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Yazar V, Yilmaz IC, Bulbul A, Klinman DM, Gursel I. Gene network landscape of mouse splenocytes reveals integrin complex as the A151 ODN-responsive hub molecule in the immune transcriptome. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:553-565. [PMID: 36895952 PMCID: PMC9989320 DOI: 10.1016/j.omtn.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
Homeostatic restoration of an inflammatory response requires quenching of the immune system after pathogen threats vanish. A continued assault orchestrated by host defense results in tissue destruction or autoimmunity. A151 is the epitome of synthetic oligodeoxynucleotides (ODNs) that curb the immune response by a subset of white corpuscles through repetitive telomere-derived TTAGGG sequences. Currently, the genuine effect of A151 on the immune cell transcriptome remains unknown. Here, we leveraged an integrative approach where weighted gene co-expression network analysis (WGCNA), differential gene expression analysis, and gene set enrichment analysis (GSEA) of our in-house microarray datasets aided our understanding of how A151 ODN suppresses the immune response in mouse splenocytes. Our bioinformatics results, together with experimental validations, indicated that A151 ODN acts on components of integrin complexes, Itgam and Itga6, to interfere with immune cell adhesion and thereby suppresses the immune response in mice. Moreover, independent lines of evidence in this work converged on the observation that cell adhesion by integrin complexes serves as a focal point for cellular response to A151 ODN treatment in immune cells. Taken together, the outcome of this study sheds light on the molecular basis of immune suppression by a clinically useful DNA-based therapeutic agent.
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Affiliation(s)
- Volkan Yazar
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Thorlab, Molecular Biology and Genetics Department, Faculty of Science, Ihsan Dogramaci Bilkent University, 06800 Ankara, Turkey
| | - Ismail Cem Yilmaz
- Thorlab, Molecular Biology and Genetics Department, Faculty of Science, Ihsan Dogramaci Bilkent University, 06800 Ankara, Turkey
- Izmir Biomedicine and Genome Center, Dokuz Eylul University, Balcova, Izmir, Turkey
| | - Artun Bulbul
- Thorlab, Molecular Biology and Genetics Department, Faculty of Science, Ihsan Dogramaci Bilkent University, 06800 Ankara, Turkey
| | - Dennis M. Klinman
- Immune Modulation Section, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Ihsan Gursel
- Thorlab, Molecular Biology and Genetics Department, Faculty of Science, Ihsan Dogramaci Bilkent University, 06800 Ankara, Turkey
- Izmir Biomedicine and Genome Center, Dokuz Eylul University, Balcova, Izmir, Turkey
- Corresponding author: Ihsan Gursel, PhD, Izmir Biomedicine and Genome Center, Dokuz Eylul University, Balcova, Izmir, Turkey.
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Yue H, Yang X, Wu X, Geng X, Ji X, Li G, Sang N. Maternal NO 2 exposure disturbs the long noncoding RNA expression profile in the lungs of offspring in time-series patterns. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 246:114140. [PMID: 36209526 DOI: 10.1016/j.ecoenv.2022.114140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/07/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Gestation is a sensitive window to nitrogen dioxide (NO2) exposure, which may disturb fetal lung development and lung function later in life. Animal and epidemiological studies indicated that long noncoding RNAs (lncRNAs) participate in abnormal lung development induced by environmental pollutant exposure. In the present study, pregnant C57BL/6J mice were exposed to 2.5 ppm NO2 (mimicking indoor occupational exposure) or clean air, and lncRNAs expression profiles in the lungs of offspring mice were determined by lncRNA-seq on embryonic day 13.5 (E13.5), E18.5, postnatal day 1 (P1), and P14. The lung histopathology examination of offspring was performed, followed by weighted gene coexpression network analysis (WGCNA), prediction of lncRNAs-target genes, and the biological processes enrichment analysis of lncRNAs. Our results indicated that maternal NO2 exposure induced hypoalveolarization on P14 and differentially expressed lncRNAs showed a time-series pattern. Following WGCNA and enrichment analysis, 2 modules participated in development-related pathways. Importantly, the expressions of related genes were altered, some of which were confirmed to be related to abnormal vascular development and even lung diseases. The research points out that the maternal NO2 exposure leads to abnormal lung development in offspring that might be related to altered lncRNAs expression profiles with time-series-pattern.
