1
|
Liu Y, Sun D, Xu C, Liu X, Tang M, Ying S. In-depth transcriptome profiling of Cherry Valley duck lungs exposed to chronic heat stress. Front Vet Sci 2024; 11:1417244. [PMID: 39104549 PMCID: PMC11298465 DOI: 10.3389/fvets.2024.1417244] [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: 04/14/2024] [Accepted: 07/08/2024] [Indexed: 08/07/2024] Open
Abstract
Amidst rising global temperatures, chronic heat stress (CHS) is increasingly problematic for the poultry industry. While mammalian CHS responses are well-studied, avian-specific research is lacking. This study uses in-depth transcriptome sequencing to evaluate the pulmonary response of Cherry Valley ducks to CHS at ambient temperatures of 20°C and a heat-stressed 29°C. We detailed the CHS-induced gene expression changes, encompassing mRNAs, lncRNAs, and miRNAs. Through protein-protein interaction network analysis, we identified central genes involved in the heat stress response-TLR7, IGF1, MAP3K1, CIITA, LCP2, PRKCB, and PLCB2. Subsequent functional enrichment analysis of the differentially expressed genes and RNA targets revealed significant engagement in immune responses and regulatory processes. KEGG pathway analysis underscored crucial immune pathways, specifically those related to intestinal IgA production and Toll-like receptor signaling, as well as Salmonella infection and calcium signaling pathways. Importantly, we determined six miRNAs-miR-146, miR-217, miR-29a-3p, miR-10926, miR-146b-5p, and miR-17-1-3p-as potential key regulators within the ceRNA network. These findings enhance our comprehension of the physiological adaptation of ducks to CHS and may provide a foundation for developing strategies to improve duck production under thermal stress.
Collapse
Affiliation(s)
- Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Dongyue Sun
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Congcong Xu
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Xiaoyong Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shijia Ying
- Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| |
Collapse
|
2
|
Song C, Hu P, Peng R, Li F, Fang Z, Xu Y. Bioenergetic dysfunction in the pathogenesis of intervertebral disc degeneration. Pharmacol Res 2024; 202:107119. [PMID: 38417775 DOI: 10.1016/j.phrs.2024.107119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/16/2024] [Accepted: 02/24/2024] [Indexed: 03/01/2024]
Abstract
Intervertebral disc (IVD) degeneration is a frequent cause of low back pain and is the most common cause of disability. Treatments for symptomatic IVD degeneration, including conservative treatments such as analgesics, physical therapy, anti-inflammatories and surgeries, are aimed at alleviating neurological symptoms. However, there are no effective treatments to prevent or delay IVD degeneration. Previous studies have identified risk factors for IVD degeneration such as aging, inflammation, genetic factors, mechanical overload, nutrient deprivation and smoking, but metabolic dysfunction has not been highlighted. IVDs are the largest avascular structures in the human body and determine the hypoxic and glycolytic features of nucleus pulposus (NP) cells. Accumulating evidence has demonstrated that intracellular metabolic dysfunction is associated with IVD degeneration, but a comprehensive review is lacking. Here, by reviewing the physiological features of IVDs, pathological processes and metabolic changes associated with IVD degeneration and the functions of metabolic genes in IVDs, we highlight that glycolytic pathway and intact mitochondrial function are essential for IVD homeostasis. In degenerated NPs, glycolysis and mitochondrial function are downregulated. Boosting glycolysis such as HIF1α overexpression protects against IVD degeneration. Moreover, the correlations between metabolic diseases such as diabetes, obesity and IVD degeneration and their underlying molecular mechanisms are discussed. Hyperglycemia in diabetic diseases leads to cell senescence, the senescence-associated phenotype (SASP), apoptosis and catabolism of extracellualr matrix in IVDs. Correcting the global metabolic disorders such as insulin or GLP-1 receptor agonist administration is beneficial for diabetes associated IVD degeneration. Overall, we summarized the recent progress of investigations on metabolic contributions to IVD degeneration and provide a new perspective that correcting metabolic dysfunction may be beneficial for treating IVD degeneration.
Collapse
Affiliation(s)
- Chao Song
- Department of Orthopaedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, China
| | - Peixuan Hu
- Department of Orthopaedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, China
| | - Renpeng Peng
- Department of Orthopaedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, China
| | - Feng Li
- Department of Orthopaedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, China.
| | - Zhong Fang
- Department of Orthopaedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, China.
| | - Yong Xu
- Department of Orthopaedic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, China.
| |
Collapse
|
3
|
Genedy HH, Humbert P, Laoulaou B, Le Moal B, Fusellier M, Passirani C, Le Visage C, Guicheux J, Lepeltier É, Clouet J. MicroRNA-targeting nanomedicines for the treatment of intervertebral disc degeneration. Adv Drug Deliv Rev 2024; 207:115214. [PMID: 38395361 DOI: 10.1016/j.addr.2024.115214] [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: 12/13/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024]
Abstract
Low back pain stands as a pervasive global health concern, afflicting almost 80% of adults at some point in their lives with nearly 40% attributable to intervertebral disc degeneration (IVDD). As only symptomatic relief can be offered to patients there is a dire need for innovative treatments.Given the accumulating evidence that multiple microRNAs (miRs) are dysregulated during IVDD, they could have a huge potential against this debilitating condition. The way miRs can profoundly modulate signaling pathways and influence several cellular processes at once is particularly exciting to tackle this multifaceted disorder. However, miR delivery encounters extracellular and intracellular biological barriers. A promising technology to address this challenge is the vectorization of miRs within nanoparticles, providing both protection and enhancing their uptake within the scarce target cells of the degenerated IVD. This comprehensive review presents the diverse spectrum of miRs' connection with IVDD and demonstrates their therapeutic potential when vectorized in nanomedicines.
Collapse
Affiliation(s)
- Hussein H Genedy
- Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR1229, Nantes, France; Univ Angers, INSERM, CNRS, MINT, SFR ICAT, F-49000 Angers, France
| | - Paul Humbert
- Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR1229, Nantes, France
| | - Bilel Laoulaou
- Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR1229, Nantes, France; Univ Angers, INSERM, CNRS, MINT, SFR ICAT, F-49000 Angers, France
| | - Brian Le Moal
- Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR1229, Nantes, France; Univ Angers, INSERM, CNRS, MINT, SFR ICAT, F-49000 Angers, France
| | - Marion Fusellier
- Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR1229, Nantes, France; Department of Diagnostic Imaging, CRIP, ONIRIS, College of Veterinary Medicine, Food Science and Engineering, Nantes F-44307, France
| | | | - Catherine Le Visage
- Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR1229, Nantes, France
| | - Jérôme Guicheux
- Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR1229, Nantes, France
| | - Élise Lepeltier
- Univ Angers, INSERM, CNRS, MINT, SFR ICAT, F-49000 Angers, France; Institut Universitaire de France (IUF), France.
