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Shi W, Yao X, Cao X, Fu Y, Wang Y. Serine/Arginine-Rich Splicing Factor 7 Knockdown Inhibits Aerobic Glycolysis and Growth in HepG2 Cells by Regulating PKM2 Expression. Curr Issues Mol Biol 2024; 46:5023-5036. [PMID: 38785569 PMCID: PMC11119032 DOI: 10.3390/cimb46050301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024] Open
Abstract
Serine/arginine-rich splicing factors (SRSFs), part of the serine/arginine-rich (SR) protein family, play a crucial role in precursor RNA splicing. Abnormal expression of SRSFs in tumors can disrupt normal RNA splicing, contributing to tumor progression. Notably, SRSF7 has been found to be upregulated in hepatocellular carcinoma (HCC), yet its specific role and molecular mechanisms in HCC pathogenesis are not fully understood. We investigated the expression and prognostic significance of SRSF7 in HCC using bioinformatics database analysis. In HepG2 cells, the expressions of SRSF7 and glycolytic enzymes were analyzed using qRT-PCR, and Western blot. Glucose uptake and lactate production were quantified using relevant reagent kits. Additionally, cell proliferation, clonogenicity, invasion, and apoptosis were evaluated using MTS assay, clonal formation assay, Transwell assay, and mitochondrial membrane potential assay, respectively. This study demonstrated significant overexpression of SRSF7 in HCC tissue, correlating with poor prognosis. Knockdown of SRSF7 in HepG2 cells resulted in inhibited proliferation, clonogenicity, and invasion, while apoptosis was enhanced. This knockdown also decreased glucose uptake and lactate production, along with a reduction in the expression of glucose transporter 1 (GLUT1) and lactate dehydrogenase A (LDHA). Furthermore, SRSF7 downregulation increased the pyruvate kinase muscle 1 (PKM1)/PKM2 ratio. The glycolytic boost due to PKM2 overexpression partially counteracted the effects of SRSF7 silencing on HepG2 cell growth. The knockdown of SRSF7 impairs aerobic glycolysis and growth in HepG2 cells by downregulating PKM2 expression.
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Affiliation(s)
- Weiye Shi
- College of Food Science and Biology, Hebei University of Science and Technology, Shijiazhuang 050018, China; (X.Y.); (X.C.); (Y.F.)
| | | | | | | | - Yingze Wang
- College of Food Science and Biology, Hebei University of Science and Technology, Shijiazhuang 050018, China; (X.Y.); (X.C.); (Y.F.)
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Mattiolo P, Gkountakos A, Centonze G, Bevere M, Piccoli P, Ammendola S, Pedrazzani C, Landoni L, Cingarlini S, Milella M, Milione M, Luchini C, Scarpa A, Simbolo M. Transcriptome analysis of primary sporadic neuroendocrine tumours of the intestine identified three different molecular subgroups. Pathol Res Pract 2023; 248:154674. [PMID: 37454491 DOI: 10.1016/j.prp.2023.154674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Intestinal neuroendocrine tumours (I-NETs) represent a non-negligible entity among intestinal neoplasms, with metastatic spreading usually present at the time of diagnosis. In this context, effective molecular actionable targets are still lacking. Through transcriptome analysis, we aim at refining the molecular taxonomy of I-NETs, also providing insights towards the identification of new therapeutic vulnerabilities. MATERIALS AND METHODS A retrospective series of 38 primary sporadic, surgically-resected I-NETs were assessed for transcriptome profiling of 20,815 genes. RESULTS Transcriptome analysis detected 643 highly expressed genes. Unsupervised hierarchical clustering, differential expression analysis and gene set enriched analysis identified three different tumour clusters (CL): CL-A, CL-B, CL-C. CL-A showed the overexpression of ARGFX, BIRC8, NANOS2, and SSTR4 genes. Its most characterizing signatures were those related to cell-junctions, and activation of mTOR and WNT pathway. CL-A was also enriched in T CD8 + lymphocytes. CL-B showed the overexpression of PCSK1, QPCT, ST18, and TPH1 genes. Its most characterizing signatures were those related to adipogenesis, neuroendocrine metabolism, and splice site machinery-related processes. CL-B was also enriched in T CD4 + lymphocytes. CL-C showed the overexpression of ALB, ANG, ARG1, and HP genes. Its most characterizing signatures were complement/coagulation and xenobiotic metabolism. CL-C was also enriched in M1/2 macrophages. These CL-based differences may have therapeutic implications in refining the management of I-NET patients. At last, we described a specific gene-set for differentiating I-NET from pancreatic NET. DISCUSSION Our data represent an additional step for refining the molecular taxonomy of I-NET, identifying novel transcriptome subgroups with different biology and therapeutic opportunities.
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Affiliation(s)
- Paola Mattiolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Anastasios Gkountakos
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Giovanni Centonze
- Pathology Unit 1, Pathology and Laboratory Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Michele Bevere
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Paola Piccoli
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Serena Ammendola
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Corrado Pedrazzani
- Division of General and Hepatobiliary Surgery, Department of Surgical Sciences, Dentistry, Gynecology, and Pediatrics, University and Hospital Trust of Verona, Verona, Italy
| | - Luca Landoni
- General and Pancreatic Surgery Department, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Sara Cingarlini
- Department of Medicine, Section of Medical Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Michele Milella
- Department of Medicine, Section of Medical Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Massimo Milione
- Pathology Unit 1, Pathology and Laboratory Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy; ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy; ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Michele Simbolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy.
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Abstract
Alternative splicing (AS) of mRNAs is an essential regulatory mechanism in eukaryotic gene expression. AS misregulation, caused by either dysregulation or mutation of splicing factors, has been shown to be involved in cancer development and progression, making splicing factors suitable targets for cancer therapy. In recent years, various types of pharmacological modulators, such as small molecules and oligonucleotides, targeting distinct components of the splicing machinery, have been under development to treat multiple disorders. Although these approaches have promise, targeting the core spliceosome components disrupts the early stages of spliceosome assembly and can lead to nonspecific and toxic effects. New research directions have been focused on targeting specific splicing factors for a more precise effect. In this Perspective, we will highlight several approaches for targeting splicing factors and their functions and suggest ways to improve their specificity.
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Affiliation(s)
- Ariel Bashari
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
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De Silva NIU, Fargason T, Zhang Z, Wang T, Zhang J. Inter-domain Flexibility of Human Ser/Arg-Rich Splicing Factor 1 Allows Variable Spacer Length in Cognate RNA’s Bipartite Motifs. Biochemistry 2022; 61:2922-2932. [DOI: 10.1021/acs.biochem.2c00565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Naiduwadura Ivon Upekala De Silva
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, Alabama35294-1240, United States
| | - Talia Fargason
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, Alabama35294-1240, United States
| | - Zihan Zhang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, Alabama35294-1240, United States
| | - Ting Wang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, Alabama35294-1240, United States
| | - Jun Zhang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, Alabama35294-1240, United States
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Yu S, Zhang J, Ding Y, Kang X, Pu X. Genome-wide identification of alternative splicing associated with histone deacetylase inhibitor in cutaneous T-cell lymphomas. Front Genet 2022; 13:937623. [PMID: 36147491 PMCID: PMC9485882 DOI: 10.3389/fgene.2022.937623] [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: 05/06/2022] [Accepted: 08/19/2022] [Indexed: 11/18/2022] Open
Abstract
Cutaneous T-cell lymphomas (CTCLs) are a kind of non-Hodgkin lymphoma that originates from skin, which is difficult to treat with traditional drugs. Human histone deacetylase inhibitors (HDACi) targeted therapy has become a promising treatment strategy in recent years, but some patients can develop resistance to the drug, leading to treatment failure. There are no public reports on whether alternative splicing (AS) and RNA binding proteins (RBP) affect the efficacy of targeted therapy. Using data from the Gene Expression Omnibus (GEO) database, we established a co-change network of AS events and RBP in CTCLs for the first time, and analyzed the potential regulatory effects of RBP on HDACi-related AS events. The dataset GSE132053, which contained the RNA sequence data for 17 HDACi samples, was downloaded and clean reads were aligned to the human GRCh38 genome by hierarchical indexing for spliced alignment of the transcripts, allowing four mismatches. Gene expression levels were evaluated using exons per million fragments mapped for each gene. Student’s t-tests were performed to evaluate the significance of changes in ratios for AS events, and regulated alternative splicing events (RASEs) were defined as events with p values less than 0.05. To sort the differentially expressed genes functional categories, Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways were identified using the KOBAS 2.0 server. The regulatory mechanisms of the RASEs and RBPs were evaluated using Pearson’s correlation coefficient. Seven indirect events of HDACi resistance or sensitivity were identified: NIR_5151_RP11-977G19.10, NIR_4557_IRAG2, NIR_11870_SUMO1, NIR_5347_ING4, NIR_17935_DNAJC2, NIR_17974_CBLL1, and NIR_422_SLC50A1. The potential regulatory relationships between RBPs and HDACi-sensitive RASEs were also analyzed. LEPR and HNRNPAO significantly affected NIR_11870_SUMO1, suggesting a potential regulatory relationship. Additionally, CNN1 may regulate NIR_5347_ING4, CNOT3 may regulate NIR_17935_DNAJC2, and DQX1 and LENG9 may regulate NIR_422_SLC5A1. Overall, our findings establish a theoretical foundation for the precise targeted treatment of CTCLs with HDACi.
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Affiliation(s)
- Shirong Yu
- Xinjiang Medical University, Urumqi, China
| | | | - Yuan Ding
- Department of Dermatology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Dermatologic Diseases, Urumqi, China
- Xinjiang Key Laboratory of Dermatology Research, Urumqi, China
| | - Xiaojing Kang
- Department of Dermatology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Dermatologic Diseases, Urumqi, China
- Xinjiang Key Laboratory of Dermatology Research, Urumqi, China
| | - Xiongming Pu
- Department of Dermatology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- Xinjiang Clinical Research Center for Dermatologic Diseases, Urumqi, China
- Xinjiang Key Laboratory of Dermatology Research, Urumqi, China
- *Correspondence: Xiongming Pu,
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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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7
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Pan YJ, Liu BW, Pei DS. The Role of Alternative Splicing in Cancer: Regulatory Mechanism, Therapeutic Strategy, and Bioinformatics Application. DNA Cell Biol 2022; 41:790-809. [PMID: 35947859 DOI: 10.1089/dna.2022.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
[Formula: see text] Alternative splicing (AS) can generate distinct transcripts and subsequent isoforms that play differential functions from the same pre-mRNA. Recently, increasing numbers of studies have emerged, unmasking the association between AS and cancer. In this review, we arranged AS events that are closely related to cancer progression and presented promising treatments based on AS for cancer therapy. Obtaining proliferative capacity, acquiring invasive properties, gaining angiogenic features, shifting metabolic ability, and getting immune escape inclination are all splicing events involved in biological processes. Spliceosome-targeted and antisense oligonucleotide technologies are two novel strategies that are hopeful in tumor therapy. In addition, bioinformatics applications based on AS were summarized for better prediction and elucidation of regulatory routines mingled in. Together, we aimed to provide a better understanding of complicated AS events associated with cancer biology and reveal AS a promising target of cancer treatment in the future.
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Affiliation(s)
- Yao-Jie Pan
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| | - Bo-Wen Liu
- Department of General Surgery, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
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8
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Öther-Gee Pohl S, Myant KB. Alternative RNA splicing in tumour heterogeneity, plasticity and therapy. Dis Model Mech 2022; 15:dmm049233. [PMID: 35014671 PMCID: PMC8764416 DOI: 10.1242/dmm.049233] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing is a process by which a single gene is able to encode multiple different protein isoforms. It is regulated by the inclusion or exclusion of introns and exons that are joined in different patterns prior to protein translation, thus enabling transcriptomic and proteomic diversity. It is now widely accepted that alternative splicing is dysregulated across nearly all cancer types. This widespread dysregulation means that nearly all cellular processes are affected - these include processes synonymous with the hallmarks of cancer - evasion of apoptosis, tissue invasion and metastasis, altered cellular metabolism, genome instability and drug resistance. Emerging evidence indicates that the dysregulation of alternative splicing also promotes a permissive environment for increased tumour heterogeneity and cellular plasticity. These are fundamental regulators of a patient's response to therapy. In this Review, we introduce the mechanisms of alternative splicing and the role of aberrant splicing in cancer, with particular focus on newfound evidence of alternative splicing promoting tumour heterogeneity, cellular plasticity and altered metabolism. We discuss recent in vivo models generated to study alternative splicing and the importance of these for understanding complex tumourigenic processes. Finally, we review the effects of alternative splicing on immune evasion, cell death and genome instability, and how targeting these might enhance therapeutic efficacy.
