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Wang X, Wei K, Wang M, Zhang L. Identification of potential key ferroptosis- and autophagy-related genes in myelomeningocele through bioinformatics analysis. Heliyon 2024; 10:e29654. [PMID: 38660270 PMCID: PMC11040124 DOI: 10.1016/j.heliyon.2024.e29654] [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: 10/08/2023] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024] Open
Abstract
Myelomeningocele is a common congenital anomaly associated with polygenic disorders worldwide. However, the intricate molecular mechanisms underlying myelomeningocele remain elusive. To investigate whether ferroptosis and ferritinophagy contribute to the pathomechanism of myelomeningocele, differentially expressed genes (DEGs) were identified as novel biomarker and potential treatment agents. The GSE101141 dataset from Gene Expression Omnibus (GEO) was analyzed using GEO2R web tool to obtain DEGs based on |log2 fold change (FC)|≥1.5 and p < 0.05. Two datasets from the Ferroptosis Database (481 genes) and Autophagy Database (551 genes) were intersected with the DEGs from the GSE101141 dataset to identify ferroptosis- and autophagy-related DEGs using Venn diagrams. Functional and pathway enrichment, protein-protein interaction (PPI) network analyses were performed, and candidate genes were selected. Transcription factors (TFs), microRNAs (miRNAs), diseases and chemicals interacting with the candidate genes were identified. Receiver operating characteristic (ROC) curve analysis was performed to validate the diagnostic value of the candidate genes. Sixty ferroptosis-related and 74 autophagy-related DEGs were identified. These DEGs are involved in FoxO signaling pathway. Six candidate genes (EGFR, KRAS, IL1B, SIRT1, ATM, and MAPK8) were selected. miRNAs such as hsa-miR-27a-3p, hsa-miR-877-5p, and hsa-miR-892b, and TFs including P53, POU3F2, TATA are involved in regulation of candidate genes. Diseases such as schizophrenia, fibrosis, and neoplasms are the most relevant to the candidate genes. Chemicals, such as resveratrol, curcumin, and quercetin may have significant implications in the treatment of myelomeningocele. The candidate genes, especially MAPK8, also showed a high diagnostic value for myelomeningocele. These results help to shed light on the molecular mechanism of myelomeningocele and may provide new insights into diagnostic biomarker in the amniotic fluid and potential therapeutic agents of myelomeningocele.
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Affiliation(s)
- Xiuwei Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Translational Medicine Laboratory, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Kaixin Wei
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Min Wang
- Department of Physiology, College of Medicine, Jiaxing University, Jiaxing, 314001, Zhejiang, China
| | - Li Zhang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
- Department of Hepatobiliary and Pancreatic Surgery and Liver Transplant Center, The First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
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2
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Piazza A, Carlone R, Spencer GE. Non-canonical retinoid signaling in neural development, regeneration and synaptic function. Front Mol Neurosci 2024; 17:1371135. [PMID: 38516042 PMCID: PMC10954794 DOI: 10.3389/fnmol.2024.1371135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/21/2024] [Indexed: 03/23/2024] Open
Abstract
Canonical retinoid signaling via nuclear receptors and gene regulation is critical for the initiation of developmental processes such as cellular differentiation, patterning and neurite outgrowth, but also mediates nerve regeneration and synaptic functions in adult nervous systems. In addition to canonical transcriptional regulation, retinoids also exert rapid effects, and there are now multiple lines of evidence supporting non-canonical retinoid actions outside of the nucleus, including in dendrites and axons. Together, canonical and non-canonical retinoid signaling provide the precise temporal and spatial control necessary to achieve the fine cellular coordination required for proper nervous system function. Here, we examine and discuss the evidence supporting non-canonical actions of retinoids in neural development and regeneration as well as synaptic function, including a review of the proposed molecular mechanisms involved.
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Affiliation(s)
| | | | - Gaynor E. Spencer
- Department of Biological Sciences, Brock University, St. Catharines, ON, Canada
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3
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Seelan RS, Pisano MM, Greene RM. MicroRNAs as Biomarkers for Birth Defects. Microrna 2022; 11:2-11. [PMID: 35168515 DOI: 10.2174/2211536611666220215123423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/03/2022] [Accepted: 01/10/2022] [Indexed: 11/22/2022]
Abstract
It is estimated that 2-4% of live births will have a birth defect (BD). The availability of biomarkers for the prenatal detection of BDs will facilitate early risk assessment, prompt medical intervention and ameliorating disease severity. miRNA expression levels are often found to be altered in many diseases. There is, thus, a growing interest in determining whether miRNAs, particularly extracellular miRNAs, can predict, diagnose, or monitor BDs. These miRNAs, typically encapsulated in exosomes, are released by cells (including those of the fetus and placenta) into the extracellular milieu, such as blood, urine, saliva and cerebrospinal fluid, thereby enabling interaction with target cells. Exosomal miRNAs are stable, protected from degradation, and retain functionality. The observation that placental and fetal miRNAs can be detected in maternal serum, provides a strong rationale for adopting miRNAs as noninvasive prenatal biomarkers for BDs. In this mini-review, we examine the current state of research involving the use of miRNAs as prognostic and diagnostic biomarkers for BD.
