/pnas.2211986120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/18/2023] [Indexed: 08/18/2023] Open
Abstract
The receptor tyrosine kinase RET plays a critical role in the fate specification of enteric neural crest-derived cells (ENCDCs) during enteric nervous system (ENS) development. RET loss of function (LoF) is associated with Hirschsprung disease (HSCR), which is marked by aganglionosis of the gastrointestinal (GI) tract. Although the major phenotypic consequences and the underlying transcriptional changes from Ret LoF in the developing ENS have been described, cell type- and state-specific effects are unknown. We performed single-cell RNA sequencing on an enriched population of ENCDCs from the developing GI tract of Ret null heterozygous and homozygous mice at embryonic day (E)12.5 and E14.5. We demonstrate four significant findings: 1) Ret-expressing ENCDCs are a heterogeneous population comprising ENS progenitors as well as glial- and neuronal-committed cells; 2) neurons committed to a predominantly inhibitory motor neuron developmental trajectory are not produced under Ret LoF, leaving behind a mostly excitatory motor neuron developmental program; 3) expression patterns of HSCR-associated and Ret gene regulatory network genes are impacted by Ret LoF; and 4) Ret deficiency leads to precocious differentiation and reduction in the number of proliferating ENS precursors. Our results support a model in which Ret contributes to multiple distinct cellular phenotypes during development of the ENS, including the specification of inhibitory neuron subtypes, cell cycle dynamics of ENS progenitors, and the developmental timing of neuronal and glial commitment.
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Affiliation(s)
- Elizabeth Vincent
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Sumantra Chatterjee
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY10016
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY10016
| | - Gabrielle H. Cannon
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Dallas Auer
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Holly Ross
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - Aravinda Chakravarti
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY10016
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY10016
| | - Loyal A. Goff
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD21205
- Kavli Neurodiscovery Institute, Johns Hopkins University, Baltimore, MD21205
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17
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Chi S, Li S, Cao G, Guo J, Han Y, Zhou Y, Zhang X, Li Y, Luo Z, Li X, Rong L, Zhang M, Li L, Tang S. The interplay of common genetic variants NRG1 rs2439302 and RET rs2435357 increases the risk of developing Hirschsprung's disease. Front Cell Dev Biol 2023; 11:1184799. [PMID: 37484916 PMCID: PMC10361661 DOI: 10.3389/fcell.2023.1184799] [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: 03/12/2023] [Accepted: 06/14/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction: As a congenital and genetically related disease, many single nucleotide polymorphisms (SNPs) have been reported to be associated with the risk of HSCR. Our previous research showed that SNP rs2439302 (NRG1) interacted with rs2435357 (RET) to increase the risk of HSCR development. However, the underlying molecular mechanism is still not well understood. Methods: SNP rs2439302 (NRG1) and rs2435357 (RET) were genotyped in 470 HSCR cases. The expression of NRG1 and RET was investigated in the colon of HSCR patients. Knockdown of the NRG1 and RET homologs was performed in zebrafish to investigate their synergistic effect on ENS development. The effect of SNP rs2439302 and rs2435357 polymorphism on neuron proliferation, migration, and differentiation were investigated in SHSY-5Y cells and IPSCs. Results: Significant downregulation of NRG1 and RET expression was noticed in the aganglionic segment of HSCR patients and SHSY-5Y cells with rs2439302 GG/rs2435357 TT genotype. NRG1 and RET double mutants caused the most severe reduction in enteric neuron numbers than NRG1 single mutant or RET single mutant in the hindgut of zebrafish. SHSY-5Y cells and IPSCs with rs2439302 GG/rs2435357 TT genotype exhibited a decreased proliferative, migration, and differentiative capacity. CTCF showed a considerably higher binding ability to SNP rs2439302 CC than GG. NRG1 reduction caused a further decrease in SOX10 expression via the PI3K/Akt pathway, which regulates RET expression by directly binding to rs2435357. Discussion: SNP rs2439302 (NRG1) GG increases the risk of developing HSCR by affecting the binding of transcription factor CTCF and interacting with rs2435357 (RET) to regulate RET expression via the PI3K/Akt/SOX10 pathway.
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Affiliation(s)
- Shuiqing Chi
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuai Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guoqing Cao
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jialing Guo
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yunqiao Han
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yun Zhou
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xi Zhang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yibo Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhibin Luo
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiangyang Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liying Rong
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mengxin Zhang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Linglu Li
- China Zebrafish Resource Center, National Aquatic Biological Resource Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shaotao Tang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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18
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Xu W, Yu H, Chen D, Pan W, Yang W, Miao J, Jia W, Zheng B, Liu Y, Chen X, Gao Y, Tian D. Identifying the potential transcriptional regulatory network in Hirschsprung disease by integrated analysis of microarray datasets. WORLD JOURNAL OF PEDIATRIC SURGERY 2023; 6:e000547. [PMID: 37082700 PMCID: PMC10111925 DOI: 10.1136/wjps-2022-000547] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/13/2023] [Indexed: 04/22/2023] Open
Abstract
Objective Hirschsprung disease (HSCR) is one of the common neurocristopathies in children, which is associated with at least 20 genes and involves a complex regulatory mechanism. Transcriptional regulatory network (TRN) has been commonly reported in regulating gene expression and enteric nervous system development but remains to be investigated in HSCR. This study aimed to identify the potential TRN implicated in the pathogenesis and diagnosis of HSCR. Methods Based on three microarray datasets from the Gene Expression Omnibus database, the multiMiR package was used to investigate the microRNA (miRNA)-target interactions, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Then, we collected transcription factors (TFs) from the TransmiR database to construct the TF-miRNA-mRNA regulatory network and used cytoHubba to identify the key modules. Finally, the receiver operating characteristic (ROC) curve was determined and the integrated diagnostic models were established based on machine learning by the support vector machine method. Results We identified 58 hub differentially expressed microRNAs (DEMis) and 16 differentially expressed mRNAs (DEMs). The robust target genes of DEMis and DEMs mainly enriched in several GO/KEGG terms, including neurogenesis, cell-substrate adhesion, PI3K-Akt, Ras/mitogen-activated protein kinase and Rho/ROCK signaling. Moreover, 2 TFs (TP53 and TWIST1), 4 miRNAs (has-miR-107, has-miR-10b-5p, has-miR-659-3p, and has-miR-371a-5p), and 4 mRNAs (PIM3, CHUK, F2RL1, and CA1) were identified to construct the TF-miRNA-mRNA regulatory network. ROC analysis revealed a strong diagnostic value of the key TRN regulons (all area under the curve values were more than 0.8). Conclusion This study suggests a potential role of the TF-miRNA-mRNA network that can help enrich the connotation of HSCR pathogenesis and diagnosis and provide new horizons for treatment.
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Affiliation(s)
- Wenyao Xu
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
- Institute of Neurobiology, Environment and Genes Related to Diseases Key Laboratory of Chinese Ministry of Education, Xi'an Jiaotong University, Xi'an, China
| | - Hui Yu
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
- Institute of Neurobiology, Environment and Genes Related to Diseases Key Laboratory of Chinese Ministry of Education, Xi'an Jiaotong University, Xi'an, China
| | - Dian Chen
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Peking University, Beijing, China
| | - Weikang Pan
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Weili Yang
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Jing Miao
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Wanying Jia
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Baijun Zheng
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Yong Liu
- Institute of Neurobiology, Environment and Genes Related to Diseases Key Laboratory of Chinese Ministry of Education, Xi'an Jiaotong University, Xi'an, China
| | - Xinlin Chen
- Institute of Neurobiology, Environment and Genes Related to Diseases Key Laboratory of Chinese Ministry of Education, Xi'an Jiaotong University, Xi'an, China
| | - Ya Gao
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Donghao Tian
- Department of Pediatric Surgery, the Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
- Institute of Neurobiology, Environment and Genes Related to Diseases Key Laboratory of Chinese Ministry of Education, Xi'an Jiaotong University, Xi'an, China
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19
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Current challenges in understanding the role of enhancers in disease. Nat Struct Mol Biol 2022; 29:1148-1158. [PMID: 36482255 DOI: 10.1038/s41594-022-00896-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/04/2022] [Indexed: 12/13/2022]
Abstract
Enhancers play a central role in the spatiotemporal control of gene expression and tend to work in a cell-type-specific manner. In addition, they are suggested to be major contributors to phenotypic variation, evolution and disease. There is growing evidence that enhancer dysfunction due to genetic, structural or epigenetic mechanisms contributes to a broad range of human diseases referred to as enhanceropathies. Such mechanisms often underlie the susceptibility to common diseases, but can also play a direct causal role in cancer or Mendelian diseases. Despite the recent gain of insights into enhancer biology and function, we still have a limited ability to predict how enhancer dysfunction impacts gene expression. Here we discuss the major challenges that need to be overcome when studying the role of enhancers in disease etiology and highlight opportunities and directions for future studies, aiming to disentangle the molecular basis of enhanceropathies.
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20
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Whole genome sequencing reveals epistasis effects within RET for Hirschsprung disease. Sci Rep 2022; 12:20423. [PMID: 36443333 PMCID: PMC9705416 DOI: 10.1038/s41598-022-24077-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/09/2022] [Indexed: 11/29/2022] Open
Abstract
Common variants in RET and NRG1 have been associated with Hirschsprung disease (HSCR), a congenital disorder characterised by incomplete innervation of distal gut, in East Asian (EA) populations. However, the allelic effects so far identified do not fully explain its heritability, suggesting the presence of epistasis, where effect of one genetic variant differs depending on other (modifier) variants. Few instances of epistasis have been documented in complex diseases due to modelling complexity and data challenges. We proposed four epistasis models to comprehensively capture epistasis for HSCR between and within RET and NRG1 loci using whole genome sequencing (WGS) data in EA samples. 65 variants within the Topologically Associating Domain (TAD) of RET demonstrated significant epistasis with the lead enhancer variant (RET+3; rs2435357). These epistatic variants formed two linkage disequilibrium (LD) clusters represented by rs2506026 and rs2506028 that differed in minor allele frequency and the best-supported epistatic model. Intriguingly, rs2506028 is in high LD with one cis-regulatory variant (rs2506030) highlighted previously, suggesting that detected epistasis might be mediated through synergistic effects on transcription regulation of RET. Our findings demonstrated the advantages of WGS data for detecting epistasis, and support the presence of interactive effects of regulatory variants in RET for HSCR.