| | - Johann Clouet
- Nantes Université, Oniris, CHU Nantes, INSERM, Regenerative Medicine and Skeleton, RMeS, UMR1229, Nantes, France
| |
Collapse
|
4
|
Li ZC, An F. ERBB2-PTGS2 axis promotes intervertebral disc degeneration by regulating senescence of nucleus pulposus cells. BMC Musculoskelet Disord 2023; 24:504. [PMID: 37340393 DOI: 10.1186/s12891-023-06625-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/10/2023] [Indexed: 06/22/2023] Open
Abstract
Intervertebral disc degeneration (IDD) is considered one of the main causes of low back pain and lumbar disc herniation. Various studies have shown that disc cell senescence plays a critical role in this process. however, its role in IDD is yet unclear. In this study, we explored the role of senescence-related genes (SR-DEGs) and its underlying mechanism in IDD. A total of 1325 differentially expressed genes (DEGs) were identified using Gene Expression Omnibus (GEO) database GSE41883. 30 SR-DEGs were identified for further functional enrichment and pathway analysis, and two hub SR-DEGs (ERBB2 and PTGS2) were selected to construct transcription factor (TF)-gene interaction and TF-miRNA coregulatory networks, and 10 candidate drugs were screened for the treatment of IDD. Last but not least, in vitro experiments show that ERBB2 expression decreased and PTGS2 expression increased in human nucleus pulposus (NP) cell senescence model treated with TNF-α. After lentivirus-mediated overexpression of ERBB2, the expression of PTGS2 decreased and the senescence level of NP cells decreased. Overexpression of PTGS2 reversed the anti-senescence effects of ERBB2. The findings in this study suggested that ERBB2 overexpression further reduced NP cell senescence by inhibiting PTGS2 levels, which ultimately alleviated IDD. Taken together, our findings provide new insights into the roles of senescence-related genes in IDD and highlight a novel target of ERBB2-PTGS2 axis for therapeutic strategies.
Collapse
Affiliation(s)
- Zhao-Cheng Li
- Department of Spine Surgery, Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, 730000, Gansu, PR China
| | - Fu An
- Department of Spine Surgery, Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, 730000, Gansu, PR China.
| |
Collapse
|
5
|
Tian R, Xue Z, Ruan D, Chen P, Xu Y, Dai C, Shen W, Ouyang H, Liu W, Lin J. MSdb: An integrated expression atlas of human musculoskeletal system. iScience 2023; 26:106933. [PMID: 37378342 PMCID: PMC10291471 DOI: 10.1016/j.isci.2023.106933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/26/2023] [Accepted: 05/16/2023] [Indexed: 06/29/2023] Open
Abstract
The global prevalence and burden of musculoskeletal (MSK) disorders are immense. Advancements in next-generation sequencing (NGS) have generated vast amounts of data, accelerating the research of pathological mechanisms and the development of therapeutic approaches for MSK disorders. However, scattered datasets across various repositories complicate uniform analysis and comparison. Here, we introduce MSdb, a database for visualization and integrated analysis of next-generation sequencing data from human musculoskeletal system, along with manually curated patient phenotype data. MSdb provides various types of analysis, including sample-level browsing of metadata information, gene/miRNA expression, and single-cell RNA-seq dataset. In addition, MSdb also allows integrated analysis for cross-samples and cross-omics analysis, including customized differentially expressed gene/microRNA analysis, microRNA-gene network, scRNA-seq cross-sample/disease integration, and gene regulatory network analysis. Overall, systematic categorizing, standardized processing, and freely accessible knowledge features MSdb a valuable resource for MSK research community.
Collapse
Affiliation(s)
- Ruonan Tian
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China
| | - Ziwei Xue
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China
| | - Dengfeng Ruan
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Pengwei Chen
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yiwen Xu
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Chao Dai
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Weiliang Shen
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Hangzhou, Zhejiang 310058, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, Zhejiang 310058, China
| | - Hongwei Ouyang
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Department of Sports Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Hangzhou, Zhejiang 310058, China
- China Orthopedic Regenerative Medicine Group (CORMed), Hangzhou, Zhejiang 310058, China
| | - Wanlu Liu
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, Zhejiang 314100, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province, Hangzhou, Zhejiang 310058, China
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junxin Lin
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine, and Department of Orthopedic Surgery of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| |
Collapse
|
6
|
Zhang Y, Zhang J, Sun Z, Wang H, Ning R, Xu L, Zhao Y, Yang K, Xi X, Tian J. MAPK8 and CAPN1 as potential biomarkers of intervertebral disc degeneration overlapping immune infiltration, autophagy, and ceRNA. Front Immunol 2023; 14:1188774. [PMID: 37325630 PMCID: PMC10266224 DOI: 10.3389/fimmu.2023.1188774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/16/2023] [Indexed: 06/17/2023] Open
Abstract
Background Intervertebral disc degeneration (IDD) is one of the most common health problems in the elderly and a major causative factor in low back pain (LBP). An increasing number of studies have shown that IDD is closely associated with autophagy and immune dysregulation. Therefore, the aim of this study was to identify autophagy-related biomarkers and gene regulatory networks in IDD and potential therapeutic targets. Methods We obtained the gene expression profiles of IDD by downloading the datasets GSE176205 and GSE167931 from the Gene Expression Omnibus (GEO) public database. Subsequently, differentially expressed genes (DEGs) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, gene ontology (GO), and gene set enrichment analysis (GSEA) were performed to explore the biological functions of DEGs. Differentially expressed autophagy-related genes (DE-ARGs) were then crossed with the autophagy gene database. The hub genes were screened using the DE-ARGs protein-protein interaction (PPI) network. The correlation between the hub genes and immune infiltration and the construction of the gene regulatory network of the hub genes were confirmed. Finally, quantitative PCR (qPCR) was used to validate the correlation of hub genes in a rat IDD model. Results We obtained 636 DEGs enriched in the autophagy pathway. Our analysis revealed 30 DE-ARGs, of which six hub genes (MAPK8, CTSB, PRKCD, SNCA, CAPN1, and EGFR) were identified using the MCODE plugin. Immune cell infiltration analysis revealed that there was an increased proportion of CD8+ T cells and M0 macrophages in IDD, whereas CD4+ memory T cells, neutrophils, resting dendritic cells, follicular helper T cells, and monocytes were much less abundant. Subsequently, the competitive endogenous RNA (ceRNA) network was constructed using 15 long non-coding RNAs (lncRNAs) and 21 microRNAs (miRNAs). In quantitative PCR (qPCR) validation, two hub genes, MAPK8 and CAPN1, were shown to be consistent with the bioinformatic analysis results. Conclusion Our study identified MAPK8 and CAPN1 as key biomarkers of IDD. These key hub genes may be potential therapeutic targets for IDD.
