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Li Y, Wang L, Zhang J, Xu B, Zhan H. Integrated multi-omics and bioinformatic methods to reveal the mechanisms of sinomenine against diabetic nephropathy. BMC Complement Med Ther 2023; 23:287. [PMID: 37580684 PMCID: PMC10424381 DOI: 10.1186/s12906-023-04119-0] [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: 05/23/2023] [Accepted: 08/05/2023] [Indexed: 08/16/2023] Open
Abstract
OBJECTIVES Diabetic Nephropathy (DN) is a serious complication of diabetes, the diagnosis and treatment of DN is still limited. Sinomenine (SIN) is an active extract of herbal medicine and has been applied into the therapy of DN. METHODS In the part of bioinformatic analyses, network pharmacology and molecular docking analyses were conducted to predict the important pathway of SIN treatment for DN. In-vivo study, DN rats were randomized to be treated with vehicle or SIN (20 mg/kg or 40 mg/kg) daily by gavage for 8 weeks. Then, the pharmacological effect of SIN on DN and the potential mechanisms were also evaluated by 24 h albuminuria, histopathological examination, transcriptomics, and metabolomics. RESULTS Firstly, network pharmacology and molecular docking were performed to show that SIN might improve DN via AGEs/RAGE, IL-17, JAK, TNF pathways. Urine biochemical parameters showed that SIN treatment could significantly reduce 24 h albuminuria of DN rats. Transcriptomics analysis found SIN could affect DN progression via inflammation and EMT pathways. Metabolic pathway analysis found SIN would mainly involve in arginine biosynthesis, linoleic acid metabolism, arachidonic acid metabolism, and glycerophospholipid metabolism to affect DN development. CONCLUSIONS We confirmed that SIN could inhibit the progression of DN via affecting multiple genes and metabolites related pathways.
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Affiliation(s)
- Yan Li
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, Xiamen, 117892, Fujian, China
- Xiamen Municipal Clinical Research Center for Immune Diseases, Xiamen, 361000, XM, China
- Xiamen Key Laboratory of Rheumatology and Clinical Immunology, Xiamen University, Xiamen, 12466, Fujian, China
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, Sichuan, China
| | - Lei Wang
- Key Laboratory of Chinese Internal Medicine of Ministry of Education and Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
| | - Jimin Zhang
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, Xiamen, 117892, Fujian, China
- Xiamen Municipal Clinical Research Center for Immune Diseases, Xiamen, 361000, XM, China
- Xiamen Key Laboratory of Rheumatology and Clinical Immunology, Xiamen University, Xiamen, 12466, Fujian, China
| | - Bojun Xu
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, Sichuan, China.
| | - Huakui Zhan
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, Sichuan, China.
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Jin Y, Huang S, Wang Z. Identify and validate RUNX2 and LAMA2 as novel prognostic signatures and correlate with immune infiltrates in bladder cancer. Front Oncol 2023; 13:1191398. [PMID: 37519798 PMCID: PMC10373733 DOI: 10.3389/fonc.2023.1191398] [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: 03/22/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023] Open
Abstract
Background Muscle-invasive bladder cancer (MIBC) develops lymph node (LN) metastasis or distant metastasis, leading to recurrence and poor prognosis. The five-year survival rate of MIBC with LN or distant metastasis is only 8.1%; therefore, there is an urgent need to identify reliable biomarkers for prognosis and treatment regimen for patients with bladder cancer (BLCA). Methods SEER database was used to select important clinical characteristics for MIBC. Then, weighted gene co-expression network analysis (WGCNA) was employed to identify differentially expressed genes (DEGs) to recognize significant co-expression modules by calculating the correlation between the modules and clinical data. Furthermore, Cox regression and lasso analysis were applied to screen prognostic hub genes and establish the risk predictive model. Bladder cancer cell lines (UMUC3 and 5637) were used for experimental validation in vitro. Results Cox analysis of 122,600 MIBC patients showed that the N stage was the most important clinical factor. A total of 4,597 DEGs were calculated between N0 and N+ patients, and WGCNA with these DEGs in 368 samples revealed that expression of turquoise was positively and strongly correlated with the N stage. Eight genes were identified as important prognostic candidates using lasso regression based on Cox analysis and STRING database. Combining GEO datasets, literature, and clinical factors, we identified LAMA2 and RUNX2 as novel prognostic biomarkers. CCK8 assay showed that depletion of LAMA2 or RUNX2 significantly inhibited the proliferation of BLCA cells, and flow cytometry indicated that knockdown of LAMA2 or RUNX2 induced the apoptosis of BLCA cells. Transwell assay also showed that silencing of LAMA2 or RUNX2 weakened the migration and invasiveness of BLCA cells. Conclusions We constructed a new eight-gene risk model to provide novel prognostic biomarkers and therapeutic targets for BLCA.
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Affiliation(s)
- Yi Jin
- Department of Radiation Oncology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- Key Laboratory of Translational Radiation Oncology, Department of Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Siwei Huang
- School of Humanities and Management, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Zhanwang Wang
- Department of Oncology, Third Xiangya Hospital of Central South University, Changsha, China
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He L, He W, Luo J, Xu M. Upregulated ENC1 predicts unfavorable prognosis and correlates with immune infiltration in endometrial cancer. Front Cell Dev Biol 2022; 10:919637. [PMID: 36531950 PMCID: PMC9751423 DOI: 10.3389/fcell.2022.919637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/17/2022] [Indexed: 07/30/2023] Open
Abstract
A better knowledge of the molecular process behind uterine corpus endometrial carcinoma (UCEC) is important for prognosis prediction and the development of innovative targeted gene therapies. The purpose of this research is to discover critical genes associated with UCEC. We analyzed the gene expression profiles of TCGA-UCEC and GSE17025, respectively, using Weighted Gene Co-expression Network Analysis (WGCNA) and differential gene expression analysis. From four sets of findings, a total of 95 overlapping genes were retrieved. On the 95 overlapping genes, KEGG pathway and GO enrichment analysis were conducted. Then, we mapped the PPI network of 95 overlapping genes using the STRING database. Twenty hub genes were evaluated using the Cytohubba plugin, including NR3C1, ATF3, KLF15, THRA, NR4A1, FOSB, PER3, HLF, NTRK3, EGR3, MAPK13, ARNTL2, PKM2, SCD, EIF5A, ADHFE1, RERGL, TUB, and ENC1. The expression levels of NR3C1, PKM2, and ENC1 were shown to be adversely linked with the survival time of UCEC patients using univariate Cox regression analysis and Kaplan-Meier survival calculation. ENC1 were also overexpressed in UCEC tumor tissues or cell lines, as shown by quantitative real-time PCR and Western blotting. Then we looked into it further and discovered that ENC1 expression was linked to tumor microenvironment and predicted various immunological checkpoints. In conclusion, our data indicate that ENC1 may be required for the development of UCEC and may serve as a future biomarker for diagnosis and therapy.
