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Aljabban J, Rohr M, Syed S, Cohen E, Hashi N, Syed S, Khorfan K, Aljabban H, Borkowski V, Segal M, Mukhtar M, Mohammed M, Boateng E, Nemer M, Panahiazar M, Hadley D, Jalil S, Mumtaz K. Dissecting novel mechanisms of hepatitis B virus related hepatocellular carcinoma using meta-analysis of public data. World J Gastrointest Oncol 2022; 14:1856-1873. [PMID: 36187396 PMCID: PMC9516659 DOI: 10.4251/wjgo.v14.i9.1856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/26/2022] [Accepted: 08/07/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) is a cause of hepatocellular carcinoma (HCC). Interestingly, this process is not necessarily mediated through cirrhosis and may in fact involve oncogenic processes. Prior studies have suggested specific oncogenic gene expression pathways were affected by viral regulatory proteins. Thus, identifying these genes and associated pathways could highlight predictive factors for HCC transformation and has implications in early diagnosis and treatment.
AIM To elucidate HBV oncogenesis in HCC and identify potential therapeutic targets.
METHODS We employed our Search, Tag, Analyze, Resource platform to conduct a meta-analysis of public data from National Center for Biotechnology Information’s Gene Expression Omnibus. We performed meta-analysis consisting of 155 tumor samples compared against 185 adjacent non-tumor samples and analyzed results with ingenuity pathway analysis.
RESULTS Our analysis revealed liver X receptors/retinoid X receptor (RXR) activation and farnesoid X receptor/RXR activation as top canonical pathways amongst others. Top upstream regulators identified included the Ras family gene rab-like protein 6 (RABL6). The role of RABL6 in oncogenesis is beginning to unfold but its specific role in HBV-related HCC remains undefined. Our causal analysis suggests RABL6 mediates pathogenesis of HBV-related HCC through promotion of genes related to cell division, epigenetic regulation, and Akt signaling. We conducted survival analysis that demonstrated increased mortality with higher RABL6 expression. Additionally, homeobox A10 (HOXA10) was a top upstream regulator and was strongly upregulated in our analysis. HOXA10 has recently been demonstrated to contribute to HCC pathogenesis in vitro. Our causal analysis suggests an in vivo role through downregulation of tumor suppressors and other mechanisms.
CONCLUSION This meta-analysis describes possible roles of RABL6 and HOXA10 in the pathogenesis of HBV-related HCC. RABL6 and HOXA10 represent potential therapeutic targets and warrant further investigation.
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Affiliation(s)
- Jihad Aljabban
- Department of Medicine, University of Wisconsin Hospital and Clinics, Madison, WI 53792, United States
| | - Michael Rohr
- Department of Medicine, University of Central Florida College of Medicine, Orlando, FL 32827, United States
| | - Saad Syed
- Department of Medicine, Northwestern Memorial Hospital, Chicago, IL 60611, United States
| | - Eli Cohen
- Department of Medicine, Vanderbilt Medical Center, Nashville, TN 37232, United States
| | - Naima Hashi
- Department of Medicine, Mayo Clinic, Rochester, MN 55905, United States
| | - Sharjeel Syed
- Department of Medicine, University of Chicago Hospitals, Chicago, IL 60637, United States
| | - Kamal Khorfan
- Department of Gastroenterology and Hepatology, University of California San Francisco-Fresno, Fresno, CA 93701, United States
| | - Hisham Aljabban
- Department of Medicine, Barry University, Miami, FL 33161, United States
| | - Vincent Borkowski
- Department of Medicine, University of Wisconsin Hospital and Clinics, Madison, WI 53792, United States
| | - Michael Segal