Collapse
Affiliation(s)
- Yuxin Zhang
- School of Medicine, Shanghai University, Shanghai, China
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiahui Zhang
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhongyi Sun
- Department of Orthopedics, BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
| | - Hui Wang
- Department of Orthopaedics, Shanghai Changzheng Hospital, Shanghai, China
| | - Ruonan Ning
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Longyu Xu
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yichen Zhao
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kai Yang
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaobing Xi
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiwei Tian
- School of Medicine, Shanghai University, Shanghai, China
- Department of Orthopedics, BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
| |
Collapse
|
7
|
Bie Y, Zheng X, Chen X, Liu X, Wang L, Sun Y, Kou J. RNA sequencing and bioinformatics analysis of differentially expressed genes in the peripheral serum of ankylosing spondylitis patients. J Orthop Surg Res 2023; 18:394. [PMID: 37254181 DOI: 10.1186/s13018-023-03871-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/21/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Ankylosing spondylitis (AS) is a chronic progressive autoimmune disease characterized by spinal and sacroiliac arthritis, but its pathogenesis and genetic basis are largely unclear. METHODS We randomly selected three serum samples each from an AS and a normal control (NC) group for high-throughput sequencing followed by using edgeR to find differentially expressed genes (DEGs). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes, Reactome pathway analyses, and Gene Set Enrichment Analysis were used to comprehensively analyze the possible functions and pathways involved with these DEGs. Protein-protein interaction (PPI) networks were constructed using the STRING database and Cytoscape. The modules and hub genes of these DEGs were identified using MCODE and CytoHubba plugins. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to validate the expression levels of candidate genes in serum samples from AS patients and healthy controls. RESULTS We successfully identified 100 significant DEGs in serum. When we compared them with the NC group, 49 of these genes were upregulated in AS patients and 51 were downregulated. GO function and pathway enrichment analysis indicated that these DEGs were mainly enriched in several signaling pathways associated with endoplasmic reticulum stress, including protein processing in the endoplasmic reticulum, unfolded protein response, and ubiquitin-mediated proteolysis. We also constructed a PPI network and identified the highly connected top 10 hub genes. The expression levels of the candidate hub genes PPARG, MDM2, DNA2, STUB1, UBTF, and SLC25A37 were then validated by RT-qPCR analysis. Finally, receiver operating characteristic curve analysis suggested that PPARG and MDM2 may be the potential biomarkers of AS. CONCLUSIONS These findings may help to further elucidate the pathogenesis of AS and provide valuable potential gene biomarkers or targets for the diagnosis and treatment of AS.
Collapse
Affiliation(s)
- Yongchen Bie
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Xiujun Zheng
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Xiaojiong Chen
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Xiangyun Liu
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Liqin Wang
- Department of Rheumatology, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Yuanliang Sun
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Jianqiang Kou
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China.
| |
Collapse
|
8
|
Yang J, Long Q, Zhang Y, Liu Y, Wu J, Zhao X, You X, Li X, Liu J, Teng Z, Zeng Y, Luo XJ. Whole transcriptome analysis reveals dysregulation of molecular networks in schizophrenia. Asian J Psychiatr 2023; 85:103649. [PMID: 37267675 DOI: 10.1016/j.ajp.2023.103649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/04/2023]
Abstract
To characterize the regulatory relationships between different types of transcripts and the altered molecular networks in schizophrenia (SCZ), we performed a whole transcriptome study by quantifying mRNAs, long noncoding RNAs (lncRNAs), miRNAs, and circular RNAs (circRNAs) in the same individuals simultaneously. A total of 807 dysregulated genes showed differential expression in SCZ cases compared with controls. Network-based analysis revealed dysregulation of molecular networks in SCZ. Finally, integration of the transcriptome data with published data identified promising SCZ candidate genes. Our study reveals that dysregulated molecular networks and regulatory relationships between different types of transcript may have a role in SCZ.
Collapse
Affiliation(s)
- Jinfeng Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Qing Long
- The Second Affiliated Hospital, Kunming Medical University, Kunming, Yunnan 650101, China
| | - Yunqiao Zhang
- The Second Affiliated Hospital, Kunming Medical University, Kunming, Yunnan 650101, China; Honghe Second People's Hospital, Honghe, Yunnan 654399, China; The Sixth Affiliated Hospital, Kunming Medical University, Yuxi, Yunnan 653100, China
| | - Yilin Liu
- The Second Affiliated Hospital, Kunming Medical University, Kunming, Yunnan 650101, China
| | - Jie Wu
- The Affiliated Mental Health Center, Kunming Medical University, Kunming, Yunnan 650224, China
| | - Xinling Zhao
- The Second Affiliated Hospital, Kunming Medical University, Kunming, Yunnan 650101, China
| | - Xu You
- Honghe Second People's Hospital, Honghe, Yunnan 654399, China
| | - Xiaoyan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Jiewei Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Zhaowei Teng
- The Second Affiliated Hospital, Kunming Medical University, Kunming, Yunnan 650101, China.
| | - Yong Zeng
- The Second Affiliated Hospital, Kunming Medical University, Kunming, Yunnan 650101, China.
| | - Xiong-Jian Luo
- Zhongda Hospital, School of Medicine, Advanced Institute for Life and Health, Southeast University, Nanjing 210096, China; Department of Neurology, Zhongda Hospital, School of Medicine, Advanced Institute for Life and Health, Southeast University, Nanjing, China.
| |
Collapse
|
9
|
Li S, Li S, Li Q, Zhou Q, Liao W, Yu L, Ouyang C, Xia H, Liu C, Li M. Identification of key genes and pathways in atherosclerosis using integrated bioinformatics analysis. BMC Med Genomics 2023; 16:102. [PMID: 37179331 PMCID: PMC10183119 DOI: 10.1186/s12920-023-01533-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Atherosclerosis (AS) is a chronic inflammatory disease that might induce severe cardiovascular events, such as myocardial infarction and cerebral infarction. These risk factors in the pathogenesis of AS remain uncertain and further research is needed. This study aims to explore the potential molecular mechanisms of AS by bioinformatics analyses. METHODS GSE100927 gene expression profiles, including 69 AS samples and 35 healthy controls, were downloaded from Gene Expression Omnibus database and indenfied for key genes and pathways in AS. RESULTS A total of 443 differentially expressed genes (DEGs) between control and AS were identified, including 323 down-regulated genes and 120 up-regulated genes. The Gene ontology terms enriched by the up-regulated DEGs were associated with the regulation of leukocyte activation, endocytic vesicle, and cytokine binding, while the down-regulated DEGs were associated with negative regulation of cell growth, extracellular matrix, and G protein-coupled receptor binding. KEGG pathway analysis showed that the up-regulated DEGs were enriched in Osteoclast differentiation and Phagosome, while the down-regulated DEGs were enriched in vascular smooth muscle contraction and cGMP-PKG signaling pathway. Using the modular analysis of Cytoscape, we identified 3 modules mainly involved in Leishmaniasis and Osteoclast differentiation. The GSEA analysis showed the up-regulated gene sets were enriched in the ribosome, ascorbated metabolism, and propanoate metabolism. The LASSO Cox regression analysis showed the top 3 genes were TNF, CX3CR1, and COL1R1. Finally, we found these immune cells were conferred significantly higher infiltrating density in the AS group. CONCLUSIONS Our data showed the pathway of Osteoclast differentiation and Leishmaniasis was involved in the AS process and we developed a three-gene model base on the prognosis of AS. These findings clarified the gene regulatory network of AS and may provide a novel target for AS therapy.
Collapse
Affiliation(s)
- Shihuan Li
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, People's Republic of China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, People's Republic of China
| | - Suqin Li
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, People's Republic of China
| | - Qingjie Li
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, People's Republic of China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, People's Republic of China
| | - Qiaofeng Zhou
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, People's Republic of China
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, People's Republic of China
| | - Wenli Liao
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, People's Republic of China
| | - Liangzhu Yu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, People's Republic of China
| | - Changhan Ouyang
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, People's Republic of China
| | - Hongli Xia
- The Central Hospital of Xianning, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, People's Republic of China
| | - Chao Liu
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, People's Republic of China.
| | - Mincai Li
- Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, People's Republic of China.
