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Zhou L, Li Y, Li J, Yao H, Huang J, Li C, Wang L. Decoding ceRNA regulatory network and autophagy-related genes in benign prostatic hyperplasia. Int J Biol Macromol 2023; 225:997-1009. [PMID: 36403772 DOI: 10.1016/j.ijbiomac.2022.11.162] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
Benign prostatic hyperplasia (BPH) is a common disease among aging males. We obtained BPH transcriptional signatures by high-throughput RNA sequencing analysis. Accordingly, we determined the differentially expressed RNAs (DERNAs) between BPH tissues and normal prostate tissues. WebGestalt and R package (clusterprofiler) was used to enrichment analysis. Clinical correlations were analyzed using Spearman's coefficient. TargetScan, ENCORI, miRNet, and miRDB databases were used to predict targets' relationships in ceRNA networks. Immunofluorescence staining and qRT-PCR analyses were performed to validate the findings. Microarray analysis of the datasets showed 369 DElncRNAs, 122 DEpseudogenes, 6 DEmiRNAs and 1358 DEmRNAs. DEmRNAs were particularly enriched in the autophagy-related pathways. Following the screening of DEmRNAs and autophagy-related genes (ARGs), 50 DEARGs were selected. MCODE analysis on Cytoscape was performed for the 50 DEARGs, and 3 hub genes (ATF4, XBP1, and PPP1R15A) were obtained. Spearman's correlation analysis showed that the mRNA expression of XBP1 correlated positively with age, total score, and storage score, but negatively with the maximum flow rate. Subsequently, the pseudogene/lncRNA- hsa-miR-222-3p-XBP1 pathway was identified. Our findings elucidate that the pseudogene/lncRNA-hsa-miR-222-3p-XBP1 pathway may play a regulatory role in the occurrence of BPH through autophagy.
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Affiliation(s)
- Liang Zhou
- Department of Urology, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Youyou Li
- Department of Urology, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Jiaren Li
- Department of Urology, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Hanyu Yao
- Department of Urology, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Jin Huang
- Department of Urology, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Cheng Li
- Department of Urology, The Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Long Wang
- Department of Urology, The Third Xiangya Hospital of Central South University, Changsha 410013, China.
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Liu J, Yao Y, Huang J, Sun H, Pu Y, Tian M, Zheng M, He H, Li Z. Comprehensive analysis of lncRNA-miRNA-mRNA networks during osteogenic differentiation of bone marrow mesenchymal stem cells. BMC Genomics 2022; 23:425. [PMID: 35672672 PMCID: PMC9172120 DOI: 10.1186/s12864-022-08646-x] [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: 12/16/2021] [Accepted: 05/19/2022] [Indexed: 11/15/2022] Open
Abstract
Background Long non-coding RNA (lncRNA) plays crucial role in osteogenic differentiation of bone marrow mesenchymal stem cells (BMMSCs), involving in regulation of competing endogenous RNA (ceRNA) mechanisms and conduction of signaling pathways. However, its mechanisms are poorly understood. This study aimed to investigate lncRNAs, miRNAs and mRNAs expression profiles in rat BMMSCs (rBMMSCs) osteogenic differentiation, screen the potential key lncRNA-miRNA-mRNA networks, explore the putative functions and identify the key molecules, as the basis of studying potential mechanism of rBMMSCs osteogenic differentiation driven by lncRNA, providing molecular targets for the management of bone defect. Methods High-throughput RNA sequencing (RNA-seq) was used to determine lncRNAs, miRNAs, and mRNAs expression profiles at 14-day rBMMSCs osteogenesis. The pivotal lncRNA-miRNA and miRNA-mRNA networks were predicted from sequencing data and bioinformatic analysis, and the results were exported by Cytoscape 3.9.0 software. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used for functional exploration. Real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was performed to validate lncRNAs, miRNAs and mRNAs. Results rBMMSCs were identified, and the osteogenic and adipogenic differentiation ability were detected. A total of 8634 lncRNAs were detected by RNA-seq, and 1524 differential expressed lncRNAs, of which 812 up-regulated and 712 down-regulated in osteo-inductive groups compared with control groups. 30 up-regulated and 61 down-regulated miRNAs, 91 miRNAs were differentially expressed in total. 2453 differentially expressed mRNAs including 1272 up-expressed and 1181 down-expressed were detected. 10 up-regulated lncRNAs were chosen to predict 21 down-regulated miRNAs and 650 up-regulated mRNAs. 49 lncRNA-miRNA and 1515 miRNA–mRNA interactive networks were constructed. GO analysis showed the most important enrichment in cell component and molecular function were “cytoplasm” and “protein binding”, respectively. Biological process related to osteogenic differentiation such as “cell proliferation”, “wound healing”, “cell migration”, “osteoblast differentiation”, “extracellular matrix organization” and “response to hypoxia” were enriched. KEGG analysis showed differentially expressed genes were mainly enriched in “PI3K-Akt signaling pathway”, “Signaling pathway regulating pluripotency of stem cells”, “cGMP-PKG signaling pathway”, “Axon guidance” and “Calcium signaling pathway”. qRT-PCR verified that lncRNA Tug1, lncRNA AABR07011996.1, rno-miR-93-5p, rno-miR-322-5p, Sgk1 and Fzd4 were consistent with the sequencing results, and 4 lncRNA-miRNA-mRNA networks based on validations were constructed, and enrichment pathways were closely related to “PI3K-Akt signaling pathway”, “Signaling pathway regulating pluripotency of stem cells” and “Wnt signaling pathway”. Conclusions lncRNAs, miRNAs and mRNAs expression profiles provide clues for future studies on their roles for BMMSCs osteogenic differentiation. Furthermore, lncRNA–miRNA–mRNA networks give more information on potential new mechanisms and targets for management on bone defect. Supplementary information The online version contains supplementary material available at 10.1186/s12864-022-08646-x.