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Affiliation(s)
- Lingling He
- Department of Obstetrics and Gynecology, Ganzhou People's Hospital, Ganzhou, China
- Department of Obstetrics and Gynecology, Ganzhou Hospital-Nanfang Hospital, Southern Medical University, Ganzhou, China
- Department of Obstetrics and Gynecology, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, China
| | - Wenjing He
- Department of Endocrinology, Baoji Gaoxin Hospital, Baoji, China
| | - Ji Luo
- Department of Obstetrics and Gynecology, Ganzhou People's Hospital, Ganzhou, China
- Department of Obstetrics and Gynecology, Ganzhou Hospital-Nanfang Hospital, Southern Medical University, Ganzhou, China
- Department of Obstetrics and Gynecology, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, China
| | - Minjuan Xu
- Department of Obstetrics and Gynecology, Ganzhou People's Hospital, Ganzhou, China
- Department of Obstetrics and Gynecology, Ganzhou Hospital-Nanfang Hospital, Southern Medical University, Ganzhou, China
- Department of Obstetrics and Gynecology, The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, China
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Hasankhani A, Bahrami A, Mackie S, Maghsoodi S, Alawamleh HSK, Sheybani N, Safarpoor Dehkordi F, Rajabi F, Javanmard G, Khadem H, Barkema HW, De Donato M. In-depth systems biological evaluation of bovine alveolar macrophages suggests novel insights into molecular mechanisms underlying Mycobacterium bovis infection. Front Microbiol 2022; 13:1041314. [PMID: 36532492 PMCID: PMC9748370 DOI: 10.3389/fmicb.2022.1041314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/04/2022] [Indexed: 08/26/2023] Open
Abstract
OBJECTIVE Bovine tuberculosis (bTB) is a chronic respiratory infectious disease of domestic livestock caused by intracellular Mycobacterium bovis infection, which causes ~$3 billion in annual losses to global agriculture. Providing novel tools for bTB managements requires a comprehensive understanding of the molecular regulatory mechanisms underlying the M. bovis infection. Nevertheless, a combination of different bioinformatics and systems biology methods was used in this study in order to clearly understand the molecular regulatory mechanisms of bTB, especially the immunomodulatory mechanisms of M. bovis infection. METHODS RNA-seq data were retrieved and processed from 78 (39 non-infected control vs. 39 M. bovis-infected samples) bovine alveolar macrophages (bAMs). Next, weighted gene co-expression network analysis (WGCNA) was performed to identify the co-expression modules in non-infected control bAMs as reference set. The WGCNA module preservation approach was then used to identify non-preserved modules between non-infected controls and M. bovis-infected samples (test set). Additionally, functional enrichment analysis was used to investigate the biological behavior of the non-preserved modules and to identify bTB-specific non-preserved modules. Co-expressed hub genes were identified based on module membership (MM) criteria of WGCNA in the non-preserved modules and then integrated with protein-protein interaction (PPI) networks to identify co-expressed hub genes/transcription factors (TFs) with the highest maximal clique centrality (MCC) score (hub-central genes). RESULTS As result, WGCNA analysis led to the identification of 21 modules in the non-infected control bAMs (reference set), among which the topological properties of 14 modules were altered in the M. bovis-infected bAMs (test set). Interestingly, 7 of the 14 non-preserved modules were directly related to the molecular mechanisms underlying the host immune response, immunosuppressive mechanisms of M. bovis, and bTB development. Moreover, among the co-expressed hub genes and TFs of the bTB-specific non-preserved modules, 260 genes/TFs had double centrality in both co-expression and PPI networks and played a crucial role in bAMs-M. bovis interactions. Some of these hub-central genes/TFs, including PSMC4, SRC, BCL2L1, VPS11, MDM2, IRF1, CDKN1A, NLRP3, TLR2, MMP9, ZAP70, LCK, TNF, CCL4, MMP1, CTLA4, ITK, IL6, IL1A, IL1B, CCL20, CD3E, NFKB1, EDN1, STAT1, TIMP1, PTGS2, TNFAIP3, BIRC3, MAPK8, VEGFA, VPS18, ICAM1, TBK1, CTSS, IL10, ACAA1, VPS33B, and HIF1A, had potential targets for inducing immunomodulatory mechanisms by M. bovis to evade the host defense response. CONCLUSION The present study provides an in-depth insight into the molecular regulatory mechanisms behind M. bovis infection through biological investigation of the candidate non-preserved modules directly related to bTB development. Furthermore, several hub-central genes/TFs were identified that were significant in determining the fate of M. bovis infection and could be promising targets for developing novel anti-bTB therapies and diagnosis strategies.
