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Li QS, Vasanthakumar A, Davis JW, Idler KB, Nho K, Waring JF, Saykin AJ. Association of peripheral blood DNA methylation level with Alzheimer's disease progression. Clin Epigenetics 2021; 13:191. [PMID: 34654479 PMCID: PMC8518178 DOI: 10.1186/s13148-021-01179-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022] Open
Abstract
Background Identifying biomarkers associated with Alzheimer’s disease (AD) progression may enable patient enrichment and improve clinical trial designs. Epigenome-wide association studies have revealed correlations between DNA methylation at cytosine-phosphate-guanine (CpG) sites and AD pathology and diagnosis. Here, we report relationships between peripheral blood DNA methylation profiles measured using Infinium® MethylationEPIC BeadChip and AD progression in participants from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort. Results The rate of cognitive decline from initial DNA sampling visit to subsequent visits was estimated by the slopes of the modified Preclinical Alzheimer Cognitive Composite (mPACC; mPACCdigit and mPACCtrailsB) and Clinical Dementia Rating Scale Sum of Boxes (CDR-SB) plots using robust linear regression in cognitively normal (CN) participants and patients with mild cognitive impairment (MCI), respectively. In addition, diagnosis conversion status was assessed using a dichotomized endpoint. Two CpG sites were significantly associated with the slope of mPACC in CN participants (P < 5.79 × 10−8 [Bonferroni correction threshold]); cg00386386 was associated with the slope of mPACCdigit, and cg09422696 annotated to RP11-661A12.5 was associated with the slope of CDR-SB. No significant CpG sites associated with diagnosis conversion status were identified. Genes involved in cognition and learning were enriched. A total of 19, 13, and 5 differentially methylated regions (DMRs) associated with the slopes of mPACCtrailsB, mPACCdigit, and CDR-SB, respectively, were identified by both comb-p and DMRcate algorithms; these included DMRs annotated to HOXA4. Furthermore, 5 and 19 DMRs were associated with conversion status in CN and MCI participants, respectively. The most significant DMR was annotated to the AD-associated gene PM20D1 (chr1: 205,818,956 to 205,820,014 [13 probes], Sidak-corrected P = 7.74 × 10−24), which was associated with both the slope of CDR-SB and the MCI conversion status. Conclusion Candidate CpG sites and regions in peripheral blood were identified as associated with the rate of cognitive decline in participants in the ADNI cohort. While we did not identify a single CpG site with sufficient clinical utility to be used by itself due to the observed effect size, a biosignature composed of DNA methylation changes may have utility as a prognostic biomarker for AD progression. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01179-2.
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Affiliation(s)
- Qingqin S Li
- Neuroscience, Janssen Research and Development, LLC, 1125 Trenton-Harbourton Road, Titusville, NJ, 08560, USA.
| | | | - Justin W Davis
- Genomics Research Center, AbbVie, North Chicago, IL, USA
| | | | - Kwangsik Nho
- Indiana Alzheimer's Disease Research Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Andrew J Saykin
- Indiana Alzheimer's Disease Research Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
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Yeh SJ, Chen SW, Chen BS. Investigation of the Genome-Wide Genetic and Epigenetic Networks for Drug Discovery Based on Systems Biology Approaches in Colorectal Cancer. Front Genet 2020; 11:117. [PMID: 32211020 PMCID: PMC7068214 DOI: 10.3389/fgene.2020.00117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/31/2020] [Indexed: 12/29/2022] Open
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed type of cancer worldwide. The mechanisms leading to the progression of CRC are involved in both genetic and epigenetic regulations. In this study, we applied systems biology methods to identify potential biomarkers and conduct drug discovery in a computational approach. Using big database mining, we constructed a candidate protein-protein interaction network and a candidate gene regulatory network, combining them into a genome-wide genetic and epigenetic network (GWGEN). With the assistance of system identification and model selection approaches, we obtain real GWGENs for early-stage, mid-stage, and late-stage CRC. Subsequently, we extracted core GWGENs for each stage of CRC from their real GWGENs through a principal network projection method, and projected them to the Kyoto Encyclopedia of Genes and Genomes pathways for further analysis. Finally, we compared these core pathways resulting in different molecular mechanisms in each stage of CRC and identified carcinogenic biomarkers for the design of multiple-molecule drugs to prevent the progression of CRC. Based on the identified gene expression signatures, we suggested potential compounds combined with known CRC drugs to prevent the progression of CRC with querying Connectivity Map (CMap).
