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Dong J, Song R, Shang X, Wang Y, Liu Q, Zhang Z, Jia H, Huang M, Zhu C, Sun Q, Du B, Xing A, Li Z, Zhang L, Pan L, Zhang Z. Identification of important modules and biomarkers in tuberculosis based on WGCNA. Front Microbiol 2024; 15:1354190. [PMID: 38389525 PMCID: PMC10882270 DOI: 10.3389/fmicb.2024.1354190] [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: 12/12/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Background Tuberculosis (TB) is a significant public health concern, particularly in China. Long noncoding RNAs (lncRNAs) can provide abundant pathological information regarding etiology and could include candidate biomarkers for diagnosis of TB. However, data regarding lncRNA expression profiles and specific lncRNAs associated with TB are limited. Methods We performed ceRNA-microarray analysis to determine the expression profile of lncRNAs in peripheral blood mononuclear cells (PBMCs). Weighted gene co-expression network analysis (WGCNA) was then conducted to identify the critical module and genes associated with TB. Other bioinformatics analyses, including Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and co-expression networks, were conducted to explore the function of the critical module. Finally, real-time quantitative polymerase chain reaction (qPCR) was used to validate the candidate biomarkers, and receiver operating characteristic analysis was used to assess the diagnostic performance of the candidate biomarkers. Results Based on 8 TB patients and 9 healthy controls (HCs), a total of 1,372 differentially expressed lncRNAs were identified, including 738 upregulated lncRNAs and 634 downregulated lncRNAs. Among all lncRNAs and mRNAs in the microarray, the top 25% lncRNAs (3729) and top 25% mRNAs (2824), which exhibited higher median expression values, were incorporated into the WGCNA. The analysis generated 16 co-expression modules, among which the blue module was highly correlated with TB. GO and KEGG analyses showed that the blue module was significantly enriched in infection and immunity. Subsequently, considering module membership values (>0.85), gene significance values (>0.90) and fold-change value (>2 or < 0.5) as selection criteria, the top 10 upregulated lncRNAs and top 10 downregulated lncRNAs in the blue module were considered as potential biomarkers. The candidates were then validated in an independent validation sample set (31 TB patients and 32 HCs). The expression levels of 8 candidates differed significantly between TB patients and HCs. The lncRNAs ABHD17B (area under the curve [AUC] = 1.000) and ENST00000607464.1 (AUC = 1.000) were the best lncRNAs in distinguishing TB patients from HCs. Conclusion This study characterized the lncRNA profiles of TB patients and identified a significant module associated with TB as well as novel potential biomarkers for TB diagnosis.
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Affiliation(s)
- Jing Dong
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Ruixue Song
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xuetian Shang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yingchao Wang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Qiuyue Liu
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- Department of Intensive Care Unit, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Zhiguo Zhang
- Changping Tuberculosis Prevent and Control Institute of Beijing, Beijing, China
| | - Hongyan Jia
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Mailing Huang
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Chuanzhi Zhu
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Qi Sun
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Boping Du
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Aiying Xing
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Zihui Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Lanyue Zhang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Liping Pan
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Zongde Zhang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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Zhang L, Dong X, Zhan Y, Ma S, Liu C, Gao Y. Expression profile of microRNAs in patients with decompensated cirrhosis by small RNA deep sequencing. Clin Biochem 2024; 123:110705. [PMID: 38159622 DOI: 10.1016/j.clinbiochem.2023.110705] [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: 09/12/2023] [Revised: 12/25/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
INTRODUCTION AND OBJECTIVE Decompensated cirrhosis (DCC) is a more advanced stage of liver cirrhosis (LC). It is important to identify biomarkers to predict DCC progression. The aim of this study was to analyze microRNA (miRNA) profiles of whole blood involved in the DCC process to gain a better understanding of the molecular mechanisms underlying its development. MATERIALS AND METHODS RNA-Seq analysis of blood samples from a discovery set, including four DCC patients and four LC individuals, was performed to identify differentially expressed miRNAs. The selected differentially expressed miRNAs were validated by using an independent validation set. RESULTS In this study, a total of 1,036 miRNAs were identified in whole blood samples. Forty differentially expressed miRNAs were identified, including 24 upregulated and 16 downregulated miRNAs. The expression levels of three upregulated miRNAs (hsa-miR-20b-5p, hsa-miR-421, and hsa-miR-1307-3p) and two downregulated miRNAs (hsa-miR-139-5p and hsa-miR-150-5p) were validated by quantitative reverse transcriptase polymerase chain reaction. The receiver operator characteristic curve for the logistic regression model based on hsa-miR-20b-5p, hsa-miR-421, and hsa-miR-150-5p could distinguish DCC patients with excellent diagnostic accuracy (area under the curve: 0.981, p < 0.01). CONCLUSION The miRNA expression profiles in patients with DCC and LC controls suggested that miR-20b-5p, miR-421, and miR-150-5p could be potential biomarkers and therapeutic targets for this condition.
