1
|
Chen H, Li S, Wang J, Ma Y, Yin H. Screening of key biomarkers in osteoporosis: Evidence from bioinformatic analysis. Int J Rheum Dis 2023; 26:69-79. [PMID: 36219533 DOI: 10.1111/1756-185x.14450] [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: 06/07/2022] [Revised: 09/02/2022] [Accepted: 09/20/2022] [Indexed: 01/04/2023]
Abstract
OBJECTIVE To analyze the expression characteristics of osteoporosis-related genes by bioinformatics and elucidate the pathogenesis of osteoporosis. METHODS The differentially expressed genes (DEGs), microRNA (miRNA), and genes with differentially methylated regions (DMRS) in promoters were identified. The protein-protein interaction (PPI) network was constructed and performed. The Clue Gene Ontology analysis and miRNA-mRNA (messenger RNA) regulatory network were constructed using Cytoscape. RESULTS Fifty-nine DEGs, 10 differential miRNAs, and 2083 genes with DMRs were screened out. The Proteasome-Modulator (PSMD) family proteins and estrogen receptor 1 (ESR1) are vital for the PPI analysis of DEGs. The interaction network of the Smad3 protein showed that the degree of connection to ESR1, PSMD11, and transcription factor 4 (TCF4) is very high. Homo sapiens (hsa)-miR-106b-5p was differential and regulated TCF4 through building the miRNA-mRNA regulatory network. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment of DEGs focused on vascular smooth muscle contraction, thyroid hormone signaling pathway, and estrogen signaling pathway. The Gene Ontology (GO) function analysis of genes with DMRs in promoters was primarily concentrated in the cell differentiation, positive regulation of CDP-diacylglycerol-serine O-phosphatidyltransferase activity, and positive regulation of C-palmitoyltransferase activity. The KEGG enrichment of genes with DMRs in promoters largely focused on glycerol phospholipid metabolism, histidine metabolism, Adenosine 5'-monophosphate-activated protein kinase signaling pathway, Hedgehog signaling pathway, and mRNA surveillance pathway. CONCLUSION Hsa-miRNA-106b-5p regulates bone formation and the pathogenesis of osteoporosis by controlling TCF4, and methylation modification of TCF4 can also affect the pathogenesis of osteoporosis.
Collapse
Affiliation(s)
- Hao Chen
- Traditional Chinese Medicine Orthopedics, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Orthopedics and Traumatology, Yancheng Dafeng Hospital of Traditional Chinese Medicine, Yancheng, China
| | - Shaoshuo Li
- Traditional Chinese Medicine Orthopedics, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jianwei Wang
- Department of Orthopedics, Wuxi TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi, China
| | - Yong Ma
- Traditional Chinese Medicine Orthopedics, Nanjing University of Chinese Medicine, Nanjing, China
| | - Heng Yin
- Department of Orthopedics, Wuxi TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Wuxi, China
| |
Collapse
|
2
|
Shakyawar S, Southekal S, Guda C. mintRULS: Prediction of miRNA–mRNA Target Site Interactions Using Regularized Least Square Method. Genes (Basel) 2022; 13:genes13091528. [PMID: 36140696 PMCID: PMC9498445 DOI: 10.3390/genes13091528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Identification of miRNA–mRNA interactions is critical to understand the new paradigms in gene regulation. Existing methods show suboptimal performance owing to inappropriate feature selection and limited integration of intuitive biological features of both miRNAs and mRNAs. The present regularized least square-based method, mintRULS, employs features of miRNAs and their target sites using pairwise similarity metrics based on free energy, sequence and repeat identities, and target site accessibility to predict miRNA-target site interactions. We hypothesized that miRNAs sharing similar structural and functional features are more likely to target the same mRNA, and conversely, mRNAs with similar features can be targeted by the same miRNA. Our prediction model achieved an impressive AUC of 0.93 and 0.92 in LOOCV and LmiTOCV settings, respectively. In comparison, other popular tools such as miRDB, TargetScan, MBSTAR, RPmirDIP, and STarMir scored AUCs at 0.73, 0.77, 0.55, 0.84, and 0.67, respectively, in LOOCV setting. Similarly, mintRULS outperformed other methods using metrics such as accuracy, sensitivity, specificity, and MCC. Our method also demonstrated high accuracy when validated against experimentally derived data from condition- and cell-specific studies and expression studies of miRNAs and target genes, both in human and mouse.