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Affiliation(s)
- Shan-Ju Yeh
- Laboratory of Automatic Control, Signaling Processing and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan.,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Shuo-Wei Chen
- Laboratory of Automatic Control, Signaling Processing and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Bor-Sen Chen
- Laboratory of Automatic Control, Signaling Processing and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
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Zheng Z, Chen B, Jin Z, Gao M, Tang C, Mao Y, Qu Y, Liu Y. Downregulation of P2Y2 and HuD during the development of the enteric nervous system in fetal rats with anorectal malformations. Mol Med Rep 2019; 20:1297-1305. [PMID: 31173231 PMCID: PMC6625457 DOI: 10.3892/mmr.2019.10356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/17/2019] [Indexed: 11/12/2022] Open
Abstract
Certain patients with anorectal malformations (ARMs) continue to suffer from postoperative dysphoria. The enteric nervous system (ENS) is closely associated with defecation. The purinergic receptor P2Y2 (P2Y2) and Hu antigen D (HuD) proteins contain multiple motifs that enable their activation and direct coupling to integrin and growth factor receptor signaling pathways; thus, they may serve as key points in ENS development. The aim of the present study was to investigate the expression pattern of P2Y2 and HuD proteins during anorectal development in ARM embryos. The embryogenesis of ARM in rats was induced by ethylenethiourea (ETU) on the 10th gestational day. The expression patterns of P2Y2 and HuD proteins were evaluated by immunohistochemistry and western blot analysis in normal, ETU and ARM rat embryos on embryonic days E17, E19 and E21; their mRNA levels were assessed via reverse transcription-quantitative polymerase chain reaction (RT-qPCR) of the distal rectum of fetal rats. Immunohistochemistry of the distal rectum demonstrated that on E17, the expression levels of the two proteins were not different between the three groups. On E19, the expression of HuD was significantly decreased in the ARM group. On E21, the two proteins were significantly decreased in the ARM group. Additionally, the expression levels of the two proteins on E17 were significantly lower than on E21 in the ARM group. Western blotting and RT-qPCR also revealed that the P2Y2 and HuD proteins and mRNA expression levels were significantly decreased in the ARM groups when compared with the normal group on E17 and E21 (P<0.01). Thus, the present study demonstrated that downregulation of P2Y2 and HuD may partly be related to the development of the ENS in ARM embryos.
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Affiliation(s)
- Zebing Zheng
- Department of Pediatric, General Thoracic and Urinary Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Bin Chen
- Department of Surgery, Dezhou Union Hospital, Dezhou, Shandong 253000, P.R. China
| | - Zhu Jin
- Department of Pediatric, General Thoracic and Urinary Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Mingjuan Gao
- Department of Pediatric, General Thoracic and Urinary Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Chengyan Tang
- Department of Pediatric, General Thoracic and Urinary Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Yuchen Mao
- Department of Pediatric, General Thoracic and Urinary Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Yan Qu
- Department of Pediatric, General Thoracic and Urinary Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Yuanmei Liu
- Department of Pediatric, General Thoracic and Urinary Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
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Qu Z, Titus ASCLS, Xuan Z, D'Mello SR. Neuroprotection by Heat Shock Factor-1 (HSF1) and Trimerization-Deficient Mutant Identifies Novel Alterations in Gene Expression. Sci Rep 2018; 8:17255. [PMID: 30467350 DOI: 10.1038/s41598-018-35610-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 11/05/2018] [Indexed: 12/17/2022] Open
Abstract
Heat shock factor-1 (HSF1) protects neurons from death caused by the accumulation of misfolded proteins by stimulating the transcription of genes encoding heat shock proteins (HSPs). This stimulatory action depends on the association of trimeric HSF1 to sequences within HSP gene promoters. However, we recently described that HSF-AB, a mutant form of HSF1 that is incapable of either homo-trimerization, association with HSP gene promoters, or stimulation of HSP expression, protects neurons just as efficiently as wild-type HSF1 suggesting an alternative neuroprotective mechanism that is activated by HSF1. To gain insight into the mechanism by which HSF1 and HSF1-AB protect neurons, we used RNA-Seq technology to identify transcriptional alterations induced by these proteins in either healthy cerebellar granule neurons (CGNs) or neurons primed to die. When HSF1 was ectopically-expressed in healthy neurons, 1,211 differentially expressed genes (DEGs) were identified with 1,075 being upregulated. When HSF1 was expressed in neurons primed to die, 393 genes were upregulated and 32 genes were downregulated. In sharp contrast, HSF1-AB altered expression of 13 genes in healthy neurons and only 6 genes in neurons under apoptotic conditions, suggesting that the neuroprotective effect of HSF1-AB may be mediated by a non-transcriptional mechanism. We validated the altered expression of 15 genes by QPCR. Although other studies have conducted RNA-Seq analyses to identify HSF1 targets, our study performed using primary neurons has identified a number of novel targets that may play a special role in brain maintenance and function.