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21
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Lin X, Liu Y, Liu S, Zhu X, Wu L, Zhu Y, Zhao D, Xu X, Chemparathy A, Wang H, Cao Y, Nakamura M, Noordermeer JN, La Russa M, Wong WH, Zhao K, Qi LS. Nested epistasis enhancer networks for robust genome regulation. Science 2022; 377:1077-1085. [PMID: 35951677 DOI: 10.1126/science.abk3512] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mammalian genomes possess multiple enhancers spanning an ultralong distance (>megabases) to modulate important genes, yet it is unclear how these enhancers coordinate to achieve this task. Here, we combine multiplexed CRISPRi screening with machine learning to define quantitative enhancer-enhancer interactions. We find that the ultralong distance enhancer network possesses a nested multi-layer architecture that confers functional robustness of gene expression. Experimental characterization reveals that enhancer epistasis is maintained by three-dimensional chromosomal interactions and BRD4 condensation. Machine learning prediction of synergistic enhancers provides an effective strategy to identify non-coding variant pairs associated with pathogenic genes in diseases beyond Genome-Wide Association Studies (GWAS) analysis. Our work unveils nested epistasis enhancer networks, which can better explain enhancer functions within cells and in diseases.
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Affiliation(s)
- Xueqiu Lin
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yanxia Liu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Shuai Liu
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute NIH, Bethesda, MD 20892, USA
| | - Xiang Zhu
- Department of Statistics, Stanford University, Stanford, CA 94305, USA.,Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lingling Wu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yanyu Zhu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Dehua Zhao
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Xiaoshu Xu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Haifeng Wang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yaqiang Cao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute NIH, Bethesda, MD 20892, USA
| | - Muneaki Nakamura
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Marie La Russa
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, Stanford, CA 94305, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute NIH, Bethesda, MD 20892, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,ChEM-H, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg BioHub, San Francisco, CA 94158, USA
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22
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Dey KK, Gazal S, van de Geijn B, Kim SS, Nasser J, Engreitz JM, Price AL. SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease. CELL GENOMICS 2022; 2:100145. [PMID: 35873673 PMCID: PMC9306342 DOI: 10.1016/j.xgen.2022.100145] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 04/03/2021] [Accepted: 05/27/2022] [Indexed: 12/11/2022]
Abstract
We assess contributions to autoimmune disease of genes whose regulation is driven by enhancer regions (enhancer-related) and genes that regulate other genes in trans (candidate master-regulator). We link these genes to SNPs using several SNP-to-gene (S2G) strategies and apply heritability analyses to draw three conclusions about 11 autoimmune/blood-related diseases/traits. First, several characterizations of enhancer-related genes using functional genomics data are informative for autoimmune disease heritability after conditioning on a broad set of regulatory annotations. Second, candidate master-regulator genes defined using trans-eQTL in blood are also conditionally informative for autoimmune disease heritability. Third, integrating enhancer-related and master-regulator gene sets with protein-protein interaction (PPI) network information magnified their disease signal. The resulting PPI-enhancer gene score produced >2-fold stronger heritability signal and >2-fold stronger enrichment for drug targets, compared with the recently proposed enhancer domain score. In each case, functionally informed S2G strategies produced 4.1- to 13-fold stronger disease signals than conventional window-based strategies.
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Affiliation(s)
- Kushal K. Dey
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Steven Gazal
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Bryce van de Geijn
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Genentech, South San Francisco, CA 94080, USA
| | - Samuel Sungil Kim
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Joseph Nasser
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jesse M. Engreitz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- BASE Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford University School of Medicine, Stanford, CA 94304, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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23
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Wang N, Xi J, Lan C, Wu Y, Zhu Y, Zuo X, Zhang Y. Association between IKBKAP polymorphisms and Hirschsprung's disease susceptibility in Chinese children. Transl Pediatr 2022; 11:789-796. [PMID: 35800263 PMCID: PMC9253937 DOI: 10.21037/tp-21-550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/22/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Hirschsprung's disease (HSCR) is a rare congenital disease in which enteric nervous system (ENS) in the distal intestine is absent. HSCR is a disease involving genetic factors and environmental factors. Despite a series of genes have been revealed to contribute to HSCR, many HSCR associated genes were yet not identified. Previous studies had identified that a potential susceptibility gene of HSCR was an inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein (IKBKAP). The study aimed to explore the association of genetic variants in IKBKAP and HSCR susceptibility in southern Chinese children. METHODS Single nucleotide polymorphism (SNPs) were genotyped by the Mass ARRAY iPLEX Gold system (Sequenom, San Diego, CA, USA) on all samples, which included 1,470 HSCR children (cases) and 1,473 healthy children (controls). The associations between SNPs and HSCR or clinical subtypes were assessed by comparing their allele frequencies in corresponding case and control samples. Different genetic models, including additive, recessive, and dominant models, were tested using PLINK 1.9 software. RESULTS Further subgroup analysis revealed rs2275630 as a total colonic aganglionosis (TCA)-specific susceptibility locus. The present study is the first to indicate that IKBKAP rs2275630 were associated with HSCR susceptibility, especially in TCA patients. CONCLUSIONS We conclude that IKBKAP rs2275630 is a susceptibility gene of HSCR.
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Affiliation(s)
- Ning Wang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jiaojiao Xi
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Chaoting Lan
- Department of Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yuxin Wu
- Department of Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yun Zhu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiaoyu Zuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yan Zhang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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24
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Perkins ML, Gandara L, Crocker J. A synthetic synthesis to explore animal evolution and development. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200517. [PMID: 35634925 PMCID: PMC9149795 DOI: 10.1098/rstb.2020.0517] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Identifying the general principles by which genotypes are converted into phenotypes remains a challenge in the post-genomic era. We still lack a predictive understanding of how genes shape interactions among cells and tissues in response to signalling and environmental cues, and hence how regulatory networks generate the phenotypic variation required for adaptive evolution. Here, we discuss how techniques borrowed from synthetic biology may facilitate a systematic exploration of evolvability across biological scales. Synthetic approaches permit controlled manipulation of both endogenous and fully engineered systems, providing a flexible platform for investigating causal mechanisms in vivo. Combining synthetic approaches with multi-level phenotyping (phenomics) will supply a detailed, quantitative characterization of how internal and external stimuli shape the morphology and behaviour of living organisms. We advocate integrating high-throughput experimental data with mathematical and computational techniques from a variety of disciplines in order to pursue a comprehensive theory of evolution. This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
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Affiliation(s)
- Mindy Liu Perkins
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Lautaro Gandara
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Justin Crocker
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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25
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Zhou T, Zhu X, Ye Z, Wang YF, Yao C, Xu N, Zhou M, Ma J, Qin Y, Shen Y, Tang Y, Yin Z, Xu H, Zhang Y, Zang X, Ding H, Yang W, Guo Y, Harley JB, Namjou B, Kaufman KM, Kottyan LC, Weirauch MT, Hou G, Shen N. Lupus enhancer risk variant causes dysregulation of IRF8 through cooperative lncRNA and DNA methylation machinery. Nat Commun 2022; 13:1855. [PMID: 35388006 PMCID: PMC8987079 DOI: 10.1038/s41467-022-29514-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Despite strong evidence that human genetic variants affect the expression of many key transcription factors involved in autoimmune diseases, establishing biological links between non-coding risk variants and the gene targets they regulate remains a considerable challenge. Here, we combine genetic, epigenomic, and CRISPR activation approaches to screen for functional variants that regulate IRF8 expression. We demonstrate that the locus containing rs2280381 is a cell-type-specific enhancer for IRF8 that spatially interacts with the IRF8 promoter. Further, rs2280381 mediates IRF8 expression through enhancer RNA AC092723.1, which recruits TET1 to the IRF8 promoter regulating IRF8 expression by affecting methylation levels. The alleles of rs2280381 modulate PU.1 binding and chromatin state to regulate AC092723.1 and IRF8 expression differentially. Our work illustrates an integrative strategy to define functional genetic variants that regulate the expression of critical genes in autoimmune diseases and decipher the mechanisms underlying the dysregulation of IRF8 expression mediated by lupus risk variants.
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Affiliation(s)
- Tian Zhou
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032 China ,Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China
| | - Xinyi Zhu
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Zhizhong Ye
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China
| | - Yong-Fei Wang
- grid.194645.b0000000121742757Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, 999077 China
| | - Chao Yao
- grid.9227.e0000000119573309Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences (SIBS), University of Chinese Academy of Sciences, Chinese Academy of Sciences (CAS), Shanghai, 200031 China
| | - Ning Xu
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Mi Zhou
- grid.16821.3c0000 0004 0368 8293Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240 China
| | - Jianyang Ma
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Yuting Qin
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Yiwei Shen
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Yuanjia Tang
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Zhihua Yin
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China
| | - Hong Xu
- grid.16821.3c0000 0004 0368 8293Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200127 China ,grid.16821.3c0000 0004 0368 8293Shanghai Key Laboratory of Gynecologic Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200127 China
| | - Yutong Zhang
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Xiaoli Zang
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Huihua Ding
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China
| | - Wanling Yang
- grid.194645.b0000000121742757Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, 999077 China
| | - Ya Guo
- grid.16821.3c0000 0004 0368 8293Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240 China
| | - John B. Harley
- grid.413848.20000 0004 0420 2128US Department of Veterans Affairs Medical Center, Cincinnati, OH 45229 USA
| | - Bahram Namjou
- grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Kenneth M. Kaufman
- grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA
| | - Leah C. Kottyan
- grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Matthew T. Weirauch
- grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.239573.90000 0000 9025 8099Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Guojun Hou
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032 China ,Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China
| | - Nan Shen
- grid.16821.3c0000 0004 0368 8293Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001 China ,grid.16821.3c0000 0004 0368 8293State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200032 China ,Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040 China ,grid.239573.90000 0000 9025 8099Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA
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26
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Yang TH, Yang YC, Tu KC. regCNN: identifying Drosophila genome-wide cis-regulatory modules via integrating the local patterns in epigenetic marks and transcription factor binding motifs. Comput Struct Biotechnol J 2022; 20:296-308. [PMID: 35035784 PMCID: PMC8724954 DOI: 10.1016/j.csbj.2021.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 11/20/2022] Open
Abstract
Transcription regulation in metazoa is controlled by the binding events of transcription factors (TFs) or regulatory proteins on specific modular DNA regulatory sequences called cis-regulatory modules (CRMs). Understanding the distributions of CRMs on a genomic scale is essential for constructing the metazoan transcriptional regulatory networks that help diagnose genetic disorders. While traditional reporter-assay CRM identification approaches can provide an in-depth understanding of functions of some CRM, these methods are usually cost-inefficient and low-throughput. It is generally believed that by integrating diverse genomic data, reliable CRM predictions can be made. Hence, researchers often first resort to computational algorithms for genome-wide CRM screening before specific experiments. However, current existing in silico methods for searching potential CRMs were restricted by low sensitivity, poor prediction accuracy, or high computation time from TFBS composition combinatorial complexity. To overcome these obstacles, we designed a novel CRM identification pipeline called regCNN by considering the base-by-base local patterns in TF binding motifs and epigenetic profiles. On the test set, regCNN shows an accuracy/auROC of 84.5%/92.5% in CRM identification. And by further considering local patterns in epigenetic profiles and TF binding motifs, it can accomplish 4.7% (92.5%–87.8%) improvement in the auROC value over the average value-based pure multi-layer perceptron model. We also demonstrated that regCNN outperforms all currently available tools by at least 11.3% in auROC values. Finally, regCNN is verified to be robust against its resizing window hyperparameter in dealing with the variable lengths of CRMs. The model of regCNN can be downloaded athttp://cobisHSS0.im.nuk.edu.tw/regCNN/.