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Affiliation(s)
| | - Kevin B. Myant
- Cancer Research UK Edinburgh Centre, Institute of Genetics of Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
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9
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Czegle I, Gray AL, Wang M, Liu Y, Wang J, Wappler-Guzzetta EA. Mitochondria and Their Relationship with Common Genetic Abnormalities in Hematologic Malignancies. Life (Basel) 2021; 11:1351. [PMID: 34947882 PMCID: PMC8707674 DOI: 10.3390/life11121351] [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: 11/01/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
Hematologic malignancies are known to be associated with numerous cytogenetic and molecular genetic changes. In addition to morphology, immunophenotype, cytochemistry and clinical characteristics, these genetic alterations are typically required to diagnose myeloid, lymphoid, and plasma cell neoplasms. According to the current World Health Organization (WHO) Classification of Tumors of Hematopoietic and Lymphoid Tissues, numerous genetic changes are highlighted, often defining a distinct subtype of a disease, or providing prognostic information. This review highlights how these molecular changes can alter mitochondrial bioenergetics, cell death pathways, mitochondrial dynamics and potentially be related to mitochondrial genetic changes. A better understanding of these processes emphasizes potential novel therapies.
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Affiliation(s)
- Ibolya Czegle
- Department of Internal Medicine and Haematology, Semmelweis University, H-1085 Budapest, Hungary;
| | - Austin L. Gray
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA; (A.L.G.); (Y.L.); (J.W.)
| | - Minjing Wang
- Independent Researcher, Diamond Bar, CA 91765, USA;
| | - Yan Liu
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA; (A.L.G.); (Y.L.); (J.W.)
| | - Jun Wang
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA; (A.L.G.); (Y.L.); (J.W.)
| | - Edina A. Wappler-Guzzetta
- Department of Pathology and Laboratory Medicine, Loma Linda University Health, Loma Linda, CA 92354, USA; (A.L.G.); (Y.L.); (J.W.)
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10
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Thompson CM, Cannon A, West S, Ghersi D, Atri P, Bhatia R, Smith L, Rachagani S, Wichman C, Kumar S, Batra SK. Mucin Expression and Splicing Determine Novel Subtypes and Patient Mortality in Pancreatic Ductal Adenocarcinoma. Clin Cancer Res 2021; 27:6787-6799. [PMID: 34615717 DOI: 10.1158/1078-0432.ccr-21-1591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/15/2021] [Accepted: 10/04/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy demonstrating aberrant and progressive expression of mucins. The contribution of individual mucins has been extensively investigated in PDAC; however, comprehensive mucin profiling including splice variants in PDAC tumors has not been reported. EXPERIMENTAL DESIGN Using publicly available RNA sequencing (RNA-seq) datasets, we assess the expression of mucin family members and their splice variants (SV) in PDAC tumor samples for the first time. Mucin SVs that are correlated with PDAC patient survival are validated in a cohort of patient tumor samples. Further, we use computational methods to derive novel pancreatic tumor subtypes using mucin expression signatures and their associated activated pathways. RESULTS Principal component analysis identified four novel mucin-based PDAC subtypes. Pathway analysis implicated specific biological signatures for each subtype, labeled (i) immune activated, (ii) progressive, (iii) pancreatitis-initiated, and (iv) anti-inflammatory/PanIN-initiated. Assessing mucin SVs, significantly longer survival is observed with higher expression of 4 MUC1 and 1 MUC13 SVs, whereas patients expressing 2 MUC4 and 1 MUC16 SVs had shorter survival. Using a whole-transcriptome correlation, a three-gene panel, including ESRP2, PTK6, and MAGEH1, is designated to assess PDAC tumor sample cellularity by PCR. One MUC4 SV and one MUC13 SV are quantified in a separate PDAC patient cohort, and their effects on survival are experimentally validated. CONCLUSIONS Altogether, we demonstrate the unique expression pattern of mucins, four mucin-based PDAC subtypes, and the contribution of MUC1, MUC4, and MUC16 SVs in PDAC patient survival.
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Affiliation(s)
- Christopher M Thompson
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Andrew Cannon
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sean West
- School of Interdisciplinary Informatics, College of Information Science and Technology, University of Nebraska, Omaha, Nebraska
| | - Dario Ghersi
- School of Interdisciplinary Informatics, College of Information Science and Technology, University of Nebraska, Omaha, Nebraska
| | - Pranita Atri
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Rakesh Bhatia
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Lynette Smith
- Department of Biostatistics, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Satyayanarayana Rachagani
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Christopher Wichman
- Department of Biostatistics, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Sushil Kumar
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska.
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska. .,The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
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11
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Non-Coding RNAs and Splicing Activity in Testicular Germ Cell Tumors. Life (Basel) 2021; 11:life11080736. [PMID: 34440480 PMCID: PMC8399856 DOI: 10.3390/life11080736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/13/2021] [Accepted: 07/22/2021] [Indexed: 01/22/2023] Open
Abstract
Testicular germ cell tumors (TGCTs) are the most common tumors in adolescent and young men. Recently, genome-wide studies have made it possible to progress in understanding the molecular mechanisms underlying the development of tumors. It is becoming increasingly clear that aberrant regulation of RNA metabolism can drive tumorigenesis and influence chemotherapeutic response. Notably, the expression of non-coding RNAs as well as specific splice variants is deeply deregulated in human cancers. Since these cancer-related RNA species are considered promising diagnostic, prognostic and therapeutic targets, understanding their function in cancer development is becoming a major challenge. Here, we summarize how the different expression of RNA species repertoire, including non-coding RNAs and protein-coding splicing variants, impacts on TGCTs’ onset and progression and sustains therapeutic resistance. Finally, the role of transcription-associated R-loop misregulation in the maintenance of genomic stability in TGCTs is also discussed.
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12
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Jbara A, Siegfried Z, Karni R. Splice-switching as cancer therapy. Curr Opin Pharmacol 2021; 59:140-148. [PMID: 34217945 DOI: 10.1016/j.coph.2021.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 12/26/2022]
Abstract
In light of recent advances in RNA splicing modulation as therapy for specific genetic diseases, there is great optimism that this approach can be applied to treatment of cancer as well. Dysregulation of alternative RNA splicing is a common aberration detected in many cancers and thus, provides an attractive target for therapeutics. Here, we present and compare two promising approaches that are currently being investigated to manipulate alternative splicing and their potential use in therapy. The first strategy makes use of splice-switching oligonucleotides, whereas the second strategy uses CRISPR (clustered regularly interspaced short palindromic repeat Cas (CRISPR-associated) technology. We will discuss both the challenges and limitations of these technologies and progress being made to implement splice-switching as a potential cancer therapy.
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Affiliation(s)
- Amina Jbara
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel.
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Auboeuf D. The Physics-Biology continuum challenges darwinism: Evolution is directed by the homeostasis-dependent bidirectional relation between genome and phenotype. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:121-139. [PMID: 34097984 DOI: 10.1016/j.pbiomolbio.2021.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/19/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
The physics-biology continuum relies on the fact that life emerged from prebiotic molecules. Here, I argue that life emerged from the coupling between nucleic acid and protein synthesis during which proteins (or proto-phenotypes) maintained the physicochemical parameter equilibria (or proto-homeostasis) in the proximity of their encoding nucleic acids (or proto-genomes). This protected the proto-genome physicochemical integrity (i.e., atomic composition) from environmental physicochemical constraints, and therefore increased the probability of reproducing the proto-genome without variation. From there, genomes evolved depending on the biological activities they generated in response to environmental fluctuations. Thus, a genome maintaining homeostasis (i.e., internal physicochemical parameter equilibria), despite and in response to environmental fluctuations, maintains its physicochemical integrity and has therefore a higher probability to be reproduced without variation. Consequently, descendants have a higher probability to share the same phenotype than their parents. Otherwise, the genome is modified during replication as a consequence of the imbalance of the internal physicochemical parameters it generates, until new mutation-deriving biological activities maintain homeostasis in offspring. In summary, evolution depends on feedforward and feedback loops between genome and phenotype, as the internal physicochemical conditions that a genome generates ─ through its derived phenotype in response to environmental fluctuations ─ in turn either guarantee its stability or direct its variation. Evolution may not be explained by the Darwinism-derived, unidirectional principle (random mutations-phenotypes-natural selection) but rather by the bidirectional relationship between genome and phenotype, in which the phenotype in interaction with the environment directs the evolution of the genome it derives from.
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Affiliation(s)
- Didier Auboeuf
- ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée D'Italie, Site Jacques Monod, F-69007, Lyon, France.
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14
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Han P, Zhu J, Feng G, Wang Z, Ding Y. Characterization of alternative splicing events and prognostic signatures in breast cancer. BMC Cancer 2021; 21:587. [PMID: 34022836 PMCID: PMC8141138 DOI: 10.1186/s12885-021-08305-6] [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: 04/14/2020] [Accepted: 05/05/2021] [Indexed: 12/22/2022] Open
Abstract
Background Breast cancer (BRCA) is one of the most common cancers worldwide. Abnormal alternative splicing (AS) frequently observed in cancers. This study aims to demonstrate AS events and signatures that might serve as prognostic indicators for BRCA. Methods Original data for all seven types of splice events were obtained from TCGA SpliceSeq database. RNA-seq and clinical data of BRCA cohorts were downloaded from TCGA database. Survival-associated AS events in BRCA were analyzed by univariate COX proportional hazards regression model. Prognostic signatures were constructed for prognosis prediction in patients with BRCA based on survival-associated AS events. Pearson correlation analysis was performed to measure the correlation between the expression of splicing factors (SFs) and the percent spliced in (PSI) values of AS events. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted to demonstrate pathways in which survival-associated AS event is enriched. Results A total of 45,421 AS events in 21,232 genes were identified. Among them, 1121 AS events in 931 genes significantly correlated with survival for BRCA. The established AS prognostic signatures of seven types could accurately predict BRCA prognosis. The comprehensive AS signature could serve as independent prognostic factor for BRCA. A SF-AS regulatory network was therefore established based on the correlation between the expression levels of SFs and PSI values of AS events. Conclusions This study revealed survival-associated AS events and signatures that may help predict the survival outcomes of patients with BRCA. Additionally, the constructed SF-AS networks in BRCA can reveal the underlying regulatory mechanisms in BRCA. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08305-6.
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Affiliation(s)
- Pihua Han
- Breast Disease Center, Shaanxi Provincial Cancer Hospital, Xi'an City, 710000, Shaan Xi Province, China
| | - Jingjun Zhu
- Department of Breast Surgery, Baotou Tumor Hospital, Inner Mongolia Autonomous Region, Baotou, 014030, China
| | - Guang Feng
- The Third Department of Burns and Plastic Surgery and Center of Wound Repair, the Fourth Medical Center of PLA General Hospital, Beijing, 100048, China
| | - Zizhang Wang
- Department of Head and Neck Surgery, Shaanxi Provincial Cancer Hospital, Xi'an City, 710000, Shaan Xi Province, China
| | - Yanni Ding
- Breast Disease Center, Shaanxi Provincial Cancer Hospital, Xi'an City, 710000, Shaan Xi Province, China.
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15
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Hajaj E, Zisman E, Tzaban S, Merims S, Cohen J, Klein S, Frankenburg S, Sade-Feldman M, Tabach Y, Yizhak K, Navon A, Stepensky P, Hacohen N, Peretz T, Veillette A, Karni R, Eisenberg G, Lotem M. Alternative Splicing of the Inhibitory Immune Checkpoint Receptor SLAMF6 Generates a Dominant Positive Form, Boosting T-cell Effector Functions. Cancer Immunol Res 2021; 9:637-650. [PMID: 33762352 DOI: 10.1158/2326-6066.cir-20-0800] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/16/2021] [Accepted: 03/22/2021] [Indexed: 11/16/2022]
Abstract
SLAMF6 is a homotypic receptor of the Ig-superfamily associated with progenitor-exhausted T cells. Here we show that in humans, SLAMF6 has three splice isoforms involving its V-domain. Although the canonical receptor inhibited T-cell activation through SAP recruitment, the short isoform SLAMF6Δ17-65 had a strong agonistic effect. The costimulatory action depended on protein phosphatase SHP1 and led to a cytotoxic molecular profile mediated by the expression of TBX21 and RUNX3. Patients treated with immune checkpoint blockade showed a shift toward SLAMF6Δ17-65 in peripheral blood T cells. We developed splice-switching antisense oligonucleotides (ASO) designed to target the relevant SLAMF6 splice junction. Our ASOs enhanced SLAMF6Δ17-65 expression in human tumor-infiltrating lymphocytes and improved their capacity to inhibit human melanoma in mice. The yin-yang relationship of SLAMF6 splice isoforms may represent a balancing mechanism that could be exploited to improve cancer immunotherapy.
