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Xie X, Sinha S. Quantitative estimates of the regulatory influence of long non-coding RNAs on global gene expression variation using TCGA breast cancer transcriptomic data. PLoS Comput Biol 2024; 20:e1012103. [PMID: 38838009 DOI: 10.1371/journal.pcbi.1012103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/24/2024] [Indexed: 06/07/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have received attention in recent years for their regulatory roles in diverse biological contexts including cancer, yet large gaps remain in our understanding of their mechanisms and global maps of their targets. In this work, we investigated a basic unanswered question of lncRNA systems biology: to what extent can gene expression variation across individuals be attributed to lncRNA-driven regulation? To answer this, we analyzed RNA-seq data from a cohort of breast cancer patients, explaining each gene's expression variation using a small set of automatically selected lncRNA regulators. A key aspect of this analysis is that it accounts for confounding effects of transcription factors (TFs) as common regulators of a lncRNA-mRNA pair, to enrich the explained gene expression for lncRNA-mediated regulation. We found that for 16% of analyzed genes, lncRNAs can explain more than 20% of expression variation. We observed 25-50% of the putative regulator lncRNAs to be in 'cis' to, i.e., overlapping or located proximally to the target gene. This led us to quantify the global regulatory impact of such cis-located lncRNAs, which was found to be substantially greater than that of trans-located lncRNAs. Additionally, by including statistical interaction terms involving lncRNA-protein pairs as predictors in our regression models, we identified cases where a lncRNA's regulatory effect depends on the presence of a TF or RNA-binding protein. Finally, we created a high-confidence lncRNA-gene regulatory network whose edges are supported by co-expression as well as a plausible mechanism such as cis-action, protein scaffolding or competing endogenous RNAs. Our work is a first attempt to quantify the extent of gene expression control exerted globally by lncRNAs, especially those located proximally to their regulatory targets, in a specific biological (breast cancer) context. It also marks a first step towards systematic reconstruction of lncRNA regulatory networks, going beyond the current paradigm of co-expression networks, going beyond the current paradigm of co-expression networks, and motivates future analyses assessing the generalizability of our findings to additional biological contexts.
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Affiliation(s)
- Xiaoman Xie
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Saurabh Sinha
- Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- H. Milton Stewart School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
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Zhang L, Zou J, Wang Z, Li L. A Subpathway and Target Gene Cluster-Based Approach Uncovers lncRNAs Associated with Human Primordial Follicle Activation. Int J Mol Sci 2023; 24:10525. [PMID: 37445702 DOI: 10.3390/ijms241310525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as a critical regulator in controlling the expression level of genes involved in cell differentiation and development. Primordial follicle activation (PFA) is the first step for follicle maturation, and excessive PFA results in premature ovarian insufficiency (POI). However, the correlation between lncRNA and cell differentiation was largely unknown, especially during PFA. In this study, we observed the expression level of lncRNA was more specific than protein-coding genes in both follicles and granulosa cells, suggesting lncRNA might play a crucial role in follicle development. Hence, a systematical framework was needed to infer the functions of lncRNAs during PFA. Additionally, an increasing number of studies indicate that the subpathway is more precise in reflecting biological processes than the entire pathway. Given the complex expression patterns of lncRNA target genes, target genes were further clustered based on their expression similarity and classification performance to reveal the activated/inhibited gene modules, which intuitively illustrated the diversity of lncRNA regulation. Moreover, the knockdown of SBF2-AS1 in the A549 cell line and ZFAS1 in the SK-Hep1 cell line further validated the function of SBF2-AS1 in regulating the Hippo signaling subpathway and ZFAS1 in the cell cycle subpathway. Overall, our findings demonstrated the importance of subpathway analysis in uncovering the functions of lncRNAs during PFA, and paved new avenues for future lncRNA-associated research.