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Affiliation(s)
- Tzu-Hsien Yang
- Department of Information Management, National University of Kaohsiung, Kaohsiung University Rd, 811 Kaohsiung, Taiwan
| | - Ya-Chiao Yang
- Department of Information Management, National University of Kaohsiung, Kaohsiung University Rd, 811 Kaohsiung, Taiwan
| | - Kai-Chi Tu
- Department of Information Management, National University of Kaohsiung, Kaohsiung University Rd, 811 Kaohsiung, Taiwan
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27
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Iskandar K, Simanjaya S, Indrawan T, Kalim AS, Marcellus, Heriyanto DS, Gunadi. Is There Any Mosaicism in REarranged During Transfection Variant in Hirschsprung Disease's Patients? Front Pediatr 2022; 10:842820. [PMID: 35359901 PMCID: PMC8960445 DOI: 10.3389/fped.2022.842820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/21/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Hirschsprung disease (HSCR) is a heterogeneous genetic disease characterized by the absence of ganglion cells in the intestinal tract. The REarranged during Transfection (RET) is the most responsible gene for its pathogenesis. RET's somatic mosaicisms have been reported for HSCR; however, they are still under-recognized. Therefore, we determined the frequency of somatic mutation of RET rs2435357 in HSCR patients at our institution. METHODS We performed RET rs2435357 genotyping from 73 HSCR formalin-fixed and paraffin-embedded (FFPE) rectal and 60 non-HSCR controls using the PCR-RFLP method. Subsequently, we compared those frequencies of genotypes for RET rs2435357 with our previous genotyping data from 93 HSCR blood specimens. RESULTS The frequencies of genotypes for RET rs2435357 in HSCR paraffin-embedded rectal were CC 0, CT 11 (15%), and TT 62 (85%), whereas their frequencies in HSCR blood samples were CC 4 (4.3%), CT 22 (23.7%), and TT 67 (72%). Those frequencies differences almost reached a significant level (p = 0.06). Moreover, the frequency of RET rs2435357 risk allele (T) was significantly higher in HSCR patients (135/146, 92.5%) than controls (46/120, 38.3%) (p = 3.4 × 10-22), with an odds ratio of 19.74 (95% confidence interval = 9.65-40.41). CONCLUSION Our study suggests somatic mosaicism in HSCR patients. These findings further imply the complexity of the pathogenesis of HSCR. Moreover, our study confirms the RET rs2435357 as a significant genetic risk factor for HSCR patients.
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Affiliation(s)
- Kristy Iskandar
- Department of Child Health/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/UGM Academic Hospital, Yogyakarta, Indonesia
| | - Susan Simanjaya
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Taufik Indrawan
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Alvin Santoso Kalim
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Marcellus
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Didik Setyo Heriyanto
- Department of Anatomical Pathology/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Gunadi
- Pediatric Surgery Division, Department of Surgery/Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada/Dr. Sardjito Hospital, Yogyakarta, Indonesia
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28
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Chatterjee S, Karasaki KM, Fries LE, Kapoor A, Chakravarti A. A multi-enhancer RET regulatory code is disrupted in Hirschsprung disease. Genome Res 2021; 31:2199-2208. [PMID: 34782358 PMCID: PMC8647834 DOI: 10.1101/gr.275667.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/05/2021] [Indexed: 01/25/2023]
Abstract
The major genetic risk factors for Hirschsprung disease (HSCR) are three common polymorphisms within cis-regulatory elements (CREs) of the receptor tyrosine kinase gene RET, which reduce its expression during enteric nervous system (ENS) development. These risk variants attenuate binding of the transcription factors RARB, GATA2, and SOX10 to their cognate CREs, reduce RET gene expression, and dysregulate other ENS and HSCR genes in the RET-EDNRB gene regulatory network (GRN). Here, we use siRNA, ChIP, and CRISPR-Cas9 deletion analyses in the SK-N-SH cell line to ask how many additional HSCR-associated risk variants reside in RET CREs that affect its gene expression. We identify 22 HSCR-associated variants in candidate RET CREs, of which seven have differential allele-specific in vitro enhancer activity, and four of these seven affect RET gene expression; of these, two enhancers are bound by the transcription factor PAX3. We also show that deleting multiple variant-containing enhancers leads to synergistic effects on RET gene expression. These, coupled with our prior results, show that common sequence variants in at least 10 RET enhancers affect HSCR risk, seven with experimental evidence of affecting RET gene expression, extending the known RET-EDNRB GRN to reveal an extensive regulatory code modulating disease risk at a single gene.
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Affiliation(s)
- Sumantra Chatterjee
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, New York 10016, USA
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, New York 10016, USA
| | - Kameko M Karasaki
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Lauren E Fries
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, New York 10016, USA
| | - Ashish Kapoor
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Aravinda Chakravarti
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, New York 10016, USA
- Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, New York 10016, USA
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29
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Kapoor A, Nandakumar P, Auer DR, Sosa MX, Ross H, Bollinger J, Yan J, Berrios C, Chakravarti A. Multiple, independent, common variants at RET, SEMA3 and NRG1 gut enhancers specify Hirschsprung disease risk in European ancestry subjects. J Pediatr Surg 2021; 56:2286-2294. [PMID: 34006365 PMCID: PMC8526751 DOI: 10.1016/j.jpedsurg.2021.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/08/2021] [Accepted: 04/06/2021] [Indexed: 11/28/2022]
Abstract
PURPOSE Hirschsprung disease (HSCR) is a developmental disorder of the enteric nervous system (ENS) characterized by congenital aganglionosis arising from coding variants in ENS genes causing partial or total loss-of-function. Low-penetrance, common, noncoding variants at RET, SEMA3 and NRG1 loci are also associated with HSCR, with small-to-moderate loss of gene expression mediated through sequence variants in cis-regulatory elements (CRE) as another causal mechanism. Since these latter variants are common, many individuals carry multiple risk variants. However, the extent and combinatorial effects of all putative CRE variants within and across these loci on HSCR is unknown. METHODS Using 583 HSCR subjects, one of the largest samples of European ancestry studied, and genotyping 56 tag variants, we evaluated association of all common variants overlapping putative gut CREs and fine-mapped causal variants at RET, SEMA3 and NRG1. RESULTS We demonstrate that 28 and 8 tag variants, several of which are genetically independent, overlap putative-enhancers at the RET and SEMA3 loci, respectively, as well as two fine-mapped tag variants at the NRG1 locus, are significantly associated with HSCR. Importantly, disease risk increases with increasing numbers of risk alleles from multiple variants within and across these loci, varying >25-fold across individuals. CONCLUSION This increasing allele number-dependent risk, we hypothesize, arises from HSCR-relevant ENS cells sensing the reduced gene expression at multiple ENS genes since their developmental effects are integrated through gene regulatory networks.
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Affiliation(s)
- Ashish Kapoor
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA; Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Priyanka Nandakumar
- McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dallas R. Auer
- McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Maria X. Sosa
- McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Holly Ross
- McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Juli Bollinger
- McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jia Yan
- McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Courtney Berrios
- McKusick-Nathans Institute of Genetic Medicine, Johns
Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA; Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY 10016, USA.
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30
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MacKenzie KC, Garritsen R, Chauhan RK, Sribudiani Y, de Graaf BM, Rugenbrink T, Brouwer R, van Ijcken WFJ, de Blaauw I, Brooks AS, Sloots CEJ, Meeuwsen CJHM, Wijnen RM, Newgreen DF, Burns AJ, Hofstra RMW, Alves MM, Brosens E. The Somatic Mutation Paradigm in Congenital Malformations: Hirschsprung Disease as a Model. Int J Mol Sci 2021; 22:12354. [PMID: 34830235 PMCID: PMC8624421 DOI: 10.3390/ijms222212354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/05/2021] [Accepted: 11/10/2021] [Indexed: 12/20/2022] Open
Abstract
Patients with Hirschsprung disease (HSCR) do not always receive a genetic diagnosis after routine screening in clinical practice. One of the reasons for this could be that the causal mutation is not present in the cell types that are usually tested-whole blood, dermal fibroblasts or saliva-but is only in the affected tissue. Such mutations are called somatic, and can occur in a given cell at any stage of development after conception. They will then be present in all subsequent daughter cells. Here, we investigated the presence of somatic mutations in HSCR patients. For this, whole-exome sequencing and copy number analysis were performed in DNA isolated from purified enteric neural crest cells (ENCCs) and blood or fibroblasts of the same patient. Variants identified were subsequently validated by Sanger sequencing. Several somatic variants were identified in all patients, but causative mutations for HSCR were not specifically identified in the ENCCs of these patients. Larger copy number variants were also not found to be specific to ENCCs. Therefore, we believe that somatic mutations are unlikely to be identified, if causative for HSCR. Here, we postulate various modes of development following the occurrence of a somatic mutation, to describe the challenges in detecting such mutations, and hypothesize how somatic mutations may contribute to 'missing heritability' in developmental defects.