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Affiliation(s)
- Huifeng Yue
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China.
| | - Xiaowen Yang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China.
| | - Xiaoyun Wu
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China.
| | - Xilin Geng
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China.
| | - Xiaotong Ji
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi 030001, PR China.
| | - Guangke Li
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China.
| | - Nan Sang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China.
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Zhu Y, Li Z, Zhang J, Liu M, Jiang X, Li B. Identification of crucial lncRNAs and mRNAs in liver regeneration after portal vein ligation through weighted gene correlation network analysis. BMC Genomics 2022; 23:665. [PMID: 36131263 PMCID: PMC9490934 DOI: 10.1186/s12864-022-08891-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Portal vein ligation (PVL)-induced liver hypertrophy increases future liver remnant (FLR) volume and improves resectability of large hepatic carcinoma. However, the molecular mechanism by which PVL facilitates liver hypertrophy remains poorly understood. METHODS To gain mechanistic insight, we established a rat PVL model and carried out a comprehensive transcriptome analyses of hepatic lobes preserving portal blood supply at 0, 1, 7, and 14-day after PVL. The differentially expressed (DE) long-non coding RNAs (lncRNAs) and mRNAs were applied to conduct weighted gene co-expression network analysis (WGCNA). LncRNA-mRNA co-expression network was constructed in the most significant module. The modules and genes associated with PVL-induced liver hypertrophy were assessed through quantitative real-time PCR. RESULTS A total of 4213 DElncRNAs and 6809 DEmRNAs probesets, identified by transcriptome analyses, were used to carry out WGCNA, by which 10 modules were generated. The largest and most significant module (marked in black_M6) was selected for further analysis. Gene Ontology (GO) analysis of the module exhibited several key biological processes associated with liver regeneration such as complement activation, IL-6 production, Wnt signaling pathway, autophagy, etc. Sixteen mRNAs (Notch1, Grb2, IL-4, Cops4, Stxbp1, Khdrbs2, Hdac2, Gnb3, Gng10, Tlr2, Sod1, Gosr2, Rbbp5, Map3k3, Golga2, and Rev3l) and ten lncRNAs (BC092620, AB190508, EF076772, BC088302, BC158675, BC100646, BC089934, L20987, BC091187, and M23890) were identified as hub genes in accordance with gene significance value, module membership value, protein-protein interaction (PPI) and lncRNA-mRNA co-expression network. Furthermore, the overexpression of 3 mRNAs (Notch1, Grb2 and IL-4) and 4 lncRNAs (BC089934, EF076772, BC092620, and BC088302) was validated in hypertrophic liver lobe tissues from PVL rats and patients undergoing hepatectomy after portal vein embolization (PVE). CONCLUSIONS Microarray and WGCNA analysis revealed that the 3 mRNAs (Notch1, Grb2 and IL-4) and the 4 lncRNAs (BC089934, EF076772, BC092620 and BC088302) may be promising targets for accelerating liver regeneration before extensive hepatectomy.
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Affiliation(s)
- Yan Zhu
- Department of Pathology, Changhai Hospital, Secondary Military Medicine University, Shanghai, 200433, China
| | - Zhishuai Li
- Biliary Tract Surgery Department I, Eastern Hepatobiliary Surgery Hospital, Secondary Military Medicine University, 225 Changhai Road, Yangpu, Shanghai, 200438, People's Republic of China
| | - Jixiang Zhang
- Biliary Tract Surgery Department I, Eastern Hepatobiliary Surgery Hospital, Secondary Military Medicine University, 225 Changhai Road, Yangpu, Shanghai, 200438, People's Republic of China
| | - Mingqi Liu
- Biliary Tract Surgery Department I, Eastern Hepatobiliary Surgery Hospital, Secondary Military Medicine University, 225 Changhai Road, Yangpu, Shanghai, 200438, People's Republic of China
| | - Xiaoqing Jiang
- Biliary Tract Surgery Department I, Eastern Hepatobiliary Surgery Hospital, Secondary Military Medicine University, 225 Changhai Road, Yangpu, Shanghai, 200438, People's Republic of China.
| | - Bin Li
- Biliary Tract Surgery Department I, Eastern Hepatobiliary Surgery Hospital, Secondary Military Medicine University, 225 Changhai Road, Yangpu, Shanghai, 200438, People's Republic of China.