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, 437100, People's Republic of China.
| |
Collapse
|
10
|
Yu J, Li C. Role of lncRNA MAGI2-AS3 in lipopolysaccharide-induced nucleus pulposus cells injury by regulating miR-374b-5p/interleukin-10 axis. Immun Inflamm Dis 2023; 11:e772. [PMID: 37102649 PMCID: PMC10108685 DOI: 10.1002/iid3.772] [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: 10/12/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Intervertebral disc degeneration (IDD) is a pathological process that occurs during the natural aging of intervertebral discs. Accumulating evidence suggests that noncoding RNAs (ncRNAs), including microRNAs and long ncRNAs (lncRNAs), participate in the pathogenesis and development of IDD. Herein, we examined the role of lncRNA MAGI2-AS3 in the pathogenic mechanism of IDD. MATERIAL AND METHODS To develop an IDD in vitro model, we treated human nucleus pulposus (NP) cells with lipopolysaccharide (LPS). Aberrant levels of lncRNA MAGI2-AS3, miR-374b-5p, interleukin (IL)-10 and extracellular matrix (ECM)-related proteins in NP cells were examined using reverse transcription-quantitative PCR and western blot analysis. LPS-induced NP cell injury and inflammatory response were confirmed using the MTT assay, flow cytometry, Caspase3 activity, and enzyme-linked immunosorbent assay. Dual-luciferase reporter assay and rescue experiments were performed to confirm targets between lncRNA MAGI2-AS3 and miR-374b-5p or miR-374b-5p and IL-10. RESULTS LPS-induced NP cells exhibited low levels of lncRNA MAGI2-AS3 and IL-10 expression, along with high miR-374b-5p expression. miR-374b-5p was a target of lncRNA MAGI2-AS3 and IL-10. LncRNA MAGI2-AS3 ameliorated injury, inflammatory response, and ECM degradation in LPS-treated NP cells by downregulating miR-374b-5p to upregulate IL-10 expression. CONCLUSIONS LncRNA MAGI2-AS3 increased IL-10 expression levels by sponging miR-374b-5p, which, in turn, alleviated LPS-triggered decreased NP cell proliferation and increased apoptosis, inflammatory response, and ECM degradation. Therefore, lncRNA MAGI2-AS3 may be a potential therapeutic target for IDD.
Collapse
Affiliation(s)
- Jiang Yu
- Department of Orthopedics Surgery, Affiliated Hospital of Jianghan University, Wuhan, China
| | - Chengjin Li
- Department of Orthopedics Surgery, Affiliated Hospital of Jianghan University, Wuhan, China
| |
Collapse
|
11
|
Common Genetic Factors and Pathways in Alzheimer's Disease and Ischemic Stroke: Evidences from GWAS. Genes (Basel) 2023; 14:genes14020353. [PMID: 36833280 PMCID: PMC9957001 DOI: 10.3390/genes14020353] [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: 12/13/2022] [Revised: 01/19/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023] Open
Abstract
Alzheimer's disease (AD) and ischemic stroke (IS) are common neurological disorders, and the comorbidity of these two brain diseases is often seen. Although AD and IS were regarded as two distinct disease entities, in terms of different etiologies and clinical presentation, recent genome-wide association studies (GWASs) revealed that there were common risk genes between AD and IS, indicating common molecular pathways and their common pathophysiology. In this review, we summarize AD and IS risk single nucleotide polymorphisms (SNPs) and their representative genes from the GWAS Catalog database, and find thirteen common risk genes, but no common risk SNPs. Furthermore, the common molecular pathways associated with these risk gene products are summarized from the GeneCards database and clustered into inflammation and immunity, G protein-coupled receptor, and signal transduction. At least seven of these thirteen genes can be regulated by 23 microRNAs identified from the TargetScan database. Taken together, the imbalance of these molecular pathways may give rise to these two common brain disorders. This review sheds light on the pathogenesis of comorbidity of AD and IS, and provides molecular targets for disease prevention, manipulation, and brain health maintenance.
Collapse
|
12
|
Moutsopoulos I, Williams EC, Mohorianu II. bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data. Brief Bioinform 2023; 24:6965538. [PMID: 36583521 PMCID: PMC9851288 DOI: 10.1093/bib/bbac591] [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: 08/11/2022] [Revised: 10/12/2022] [Accepted: 12/02/2022] [Indexed: 12/31/2022] Open
Abstract
Bulk sequencing experiments (single- and multi-omics) are essential for exploring wide-ranging biological questions. To facilitate interactive, exploratory tasks, coupled with the sharing of easily accessible information, we present bulkAnalyseR, a package integrating state-of-the-art approaches using an expression matrix as the starting point (pre-processing functions are available as part of the package). Static summary images are replaced with interactive panels illustrating quality-checking, differential expression analysis (with noise detection) and biological interpretation (enrichment analyses, identification of expression patterns, followed by inference and comparison of regulatory interactions). bulkAnalyseR can handle different modalities, facilitating robust integration and comparison of cis-, trans- and customised regulatory networks.
Collapse
Affiliation(s)
- Ilias Moutsopoulos
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK
| | - Eleanor C Williams
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK
| | - Irina I Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK
| |
Collapse
|
13
|
Li X, An Y, Wang Q, Han X. The new ceRNA crosstalk between mRNAs and miRNAs in intervertebral disc degeneration. Front Cell Dev Biol 2022; 10:1083983. [DOI: 10.3389/fcell.2022.1083983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
Abstract
Degeneration of the intervertebral disc has been linked to lower back pain. To date, pathophysiological mechanisms of intervertebral disc degeneration (IDD) remain unclear; it is meaningful to find effective diagnostic biomarkers and new therapeutic strategies for IDD. This study aimed to reveal the molecular mechanism of IDD pathogenesis from the multidimensional transcriptomics perspective. Here, we acquired IDD bulk omics datasets (GSE67567 and GSE167199) including mRNA, microRNA expression profiles, and single-cell RNA sequencing (GSE199866) from the public Gene Expression Omnibus (GEO) database. Through principal component analysis and Venn analysis, we found different expression patterns in the IDD transcription level and identified 156 common DEGs in both bulk datasets. GO and KEGG functional analyses showed these dysregulators were mostly enriched in the collagen-containing extracellular matrix, cartilage development, chondrocyte differentiation, and immune response pathways. We also constructed a potentially dysregulated competing endogenous RNA (ceRNA) network between mRNAs and miRNAs related to IDD based on microRNA target information and co-expression analysis of RNA profiles and identified 36 ceRNA axes including ZFP36/miR-155-5p/FOS, BTG2/hsa-miR-185-5p/SOCS3, and COL9A2/hsa-miR-664a-5p/IBA57. Finally, in integrating bulk and single-cell transcriptome data analyses, a total of three marker genes, COL2A1, PAX1, and ZFP36L2, were identified. In conclusion, the key genes and the new ceRNA crosstalk we identified in intervertebral disc degeneration may provide new targets for the treatment of IDD.