Collapse
Affiliation(s)
- Sushil Shakyawar
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Siddesh Southekal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Center for Biomedical Informatics Research and Innovation (CBIRI), University of Nebraska Medical Center, Omaha, NE 68198, USA
- Correspondence:
| |
Collapse
|
3
|
Abstract
MicroRNAs (miRNAs) are small noncoding elements that play essential roles in the posttranscriptional regulation of biochemical processes. miRNAs recognize and target multiple mRNAs; therefore, investigating miRNA dysregulation is an indispensable strategy to understand pathological conditions and to design innovative drugs. Targeting miRNAs in diseases improve outcomes of several therapeutic strategies thus, this present study highlights miRNA targeting methods through experimental assays and bioinformatics tools. The first part of this review focuses on experimental miRNA targeting approaches for elucidating key biochemical pathways. A growing body of evidence about the miRNA world reveals the fact that it is not possible to uncover these molecules' structural and functional characteristics related to the biological processes with a deterministic approach. Instead, a systemic point of view is needed to truly understand the facts behind the natural complexity of interactions and regulations that miRNA regulations present. This task heavily depends both on computational and experimental capabilities. Fortunately, several miRNA bioinformatics tools catering to nonexperts are available as complementary wet-lab approaches. For this purpose, this work provides recent research and information about computational tools for miRNA targeting research.
Collapse
Affiliation(s)
- Hossein Ghanbarian
- Biotechnology Department & Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehmet Taha Yıldız
- Division of Molecular Medicine, Hamidiye Institute of Health Sciences, University of Health Sciences-Turkey, Istanbul, Turkey
| | - Yusuf Tutar
- Division of Biochemistry, Department of Basic Pharmaceutical Sciences, Hamidiye Faculty of Pharmacy & Division of Molecular Medicine, Hamidiye Institute of Health Sciences, University of Health Sciences-Turkey, Istanbul, Turkey.
| |
Collapse
|
4
|
Feng X, Bao J, Song C, Xie L, Tan X, Li J, Jia H, Tian M, Qi J, Qin C, Bian H. Functional role of miR‑155 in physiological and pathological processes of liver injury (Review). Mol Med Rep 2021; 24:714. [PMID: 34396452 DOI: 10.3892/mmr.2021.12353] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/09/2021] [Indexed: 11/05/2022] Open
Abstract
There are several types of liver injury, including alcohol‑induced liver injury, drug‑induced liver injury, infectious liver injury, cirrhosis, liver ischemia/reperfusion injury and liver failure. In recent years, accumulated data have demonstrated that microRNAs (miRNAs/miRs) may be involved in the occurrence and development of a variety of systemic diseases, such as immune diseases, tumors and nervous system diseases. miR‑155 is a key miRNA, which has been studied extensively and has been shown to target different genes. In the present review, the potential effects and mechanisms of miR‑155 on the physiological and pathological processes of liver injury were reviewed from the perspective of cell stress, inflammation and activation of fibrosis. In addition, the potential benefits of miR‑155 as a therapeutic target and predictor of liver injury were summarized.
Collapse
Affiliation(s)
- Xiao Feng
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Jiaying Bao
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Chunxia Song
- Department of Emergency Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Ling Xie
- Department of Obstetrics and Gynecology, Jinan Zhangqiu District Maternal and Child Health Hospital, Jinan, Shandong 250200, P.R. China
| | - Xu Tan
- Department of Gynecology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Jiaqi Li
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Huimin Jia
- Department of Emergency Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Miaomiao Tian
- Department of Immunology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Jianni Qi
- Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Chengyong Qin
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Hongjun Bian
- Department of Emergency Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| |
Collapse
|
5
|
Jin FE, Xie B, Xian HZ, Wang JH. Knockdown of miR-125b-5p inhibits the proliferation and invasion of gastric carcinoma cells by targeting RYBP. Kaohsiung J Med Sci 2021; 37:863-871. [PMID: 34337862 DOI: 10.1002/kjm2.12425] [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: 11/14/2020] [Revised: 04/12/2021] [Accepted: 06/14/2021] [Indexed: 11/08/2022] Open
Abstract
Gastric carcinoma, one of the most aggressive and lethal human malignancies, is associated with poor prognosis despite progress in therapeutic strategies. This study examined the potential function and mechanism of action of microRNA-125b-5p (miR-125b-5p) in the pathogenesis of gastric carcinoma. We recognized that miR-125b-5p was elevated in gastric carcinoma, and its decreased expression was associated with a better prognosis. Loss-of-function assays showed that miR-125b-5p suppression inhibited the proliferative and invasive abilities of gastric cancer cells. Furthermore, RING1 and YY1-binding protein (RYBP) was found to be target gene for miR-125b-5p action; miR-125b-5p negatively regulates RYBP expression. According to the results of rescue experiments, RYBP downregulation partially counteracted the miR-125b-5p silence-mediated inhibitory function in gastric cancer progression. Collectively, these data elucidated the molecular mechanisms of the miR-125b-5p/RYBP axis in gastric cancer invasion and growth.