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Affiliation(s)
- Katherine C. MacKenzie
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (K.C.M.); (R.G.); (R.K.C.); (Y.S.); (B.M.d.G.); (T.R.); (A.S.B.); (A.J.B.); (R.M.W.H.)
| | - Rhiana Garritsen
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (K.C.M.); (R.G.); (R.K.C.); (Y.S.); (B.M.d.G.); (T.R.); (A.S.B.); (A.J.B.); (R.M.W.H.)
- Department of Pediatric Surgery, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (I.d.B.); (C.E.J.S.); (C.J.H.M.M.); (R.M.W.)
| | - Rajendra K. Chauhan
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (K.C.M.); (R.G.); (R.K.C.); (Y.S.); (B.M.d.G.); (T.R.); (A.S.B.); (A.J.B.); (R.M.W.H.)
- Fluidigm Europe B.V., 1101 CM Amstelveen, The Netherlands
| | - Yunia Sribudiani
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (K.C.M.); (R.G.); (R.K.C.); (Y.S.); (B.M.d.G.); (T.R.); (A.S.B.); (A.J.B.); (R.M.W.H.)
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Universitas of Padjadjaran, Bandung 45363, Indonesia
| | - Bianca M. de Graaf
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (K.C.M.); (R.G.); (R.K.C.); (Y.S.); (B.M.d.G.); (T.R.); (A.S.B.); (A.J.B.); (R.M.W.H.)
| | - Tim Rugenbrink
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (K.C.M.); (R.G.); (R.K.C.); (Y.S.); (B.M.d.G.); (T.R.); (A.S.B.); (A.J.B.); (R.M.W.H.)
| | - Rutger Brouwer
- Department of Cell Biology & Center for Biomics, Erasmus University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (R.B.); (W.F.J.v.I.)
| | - Wilfred F. J. van Ijcken
- Department of Cell Biology & Center for Biomics, Erasmus University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (R.B.); (W.F.J.v.I.)
| | - Ivo de Blaauw
- Department of Pediatric Surgery, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (I.d.B.); (C.E.J.S.); (C.J.H.M.M.); (R.M.W.)
- Department of Paediatric Surgery, Amalia Children’s Hospital, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Alice S. Brooks
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (K.C.M.); (R.G.); (R.K.C.); (Y.S.); (B.M.d.G.); (T.R.); (A.S.B.); (A.J.B.); (R.M.W.H.)
| | - Cornelius E. J. Sloots
- Department of Pediatric Surgery, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (I.d.B.); (C.E.J.S.); (C.J.H.M.M.); (R.M.W.)
| | - Conny J. H. M. Meeuwsen
- Department of Pediatric Surgery, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (I.d.B.); (C.E.J.S.); (C.J.H.M.M.); (R.M.W.)
| | - René M. Wijnen
- Department of Pediatric Surgery, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (I.d.B.); (C.E.J.S.); (C.J.H.M.M.); (R.M.W.)
| | - Donald F. Newgreen
- Department of Cell Biology, Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, VIC 3052, Australia;
| | - Alan J. Burns
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (K.C.M.); (R.G.); (R.K.C.); (Y.S.); (B.M.d.G.); (T.R.); (A.S.B.); (A.J.B.); (R.M.W.H.)
- Department of Stem Cells and Regenerative Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Takeda Pharmaceuticals, Cambridge, MA 02139, USA
| | - Robert M. W. Hofstra
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (K.C.M.); (R.G.); (R.K.C.); (Y.S.); (B.M.d.G.); (T.R.); (A.S.B.); (A.J.B.); (R.M.W.H.)
- Department of Stem Cells and Regenerative Medicine, UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | - Maria M. Alves
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (K.C.M.); (R.G.); (R.K.C.); (Y.S.); (B.M.d.G.); (T.R.); (A.S.B.); (A.J.B.); (R.M.W.H.)
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children’s Hospital, 3000 CA Rotterdam, The Netherlands; (K.C.M.); (R.G.); (R.K.C.); (Y.S.); (B.M.d.G.); (T.R.); (A.S.B.); (A.J.B.); (R.M.W.H.)
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Liu Y, Lan C, Li B, Wang N, Zuo X, Huang L, Wu Y, Zhu Y. Associations of CYP2B6 genetic polymorphisms with Hirschsprung's disease in a southern Chinese population. J Clin Lab Anal 2021; 35:e24074. [PMID: 34752660 PMCID: PMC8649360 DOI: 10.1002/jcla.24074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/08/2021] [Accepted: 10/17/2021] [Indexed: 11/11/2022] Open
Abstract
Background Hirschsprung’s disease (HSCR) is an enteric nervous system birth defect partially caused by a genetic disorder. Single‐nucleotide polymorphisms (SNPs) of the cytochrome P450 family 2 subfamily B member 6 (CYP2B6) gene are reported to be associated with HSCR. Methods We evaluated the association of rs2054675, rs707265, and rs1042389 with HSCR susceptibility in southern Chinese children including 1470 HSCR patients and 1473 controls using the TaqMan SNP Genotyping Assay. Results rs2054675 C allele and the rs707265 G allele were risk SNPs for total colonic aganglionosis (OR = 1.82, 95% CI 1.29 ~ 2.55, P_adj < 0.001 and OR = 0.68, 95% CI 0.48 ~ 0.97, P_adj = 0.034). These results suggested that CYP2B6 rs2054675 and rs707265 polymorphisms were associated with increased susceptibility to the severe HSCR subtype in southern Chinese children. Conclusion We suggest that CYP2B6 rs2054675 and rs707265 polymorphisms are associated with increased susceptibility to the severe HSCR subtype in southern Chinese children.
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Affiliation(s)
- Yanqing Liu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Chaoting Lan
- The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Bingxiao Li
- The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Ning Wang
- Guangzhou Medical University, Guangzhou, China
| | - Xiaoyu Zuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Lihua Huang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yuxin Wu
- The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yun Zhu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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Yan H, Tian S, Kleinstern G, Wang Z, Lee JH, Boddicker NJ, Cerhan JR, Kay NE, Braggio E, Slager SL. Chronic lymphocytic leukemia (CLL) risk is mediated by multiple enhancer variants within CLL risk loci. Hum Mol Genet 2021; 29:2761-2774. [PMID: 32744316 DOI: 10.1093/hmg/ddaa165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 07/02/2020] [Accepted: 07/25/2020] [Indexed: 12/12/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common adult leukemia in Western countries. It has a strong genetic basis, showing a ~ 8-fold increased risk of CLL in first-degree relatives. Genome-wide association studies (GWAS) have identified 41 risk variants across 41 loci. However, for a majority of the loci, the functional variants and the mechanisms underlying their causal roles remain undefined. Here, we examined the genetic and epigenetic features associated with 12 index variants, along with any correlated (r2 ≥ 0.5) variants, at the CLL risk loci located outside of gene promoters. Based on publicly available ChIP-seq and chromatin accessibility data as well as our own ChIP-seq data from CLL patients, we identified six candidate functional variants at six loci and at least two candidate functional variants at each of the remaining six loci. The functional variants are predominantly located within enhancers or super-enhancers, including bi-directionally transcribed enhancers, which are often restricted to immune cell types. Furthermore, we found that, at 78% of the functional variants, the alternative alleles altered the transcription factor binding motifs or histone modifications, indicating the involvement of these variants in the change of local chromatin state. Finally, the enhancers carrying functional variants physically interacted with genes enriched in the type I interferon signaling pathway, apoptosis, or TP53 network that are known to play key roles in CLL. These results support the regulatory roles for inherited noncoding variants in the pathogenesis of CLL.
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Affiliation(s)
- Huihuang Yan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Shulan Tian
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Geffen Kleinstern
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhiquan Wang
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jeong-Heon Lee
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Neil E Kay
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Esteban Braggio
- Division of Hematology/Oncology, Department of Medicine, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
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33
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Claringbould A, Zaugg JB. Enhancers in disease: molecular basis and emerging treatment strategies. Trends Mol Med 2021; 27:1060-1073. [PMID: 34420874 DOI: 10.1016/j.molmed.2021.07.012] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
Enhancers are genomic sequences that play a key role in regulating tissue-specific gene expression levels. An increasing number of diseases are linked to impaired enhancer function through chromosomal rearrangement, genetic variation within enhancers, or epigenetic modulation. Here, we review how these enhancer disruptions have recently been implicated in congenital disorders, cancers, and common complex diseases and address the implications for diagnosis and treatment. Although further fundamental research into enhancer function, target genes, and context is required, enhancer-targeting drugs and gene editing approaches show great therapeutic promise for a range of diseases.
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Affiliation(s)
- Annique Claringbould
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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34
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Chakravarti A. Magnitude of Mendelian versus complex inheritance of rare disorders. Am J Med Genet A 2021; 185:3287-3293. [PMID: 34418293 DOI: 10.1002/ajmg.a.62463] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 11/10/2022]
Abstract
In medical genetics, the vast majority of patients with a currently known genetic basis harbor a rare deleterious allele explaining its Mendelian inheritance. Increasingly, for these phenotypes, we recognize exceptions to Mendelian expectations from non-penetrance of clinical disease to significant inter-individual variation in clinical manifestations, likely reflecting the actions of additional modifier genes. Despite recent progress, we still remain ignorant about the molecular basis for many rare disorders presumed to be Mendelian. The molecular evidence increasingly suggests a role for multiple genes in some of these cases, but for how many? In this article, I discuss why equating a phenotype as Mendelian or complex may be short-sighted or even erroneous. As we learn more about the functions of the human genome with its genes in networks, we should view the phenotype of an individual patient as arising from his or her total genomic deleterious burden in a set of functionally inter-related genes affecting that phenotype. This can sometimes arise from deleterious allele(s) at a single gene (Mendelian inheritance) creating a specific biochemical deficiency (or excess) but could just as frequently arise from the cumulative effects of multiple disease alleles (complex inheritance) leading to the same biochemical deficiency (or excess).