Collapse
|
14
|
Pu Y, Wei J, Wu Y, Zhao K, Wu Y, Wu S, Yang X, Xing C. THUMPD3-AS1 facilitates cell growth and aggressiveness by the miR-218-5p/SKAP1 axis in colorectal cancer. Cell Biochem Biophys 2022; 80:483-494. [PMID: 35538197 DOI: 10.1007/s12013-022-01074-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 04/22/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is a malignant cancer with a high mortality. Accumulating studies have revealed that mRNAs involved in ceRNA (competing endogenous RNA) network are implicated in the tumorigenesis and development of CRC. Here, we aimed to elucidate the ceRNA network involving Src kinase associated phosphoprotein 1 (SKAP1) in the biological characteristics of CRC. METHODS Expression levels of genes in colon adenocarcinoma (COAD) samples and prognosis of COAD patients were predicted using publicly available online tool. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), clony formation and Transwell assays were conducted to test the biological functions of SKAP1 and THUMPD3 antisense RNA 1 (THUMPD3-AS1) in CRC cells. Western blot was used to measure the protein levels of SKAP1. Gene expression in CRC cells was detected by reverse transcription quantitative polymerase chain reaction (RT-qPCR). The interaction between miR-218-5p and THUMPD3-AS1 (or SKAP1) was verified by RNA pulldown and luciferase reporter assays. RESULTS SKAP1 was upregulated in COAD tissues and CRC cells and it reflected a poor prognosis in patients with COAD. SKAP1 knockdown inhibited CRC (HT-29 and HCT-116) cell proliferation, migration and invasion. Mechanistically, THUMPD3-AS1 acted as a ceRNA to sponge miR-218-5p and subsequently upregulated SKAP1 expression in CRC cells. SKAP1 overexpression reversed the suppressive effect of THUMPD3-AS1 knockdown on proliferation, migration and invision of CRC cells. CONCLUSIONS THUMPD3-AS1 promotes CRC cell growth and aggressiveness by regulating the miR-218-5p/SKAP1 axis.
Collapse
Affiliation(s)
- Yuwei Pu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Jinrong Wei
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Yong Wu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Kui Zhao
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Yongyou Wu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Shu Wu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Xiaodong Yang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China.
| | - Chungen Xing
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China.
| |
Collapse
|
15
|
Significance of Immune-Related Genes in the Diagnosis and Classification of Intervertebral Disc Degeneration. J Immunol Res 2022; 2022:2616260. [PMID: 36081453 PMCID: PMC9448583 DOI: 10.1155/2022/2616260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Background With the extensive development of intervertebral disc degeneration (IDD) research, IDD has been found to be a complex disease associated with immune-related gene (IRGs) changes. Nonetheless, the roles of IRGs in IDD are unclear. Methods In our study, 11 IRGs were chosen using differential analysis between nondisc degeneration and degenerative patients from the GEO database. Then, we utilized a random forest (RF) model to screen six candidate IRGs to predict the risk of IDD. A nomogram was developed on the basis of six candidate IRGs, and DCA showed that patients could benefit from the nomogram. Based on the selected significant IRGs, a consensus clustering approach was used to differentiate disc degeneration patients into two immune patterns (immune cluster A and B). The PCA algorithm was constructed to compute immune scores for every sample, to quantify immune patterns. The immune scores of immune cluster B patients were higher than those of immune cluster A. Results Through differential expression analysis between healthy and IDD samples, 11 significant IRGs (CTSS, S100Z, STAT3, KLRK1, FPR1, C5AR2, RLN1, IFGR2, IL2RB, IL17RA, and IL6R) were recognized through significant IRGs. The “Reverse Cumulative Distribution of Residual” and “Boxplots of Residual” indicate that the RF model has minimal residuals. The majority of samples in the model have relatively small residuals, demonstrating that the model is better. Besides, the nomogram model was constructed based on importance and the IRGs with importance scores greater than 2 (FPR1, RLN1, S100Z, IFNGR2, KLRK1, and CTSS). The nomogram model revealed that decision-making based on an established model might be beneficial for IDD patients, and the predictive power of the nomogram model was significant. In addition, we identified two different immune cluster patterns (immune cluster A and immune cluster B) based on the 11 IRGs. We found that immune cluster A had significantly higher levels of MDSC, neutrophil, plasmacytoid dendritic cell, and type 17 T helper cell expression than immune cluster B. And we calculated the score for each sample to quantify the gene patterns. The patients in immune cluster B or gene cluster B had higher immune scores than those in immune cluster A or gene cluster A. Conclusion In conclusion, IRGs play an extremely significant role in the occurrence of IDD. Our study of immune patterns may guide the strategies of prevention and treatment for IDD in the future.
Collapse
|
16
|
Yu B, Zhu Z, Hu T, Lu J, Shen B, Wu T, Guo K, Chaudhary SK, Feng H, Zhao W, Wu D. Construction of a circular RNA-based competing endogenous RNA network to screen biomarkers related to intervertebral disc degeneration. BMC Musculoskelet Disord 2022; 23:675. [PMID: 35840955 PMCID: PMC9284696 DOI: 10.1186/s12891-022-05579-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 06/06/2022] [Indexed: 12/03/2022] Open
Abstract
Background Intervertebral disc degeneration (IDD) is a leading cause of disability with limited treatment strategies. A better understanding of the mechanism of IDD might enable less invasive and more targeted treatments. This study aimed to identify the circular RNA (circRNA)–microRNA (miRNA)–messenger RNA (mRNA) competing endogenous RNA (ceRNA) regulatory mechanisms in IDD. Methods The GSE67567 microarray dataset was downloaded from the Gene Expression Omnibus database. After data preprocessing, differentially expressed circRNAs, miRNAs and mRNAs between IDD and controls were identified. A ceRNA network was constructed on the basis of the interaction between circRNAs and miRNAs, and miRNAs and mRNAs. Pathway enrichment analysis was performed on the mRNAs in the ceRNA network. Then, with ‘intervertebral disc degeneration’ as keywords, IDD-related Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were searched for in the Comparative Toxicogenomics Database. Results A total of 105 differentially expressed circRNAs, 84 miRNAs and 967 mRNAs were identified. After analysis, 86 circRNA–miRNA, and 126 miRNA–mRNA regulatory relationship pairs were obtained to construct a ceRNA network. The mRNAs were enriched in six KEGG signalling pathways, and four were associated with IDD: the hsa04350: TGF-beta signalling pathway, hsa04068: FoxO signalling pathway, hsa05142: Chagas disease (American trypanosomiasis) and hsa04380: Osteoclast differentiation. An IDD-related ceRNA network was constructed involving four circRNAs, three miRNAs and 11 mRNAs. Auxiliary validation showed that the expression levels of miR-185-5p, miR-486-5p, ACVR1B, FOXO1, SMAD2 and TGFB1 were consistent in different databases. Conclusions Our study identified some circRNA–miRNA–mRNA interaction axes potentially associated with the progression of IDD, viz.: circRNA_100086–miR-509-3p–MAPK1, circRNA_000200–miR-185-5p–TGFB1, circRNA_104308–miR-185-5p–TGFB1, circRNA_400090–miR-486-5p–FOXO1 and circRNA_400090–miR-486-5p–SMAD2. Supplementary Information The online version contains supplementary material available at 10.1186/s12891-022-05579-0. 1. An IDD-related ceRNA network involving four circRNAs, three miRNAs and 11 mRNAs was constructed. 2. The expression levels of miR-185-5p, miR-486-5p, FOXO1, SMAD2 and TGFB1 were consistent in different databases. 3. Our study identified IDD-related circRNA–miRNA–mRNA interaction axes, including circRNA_100086–miR-509-3p–MAPK1.