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Affiliation(s)
- Emma Hajaj
- Sharett Institute of Oncology, Hadassah Hebrew University Hospital, Jerusalem, Israel.,Wohl Institute for Translational Medicine, Hadassah Medical Organization, Jerusalem, Israel.,Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Elad Zisman
- Sharett Institute of Oncology, Hadassah Hebrew University Hospital, Jerusalem, Israel.,Wohl Institute for Translational Medicine, Hadassah Medical Organization, Jerusalem, Israel.,Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Shay Tzaban
- Sharett Institute of Oncology, Hadassah Hebrew University Hospital, Jerusalem, Israel.,Wohl Institute for Translational Medicine, Hadassah Medical Organization, Jerusalem, Israel.,Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Sharon Merims
- Sharett Institute of Oncology, Hadassah Hebrew University Hospital, Jerusalem, Israel.,Wohl Institute for Translational Medicine, Hadassah Medical Organization, Jerusalem, Israel
| | - Jonathan Cohen
- Sharett Institute of Oncology, Hadassah Hebrew University Hospital, Jerusalem, Israel.,Wohl Institute for Translational Medicine, Hadassah Medical Organization, Jerusalem, Israel.,Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Shiri Klein
- Sharett Institute of Oncology, Hadassah Hebrew University Hospital, Jerusalem, Israel.,Wohl Institute for Translational Medicine, Hadassah Medical Organization, Jerusalem, Israel.,Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Shoshana Frankenburg
- Sharett Institute of Oncology, Hadassah Hebrew University Hospital, Jerusalem, Israel.,Wohl Institute for Translational Medicine, Hadassah Medical Organization, Jerusalem, Israel
| | - Moshe Sade-Feldman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Yuval Tabach
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Keren Yizhak
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Ami Navon
- Department of Biological Regulation, Faculty of Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Polina Stepensky
- Department of Bone Marrow Transplantation, Hadassah Medical Organization, Jerusalem, Israel
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Medicine, Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Tamar Peretz
- Sharett Institute of Oncology, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - André Veillette
- IRCM, Montreal Clinical Research Institute, Montreal, Quebec, Canada
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Galit Eisenberg
- Sharett Institute of Oncology, Hadassah Hebrew University Hospital, Jerusalem, Israel.,Wohl Institute for Translational Medicine, Hadassah Medical Organization, Jerusalem, Israel.,Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Michal Lotem
- Sharett Institute of Oncology, Hadassah Hebrew University Hospital, Jerusalem, Israel. .,Wohl Institute for Translational Medicine, Hadassah Medical Organization, Jerusalem, Israel.,Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, Hebrew University, Jerusalem, Israel
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16
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Al Abo M, Hyslop T, Qin X, Owzar K, George DJ, Patierno SR, Freedman JA. Differential alternative RNA splicing and transcription events between tumors from African American and White patients in The Cancer Genome Atlas. Genomics 2021; 113:1234-1246. [PMID: 33705884 DOI: 10.1016/j.ygeno.2021.02.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/15/2021] [Accepted: 02/01/2021] [Indexed: 11/26/2022]
Abstract
Individuals of African ancestry suffer disproportionally from higher incidence, aggressiveness, and mortality for particular cancers. This disparity likely results from an interplay among differences in multiple determinants of health, including differences in tumor biology. We used The Cancer Genome Atlas (TCGA) SpliceSeq and TCGA aggregate expression datasets and identified differential alternative RNA splicing and transcription events (ARS/T) in cancers between self-identified African American (AA) and White (W) patients. We found that retained intron events were enriched among race-related ARS/T. In addition, on average, 12% of the most highly ranked race-related ARS/T overlapped between any two analyzed cancers. Moreover, the genes undergoing race-related ARS/T functioned in cancer-promoting pathways, and a number of race-related ARS/T were associated with patient survival. We built a web-application, CanSplice, to mine genomic datasets by self-identified race. The race-related targets have the potential to aid in the development of new biomarkers and therapeutics to mitigate cancer disparity.
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Affiliation(s)
- Muthana Al Abo
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Terry Hyslop
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Xiaodi Qin
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kouros Owzar
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Daniel J George
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Medicine, Division of Medical Oncology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Steven R Patierno
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Medicine, Division of Medical Oncology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jennifer A Freedman
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Medicine, Division of Medical Oncology, Duke University School of Medicine, Durham, NC, 27710, USA.
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17
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Alternative splicing events implicated in carcinogenesis and prognosis of thyroid gland cancer. Sci Rep 2021; 11:4841. [PMID: 33649373 PMCID: PMC7921437 DOI: 10.1038/s41598-021-84403-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/16/2021] [Indexed: 02/08/2023] Open
Abstract
Alternative splicing (AS), a critical post-transcriptional regulatory mechanism, expands gene expression patterns, thereby leading to increased protein diversity. Indeed, more than 95% of human genes undergo alternative splicing events (ASEs). In this study, we drew an all-around AS profile of thyroid cancer cells based on RNA-seq data. In total, there were 45,150 AS in 10,446 thyroid cancer cell genes derived from 506 patients, suggesting that ASEs is a common process in TC. Moreover, 1819 AS signatures were found to be significantly associated with the overall survival (OS) of TC patients. Kaplan–Meier survival analyses suggested that seven types of ASEs were associated with poor prognosis of TC (P < 0.05). Among them, exon skipping (ES) was the most common, with alternate promoter (AP) and alternate terminator (AT) coming second and third, respectively. Our results indicated that acceptor sites (AA) (AUC: 0.937), alternate donor sites (AD) (AUC: 0.965), AT (AUC: 0.964), ES (AUC: 0.999), mutually exclusive exons (ME) (AUC: 0.999), and retained intron (RI) (AUC: 0.837) exhibited an AUC greater than 0.6. In addition, age and risk score (All) were risk factors for TC patients. We also evaluated whether TC-ASEs are regulated by various splicing factors (SFs). We found that the expression of 90 SFs was associated with 469 ASEs and OS of TC patients. Our findings provide an insight into the role of spliceosomes in TC, which may offer novel perspectives in tumor research.
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18
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Grinev VV, Barneh F, Ilyushonak IM, Nakjang S, Smink J, van Oort A, Clough R, Seyani M, McNeill H, Reza M, Martinez-Soria N, Assi SA, Ramanouskaya TV, Bonifer C, Heidenreich O. RUNX1/RUNX1T1 mediates alternative splicing and reorganises the transcriptional landscape in leukemia. Nat Commun 2021; 12:520. [PMID: 33483506 PMCID: PMC7822815 DOI: 10.1038/s41467-020-20848-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/14/2020] [Indexed: 01/30/2023] Open
Abstract
The fusion oncogene RUNX1/RUNX1T1 encodes an aberrant transcription factor, which plays a key role in the initiation and maintenance of acute myeloid leukemia. Here we show that the RUNX1/RUNX1T1 oncogene is a regulator of alternative RNA splicing in leukemic cells. The comprehensive analysis of RUNX1/RUNX1T1-associated splicing events identifies two principal mechanisms that underlie the differential production of RNA isoforms: (i) RUNX1/RUNX1T1-mediated regulation of alternative transcription start site selection, and (ii) direct or indirect control of the expression of genes encoding splicing factors. The first mechanism leads to the expression of RNA isoforms with alternative structure of the 5'-UTR regions. The second mechanism generates alternative transcripts with new junctions between internal cassettes and constitutive exons. We also show that RUNX1/RUNX1T1-mediated differential splicing affects several functional groups of genes and produces proteins with unique conserved domain structures. In summary, this study reveals alternative splicing as an important component of transcriptome re-organization in leukemia by an aberrant transcriptional regulator.
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Affiliation(s)
- Vasily V. Grinev
- grid.17678.3f0000 0001 1092 255XDepartment of Genetics, Faculty of Biology, Belarusian State University, 220030 Minsk, Republic of Belarus
| | - Farnaz Barneh
- grid.487647.ePrincess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Ilya M. Ilyushonak
- grid.17678.3f0000 0001 1092 255XDepartment of Genetics, Faculty of Biology, Belarusian State University, 220030 Minsk, Republic of Belarus
| | - Sirintra Nakjang
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Job Smink
- grid.487647.ePrincess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Anita van Oort
- grid.487647.ePrincess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Richard Clough
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Michael Seyani
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Hesta McNeill
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Mojgan Reza
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Natalia Martinez-Soria
- grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Salam A. Assi
- grid.6572.60000 0004 1936 7486Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Tatsiana V. Ramanouskaya
- grid.17678.3f0000 0001 1092 255XDepartment of Genetics, Faculty of Biology, Belarusian State University, 220030 Minsk, Republic of Belarus
| | - Constanze Bonifer
- grid.6572.60000 0004 1936 7486Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Olaf Heidenreich
- grid.487647.ePrincess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands ,grid.1006.70000 0001 0462 7212Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE1 7RU UK ,grid.1006.70000 0001 0462 7212Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
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19
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Chen X, Wang Y, Qu X, Bie F, Wang Y, Du J. TRIM58 is a prognostic biomarker remodeling the tumor microenvironment in KRAS-driven lung adenocarcinoma. Future Oncol 2021; 17:565-579. [PMID: 33406903 DOI: 10.2217/fon-2020-0645] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aim: To comprehensively analyze the expression profiles of ubiquitin-related genes (URGs) and determine potential biomarkers in KRAS-driven lung adenocarcinoma (LUAD). Materials & methods: Differential expression analyses were performed between KRAS-wild and KRAS-mutant LUAD samples from The Cancer Genome Atlas database, and 34 URGs were screened out. ESTIMATE and CIBERSORT methods were used to calculate the ratio of immune and stromal components. Results & conclusion: TRIM58 was positively correlated with abundances of M2 macrophages and resting mast cells and negatively correlated with follicular helper T-cell abundances in KRAS-driven LUAD. TRIM58 was a potential prognosis-associated indicator for tumor microenvironment modulation and played a key role in TME-specific AS landscapes alterations in KRAS-driven LUAD.
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Affiliation(s)
- Xiaowei Chen
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250021, China
| | - Yu Wang
- Department of Respiratory Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, China
| | - Xiao Qu
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250021, China
| | - Fenglong Bie
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250021, China
| | - Yadong Wang
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250021, China
| | - Jiajun Du
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250021, China.,Department of Thoracic Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250021, China
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20
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Du JX, Liu YL, Zhu GQ, Luo YH, Chen C, Cai CZ, Zhang SJ, Wang B, Cai JL, Zhou J, Fan J, Dai Z, Zhu W. Profiles of alternative splicing landscape in breast cancer and their clinical significance: an integrative analysis based on large-sequencing data. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:58. [PMID: 33553351 PMCID: PMC7859793 DOI: 10.21037/atm-20-7203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background Alternative splicing (AS) is closely correlated with the initiation and progression of carcinoma. The systematic analysis of its biological and clinical significance in breast cancer (BRCA) is, however, lacking. Methods Clinical data and RNA-seq were obtained from the TCGA dataset and differentially expressed AS (DEAS) events between tumor and paired normal BRCA tissues were identified. Enrichment analysis was then used to reveal the potential biological functions of DEAS events. We performed protein-protein interaction (PPI) analysis of DEAS events by using STRING and the correlation network between splicing factors (SFs) and AS events was constructed. The LASSO Cox model, Kaplan-Meier and log-rank tests were used to construct and evaluate DEAS-related risk signature, and the association between DEAS events and clinicopathological features were then analyzed. Results After strict filtering, 35,367 AS events and 973 DEAS events were detected. DEAS corresponding genes were significantly enriched in pivotal pathways including cell adhesion, cytoskeleton organization, and extracellular matrix organization. A total of 103 DEAS events were correlated with disease free survival. The DEAS-related risk signature stratified BRCA patients into two groups and the area under curve (AUC) was 0.754. Moreover, patients in the high-risk group had enriched basel-like subtype, advanced clinical stages, proliferation, and metastasis potency. Conclusions Collectively, the profile of DEAS landscape in BRCA revealed the potential biological function and prognostic value of DEAS events.