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Affiliation(s)
- Aravinda Chakravarti
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, New York, USA
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35
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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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36
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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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37
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Uesaka T, Okamoto M, Nagashimada M, Tsuda Y, Kihara M, Kiyonari H, Enomoto H. Enhanced enteric neurogenesis by Schwann cell precursors in mouse models of Hirschsprung disease. Glia 2021; 69:2575-2590. [PMID: 34272903 DOI: 10.1002/glia.24059] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/21/2021] [Accepted: 07/05/2021] [Indexed: 12/31/2022]
Abstract
Hirschsprung disease (HSCR) is characterized by congenital absence of enteric neurons in distal portions of the gut. Although recent studies identified Schwann cell precursors (SCPs) as a novel cellular source of enteric neurons, it is unknown how SCPs contribute to the disease phenotype of HSCR. Using Schwann cell-specific genetic labeling, we investigated SCP-derived neurogenesis in two mouse models of HSCR; Sox10 haploinsufficient mice exhibiting distal colonic aganglionosis and Ednrb knockout mice showing small intestinal aganglionosis. We also examined Ret dependency in SCP-derived neurogenesis using mice displaying intestinal aganglionosis in which Ret expression was conditionally removed in the Schwann cell lineage. SCP-derived neurons were abundant in the transition zone lying between the ganglionated and aganglionic segments, although SCP-derived neurogenesis was scarce in the aganglionic region. In the transition zone, SCPs mainly gave rise to nitrergic neurons that are rarely observed in the SCP-derived neurons under the normal condition. Enhanced SCP-derived neurogenesis was also detected in the transition zone of mice lacking RET expression in the Schwann cell lineage. Increased SCP-derived neurogenesis in the transition zone suggests that reduction in the vagal neural crest-derived enteric neurons promotes SCP-derived neurogenesis. SCPs may adopt a neuronal subtype by responding to changes in the gut environment. Robust SCP-derived neurogenesis can occur in a Ret-independent manner, which suggests that SCPs are a cellular source to compensate for missing enteric neurons in HSCR.
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Affiliation(s)
- Toshihiro Uesaka
- Division for Neural Differentiation and Regeneration, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Mitsumasa Okamoto
- Division for Neural Differentiation and Regeneration, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan.,Department of Pediatric Surgery, Japanese Red Cross Society, Himeji Hospital, Himeji, Hyogo, Japan
| | - Mayumi Nagashimada
- Division for Neural Differentiation and Regeneration, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan.,Division of Health Science, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Yoshihiro Tsuda
- Division for Neural Differentiation and Regeneration, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Miho Kihara
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Hideki Enomoto
- Division for Neural Differentiation and Regeneration, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
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38
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Padhi EM, Hayeck TJ, Cheng Z, Chatterjee S, Mannion BJ, Byrska-Bishop M, Willems M, Pinson L, Redon S, Benech C, Uguen K, Audebert-Bellanger S, Le Marechal C, Férec C, Efthymiou S, Rahman F, Maqbool S, Maroofian R, Houlden H, Musunuri R, Narzisi G, Abhyankar A, Hunter RD, Akiyama J, Fries LE, Ng JK, Mehinovic E, Stong N, Allen AS, Dickel DE, Bernier RA, Gorkin DU, Pennacchio LA, Zody MC, Turner TN. Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism. Hum Genomics 2021; 15:44. [PMID: 34256850 PMCID: PMC8278787 DOI: 10.1186/s40246-021-00342-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/17/2021] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2671 families with autism (discovery cohort of 516 families, replication cohort of 2155 families). We focused on DNVs in enhancers with characterized in vivo activity in the brain and identified an excess of DNVs in an enhancer named hs737. RESULTS We adapted the fitDNM statistical model to work in noncoding regions and tested enhancers for excess of DNVs in families with autism. We found only one enhancer (hs737) with nominal significance in the discovery (p = 0.0172), replication (p = 2.5 × 10-3), and combined dataset (p = 1.1 × 10-4). Each individual with a DNV in hs737 had shared phenotypes including being male, intact cognitive function, and hypotonia or motor delay. Our in vitro assessment of the DNVs showed they all reduce enhancer activity in a neuronal cell line. By epigenomic analyses, we found that hs737 is brain-specific and targets the transcription factor gene EBF3 in human fetal brain. EBF3 is genome-wide significant for coding DNVs in NDDs (missense p = 8.12 × 10-35, loss-of-function p = 2.26 × 10-13) and is widely expressed in the body. Through characterization of promoters bound by EBF3 in neuronal cells, we saw enrichment for binding to NDD genes (p = 7.43 × 10-6, OR = 1.87) involved in gene regulation. Individuals with coding DNVs have greater phenotypic severity (hypotonia, ataxia, and delayed development syndrome [HADDS]) in comparison to individuals with noncoding DNVs that have autism and hypotonia. CONCLUSIONS In this study, we identify DNVs in the hs737 enhancer in individuals with autism. Through multiple approaches, we find hs737 targets the gene EBF3 that is genome-wide significant in NDDs. By assessment of noncoding variation and the genes they affect, we are beginning to understand their impact on gene regulatory networks in NDDs.
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Affiliation(s)
- Evin M Padhi
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA
| | - Tristan J Hayeck
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Zhang Cheng
- Center for Epigenomics, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Sumantra Chatterjee
- Center for Human Genetics and Genomics, NYU School of Medicine, New York, NY, 10016, USA
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Marjolaine Willems
- University of Montpellier, département de Génétique, maladies rares médecine personnalisée, U 1298, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Lucile Pinson
- University of Montpellier, département de Génétique, maladies rares médecine personnalisée, U 1298, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Sylvia Redon
- CHU Brest, Inserm, Univ Brest, EFS,UMR 1078, GGB, F-29200, Brest, France
| | - Caroline Benech
- CHU Brest, Inserm, Univ Brest, EFS,UMR 1078, GGB, F-29200, Brest, France
| | - Kevin Uguen
- CHU Brest, Inserm, Univ Brest, EFS,UMR 1078, GGB, F-29200, Brest, France
| | | | - Cédric Le Marechal
- CHU Brest, Inserm, Univ Brest, EFS,UMR 1078, GGB, F-29200, Brest, France
| | - Claude Férec
- CHU Brest, Inserm, Univ Brest, EFS,UMR 1078, GGB, F-29200, Brest, France
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Fatima Rahman
- Development and Behavioral Pediatrics Department, Institute of Child Health and Children Hospital, Lahore, Pakistan
| | - Shazia Maqbool
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- Development and Behavioral Pediatrics Department, Institute of Child Health and Children Hospital, Lahore, Pakistan
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | | | | | | | - Riana D Hunter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jennifer Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Lauren E Fries
- Center for Human Genetics and Genomics, NYU School of Medicine, New York, NY, 10016, USA
| | - Jeffrey K Ng
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA
| | - Elvisa Mehinovic
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA
| | - Nick Stong
- Institute for Genomic Medicine, Columbia University, New York, NY, 10027, USA
| | - Andrew S Allen
- Center for Statistical Genetics and Genomics, Duke University, Durham, NC, 27708, USA
- Division of Integrative Genomics, Duke University, Durham, NC, 27708, USA
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, 27708, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA
| | - David U Gorkin
- Center for Epigenomics, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA.
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Gao T, Wright-Jin EC, Sengupta R, Anderson JB, Heuckeroth RO. Cell-autonomous retinoic acid receptor signaling has stage-specific effects on mouse enteric nervous system. JCI Insight 2021; 6:145854. [PMID: 33848271 PMCID: PMC8262371 DOI: 10.1172/jci.insight.145854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/07/2021] [Indexed: 12/11/2022] Open
Abstract
Retinoic acid (RA) signaling is essential for enteric nervous system (ENS) development, since vitamin A deficiency or mutations in RA signaling profoundly reduce bowel colonization by ENS precursors. These RA effects could occur because of RA activity within the ENS lineage or via RA activity in other cell types. To define cell-autonomous roles for retinoid signaling within the ENS lineage at distinct developmental time points, we activated a potent floxed dominant-negative RA receptor α (RarαDN) in the ENS using diverse CRE recombinase–expressing mouse lines. This strategy enabled us to block RA signaling at premigratory, migratory, and postmigratory stages for ENS precursors. We found that cell-autonomous loss of RA receptor (RAR) signaling dramatically affected ENS development. CRE activation of RarαDN expression at premigratory or migratory stages caused severe intestinal aganglionosis, but at later stages, RarαDN induced a broad range of phenotypes including hypoganglionosis, submucosal plexus loss, and abnormal neural differentiation. RNA sequencing highlighted distinct RA-regulated gene sets at different developmental stages. These studies show complicated context-dependent RA-mediated regulation of ENS development.
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Affiliation(s)
- Tao Gao
- Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Elizabeth C Wright-Jin
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rajarshi Sengupta
- Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Jessica B Anderson
- Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Robert O Heuckeroth
- Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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40
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Li Y, Lv X, Chen H, Zhi Z, Wei Z, Wang B, Zhou L, Li H, Tang W. Peptide Derived from AHNAK Inhibits Cell Migration and Proliferation in Hirschsprung's Disease by Targeting the ERK1/2 Pathway. J Proteome Res 2021; 20:2308-2318. [PMID: 33853325 DOI: 10.1021/acs.jproteome.0c00811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Hirschsprung's disease (HSCR) is characterized by the lack of ganglion cells in the distal part of the digestive tract. It occurs due to migration disorders of enteric neural crest cells (ENCCs) from 5 to 12 weeks of embryonic development. More and more studies show that HSCR is a result of the interaction of multiple genes and the microenvironments, but its specific pathogenesis has not been fully elucidated. Studies have confirmed that many substances in the intestinal microenvironment, such as laminin and β1-integrin, play a vital regulatory role in cell growth and disease progression. In addition to these high-molecular-weight proteins, research on endogenous polypeptides derived from these proteins has been increasing in recent years. However, it is unclear whether these endogenous peptides have effects on the migration of ENCCs and thus participate in the occurrence of HSCR. Previously, our research group found that compared with the normal intestinal tissue, the expression of AHNAK protein in the stenosed intestinal tissue of HSCR patients was significantly upregulated, and overexpression of AHNAK could inhibit cell migration and proliferation. In this study, endogenous peptides were extracted from the normal control intestinal tissue and the stenosed HSCR intestinal tissue. The endogenous polypeptide expression profile was analyzed by liquid chromatography-mass spectrometry, and multiple peptides derived from AHNAK protein were found. We selected one of them, "EGPEVDVNLPK", for research. Because there is no uniform naming system, this peptide is temporarily named PDAHNAK (peptide derived from AHNAK). This project aims to clarify the potential role of PDAHNAK in the development of HSCR and to further understand its relationship with its precursor protein AHNAK and how they contribute to the development of HSCR.