- Department of Medicine, University of Wisconsin Hospital and Clinics, Madison, WI 53792, United States
| | - Mohamed Mukhtar
- Department of Medicine, Michigan State University College of Human Medicine, Lansing, MI 49503, United States
| | - Mohammed Mohammed
- Department of Medicine, Windsor University School of Medicine, Frankfort, IL 60423, United States
| | - Emmanuel Boateng
- Department of Medicine, Vanderbilt Medical Center, Nashville, TN 37232, United States
| | - Mary Nemer
- Department of Medicine, University of Wisconsin Hospital and Clinics, Madison, WI 53792, United States
| | - Maryam Panahiazar
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, United States
| | - Dexter Hadley
- Department of Pathology, University of Central Florida College of Medicine, Orlando, FL 32827, United States
| | - Sajid Jalil
- Department of Gastroenterology and Hepatology, Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
| | - Khalid Mumtaz
- Department of Gastroenterology and Hepatology, Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
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Chen XX, Zhang BH, Lu YC, Li ZQ, Chen CY, Yang YC, Chen YJ, Ma D. A novel 16-gene alternative mRNA splicing signature predicts tumor relapse and indicates immune activity in stage I–III hepatocellular carcinoma. Front Pharmacol 2022; 13:939912. [PMID: 36147313 PMCID: PMC9485890 DOI: 10.3389/fphar.2022.939912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a lethal disease with high relapse and dismal survival rates. Alternative splicing (AS) plays a crucial role in tumor progression. Herein, we aim to integratedly analyze the relapse-associated AS events and construct a signature predicting tumor relapse in stage I–III HCC. Methods: AS events of stage I–III HCC with tumor relapse or long-term relapse-free survival were profiled to identify the relapse-associated AS events. A splicing network was set up to analyze the correlation between the relapse-associated AS events and splicing factors. Cox regression analysis and receiver operating characteristic curve were performed to develop and validate the relapse-predictive AS signature. Single-sample gene set enrichment analysis (ssGSEA) and the ESTIMATE algorithm were used to assess the immune infiltration status of the HCC microenvironment between different risk subgroups. Unsupervised cluster analysis was conducted to assess the relationship between molecular subtypes and local immune status and clinicopathological features. Results: In total, 2441 ASs derived from 1634 mRNA were identified as relapse-associated AS events. By analyzing the proteins involved in the relapse-associated AS events, 1573 proteins with 11590 interactions were included in the protein–protein interaction (PPI) network. In total, 16 splicing factors and 61 relapse-associated AS events with 85 interactions were involved in the splicing network. The relevant genes involved in the PPI network and splicing network were also analyzed by Gene Ontology enrichment analysis. Finally, we established a robust 16-gene AS signature for predicting tumor relapse in stage I–III HCC with considerable AUC values in all of the training cohort, testing cohort, and entire cohort. The ssGSEA and ESTIMATE analyses showed that the AS signature was significantly associated with the immune status of the HCC microenvironment. Moreover, four molecular subgroups with distinguishing tumor relapse modes and local immune status were also revealed. Conclusion: Our study built a novel 16-gene AS signature that robustly predicts tumor relapse and indicates immune activity in stage I–III HCC, which may facilitate the deep mining of the mechanisms associated with tumor relapse and tumor immunity and the development of novel individualized treatment targets for HCC.