Collapse
Affiliation(s)
- Bin Yu
- Department of Spine Surgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai, 200092, China
| | - Ziqi Zhu
- Department of Spine Surgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai, 200092, China
| | - Tao Hu
- Department of Spine Surgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai, 200092, China
| | - Jiawei Lu
- Department of Spine Surgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai, 200092, China
| | - Beiduo Shen
- Department of Spine Surgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai, 200092, China
| | - Tongde Wu
- Department of Spine Surgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai, 200092, China
| | - Kai Guo
- Department of Spine Surgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai, 200092, China
| | - Surendra Kumar Chaudhary
- Department of Spine Surgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai, 200092, China
| | - Hang Feng
- Department of Surgery of Spine and Spinal Cord, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou, 450003, Henan, China
| | - Weidong Zhao
- Department of Spine Surgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai, 200092, China.
| | - Desheng Wu
- Department of Spine Surgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai, 200092, China.
| |
Collapse
|
17
|
Cui Y, Zhao X, Wu Y. Circ_0005918 Sponges miR-622 to Aggravate Intervertebral Disc Degeneration. Front Cell Dev Biol 2022; 10:905213. [PMID: 35874804 PMCID: PMC9304550 DOI: 10.3389/fcell.2022.905213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Intervertebral discdegeneration (IDD) is the most common cause of lower back pain, but the exact molecular mechanism of IDD is still unknown. Recently, studies have shown that circular RNAs (circRNAs) regulate diverse biological procedures such as cell metastasis, growth, metabolism, migration, apoptosis, and invasion. We demonstrated that IL-1β and TNF-α induced circ_0005918 expression in the NP cell, and circ_0005918 was overexpressed in the IDD group compared with the control group. Moreover, the upregulated expression of circ_0005918 was associated with disc degeneration degree. The elevated expression of circ_0005918 promoted cell growth and ECM degradation, and it induced secretion of inflammatory cytokines including IL-1β, IL-6, and TNF-α. Moreover, we found that circ_0005918 sponged miR-622 in the NP cell. In addition, the exposure to IL-1β and TNF-α suppressed the expression of miR-622, which was downregulated in the IDD group compared with the control group. Furthermore, the downregulated expression of miR-622 was associated with disc degeneration degree. The expression level of miR-622 was negatively associated with circ_0005918 expression in the IDD group. In conclusion, circ_0005918 regulated cell growth, ECM degradation, and secretion of inflammatory cytokines by regulating miR-622 expression. These data suggested that circ_0005918 played important roles in the development of IDD via sponging miR-622.
Collapse
|
18
|
Ren W, Yuan Y, Chen X, Zhai H, An Y, Tang L, Wang J, Zhang D, Zhang L, Cheng W, Wang X, Duan L, Mutti L, Han B, Wang P. Identification and Validation of Long Non-Coding RNA LCIIAR as a Biomarker in LUAD. Front Oncol 2022; 12:933071. [PMID: 35860557 PMCID: PMC9293053 DOI: 10.3389/fonc.2022.933071] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related death worldwide. Therapies for lung cancer have relatively poor outcomes and need to be improved. Lung cancer immune cell infiltration associated RNA (LCIIAR) is a long noncoding RNA (lncRNA), which is overexpressed in human cancers. However, the clinical significance and functional role of LCIIAR in Lung Adenocarcinoma remain unclear. Here, we identified a novel long non-coding RNA (ENSG00000256802), termed LCIIAR (lung cancer immune cell infiltration associated lncRNA), up-regulated in lung cancer tissue and cell lines. We show that increase LCIIAR expression correlated with poor clinical stage and adverse clinical outcomes and that could also serve as an independent unfavorable prognostic factor in patients with Lung Adenocarcinima. GSEA analysis demonstrated that LCIIAR is mainly involved in the regulation of the immune response. We uncovered that elevate LCIIAR expression positively correlated with immune infiltration and immune modulator in Lung Adenocarcinoma. More importantly, we confirmed that silencing of LCIIAR expression significantly inhibits the proliferation, and migration abilities of these tumour cells. We also demonstrated that the LCIIAR/hsa-miR184/SLC16A3/CDCP1 network regulates SLC16A3/CDCP1 overexpression in and is associated with poor prognosis in this tumour. Therefore our findings revealed the critical role of LCIIAR in Lung Adenocarcinoma progression, which may also serve as a prognostic biomarker and novel therapeutic target.
Collapse
Affiliation(s)
- Wenjun Ren
- Department of Thoracic Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
- Department of Cardiovascular Surgery, The First People’s Hospital of Yunnan Province, the Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Yixiao Yuan
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xi Chen
- First Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Haoqing Zhai
- First Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yin An
- Department of Gastroenterology, The First People's Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Lin Tang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Juan Wang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Dahang Zhang
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Liren Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Wanli Cheng
- Department of Thoracic Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xin Wang
- Department of Cardiovascular Surgery, The First People’s Hospital of Yunnan Province, the Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Lincan Duan
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Luciano Mutti
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, United States
- *Correspondence: Ping Wang, ; Bin Han, ; Luciano Mutti,
| | - Bin Han
- Department of Emergency, The First People’s Hospital Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
- *Correspondence: Ping Wang, ; Bin Han, ; Luciano Mutti,
| | - Ping Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
- *Correspondence: Ping Wang, ; Bin Han, ; Luciano Mutti,
| |
Collapse
|
19
|
Mechanisms and functions of long noncoding RNAs in intervertebral disc degeneration. Pathol Res Pract 2022; 235:153959. [DOI: 10.1016/j.prp.2022.153959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/04/2022] [Accepted: 05/25/2022] [Indexed: 01/17/2023]
|
20
|
Zhang L, Zhang Y, Miao M, Hu S, Wang X, Zhao L, Huang X, Cao G, Shou D. Erxian herbal pair enhances bone formation in infected bone nonunion models and attenuates lipopolysaccharide-induced osteoblastinhibition by regulating miRNA-34a-5p. Bioengineered 2022; 13:14339-14356. [PMID: 36694425 PMCID: PMC9995130 DOI: 10.1080/21655979.2022.2085388] [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: 01/26/2023] Open
Abstract
Bacterium-induced inflammatory responses cause bone nonunion. Although antibiotics suppress infection, bone loss after antibacterial treatment remains a critical challenge. Erxian herbal pair (EHP) has been proven effective in promoting bone formation. Our study aimed to investigate the effect of EHP on bone repair after anti-infection treatment, explore its effect on a lipopolysaccharide (LPS)-induced osteoblast. We evaluated effects of EHP on bone repair with Micro-CT, and morphology detecting. Chemical constituents of EHP and EHP-containing serum (EHP-CS) were identified by UHPLC-Q/TOF-MS. In addition, osteoblast induced by LPS was established and administrated with EHP-CS. Cell proliferationwas assessed by MTT. Target prediction identified SMAD2 as a potential target of miRNA-34a-5p. MiRNA mimic, inhibitor and siRNA were transiently transfected into osteoblasts. The mRNA levels and protein expressions of miRNA-34a-5p, BMP2, Runx2, SMAD2 were assessed. The results showed that the main biocactivity ingredients in EHP-CS were Baohuoside Ι and Orcinol Glucoside. EHP could promote bone remolding after anti-infection therapy and restore the activity of LPS-induced osteoblasts. Moreover, miRNA-34a-5p was dramatically downregulated and SMAD2 was upregulated after LPS stimulation, while EHP resisted the inhibition of LPS by promoting miRNA-34a-5p, ALP, and BMP2 expressions. Whereas downregulation of miRNA-34a-5p reversed these effects. Silencing endogenous SMAD2 expression markedly promoted BMP2 and ALP activity and enhanced osteogenesis. Taken together, EHP restored LPS-induced bone loss by regulating miRNA-34a-5p levels and repressing its target gene SMAD2. EHP might be a potential adjuvant herbal remedy for the treatment of bone nonunion, and miRNA-34a-5p is a novel target for controlling bone and metabolic diseases.