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Affiliation(s)
- Yuhan Li
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China.,Department of Pediatric Surgery, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiurui Lv
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China.,School of Medicine & Dentistry, University of Rochester, Rochester 14642, United States
| | - Huan Chen
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China.,State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhengke Zhi
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China.,State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhonghong Wei
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Binyu Wang
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China.,State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - LingLing Zhou
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Hongxing Li
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China.,State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Weibing Tang
- Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China.,State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
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Kang YN, Fung C, Vanden Berghe P. Gut innervation and enteric nervous system development: a spatial, temporal and molecular tour de force. Development 2021; 148:148/3/dev182543. [PMID: 33558316 DOI: 10.1242/dev.182543] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During embryonic development, the gut is innervated by intrinsic (enteric) and extrinsic nerves. Focusing on mammalian ENS development, in this Review we highlight how important the different compartments of this innervation are to assure proper gut function. We specifically address the three-dimensional architecture of the innervation, paying special attention to the differences in development along the longitudinal and circumferential axes of the gut. We review recent information about the formation of both intrinsic innervation, which is fairly well-known, as well as the establishment of the extrinsic innervation, which, despite its importance in gut-brain signaling, has received much less attention. We further discuss how external microbial and nutritional cues or neuroimmune interactions may influence development of gut innervation. Finally, we provide summary tables, describing the location and function of several well-known molecules, along with some newer factors that have more recently been implicated in the development of gut innervation.
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Affiliation(s)
- Yi-Ning Kang
- Laboratory for Enteric NeuroScience (LENS), Translational Research Center for Gastrointestinal Disorders (TARGID), University of Leuven, Leuven 3000, Belgium
| | - Candice Fung
- Laboratory for Enteric NeuroScience (LENS), Translational Research Center for Gastrointestinal Disorders (TARGID), University of Leuven, Leuven 3000, Belgium
| | - Pieter Vanden Berghe
- Laboratory for Enteric NeuroScience (LENS), Translational Research Center for Gastrointestinal Disorders (TARGID), University of Leuven, Leuven 3000, Belgium
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42
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Chang H, Cai X, Li HJ, Liu WP, Zhao LJ, Zhang CY, Wang JY, Liu JW, Ma XL, Wang L, Yao YG, Luo XJ, Li M, Xiao X. Functional Genomics Identify a Regulatory Risk Variation rs4420550 in the 16p11.2 Schizophrenia-Associated Locus. Biol Psychiatry 2021; 89:246-255. [PMID: 33246552 DOI: 10.1016/j.biopsych.2020.09.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 09/17/2020] [Accepted: 09/17/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Genome-wide association studies (GWASs) have reported hundreds of genomic loci associated with schizophrenia, yet identifying the functional risk variations is a key step in elucidating the underlying mechanisms. METHODS We applied multiple bioinformatics and molecular approaches, including expression quantitative trait loci analyses, epigenome signature identification, luciferase reporter assay, chromatin conformation capture, homology-directed genome editing by CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/Cas9), RNA sequencing, and ATAC-Seq (assay for transposase-accessible chromatin using sequencing). RESULTS We found that the schizophrenia GWAS risk variations at 16p11.2 were significantly associated with messenger RNA levels of multiple genes in human brain, and one of the leading expression quantitative trait loci genes, MAPK3, is located ∼200 kb away from these risk variations in the genome. Further analyses based on the epigenome marks in human brain and cell lines suggested that a noncoding single nucleotide polymorphism, rs4420550 (p = 2.36 × 10-9 in schizophrenia GWAS), was within a DNA enhancer region, which was validated via in vitro luciferase reporter assays. The chromatin conformation capture experiment showed that the rs4420550 region physically interacted with the MAPK3 promoter and TAOK2 promoter. Precise CRISPR/Cas9 editing of a single base pair in cells followed by RNA sequencing further confirmed the regulatory effects of rs4420550 on the transcription of 16p11.2 genes, and ATAC-Seq demonstrated that rs4420550 affected chromatin accessibility at the 16p11.2 region. The rs4420550-[A/A] cells showed significantly higher proliferation rates compared with rs4420550-[G/G] cells. CONCLUSIONS These results together suggest that rs4420550 is a functional risk variation, and this study illustrates an example of comprehensive functional characterization of schizophrenia GWAS risk loci.
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Affiliation(s)
- Hong Chang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China
| | - Xin Cai
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Hui-Juan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Wei-Peng Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Li-Juan Zhao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Chu-Yi Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Jun-Yang Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Jie-Wei Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China
| | - Xiao-Lei Ma
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China
| | - Lu Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China; KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China; KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Shanghai, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China; KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Shanghai, China.
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Jiang Q, Wang Y, Gao Y, Wang H, Zhang Z, Li Q, Xu S, Cai W, Li L. RET compound inheritance in Chinese patients with Hirschsprung disease: lack of penetrance from insufficient gene dysfunction. Hum Genet 2021; 140:813-825. [PMID: 33433679 DOI: 10.1007/s00439-020-02247-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/11/2020] [Indexed: 11/30/2022]
Abstract
Hirschsprung disease (HSCR) is a neurocristopathy characterized by the absence of enteric ganglia along variable lengths of the intestine. Genetic defects play a major role in HSCR pathogenesis with nearly 50% of patients having a structural or regulatory deficiency in the major susceptibility gene RET. However, complete molecular defects remain poorly characterized in most patients. Here, we performed detailed genetic, molecular, and populational investigations of rare null mutations and modifiers at the RET locus. We first verified the pathogenicity of three RET splice site mutants (c.1879 + 1G > A, c.2607 + 5G > A and c.2608-3C > G) at the RNA level. We also identified significantly higher risk allele (genotype) frequencies, and their over-transmission, from unaffected parents to affected offspring of three functionally independent enhancer variants (rs2506030, rs7069590 and rs2435357, with odd ratios (OR) of 2.09, 2.71 and 7.59, respectively, P < 0.001). These three common variants are in significant (P < 4.64 × 10-186) linkage disequilibrium in the Han Chinese population with ~ 60% of them carrying at least one copy and > 10% with two copies. We show that RET compound inheritance of rare and common variants prevails in 64% (seven out of 11) of Chinese HSCR families. This study supports the idea that common RET variants can modify the penetrance of rare null RET mutations in HSCR, and the combined high susceptibility allele dosage may constitute the unique raised "risk baseline" among the Chinese population.
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Affiliation(s)
- Qian Jiang
- Department of Medical Genetics, Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Yang Wang
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai Institute for Pediatric Research, Shanghai, 200092, China
| | - Yang Gao
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Hui Wang
- Department of Medical Genetics, Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Zhen Zhang
- Department of General Surgery, Capital Institute of Pediatrics Affiliated Children's Hospital, No. 2 Yabao Rd., Chaoyang District, Beijing, 100020, China
| | - Qi Li
- Department of General Surgery, Capital Institute of Pediatrics Affiliated Children's Hospital, No. 2 Yabao Rd., Chaoyang District, Beijing, 100020, China
| | - Shuhua Xu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Wei Cai
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai Institute for Pediatric Research, Shanghai, 200092, China.
| | - Long Li
- Department of General Surgery, Capital Institute of Pediatrics Affiliated Children's Hospital, No. 2 Yabao Rd., Chaoyang District, Beijing, 100020, China.
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Tan M, Yang T, Liu H, Xiao L, Li C, Zhu J, Chen J, Li T. Maternal vitamin A deficiency impairs cholinergic and nitrergic neurons, leading to gastrointestinal dysfunction in rat offspring via RARβ. Life Sci 2020; 264:118688. [PMID: 33130074 DOI: 10.1016/j.lfs.2020.118688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023]
Abstract
AIMS Many gastrointestinal (GI) disorders are developmental in origin and are caused by abnormal enteric nervous system (ENS) formation. Maternal vitamin A deficiency (VAD) during pregnancy affects multiple central nervous system developmental processes during embryogenesis and fetal life. Here, we evaluated whether maternal diet-induced VAD during pregnancy alone can cause changes in the ENS that lead to GI dysfunction in rat offspring. MAIN METHODS Rats were selected to construct animal models of normal VA, VA deficiency and VA supplementation. The fecal water content, total gastrointestinal transmission time and colonic motility were measured to evaluate gastrointestinal function of eight-week-old offspring rats. The expression levels of RARβ, SOX10, cholinergic (ChAT) and nitrergic (nNOS) enteric neurons in colon tissues were detected through western blot and immunofluorescence. Primary enteric neurospheres were treated with retinoic acid (RA), infection with Ad-RARβ and siRARβ adenovirus, respectively. KEY FINDINGS Our data revealed marked reductions in the mean densities of cholinergic and nitrergic enteric neurons in the colon and GI dysfunction evidenced by mild intestinal flatulence, increased fecal water content, prolonged total GI transit time and reduced colon motility in adult offspring of the VAD group. Interestingly, maternal VA supplementation (VAS) during pregnancy rescued these changes. In addition, in vitro experiments demonstrated that exposure to appropriate doses of RA promoted enteric neurosphere differentiation into cholinergic and nitrergic neurons, possibly by upregulating RARβ expression, leading to enhanced SOX10 expression. SIGNIFICANCE Maternal VAD during pregnancy is an environmental risk factor for GI dysfunction in rat offspring.