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Affiliation(s)
- Xu-Xiao Chen
- Department of General Surgery, Hepatobiliary Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Xu-Xiao Chen, ; Yong-Jun Chen, ; Di Ma,
| | - Bao-Hua Zhang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Yan-Cen Lu
- Department of General Surgery, Hepatobiliary Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zi-Qiang Li
- Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cong-Yan Chen
- Department of General Surgery, Hepatobiliary Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu-Chen Yang
- Department of General Surgery, Hepatobiliary Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yong-Jun Chen
- Department of General Surgery, Hepatobiliary Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Xu-Xiao Chen, ; Yong-Jun Chen, ; Di Ma,
| | - Di Ma
- Department of General Surgery, Hepatobiliary Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Xu-Xiao Chen, ; Yong-Jun Chen, ; Di Ma,
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Dolicka D, Zahoran S, Correia de Sousa M, Gjorgjieva M, Sempoux C, Fournier M, Maeder C, Collart MA, Foti M, Sobolewski C. TIA1 Loss Exacerbates Fatty Liver Disease but Exerts a Dual Role in Hepatocarcinogenesis. Cancers (Basel) 2022; 14:cancers14071704. [PMID: 35406476 PMCID: PMC8997004 DOI: 10.3390/cancers14071704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 11/16/2022] Open
Abstract
Alterations in specific RNA-binding protein expression/activity importantly contribute to the development of fatty liver disease (FLD) and hepatocellular carcinoma (HCC). In particular, adenylate–uridylate-rich element binding proteins (AUBPs) were reported to control the post-transcriptional regulation of genes involved in both metabolic and cancerous processes. Herein, we investigated the pathophysiological functions of the AUBP, T-cell-restricted intracellular antigen-1 (TIA1) in the development of FLD and HCC. Analysis of TIA1 expression in mouse and human models of FLD and HCC indicated that TIA1 is downregulated in human HCC. In vivo silencing of TIA1 using AAV8-delivered shRNAs in mice worsens hepatic steatosis and fibrosis induced by a methionine and choline-deficient diet and increases the hepatic tumor burden in liver-specific PTEN knockout (LPTENKO) mice. In contrast, our in vitro data indicated that TIA1 expression promoted proliferation and migration in HCC cell lines, thus suggesting a dual and context-dependent role for TIA1 in tumor initiation versus progression. Consistent with a dual function of TIA1 in tumorigenesis, translatome analysis revealed that TIA1 appears to control the expression of both pro- and anti-tumorigenic factors in hepatic cancer cells. This duality of TIA1′s function in hepatocarcinogenesis calls for cautiousness when considering TIA1 as a therapeutic target or biomarker in HCC.
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Affiliation(s)
- Dobrochna Dolicka
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Szabolcs Zahoran
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (S.Z.); (M.A.C.)
| | - Marta Correia de Sousa
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Monika Gjorgjieva
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Christine Sempoux
- Service of Clinical Pathology, Institute of Pathology, Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland;
| | - Margot Fournier
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Christine Maeder
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Martine A. Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (S.Z.); (M.A.C.)
| | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Cyril Sobolewski
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
- Correspondence: or
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The Multifunctional Faces of T-Cell Intracellular Antigen 1 in Health and Disease. Int J Mol Sci 2022; 23:ijms23031400. [PMID: 35163320 PMCID: PMC8836218 DOI: 10.3390/ijms23031400] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/22/2022] [Indexed: 02/06/2023] Open
Abstract
T-cell intracellular antigen 1 (TIA1) is an RNA-binding protein that is expressed in many tissues and in the vast majority of species, although it was first discovered as a component of human cytotoxic T lymphocytes. TIA1 has a dual localization in the nucleus and cytoplasm, where it plays an important role as a regulator of gene-expression flux. As a multifunctional master modulator, TIA1 controls biological processes relevant to the physiological functioning of the organism and the development and/or progression of several human pathologies. This review summarizes our current knowledge of the molecular aspects and cellular processes involving TIA1, with relevance for human pathophysiology.