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Affiliation(s)
- Aliakbar Hasankhani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
- Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Shayan Mackie
- Faculty of Science, Earth Sciences Building, University of British Columbia, Vancouver, BC, Canada
| | - Sairan Maghsoodi
- Faculty of Paramedical Sciences, Kurdistan University of Medical Sciences, Kurdistan, Iran
| | - Heba Saed Kariem Alawamleh
- Department of Basic Scientific Sciences, AL-Balqa Applied University, AL-Huson University College, AL-Huson, Jordan
| | - Negin Sheybani
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Farhad Safarpoor Dehkordi
- Halal Research Center of IRI, FDA, Tehran, Iran
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Fatemeh Rajabi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Ghazaleh Javanmard
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Hosein Khadem
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Herman W. Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Marcos De Donato
- Regional Department of Bioengineering, Tecnológico de Monterrey, Monterrey, Mexico
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Hou M. Exploring novel independent prognostic biomarkers for hepatocellular carcinoma based on TCGA and GEO databases. Medicine (Baltimore) 2022; 101:e31376. [PMID: 36316888 PMCID: PMC9622571 DOI: 10.1097/md.0000000000031376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) has become the fifth most common cancer globally, with the second-highest mortality rate and poor survival outcomes. In our research, we aimed to use The Cancer Genome Atlas and gene expression omnibus databases to identify potential genetic biomarkers to predict and improve the survival rate of HCC patients. METHODS In GSE60502, GSE76427, and GSE84402, we performed differential expression analysis to obtain differentially expressed genes (DEGs). In the The Cancer Genome Atlas database, the FPKM expression profile was subjected to weighted gene co-expression analysis to obtain modules closely related to HCC. We received common genes by intersecting the genes in the module with the differential genes. Then, we fused the common genes' expression profiles, survival time, and survival status for univariate, Least Absolute Shrinkage and Selection Operator, and multivariate COX regression analysis to obtain prognostic genes. Predictive genes were performed in K-M survival analysis and combined with clinical data for independent predictive analysis. RESULTS After differential expression analysis, GSE60502 obtained 1107 DEGs, GSE76427 obtained 424 DEGs, and GSE84402 obtained 1668 DEGs. Through weighted gene co-expression analysis analysis, we can see that the blue and brown modules were closely associated with HCC. After single and multivariate COX regression analysis, we found that suppressor of cytokine signaling 2 (SOCS2) and SERPINF2 were independent prognostic genes for HCC. After survival analysis, HCC patients with high expression of SOCS2 and SERPINF2 had a longer survival time. These 2 genes in normal liver tissues were higher than in HCC at the transcriptional level. CONCLUSION SOCS2 and SERPINF2 were new independent prognostic genes of HCC. So, they may provide new treatment methods and measures for diagnosing HCC.
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Affiliation(s)
- Miaomiao Hou
- Microimmune, 3201 Hospital, Hanzhong City, Shaanxi Province, China
- *Correspondence: Miaomiao Hou, Microimmune, 3201 Hospital, Hanzhong City, Shaanxi Province, China (e-mail: )
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Lin L, Zeng X, Liang S, Wang Y, Dai X, Sun Y, Wu Z. Construction of a co-expression network and prediction of metastasis markers in colorectal cancer patients with liver metastasis. J Gastrointest Oncol 2022; 13:2426-2438. [PMID: 36388701 PMCID: PMC9660078 DOI: 10.21037/jgo-22-965] [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: 09/23/2022] [Accepted: 10/18/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a common global malignancy associated with high invasiveness, high metastasis, and poor prognosis. CRC commonly metastasizes to the liver, where the treatment of metastasis is both difficult and an important topic in current CRC management. METHODS Microarrays data of human CRC with liver metastasis (CRCLM) were downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database to identify potential key genes. Differentially expressed (DE) genes (DEGs) and DEmiRNAs of primary CRC tumor tissues and metastatic liver tissues were identified. Microenvironment Cell Populations (MCP)-counter was used to estimate the abundance of immune cells in the tumor micro-environment (TME), and weighted gene correlation network analysis (WGCNA) was used to construct the co-expression network analysis. Gene Ontology and Kyoto Encyclopaedia of Gene and Genome (KEGG) pathway enrichment analyses were conducted, and the protein-protein interaction (PPI) network for the DEGs were constructed and gene modules were screened. RESULTS Thirty-five pairs of matched colorectal primary cancer and liver metastatic gene expression profiles were screened, and 610 DEGs (265 up-regulated and 345 down-regulated) and 284 DEmiRNAs were identified. The DEGs were mainly enriched in the complement and coagulation cascade pathways and renin secretion. Immune infiltrating cells including neutrophils, monocytic lineage, and cancer-associated fibroblasts (CAFs) differed significantly between primary tumor tissues and metastatic liver tissues. WGCN analysis obtained 12 modules and identified 62 genes with significant interactions which were mainly related to complement and coagulation cascade and the focal adhesion pathway. The best subset regression analysis and backward stepwise regression analysis were performed, and eight genes were determined, including F10, FGG, KNG1, MBL2, PROC, SERPINA1, CAV1, and SPP1. Further analysis showed four genes, including FGG, KNG1, CAV1, and SPP1 were significantly associated with CRCLM. CONCLUSIONS Our study implies complement and coagulation cascade and the focal adhesion pathway play a significant role in the development and progression of CRCLM, and FGG, KNG1, CAV1, and SPP1 may be metastatic markers for its early diagnosis.
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Affiliation(s)
- Lihong Lin
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Xiuxiu Zeng
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Shanyan Liang
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Yunzhi Wang
- School of Health Sciences, University of Sydney, Lidcombe, NSW, Australia
| | - Xiaoyu Dai
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Yuechao Sun
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China;,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Zhou Wu
- Department of Anorectal Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
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Liu Z, Liu Z, Mu Q, Zhao M, Cai T, Xie Y, Zhao C, Qin Q, Zhang C, Xu X, Lan M, Zhang Y, Su R, Wang Z, Wang R, Wang Z, Li J, Zhao Y. Identification of key pathways and genes that regulate cashmere development in cashmere goats mediated by exogenous melatonin. Front Vet Sci 2022; 9:993773. [PMID: 36246326 PMCID: PMC9558121 DOI: 10.3389/fvets.2022.993773] [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: 07/14/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
The growth of secondary hair follicles in cashmere goats follows a seasonal cycle. Melatonin can regulate the cycle of cashmere growth. In this study, melatonin was implanted into live cashmere goats. After skin samples were collected, transcriptome sequencing and histological section observation were performed, and weighted gene co-expression network analysis (WGCNA) was used to identify key genes and establish an interaction network. A total of 14 co-expression modules were defined by WGCNA, and combined with previous analysis results, it was found that the blue module was related to the cycle of cashmere growth after melatonin implantation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the first initiation of exogenous melatonin-mediated cashmere development was related mainly to the signaling pathway regulating stem cell pluripotency and to the Hippo, TGF-beta and MAPK signaling pathways. Via combined differential gene expression analyses, 6 hub genes were identified: PDGFRA, WNT5A, PPP2R1A, BMPR2, BMPR1A, and SMAD1. This study provides a foundation for further research on the mechanism by which melatonin regulates cashmere growth.