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Affiliation(s)
- Li Zhang
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiyuan Zou
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zhihao Wang
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lin Li
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
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Xie C, Wang S, Zhang H, Zhu Y, Jiang P, Shi S, Si Y, Chen J. Lnc-AIFM2-1 promotes HBV immune escape by acting as a ceRNA for miR-330-3p to regulate CD244 expression. Front Immunol 2023; 14:1121795. [PMID: 36845111 PMCID: PMC9946971 DOI: 10.3389/fimmu.2023.1121795] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/13/2023] [Indexed: 02/11/2023] Open
Abstract
Chronic hepatitis B (CHB) virus infection is a major risk factor for cirrhosis and hepatocellular carcinoma (HCC). Hepatitis B virus (HBV) immune escape is regulated by the exhaustion of virus-specific CD8+ T cells, which is associated with abnormal expression of negative regulatory molecule CD244. However, the underlying mechanisms are unclear. To investigate the important roles of non-coding RNAs play in CD244 regulating HBV immune escape, we performed microarray analysis to determine the differential expression profiles of long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs in patients with CHB and patients with spontaneous clearance of HBV. Competing endogenous RNA (ceRNA) was analyzed by bioinformatics methods and confirmed by the dual-luciferase reporter assay. Furthermore, gene silencing and overexpression experiments were used to further identify the roles of lncRNA and miRNA in HBV immune escape through CD244 regulation. The results showed that the expression of CD244 on the surface of CD8+ T cells was significantly increased in CHB patients and in the co-culture system of T cells and HBV-infected HepAD38 cells, which was accompanied by the reduction of miR-330-3p and the elevation of lnc-AIFM2-1. The down-regulated miR-330-3p induced the apoptosis of T cells by lifting the inhibition of CD244, which was reversed by miR-330-3p mimic or CD244-siRNA. Lnc-AIFM2-1 promotes the accumulation of CD244, which is mediated by decreased miR-330-3p, and then reduced the clearance ability of CD8+ T cells to HBV through regulated CD244 expression. And the injury in the ability of CD8+ T cells to clear HBV can be reversed by lnc-AIFM2-1-siRNA, miR-330-3p mimic, or CD244-siRNA. Collectively, our findings indicate that lnc-AIFM2-1 on CD244 by acting as a ceRNA of miR-330-3p contributes to HBV immune escape, which may provide novel insights into the roles of interaction networks among lncRNA, miRNA, and mRNA in HBV immune escape, highlighting potential applications of lnc-AIFM2-1 and CD244 for diagnosis and treatment in CHB.
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Affiliation(s)
| | | | | | | | | | | | | | - Jie Chen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
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4
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Tourkochristou E, Assimakopoulos SF, Thomopoulos K, Marangos M, Triantos C. NAFLD and HBV interplay - related mechanisms underlying liver disease progression. Front Immunol 2022; 13:965548. [PMID: 36544761 PMCID: PMC9760931 DOI: 10.3389/fimmu.2022.965548] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/15/2022] [Indexed: 12/08/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) and Hepatitis B virus infection (HBV) constitute common chronic liver diseases with worldwide distribution. NAFLD burden is expected to grow in the coming decade, especially in western countries, considering the increased incidence of diabetes and obesity. Despite the organized HBV vaccinations and use of anti-viral therapies globally, HBV infection remains endemic and challenging public health issue. As both NAFLD and HBV have been associated with the development of progressive fibrosis, cirrhosis and hepatocellular carcinoma (HCC), the co-occurrence of both diseases has gained great research and clinical interest. The causative relationship between NAFLD and HBV infection has not been elucidated so far. Dysregulated fatty acid metabolism and lipotoxicity in NAFLD disease seems to initiate activation of signaling pathways that enhance pro-inflammatory responses and disrupt hepatocyte cell homeostasis, promoting progression of NAFLD disease to NASH, fibrosis and HCC and can affect HBV replication and immune encountering of HBV virus, which may further have impact on liver disease progression. Chronic HBV infection is suggested to have an influence on metabolic changes, which could lead to NAFLD development and the HBV-induced inflammatory responses and molecular pathways may constitute an aggravating factor in hepatic steatosis development. The observed altered immune homeostasis in both HBV infection and NAFLD could be associated with progression to HCC development. Elucidation of the possible mechanisms beyond HBV chronic infection and NAFLD diseases, which could lead to advanced liver disease or increase the risk for severe complications, in the case of HBV-NAFLD co-existence is of high clinical significance in the context of designing effective therapeutic targets.
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Affiliation(s)
- Evanthia Tourkochristou
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Stelios F. Assimakopoulos
- Division of Infectious Diseases, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece,*Correspondence: Stelios F. Assimakopoulos,
| | - Konstantinos Thomopoulos
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Markos Marangos
- Division of Infectious Diseases, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Christos Triantos
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
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Wang X, Kang M, Liu C, Lin T, Han X, Jiang X. Current State and Progress of Research on the Role of lncRNA in HBV-Related Liver Cancer. Front Cell Infect Microbiol 2021; 11:714895. [PMID: 34869051 PMCID: PMC8636595 DOI: 10.3389/fcimb.2021.714895] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/01/2021] [Indexed: 01/04/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a malignant tumor with the highest mortality rate in the world, and hepatitis B virus (HBV) plays an important role in its development. Long noncoding RNA (lncRNA) is highly related to the inactivation of tumor suppressor genes and the activation of oncogenes in HCC. Researchers have used high-throughput sequencing technology to identify many noncoding transcripts related to the development of HCC and have studied the interaction between these transcripts and DNA, RNA, or protein to determine the relevant mechanism in the development of HCC. In general, the research on lncRNA represents a new field of cancer research, and the imbalance in lncRNA plays an pivotal role in the occurrence of liver cancer. In this review, we summarize some of the dysfunctional lncRNAs in human HCC associated with HBV infection. Their regulatory pathways, functions, and potential molecular mechanisms in the occurrence and development of HCC are discussed.