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Affiliation(s)
- Jun-Xian Du
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Yong-Lei Liu
- Research Center, Zhongshan Hospital Qingpu Branch, Fudan University, Shanghai, China
| | - Gui-Qi Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Yi-Hong Luo
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Cong Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Cheng-Zhe Cai
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Si-Jia Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Biao Wang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Jia-Liang Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Jian Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Zhi Dai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, China
| | - Wei Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
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21
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Du JX, Zhu GQ, Cai JL, Wang B, Luo YH, Chen C, Cai CZ, Zhang SJ, Zhou J, Fan J, Zhu W, Dai Z. Splicing factors: Insights into their regulatory network in alternative splicing in cancer. Cancer Lett 2020; 501:83-104. [PMID: 33309781 DOI: 10.1016/j.canlet.2020.11.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/18/2022]
Abstract
More than 95% of all human genes are alternatively spliced after transcription, which enriches the diversity of proteins and regulates transcript and/or protein levels. The splicing isoforms produced from the same gene can manifest distinctly, even exerting opposite effects. Mounting evidence indicates that the alternative splicing (AS) mechanism is ubiquitous in various cancers and drives the generation and maintenance of various hallmarks of cancer, such as enhanced proliferation, inhibited apoptosis, invasion and metastasis, and angiogenesis. Splicing factors (SFs) play pivotal roles in the recognition of splice sites and the assembly of spliceosomes during AS. In this review, we mainly discuss the similarities and differences of SF domains, the details of SF function in AS, the effect of SF-driven pathological AS on different hallmarks of cancer, and the main drivers of SF expression level and subcellular localization. In addition, we briefly introduce the application prospects of targeted therapeutic strategies, including small-molecule inhibitors, siRNAs and splice-switching oligonucleotides (SSOs), from three perspectives (drivers, SFs and pathological AS). Finally, we share our insights into the potential direction of research on SF-centric AS-related regulatory networks.
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Affiliation(s)
- Jun-Xian Du
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Gui-Qi Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia-Liang Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Biao Wang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Yi-Hong Luo
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cong Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cheng-Zhe Cai
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Si-Jia Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Jian Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Wei Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
| | - Zhi Dai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China.
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22
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Cai Q, He B, Zhang P, Zhao Z, Peng X, Zhang Y, Xie H, Wang X. Exploration of predictive and prognostic alternative splicing signatures in lung adenocarcinoma using machine learning methods. J Transl Med 2020; 18:463. [PMID: 33287830 PMCID: PMC7720605 DOI: 10.1186/s12967-020-02635-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/27/2020] [Indexed: 12/25/2022] Open
Abstract
Background Alternative splicing (AS) plays critical roles in generating protein diversity and complexity. Dysregulation of AS underlies the initiation and progression of tumors. Machine learning approaches have emerged as efficient tools to identify promising biomarkers. It is meaningful to explore pivotal AS events (ASEs) to deepen understanding and improve prognostic assessments of lung adenocarcinoma (LUAD) via machine learning algorithms. Method RNA sequencing data and AS data were extracted from The Cancer Genome Atlas (TCGA) database and TCGA SpliceSeq database. Using several machine learning methods, we identified 24 pairs of LUAD-related ASEs implicated in splicing switches and a random forest-based classifiers for identifying lymph node metastasis (LNM) consisting of 12 ASEs. Furthermore, we identified key prognosis-related ASEs and established a 16-ASE-based prognostic model to predict overall survival for LUAD patients using Cox regression model, random survival forest analysis, and forward selection model. Bioinformatics analyses were also applied to identify underlying mechanisms and associated upstream splicing factors (SFs). Results Each pair of ASEs was spliced from the same parent gene, and exhibited perfect inverse intrapair correlation (correlation coefficient = − 1). The 12-ASE-based classifier showed robust ability to evaluate LNM status of LUAD patients with the area under the receiver operating characteristic (ROC) curve (AUC) more than 0.7 in fivefold cross-validation. The prognostic model performed well at 1, 3, 5, and 10 years in both the training cohort and internal test cohort. Univariate and multivariate Cox regression indicated the prognostic model could be used as an independent prognostic factor for patients with LUAD. Further analysis revealed correlations between the prognostic model and American Joint Committee on Cancer stage, T stage, N stage, and living status. The splicing network constructed of survival-related SFs and ASEs depicts regulatory relationships between them. Conclusion In summary, our study provides insight into LUAD researches and managements based on these AS biomarkers.
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Affiliation(s)
- Qidong Cai
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Boxue He
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Pengfei Zhang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Zhenyu Zhao
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Xiong Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Yuqian Zhang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Hui Xie
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China. .,Hunan Key Laboratory of Early Diagnosis and Precision Therapy, Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, China.
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23
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Fuentes-Fayos AC, Vázquez-Borrego MC, Jiménez-Vacas JM, Bejarano L, Pedraza-Arévalo S, L-López F, Blanco-Acevedo C, Sánchez-Sánchez R, Reyes O, Ventura S, Solivera J, Breunig JJ, Blasco MA, Gahete MD, Castaño JP, Luque RM. Splicing machinery dysregulation drives glioblastoma development/aggressiveness: oncogenic role of SRSF3. Brain 2020; 143:3273-3293. [PMID: 33141183 PMCID: PMC7904102 DOI: 10.1093/brain/awaa273] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/17/2020] [Accepted: 07/05/2020] [Indexed: 12/11/2022] Open
Abstract
Glioblastomas remain the deadliest brain tumour, with a dismal ∼12–16-month survival from diagnosis. Therefore, identification of new diagnostic, prognostic and therapeutic tools to tackle glioblastomas is urgently needed. Emerging evidence indicates that the cellular machinery controlling the splicing process (spliceosome) is altered in tumours, leading to oncogenic splicing events associated with tumour progression and aggressiveness. Here, we identify for the first time a profound dysregulation in the expression of relevant spliceosome components and splicing factors (at mRNA and protein levels) in well characterized cohorts of human high-grade astrocytomas, mostly glioblastomas, compared to healthy brain control samples, being SRSF3, RBM22, PTBP1 and RBM3 able to perfectly discriminate between tumours and control samples, and between proneural-like or mesenchymal-like tumours versus control samples from different mouse models with gliomas. Results were confirmed in four additional and independent human cohorts. Silencing of SRSF3, RBM22, PTBP1 and RBM3 decreased aggressiveness parameters in vitro (e.g. proliferation, migration, tumorsphere-formation, etc.) and induced apoptosis, especially SRSF3. Remarkably, SRSF3 was correlated with patient survival and relevant tumour markers, and its silencing in vivo drastically decreased tumour development and progression, likely through a molecular/cellular mechanism involving PDGFRB and associated oncogenic signalling pathways (PI3K-AKT/ERK), which may also involve the distinct alteration of alternative splicing events of specific transcription factors controlling PDGFRB (i.e. TP73). Altogether, our results demonstrate a drastic splicing machinery-associated molecular dysregulation in glioblastomas, which could potentially be considered as a source of novel diagnostic and prognostic biomarkers as well as therapeutic targets for glioblastomas. Remarkably, SRSF3 is directly associated with glioblastoma development, progression, aggressiveness and patient survival and represents a novel potential therapeutic target to tackle this devastating pathology.
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Affiliation(s)
- Antonio C Fuentes-Fayos
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain.,Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain.,Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.,CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain.,Agrifood Campus of International Excellence (ceiA3), 14004 Cordoba, Spain
| | - Mari C Vázquez-Borrego
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain.,Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain.,Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.,CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain.,Agrifood Campus of International Excellence (ceiA3), 14004 Cordoba, Spain
| | - Juan M Jiménez-Vacas
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain.,Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain.,Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.,CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain.,Agrifood Campus of International Excellence (ceiA3), 14004 Cordoba, Spain
| | - Leire Bejarano
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Sergio Pedraza-Arévalo
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain.,Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain.,Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.,CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain.,Agrifood Campus of International Excellence (ceiA3), 14004 Cordoba, Spain
| | - Fernando L-López
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain.,Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain.,Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.,CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain.,Agrifood Campus of International Excellence (ceiA3), 14004 Cordoba, Spain
| | - Cristóbal Blanco-Acevedo
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain.,Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.,Department of Neurosurgery, Reina Sofia University Hospital, 14004 Cordoba, Spain
| | - Rafael Sánchez-Sánchez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain.,Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.,Pathology Service, Reina Sofia University Hospital, 14004 Cordoba, Spain
| | - Oscar Reyes
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain.,Department of Computer Sciences, University of Cordoba, 14004 Cordoba, Spain
| | - Sebastián Ventura
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain.,Department of Computer Sciences, University of Cordoba, 14004 Cordoba, Spain
| | - Juan Solivera
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain.,Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.,Department of Neurosurgery, Reina Sofia University Hospital, 14004 Cordoba, Spain
| | - Joshua J Breunig
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Center for Neural Sciences in Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.,Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - María A Blasco
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Manuel D Gahete
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain.,Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain.,Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.,CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain.,Agrifood Campus of International Excellence (ceiA3), 14004 Cordoba, Spain
| | - Justo P Castaño
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain.,Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain.,Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.,CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain.,Agrifood Campus of International Excellence (ceiA3), 14004 Cordoba, Spain
| | - Raúl M Luque
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain.,Department of Cell Biology, Physiology and Immunology, University of Cordoba, 14004 Cordoba, Spain.,Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain.,CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain.,Agrifood Campus of International Excellence (ceiA3), 14004 Cordoba, Spain
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24
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Silva GR, Mattos DS, Bastos ACF, Viana BPPB, Brum MCM, Ferreira LB, Gimba ERP. Osteopontin-4 and Osteopontin-5 splice variants are expressed in several tumor cell lines. Mol Biol Rep 2020; 47:8339-8345. [PMID: 33006711 DOI: 10.1007/s11033-020-05867-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/25/2020] [Indexed: 02/07/2023]
Abstract
Among osteopontin splice variants (OPN-SV), the expression profile of osteopontin-4 (OPN4) and osteopontin-5 (OPN5) has not been addressed in distinct cancer types. We herein aimed to investigate their expression in several cancer cell lines, besides comparing it in relation to the three previously described OPN-SV: OPNa, OPNb and OPNc. Total RNA from cancer cell lines, including prostate (PC3 and DU145), ovarian (A2780), breast (MCF-7 and MDA-MB-231), colorectal (Caco-2, HT-29 and HCT-116), thyroid (TT, TPC1 and 8505c) and lung (A549 and NCI-H460) was extracted, followed by cDNA synthesis. OPN-SV transcript analysis by RT-PCR or RT-qPCR were performed using OPN-SV specific oligonucleotides and gapdh and actin transcripts were used as housekeeping controls. OPN4 and OPN5 transcripts displayed co-expression in most tested cell lines. OPN4 was found expressed in similar or higher levels in relation to OPN5. Moreover, in most tested cell lines, OPN4 is also expressed in similar levels to OPNa or OPNb. The expression of OPN5 is also generally variable in relation to the other OPN-SV, but expressed in similar or higher levels in relation to OPNc, depending on each tested cell line. OPN4 and OPN5 seem to be co-expressed in several tumor types and OPN4 is one of the most overexpressed OPN-SV in distinct tumor cell lines. Once both OPN4 and OPN5 are differentially expressed and also evidence tumor-specific expression patterns, we hypothesize that similarly to the other OPN-SV, they also possibly contribute to key aspects of tumor progression, what should be further functionally investigated in distinct tumor models.