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Affiliation(s)
- Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Goat Genetics and Breeding Engineering Technology Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhichen Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Qing Mu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Meng Zhao
- Inner Mongolia Autonomous Region Agriculture and Animal Husbandry Technology Extension Center, Hohhot, China
| | - Ting Cai
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Yuchun Xie
- Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Cun Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Qing Qin
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Chongyan Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaolong Xu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingxi Lan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhixin Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Goat Genetics and Breeding Engineering Technology Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanhong Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Goat Genetics and Breeding Engineering Technology Research Center, Inner Mongolia Agricultural University, Hohhot, China
- *Correspondence: Yanhong Zhao
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Ahmadi-Beni R, Shahbazi S, Khoshnevisan A. An integrative bioinformatics investigation and experimental validation of critically involved genes in high-grade gliomas. Diagn Pathol 2022; 17:73. [PMID: 36153549 PMCID: PMC9508723 DOI: 10.1186/s13000-022-01253-0] [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: 05/05/2021] [Accepted: 09/15/2022] [Indexed: 11/10/2022] Open
Abstract
Background Lack of knowledge around underlying mechanisms of gliomas mandates intense research efforts to improve the disease outcomes. Identification of high-grade gliomas pathogenesis which is known for poor prognosis and low survival is of particular importance. Distinguishing the differentially expressed genes is one of the core approaches to clarify the causative factors. Methods Microarray datasets of the treatment-naïve gliomas were provided from the Gene Expression Omnibus considering the similar platform and batch effect removal. Interacting recovery of the top differentially expressed genes was performed on the STRING and Cytoscape platforms. Kaplan–Meier analysis was piloted using RNA sequencing data and the survival rate of glioma patients was checked considering selected genes. To validate the bioinformatics results, the gene expression was elucidated by real-time RT-qPCR in a series of low and high-grade fresh tumor samples. Results We identified 323 up-regulated and 253 down-regulated genes. The top 20 network analysis indicated that PTX3, TIMP1, CHI3L1, LTF and IGFBP3 comprise a crucial role in gliomas progression. The survival was inversely linked to the levels of all selected genes. Further analysis of RNA sequencing data indicated a significant increase in all five genes in high-grade tumors. Among them, PTX3, TIMP1 and LTF did not show any change in low-grade versus controls. Real-time RT-qPCR confirmed the in-silico results and revealed significantly higher expression of selected genes in high-grade samples compared to low-grade. Conclusions Our results highlighted the role of PTX3 and TIMP1 which were previously considered in glioma tumorigenesis as well as LTF as a new potential biomarker.
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Analysis of Dormancy-Associated Transcriptional Networks Reveals a Shared Quiescence Signature in Lung and Colorectal Cancer. Int J Mol Sci 2022; 23:ijms23179869. [PMID: 36077264 PMCID: PMC9456317 DOI: 10.3390/ijms23179869] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
Quiescent cancer cells (QCCs) are a common feature of solid tumors, representing a major obstacle to the long-term success of cancer therapies. We isolated QCCs ex vivo from non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) xenografts with a label-retaining strategy and compared QCCs gene expression profiles to identify a shared “quiescence signature”. Principal Component Analysis (PCA) revealed a specific component neatly discriminating quiescent and replicative phenotypes in NSCLC and CRC. The discriminating component showed significant overlapping, with 688 genes in common including ZEB2, a master regulator of stem cell plasticity and epithelial-to-mesenchymal transition (EMT). Gene set enrichment analysis showed that QCCs of both NSCLC and CRC had an increased expression of factors related to stemness/self renewal, EMT, TGF-β, morphogenesis, cell adhesion and chemotaxis, whereas proliferating cells overexpressed Myc targets and factors involved in RNA metabolism. Eventually, we analyzed in depth by means of a complex network approach, both the ‘morphogenesis module’ and the subset of differentially expressed genes shared by NCSLC and CRC. This allowed us to recognize different gene regulation network wiring for quiescent and proliferating cells and to underpin few genes central for network integration that may represent new therapeutic vulnerabilities. Altogether, our results highlight common regulatory pathways in QCCs of lung and colorectal tumors that may be the target of future therapeutic interventions.
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Chen H, Li X, Sun Y, Du Y, Wu S, Wu Y, Liu H, Liu Y, Wang Y, Zhao Q, Yin S. HAO1 negatively regulates liver macrophage activation via the NF-κB pathway in alcohol-associated liver disease. Cell Signal 2022; 99:110436. [PMID: 35953025 DOI: 10.1016/j.cellsig.2022.110436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/19/2022] [Accepted: 08/05/2022] [Indexed: 11/24/2022]
Abstract
Inflammation is a key factor contributing to the progression of alcohol-associated liver disease (ALD). Accumulating data have shown that ethyl alcohol (EtOH) induced liver macrophages activation along with an inflammatory response that contributes to the development of ALD. The liver-specific peroxisomal enzyme hydroxyacid oxidase 1 (HAO1) has been found to be associated with chronic liver disease. But the role of HAO1 remains unknown in ALD. In our study, HAO1 was found to be decreased in ALD patients and EtOH-fed mice. Interestingly, HAO1 expression was reduced in primary hepatocytes, whereas HAO1 was elevated in peripheral blood monocytes from ALD patients and EtOH-fed mice liver macrophages as well as LPS-treated RAW264.7 cells. Moreover, HAO1 knockdown exacerbated the inflammatory response, while HAO1 overexpression inhibited inflammation in LPS-stimulated RAW264.7 cells. Additionally, overexpression or silencing of HAO1 in vitro significantly affected NF-κB signaling pathway. Collectively, the results revealed a key role of HAO1-mediated macrophage activation and may provide a potential target for treating ALD.