Collapse
Affiliation(s)
- Fu-E Jin
- Department of Health Management, Qingdao Huangdao District Center Hospital, Qingdao, China
| | - Bo Xie
- Gastrointestinal Surgery, Liaocheng People's Hospital, Liaocheng, China
| | - Hong-Zhen Xian
- Department of Gastroenterology, Jimo People's Hospital of Qingdao City, Qingdao, China
| | - Ji-Hai Wang
- Surgery Staff Room, Shandong Medical College, Linyi, China
| |
Collapse
|
6
|
Ling Z, Chen M, Li T, Qian Y, Li C. MiR-141-3p downregulation promotes tube formation, migration, invasion and inhibits apoptosis in hypoxia-induced human umbilical vein endothelial cells by targeting Notch2. Reprod Biol 2021; 21:100483. [PMID: 33631423 DOI: 10.1016/j.repbio.2021.100483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 01/11/2021] [Accepted: 01/25/2021] [Indexed: 12/15/2022]
Abstract
Vascular endothelial cell damage is regarded as the carrier in the progression of the pathological changes of preeclampsia (PE) from the placenta to maternal organs. MicroRNA (miR)-141-3p was aberrantly expressed during PE pathogenesis. We investigated the role of miR-141-3p in regulating the biological behaviors of endothelial cells in PE. Human umbilical vein endothelial cells (HUVECs) were isolated from the human umbilical cords and cultured under hypoxia condition to establish PE models. The binding of miR-141-3p and Notch2 was confirmed by dual-luciferase reporter assay. HUVECs were transfected with miR-141-3p inhibitor and siRNA-Notch2. The viability, vascularization capability, migration, and invasion of HUVECs were evaluated by MTT, tube formation, and Transwell assays. Cell apoptosis was measured via flow cytometry. The expressions of miR-141-3p, Notch2, Bcl-2, Bax and cleaved caspase-3 were assessed by qRT-PCR or Western blot. MiR-141-3p expression was upregulated in the HUVECs isolated from PE tissues and hypoxia-induced HUVECs. Hypoxia treatment inhibited viability, tube formation, migration, and invasion, and promoted apoptosis in HUVECS, as well as increased Bax and cleaved caspase-3 expressions and decreased Bcl-2 expression. Downregulating miR-141-3p expression promoted viability, tube formation, migration and invasion, and inhibited apoptosis in HUVECs, counteracting the effect of hypoxia on HUVECs. MiR-141-3p directly targeted Notch2. Silencing Notch2 reversed the promoting effect of downregulated miR-141-3p expression on HUVECs. In conclusion, downregulating miR-141-3p expression during hypoxia promotes tube formation, migration, and invasion and inhibits apoptosis in HUVECs by targeting Notch2.
Collapse
Affiliation(s)
- Zhonghui Ling
- Department of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing, China
| | - Min Chen
- Department of Gynaecology and Obstetrics, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, No.123, Tianfei Alley, Qinhuai District, Nanjing, Jiangsu 210000, China
| | - Ting Li
- Department of Gynaecology and Obstetrics, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, No.123, Tianfei Alley, Qinhuai District, Nanjing, Jiangsu 210000, China
| | - Yating Qian
- Department of Gynaecology and Obstetrics, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, No.123, Tianfei Alley, Qinhuai District, Nanjing, Jiangsu 210000, China
| | - Chanjuan Li
- Department of Gynaecology and Obstetrics, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, No.123, Tianfei Alley, Qinhuai District, Nanjing, Jiangsu 210000, China.
| |
Collapse
|
7
|
Videm P, Kumar A, Zharkov O, Grüning BA, Backofen R. ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data. Gigascience 2021; 10:6123621. [PMID: 33511995 PMCID: PMC7844879 DOI: 10.1093/gigascience/giaa158] [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: 08/20/2020] [Revised: 11/26/2020] [Accepted: 12/15/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND With the advances in next-generation sequencing technologies, it is possible to determine RNA-RNA interaction and RNA structure predictions on a genome-wide level. The reads from these experiments usually are chimeric, with each arm generated from one of the interaction partners. Owing to short read lengths, often these sequenced arms ambiguously map to multiple locations. Thus, inferring the origin of these can be quite complicated. Here we present ChiRA, a generic framework for sensitive annotation of these chimeric reads, which in turn can be used to predict the sequenced hybrids. RESULTS Grouping reference loci on the basis of aligned common reads and quantification improved the handling of the multi-mapped reads in contrast to common strategies such as the selection of the longest hit or a random choice among all hits. On benchmark data ChiRA improved the number of correct alignments to the reference up to 3-fold. It is shown that the genes that belong to the common read loci share the same protein families or similar pathways. In published data, ChiRA could detect 3 times more new interactions compared to existing approaches. In addition, ChiRAViz can be used to visualize and filter large chimeric datasets intuitively. CONCLUSION ChiRA tool suite provides a complete analysis and visualization framework along with ready-to-use Galaxy workflows and tutorials for RNA-RNA interactome and structurome datasets. Common read loci built by ChiRA can rescue multi-mapped reads on paralogous genes without requiring any information on gene relations. We showed that ChiRA is sensitive in detecting new RNA-RNA interactions from published RNA-RNA interactome datasets.