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Affiliation(s)
- Xueke Wang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Meisong Kang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Chun Liu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Ting Lin
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Xiwen Jiang
- DAAN Gene Co., Ltd. of Sun Yat-sen University, Guangzhou, China
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LncRNA-mRNA co-expression network revealing the regulatory roles of lncRNAs in melanogenesis in vitiligo. J Hum Genet 2021; 67:247-252. [PMID: 34815525 DOI: 10.1038/s10038-021-00993-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 11/08/2022]
Abstract
Vitiligo is characterized by the progressive disappearance of melanocytes, resulting in depigmentation. Long noncoding RNAs (lncRNAs) are a class of noncoding RNAs that play an essential role in the regulation of inflammation and immunity. Published reports on the expression profile of lncRNAs in vitiligo cases and the potential biological function of lncRNAs in vitiligo are lacking. We performed RNA-Seq to identify the functions of lncRNAs in vitiligo. In total, 32 upregulated lncRNAs and 78 downregulated lncRNAs were identified in skin lesions with vitiligo. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis demonstrated that mRNAs regulated by abnormally expressed lncRNAs are most relevant to melanocyte function and melanogenesis. We identified 14 aberrantly expressed lncRNAs through the co-expression pattern that regulate the melanogenesis-related genes DCT, TYR, and TYRP1. Therefore, we speculate that these hub genes may be involved in pathological mechanisms in melanocytes in vitiligo. These genes are closely related to melanogenesis in vitiligo. Abnormally expressed lncRNAs directly or indirectly act on these target genes to regulate melanogenesis. Identifying lncRNAs and clarifying the regulatory roles of the lncRNA-mRNA network may be helpful to develop novel diagnoses or treatment targets for vitiligo.
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Liu WN, Wu KX, Wang XT, Lin LR, Tong ML, Liu LL. LncRNA- ENST00000421645 promotes T cells to secrete IFN-γ by sponging PCM1 in neurosyphilis. Epigenomics 2021; 13:1187-1203. [PMID: 34382410 DOI: 10.2217/epi-2021-0163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aim: Neurosyphilis patients exhibited significant expression of long noncoding RNA (lncRNA) in peripheral blood T lymphocytes. In this study, we further clarified the role of lncRNA-ENST00000421645 in the pathogenic mechanism of neurosyphilis. Methods: lncRNA-ENST00000421645 was transfected into Jurkat-E6-1 cells, namely lentivirus (Lv)-1645 cells. RNA pull-down assay, flow cytometry, RT-qPCR, ELISA (Neobioscience Technology Co Ltd, Shenzhen, China) and RNA immunoprecipitation chip assay were used to analyze the function of lncRNA-ENST00000421645. Results: The expression of IFN-γ in Lv-1645 cells was significantly increased compared to that in Jurkat-E6-1 cells stimulated by phorbol-12-myristate-13-acetate (PMA). Then, it was suggested that lncRNA-ENST00000421645 interacts with PCM1 protein. Silencing PCM1 significantly increased the level of IFN-γ in Lv-1645 cells stimulated by PMA. Conclusion: This study revealed that lncRNA-ENST00000421645 mediates the production of IFN-γ by sponging PCM1 protein after PMA stimulation.