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Affiliation(s)
- Jialin Liu
- Department of Prosthodontics and Implant Dentistry, The First Affiliated Hospital of Xinjiang Medical University, Xin Jiang Uygur Autonomous Region, 830054, Urumqi, China.,Affiliated Stomatological Hospital of Xinjiang Medical University, Xin Jiang Uygur Autonomous Region, 830054, Urumqi, China.,Stomatology Research Institute of Xinjiang Uygur Autonomous Region, Xin Jiang Uygur Autonomous Region, 830054, Urumqi, China
| | - Yuan Yao
- Department of Prosthodontics and Implant Dentistry, The First Affiliated Hospital of Xinjiang Medical University, Xin Jiang Uygur Autonomous Region, 830054, Urumqi, China.,Affiliated Stomatological Hospital of Xinjiang Medical University, Xin Jiang Uygur Autonomous Region, 830054, Urumqi, China.,Stomatology Research Institute of Xinjiang Uygur Autonomous Region, Xin Jiang Uygur Autonomous Region, 830054, Urumqi, China
| | - Jinyong Huang
- Department of Trauma Orthopedics, The First Affiliated Hospital of Xinjiang Medical University, Xin Jiang Uygur Autonomous Region, 830054, Urumqi, China
| | - Hao Sun
- Department of Prosthodontics and Implant Dentistry, The First Affiliated Hospital of Xinjiang Medical University, Xin Jiang Uygur Autonomous Region, 830054, Urumqi, China
| | - Yixuan Pu
- Department of Prosthodontics and Implant Dentistry, The First Affiliated Hospital of Xinjiang Medical University, Xin Jiang Uygur Autonomous Region, 830054, Urumqi, China
| | - Mengting Tian
- Department of Prosthodontics and Implant Dentistry, The First Affiliated Hospital of Xinjiang Medical University, Xin Jiang Uygur Autonomous Region, 830054, Urumqi, China
| | - Meijie Zheng
- Department of Prosthodontics and Implant Dentistry, The First Affiliated Hospital of Xinjiang Medical University, Xin Jiang Uygur Autonomous Region, 830054, Urumqi, China
| | - Huiyu He
- Department of Prosthodontics and Implant Dentistry, The First Affiliated Hospital of Xinjiang Medical University, Xin Jiang Uygur Autonomous Region, 830054, Urumqi, China.
| | - Zheng Li
- Department of Prosthodontics and Implant Dentistry, The First Affiliated Hospital of Xinjiang Medical University, Xin Jiang Uygur Autonomous Region, 830054, Urumqi, China.
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Yuan G, Yang S. Effect of Regulator of G Protein Signaling Proteins on Bone. Front Endocrinol (Lausanne) 2022; 13:842421. [PMID: 35573989 PMCID: PMC9098968 DOI: 10.3389/fendo.2022.842421] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/01/2022] [Indexed: 01/08/2023] Open
Abstract
Regulator of G protein signaling (RGS) proteins are critical negative molecules of G protein-coupled receptor (GPCR) signaling, which mediates a variety of biological processes in bone homeostasis and diseases. The RGS proteins are divided into nine subfamilies with a conserved RGS domain which plays an important role in regulating the GTPase activity. Mutations of some RGS proteins change bone development and/or metabolism, causing osteopathy. In this review, we summarize the recent findings of RGS proteins in regulating osteoblasts, chondrocytes, and osteoclasts. We also highlight the impacts of RGS on bone development, bone remodeling, and bone-related diseases. Those studies demonstrate that RGS proteins might be potential drug targets for bone diseases.
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Affiliation(s)
- Gongsheng Yuan
- Department of Basic and Translational Sciences, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Shuying Yang
- Department of Basic and Translational Sciences, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA, United States
- The Penn Center for Musculoskeletal Disorders, Penn Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Center for Innovation and Precision Dentistry, Penn Dental Medicine, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, United States
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Bortezomib Rescues Ovariectomy-Induced Bone Loss via SMURF-Mediated Ubiquitination Pathway. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2021:9661200. [PMID: 35003523 PMCID: PMC8741347 DOI: 10.1155/2021/9661200] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/17/2021] [Accepted: 11/29/2021] [Indexed: 12/28/2022]
Abstract
A balance between bone formation by osteoblasts and bone resorption by osteoclasts is necessary to maintain bone health and homeostasis. As a cancer of plasma cells, multiple myeloma (MM) is accompanied with rapid bone loss and fragility fracture. Bortezomib has been used as a first-line for treating MM for decades. Recently, the potential protection of bortezomib on osteoporosis (OP) is reported; however, the specific mechanism involving bortezomib-mediated antiosteoporotic effect is undetermined. In the present study, we assessed the effects of in vitro bortezomib treatment on osteogenesis and osteoclastogenesis and the protective effect on bone loss in ovariectomized (OVX) mice. Our results indicated that bortezomib treatment increased osteogenic differentiation of MC3T3-E1 cells as evidenced by increased levels of matrix mineralization and osteoblast-specific markers. In bortezomib-treated bone marrow monocytes (BMMs), osteoclast differentiation was suppressed, substantiated by downregulated tartrate-resistant acid phosphatase- (TRAP-) positive multinucleated cells, areas of actin rings, pit formation, and osteoclast-specific genes. Mechanistically, bortezomib exerted a protective effect against OP through the Smad ubiquitination regulatory factor- (SMURF-) mediated ubiquitination pathway. Furthermore, in vivo intraperitoneal injection of bortezomib attenuated the bone microarchitecture in OVX mice. Accordingly, our findings corroborated that bortezomib might have future applications in the treatment of postmenopausal OP.
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