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Huang C, He J, Dong Y, Huang L, Chen Y, Peng A, Huang H. Identification of Novel Prognostic Markers Associated With Laryngeal Squamous Cell Carcinoma Using Comprehensive Analysis. Front Oncol 2022; 11:779153. [PMID: 35087752 PMCID: PMC8787159 DOI: 10.3389/fonc.2021.779153] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/13/2021] [Indexed: 01/02/2023] Open
Abstract
Background Laryngeal squamous cell carcinoma (LSCC) is a leading malignant cancer of the head and neck. Patients with LSCC, in which the cancer has infiltrated and metastasized, have a poor prognosis. Therefore, there is an urgent need to identify more potential targets for drugs and biomarkers for early diagnosis. Methods RNA sequence data from LSCC and patients’ clinical traits were obtained from the Gene Expression Omnibus (GEO) (GSE142083) and The Cancer Genome Atlas (TCGA) database. Differentially expressed gene (DEG) analysis and weighted gene co-expression network analysis (WGCNA) were performed to identify hub genes. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, prognostic value analysis, receiver operating characteristic (ROC) curve analysis, gene mutation analysis, tumor-infiltrating immune cell abundance profile estimation, gene set variation analysis (GSVA), and gene set enrichment analysis (GSEA) were performed. Single-gene RNA sequencing data were obtained from the GSE150321 dataset. Cell proliferation and viability were confirmed by the CCK-8 assay and real-time PCR. Results A total of 701 DEGs, including 329 upregulated and 372 downregulated genes, were screened in the GSE142083 dataset. Using WGCNA, three modules were identified to be closely related to LSCC. After intersecting the DEGs and performing univariate and multivariate Cox analyses, a novel prognostic model based on three genes (SLC35C1, HOXB7, and TEDC2) for LSCC was established. Interfering TEDC2 expression inhibited tumor cell proliferation and migration. Conclusions Our results show that SLC35C1, HOXB7, and TEDC2 have the potential to become new therapeutic targets and prognostic biomarkers for LSCC.
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Affiliation(s)
- Chao Huang
- Department of Otolaryngology-Head and Neck Surgery, Second Xiangya Hospital Central South University, Changsha, China
| | - Jun He
- Department of Otolaryngology-Head and Neck Surgery, Second Xiangya Hospital Central South University, Changsha, China
| | - Yi Dong
- Department of Nephrology, Xiangya Hospital Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China
| | - Li Huang
- Department of Otolaryngology-Head and Neck Surgery, Second Xiangya Hospital Central South University, Changsha, China
| | - Yichao Chen
- Department of Otolaryngology-Head and Neck Surgery, Second Xiangya Hospital Central South University, Changsha, China
| | - Anquan Peng
- Department of Otolaryngology-Head and Neck Surgery, Second Xiangya Hospital Central South University, Changsha, China
| | - Hao Huang
- Department of Nephrology, Xiangya Hospital Central South University, Changsha, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Organ Fibrosis, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital Central South University, Changsha, China
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Zhang L, Yu H, Deng T, Ling L, Wen J, Lv M, Ou R, Wang Q, Xu Y. FNDC3B and BPGM Are Involved in Human Papillomavirus-Mediated Carcinogenesis of Cervical Cancer. Front Oncol 2021; 11:783868. [PMID: 34976823 PMCID: PMC8716600 DOI: 10.3389/fonc.2021.783868] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/17/2021] [Indexed: 12/11/2022] Open
Abstract
Human papillomavirus (HPV)-mediated cervical carcinogenesis is a multistep progressing from persistent infection, precancerous lesion to cervical cancer (CCa). Although molecular alterations driven by viral oncoproteins are necessary in cervical carcinogenesis, the key regulators behind the multistep process remain not well understood. It is pivotal to identify the key genes involved in the process for early diagnosis and treatment of this disease. Here we analyzed the mRNA expression profiles in cervical samples including normal, cervical intraepithelial neoplasia (CIN), and CCa. A co-expression network was constructed using weighted gene co-expression