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Lucena-Padros H, Bravo-Gil N, Tous C, Rojano E, Seoane-Zonjic P, Fernández RM, Ranea JAG, Antiñolo G, Borrego S. Bioinformatics Prediction for Network-Based Integrative Multi-Omics Expression Data Analysis in Hirschsprung Disease. Biomolecules 2024; 14:164. [PMID: 38397401 PMCID: PMC10886964 DOI: 10.3390/biom14020164] [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: 12/05/2023] [Revised: 01/15/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
Hirschsprung's disease (HSCR) is a rare developmental disorder in which enteric ganglia are missing along a portion of the intestine. HSCR has a complex inheritance, with RET as the major disease-causing gene. However, the pathogenesis of HSCR is still not completely understood. Therefore, we applied a computational approach based on multi-omics network characterization and clustering analysis for HSCR-related gene/miRNA identification and biomarker discovery. Protein-protein interaction (PPI) and miRNA-target interaction (MTI) networks were analyzed by DPClusO and BiClusO, respectively, and finally, the biomarker potential of miRNAs was computationally screened by miRNA-BD. In this study, a total of 55 significant gene-disease modules were identified, allowing us to propose 178 new HSCR candidate genes and two biological pathways. Moreover, we identified 12 key miRNAs with biomarker potential among 137 predicted HSCR-associated miRNAs. Functional analysis of new candidates showed that enrichment terms related to gene ontology (GO) and pathways were associated with HSCR. In conclusion, this approach has allowed us to decipher new clues of the etiopathogenesis of HSCR, although molecular experiments are further needed for clinical validations.
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Affiliation(s)
- Helena Lucena-Padros
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
| | - Nereida Bravo-Gil
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Cristina Tous
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Elena Rojano
- Department of Molecular Biology and Biochemistry, University of Malaga, 29010 Malaga, Spain
- Biomedical Research Institute of Malaga, IBIMA, 29010 Malaga, Spain
| | - Pedro Seoane-Zonjic
- Department of Molecular Biology and Biochemistry, University of Malaga, 29010 Malaga, Spain
- Biomedical Research Institute of Malaga, IBIMA, 29010 Malaga, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 29071 Malaga, Spain
| | - Raquel María Fernández
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Juan A. G. Ranea
- Department of Molecular Biology and Biochemistry, University of Malaga, 29010 Malaga, Spain
- Biomedical Research Institute of Malaga, IBIMA, 29010 Malaga, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 29071 Malaga, Spain
- Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, 41013 Seville, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), 41013 Seville, Spain
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Hegde SG, Devi S, Pasanna RM, Padashetty C, Shubha AM, Mukhopadhyay A, Kurpad AV. Untargeted Maternal Plasma Metabolomics in Hirschsprung Disease: A Pilot Study. J Indian Assoc Pediatr Surg 2024; 29:6-12. [PMID: 38405248 PMCID: PMC10883180 DOI: 10.4103/jiaps.jiaps_134_23] [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: 06/15/2023] [Revised: 09/11/2023] [Accepted: 09/28/2023] [Indexed: 02/27/2024] Open
Abstract
Background and Aims Hirschsprung disease (HSCR) is a congenital disorder of unknown etiology affecting the enteric nervous system (ENS). Since the early gestational development of the ENS is dependent on the prenatal maternal metabolic environment, the objective of this pilot study was to explore the role of specific maternal plasma metabolites in the etiology of HSCR. Methods In this cross-sectional study, postnatal (as a surrogate for prenatal) plasma samples were obtained from mothers of children diagnosed with HSCR (n = 7) and age-matched mothers of normal children (n = 6). The plasma metabolome was analyzed by ultra-high-pressure liquid chromatography and mass spectrometry. Metabolites were identified by mzCloud using Compound Discoverer software. Using an untargeted metabolomics workflow, metabolites with case versus control group differences were identified. Results A total of 268 unique plasma metabolites were identified and annotated in maternal plasma. Of these, 57 were significantly different between case and control groups (P < 0.05, t-test). Using a false discovery rate corrected cutoff of 10% to adjust for multiple comparisons, 19 metabolites were significantly different in HSCR cases, including carnitines, medium-chain fatty acids, and glutamic acid. Pathways affected were for amino acid and lipid metabolism. Conclusion Disordered prenatal metabolic pathways may be involved in the etiopathogenesis of HSCR in the developing fetus. This is the first study to assess maternal plasma metabolomics in HSCR.