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Affiliation(s)
- Gabriela Ribeiro Silva
- Programa de Oncobiologia Celular e Molecular, Instituto Nacional de Câncer, Rua André Cavalcanti, 37, 3° andar, Rio de Janeiro, CEP: 20 231 050, Brazil.,Programa de Pós-Graduação Em Ciências Biomédicas, Fisiologia E Farmacologia, Instituto Biomédico, Av. Prof. Hernani Melo, Niterói, 101, CEP24210-130, Brazil
| | - Daniella Santos Mattos
- Programa de Oncobiologia Celular e Molecular, Instituto Nacional de Câncer, Rua André Cavalcanti, 37, 3° andar, Rio de Janeiro, CEP: 20 231 050, Brazil.,Programa de Pós-Graduação Stricto Sensu em Oncologia, Instituto Nacional de Câncer, Rua André Cavalcanti, 37, 3° andar, Rio de Janeiro, CEP: 20 231 050, Brazil
| | - Ana Clara Fonseca Bastos
- Programa de Oncobiologia Celular e Molecular, Instituto Nacional de Câncer, Rua André Cavalcanti, 37, 3° andar, Rio de Janeiro, CEP: 20 231 050, Brazil.,Programa de Pós-Graduação Stricto Sensu em Oncologia, Instituto Nacional de Câncer, Rua André Cavalcanti, 37, 3° andar, Rio de Janeiro, CEP: 20 231 050, Brazil
| | - Bruna Prunes Pena Baroni Viana
- Programa de Oncobiologia Celular e Molecular, Instituto Nacional de Câncer, Rua André Cavalcanti, 37, 3° andar, Rio de Janeiro, CEP: 20 231 050, Brazil.,Programa de Pós-Graduação Stricto Sensu em Oncologia, Instituto Nacional de Câncer, Rua André Cavalcanti, 37, 3° andar, Rio de Janeiro, CEP: 20 231 050, Brazil
| | - Mariana Concentino Menezes Brum
- Programa de Oncobiologia Celular e Molecular, Instituto Nacional de Câncer, Rua André Cavalcanti, 37, 3° andar, Rio de Janeiro, CEP: 20 231 050, Brazil.,Programa de Pós-Graduação Stricto Sensu em Oncologia, Instituto Nacional de Câncer, Rua André Cavalcanti, 37, 3° andar, Rio de Janeiro, CEP: 20 231 050, Brazil
| | - Luciana Bueno Ferreira
- Programa de Oncobiologia Celular e Molecular, Instituto Nacional de Câncer, Rua André Cavalcanti, 37, 3° andar, Rio de Janeiro, CEP: 20 231 050, Brazil.,Programa de Pós-Graduação Stricto Sensu em Oncologia, Instituto Nacional de Câncer, Rua André Cavalcanti, 37, 3° andar, Rio de Janeiro, CEP: 20 231 050, Brazil
| | - Etel Rodrigues Pereira Gimba
- Programa de Oncobiologia Celular e Molecular, Instituto Nacional de Câncer, Rua André Cavalcanti, 37, 3° andar, Rio de Janeiro, CEP: 20 231 050, Brazil. .,Programa de Pós-Graduação Stricto Sensu em Oncologia, Instituto Nacional de Câncer, Rua André Cavalcanti, 37, 3° andar, Rio de Janeiro, CEP: 20 231 050, Brazil. .,Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rua André Cavalcanti, 37, 3° andar, Rio de Janeiro, CEP: 20 231 050, Brazil. .,Departamento de Ciências da Natureza, Instituto de Humanidades E Saúde, Universidade Federal Fluminense, Rua Recife 1-7, Bairro Bela Vista, Rio das Ostras, RJ, CEP 28880-000, Brazil. .,Programa de Pós-Graduação Em Ciências Biomédicas, Fisiologia E Farmacologia, Instituto Biomédico, Av. Prof. Hernani Melo, Niterói, 101, CEP24210-130, Brazil.
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25
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Zhao Z, Li GZ, Liu YQ, Huang RY, Wang KY, Jiang HY, Li RP, Chai RC, Zhang CB, Wu F. Characterization and prognostic significance of alternative splicing events in lower-grade diffuse gliomas. J Cell Mol Med 2020; 24:13171-13180. [PMID: 33006444 PMCID: PMC7701518 DOI: 10.1111/jcmm.15924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/03/2020] [Accepted: 09/10/2020] [Indexed: 01/17/2023] Open
Abstract
Alternative splicing (AS) is assumed to play important roles in the progression and prognosis of cancer. Currently, the comprehensive analysis and clinical relevance of AS in lower-grade diffuse gliomas have not been systematically addressed. Here, we gathered alternative splicing data of lower-grade diffuse gliomas from SpliceSeq. Based on the Percent Spliced In (PSI) values of 515 lower-grade diffuse glioma patients from the Cancer Genome Atlas (TCGA), we performed subtype-differential AS analysis and consensus clustering to determine robust clusters of patients. A total of 48 050 AS events in 10 787 genes in lower-grade diffuse gliomas were profiled. Subtype-differential splicing analysis and functional annotation revealed that spliced genes were significantly enriched in numerous cancer-related biological phenotypes and signalling pathways. Consensus clustering using AS events identified three robust clusters of patients with distinguished pathological and prognostic features. Moreover, each cluster was also associated with distinct genomic alterations. Finally, we developed and validated an AS-related signature with Cox proportional hazards model. The signature, significantly associated with clinical and molecular features, could serve as an independent prognostic factor for lower-grade diffuse gliomas. Thus, our results indicated that AS events could discriminate molecular subtypes and have prognostic impact in lower-grade diffuse gliomas.
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Affiliation(s)
- Zheng Zhao
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guan-Zhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yu-Qing Liu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ruo-Yu Huang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Kuan-Yu Wang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Hao-Yu Jiang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ren-Peng Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Rui-Chao Chai
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Chuan-Bao Zhang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fan Wu
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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26
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Liu Y, Jia W, Li J, Zhu H, Yu J. Identification of Survival-Associated Alternative Splicing Signatures in Lung Squamous Cell Carcinoma. Front Oncol 2020; 10:587343. [PMID: 33117720 PMCID: PMC7561379 DOI: 10.3389/fonc.2020.587343] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 08/28/2020] [Indexed: 02/05/2023] Open
Abstract
Purpose: Alternative splicing (AS) is a post-transcriptional process that plays a significant role in enhancing the diversity of transcription and protein. Accumulating evidences have demonstrated that dysregulation of AS is associated with oncogenic processes. However, AS signature specifically in lung squamous cell carcinoma (LUSC) remains unknown. This study aimed to evaluate the prognostic values of AS events in LUSC patients. Methods: The RNA-seq data, AS events data and corresponding clinical information were obtained from The Cancer Genome Atlas (TCGA) database. Univariate Cox regression analysis was performed to identify survival-related AS events and survival-related parent genes were subjected to Gene Ontology enrichment analysis and gene network analysis. The least absolute shrinkage and selection operator (LASSO) method and multivariate Cox regression analysis were used to construct prognostic prediction models, and their predictive values were assessed by Kaplan-Meier analysis and receiver operating characteristic (ROC) curves. Then a nomogram was established to predict the survival of LUSC patients. And the interaction network of splicing factors (SFs) and survival-related AS events was constructed by Spearman correlation analysis and visualized by Cytoscape. Results: Totally, 467 LUSC patients were included in this study and 1,991 survival-related AS events within 1,433 genes were identified. SMAD4, FOS, POLR2L, and RNPS1 were the hub genes in the gene interaction network. Eight prognostic prediction models (seven types of AS and all AS) were constructed and all exhibited high efficiency in distinguishing good or poor survival of LUSC patients. The final integrated prediction model including all types of AS events exhibited the best prognostic power with the maximum AUC values of 0.778, 0.816, 0.814 in 1, 3, 5 years ROC curves, respectively. Meanwhile, the nomogram performed well in predicting the 1-, 3-, and 5-year survival of LUSC patients. In addition, the SF-AS regulatory network uncovered a significant correlation between SFs and survival-related AS events. Conclusion: This is the first comprehensive study to analyze the role of AS events in LUSC specifically, which improves our understanding of the prognostic value of survival-related AS events for LUSC. And these survival-related AS events might serve as novel prognostic biomarkers and drug therapeutic targets for LUSC.
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Affiliation(s)
- Yang Liu
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wenxiao Jia
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Ji Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.,Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Hui Zhu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Jinming Yu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
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27
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Wang L, Bi J, Li X, Wei M, He M, Zhao L. Prognostic alternative splicing signature reveals the landscape of immune infiltration in Pancreatic Cancer. J Cancer 2020; 11:6530-6544. [PMID: 33046974 PMCID: PMC7545682 DOI: 10.7150/jca.47877] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Pancreatic cancer (PC) is an aggressive cancer with worse survival in the world. Emerging evidence suggested that the imbalance of alternative splicing (AS) is a hallmark of cancer and indicated poor prognosis of patients. Genes-derived splicing events can produce neoepitopes for immunotherapy. However, the profound study of splicing profiling in PC is still elusive. We aimed to identification of novel prognostic signature across a comprehensive splicing landscape and reveal their relationship with tumor-infiltrating immune cells in pancreatic cancer microenvironment. Methods: Based on integrated analysis of splicing profiling and clinical data, differentially splicing events were filtered out. Then, stepwise Cox regression analysis was applied to identify survival-related splicing events and construct prognostic signature. Functional enrichment analysis was performed to explore biology function. Kaplan-Meier curves and receiver operating characteristic (ROC) curves were performed to validate the predictive effect of predictive signature. We also verified the clinical value of prognostic signature under the influence of different clinical parameters. For deeper analysis, we evaluated the correlation between prognostic signature and infiltrating immune cells by CIBERSORT. Results: According to systematic analyzing, a final six splicing events were identified and validated the good prognostic capability in entire TCGA dataset, validation set 1 and validation set 2 by Kaplan-Meier curves (P < 0.0001). The area under the curve (AUC) of ROC curves were also confirmed the high predictive efficiency of the prognostic signature in these three cohorts (AUC = 0.857, 0.895 and 0.788). In order to validate whether prognostic signature highlights a correlation between AS and immune contexture, CIBERSORT was performed to analyze the proportion of tumor-infiltrating immune cells in PC. Based on prognostic signature, we identified survival-related immune cells including CD8 T cells (P = 0.0111), activated CD4 memory T cells (P = 0.0329) and resting mast cells (P = 0.0352). Conclusion: In conclusion, our study contribute to provide a promising prognostic signature based on six splicing events and revealed prognosis-related immune cells which indeed represented novel tumor drivers and provide potential targets for personalized therapeutic.
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Affiliation(s)
- Lin Wang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education; China Medical University, Shenyang, Liaoning Province, China
| | - Jia Bi
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education; China Medical University, Shenyang, Liaoning Province, China
| | - Xueping Li
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education; China Medical University, Shenyang, Liaoning Province, China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education; China Medical University, Shenyang, Liaoning Province, China
| | - Miao He
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education; China Medical University, Shenyang, Liaoning Province, China
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation; Liaoning Cancer immune peptide drug Engineering Technology Research Center; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education; China Medical University, Shenyang, Liaoning Province, China
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Lv J, He Y, Li L, Wang Z. Alternative Splicing Events and Splicing Factors Are Prognostic in Adrenocortical Carcinoma. Front Genet 2020; 11:918. [PMID: 33101358 PMCID: PMC7494975 DOI: 10.3389/fgene.2020.00918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 07/23/2020] [Indexed: 01/22/2023] Open
Abstract
Alternative splicing is involved in the pathogenesis of human diseases, including cancer. Here, we investigated the potential application of alternative splicing events (ASEs) and splicing factors (SFs) in the prognosis of adrenocortical carcinoma (ACC). Transcriptome data from 79 ACC cases were downloaded from The Cancer Genome Atlas database, and percent spliced-in values of seven splicing types were downloaded from The Cancer Genome Atlas SpliceSeq database. By the univariate Cox regression analysis, 1,839 survival-related ASEs were identified. Prognostic indices based on seven types of survival-related ASEs were calculated by multivariate Cox regression analysis. Survival curves and receiver operating characteristic curves were used to assess the diagnostic value of the prognostic model. Independent prognosis analysis identified several ASEs (e.g., THNSL2| 54469| ME) that could be used as biomarkers to predict the prognosis of patients with ACC accurately. By analyzing the co-expression correlation between SFs and ASEs, 188 highly correlated interactions were established. From the protein interaction network, we finally screened six hub SFs, including YBX1, SART1, PRCC, SNRPG, SNRPE, and SF3B4, whose expression levels were significantly related to the overall survival and prognosis of ACC. Our findings provide a reliable model for predicting the prognosis of ACC patients based on aberrant alternative splicing patterns.
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Affiliation(s)
- Jian Lv
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China.,Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuan He
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lili Li
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhihua Wang
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China.,Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China
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29
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Cao R, Zhang J, Jiang L, Wang Y, Ren X, Cheng B, Xia J. Comprehensive Analysis of Prognostic Alternative Splicing Signatures in Oral Squamous Cell Carcinoma. Front Oncol 2020; 10:1740. [PMID: 32984057 PMCID: PMC7485395 DOI: 10.3389/fonc.2020.01740] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/04/2020] [Indexed: 12/17/2022] Open
Abstract
Background Alternative splicing (AS) plays an essential role in tumorigenesis and progression. This study aimed to develop a novel prognostic model based on the AS events to obtain more accurate survival prediction and search for potential therapeutic targets in oral squamous cell carcinoma (OSCC). Methods Seven types of AS events in 326 OSCC patients with RNA-seq were obtained from the TCGA SpliceSeq tool and the TCGA database. Cox analysis, the least absolute shrinkage and selection operator Cox regression and random forest were employed to establish prognostic models. Genomics of Drug Sensitivity in Cancer (GDSC) was adopted to estimate the possible drug sensiticity. Prognostic splicing factor (SF)-AS network was constructed by Cytoscape. Results The final model included 12 AS events, showing satisfactory performance. The area under the curve for 3- and 5-year survival in the training cohort was 0.83 and 0.82, respectively while that in internal validation was 0.83 and 0.82 accordingly. The calibration curve also indicated a satisfactory agreement between the observation and the predictive values. Low-risk patients stratified by the final model presented higher sensitivity to three chemo drugs. Besides, the prognostic SF-AS regulatory network contained five key SFs and 62 AS events. Conclusions We developed a powerful prognostic AS signature for OSCC and deepened the understanding of SF-AS network regulatory mechanisms. Low-risk patients tended to be more sensitive to the three chemo drugs while five key SFs including CELF2, TIA1, HNRNPC, HNRNPK, and SRSF9 were identified as potential prognostic biomarkers, which may offer new prospects for effective therapies of OSCC.