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Affiliation(s)
- Mei Tan
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Child Nutrition and Health, China; Ministry of Education Key Laboratory of Child Development and Disorders, China; National Clinical Research Center for Child Health and Disorder, China; China International Science and Technology Cooperation Base of Child Development and Critical Disorders, China
| | - Ting Yang
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Child Nutrition and Health, China; Ministry of Education Key Laboratory of Child Development and Disorders, China; National Clinical Research Center for Child Health and Disorder, China; China International Science and Technology Cooperation Base of Child Development and Critical Disorders, China
| | - Huan Liu
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Child Nutrition and Health, China; Ministry of Education Key Laboratory of Child Development and Disorders, China; National Clinical Research Center for Child Health and Disorder, China; China International Science and Technology Cooperation Base of Child Development and Critical Disorders, China
| | - Lu Xiao
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Child Nutrition and Health, China; Ministry of Education Key Laboratory of Child Development and Disorders, China; National Clinical Research Center for Child Health and Disorder, China; China International Science and Technology Cooperation Base of Child Development and Critical Disorders, China
| | - Cheng Li
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Child Nutrition and Health, China; Ministry of Education Key Laboratory of Child Development and Disorders, China; National Clinical Research Center for Child Health and Disorder, China; China International Science and Technology Cooperation Base of Child Development and Critical Disorders, China
| | - Jiang Zhu
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Child Nutrition and Health, China; Ministry of Education Key Laboratory of Child Development and Disorders, China; National Clinical Research Center for Child Health and Disorder, China; China International Science and Technology Cooperation Base of Child Development and Critical Disorders, China
| | - Jie Chen
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Child Nutrition and Health, China; Ministry of Education Key Laboratory of Child Development and Disorders, China; National Clinical Research Center for Child Health and Disorder, China; China International Science and Technology Cooperation Base of Child Development and Critical Disorders, China.
| | - Tingyu Li
- Children's Nutrition Research Center, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Child Nutrition and Health, China; Ministry of Education Key Laboratory of Child Development and Disorders, China; National Clinical Research Center for Child Health and Disorder, China; China International Science and Technology Cooperation Base of Child Development and Critical Disorders, China.
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Sahlén P, Spalinskas R, Asad S, Mahapatra KD, Höjer P, Anil A, Eisfeldt J, Srivastava A, Nikamo P, Mukherjee A, Kim KH, Bergman O, Ståhle M, Sonkoly E, Pivarcsi A, Wahlgren CF, Nordenskjöld M, Taylan F, Bradley M, Tapia-Páez I. Chromatin interactions in differentiating keratinocytes reveal novel atopic dermatitis- and psoriasis-associated genes. J Allergy Clin Immunol 2020; 147:1742-1752. [PMID: 33069716 DOI: 10.1016/j.jaci.2020.09.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/14/2020] [Accepted: 09/17/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Hundreds of variants associated with atopic dermatitis (AD) and psoriasis, 2 common inflammatory skin disorders, have previously been discovered through genome-wide association studies (GWASs). The majority of these variants are in noncoding regions, and their target genes remain largely unclear. OBJECTIVE We sought to understand the effects of these noncoding variants on the development of AD and psoriasis by linking them to the genes that they regulate. METHODS We constructed genomic 3-dimensional maps of human keratinocytes during differentiation by using targeted chromosome conformation capture (Capture Hi-C) targeting more than 20,000 promoters and 214 GWAS variants and combined these data with transcriptome and epigenomic data sets. We validated our results with reporter assays, clustered regularly interspaced short palindromic repeats activation, and examination of patient gene expression from previous studies. RESULTS We identified 118 target genes of 82 AD and psoriasis GWAS variants. Differential expression of 58 of the 118 target genes (49%) occurred in either AD or psoriatic lesions, many of which were not previously linked to any skin disease. We highlighted the genes AFG1L, CLINT1, ADO, LINC00302, and RP1-140J1.1 and provided further evidence for their potential roles in AD and psoriasis. CONCLUSIONS Our work focused on skin barrier pathology through investigation of the interaction profile of GWAS variants during keratinocyte differentiation. We have provided a catalogue of candidate genes that could modulate the risk of AD and psoriasis. Given that only 35% of the target genes are the gene nearest to the known GWAS variants, we expect that our work will contribute to the discovery of novel pathways involved in AD and psoriasis.
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Affiliation(s)
- Pelin Sahlén
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden.
| | - Rapolas Spalinskas
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Samina Asad
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kunal Das Mahapatra
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Pontus Höjer
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Anandashankar Anil
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ankit Srivastava
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Pernilla Nikamo
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anaya Mukherjee
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kyu-Han Kim
- Basic Research and Innovation Division, Research and Development Unit, AmorePacific Corporation, Yongin-si, Korea
| | - Otto Bergman
- Division of Cardiovascular Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Mona Ståhle
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Enikö Sonkoly
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Dermatology Unit, Karolinska University Hospital, Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andor Pivarcsi
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Carl-Fredrik Wahlgren
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Bradley
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Dermatology Unit, Karolinska University Hospital, Stockholm, Sweden
| | - Isabel Tapia-Páez
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease. Genome Res 2020; 30:1618-1632. [PMID: 32948616 PMCID: PMC7605255 DOI: 10.1101/gr.264473.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/14/2020] [Indexed: 12/16/2022]
Abstract
It is widely recognized that noncoding genetic variants play important roles in many human diseases, but there are multiple challenges that hinder the identification of functional disease-associated noncoding variants. The number of noncoding variants can be many times that of coding variants; many of them are not functional but in linkage disequilibrium with the functional ones; different variants can have epistatic effects; different variants can affect the same genes or pathways in different individuals; and some variants are related to each other not by affecting the same gene but by affecting the binding of the same upstream regulator. To overcome these difficulties, we propose a novel analysis framework that considers convergent impacts of different genetic variants on protein binding, which provides multiscale information about disease-associated perturbations of regulatory elements, genes, and pathways. Applying it to our whole-genome sequencing data of 918 short-segment Hirschsprung disease patients and matched controls, we identify various novel genes not detected by standard single-variant and region-based tests, functionally centering on neural crest migration and development. Our framework also identifies upstream regulators whose binding is influenced by the noncoding variants. Using human neural crest cells, we confirm cell stage-specific regulatory roles of three top novel regulatory elements on our list, respectively in the RET, RASGEF1A, and PIK3C2B loci. In the PIK3C2B regulatory element, we further show that a noncoding variant found only in the patients affects the binding of the gliogenesis regulator NFIA, with a corresponding up-regulation of multiple genes in the same topologically associating domain.
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MacKenzie KC, de Graaf BM, Syrimis A, Zhao Y, Brosens E, Mancini GMS, Schot R, Halley D, Wilke M, Vøllo A, Flinter F, Green A, Mansour S, Pilch J, Stark Z, Zamba-Papanicolaou E, Christophidou-Anastasiadou V, Hofstra RMW, Jongbloed JDH, Nicolaou N, Tanteles GA, Brooks AS, Alves MM. Goldberg-Shprintzen syndrome is determined by the absence, or reduced expression levels, of KIFBP. Hum Mutat 2020; 41:1906-1917. [PMID: 32939943 PMCID: PMC7693350 DOI: 10.1002/humu.24097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 03/12/2020] [Accepted: 08/04/2020] [Indexed: 12/19/2022]
Abstract
Goldberg-Shprintzen syndrome (GOSHS) is caused by loss of function variants in the kinesin binding protein gene (KIFBP). However, the phenotypic range of this syndrome is wide, indicating that other factors may play a role. To date, 37 patients with GOSHS have been reported. Here, we document nine new patients with variants in KIFBP: seven with nonsense variants and two with missense variants. To our knowledge, this is the first time that missense variants have been reported in GOSHS. We functionally investigated the effect of the variants identified, in an attempt to find a genotype-phenotype correlation. We also determined whether common Hirschsprung disease (HSCR)-associated single nucleotide polymorphisms (SNPs), could explain the presence of HSCR in GOSHS. Our results showed that the missense variants led to reduced expression of KIFBP, while the truncating variants resulted in lack of protein. However, no correlation was found between the severity of GOSHS and the location of the variants. We were also unable to find a correlation between common HSCR-associated SNPs, and HSCR development in GOSHS. In conclusion, we show that reduced, as well as lack of KIFBP expression can lead to GOSHS, and our results suggest that a threshold expression of KIFBP may modulate phenotypic variability of the disease.
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Affiliation(s)
- Katherine C MacKenzie
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Bianca M de Graaf
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Andreas Syrimis
- Department of Clinical Genetics, The Cyprus Institute of Neurology & Genetics and Archbishop Makarios III Medical Centre, Nicosia, Cyprus
| | - Yuying Zhao
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Rachel Schot
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Dicky Halley
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Arve Vøllo
- Department of Paediatrics, Sykehuset Østfold HF, Fredrikstad, Norway
| | - Frances Flinter
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Andrew Green
- Department of Clinical Genetics, Children's Hospital Ireland at Crumlin, Dublin, Ireland
| | - Sahar Mansour
- South West Thames Regional Genetic Service, St George's Hospital Medical School, London, UK
| | - Jacek Pilch
- Department of Child Neurology, Medical University of Silesia, Katowice, Poland
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | | | | | - Robert M W Hofstra
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Jan D H Jongbloed
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
| | - Nayia Nicolaou
- Department of Clinical Genetics, The Cyprus Institute of Neurology & Genetics and Archbishop Makarios III Medical Centre, Nicosia, Cyprus
| | - George A Tanteles
- Department of Clinical Genetics, The Cyprus Institute of Neurology & Genetics and Archbishop Makarios III Medical Centre, Nicosia, Cyprus
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Maria M Alves
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, The Netherlands
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Identification and Characterization of a Transcribed Distal Enhancer Involved in Cardiac Kcnh2 Regulation. Cell Rep 2020; 28:2704-2714.e5. [PMID: 31484079 DOI: 10.1016/j.celrep.2019.08.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 06/05/2019] [Accepted: 07/30/2019] [Indexed: 12/26/2022] Open
Abstract
The human ether-a-go-go-related gene KCNH2 encodes the voltage-gated potassium channel underlying IKr, a current critical for the repolarization phase of the cardiac action potential. Mutations in KCNH2 that cause a reduction of the repolarizing current can result in cardiac arrhythmias associated with long-QT syndrome. Here, we investigate the regulation of KCNH2 and identify multiple active enhancers. A transcribed enhancer ∼85 kbp downstream of Kcnh2 physically contacts the promoters of two Kcnh2 isoforms in a cardiac-specific manner in vivo. Knockdown of its ncRNA transcript results in reduced expression of Kcnh2b and two neighboring mRNAs, Nos3 and Abcb8, in vitro. Genomic deletion of the enhancer, including the ncRNA transcription start site, from the mouse genome causes a modest downregulation of both Kcnh2a and Kcnh2b in the ventricles. These findings establish that the regulation of Kcnh2a and Kcnh2b is governed by a complex regulatory landscape that involves multiple partially redundantly acting enhancers.