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Affiliation(s)
- Li Zhang
- Department of Infectious Diseases, First Affiliated Hospital, Bengbu Medical College, Bengbu, China
| | - Xiang Dong
- Department of Biotechnology, School of Life Science, Bengbu Medical College, Bengbu, China; Bengbu Medical College Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, Bengbu Medical College, Bengbu, China
| | - Yuling Zhan
- Department of Biotechnology, School of Life Science, Bengbu Medical College, Bengbu, China; Bengbu Medical College Key Laboratory of Cancer Research and Clinical Laboratory Diagnosis, Bengbu Medical College, Bengbu, China
| | - Shasha Ma
- Department of Infectious Diseases, First Affiliated Hospital, Bengbu Medical College, Bengbu, China
| | - Chuanmiao Liu
- Department of Infectious Diseases, First Affiliated Hospital, Bengbu Medical College, Bengbu, China
| | - Yu Gao
- Department of Biotechnology, School of Life Science, Bengbu Medical College, Bengbu, China; Anhui Province Key Laboratory of Translational Cancer Research, Bengbu Medical College, Bengbu, China; Research Center for Laboratory Animal Science, Bengbu Medical College, Bengbu, China.
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He Z, Zhang J, Huang W. Diagnostic role and immune correlates of programmed cell death-related genes in hepatocellular carcinoma. Sci Rep 2023; 13:20509. [PMID: 37993470 PMCID: PMC10665317 DOI: 10.1038/s41598-023-47560-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/15/2023] [Indexed: 11/24/2023] Open
Abstract
Programmed cell death (PCD) is thought to have multiple roles in tumors. Here, the roles of PCD-related genes were comprehensively analyzed to evaluate their values in hepatocellular carcinoma (HCC) diagnosis and prognosis. Gene expression and single-cell data of HCC patients, and PCD-related genes were collected from public databases. The diagnostic and prognostic roles of differentially expressed PCD-related genes in HCC were explored by univariate and multivariate Cox regression analyses. Single-cell data were further analyzed for the immune cells and expression of feature genes. Finally, we evaluated the expression of genes by quantitative real-time polymerase chain reaction and Western blot, and the proportion of immune cells was detected by flow cytometry in HCC samples. We obtained 52 differentially expressed PCD-related genes in HCC, based on which the consensus clustering analysis cluster 2 was found to have a worse prognosis than cluster 1. Then 10 feature genes were identified using LASSO analysis, and programmed cell death index (PCDI) was calculated to divided HCC patients into high-PCDI and low-PCDI groups. Worse prognosis was observed in high-PCDI group. Cox regression analysis showed that PCDI is an independent prognostic risk factor for HCC patients. Additionally, SERPINE1 and G6PD of feature genes significantly affect patient survival. Macrophages and Tregs were significantly positively correlated with PCDI. G6PD mainly expressed in macrophages, SERPINE1 mainly expressed in fibroblast. The experimental results confirmed the high expression of SERPINE1 and G6PD in HCC compared with the control, and the infiltration level of macrophages and Treg in HCC was also obviously elevated. PCDI may be a new predictor for the diagnosis of patients with HCC. The association of SERPINE1 and G6PD with the immune environment will provide new clues for HCC therapy.
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Affiliation(s)
- Zhanao He
- Department of Interventional Diagnosis and Treatment, The Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, 830011, China
| | - Jie Zhang
- Department of Hepatobiliary Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Ürümqi, 830011, China
| | - Wukui Huang
- Department of Interventional Diagnosis and Treatment, The Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, 830011, China.