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Affiliation(s)
- Ruoyan Cao
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Jiayu Zhang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Laibo Jiang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Yanting Wang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Xianyue Ren
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Bin Cheng
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Juan Xia
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China.,Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
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30
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Lu J, Wei S, Lou J, Yin S, Zhou L, Zhang W, Zheng S. Systematic Analysis of Alternative Splicing Landscape in Pancreatic Adenocarcinoma Reveals Regulatory Network Associated with Tumorigenesis and Immune Response. Med Sci Monit 2020; 26:e925733. [PMID: 32706768 PMCID: PMC7709468 DOI: 10.12659/msm.925733] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive gastrointestinal tumors and has an extremely high mortality rate. Recent studies indicate that alternative splicing (AS), a common post-transcriptional process, has important roles in tumor biological behaviors and may provide novel immunotherapeutic targets. This study systematically analyzes AS profiles in PDAC and reveals their potential regulatory effects on cancer immune response. MATERIAL AND METHODS AS event, RNA sequencing, and splicing factor (SF) data were extracted from SpliceSeq, The Cancer Genome Atlas, and SpliceAid2, respectively. Overall survival (OS)-associated AS events and SFs were identified with univariate analysis. The LASSO method and multivariate Cox regression analysis were used to construct predictive signatures for the prediction of patient prognosis. The proportions of immune cells within PDAC samples were evaluated using the CIBERSORT algorithm. The correlations among AS events, SFs, and immune cell proportions were calculated using Spearman correlation analysis. Consensus clustering and immune classification were performed on the PDAC cohort. RESULTS A total of 4812 OS-related AS events from 3341 parent genes were identified, and 8 AS-based predictive models were constructed for PDAC. An OS-related SF-AS regulatory network was constructed. The AS events regulated by ELAVL4 exhibited strong correlations with CD8 T cells and regulatory T cells. In addition, AS-based clusters demonstrated distinct OS outcomes and immune features. CONCLUSIONS AS-based predictive models with high accuracy were constructed to facilitate prognosis prediction and treatment of PDAC. An SF-AS regulatory network was constructed, revealing the potential relationships among SF, AS, and immune response.
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Affiliation(s)
- Jiahua Lu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China (mainland).,NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, Zhejiang, China (mainland).,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, Zhejiang, China (mainland).,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang, China (mainland)
| | - Shenyu Wei
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China (mainland)
| | - Jianying Lou
- Department of Hepato-Pancreato-Biliary Surgery, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China (mainland)
| | - Shengyong Yin
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China (mainland).,NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, Zhejiang, China (mainland).,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, Zhejiang, China (mainland).,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang, China (mainland)
| | - Lin Zhou
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China (mainland).,NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, Zhejiang, China (mainland).,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, Zhejiang, China (mainland).,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang, China (mainland)
| | - Wu Zhang
- Shulan (Hangzhou) Hospital, Hangzhou, Zhejiang, China (mainland).,School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China (mainland)
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China (mainland).,NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, Zhejiang, China (mainland).,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019), Hangzhou, Zhejiang, China (mainland).,Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Hangzhou, Zhejiang, China (mainland)
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Zhang Z, Feng Q, Jia C, Zheng P, Lv Y, Mao Y, Xu Y, He G, Xu J. Analysis of relapse-associated alternative mRNA splicing and construction of a prognostic signature predicting relapse in I-III colon cancer. Genomics 2020; 112:4032-4040. [PMID: 32645524 DOI: 10.1016/j.ygeno.2020.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 12/22/2022]
Abstract
The literature comprehensively analyzed alternative splicing (AS) events in colon cancer is little and corresponding prognostic signature is still a lack. Based on data of TCGA, the relapse-associated ASs were comprehensively analyzed and a signature was further constructed to predict the relapse in I-III colon cancer. In total 1912 ASs of 1384 mRNA were identified as relapse-associated ASs, protein-protein interactions (PPI) and ASs-splicing factors (SF) interactions network were identified. We finally built a robust signature to predict the relapse of I-III colon cancer with a considerable AUC value in both the training group and the test group. The AUC in the entire set at 1, 3 and 5 year was 0.85, 0.83 and 0.836. Our study provided a profile of relapse-associated ASs in I-III colon cancer and built a robust signature to predict the relapse of I-III colon cancer.
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Affiliation(s)
- Zhiyuan Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qingyang Feng
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Caiwei Jia
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Peng Zheng
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yang Lv
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yihao Mao
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuqiu Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Guodong He
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianmin Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
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32
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Zhang Z, Ji M, Lv Y, Feng Q, Zheng P, Mao Y, Xu Y, He G, Xu J. A signature predicting relapse based on integrated analysis on relapse-associated alternative mRNA splicing in I-III rectal cancer. Genomics 2020; 112:3274-3283. [PMID: 32544549 DOI: 10.1016/j.ygeno.2020.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/03/2020] [Accepted: 06/10/2020] [Indexed: 12/22/2022]
Abstract
Researches focusing on the effects of alternative splicing (AS) on relapse of rectal cancer is little and signature based on the AS is blank. In this study, bioinformatic analysis was performed to identify and analyze the relapse-associated ASs, a signature was also constructed. In conclusion, 829 relapse-associated ASs of 676 mRNA were identified. 603 proteins with 2119 interactions were involved in the PPI (protein-protein interactions) network. 43 relapse-associated ASs and 64 SFs (splicing factors) with 160 interactions were indicated. Finally, we built a robust signature to predict the relapse of I-III rectal cancer with a high AUC (0.98) of ROC at 1 year. Based on the ASs involved in the signature, 4 molecular subgroups that could distinguish the relapse rate in diverse groups were identified. Our research provided an overview of relapse-associated ASs in I-III rectal cancer.
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Affiliation(s)
- Zhiyuan Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Meiling Ji
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yang Lv
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qingyang Feng
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peng Zheng
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yihao Mao
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuqiu Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Guodong He
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianmin Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
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33
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Jing L, Feng L, Zhou Z, Shi S, Deng R, Wang Z, Zhang Y, Ren Z, Liu Y. TNNT2 as a potential biomarker for the progression and prognosis of colorectal cancer. Oncol Rep 2020; 44:628-636. [PMID: 32627044 PMCID: PMC7336514 DOI: 10.3892/or.2020.7637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 02/26/2020] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide. At present, there are limited effective biomarkers of CRC. The present study aimed to identify potential signatures associated with the tumorigenesis and prognosis of CRC using publicly available databases, and further validate the identified biomarkers in CRC cell lines. Identification of differentially expressed mRNAs between CRC and paracancerous samples was conducted based on data from The Cancer Genome Atlas (TCGA; 471 tumor samples and 41 normal samples). Survival analysis was performed to explore the prognostic value of troponin 2 (TNNT2) in the TCGA training set, which was further validated in an external dataset, GSE17531. Functional enrichment analysis was conducted to determine the possible biological functions using GSEA 3.0. Reverse transcription-quantitative PCR (RT-qPCR) and western blotting were utilized to detect the mRNA and protein expression levels of TNNT2 between CRC and normal colorectal cells. Immunohistochemistry was performed to detect the protein expression of TNNT2 in CRC and normal tissues. TNNT2 was significantly upregulated in CRC samples compared with adjacent normal samples in the TCGA dataset. Increased expression of TNNT2 was associated with inferior prognosis in the TCGA training dataset and GSE17531 validation dataset. Functional enrichment analysis revealed that the ErbB signaling pathway and glycerophospholipid metabolism pathway were significantly activated in the TNNT2 high expression group. Overexpression of TNNT2 mRNA and TNNT2 protein in CRC tumor cells was confirmed by RT-qPCR and western blotting, respectively. Immunohistochemistry indicated increased protein expression levels of TNNT2 in CRC tissues in comparison with normal tissues. TNNT2 was associated with the tumorigenesis and prognosis of CRC, which may be useful for novel biomarker identification and targeted therapeutic strategy development.
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Affiliation(s)
- Li Jing
- Department of Medical Oncology, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Li Feng
- Department of Medical Oncology, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Zhiguo Zhou
- Department of Radiotherapy, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Shuai Shi
- Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Ruoying Deng
- Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Zhicong Wang
- Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Yi Zhang
- Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Zhixue Ren
- The Seven People's Hospital of Hebei Province, Dingzhou, Hebei 073000, P.R. China
| | - Yibing Liu
- Department of Medical Oncology, Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
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Ding Y, Feng G, Yang M. Prognostic role of alternative splicing events in head and neck squamous cell carcinoma. Cancer Cell Int 2020; 20:168. [PMID: 32467664 PMCID: PMC7227031 DOI: 10.1186/s12935-020-01249-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
Background Aberrant alternative splicing (AS) is implicated in biological processes of cancer. This study aims to reveal prognostic AS events and signatures that may serve as prognostic predictors for head and neck squamous cell carcinoma (HNSCC). Methods Prognostic AS events in HNSCC were identified by univariate COX analysis. Prognostic signatures comprising prognostic AS events were constructed for prognosis prediction in patients with HNSCC. The correlation between the percent spliced in (PSI) values of AS events and the expression of splicing factors (SFs) was analyzed by Pearson correlation analysis. Gene functional annotation analysis was performed to reveal pathways in which prognostic AS is enriched. Results A total of 27,611 AS events in 15,873 genes were observed, and there were 3433 AS events in 2624 genes significantly associated with overall survival (OS) for HNSCC. Moreover, we found that AS prognostic signatures could accurately predict HNSCC prognosis. SF-AS regulatory networks were constructed according to the correlation between PSI values of AS events and the expression levels of SFs. Conclusions Our study identified prognostic AS events and signatures. Furthermore, it established SF-AS networks in HNSCC that were valuable in predicting the prognosis of patients with HNSCC and elucidating the regulatory mechanisms underlying AS in HNSCC.
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Affiliation(s)
- Yanni Ding
- Department of Breast Surgery, Shaan Xi Provincial Tumor Hospital, Xi'an City, Shaan Xi Province 710000 China
| | - Guang Feng
- 2The Third Department of Burns and Plastic Surgery and Center of Wound Repair, The Fourth Medical Center of PLA General Hospital, Beijing, 100048 China
| | - Min Yang
- Department of Breast Surgery, Shaan Xi Provincial Tumor Hospital, Xi'an City, Shaan Xi Province 710000 China
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35
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Zhao X, Si S, Li X, Sun W, Cui L. Identification and validation of an alternative splicing-based prognostic signature for head and neck squamous cell carcinoma. J Cancer 2020; 11:4571-4580. [PMID: 32489474 PMCID: PMC7255372 DOI: 10.7150/jca.44746] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 03/28/2020] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence has demonstrated that changes in alternative splicing (AS) events are closely associated with the initiation and progression of cancer. However, the concrete role of AS in tumorigenesis of head and neck squamous cell carcinoma (HNSCC) is poorly known. In this study, we aimed to investigate the AS profile in HNSCC, and build up a robust AS-based prognostic signature for HNSCC. Our results revealed a total of 4068 overall survival (OS) associated AS events in the TCGA HNSCC cohort. The whole TCGA HNSCC cohort was randomly divided into discovery cohort and validation cohort. A prognostic signature including five AS events was developed with the discovery cohort based on the most significant OS-associated AS events. Then it was further successfully validated in the validation cohort. The AS-based risk signature was an independent prognostic indicator in both discovery cohort and validation cohort. This prognostic signature-based nomogram model showed excellent performance for predicting the OS of HNSCC. Splicing network analysis have identified the most correlated splicing factor-AS network in HNSCC. Collectively, we have constructed a robust AS-based prognostic signature which might contribute to improve the clinical outcome of HNSCC.