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Kim JH, Jung SM, Shin JG, Cheong HS, Seo JM, Kim DY, Oh JT, Kim HY, Jung K, Shin HD. Potential association between ITPKC genetic variations and Hirschsprung disease. Mol Biol Rep 2017; 44:307-313. [PMID: 28664405 DOI: 10.1007/s11033-017-4111-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 06/24/2017] [Indexed: 02/03/2023]
Abstract
Hirschsprung disease (HSCR) is a congenital and complex disorder characterized by intestinal obstruction due to the absence of enteric neurons along variable lengths of the hindgut. Our recent genome-wide association study (GWAS) has revealed regional associations with HSCR at several loci of inositol-trisphosphate 3-kinase C (ITPKC). For fine mapping, we additionally selected and genotyped a total of 12 single nucleotide polymorphisms (SNPs) of ITPKC in 187 HSCR patients and 283 unaffected controls, and performed a further combined imputation analysis based on genotype data from this second stage of fine mapping and our previous GWAS stage, totaling 902 subjects (187 HSCR cases and 715 controls). As a result, several SNPs (minimum P = 0.004) and a haplotype (P = 0.02) were found to be significantly associated with HSCR. In further in silico analyses to ascertain the potential functions of the significant variants, the change from the common allele to the rare allele of the highly conserved nonsynonymous rs76785336 showed a difference in mRNA folding structure. In the case of intronic SNPs, rs2607420 with a high consensus value was predicted to be a new splice site. Although this study has limitations (such as lack of functional evaluations, small number of cases, and further need of replication in other cohorts), our findings suggest that genetic variants of ITPKC may have a potential association with HSCR susceptibility and/or developmental diseases related to enteric nervous system development.
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Affiliation(s)
- Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Soo-Min Jung
- Department of Surgery, Konkuk University Medical Center, Seoul, 05030, Republic of Korea
| | - Joong-Gon Shin
- Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, 04107, Republic of Korea
| | - Jeong-Meen Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Dae-Yeon Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Jung-Tak Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Hyun-Young Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, 03080, Republic of Korea
| | - Kyuwhan Jung
- Department of Surgery, Jeju National University Hospital, Jeju, 63241, Republic of Korea
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul, 04107, Republic of Korea. .,Department of Life Science, Sogang University, Seoul, 04107, Republic of Korea.
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Kim LH, Cheong HS, Shin JG, Seo JM, Kim DY, Oh JT, Kim HY, Jung K, Koh I, Kim JH, Shin HD. Genetic variants of IL-11 associated with risk of Hirschsprung disease. Neurogastroenterol Motil 2015; 27:1371-7. [PMID: 26172388 DOI: 10.1111/nmo.12629] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 06/15/2015] [Indexed: 02/08/2023]
Abstract
BACKGROUND Hirschsprung disease (HSCR) is a congenital and heterogeneous disorder characterized by the absence of enteric ganglia during enteric nervous system (ENS) development. Our recent genome-wide association study has identified a variant (rs6509940) of interleukin-11 (IL-11) as a potential susceptible locus for HSCR. As interleukins play important roles in the ENS, we further studied associations with HSCR of nine common single nucleotide polymorphisms (SNPs) on IL-11. METHODS Biopsy specimens or surgical materials from all patients that were tested for histological examination based on the absence of the enteric ganglia were collected. A total of nine SNPs on IL-11 were genotyped in 187 HSCR patients and 283 unaffected controls using TaqMan genotyping assay. KEY RESULTS Combined analysis revealed that several SNPs (minimum p = 1.57 × 10(-7) ) showed statistically significant associations with HSCR, even after Bonferroni correction (pcorr = 1.73 × 10(-6) for the SNP). Moreover, the most common haplotype was strongly associated with HSCR (pcorr = 2.20 × 10(-6) ). In further analysis among three HSCR subtypes (short segment, S-HSCR; long segment, L-HSCR; total colonic aganglionosis, TCA) based on the extent of aganglionic segment, the result showed a different association pattern depending on the subtypes (minimum pcorr = 6.12 × 10(-5) for rs6509940 in S-HSCR; but no significant SNP in L-HSCR and TCA). CONCLUSIONS & INFERENCES Although further replication in a larger cohort and functional evaluations are needed, our findings suggest that genetic variations of IL-11 may be associated with the risk of HSCR and/or the mechanisms related to ENS development.