network analysis (WGCNA) to reveal the crucial modules in the dynamic process from HPV infection to CCa development. Furthermore, the differentially expressed genes (DEGs) that could distinguish all stages of progression of CCa were screened. The key genes involved in HPV-CCa were identified. It was found that the genes involved in DNA replication/repair and cell cycle were upregulated in CIN compared with normal control, and sustained in CCa, accompanied by substantial metabolic shifts. We found that upregulated fibronectin type III domain-containing 3B (FNDC3B) and downregulated bisphosphoglycerate mutase (BPGM) could differentiate all stages of CCa progression. In patients with CCa, a higher expression of FNDC3B or lower expression of BPGM was closely correlated with a shorter overall survival (OS) and disease-free survival (DFS). A receiver operating characteristic (ROC) analysis of CIN and CCa showed that FNDC3B had the highest sensitivity and specificity for predicting CCa development. Taken together, the current data showed that FNDC3B and BPGM were key genes involved in HPV-mediated transformation from normal epithelium to precancerous lesions and CCa.
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Affiliation(s)
- Luhan Zhang
- School of Basic Medicine, Southwest Medical University, Luzhou, China
- Department of Dermatovenerology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Hong Yu
- School of Basic Medicine, Southwest Medical University, Luzhou, China
| | - Tian Deng
- Department of Stomatology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Li Ling
- Department of Stomatology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Juan Wen
- Department of Dermatovenerology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Mingfen Lv
- Department of Dermatovenerology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Rongying Ou
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, China
| | - Qiaozhi Wang
- School of Basic Medicine, Southwest Medical University, Luzhou, China
- *Correspondence: Qiaozhi Wang, ; Yunsheng Xu,
| | - Yunsheng Xu
- Department of Dermatovenerology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- *Correspondence: Qiaozhi Wang, ; Yunsheng Xu,
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Hernandez-Toledano D, Vega L. The cytoskeleton as a non-cholinergic target of organophosphate compounds. Chem Biol Interact 2021; 346:109578. [PMID: 34265256 DOI: 10.1016/j.cbi.2021.109578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/19/2021] [Accepted: 07/12/2021] [Indexed: 12/29/2022]
Abstract
Current organophosphate (OP) toxicity research now considers potential non-cholinergic mechanisms for these compounds, since the inhibition of acetylcholinesterase (AChE) cannot completely explain all the adverse biological effects of OP. Thanks to the development of new strategies for OP detection, some potential molecular targets have been identified. Among these molecules are several cytoskeletal proteins, including actin, tubulin, intermediate filament proteins, and associated proteins, such as motor proteins, microtubule-associated proteins (MAPs), and cofilin. in vitro, ex vivo, and some in vivo reports have identified alterations in the cytoskeleton following OP exposure, including cell morphology defects, cells detachments, intracellular transport disruption, aberrant mitotic spindle formation, modification of cell motility, and reduced phagocytic capability, which implicate the cytoskeleton in OP toxicity. Here, we reviewed the evidence indicating the cytoskeletal targets of OP compounds, including their strategies, the potential effects of their alterations, and their possible participation in neurotoxicity, embryonic development, cell division, and immunotoxicity related to OP compounds exposure.
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Affiliation(s)
- David Hernandez-Toledano
- Department of Toxicology, Center for Research and Advanced Studies of the National Polytechnic Institute. Av. IPN 2508, San Pedro Zacatenco, C.P. 07360, Mexico City, Mexico
| | - Libia Vega
- Department of Toxicology, Center for Research and Advanced Studies of the National Polytechnic Institute. Av. IPN 2508, San Pedro Zacatenco, C.P. 07360, Mexico City, Mexico.
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