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Affiliation(s)
- Xinyuan Zhao
- Stomatological Hospital, Southern Medical University, Guangzhou 510280, China
| | - Shanshan Si
- Stomatological Hospital, Southern Medical University, Guangzhou 510280, China
| | - Xiaona Li
- Stomatological Hospital, Southern Medical University, Guangzhou 510280, China
| | - Wenjuan Sun
- Department of Stomatology, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Li Cui
- UCLA School of Dentistry, Los Angeles, CA 90095, USA
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36
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Roles and mechanisms of alternative splicing in cancer - implications for care. Nat Rev Clin Oncol 2020; 17:457-474. [PMID: 32303702 DOI: 10.1038/s41571-020-0350-x] [Citation(s) in RCA: 360] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2020] [Indexed: 12/14/2022]
Abstract
Removal of introns from messenger RNA precursors (pre-mRNA splicing) is an essential step for the expression of most eukaryotic genes. Alternative splicing enables the regulated generation of multiple mRNA and protein products from a single gene. Cancer cells have general as well as cancer type-specific and subtype-specific alterations in the splicing process that can have prognostic value and contribute to every hallmark of cancer progression, including cancer immune responses. These splicing alterations are often linked to the occurrence of cancer driver mutations in genes encoding either core components or regulators of the splicing machinery. Of therapeutic relevance, the transcriptomic landscape of cancer cells makes them particularly vulnerable to pharmacological inhibition of splicing. Small-molecule splicing modulators are currently in clinical trials and, in addition to splice site-switching antisense oligonucleotides, offer the promise of novel and personalized approaches to cancer treatment.
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37
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Boer RE, Torrey ZR, Schneekloth JS. Chemical Modulation of Pre-mRNA Splicing in Mammalian Systems. ACS Chem Biol 2020; 15:808-818. [PMID: 32191432 DOI: 10.1021/acschembio.0c00001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
RNA splicing is a key component of gene expression and proteomic diversity in humans. The spliceosome assembles on and processes individual nascent pre-mRNA transcripts into distinct mature mRNAs that can code for different proteins. Splicing programs can be affected by somatic mutations and changes in response to exogenous stimuli. Importantly, alterations in splicing can be direct drivers of diseases including cancers. This Review describes recent advances and the potential for targeting and controlling pre-mRNA splicing in humans with small molecules, ranging from targeting spliceosomal proteins to direct targeting of individual RNA transcripts.
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Affiliation(s)
- Robert E. Boer
- Chemical Biology Laboratory, National Cancer Institute, Frederick Maryland 21702, United States
| | - Zachary R. Torrey
- Chemical Biology Laboratory, National Cancer Institute, Frederick Maryland 21702, United States
| | - John S. Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick Maryland 21702, United States
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38
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Zhao D, Zhang C, Jiang M, Wang Y, Liang Y, Wang L, Qin K, Rehman FU, Zhang X. Survival-associated alternative splicing signatures in non-small cell lung cancer. Aging (Albany NY) 2020; 12:5878-5893. [PMID: 32282333 PMCID: PMC7185095 DOI: 10.18632/aging.102983] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 03/24/2020] [Indexed: 12/24/2022]
Abstract
Alternative splicing (AS) is fundamental to transcriptome and proteome richness, and data from recent studies suggested a critical association between AS and oncogenic processes. To date, no systematic analysis has been conducted on AS from the perspective of different sexes and subtypes in non-small-cell lung cancer (NSCLC). Thus, we integrated the information of NSCLC patients from The Cancer Genome Atlas (TCGA) and evaluated AS profiles from the perspectives of sex and subtype. Eventually, a total of 813 and 1020 AS events were found to be significantly related to the overall survival (OS) of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) patients. Four prognostic prediction models performed well at 1, 3, and 5 years, with an area under the receiver operating characteristic (ROC) curve (AUC) greater than 0.75. Notably, we explored the upstream splicing factors (SFs) and downstream regulatory mechanisms of the OS-associated AS events and verified four differentially expressed alternative splicing (DEAS) events via qPCR. These findings can provide important guidance for subsequent studies. In addition, we also constructed nomograms to facilitate early screening by clinicians and to determine patient outcomes in NSCLC.
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Affiliation(s)
- Deze Zhao
- Department of Medical Oncology, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266003, China
| | - Chuantao Zhang
- Department of Medical Oncology, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266003, China
| | - Man Jiang
- Department of Medical Oncology, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266003, China
| | - Yongjie Wang
- Department of Thoracic Surgery; The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266003, China
| | - Yu Liang
- Department of Medical Oncology, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266003, China
| | - Li Wang
- Department of Medical Oncology, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266003, China
| | - Kang Qin
- Department of Medical Oncology, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266003, China
| | - Faisal Ul Rehman
- Department of Medical Oncology, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266003, China
| | - Xiaochun Zhang
- Department of Medical Oncology, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266003, China.,Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China
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Martinez BA, Reis Rodrigues P, Nuñez Medina RM, Mondal P, Harrison NJ, Lone MA, Webster A, Gurkar AU, Grill B, Gill MS. An alternatively spliced, non-signaling insulin receptor modulates insulin sensitivity via insulin peptide sequestration in C. elegans. eLife 2020; 9:49917. [PMID: 32096469 PMCID: PMC7041946 DOI: 10.7554/elife.49917] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/10/2020] [Indexed: 01/05/2023] Open
Abstract
In the nematode C. elegans, insulin signaling regulates development and aging in response to the secretion of numerous insulin peptides. Here, we describe a novel, non-signaling isoform of the nematode insulin receptor (IR), DAF-2B, that modulates insulin signaling by sequestration of insulin peptides. DAF-2B arises via alternative splicing and retains the extracellular ligand binding domain but lacks the intracellular signaling domain. A daf-2b splicing reporter revealed active regulation of this transcript through development, particularly in the dauer larva, a diapause stage associated with longevity. CRISPR knock-in of mScarlet into the daf-2b genomic locus confirmed that DAF-2B is expressed in vivo and is likely secreted. Genetic studies indicate that DAF-2B influences dauer entry, dauer recovery and adult lifespan by altering insulin sensitivity according to the prevailing insulin milieu. Thus, in C. elegans alternative splicing at the daf-2 locus generates a truncated IR that fine-tunes insulin signaling in response to the environment.
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Affiliation(s)
- Bryan A Martinez
- Department of Molecular Medicine, The Scripps Research Institute - Scripps Florida, Jupiter, United States
| | - Pedro Reis Rodrigues
- Department of Molecular Medicine, The Scripps Research Institute - Scripps Florida, Jupiter, United States
| | - Ricardo M Nuñez Medina
- Department of Molecular Medicine, The Scripps Research Institute - Scripps Florida, Jupiter, United States
| | - Prosenjit Mondal
- Department of Molecular Medicine, The Scripps Research Institute - Scripps Florida, Jupiter, United States
| | - Neale J Harrison
- Department of Molecular Medicine, The Scripps Research Institute - Scripps Florida, Jupiter, United States
| | - Museer A Lone
- Department of Molecular Medicine, The Scripps Research Institute - Scripps Florida, Jupiter, United States
| | - Amanda Webster
- Department of Molecular Medicine, The Scripps Research Institute - Scripps Florida, Jupiter, United States
| | - Aditi U Gurkar
- Department of Molecular Medicine, The Scripps Research Institute - Scripps Florida, Jupiter, United States
| | - Brock Grill
- Department of Neuroscience, The Scripps Research Institute - Scripps Florida, Jupiter, United States
| | - Matthew S Gill
- Department of Molecular Medicine, The Scripps Research Institute - Scripps Florida, Jupiter, United States
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40
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Huang R, Li Z, Li C, Wang G, Yan P, Peng L, Wang J, Zhu X, Hu P, Zhang J, Chang Z, Huang Z, Cheng L, Zhang J. Germ Cell-Specific Gene 1-Like Protein Regulated by Splicing Factor CUGBP Elav-Like Family Member 5 and Primary Bile Acid Biosynthesis are Prognostic in Glioblastoma Multiforme. Front Genet 2020; 10:1380. [PMID: 32117422 PMCID: PMC7010853 DOI: 10.3389/fgene.2019.01380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/18/2019] [Indexed: 12/11/2022] Open
Abstract
Background Alternative splicing (AS) modifies 92-94% human genes, abnormal splicing events might relate to tumor development and invasion. Glioblastoma Multiforme (GBM) is a fatal, invasive, and malignant tumor in nervous system. The recurrence and development leads to poor prognosis. However, few studies have focused on AS in GBM. Methods RNA-seq and Alternative splicing events (ASEs) data of GBM samples were downloaded from The Cancer Genome Atlas (TCGA) and TCGASpliceSeq databases, respectively. Firstly, the Cox regression analysis was utilized to identify the overall survival splicing events (OS-SEs). Secondly, a multivariable model was applied to access the prognostic value of risk score. Then, we constructed a co-expressed network between splicing factors (SFs) and overall survival alternative splicing events (OS-SEs). Additionally, to explore the relationship between the potential prognostic signaling pathways and OS-SEs, we constructed a network between these pathways and OS-SEs. Ultimately, to better explain the results, validations from multi-dimension platforms were applied. Results In the first step, 1,062 OS-SEs were selected by Cox regression. Then, 11 OS-SEs were integrated in a multivariate model by Lasso regression. The area under the curve (AUC) of receiver operator characteristic (ROC) curve was 0.861. In addition, the risk score generated from the multivariate model was confirmed to be an independent prognostic factor (P < 0.001). What's more, in the network of SFs and ASEs, CELF5 significantly regulated GSG1L|35696|AP and GSG1L|35698|AP (P < 0.001, R = 0.511 and = -0.492). Additionally, GSG1L|35696|AP (P = 0.006) and GSG1L|35698|AP (P = 0.007) showed a significant relationship with cancer status. Eventually, KEGG pathways related to prognosis of GBM were selected by GSVA. The primary bile acid synthesis (P < 0.001, R = 0.420) was the significant pathway co-expressed with Germ Cell-Specific Gene 1-Like Protein (GSG1L). Conclusions Based on the comprehensive bioinformatics analysis, we proposed that aberrant splicing factor CUGBP Elav-like family member 5 (CELF5) significantly, positively and negatively, regulated ASE of GSG1L, and the primary bile acid synthesis pathway might play an important role in tumorigenesis and prognosis of GBM.
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Affiliation(s)
- Runzhi Huang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.,Division of Spine, Department of Orthopedics, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai, China
| | - Zhenyu Li
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Chen Li
- Division of Spine, Department of Orthopedics, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai, China
| | - Guanghua Wang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Penghui Yan
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Li Peng
- Shanghai Key Laboratory of Meteorology and Health, Shanghai, China
| | - Jiaqi Wang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Xiaolong Zhu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Peng Hu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junfang Zhang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Zhengyan Chang
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Liming Cheng
- Division of Spine, Department of Orthopedics, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai, China
| | - Jie Zhang
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
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41
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Dou XQ, Chen XJ, Zhou Q, Wen MX, Zhang SZ, Zhang SQ. miR-335 modulates Numb alternative splicing via targeting RBM10 in endometrial cancer. Kaohsiung J Med Sci 2020; 36:171-177. [PMID: 31894898 DOI: 10.1002/kjm2.12149] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 10/13/2019] [Indexed: 12/19/2022] Open
Abstract
Numb is a conserved protein plays important roles in the development of cancer. Two Numb isoforms have been found produced by alternative splicing and play contrast roles in regulating cellular functions. It is reported that the expression of Numb long isoform (Numb-L) was increased in various kinds of cancers, but in endometrial cancer, the condition is still unknown. The level of two Numb transcripts and protein isoforms were detected by semiquantitative polymerase chain reaction and immunoblotting in 47 paired endometrial tumor and adjacent non-tumor control tissues. The level of three alternative splicing related proteins: RBM5, RBM6, and RBM10 was determined by immunoblotting. MiRNAs targeting RBM10 were predicted by bioinformatics tools and their interaction with RBM10 was confirmed by luciferase assay and immunoblotting. The function of miR-335 in endometrial cancer was examined in xenograft mouse model. Numb-L level was increased in tumors and negatively correlated with RBM10 protein level. RBM10 mRNA level was not significantly altered in endometrial tumors suggesting its expression may regulated by post transcriptional regulators such as miRNAs. We identified miR-133a, miR-133b, and miR-335 directly target RBM10, but only miR-335 level increased in tumors and negatively correlated with RBM10 protein level. miR-335 overexpression promoted tumor growth by downregulating RBM10 and upregulating Numb-L level in xenograft mouse model. miR-335 overexpression promoted Numb-L expression via targeting RBM10 in endometrial cancer, which may provide new biomarkers for EC diagnosis.