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49
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Adiponectin GWAS loci harboring extensive allelic heterogeneity exhibit distinct molecular consequences. PLoS Genet 2020; 16:e1009019. [PMID: 32915782 PMCID: PMC7511027 DOI: 10.1371/journal.pgen.1009019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/23/2020] [Accepted: 07/29/2020] [Indexed: 02/06/2023] Open
Abstract
Loci identified in genome-wide association studies (GWAS) can include multiple distinct association signals. We sought to identify the molecular basis of multiple association signals for adiponectin, a hormone involved in glucose regulation secreted almost exclusively from adipose tissue, identified in the Metabolic Syndrome in Men (METSIM) study. With GWAS data for 9,262 men, four loci were significantly associated with adiponectin: ADIPOQ, CDH13, IRS1, and PBRM1. We performed stepwise conditional analyses to identify distinct association signals, a subset of which are also nearly independent (lead variant pairwise r2<0.01). Two loci exhibited allelic heterogeneity, ADIPOQ and CDH13. Of seven association signals at the ADIPOQ locus, two signals colocalized with adipose tissue expression quantitative trait loci (eQTLs) for three transcripts: trait-increasing alleles at one signal were associated with increased ADIPOQ and LINC02043, while trait-increasing alleles at the other signal were associated with decreased ADIPOQ-AS1. In reporter assays, adiponectin-increasing alleles at two signals showed corresponding directions of effect on transcriptional activity. Putative mechanisms for the seven ADIPOQ signals include a missense variant (ADIPOQ G90S), a splice variant, a promoter variant, and four enhancer variants. Of two association signals at the CDH13 locus, the first signal consisted of promoter variants, including the lead adipose tissue eQTL variant for CDH13, while a second signal included a distal intron 1 enhancer variant that showed ~2-fold allelic differences in transcriptional reporter activity. Fine-mapping and experimental validation demonstrated that multiple, distinct association signals at these loci can influence multiple transcripts through multiple molecular mechanisms. Many DNA variants affect common human traits, and distinct variants can have different effects on the function or expression level of the same gene. We identified variants associated with levels of adiponectin, a hormone involved in glucose regulation. Among these variants, we specifically studied the sets of variants located near two genes, ADIPOQ and CDH13, to determine how the variants affect gene expression or function. We focused on sets of variants that can be inherited together but are not always inherited together. Of the variants associated with adiponectin and located near ADIPOQ, one set were also associated with higher expression levels of the protein-coding ADIPOQ gene and a nearby non-coding gene, a second set of variants were associated with lower levels of the ADIPOQ-AS1 antisense gene, and additional variants changed the amino acid sequence or size of the adiponectin protein. Our examples show the benefits of identifying multiple sets of trait-associated variants in the same DNA region. These variants explain more trait variation, help identify genes that affect the trait, and guide studies of gene regulation and biological processes.
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50
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Abstract
In celebration of the 20th anniversary of Nature Reviews Genetics, we asked 12 leading researchers to reflect on the key challenges and opportunities faced by the field of genetics and genomics. Keeping their particular research area in mind, they take stock of the current state of play and emphasize the work that remains to be done over the next few years so that, ultimately, the benefits of genetic and genomic research can be felt by everyone. To celebrate the first 20 years of Nature Reviews Genetics, we asked 12 leading scientists to reflect on the key challenges and opportunities faced by the field of genetics and genomics. Amy L. McGuire is the Leon Jaworski Professor of Biomedical Ethics and Director of the Center for Medical Ethics and Health Policy at Baylor College of Medicine. She has received numerous teaching awards at Baylor College of Medicine, was recognized by the Texas Executive Women as a Woman on the Move in 2016 and was invited to give a TedMed talk titled “There is No Genome for the Human Spirit” in 2014. In 2020, she was elected as a Hastings Center Fellow. Her research focuses on ethical and policy issues related to emerging technologies, with a particular focus on genomic research, personalized medicine and the clinical integration of novel neurotechnologies. Stacey Gabriel is the Senior Director of the Genomics Platform at the Broad Institute since 2012 and has led platform development, execution and operation since its founding. She is Chair of Institute Scientists and serves on the institute’s executive leadership team. She is widely recognized as a leader in genomic technology and project execution. She has led the Broad’s contributions to numerous flagship projects in human genetics, including the International HapMap Project, the 1000 Genomes Project, The Cancer Genome Atlas, the National Heart, Lung, and Blood Institute’s Exome Sequencing Project and the TOPMed programme. She is Principal Investigator of the Broad’s All of Us (AoU) Genomics Center and serves on the AoU Program Steering Committee. Sarah A. Tishkoff is the David and Lyn Silfen University Associate Professor in Genetics and Biology at the University of Pennsylvania, Philadelphia, USA, and holds appointments in the School of Medicine and the School of Arts and Sciences. She is a member of the US National Academy of Sciences and a recipient of an NIH Pioneer Award, a David and Lucile Packard Career Award, a Burroughs/Wellcome Fund Career Award and an American Society of Human Genetics Curt Stern Award. Her work focuses on genomic variation in Africa, human evolutionary history, the genetic basis of adaptation and phenotypic variation in Africa, and the genetic basis of susceptibility to infectious disease in Africa. Ambroise Wonkam is Professor of Medical Genetics, Director of GeneMAP (Genetic Medicine of African Populations Research Centre) and Deputy Dean Research in the Faculty of Health Sciences, University of Cape Town, South Africa. He has successfully led numerous NIH- and Wellcome Trust-funded projects over the past decade to investigate clinical variability in sickle cell disease, hearing impairment genetics and the return of individual findings in genetic research in Africa. He won the competitive Clinical Genetics Society International Award for 2014 from the British Society of Genetic Medicine. He is president of the African Society of Human Genetics. Aravinda Chakravarti is Director of the Center for Human Genetics and Genomics, the Muriel G. and George W. Singer Professor of Neuroscience and Physiology, and Professor of Medicine at New York University School of Medicine. He is an elected member of the US National Academy of Sciences, the US National Academy of Medicine and the Indian National Science Academy. He has been a key participant in the Human Genome Project, the International HapMap Project and the 1000 Genomes Project. His research attempts to understand the molecular basis of multifactorial disease. He was awarded the 2013 William Allan Award by the American Society of Human Genetics and the 2018 Chen Award by the Human Genome Organization. Eileen E. M. Furlong is Head of the Genome Biology Department at the European Molecular Biology Laboratory (EMBL) and a member of the EMBL Directorate. She is an elected member of the European Molecular Biology Organization (EMBO) and the Academia Europaea, and a European Research Council (ERC) advanced investigator. Her group dissects fundamental principles of how the genome is regulated and how it drives cell fate decisions during embryonic development, including how developmental enhancers are organized and function within the 3D nucleus. Her work combines genetics, (single-cell) genomics, imaging and computational approaches to understand these processes. Her research has advanced the development of genomic methods for use in complex multicellular organisms. Barbara Treutlein is Associate Professor of Quantitative Developmental Biology in the Department of Biosystems Science and Engineering of ETH Zurich in Basel, Switzerland. Her group uses and develops single-cell genomics approaches in combination with stem cell-based 2D and 3D culture systems to study how human organs develop and regenerate and how cell fate is regulated. For her work, Barbara has received multiple awards, including the Friedmund Neumann Prize of the Schering Foundation, the Dr. Susan Lim Award for Outstanding Young Investigator of the International Society of Stem Cell Research and the EMBO Young Investigator Award. Alexander Meissner is a scientific member of the Max Planck Society and currently Managing Director of the Max Planck Institute (MPI) for Molecular Genetics in Berlin, Germany. He heads the Department of Genome Regulation and is a visiting scientist in the Department of Stem Cell and Regenerative Biology at Harvard University. Before his move to the MPI, he was a tenured professor at Harvard University and a senior associate member of the Broad Institute, where he co-directed the epigenomics programme. In 2018, he was elected as an EMBO member. His laboratory uses genomic tools to study developmental and disease biology with a particular focus on epigenetic regulation. Howard Y. Chang is the Virginia and D. K. Ludwig Professor of Cancer Genomics at Stanford University and an investigator at the Howard Hughes Medical Institute. He is a physician–scientist who has focused on deciphering the hidden information in the non-coding genome. His laboratory is best known for studies of long non-coding RNAs in gene regulation and development of new epigenomic technologies. He is an elected member of the US National Academy of Sciences, the US National Academy of Medicine, and the American Academy of Arts and Sciences. Núria López-Bigas is ICREA research Professor at the Institute for Research in Biomedicine and Associate Professor at the University Pompeu Fabra. She obtained an ERC Consolidator Grant in 2015 and was elected as an EMBO member in 2016. Her work has been recognized with the prestigious Banc de Sabadell Award for Research in Biomedicine, the Catalan National Award for Young Research Talent and the Career Development Award from the Human Frontier Science Program. Her research focuses on the identification of cancer driver mutations, genes and pathways across tumour types and in understanding the mutational processes that lead to the accumulation of mutations in cancer cells. Eran Segal is Professor in the Department of Computer Science and Applied Mathematics at the Weizmann Institute of Science, heading a multidisciplinary laboratory with extensive experience in machine learning, computational biology and analysis of heterogeneous high-throughput genomic data. His research focuses on the microbiome, nutrition and genetics, and their effect on health and disease and aims to develop personalized medicine based on big data from human cohorts. He has published more than 150 publications and received several awards and honours for his work, including the Overton and the Michael Bruno awards. He was recently elected as an EMBO member and as a member of the Israel Young Academy. Jin-Soo Kim is Director of the Center for Genome Engineering in the Institute for Basic Science in Daejon, South Korea. He has received numerous awards, including the 2017 Asan Award in Medicine, the 2017 Yumin Award in Science and the 2019 Research Excellence Award (Federation of Asian and Oceanian Biochemists and Molecular Biologists). He was featured as one of ten Science Stars of East Asia in Nature (558, 502–510 (2018)) and has been recognized as a highly cited researcher by Clarivate Analytics since 2018. His work focuses on developing tools for genome editing in biomedical research.
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