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Affiliation(s)
- Shalini G Hegde
- Department of Paediatric Surgery, Bengaluru, Karnataka, India
| | - Sarita Devi
- Department of Paediatric Surgery, Bengaluru, Karnataka, India
| | | | | | | | | | - Anura V Kurpad
- Department of Division of Nutrition, St. John's Research Institute, Bengaluru, Karnataka, India
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Wang J, Zhi Z, Ding J, Jia N, Hu Y, Cai J, Li H, Tang J, Tang W, Mao X. Suppression of PGE2/EP2 signaling alleviates Hirschsprung disease by upregulating p38 mitogen-activated protein kinase activity. J Mol Med (Berl) 2023; 101:1125-1139. [PMID: 37522903 DOI: 10.1007/s00109-023-02353-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/11/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023]
Abstract
Hirschsprung disease (HSCR) is a congenital disorder caused by the failure of enteric neural crest cells (ENCCs) to colonize the distal bowel, resulting in absence of enteric nervous system. While a range of molecules and signaling pathways have been found to contribute to HSCR development, the risk factors and pathogenesis of this disease in many patients remain unknown. We previously demonstrated that increased activity of the prostaglandin E2 (PGE2)/PGE2 receptor subtype EP2 pathway can be a risk factor for HSCR. In this study, an Ednrb-deficient mouse model of HSCR was generated and used to investigate if PGE2/EP2 pathway could be a potential therapeutic target for HSCR. We found that downregulation of PGE2/EP2 signaling by siRNA-mediated ablation of a PGE2 synthase or pharmacologic blockage of EP2 enhanced ENCC colonization in the distal bowel of Ednrb-/- mice and alleviated their HSCR-like symptoms. Furthermore, blockage of EP2 was shown to promote ENCC migration through upregulating p38 mitogen-activated protein kinase activity, which was downregulated in the colon of Ednrb-/- mice and in the distal aganglionic bowel of HSCR patients. These data provide evidence that maternal exposure during embryonic development to an environment with dysregulated activation of the PGE2/EP2 pathway may predispose genetically susceptible offspring to HSCR, and avoidance or early disruption of maternal events (e.g. inflammation) that possibly enhance PGE2/EP2 signaling during pregnancy would reduce the occurrence and severity of this disease. KEY MESSAGES : Knockdown of PTGES alleviates HSCR severity in Ednrb-/- mice. Blockage of EP2-mediated PGE2 signaling alleviates HSCR severity in Ednrb-/- mice. Blockage of EP2-mediated PGE2 signaling promotes ENCC migration via enhancing p38 activity.
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Affiliation(s)
- Jiao Wang
- School of Life Science and Technology, Key Laboratory of Ministry of Education for Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Zhengke Zhi
- Department of Pediatric Surgery, Childrens Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210008, China
| | - Jie Ding
- Department of Biochemistry and Molecular Biology, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Na Jia
- School of Life Science and Technology, Key Laboratory of Ministry of Education for Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Yuqing Hu
- Department of Biochemistry and Molecular Biology, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Jiali Cai
- School of Life Science and Technology, Key Laboratory of Ministry of Education for Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Hongxing Li
- Department of Pediatric Surgery, Childrens Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210008, China
| | - Jie Tang
- Department of Pediatric Surgery, Childrens Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210008, China
| | - Weibing Tang
- Department of Pediatric Surgery, Childrens Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210008, China.
| | - Xiaohua Mao
- School of Life Science and Technology, Key Laboratory of Ministry of Education for Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, 210096, China.
- Department of Biochemistry and Molecular Biology, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China.