Collapse
Affiliation(s)
- Li Zhang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.,Department of Pharmacy, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou 310006, China
| | - Yang Zhang
- Institute of Orthopadics and Traumatology, the First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310053,China
| | - Maomao Miao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Shaoqi Hu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xuping Wang
- Department of Medicine, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou 310007, China
| | - Lisha Zhao
- Department of Medicine, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou 310007, China
| | - Xiaowen Huang
- Department of Medicine, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou 310007, China
| | - Gang Cao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Dan Shou
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.,Department of Medicine, Zhejiang Academy of Traditional Chinese Medicine, Hangzhou 310007, China
| |
Collapse
|
21
|
Zheng X, Gan S, Su C, Zheng Z, Liao Y, Shao J, Zhu Z, Chen W. Screening and preliminary identification of long non-coding RNAs critical for osteogenic differentiation of human umbilical cord mesenchymal stem cells. Bioengineered 2022; 13:6880-6894. [PMID: 35249446 PMCID: PMC8973756 DOI: 10.1080/21655979.2022.2044274] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Human umbilical cord mesenchymal stem cells (hUCMSCs) are attractive therapeutic cells for tissue engineering to treat bone defects. However, how the cells can differentiate into bone remains unclear. Long non-coding RNAs (lncRNAs) are non-coding RNAs that participate in many biological processes, including stem cell differentiation. In this study, we investigated the profiles and functions of lncRNAs in the osteogenic differentiation of hUCMSCs. We identified 343 lncRNAs differentially expressed during osteogenic differentiation, of which 115 were upregulated and 228 were downregulated. We further analyzed these lncRNAs using bioinformatic analyses, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. GO and KEGG pathway analysis showed that ‘intracellular part’ and ‘Phosphatidylinositol signaling system’ were the most correlated molecular function and pathway, respectively. We selected the top 10 upregulated lncRNAs to construct six competing endogenous RNA networks. We validated the impact of the lncRNA H19 on osteogenic differentiation by overexpressing it in hUCMSCs. Overall, our results pave the way to detailed studies of the molecular mechanisms of hUCMSC osteogenic differentiation, and they provide a new theoretical basis to guide the therapeutic application of hUCMSCs.
Collapse
Affiliation(s)
- Xiao Zheng
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.,Department of Oral Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.,Department of Pediatric Dentistry, Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, Guangdong, China
| | - Shuaiqi Gan
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.,Department of Oral Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Cheng Su
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.,Department of Oral Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Zheng Zheng
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.,Department of Oral Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yihan Liao
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.,Department of Oral Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Jingjing Shao
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.,Department of Oral Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Zhimin Zhu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.,Department of Oral Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Wenchuan Chen
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China.,Department of Oral Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| |
Collapse
|
22
|
Xu W, Zhang H, Zhang Q, Xu J. β-Amyrin ameliorates diabetic nephropathy in mice and regulates the miR-181b-5p/HMGB2 axis in high glucose-stimulated HK-2 cells. ENVIRONMENTAL TOXICOLOGY 2022; 37:637-649. [PMID: 34894065 DOI: 10.1002/tox.23431] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 06/14/2023]
Abstract
Diabetic nephropathy (DN) is a diabetic complication that can cause renal failure. β-amyrin has been identified to possess anti-diabetic property. This study was designed to evaluate the potential role of β-amyrin in DN and its underlying mechanism. Streptozotocin-induced diabetic mice were used as the in vivo model, and high glucose (HG)-stimulated human proximal tubular HK-2 cells were utilized as the in vitro model. Renal histological changes in mice were assessed by hematoxylin-eosin and periodic acid-Schiff staining. HK-2 cell viability and apoptosis were detected by Cell Counting Kit-8 assay and flow cytometry analysis, respectively. β-amyrin was found to ameliorate kidney injury in DN mice and suppressed inflammatory response as well as apoptosis of HG-stimulated HK-2 cells. miR-181-5p expression in murine renal tissues and HK-2 cells was detected by in situ hybridization (ISH) and fluorescence in situ hybridization (FISH). MiR-181b-5p, a previously identified target for diabetic kidney disease, was downregulated in renal tissues and HG stimulated HK-2 cells, and β-amyrin induced the upregulation of miR-181b-5p. Binding relationship between miR-181b-5p and high mobility group box 2 (HMGB2) was confirmed by luciferase reporter assay. MiR-181b-5p bound to 3' untranslated region of HMGB2 to suppress its expression. As shown by immunohistochemical staining and immunofluorescence staining, HMGB2 was upregulated in the in vivo and in vitro models of DN, and β-amyrin induced the downregulation of HMGB2. Moreover, HMGB2 overexpression neutralized the suppressive effects of miR-181b-5p elevation on the inflammatory response and apoptosis of HG-treated HK-2 cells. Overall, β-amyrin ameliorates DN in mice and suppresses inflammatory response and apoptosis of HG-stimulated HK-2 cells via the miR-181b-5p/HMGB2 axis.
Collapse
Affiliation(s)
- Wenhua Xu
- Preventive Treatment Center, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, Guangdong, China
| | - Hongwu Zhang
- Department of Endocrinology, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, Guangdong, China
| | - Qinfeng Zhang
- Department of Endocrinology, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, Guangdong, China
| | - Jialan Xu
- Preventive Treatment Center, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, Guangdong, China
| |
Collapse
|
23
|
Tang Y, Cai J, Lv B. LncRNA ubiquitin-binding protein domain protein 10 antisense RNA 1 inhibits colon adenocarcinoma progression via the miR-515-5p/slit guidance ligand 3 axis. Bioengineered 2022; 13:2308-2320. [PMID: 35034539 PMCID: PMC8974015 DOI: 10.1080/21655979.2021.2024396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Dysregulated long non-coding RNAs (lncRNAs) play an important role in cancer progression. However, there have been limited reports to date of the involvement of ubiquitin-binding protein domain protein 10 antisense RNA 1 (UBXN10-AS1) in cancer. Our aim was to explore the role and underlying mechanism of UBXN10-AS1 in the occurrence of colon adenocarcinoma (COAD). Real-time quantitative PCR and Western blotting were performed to determine the expression of UBXN10-AS1, miR-515-5p, and Slit guidance ligand 3 (SLIT3). Cell Counting Kit-8 and wound healing scratch assays were performed to measure COAD cell proliferation and migration. A xenograft assay was performed to examine tumor growth in vivo. Luciferase reporter and RNA immunoprecipitation (RIP) assays were used to determine the binding interaction among miR-515-5p, UBXN10-AS1, and SLIT3. The results showed that UBXN10-AS1 and SLIT3 were expressed at low levels in COAD tissues, while miR-515-5p was expressed at high levels. UBXN10-AS1 overexpression suppressed tumor growth in vitro and in vivo. The luciferase reporter and RNA RIP assays demonstrated that UBXN10-AS1 targeted miR-515-5p, which in turn targeted SLIT3. Functionally, miR-515-5p overexpression reversed the inhibition of COAD cell proliferation and migration by UBXN10-AS1 overexpression, and SLIT3 overexpression counteracted the oncogenicity of miR-515-5p. Our study shows that UBXN10-AS1 modulates the miR-515-5p/SLIT3 axis, thereby resulting in the inhibition of COAD cell proliferation and migration.