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Affiliation(s)
- L H Kim
- Department of Life Science, Sogang University, Seoul, Korea
| | - H S Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Korea
| | - J-G Shin
- Department of Life Science, Sogang University, Seoul, Korea
| | - J-M Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - D-Y Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - J-T Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - H-Y Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, Korea
| | - K Jung
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Korea
| | - I Koh
- Department of Physiology, College of Medicine, Hanyang University, Seoul, Korea
| | - J-H Kim
- Research Institute for Basic Science, Sogang University, Seoul, Korea
| | - H D Shin
- Department of Life Science, Sogang University, Seoul, Korea.,Research Institute for Basic Science, Sogang University, Seoul, Korea
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Bonora E, Bianco F, Cordeddu L, Bamshad M, Francescatto L, Dowless D, Stanghellini V, Cogliandro RF, Lindberg G, Mungan Z, Cefle K, Ozcelik T, Palanduz S, Ozturk S, Gedikbasi A, Gori A, Pippucci T, Graziano C, Volta U, Caio G, Barbara G, D'Amato M, Seri M, Katsanis N, Romeo G, De Giorgio R. Mutations in RAD21 disrupt regulation of APOB in patients with chronic intestinal pseudo-obstruction. Gastroenterology 2015; 148:771-782.e11. [PMID: 25575569 PMCID: PMC4375026 DOI: 10.1053/j.gastro.2014.12.034] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 12/03/2014] [Accepted: 12/23/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Chronic intestinal pseudo-obstruction (CIPO) is characterized by severe intestinal dysmotility that mimics a mechanical subocclusion with no evidence of gut obstruction. We searched for genetic variants associated with CIPO to increase our understanding of its pathogenesis and to identify potential biomarkers. METHODS We performed whole-exome sequencing of genomic DNA from patients with familial CIPO syndrome. Blood and lymphoblastoid cells were collected from patients and controls (individuals without CIPO); levels of messenger RNA (mRNA) and proteins were analyzed by quantitative reverse-transcription polymerase chain reaction, immunoblot, and mobility shift assays. Complementary DNAs were transfected into HEK293 cells. Expression of rad21 was suppressed in zebrafish embryos using a splice-blocking morpholino (rad21a). Gut tissues were collected and analyzed. RESULTS We identified a homozygous mutation (p.622, encodes Ala>Thr) in RAD21 in patients from a consanguineous family with CIPO. Expression of RUNX1, a target of RAD21, was reduced in cells from patients with CIPO compared with controls. In zebrafish, suppression of rad21a reduced expression of runx1; this phenotype was corrected by injection of human RAD21 mRNA, but not with the mRNA from the mutated p.622 allele. rad21a Morpholino zebrafish had delayed intestinal transit and greatly reduced numbers of enteric neurons, similar to patients with CIPO. This defect was greater in zebrafish with suppressed expression of ret and rad21, indicating their interaction in the regulation of gut neurogenesis. The promoter region of APOB bound RAD21 but not RAD21 p.622 Ala>Thr; expression of wild-type RAD21 in HEK293 cells repressed expression of APOB, compared with control vector. The gut-specific isoform of APOB (APOB48) is overexpressed in sera from patients with CIPO who carry the RAD21 mutation. APOB48 also is overexpressed in sporadic CIPO in sera and gut biopsy specimens. CONCLUSIONS Some patients with CIPO carry mutations in RAD21 that disrupt the ability of its product to regulate genes such as RUNX1 and APOB. Reduced expression of rad21 in zebrafish, and dysregulation of these target genes, disrupts intestinal transit and the development of enteric neurons.