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Yang S, Yang H, Huang Y, Chen G, Shen C, Zheng S. Serum Metabolomic Signatures of Hirschsprung's Disease Based on GC-MS and LC-MS. J Proteome Res 2023. [PMID: 37235583 DOI: 10.1021/acs.jproteome.3c00008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Hirschsprung's disease (HSCR) is a congenital digestive tract malformation characterized by the absence of intramural ganglion cells in the myenteric and submucosal plexuses along variable lengths of the gastrointestinal tract. Although the improvement of surgical methods has allowed great progress in the treatment of HSCR, its incidence and postoperative prognosis are still not ideal. The pathogenesis of HSCR remains unclear to date. In this study, metabolomic profiling of HSCR serum samples was performed by an integrated analysis of gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-high-resolution tandem mass spectrometry (LC-HRMS/MS) as well as multivariate statistical analyses. Based on the random forest algorithm and receiver operator characteristic analysis, 21 biomarkers related to HSCR were optimized. Several amino acid metabolism pathways were identified as important disordered pathways of HSCR, among which tryptophan metabolism was crucial. To our knowledge, this is the first serum metabolomics study focusing on HSCR, and it provides a new perspective for explaining the mechanism of HSCR.
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Affiliation(s)
- Shaobo Yang
- Department of Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Hong Yang
- Department of Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Yanlei Huang
- Department of Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Gong Chen
- Department of Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Chun Shen
- Department of Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Shan Zheng
- Department of Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
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He S, Wang J, Huang Y, Kong F, Yang R, Zhan Y, Li Z, Ye C, Meng L, Ren Y, Zhou Y, Chen G, Shen Z, Sun S, Zheng S, Dong R. Intestinal fibrosis in aganglionic segment of Hirschsprung's disease revealed by single-cell RNA sequencing. Clin Transl Med 2023; 13:e1193. [PMID: 36738110 PMCID: PMC9898741 DOI: 10.1002/ctm2.1193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/15/2023] [Accepted: 01/19/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Hirschsprung's disease (HSCR) is a relatively common congenital disability. Accumulating extracellular matrix (ECM) prompts intestinal fibrosis remodelling in the aganglionic segments of HSCR. The contributions of various cellular subsets in the fibrogenesis of HSCR segments are poorly understood. METHODS Single-cell transcriptomics from 8 aganglionic segments and 5 normal segments of 7 HSCR subjects and 26 healthy segments of seven healthy donors were analysed. Fibrotic phenotype and alterations were explored using differential expression analysis and single-cell trajectory analysis. Fibrosis-related transcription factors were inferred through single-cell regulatory network inference. Bulk transcriptomic data, proteomic data, immunohistochemistry (IHC) and real-time polymerase chain reaction were used to validate the alterations in the HSCR intestine. RESULTS Various collagen, fibronectin and laminin protein-coding genes expression were up-regulated in the stromal and glial cells of the HSCR intestine. The number of fibroblasts and myofibroblasts in the aganglionic segments increased, and more myofibroblasts were activated at an earlier stage in HSCR segments, which infers that there is an intestinal fibrosis phenotype in HSCR segments. The fibrotic regulators POSTN, ANXA1 and HSP70 were highly expressed in the ECM-related cellular subsets in the transitional segments and aganglionic segments. The transcription factor regulatory network revealed that fibrosis-related and megacolon-related NR2F1 in the fibroblasts and glial subsets was up-regulated in the aganglionic segment. CONCLUSIONS This work identifies intestinal fibrosis and related regulators in aganglionic segments of HSCR; hence, anti-fibrotic therapy may be considered to prevent HSCR-associated enterocolitis (HAEC), relieve intestinal stricture and improve cell therapy.