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Affiliation(s)
- Ratnam S Seelan
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, School of Dentistry, University of Louisville, Louisville, KY 40202, USA
| | - M Michele Pisano
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, School of Dentistry, University of Louisville, Louisville, KY 40202, USA
| | - Robert M Greene
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, School of Dentistry, University of Louisville, Louisville, KY 40202, USA
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4
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Li Z, Feng J, Yuan Z. Key Modules and Hub Genes Identified by Coexpression Network Analysis for Revealing Novel Biomarkers for Spina Bifida. Front Genet 2020; 11:583316. [PMID: 33343629 PMCID: PMC7738565 DOI: 10.3389/fgene.2020.583316] [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: 07/14/2020] [Accepted: 11/09/2020] [Indexed: 11/13/2022] Open
Abstract
Spina bifida is a common neural tube defect (NTD) accounting for 5–10% of perinatal mortalities. As a polygenic disease, spina bifida is caused by a combination of genetic and environmental factors, for which the precise molecular pathogenesis is still not systemically understood. In the present study, we aimed to identify the related gene module that might play a vital role in the occurrence and development of spina bifida by using weighted gene co-expression network analysis (WGCNA). Transcription profiling according to an array of human amniocytes from patients with spina bifida and healthy controls was downloaded from the Gene Expression Omnibus database. First, outliers were identified and removed by principal component analysis (PCA) and sample clustering. Then, genes in the top 25% of variance in the GSE4182 dataset were then determined in order to explore candidate genes in potential hub modules using WGCNA. After data preprocessing, 5407 genes were obtained for further WGCNA. Highly correlated genes were divided into nineteen modules. Combined with a co-expression network and significant differentially expressed genes, 967 candidate genes were identified that may be involved in the pathological processes of spina bifida. Combined with our previous microRNA (miRNA) microarray results, we constructed an miRNA–mRNA network including four miRNAs and 39 mRNA among which three key genes were, respectively, linked to two miRNA-associated gene networks. Following the verification of qRT-PCR and KCND3 was upregulated in the spina bifida. KCND3 and its related miR-765 and miR-142-3p are worthy of further study. These findings may be conducive for early detection and intervention in spina bifida, as well as be of great significance to pregnant women and clinical staff.
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Affiliation(s)
- Zijian Li
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, China
| | - Juan Feng
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, China
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Abstract
Retinoic acid (RA), the biologically active metabolite of vitamin A, regulates a vast spectrum of biological processes, such as cell differentiation, proliferation, apoptosis, and morphogenesis. microRNAs (miRNAs) play a crucial role in regulating gene expression by binding to messenger RNA (mRNA) which leads to mRNA degradation and/or translational repression. Like RA, miRNAs regulate multiple biological processes, including proliferation, differentiation, apoptosis, neurogenesis, tumorigenesis, and immunity. In fact, RA regulates the expression of many miRNAs to exert its biological functions. miRNA and RA regulatory networks have been studied in recent years. In this manuscript, we summarize literature that highlights the impact of miRNAs in RA-regulated molecular networks included in the PubMed.
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Affiliation(s)
- Lijun Wang
- Department of Pathology and Laboratory Medicine, University of California Davis Health, Sacramento, CA, United States
| | - Atharva Piyush Rohatgi
- Department of Pathology and Laboratory Medicine, University of California Davis Health, Sacramento, CA, United States
| | - Yu-Jui Yvonne Wan
- Department of Pathology and Laboratory Medicine, University of California Davis Health, Sacramento, CA, United States.
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Zhang J, Yang L, Yu J, Yang Q, Mu J, Xie J. Alteration of the microRNA expression profile and identification of miRNA/mRNA negative regulation pairs in neural tube defects. Acta Biochim Biophys Sin (Shanghai) 2019; 51:761-765. [PMID: 31169880 DOI: 10.1093/abbs/gmz050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Indexed: 11/14/2022] Open
Affiliation(s)
- Juan Zhang
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
| | - Lihong Yang
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
| | - Juan Yu
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
| | - Qiaoyan Yang
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, China
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Darzi L, Boshtam M, Shariati L, Kouhpayeh S, Gheibi A, Mirian M, Rahimmanesh I, Khanahmad H, Tabatabaiefar MA. The silencing effect of miR-30a on ITGA4 gene expression in vitro: an approach for gene therapy. Res Pharm Sci 2017; 12:456-464. [PMID: 29204174 PMCID: PMC5691572 DOI: 10.4103/1735-5362.217426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Integrins are adhesion molecules which play crucial roles in cell-cell and cell-extracellular matrix interactions. Very late antigen-4 or α4β1 and lymphocyte Peyer’s patch adhesion molecule-1 or α4β7, are key factors in the invasion of tumor cells and metastasis. Based on the previous reports, integrin α4 (ITGA4) is overexpressed in some immune disorders and cancers. Thus, inhibition of ITGA4 could be a therapeutic strategy. In the present study, miR-30a was selected in order to suppress ITGA4 expression. The ITGA4 3' UTR was amplified, cloned in the Z2827-M67-(ITGA4) plasmid and named as Z2827-M67/3'UTR. HeLa cells were divided into five groups; (1) untreated without any transfection, (2) mock with Z2827-M67/3'UTR transfection and X-tremeGENE reagent, (3) negative control with Z2827-M67/3'UTR transfection alone, (4) test with miR-30a mimic and Z2827-M67/3'UTR transfection and (5) scramble with miR-30a scramble and Z2827-M67/3'UTR transfection. The MTT assay was performed to evaluate cell survival and cytotoxicity in each group. Real-time RT-PCR was applied for the ITGA4 expression analysis. The findings of this study showed that miR-30a downregulated ITGA4 expression and had no effect on the cell survival. Due to the silencing effect of miR-30a on the ITGA4 gene expression, this agent could be considered as a potential tool for cancer and immune disorders therapy.
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Affiliation(s)
- Leila Darzi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Maryam Boshtam
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Laleh Shariati
- Isfahan Cardiovascular Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Shirin Kouhpayeh
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Azam Gheibi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, I.R. Iran
| | - Mina Mirian
- Department of Pharmaceutical Biotechnology and Isfahan Pharmaceutical Science Research Center, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Ilnaz Rahimmanesh
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran.,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I.R. Iran.,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, I.R. Iran
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