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Affiliation(s)
- Hao Chen
- Department of Pharmacy, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China; The Grade 3 Pharmaceutical Chemistry Laboratory of State Administration of Traditional Chinese Medicine, Hefei, Anhui, China
| | - Xiaofeng Li
- The Key Laboratory of Major Autoimmune Diseases of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, China
| | - Yingyin Sun
- Department of Oncology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yan Du
- Department of Pharmacy, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China; The Grade 3 Pharmaceutical Chemistry Laboratory of State Administration of Traditional Chinese Medicine, Hefei, Anhui, China
| | - Sha Wu
- The Key Laboratory of Major Autoimmune Diseases of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, China
| | - Yuanyuan Wu
- The Key Laboratory of Major Autoimmune Diseases of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, China
| | - Huiping Liu
- The Key Laboratory of Major Autoimmune Diseases of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, Anhui, China
| | - Yaru Liu
- Department of Pharmacy, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China; The Grade 3 Pharmaceutical Chemistry Laboratory of State Administration of Traditional Chinese Medicine, Hefei, Anhui, China
| | - Yongmei Wang
- Department of Nursing, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Qihang Zhao
- First Clinical Medical College of Anhui Medical University, Hefei, Anhui, China
| | - Shi Yin
- Department of Geriatrics, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
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11
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Identification of the shared gene signatures and pathways between polycystic ovary syndrome and endometrial cancer: An omics data based combined approach. PLoS One 2022; 17:e0271380. [PMID: 35830453 PMCID: PMC9278750 DOI: 10.1371/journal.pone.0271380] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 06/30/2022] [Indexed: 12/24/2022] Open
Abstract
Objective Polycystic ovary syndrome (PCOS) is a common endocrine disorder with high incidence. Recently it has been implicated as a significant risk factor for endometrial cancer (EC). Our study aims to detect shared gene signatures and biological mechanism between PCOS and EC by bioinformatics analysis. Methods Bioinformatics analysis based on GEO database consisted of data integration, network construction and functional enrichment analysis was applied. In addition, the pharmacological methodology and molecular docking was also performed. Results Totally 10 hub common genes, MRPL16, MRPL22, MRPS11, RPL26L1, ESR1, JUN, UBE2I, MRPL17, RPL37A, GTF2H3, were considered as shared gene signatures for EC and PCOS. The GO and KEGG pathway analysis of these hub genes showed that “mitochondrial translational elongation”, “ribosomal subunit”, “structural constituent of ribosome” and “ribosome” were highly correlated. Besides, associated transcription factors (TFs) and miRNAs network were constructed. We identified candidate drug molecules including fenofibrate, cinnarizine, propanil, fenthion, clindamycin, chloramphenicol, demeclocycline, hydrochloride, azacitidine, chrysene and artenimol according to these hub genes. Molecular docking analysis verified a good binding interaction of fenofibrate against available targets (JUN, ESR1, UBE2I). Conclusion Gene signatures and regulatory biological pathways were identified through bioinformatics analysis. Moreover, the molecular mechanisms of these signatures were explored and potential drug molecules associated with PCOS and EC were screened out.
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Nayak C, Singh SK. Integrated Transcriptome Profiling Identifies Prognostic Hub Genes as Therapeutic Targets of Glioblastoma: Evidenced by Bioinformatics Analysis. ACS OMEGA 2022; 7:22531-22550. [PMID: 35811900 PMCID: PMC9260928 DOI: 10.1021/acsomega.2c01820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Glioblastoma (GBM) is the most devastating and frequent type of primary brain tumor with high morbidity and mortality. Despite the use of surgical resection followed by radio- and chemotherapy as standard therapy, the progression of GBM remains dismal with a median overall survival of <15 months. GBM embodies a populace of cancer stem cells (GSCs) that is associated with tumor initiation, invasion, therapeutic resistance, and post-treatment reoccurrence. However, understanding the potential mechanisms of stemness and their candidate biomarkers remains limited. Hence in this investigation, we aimed to illuminate potential candidate hub genes and key pathways associated with the pathogenesis of GSC in the development of GBM. The integrated analysis discovered differentially expressed genes (DEGs) between the brain cancer tissues (GBM and GSC) and normal brain tissues. Multiple approaches, including gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, were employed to functionally annotate the DEGs and visualize them through the R program. The significant hub genes were identified through the protein-protein interaction network, Venn diagram analysis, and survival analysis. We observed that the upregulated DEGs were prominently involved in the ECM-receptor interaction pathway. The downregulated genes were mainly associated with the axon guidance pathway. Five significant hub genes (CTNNB1, ITGB1, TNC, EGFR, and SHOX2) were screened out through multiple analyses. GO and KEGG analyses of hub genes uncovered that these genes were primarily enriched in disease-associated pathways such as the inhibition of apoptosis and the DNA damage repair mechanism, activation of the cell cycle, EMT (epithelial-mesenchymal transition), hormone AR (androgen receptor), hormone ER (estrogen receptor), PI3K/AKT (phosphatidylinositol 3-kinase and AKT), RTK (receptor tyrosine kinase), and TSC/mTOR (tuberous sclerosis complex and mammalian target of rapamycin). Consequently, the epigenetic regulatory network disclosed that hub genes played a vital role in the progression of GBM. Finally, candidate drugs were predicted that can be used as possible drugs to treat GBM patients. Overall, our investigation offered five hub genes (CTNNB1, ITGB1, TNC, EGFR, and SHOX2) that could be used as precise diagnostic and prognostic candidate biomarkers of GBM and might be used as personalized therapeutic targets to obstruct gliomagenesis.