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Affiliation(s)
- Shiwei He
- Department of Pediatric SurgeryShanghai Key Laboratory of Birth DefectChildren's Hospital of Fudan UniversityMinistry of HealthShanghaiChina
| | - Junfeng Wang
- Department of Pediatric SurgeryShanghai Key Laboratory of Birth DefectChildren's Hospital of Fudan UniversityMinistry of HealthShanghaiChina
| | - Yanlei Huang
- Department of Pediatric SurgeryShanghai Key Laboratory of Birth DefectChildren's Hospital of Fudan UniversityMinistry of HealthShanghaiChina
| | - Fanyang Kong
- Department of Pediatric SurgeryShanghai Key Laboratory of Birth DefectChildren's Hospital of Fudan UniversityMinistry of HealthShanghaiChina
| | - Ran Yang
- Department of Pediatric SurgeryShanghai Key Laboratory of Birth DefectChildren's Hospital of Fudan UniversityMinistry of HealthShanghaiChina
| | - Yong Zhan
- Department of Pediatric SurgeryShanghai Key Laboratory of Birth DefectChildren's Hospital of Fudan UniversityMinistry of HealthShanghaiChina
| | - Zifeng Li
- Department of Pediatric SurgeryShanghai Key Laboratory of Birth DefectChildren's Hospital of Fudan UniversityMinistry of HealthShanghaiChina
| | - Chunjing Ye
- Department of Pediatric SurgeryShanghai Key Laboratory of Birth DefectChildren's Hospital of Fudan UniversityMinistry of HealthShanghaiChina
| | - Lingdu Meng
- Department of Pediatric SurgeryShanghai Key Laboratory of Birth DefectChildren's Hospital of Fudan UniversityMinistry of HealthShanghaiChina
| | - Yankang Ren
- Department of Pediatric SurgeryShanghai Key Laboratory of Birth DefectChildren's Hospital of Fudan UniversityMinistry of HealthShanghaiChina
| | - Ying Zhou
- Department of Pediatric SurgeryShanghai Key Laboratory of Birth DefectChildren's Hospital of Fudan UniversityMinistry of HealthShanghaiChina
| | - Gong Chen
- Department of Pediatric SurgeryShanghai Key Laboratory of Birth DefectChildren's Hospital of Fudan UniversityMinistry of HealthShanghaiChina
| | - Zhen Shen
- Department of Pediatric SurgeryShanghai Key Laboratory of Birth DefectChildren's Hospital of Fudan UniversityMinistry of HealthShanghaiChina
| | - Song Sun
- Department of Pediatric SurgeryShanghai Key Laboratory of Birth DefectChildren's Hospital of Fudan UniversityMinistry of HealthShanghaiChina
| | - Shan Zheng
- Department of Pediatric SurgeryShanghai Key Laboratory of Birth DefectChildren's Hospital of Fudan UniversityMinistry of HealthShanghaiChina
| | - Rui Dong
- Department of Pediatric SurgeryShanghai Key Laboratory of Birth DefectChildren's Hospital of Fudan UniversityMinistry of HealthShanghaiChina
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Hong M, Li X, Li Y, Zhou Y, Li Y, Chi S, Cao G, Li S, Tang S. Hirschsprung's disease: key microRNAs and target genes. Pediatr Res 2022; 92:737-747. [PMID: 34880446 DOI: 10.1038/s41390-021-01872-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/01/2021] [Accepted: 11/13/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND This study aimed to identify key microRNAs (miRNAs), pathways, and target genes mediating Hirschsprung's disease (HSCR) pathogenesis and identify the diagnostic potential of miRNAs. METHODS The Gene Expression Omnibus database and reverse transcription-quantitative PCR were used to compare miRNA expression between ganglionic and aganglionic colon tissues of children with HSCR, and the TAM 2.0 database was used to identify colon tissue-specific miRNAs. The StarBase database, TargetScan database, luciferase reporter, and western blot assays were used to analyze miRNA-messenger RNA interactions. OmicShare was used to perform functional and pathway enrichment analyses of the target genes. Migration assays were performed to validate the functions of the miRNAs. RESULTS The TAM 2.0 database analysis and reverse transcription-quantitative PCR showed that hsa-miR-192-5p, hsa-miR-200a-3p, and hsa-miR-200b-3p were colon tissue-specific and upregulated in aganglionic colon tissue compared to paired ganglionic colon tissue. These three miRNAs effectively reduced cell viability and migration. Luciferase reporter and western blot assays verified the direct interaction between these three miRNAs and the target genes of ZEB2 and FNDC3B. Furthermore, the plasma levels of these miRNAs were higher in HSCR patients than in non-HSCR patients. CONCLUSIONS Three plasma miRNAs (hsa-miR-192-5p, hsa-miR-200a-3p, and hsa-miR-200b-3p) are potential peripheral HSCR biomarkers. IMPACT The molecular mechanisms underlying HSCR are unclear. HSCR is most accurately diagnosed using rectal biopsy samples, and no consensus has been reached on the use of blood-based tests for HSCR diagnosis. Circulating miRNAs may be candidate diagnostic HSCR biomarkers because they are typically easily detectable, stable, and tissue-specific. Three plasma miRNAs (miR-200a-3p, miR-192-5p, and miR-200b-3p) are potential peripheral HSCR biomarkers.
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Affiliation(s)
- Mei Hong
- 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
| | - Yuan Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, 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
| | - Yibo Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuiqing Chi
- 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
| | - Shuai Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 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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