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Affiliation(s)
- Wen-Na Liu
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medical, Xiamen University, Xiamen, Fujian Province, China.,Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science & Technology of China, Chengdu, China
| | - Kai-Xuan Wu
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medical, Xiamen University, Xiamen, Fujian Province, China
| | - Xiao-Tong Wang
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medical, Xiamen University, Xiamen, Fujian Province, China
| | - Li-Rong Lin
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medical, Xiamen University, Xiamen, Fujian Province, China
| | - Man-Li Tong
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medical, Xiamen University, Xiamen, Fujian Province, China
| | - Li-Li Liu
- Center of Clinical Laboratory, Zhongshan Hospital, School of Medical, Xiamen University, Xiamen, Fujian Province, China
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Hao Q, Wang Z, Wang Q, Chen B, Qian H, Liu X, Cao H, Xia W, Jiang J, Lu Z. Identification and characterization of lncRNA AP000253 in occult hepatitis B virus infection. Virol J 2021; 18:125. [PMID: 34112188 PMCID: PMC8194241 DOI: 10.1186/s12985-021-01596-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Recent studies suggest that lncRNAs may play significant roles in the development of hepatitis B virus (HBV) infection. However, as a special stage of HBV infection, the lncRNA expression in occult HBV infection (OBI) remains unclear. METHODS The plasma level of 15 HBV infection-related lncRNAs was initially detected using qRT-PCR in 10 OBI and 10 healthy controls (HCs) in discovery phase. Significantly dysregulated lncRNAs were subsequently validated in another 64 OBI, 20 HCs, 31 chronic hepatitis B (CHB) and 20 asymptomatic HBsAg carriers (ASC). Moreover, the AP000253 expression in liver tissues and its potential biological functions in HBV infection were further investigate with public transcriptomic data and HBV-expressing cell lines. RESULTS Among candidate lncRNAs, the plasma level of AP000253 decreased significantly in OBI, ASC and CHB patients compared to HCs, while no difference was found among OBI, ASC and CHB patients. In liver tissues, similar AP000253 expression was also observed from the GSE83148 dataset, while that in HBV-expressing hepatoma cells was opposite. ROC curve analysis indicated that plasma AP000253 yielded an AUC of 0.73 with 60% sensitivity and 75% specificity when differentiating OBI from HCs, but it could not specifically separate the stage of chronic HBV infection. Furthermore, functional experiments suggested that AP000253 could promote HBV transcription and replication in hepatoma cell lines. CONCLUSIONS AP000253 might be involved in HBV replication, and be served as a potential biomarker for HBV infection. In the setting of blood donations, plasma AP000253 would be more useful to moderately distinguish OBI in HBsAg-negative donors. However, the AP000253 expression in liver tissues and associated molecular mechanism of HBV infection deserve further study in future.
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Affiliation(s)
- Qingqin Hao
- Department of Clinical Laboratory, Wuxi Red Cross Blood Center, 109 Xinmin Road, Wuxi, 214000, China
| | - Zheng Wang
- Department of Liver Disease, Wuxi No.5 People's Hospital Affiliated to Jiangnan University, 1215 Guangrui Road, Wuxi, 214000, China
| | - Qinghui Wang
- Department of Clinical Laboratory, Wuxi Red Cross Blood Center, 109 Xinmin Road, Wuxi, 214000, China
| | - Bo Chen
- Department of Clinical Laboratory, Wuxi Red Cross Blood Center, 109 Xinmin Road, Wuxi, 214000, China
| | - Huizhong Qian
- Department of Clinical Laboratory, Wuxi Red Cross Blood Center, 109 Xinmin Road, Wuxi, 214000, China
| | - Xiao Liu
- Department of Clinical Laboratory, Wuxi Red Cross Blood Center, 109 Xinmin Road, Wuxi, 214000, China
| | - Hong Cao
- Department of Liver Disease, Wuxi No.5 People's Hospital Affiliated to Jiangnan University, 1215 Guangrui Road, Wuxi, 214000, China
| | - Wei Xia
- Department of Clinical Laboratory, Wuxi Red Cross Blood Center, 109 Xinmin Road, Wuxi, 214000, China.
| | - Jian Jiang
- Department of Clinical Laboratory, Wuxi Red Cross Blood Center, 109 Xinmin Road, Wuxi, 214000, China.
| | - Zhonghua Lu
- Department of Liver Disease, Wuxi No.5 People's Hospital Affiliated to Jiangnan University, 1215 Guangrui Road, Wuxi, 214000, China.