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Jiang Y, Li X, Liu J, Zhang W, Zhou M, Wang J, Liu L, Su S, Zhao F, Chen H, Wang C. Genome-wide detection of genetic structure and runs of homozygosity analysis in Anhui indigenous and Western commercial pig breeds using PorcineSNP80k data. BMC Genomics 2022; 23:373. [PMID: 35581549 PMCID: PMC9115978 DOI: 10.1186/s12864-022-08583-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/22/2022] [Indexed: 11/25/2022] Open
Abstract
Background Runs of homozygosity (ROH) are continuous homozygous regions typically located in the DNA sequence of diploid organisms. Identifications of ROH that lead to reduced performance can provide valuable insight into the genetic architecture of complex traits. Here, we systematically investigated the population genetic structure of five Anhui indigenous pig breeds (AHIPs), and compared them to those of five Western commercial pig breeds (WECPs). Furthermore, we examined the occurrence and distribution of ROHs in the five AHIPs and estimated the inbreeding coefficients based on the ROHs (FROH) and homozygosity (FHOM). Finally, we identified genomic regions with high frequencies of ROHs and annotated candidate genes contained therein. Results The WECPs and AHIPs were clearly differentiated into two separate clades consistent with their geographical origins, as revealed by the population structure and principal component analysis. We identified 13,530 ROHs across all individuals, of which 4,555 and 8,975 ROHs were unique to AHIPs and WECPs, respectively. Most ROHs identified in our study were short (< 10 Mb) or medium (10–20 Mb) in length. WECPs had significantly higher numbers of short ROHs, and AHIPs generally had longer ROHs. FROH values were significantly lower in AHIPs than in WECPs, indicating that breed improvement and conservation programmes were successful in AHIPs. On average, FROH and FHOM values were highly correlated (0.952–0.991) in AHIPs and WECPs. A total of 27 regions had a high frequency of ROHs and contained 17 key candidate genes associated with economically important traits in pigs. Among these, nine candidate genes (CCNT2, EGR2, MYL3, CDH13, PROX1, FLVCR1, SETD2, FGF18, and FGF20) found in WECPs were related to muscular and skeletal development, whereas eight candidate genes (CSN1S1, SULT1E1, TJP1, ZNF366, LIPC, MCEE, STAP1, and DUSP) found in AHIPs were associated with health, reproduction, and fatness traits. Conclusion Our findings provide a useful reference for the selection and assortative mating of pig breeds, laying the groundwork for future research on the population genetic structures of AHIPs, ultimately helping protect these local varieties. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08583-9.
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Affiliation(s)
- Yao Jiang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Xiaojin Li
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Jiali Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wei Zhang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Mei Zhou
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Jieru Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Linqing Liu
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Shiguang Su
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Fuping Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hongquan Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Chonglong Wang
- Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
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Usman M, Okla MK, Asif HM, AbdElgayed G, Muccee F, Ghazanfar S, Ahmad M, Iqbal MJ, Sahar AM, Khaliq G, Shoaib R, Zaheer H, Hameed Y. A pan-cancer analysis of GINS complex subunit 4 to identify its potential role as a biomarker in multiple human cancers. Am J Cancer Res 2022; 12:986-1008. [PMID: 35411239 PMCID: PMC8984884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023] Open
Abstract
This study was initiated to explore the expression variation, clinical significance, and biological importance of the GINS complex subunit 4 (GINS4) in different human cancers as a shared biomarker via pan-cancer analysis through different platforms including UALCAN, Kaplan Meier (KM) plotter, TNMplot, GENT2, GEPIA, DriverDBv3, Human Protein Atlas (HPA), MEXPRESS, cBioportal, STRING, DAVID, MuTarge, Enrichr, TIMER, and CTD. Our findings have verified the up-regulation of GINS4 in 24 major subtypes of human cancers, and its overexpression was found to be substantially associated with poor overall survival (OS), relapse-free survival (RFs), and metastasis in ESCA, KIRC, LIHC, LUAD, and UCEC. This suggested that GINS4 plays a significant role in the development and progression of these five cancers. Furthermore, we noticed that GINS4 is also overexpressed in ESCA, KIRC, LIHC, LUAD, and UCEC patients with different clinicopathological characteristics. Enrichment analysis revealed the involvement of GINS4 associated genes in a variety of diverse GO and KEGG terms. We also explored few significant correlations between GINS4 expression and promoter methylation, genetic alterations, CNVs, other mutant genes, tumor purity, and immune cells infiltration. In conclusion, our results elucidated that GINS4 can serve as a shared diagnostic, prognostic biomarker, and a potential therapeutic target in ESCA, KIRC, LIHC, LUAD, and UCEC patients with different clinicopathological characteristics.
