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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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Shirai R, Cho M, Isogai M, Fukatsu S, Okabe M, Okawa M, Miyamoto Y, Torii T, Yamauchi J. FTD/ALS Type 7-Associated Thr104Asn Mutation of CHMP2B Blunts Neuronal Process Elongation, and Is Recovered by Knockdown of Arf4, the Golgi Stress Regulator. Neurol Int 2023; 15:980-993. [PMID: 37606396 PMCID: PMC10443297 DOI: 10.3390/neurolint15030063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/23/2023] Open
Abstract
Frontotemporal dementia and/or amyotrophic lateral sclerosis type 7 (FTD/ALS7) is an autosomal dominant neurodegenerative disorder characterized by the onset of FTD and/or ALS, mainly in adulthood. Patients with some types of mutations, including the Thr104Asn (T104N) mutation of charged multivesicular body protein 2B (CHMP2B), have predominantly ALS phenotypes, whereas patients with other mutations have predominantly FTD phenotypes. A few mutations result in patients having both phenotypes approximately equally; however, the reason why phenotypes differ depending on the position of the mutation is unknown. CHMP2B comprises one part of the endosomal sorting complexes required for transport (ESCRT), specifically ESCRT-III, in the cytoplasm. We describe here, for the first time, that CHMP2B with the T104N mutation inhibits neuronal process elongation in the N1E-115 cell line, a model line undergoing neuronal differentiation. This inhibitory phenotype was accompanied by changes in marker protein expression. Of note, CHMP2B with the T104N mutation, but not the wild-type form, was preferentially accumulated in the Golgi body. Of the four major Golgi stress signaling pathways currently known, the pathway through Arf4, the small GTPase, was specifically upregulated in cells expressing CHMP2B with the T104N mutation. Conversely, knockdown of Arf4 with the cognate small interfering (si)RNA recovered the neuronal process elongation inhibited by the T104N mutation. These results suggest that the T104N mutation of CHMP2B inhibits morphological differentiation by triggering Golgi stress signaling, revealing a possible therapeutic molecular target for recovering potential molecular and cellular phenotypes underlying FTD/ALS7.
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Affiliation(s)
- Remina Shirai
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (R.S.); (Y.M.)
| | - Mizuka Cho
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (R.S.); (Y.M.)
| | - Mikinori Isogai
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (R.S.); (Y.M.)
| | - Shoya Fukatsu
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (R.S.); (Y.M.)
| | - Miyu Okabe
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (R.S.); (Y.M.)
| | - Maho Okawa
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (R.S.); (Y.M.)
| | - Yuki Miyamoto
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (R.S.); (Y.M.)
- Department of Pharmacology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Tomohiro Torii
- Laboratory of Ion Channel Pathophysiology, Doshisha University Graduate School of Brain Science, Kyoto 610-0394, Japan;
| | - Junji Yamauchi
- Laboratory of Molecular Neurology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan; (R.S.); (Y.M.)
- Department of Pharmacology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
- Diabetic Neuropathy Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
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Enteric Neuromics: How High-Throughput "Omics" Deepens Our Understanding of Enteric Nervous System Genetic Architecture. Cell Mol Gastroenterol Hepatol 2022; 15:487-504. [PMID: 36368612 PMCID: PMC9792566 DOI: 10.1016/j.jcmgh.2022.10.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/09/2022]
Abstract
Recent accessibility to specialized high-throughput "omics" technologies including single cell RNA sequencing allows researchers to capture cell type- and subtype-specific expression signatures. These omics methods are used in the enteric nervous system (ENS) to identify potential subtypes of enteric neurons and glia. ENS omics data support the known gene and/or protein expression of functional neuronal and glial cell subtypes and suggest expression patterns of novel subtypes. Gene and protein expression patterns can be further used to infer cellular function and implications in human disease. In this review we discuss how high-throughput "omics" data add additional depth to the understanding of established functional subtypes of ENS cells and raise new questions by suggesting novel ENS cell subtypes with unique gene and protein expression patterns. Then we investigate the changes in these expression patterns during pathology observed by omics research. Although current ENS omics studies provide a plethora of novel data and therefore answers, they equally create new questions and routes for future study.