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Affiliation(s)
- Elena Bonora
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Francesca Bianco
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | | | - Michael Bamshad
- University of Washington Center for Mendelian Genomics, Seattle, USA
| | | | - Dustin Dowless
- Center for Human Disease Modeling Duke University, Durham, USA
| | - Vincenzo Stanghellini
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Rosanna F. Cogliandro
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | | | | | - Kivanc Cefle
- Istanbul Medical Faculty, Dept. of Internal Medicine, Division of Medical Genetics
| | | | - Sukru Palanduz
- Istanbul Medical Faculty, Dept. of Internal Medicine, Division of Medical Genetics
| | - Sukru Ozturk
- Istanbul Medical Faculty, Dept. of Internal Medicine, Division of Medical Genetics
| | - Asuman Gedikbasi
- Istanbul Medical Faculty, Dept. of Internal Medicine, Division of Medical Genetics
| | - Alessandra Gori
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Tommaso Pippucci
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Claudio Graziano
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Umberto Volta
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Giacomo Caio
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Giovanni Barbara
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | | | - Marco Seri
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy
| | | | - Giovanni Romeo
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy.
| | - Roberto De Giorgio
- Department of Medical and Surgical Sciences, University of Bologna, and St. Orsola-Malpighi Hospital, Bologna, Italy; Centro Unificato di Ricerca Biomedica Applicata, Bologna, Italy.
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Kim JH, Cheong HS, Sul JH, Seo JM, Kim DY, Oh JT, Park KW, Kim HY, Jung SM, Jung K, Cho MJ, Bae JS, Shin HD. A genome-wide association study identifies potential susceptibility loci for Hirschsprung disease. PLoS One 2014; 9:e110292. [PMID: 25310821 PMCID: PMC4195606 DOI: 10.1371/journal.pone.0110292] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 09/11/2014] [Indexed: 12/30/2022] Open
Abstract
Hirschsprung disease (HSCR) is a congenital and heterogeneous disorder characterized by the absence of intramural nervous plexuses along variable lengths of the hindgut. Although RET is a well-established risk factor, a recent genome-wide association study (GWAS) of HSCR has identified NRG1 as an additional susceptibility locus. To discover additional risk loci, we performed a GWAS of 123 sporadic HSCR patients and 432 unaffected controls using a large-scale platform with coverage of over 1 million polymorphic markers. The result was that our study replicated the findings of RET-CSGALNACT2-RASGEF1A genomic region (rawP = 5.69×10−19 before a Bonferroni correction; corrP = 4.31×10−13 after a Bonferroni correction) and NRG1 as susceptibility loci. In addition, this study identified SLC6A20 (adjP = 2.71×10−6), RORA (adjP = 1.26×10−5), and ABCC9 (adjP = 1.86×10−5) as new potential susceptibility loci under adjusting the already known loci on the RET-CSGALNACT2-RASGEF1A and NRG1 regions, although none of the SNPs in these genes passed the Bonferroni correction. In further subgroup analysis, the RET-CSGALNACT2-RASGEF1A genomic region was observed to have different significance levels among subgroups: short-segment (S-HSCR, corrP = 1.71×10−5), long-segment (L-HSCR, corrP = 6.66×10−4), and total colonic aganglionosis (TCA, corrP>0.05). This differential pattern in the significance level suggests that other genomic loci or mechanisms may affect the length of aganglionosis in HSCR subgroups during enteric nervous system (ENS) development. Although functional evaluations are needed, our findings might facilitate improved understanding of the mechanisms of HSCR pathogenesis.
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Affiliation(s)
- Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea; Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Republic of Korea
| | - Jae Hoon Sul
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jeong-Meen Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Dae-Yeon Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jung-Tak Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kwi-Won Park
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Hyun-Young Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Soo-Min Jung
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyuwhan Jung
- Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Gyeonggi, Republic of Korea
| | - Min Jeng Cho
- Department of Surgery, Konkuk University Medical Center, Seoul, Republic of Korea
| | - Joon Seol Bae
- Laboratory of Translational Genomics, Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea; Department of Life Science, Sogang University, Seoul, Republic of Korea; Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Republic of Korea
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