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Bayat Z, Ahmadi-Motamayel F, Parsa MS, Taherkhani A. Potential biomarkers and signaling pathways associated with the pathogenesis of primary salivary gland carcinoma: a bioinformatics study. Genomics Inform 2022; 19:e42. [PMID: 35012286 PMCID: PMC8752977 DOI: 10.5808/gi.21052] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/08/2021] [Indexed: 01/21/2023] Open
Abstract
Salivary gland carcinoma (SGC) is rare cancer, constituting 6% of neoplasms in the head and neck area. The most responsible genes and pathways involved in the pathology of this disorder have not been fully understood. We aimed to identify differentially expressed genes (DEGs), the most critical hub genes, transcription factors, signaling pathways, and biological processes (BPs) associated with the pathogenesis of primary SGC. The mRNA dataset GSE153283 in the Gene Expression Omnibus database was re-analyzed for determining DEGs in cancer tissue of patients with primary SGC compared to the adjacent normal tissue (adjusted p-value < 0.001; |Log2 fold change| > 1). A protein interaction map (PIM) was built, and the main modules within the network were identified and focused on the different pathways and BP analyses. The hub genes of PIM were discovered, and their associated gene regulatory network was built to determine the master regulators involved in the pathogenesis of primary SGC. A total of 137 genes were found to be differentially expressed in primary SGC. The most significant pathways and BPs that were deregulated in the primary disease condition were associated with the cell cycle and fibroblast proliferation procedures. TP53, EGF, FN1, NOTCH1, EZH2, COL1A1, SPP1, CDKN2A, WNT5A, PDGFRB, CCNB1, and H2AFX were demonstrated to be the most critical genes linked with the primary SGC. SPIB, FOXM1, and POLR2A significantly regulate all the hub genes. This study illustrated several hub genes and their master regulators that might be appropriate targets for the therapeutic aims of primary SGC.
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Affiliation(s)
- Zeynab Bayat
- Department of Oral and Maxillofacial Medicine, Faculty of Dentistry, Hamadan University of Medical Sciences, Hamadan 6517838678, Iran
| | - Fatemeh Ahmadi-Motamayel
- Dental Implants Research Center and Dental Research Center, Department of Oral Medicine, Hamadan University of Medical Sciences, Hamadan 6517838678, Iran
| | - Mohadeseh Salimi Parsa
- Department of Oral and Maxillofacial Medicine, Faculty of Dentistry, Hamadan University of Medical Sciences, Hamadan 6517838678, Iran
| | - Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan 6517838678, Iran
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Saidijam M, Afshar S, Taherkhani A. Identifying Potential Biomarkers in Colorectal Cancer and Developing Non-invasive Diagnostic Models Using Bioinformatics Approaches. AVICENNA JOURNAL OF MEDICAL BIOCHEMISTRY 2020. [DOI: 10.34172/ajmb.2020.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Background: Colorectal cancer (CRC) is one of the most frequent causes of gastrointestinal tumors. Due to the invasiveness of the current diagnostic methods, there is an urgent need to develop non-invasive diagnostic approaches for CRC. The exact mechanisms and the most important genes associated with the development of CRC are not fully demonstrated. Objectives: This study aimed to identify differentially expressed miRNAs (DEMs), key genes, and their regulators associated with the pathogenesis of CRC. The signaling pathways and biological processes (BPs) that were significantly affected in CRC were also indicated. Moreover, two non-invasive models were constructed for CRC diagnosis. Methods: The miRNA dataset GSE59856 was downloaded from the Gene Expression Omnibus (GEO) database and analyzed to identify DEMs in CRC patients compared with healthy controls (HCs). A protein-protein interaction (PPI) network was built and analyzed. Significant clusters in the PPI networks were identified, and the BPs and pathways associated with these clusters were studied. The hub genes in the PPI network, as well as their regulators were identified. Results: A total of 569 DEMs were demonstrated with the criteria of P value <0.001. A total of 110 essential genes and 30 modules were identified in the PPI network. Functional analysis revealed that 1005 BPs, 9 molecular functions (MFs), 14 cellular components (CCs), and 887 pathways were significantly affected in CRC. A total of 22 transcription factors (TFs) were demonstrated as the regulators of the hubs. Conclusion: Our results may provide new insight into the pathogenesis of CRC and advance the diagnostic and therapeutic methods of the disease. However, confirmation is required in the future.
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Affiliation(s)
- Massoud Saidijam
- Department of Molecular Medicine and Genetics, Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Saeid Afshar
- Department of Molecular Medicine and Genetics, Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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