Collapse
Affiliation(s)
- Yu Tang
- Department of General Surgery, Clinical Medical College & Affiliated Hospital of Chengdu University, Chengdu, Sichuan, China
| | - Jingxuan Cai
- Department of General Surgery, Chengdu Western Hospital, Chengdu, Sichuan, China
| | - Bo Lv
- Department of General Surgery, Clinical Medical College & Affiliated Hospital of Chengdu University, Chengdu, Sichuan, China
| |
Collapse
|
24
|
Guo H, Li T, Peng C, Mao Q, Shen B, Shi M, Lu H, Xiao T, Yang A, Liu Y. Overexpression of lncRNA A2M-AS1 inhibits cell growth and aggressiveness via regulating the miR-587/bone morphogenetic protein 3 axis in lung adenocarcinoma. Hum Exp Toxicol 2022; 41:9603271221138971. [PMID: 36461613 DOI: 10.1177/09603271221138971] [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: 12/04/2022]
Abstract
Lung adenocarcinoma (LUAD) is a malignant tumor that occurs in the lungs. Numerous reports have substantiated the participation of long non-coding RNAs (lncRNAs) in the tumorigenesis of LUAD. Previously, lncRNA alpha-2-macroglobulin antisense RNA 1 (A2M-AS1) was confirmed to be an important regulator in the biological processes of LUAD and dysregulation of A2M-AS1 was associated with non-small cell lung cancer (NSCLC) progression. However, the precise mechanism of A2M-AS1 in LUAD has not been elucidated. Therefore, our study was designed to investigate the detailed molecular mechanism of A2M-AS1 in LUAD. Herein, the expression of lncRNA A2M-AS1, microRNA (miRNA) miR-587, and bone morphogenetic protein 3 (BMP3) in LUAD cell lines and tissues were detected by real-time quantitative polymerase chain reaction (RT-qPCR) and western blotting. The viability, proliferation, migration and invasion of LUAD cells were tested by cell counting kit-8 (CCK-8), colony formation and Transwell assays. In vivo tumor growth was investigated by xenograft animal experiment. Interactions among A2M-AS1, miR-587 and BMP3 were measured by RNA pulldown and luciferase reporter assays. In this study, A2M-AS1 was downregulated in LUAD tissues and cells and related to poor prognosis in LUAD patients. A2M-AS1 overexpression suppressed LUAD cell proliferation, migration and invasion in vitro and inhibited tumor growth in vivo. Mechanistically, A2M-AS1 directly bound with miR-587 to promote BMP3 expression in LUAD cells. Low expression of BMP3 was found in LUAD tissues and cells and was closely correlated with poor prognosis in LUAD patients. BMP3 deficiency reserved the inhibitory influence of A2M-AS1 overexpression on LUAD cell behaviors. Overall, A2M-AS1 inhibits cell growth and aggressiveness via regulating the miR-587/BMP3 axis in LUAD.
Collapse
Affiliation(s)
- Hongfei Guo
- School of Basic Medical Sciences, 271667Nanjing Medical University, Nanjing, China
| | - Tao Li
- Department of Oncology, 377323Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Chunlei Peng
- Department of Oncology, 377323Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Qinghua Mao
- Department of Thoracic Surgery, 377323Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Biao Shen
- Department of Thoracic Surgery, 377323Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Minxin Shi
- Department of Thoracic Surgery, 377323Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Haimin Lu
- Department of Thoracic Surgery, 377323Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Ting Xiao
- Department of Thoracic Surgery, North Hospital, 377323Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Aimin Yang
- Department of Thoracic Surgery, South Hospital, 377323Tumor Hospital Affiliated to Nantong University, Nantong, China
| | - Yupeng Liu
- Department of Thoracic Surgery, 377323Tumor Hospital Affiliated to Nantong University, Nantong, China
| |
Collapse
|
25
|
Wang W, Bo H, Liang Y, Li G. LINC00467 Is Upregulated by DNA Copy Number Amplification and Hypomethylation and Shows ceRNA Potential in Lung Adenocarcinoma. Front Endocrinol (Lausanne) 2021; 12:802463. [PMID: 35095769 PMCID: PMC8792904 DOI: 10.3389/fendo.2021.802463] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/21/2021] [Indexed: 12/25/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common histological lung cancer, and it is the leading cause of cancer-related deaths worldwide. Long noncoding RNAs (lncRNAs) have been implicated in tumorigenesis. LINC00467 is a novel lncRNA that is abnormally expressed in several cancer types including LUAD. However, its function and regulatory mechanism in LUAD progression remain unclear. In this study, based on The Cancer Genome Atlas data mining, we demonstrated that DNA copy number amplification and hypomethylation was positively correlated with LINC00467 expression in LUAD. In addition, DNA copy number amplification was significantly associated with distant metastasis, immune infiltration and poor survival. Microarray analysis demonstrated that LINC00467 knockdown in the LUAD A549 cell line led to a distinct microRNA expression profile that impacted various target genes involved in multiple biological processes. This finding suggests that LINC00467 may regulate LUAD progression by functioning as a competing endogenous RNA (ceRNA). Finally, we constructed a ceRNA network that included two microRNAs (hsa-miR-1225-5p, hsa-miR-575) and five mRNAs (BARX2, BCL9, KCNK1, KIAA1324, TMEM182) specific to LINC00467 in LUAD. Subsequent Kaplan-Meier survival analysis in both The Cancer Genome Atlas and Gene Expression Omnibus databases revealed that two genes, BARX2 and BCL9, were potential prognostic biomarkers for LUAD patients. In conclusion, our data provide possible mechanisms underlying the abnormal upregulation of LINC00467 as well as a comprehensive view of the LINC00467-mediated ceRNA network in LUAD, thereby highlighting its potential role in diagnosis and therapy.
Collapse
Affiliation(s)
- Wen Wang
- Department of Cardio-Thoracic Surgery, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Hao Bo
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Yumei Liang
- Department of Nephrology and Laboratory of Kidney Disease, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
- Changsha Clinical Research Center for Kidney Disease, Changsha, China
- Hunan Clinical Research Center for Chronic Kidney Disease, Changsha, China
| | - Guoli Li
- Department of Nephrology and Laboratory of Kidney Disease, Hunan Provincial People’s Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
- Changsha Clinical Research Center for Kidney Disease, Changsha, China
- Hunan Clinical Research Center for Chronic Kidney Disease, Changsha, China
- *Correspondence: Guoli Li,
| |
Collapse
|