Collapse
Affiliation(s)
- Pavankumar Videm
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Anup Kumar
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Oleg Zharkov
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Björn Andreas Grüning
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
| |
Collapse
|
8
|
Cao H, Baranova A, Yue W, Yu H, Zhu Z, Zhang F, Liu D. miRNA-Coordinated Schizophrenia Risk Network Cross-Talk With Cardiovascular Repair and Opposed Gliomagenesis. Front Genet 2020; 11:149. [PMID: 32194626 PMCID: PMC7064629 DOI: 10.3389/fgene.2020.00149] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 02/10/2020] [Indexed: 12/17/2022] Open
Abstract
Background Schizophrenia risk genes are widely investigated, but a systemic analysis of miRNAs contributing to schizophrenia is lacking. Methods Schizophrenia-associated genetic loci profiles were derived from a genome-wide association study (GWAS) from the Schizophrenia Working Group of the Psychiatric Genomics Consortium (PGC) dataset. Experimentally confirmed relationships between miRNAs and their target genes were retrieved from a miRTarBase. A competitive gene set association analysis for miRNA-target regulations was conducted by the Multi-marker Analysis of GenoMic Annotation (MAGMA) and further validated by literature-based functional pathway analysis using Pathway Studio. The association between the targets of three miRNAs and schizophrenia was further validated using a GWAS of antipsychotic treatment responses. Results Three novel schizophrenia-risk miRNAs, namely, miR-208b-3p, miR-208a-3p, and miR-494-5p, and their targetomes converged on calcium voltage-gated channel subunit alpha1 C (CACNA1C) and B-cell lymphoma 2 (BCL2), and these are well-known contributors to schizophrenia. Both miR-208a-3p and miR-208b-3p reduced the expression of the RNA-binding protein Quaking (QKI), whose suppression commonly contributes to demyelination of the neurons and to ischemia/reperfusion injury. On the other hand, both QKI and hsa-miR-494-5p were involved in gliomagenesis. Conclusion Presented results point at an orchestrating role of miRNAs in the pathophysiology of schizophrenia. The sharing of regulatory networks between schizophrenia and other pathologies may explain higher cardiovascular mortality and lower odds of glioma previously reported in psychiatric patients.
Collapse
Affiliation(s)
- Hongbao Cao
- Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China.,Department of Genomics Research, R&D Solutions, Elsevier Inc., Rockville, MD, United States.,School of Systems Biology, George Mason University (GMU), Fairfax, VA, United States
| | - Ancha Baranova
- School of Systems Biology, George Mason University (GMU), Fairfax, VA, United States.,Research Center for Medical Genetics, Moscow, Russia
| | - Weihua Yue
- Department of Psychiatry Institute of Mental Health, Peking University, Bejing, China
| | - Hao Yu
- Department of Psychiatry, Jining Medical University, Jining, China
| | - Zufu Zhu
- Department of Neurology, Jiangyin People's Hospital Affiliated to Southeast University, Jiangyin, China
| | - Fuquan Zhang
- Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Dongbai Liu
- Department of Neurology, Jiangyin People's Hospital Affiliated to Southeast University, Jiangyin, China
| |
Collapse
|
9
|
Predicting miRNA-lncRNA interactions and recognizing their regulatory roles in stress response of plants. Math Biosci 2019; 312:67-76. [PMID: 31034845 DOI: 10.1016/j.mbs.2019.04.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 03/28/2019] [Accepted: 04/23/2019] [Indexed: 02/02/2023]
Abstract
It has been found that each non-coding RNA (ncRNA) can act not only through its target gene, but also interact with each other to act on biological traits, and this interaction is more common. Many studies focus mainly on the analysis of microRNA(miRNA) and message RNA (mRNA) interactions. In this study, we investigated miRNA and long non-coding RNA (lncRNA) interactions using support vector regression (SVR) for prediction of new target genes in Arabidopsis thaliana and identify some regulatory roles in stress response. The networks of miRNA-mRNA, miRNA-lncRNA and miRNA-mRNA-lncRNA were constructed. They were further analyzed and interpreted in R. We showed that miRNA with low sequence number, targeted lncRNA with high sequence number and miRNA with high sequence number targeted lncRNA with low sequence number. The experimental results showed that there is a regulatory relationship between miRNA-lncRNA. New RNA targets were predicted using SVR with new gene expression mechanism and the stress related functions were annotated.
Collapse
|