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Affiliation(s)
- Muhammad Usman
- Department of Biochemistry and Biotechnology, The Islamia University of BahawalpurBahawalpur 63100, Pakistan, Pakistan
| | - Mohammad K Okla
- Department of Botany and Microbiology, College of Science, King Saud UniversityRiyadh 11451, Saudi Arabia
| | - Hafiz Muhammad Asif
- University College of Conventional Medicine, Faculty of Pharmacy and Alternative Medicine, The Islamia University of BahawalpurBahawalpur 63100, Pakistan
| | - Gehad AbdElgayed
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp2020 Antwerp, Belgium
| | - Fatima Muccee
- Department of Biotechnology, Virtual University of PakistanLahore 54000, Pakistan
| | - Shakira Ghazanfar
- Functional Genomics and Bioinformatics, National Agricultural Research CentreIslamabad 45500, Pakistan
| | - Mukhtiar Ahmad
- Department of Biochemistry and Biotechnology, The Islamia University of BahawalpurBahawalpur 63100, Pakistan, Pakistan
| | | | - Aamina Murad Sahar
- Department of Biosciences, COMSATS University IslamabadIslamabad 4400, Pakistan
| | - Ghania Khaliq
- Department of Zoology, Cholistan University of Veterinary and Animal Sciences BahawalpurBahawalpur 63100, Pakistan
| | - Rabbia Shoaib
- Department of Chemistry, Government College University FaisalabadFaisalabad 3800, Pakistan
| | - Hira Zaheer
- Department of Biochemistry and Biotechnology, The Islamia University of BahawalpurBahawalpur 63100, Pakistan, Pakistan
| | - Yasir Hameed
- Department of Biochemistry and Biotechnology, The Islamia University of BahawalpurBahawalpur 63100, Pakistan, Pakistan
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Hasan I, Hossain A, Bhuiyan P, Miah S, Rahman H. A system biology approach to determine therapeutic targets by identifying molecular mechanisms and key pathways for type 2 diabetes that are linked to the development of tuberculosis and rheumatoid arthritis. Life Sci 2022; 297:120483. [DOI: 10.1016/j.lfs.2022.120483] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 12/17/2022]
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Ding S, Wang X, Lv D, Tao Y, Liu S, Chen C, Huang Z, Zheng S, Wei Y, Kang T, Xia Y. EBF3 reactivation by inhibiting the EGR1/EZH2/HDAC9 complex promotes metastasis via transcriptionally enhancing vimentin in nasopharyngeal carcinoma. Cancer Lett 2021; 527:49-65. [PMID: 34906623 DOI: 10.1016/j.canlet.2021.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/18/2021] [Accepted: 12/08/2021] [Indexed: 01/31/2023]
Abstract
Metastasis is the major reason for treatment failure and accounts for cancer-related death in patients with nasopharyngeal carcinoma. However, the genetic alterations and molecular mechanisms that cause nasopharyngeal carcinoma metastasis are elusive. Herein, we performed RNA sequencing in patients with or without metastasis, and found that the early B-cell factor 3 (EBF3) was significantly elevated in the samples with metastasis. Mechanistically, EBF3 promoted metastasis by directly combining with the promoter of Vimentin and transcriptionally upregulating it. In addition, EBF3 was epigenetically silenced by EGR1/EZH2/HDAC9 complexes via sustaining the high level of H3K27-Me3 at its promoter. Clinically, there was a positive correlation between EBF3 and Vimentin in nasopharyngeal carcinoma tissues. Moreover, high expression of EBF3 or Vimentin was correlated with poor overall survival, while the combination of high EBF3 and Vimentin expression was associated with more significant poor prognosis. Therefore, specific agents targeting EBF3 or stabilizing the EGR1/EZH2/HDAC9 complex could be novel therapeutic strategies for cancer metastasis.
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Affiliation(s)
- Shirong Ding
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China; Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Xin Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China; The Department of Liver Surgery, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Dongming Lv
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yalan Tao
- Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Songran Liu
- Department of Pathology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Chen Chen
- Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Zilu Huang
- Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Shuohan Zheng
- Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Yinghong Wei
- Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Yunfei Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China; Department of Radiation Oncology, Sun Yat-sen University Cancer Centre, Guangzhou, China.
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Lv X, Sun Y, Tan W, Liu Y, Wen N, Fu S, Yu L, Liu T, Qi X, Shu N, Du Y, Zhang W, Meng Y. NONMMUT140591.1 may serve as a ceRNA to regulate Gata5 in UT-B knockout-induced cardiac conduction block. Open Life Sci 2021; 16:1240-1251. [PMID: 34901457 PMCID: PMC8627919 DOI: 10.1515/biol-2021-0106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/22/2021] [Accepted: 07/30/2021] [Indexed: 01/16/2023] Open
Abstract
We intended to explore the potential molecular mechanisms underlying the cardiac conduction block inducted by urea transporter (UT)-B deletion at the transcriptome level. The heart tissues were harvested from UT-B null mice and age-matched wild-type mice for lncRNA sequencing analysis. Based on the sequencing data, the differentially expressed mRNAs (DEMs) and lncRNAs (DELs) between UT-B knockout and control groups were identified, followed by function analysis and mRNA-lncRNA co-expression analysis. The miRNAs were predicted, and then the competing endogenous RNA (ceRNA) network was constructed. UT-B deletion results in the aberrant expression of 588 lncRNAs and 194 mRNAs. These DEMs were significantly enriched in the inflammation-related pathway. A lncRNA-mRNA co-expression network and a ceRNA network were constructed on the basis of the DEMs and DELs. The complement 7 (C7)-NONMMUT137216.1 co-expression pair had the highest correlation coefficient in the co-expression network. NONMMUT140591.1 had the highest degree in the ceRNA network and was involved in the ceRNA of NONMMUT140591.1-mmu-miR-298-5p-Gata5 (GATA binding protein 5). UT-B deletion may promote cardiac conduction block via inflammatory process. The ceRNA NONMMUT140591.1-mmu-miR-298-5p-Gata5 may be a potential molecular mechanism of UT-B knockout-induced cardiac conduction block.