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Cai X, Yang C, Chen J, Gong W, Yi F, Liao W, Huang R, Xie L, Zhou J. Proteomic Insights Into Susceptibility and Resistance to Chronic-Stress-Induced Depression or Anxiety in the Rat Striatum. Front Mol Biosci 2021; 8:730473. [PMID: 34676246 PMCID: PMC8523913 DOI: 10.3389/fmolb.2021.730473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/27/2021] [Indexed: 11/13/2022] Open
Abstract
Chronic stress is a key factor for the onset of anxiety and depression disorders. However, the stress-induced common and unique molecular basis of the two psychiatric disorders is not fully known and still needs to be explored. Previously, we employed a chronic mild stress (CMS) procedure to induce a rat model including depression-susceptible (Dep-Sus), anxiety-susceptible (Anx-Sus), and insusceptible (Insus) cohorts. In this work, we continuously analyze the striatal proteomes of the three stressed cohorts by the use of comparative proteomics and bioinformatics approaches. Through isobaric tags for relative and absolute quantitation (iTRAQ)-based analysis, 386 abnormally expressed proteins in total were identified. These deregulated proteins are involved in various biological functions and significant pathways that are potentially connected with resistance and susceptibility to CMS-caused anxious- or depressive-like behaviors and, hence, could act as suggestive protein targets. A further parallel reaction monitoring-based independent investigation shows that alterations in Pak5, Dgkg, Scn4b, Rb1cc1, and Acin1; Ggps1, Fntb, Nudt19, Ufd1, and Ndufab1; and Dnajb12, Hbb2, Ap2s1, Ip6k1, and Stk4 were specifically connected with Dep-Sus, Anx-Sus, or Insus groups, respectively, potentially indicating that identical CMS treatment results in the different changes in the striatal protein regulations. Overall, our current proteomics study of the striatum provides an important molecular foundation and comprehensive insights into common and specific deregulations correlated with pathophysiological mechanisms that underlie resistance and susceptibility to chronic stress-induced anxiety or depression.
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Affiliation(s)
- Xiao Cai
- Basic Medical College, Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Chen Yang
- Basic Medical College, Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Jin Chen
- Basic Medical College, Institute of Neuroscience, Chongqing Medical University, Chongqing, China.,Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Weibo Gong
- Basic Medical College, Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Faping Yi
- Basic Medical College, Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Wei Liao
- Basic Medical College, Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Rongzhong Huang
- Statistics Laboratory, ChuangXu Institute of Life Science, Chongqing, China.,Chongqing Institute of Life Science, Chongqing, China
| | - Liang Xie
- Basic Medical College, Institute of Neuroscience, Chongqing Medical University, Chongqing, China.,Department of Neurology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jian Zhou
- Basic Medical College, Institute of Neuroscience, Chongqing Medical University, Chongqing, China
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Gong W, Liao W, Fang C, Liu Y, Xie H, Yi F, Huang R, Wang L, Zhou J. Analysis of Chronic Mild Stress-Induced Hypothalamic Proteome: Identification of Protein Dysregulations Associated With Vulnerability and Resiliency to Depression or Anxiety. Front Mol Neurosci 2021; 14:633398. [PMID: 33737865 PMCID: PMC7960925 DOI: 10.3389/fnmol.2021.633398] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
Chronic stress as a known risk factor leads to hyperactivity of the hypothalamus-pituitary-adrenal (HPA) axis in both depression and anxiety. However, the stress-induced dysfunction of the HPA axis in these disorders especially the common and unique molecular dysregulations have not been well-explored. Previously, we utilized a chronic mild stress (CMS) paradigm to segregate and gain depression-susceptible, anxiety-susceptible, and insusceptible groups. In this study, we continue to examine the possible protein expression alterations of the hypothalamus as the center of the HPA axis in these three groups by using a proteomic approach. Though isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative analysis, a total of 593 dysregulated proteins were identified. These were potentially associated with vulnerability and adaptability of CMS-caused depression or anxiety and therefore might become novel investigative protein targets. Further independent analysis using parallel reaction monitoring (PRM) indicated that 5, 7, and 21 dysregulated proteins were specifically associated with depression-susceptible, anxiety-susceptible, and insusceptible groups, respectively, suggesting that the same CMS differently affected the regulation system of the rat hypothalamic proteome. In summary, the current proteomic research on the hypothalamus provided insights into the specific and common molecular basis for the HPA dysfunction mechanisms that underlie resiliency and vulnerability to stress-induced depression or anxiety.
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Affiliation(s)
- Weibo Gong
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China.,Basic Medical College, Chongqing Medical University, Chongqing, China
| | - Wei Liao
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China.,Basic Medical College, Chongqing Medical University, Chongqing, China
| | - Chui Fang
- Shenzhen Wininnovate Bio-Tech Co., Ltd., Shenzhen, China
| | - Yanchen Liu
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China.,Basic Medical College, Chongqing Medical University, Chongqing, China
| | - Hong Xie
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China.,Department of Pharmacy, Chongqing Renji Hospital, University of Chinese Academy of Sciences, Chongqing, China
| | - Faping Yi
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China.,Basic Medical College, Chongqing Medical University, Chongqing, China
| | | | - Lixiang Wang
- Shenzhen Wininnovate Bio-Tech Co., Ltd., Shenzhen, China
| | - Jian Zhou
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China.,Basic Medical College, Chongqing Medical University, Chongqing, China
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