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Li JZ, Ye LH, Wang DH, Zhang HC, Li TY, Liu ZQ, Dai EH, Li MR. The identify role and molecular mechanism of the MALAT1/hsa-mir-20b-5p/TXNIP axis in liver inflammation caused by CHB in patients with chronic HBV infection complicated with NAFLD. Virus Res 2021; 298:198405. [PMID: 33775752 DOI: 10.1016/j.virusres.2021.198405] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND/AIMS To identify the inflammatory damage caused by chronic hepatitis B (CHB) in patients of chronic hepatitis B virus (HBV) infection complicated with non-alcoholic fatty liver disease (NAFLD), then guiding clinicians to carry out antiviral treatment. METHODS According to the pathological features of liver biopsy, treatment-naïve obese patients of chronic HBV infection complicated with NAFLD who had elevated alanine transaminase (ALT) were divided into CHB group and NASH group. Transcriptome chips were used to analyze the expression profiles of long non-coding RNA (lncRNA) and mRNA in liver puncture tissues from the two groups. The chip data of CHB and NASH groups were analyzed for differential expression analysis, gene function analysis, signal pathway analysis, target gene prediction and competing endogenous RNAs (ceRNA) network analysis. RESULTS By comparing CHB group with NASH group, a total of 44 differentially expressed lncRNAs and 567 differentially expressed mRNAs were screened. GO analysis predicted that the differentially expressed mRNAs may affect monooxygenase activity and oxidoreductase activity. KEGG analysis predicted that the differentially expressed mRNAs may be related to signaling pathways involved in oxidative phosphorylation, phagosomes, and NAFLD. Differential analysis of lncRNA shown that the expression of metastasis associated in lung adenocarcinoma transcript 1 (MALAT1) in CHB group was significantly upregulated. Subsequently, through target gene prediction and ceRNA network analysis, we found thioredoxin interacting protein (TXNIP), which was significantly upregulated in the CHB group and had a ceRNA relationship with MALAT1. It is predicted that there may be a ceRNA regulation relationship of MALAT1/hsa-miR- 20b-5p/TXNIP. CONCLUSION The MALAT1/hsa-miR-20b-5p/TXNIP axis may mediate CHB-induced inflammatory damage in chronic HBV infection complicated with NAFLD, and the mechanism may be related to the activation of NLRP3 inflammatory bodies and downstream inflammatory responses.
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Affiliation(s)
- Jin-Zhong Li
- Division of Infectious Disease, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Li-Hong Ye
- Division of Pathology, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China
| | - De-Hua Wang
- Division of Oncology, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China
| | - Hai-Cong Zhang
- Division of Pathology, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China
| | - Tao-Yuan Li
- Division of Infectious Disease, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Zhi-Quan Liu
- Division of Pathology, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China
| | - Er-Hei Dai
- Division of Liver Disease, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, China.
| | - Min-Ran Li
- Division of Infectious Disease, The First Affiliated Hospital of Jinan University, Guangzhou, China.
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Li T, Hu D, Gong Y. Identification of potential lncRNAs and co-expressed mRNAs in gestational diabetes mellitus by RNA sequencing. J Matern Fetal Neonatal Med 2021; 35:5125-5139. [PMID: 33618585 DOI: 10.1080/14767058.2021.1875432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AIM Gestational diabetes mellitus is common during pregnancy, impacting maternal health and fetal development. The aim of this study was to identify potential long non-coding RNAs (lncRNAs) and mRNAs in gestational diabetes mellitus. METHODS The placenta tissues from four women patients with gestational diabetes mellitus and three healthy pregnant women were used for RNA sequencing. Differentially expressed lncRNAs and mRNAs were obtained. Then, interaction networks of lncRNA-nearby targeted mRNA and lncRNA-co-expressed mRNA were constructed, followed by functional annotation of co-expressed mRNAs. Third, GSE51546 dataset was utilized to validate the expression of selected co-expressed mRNAs. In addition, in vitro experiment was applied to expression validation of lncRNAs and mRNAs. Finally, GSE70493 dataset was utilized for diagnostic analysis of selected co-expressed mRNAs. RESULTS A total of 78 differentially expressed lncRNAs and 647 differentially expressed mRNAs in gestational diabetes mellitus were obtained. Several interaction pairs of lncRNA-co-expressed mRNA including LINC01504-CASP8, FUT8-AS1-TLR5/GDF15, GATA2-AS1-PQLC3/KIAA2026, and EGFR-AS1-HLA-G were identified. Endocytosis (involved HLA-G) and toll-like receptor signaling pathway (involved TLR5 and CASP8) were remarkably enriched signaling pathways of co-expressed mRNAs. It is noted that CASP8, TLR5, and PQLC3 had a significant prognosis value for gestational diabetes mellitus. CONCLUSIONS Our study identified several differentially expressed lncRNAs and mRNAs, and their interactions, especially co-expression, may be associated with gestational diabetes mellitus.
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Affiliation(s)
- Tao Li
- Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, P. R. China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, P. R. China
| | - Die Hu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, P. R. China.,Department of Outpatient, West China Second University Hospital, Sichuan University, Chengdu, P. R. China
| | - Yunhui Gong
- Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, P. R. China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, P. R. China
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