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Affiliation(s)
- Xuejiao Lv
- Department of Respiratory Medicine and Pathophysiology, Jilin University, No. 218, Ziqiang Road, Nanguan District, Changchun, 130041 Jilin, China
| | - Yuxin Sun
- Department of Otolaryngology, Jilin University, Changchun, Jilin, 130021, China
| | - Wenxi Tan
- Department of Respiratory Medicine and Pathophysiology, Jilin University, No. 218, Ziqiang Road, Nanguan District, Changchun, 130041 Jilin, China
| | - Yang Liu
- Department of Respiratory Medicine and Pathophysiology, Jilin University, No. 218, Ziqiang Road, Nanguan District, Changchun, 130041 Jilin, China
| | - Naiyan Wen
- Department of Nursing, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Shuang Fu
- Department of Pathology and Pathophysiology, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Lanying Yu
- Department of Pathology and Pathophysiology, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Tiantian Liu
- Department of Pathology and Pathophysiology, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Xiaocui Qi
- Department of Pathology and Pathophysiology, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Nanqi Shu
- Department of Pathology and Pathophysiology, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Yanwei Du
- Department of Pathology and Pathophysiology, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Wenfeng Zhang
- Department of Prescriptions, Changchun University of Chinese Medicine, Changchun, Jilin, 130117, China
| | - Yan Meng
- Department of Respiratory Medicine and Pathophysiology, Jilin University, No. 218, Ziqiang Road, Nanguan District, Changchun, 130041 Jilin, China
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Jia H, Ma T, Jia S, Ouyang Y. AKT3 and related molecules as potential biomarkers responsible for cryptorchidism and cryptorchidism-induced azoospermia. Transl Pediatr 2021; 10:1805-1817. [PMID: 34430428 PMCID: PMC8349953 DOI: 10.21037/tp-21-31] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/01/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Cryptorchidism is a common congenital malformation strongly related to future oligospermia and male infertility. Normally functioning early-stage spermatogonia are vital to ensure fertility. The present study aimed to identify new differentially expressed genes (DEGs) associated with signaling pathways related to spermatogonial stem cell (SSC) maintenance during early spermatogenesis. METHODS GEO2R was used to screen for genes differentially regulated in cryptorchidism using mRNA expression profiling data in the GEO database. DAVID was used to perform GO and KEGG enrichment analysis of DEGs to analyze their functions. A protein-protein interaction (PPI) network of DEGs was constructed using the STRING database. The hub genes in the PPI networks were identified using Maximal Clique Centrality (MCC) in Cytohubba, and the top 50 genes were displayed as hub genes using Cytoscape software. Then, the miRNAs targeting hub genes were predicted using miRWalk and an mRNA-miRNA interaction network was constructed using Cytoscape. We took the intersection of these target miRNAs and the differentially expressed miRNAs identified from a non-coding RNA sequencing dataset, GSE149084. Furthermore, the intersected miRNAs and their predicted target genes were validated in the testicular tissue of rats with cryptorchidism. RESULTS A total of 474 DEGs were identified, most of which were annotated to the PI3K-AKT-mTOR signaling pathway. Hub genes related to the pathway were predicted to be targeted by 27 miRNAs. Further miRNA mining revealed that miRNA-7-5p and miRNA-519d-3p were both dysregulated in cryptorchidism patients. Further, we found that these two miRNAs were predicted with high confidence to share a common target gene, AKT3. In the testicular tissue of rats with cryptorchidism, miRNA-519d-3p was upregulated while miRNA-7-5p and AKT3 were downregulated. We also found that AKT3 plays an essential role in regulating SSC state through the PI3K-AKT-mTOR signaling pathway and that AKT3 is one of the key genes related to SSC self-renewal, proliferation, and differentiation. CONCLUSIONS The PI3K-AKT-mTOR signaling pathway functions in SSC maintenance, and alterations in this pathway may explain defects in spermatogenesis. AKT3-related miRNAs, including hsa-miR-7-5p and hsa-miR-519d-3p, might be responsible for cryptorchidism and cryptorchidism-induced azoospermia and serve as potential biomarkers.
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Affiliation(s)
- Hongshuai Jia
- Department of Urology, Capital Institute of Pediatrics, Beijing, China.,Department of Urology, Tianjin Children's Hospital, Tianjin, China
| | - Tiantian Ma
- Department of Nephrology, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Shujing Jia
- Central Laboratory, the First Hospital of Handan, Handan, China
| | - Yuru Ouyang
- Department of Urology, Capital Institute of Pediatrics, Beijing, China
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Zhang Y, Lin Z, Lin X, Zhang X, Zhao Q, Sun Y. A gene module identification algorithm and its applications to identify gene modules and key genes of hepatocellular carcinoma. Sci Rep 2021; 11:5517. [PMID: 33750838 PMCID: PMC7943822 DOI: 10.1038/s41598-021-84837-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/18/2021] [Indexed: 12/19/2022] Open
Abstract
To further improve the effect of gene modules identification, combining the Newman algorithm in community detection and K-means algorithm framework, a new method of gene module identification, GCNA-Kpca algorithm, was proposed. The core idea of the algorithm was to build a gene co-expression network (GCN) based on gene expression data firstly; Then the Newman algorithm was used to initially identify gene modules based on the topology of GCN, and the number of clusters and clustering centers were determined; Finally the number of clusters and clustering centers were input into the K-means algorithm framework, and the secondary clustering was performed based on the gene expression profile to obtain the final gene modules. The algorithm took into account the role of modularity in the clustering process, and could find the optimal membership module for each gene through multiple iterations. Experimental results showed that the algorithm proposed in this paper had the best performance in error rate, biological significance and CNN classification indicators (Precision, Recall and F-score). The gene module obtained by GCNA-Kpca was used for the task of key gene identification, and these key genes had the highest prognostic significance. Moreover, GCNA-Kpca algorithm was used to identify 10 key genes in hepatocellular carcinoma (HCC): CDC20, CCNB1, EIF4A3, H2AFX, NOP56, RFC4, NOP58, AURKA, PCNA, and FEN1. According to the validation, it was reasonable to speculate that these 10 key genes could be biomarkers for HCC. And NOP56 and NOP58 are key genes for HCC that we discovered for the first time.
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Affiliation(s)
- Yan Zhang
- College of Environmental Science and Engineering, Dalian Martime University, Linghai Road, Dalian, 116026, Liaoning, China
| | - Zhengkui Lin
- College of Information Science and Technology, Dalian Maritime University, Linghai Road, Dalian, 116026, Liaoning, China
| | - Xiaofeng Lin
- College of Information Science and Technology, Dalian Maritime University, Linghai Road, Dalian, 116026, Liaoning, China
| | - Xue Zhang
- College of Information Science and Technology, Dalian Maritime University, Linghai Road, Dalian, 116026, Liaoning, China
| | - Qian Zhao
- College of Information Science and Technology, Dalian Maritime University, Linghai Road, Dalian, 116026, Liaoning, China.
| | - Yeqing Sun
- College of Environmental Science and Engineering, Dalian Martime University, Linghai Road, Dalian, 116026, Liaoning, China.
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