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GOU L, HE Y, QIU P, HUANG B. [Mechanism Research of lncRNA miR143HG on Regulating the Biological Behavior
of Lung Squamous Cell Carcinoma H520 Cells]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2023; 26:741-752. [PMID: 37989337 PMCID: PMC10663781 DOI: 10.3779/j.issn.1009-3419.2023.106.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND There is a high morbidity, mortality, and poor clinical prognosis of lung squamous cell carcinoma (LUSC). However, there is currently no effective targeted treatment plan for LUSC. As a long non-coding RNA (lncRNA), lncRNA miR143HG has been proven to play an important role in the occurrence and development of various tumors. However, the biological role played by lncRNA miR143HG in LUSC cells is still unclear. Therefore, this study aimed to investigate the mechanism of lncRNA miR143HG on regulating the biological behavior of LUSC H520 cells. METHODS Pan-cancer analysis and differential expression analysis of lncRNA miR143HG were performed based on The Cancer Genome Atlas (TCGA) database. The predictive effect of lncRNA miR143HG on the diagnosis and prognosis of LUSC was evaluated by adopting the receiver operating characteristic (ROC) curve and timeROC curve. The enrichment degree of each pathway to lncRNA miR143HG was determined. The expression of lncRNA miR143HG and miR-155 in BEAS-2B cells and H520 cells was detected using quantitative real-time polymerase chain reaction (qRT-PCR). H520 cells were randomly divided into blank control group (without any treatment), negative control group (transfected with lncRNA-NC), lncRNA miR143HG group (transfected with lncRNA miR143HG), and lncRNA miR143HG+miR-155 group (co-transfected with lncRNA miR143HG and miR-155). The approaches of CCK-8, wound healing test, Transwell assay, flow cytometry, qRT-PCR, and Western blot were respectively employed to detect the cell proliferation ability, cell migration ability, cell invasion ability, cell apoptosis rate, and expression level of related genes and proteins of the Wnt/β-Catenin pathway. RESULTS The results of pan-cancer analysis and differential analysis collectively showed that except for renal clear cell carcinoma, the expression of lncRNA miR143HG in other cancer tissues was higher than that in healthy tissues, and the differences were significant in LUSC. The evaluation results of the ROC curve and timeROC curve suggested that lncRNA miR143HG was of great significance in the prediction of diagnosis and prognosis of LUSC. The pathways enriched in high expression of lncRNA miR143HG mainly included focal adhesion, vascular smooth muscle contraction, calcium signaling pathways, and so on; the pathways enriched in the low expression of lncRNA miR143HG embraced oxidative phosphorylation, cell cycle, basic transcription factors, etc. The qRT-PCR results showed that lncRNA miR143HG was low expressed but miR-155 was highly expressed in H520 cells when compared to BEAS-2B cells (P<0.05). Compared with the negative control group, the expression levels of the gene of lncRNA miR143HG, the gene and protein of Wnt, as well as the gene and protein of β-Catenin were significantly increased, while the gene expression of miR-155, the ability of cell proliferation, cell migration, and cell invasion were significantly reduced, but the cell apoptosis rate was dominantly elevated in cells of lncRNA miR143HG group (P<0.05). In addition, compared with the lncRNA miR143HG group, overexpression of miR-155 could reverse the biological behavior mediated by lncRNA miR143HG, and the difference was statistically significant (P<0.05). CONCLUSIONS LncRNA miR143HG was of great significance for the biological behavior of H520 cells. LncRNA miR143HG inhibited the ability of proliferation, migration, and invasion, as well as enhanced the apoptosis of H520 cells by downregulating miR-155 expression, which may be related to the Wnt/β-Catenin pathway.
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Chen D, Aierken A, Li H, Chen R, Ren L, Wang K. Identification of subclusters and prognostic genes based on glycolysis/gluconeogenesis in hepatocellular carcinoma. Front Immunol 2023; 14:1232390. [PMID: 37881434 PMCID: PMC10597634 DOI: 10.3389/fimmu.2023.1232390] [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: 05/31/2023] [Accepted: 09/19/2023] [Indexed: 10/27/2023] Open
Abstract
Background This study aimed to examine glycolysis/gluconeogenesis-related genes in hepatocellular carcinoma (HCC) and evaluate their potential roles in HCC progression and immunotherapy response. Methods Data analyzed in this study were collected from GSE14520, GSE76427, GSE174570, The Cancer Genome Atlas (TCGA), PXD006512, and GSE149614 datasets, metabolic pathways were collected from MSigDB database. Differentially expressed genes (DEGs) were identified between HCC and controls. Differentially expressed glycolysis/gluconeogenesis-related genes (candidate genes) were obtained and consensus clustering was performed based on the expression of candidate genes. Bioinformatics analysis was used to evaluate candidate genes and screen prognostic genes. Finally, the key results were tested in HCC patients. Results Thirteen differentially expressed glycolysis/gluconeogenesis-related genes were validated in additional datasets. Consensus clustering analysis identified two distinct patient clusters (C1 and C2) with different prognoses and immune microenvironments. Immune score and tumor purity were significantly higher in C1 than in C2, and CD4+ memory activated T cell, Tfh, Tregs, and macrophage M0 were higher infiltrated in HCC and C1 group. The study also identified five intersecting DEGs from candidate genes in TCGA, GSE14520, and GSE141198 as prognostic genes, which had a protective role in HCC patient prognosis. Compared with the control group, the prognostic genes all showed decreased expression in HCC patients in RT-qPCR and Western blot analyses. Flow cytometry verified the abnormal infiltration level of immune cells in HCC patients. Conclusion Results showed that glycolysis/gluconeogenesis-related genes were associated with patient prognosis, immune microenvironment, and response to immunotherapy in HCC. It suggests that the model based on five prognostic genes may valuable for predicting the prognosis and immunotherapy response of HCC patients.
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Affiliation(s)
- Dan Chen
- School of Public Health, Xinjiang Medical University, Urumqi, China
| | - Ayinuer Aierken
- Department of Hepatobiliary Hydatid Disease, the First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Hui Li
- Central Laboratory, Xinjiang Medical University, Urumqi, China
| | - Ruihua Chen
- Center of Animal Experiments, Xinjiang Medical University, Urumqi, China
| | - Lei Ren
- Department of Burns, the First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Kai Wang
- Department of Medical Engineering and Technology, Xinjiang Medical University, Urumqi, China
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