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Affiliation(s)
- Xiao-Qing Dou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China.,Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Shandong University, Jinan, China
| | - Xiu-Juan Chen
- Department of Obstetrics and Gynecology, People's Hospital of Rizhao, Rizhao, China
| | - Qun Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Ming-Xiao Wen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Shu-Zhen Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Shi-Qian Zhang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Shandong University, Jinan, China
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42
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An Intricate Connection between Alternative Splicing and Phenotypic Plasticity in Development and Cancer. Cells 2019; 9:cells9010034. [PMID: 31877720 PMCID: PMC7016785 DOI: 10.3390/cells9010034] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 12/12/2022] Open
Abstract
During tumor progression, hypoxia, nutrient deprivation or changes in the extracellular environment (i.e., induced by anti-cancer drugs) elicit adaptive responses in cancer cells. Cellular plasticity increases the chance that tumor cells may survive in a challenging microenvironment, acquire new mechanisms of resistance to conventional drugs, and spread to distant sites. Re-activation of stem pathways appears as a significant cause of cellular plasticity because it promotes the acquisition of stem-like properties through a profound phenotypic reprogramming of cancer cells. In addition, it is a major contributor to tumor heterogeneity, depending on the coexistence of phenotypically distinct subpopulations in the same tumor bulk. Several cellular mechanisms may drive this fundamental change, in particular, high-throughput sequencing technologies revealed a key role for alternative splicing (AS). Effectively, AS is one of the most important pre-mRNA processes that increases the diversity of transcriptome and proteome in a tissue- and development-dependent manner. Moreover, defective AS has been associated with several human diseases. However, its role in cancer cell plasticity and tumor heterogeneity remains unclear. Therefore, unravelling the intricate relationship between AS and the maintenance of a stem-like phenotype may explain molecular mechanisms underlying cancer cell plasticity and improve cancer diagnosis and treatment.
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43
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Dou XQ, Chen XJ, Wen MX, Zhang SZ, Zhou Q, Zhang SQ. Alternative splicing of VEGFA is regulated by RBM10 in endometrial cancer. Kaohsiung J Med Sci 2019; 36:13-19. [PMID: 31587503 DOI: 10.1002/kjm2.12127] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 08/11/2019] [Indexed: 12/31/2022] Open
Abstract
Vascular endothelial growth factor A (VEGFA) gene has three alternative exons which results in multiple isoforms. VEGFA has been found overexpressed in patients with endometrial cancer, but the VEGFA expression pattern and how it is regulated are still unknown. The level of VEGFA transcripts and protein isoforms were detected by semi-quantitative Polymerase chain reaction (PCR) and immunoblotting in 29 paired endometrial tumor and adjacent nontumor control tissues. The level of three alternative splicing related proteins: RBM5, RBM6, and RBM10 was determined by immunoblotting. The H3K27Ac level in RBM10 promoter region was detected by ChIP-PCR. The RBM10 promoter region methylation level were quantified by methylation-sensitive high resolution melting. VEGFA165a was overexpressed and VEGFA165b level was reduced in tumors. RBM10 level was reduced in tumors. RBM10 level was negatively correlated with VEGFA165a level and positively correlated with VEGFA165b level in tumors. Using HEC-1-A and RL95-2 cells, we confirmed that VEGFA165a/b expressed pattern was controlled by RBM10. MALAT1 level was increased in tumors but not involved in VEGFA alternative splicing. Reduced H3K27Ac level and increased DNA methylation in the promoter region controlled RBM10 expression in tumors. VEGFA alternative splicing in endometrial cancer was regulated by RBM10, the expression of which was controlled by histone acetylation and DNA methylation.
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Affiliation(s)
- Xiao-Qing Dou
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Shandong University, Jinan, China.,Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiu-Juan Chen
- Department of Obstetrics and Gynecology, People's Hospital of Rizhao, Rizhao, China
| | - Ming-Xiao Wen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Shu-Zhen Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Qun Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Shi-Qian Zhang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Shandong University, Jinan, China
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44
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Zuo Y, Zhang L, Tang W, Tang W. Identification of prognosis-related alternative splicing events in kidney renal clear cell carcinoma. J Cell Mol Med 2019; 23:7762-7772. [PMID: 31489763 PMCID: PMC6815842 DOI: 10.1111/jcmm.14651] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/22/2019] [Accepted: 08/10/2019] [Indexed: 02/05/2023] Open
Abstract
Alternative splicing (AS) contributes to protein diversity by modifying most gene transcriptions. Cancer generation and progression are associated with specific splicing events. However, AS signature in kidney renal clear cell carcinoma (KIRC) remains unknown. In this study, genome‐wide AS profiles were generated in 537 patients with KIRC in the cancer genome atlas. With a total of 42 522 mRNA AS events in 10 600 genes acquired, 8164 AS events were significantly associated with the survival of patients with KIRC. Logistic regression analysis of the least absolute shrinkage and selection operator was conducted to identify an optimized multivariate prognostic predicting mode containing four predictors. In this model, the receptor‐operator characteristic curves of the training set were built, and the areas under the curves (AUCs) at different times were >0.88, thus indicating a stable and powerful ability in distinguishing patients' outcome. Similarly, the AUCs of the test set at different times were >0.73, verifying the results of the training set. Correlation and gene ontology analyses revealed some potential functions of prognostic AS events. This study provided an optimized survival‐predicting model and promising data resources for future in‐depth studies on AS mechanisms in KIRC.
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Affiliation(s)
- Yongdi Zuo
- Department of NephrologyWest China HospitalSichuan UniversityChengduChina
| | - Liang Zhang
- Department of NephrologyWest China HospitalSichuan UniversityChengduChina
| | | | - Wanxin Tang
- Department of NephrologyWest China HospitalSichuan UniversityChengduChina
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45
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Zhou YJ, Zhu GQ, Zhang QW, Zheng KI, Chen JN, Zhang XT, Wang QW, Li XB. Survival-Associated Alternative Messenger RNA Splicing Signatures in Pancreatic Ductal Adenocarcinoma: A Study Based on RNA-Sequencing Data. DNA Cell Biol 2019; 38:1207-1222. [PMID: 31483163 DOI: 10.1089/dna.2019.4862] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Multiple studies have shown that cancer-specific alternative splicing (AS) alterations are associated with clinical outcome. In this study, we aimed to profile prognostic AS signatures for pancreatic ductal adenocarcinoma (PDAC). We integrated the percent-spliced-in (PSI) data of AS in 140 PDAC patients based on the Cancer Genome Atlas (TCGA) dataset. We identified overall survival (OS)-associated AS events using univariate Cox regression analysis. Then, prognostic AS signatures were constructed for OS and chemoresistance prediction using the least absolute shrinkage and selection operator (LASSO) method. We also analyzed splicing factors (SFs) regulatory networks by Pearson's correlation. We detected 677 OS-related AS events in 485 genes by profiling 10,354 AS events obtained from 140 PDAC patients. Gene functional enrichment analysis demonstrated the pathways enriched by survival-associated AS. The AS signatures constructed with significant survival-associated AS events revealed high performance in predicting PDAC survival and gemcitabine chemoresistance. The area under the receiver operator characteristic curve was 0.937 in training cohort and 0.748 in validation cohort at 2000 days of OS. Furthermore, we identified prognostic SFs (e.g., ESRP1 and HNRNPC) to build the AS regulatory network. We constructed AS signatures for OS and gemcitabine chemoresistance in PDAC patients, which may provide clues for further experiment-based mechanism study.
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Affiliation(s)
- Yu-Jie Zhou
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, China
| | - Gui-Qi Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Qing-Wei Zhang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, China
| | - Kenneth I Zheng
- Department of Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jin-Nan Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, China
| | - Xin-Tian Zhang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, China
| | - Qi-Wen Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Bo Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, China
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46
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Liang Y, Song J, He D, Xia Y, Wu Y, Yin X, Liu J. Systematic analysis of survival-associated alternative splicing signatures uncovers prognostic predictors for head and neck cancer. J Cell Physiol 2019; 234:15836-15846. [PMID: 30740675 PMCID: PMC6618130 DOI: 10.1002/jcp.28241] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/10/2019] [Accepted: 01/16/2019] [Indexed: 01/24/2023]
Abstract
BACKGROUND Previous studies have shown that alternative splicing (AS) plays a key role in carcinogenesis and prognosis of cancer. However, systematic profiles of AS signatures in head and neck cancer (HNC) have not yet been reported. METHODS In this study, AS data, RNA-Seq data, and corresponding clinicopathological information of 489 HNC patients were downloaded from The Cancer Genome Atlas. Univariate and multivariate Cox regression analyses were performed to screen for survival-associated AS events. Functional and pathway enrichment analysis was also performed. The prognostic models and splicing networks were constructed using integrated bioinformatics analysis tools. RESULTS Among the 42,849 alternating splicing events identified in 10,121 genes, 5,165 survival-associated AS events in 2,419 genes were observed in univariate Cox regression analysis. Among the seven types, alternate terminator events were the most powerful prognostic factors. Multivariate Cox analysis was then used to screen for the AS genes with prognostic value. Four candidate genes (TPM1, CLASRP, PRRC1, and DNASE1L1) were found to be independent prognostic factors for HNC patients. A prognostic prediction model was built based on the four genes. The area under the receiver operating characteristic risk score curve for predicting the survival status of HNC patients was 0.704. In addition, splicing interaction network indicated that the splicing factors have significant functions in HNC. CONCLUSION A comprehensive analysis of AS events in HNC was performed. A powerful prognostic predictor for HNC patients was established based on AS events could.
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Affiliation(s)
- Ying Liang
- Department of Orthodontics, Guiyang Hospital of Stomatology, Medical CollegeGuiyangChina,Guiyang Stomatological Hospital Affiliated to Zunyi Medical UniversityGuizhouChina
| | - Jukun Song
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's HospitalGuizhouChina
| | - Dengqi He
- Department of Stomatology, First Hospital of Lanzhou UniversityLanzhouChina
| | - Yu Xia
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's HospitalGuizhouChina
| | - Yadong Wu
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's HospitalGuizhouChina
| | - Xinhai Yin
- Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's HospitalGuizhouChina
| | - Jianguo Liu
- Special Key Laboratory of Oral Diseases Research, Stomatological Hospital Affiliated to Zunyi Medical UniversityGuizhouChina
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47
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Park J, Chung YJ. Identification of neoantigens derived from alternative splicing and RNA modification. Genomics Inform 2019; 17:e23. [PMID: 31610619 PMCID: PMC6808645 DOI: 10.5808/gi.2019.17.3.e23] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 05/09/2019] [Indexed: 01/02/2023] Open
Abstract
The acquisition of somatic mutations is the most common event in cancer. Neoantigens expressed from genes with mutations acquired during carcinogenesis can be tumor-specific. Since the immune system recognizes tumor-specific peptides, they are potential targets for personalized neoantigen-based immunotherapy. However, the discovery of druggable neoantigens remains challenging, suggesting that a deeper understanding of the mechanism of neoantigen generation and better strategies to identify them will be required to realize the promise of neoantigen-based immunotherapy. Alternative splicing and RNA editing events are emerging mechanisms leading to neoantigen production. In this review, we outline recent work involving the large-scale screening of neoantigens produced by alternative splicing and RNA editing. We also describe strategies to predict and validate neoantigens from RNA sequencing data.
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Affiliation(s)
- Jiyeon Park
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Yeun-Jun Chung
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.,Departments of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
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48
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Song J, Liu YD, Su J, Yuan D, Sun F, Zhu J. Systematic analysis of alternative splicing signature unveils prognostic predictor for kidney renal clear cell carcinoma. J Cell Physiol 2019; 234:22753-22764. [PMID: 31140607 PMCID: PMC6771988 DOI: 10.1002/jcp.28840] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/27/2019] [Accepted: 04/30/2019] [Indexed: 01/28/2023]
Abstract
There is growing evidence that alternative splicing (AS) plays an important role in cancer development. However, a comprehensive analysis of AS signatures in kidney renal clear cell carcinoma (KIRC) is lacking and urgently needed. It remains unclear whether AS acts as diagnostic biomarkers in predicting the prognosis of KIRC patients. In the work, gene expression and clinical data of KIRC were obtained from The Cancer Genome Atlas (TCGA), and profiles of AS events were downloaded from the SpliceSeq database. The RNA sequence/AS data and clinical information were integrated, and we conducted the Cox regression analysis to screen survival‐related AS events and messenger RNAs (mRNAs). Correlation between prognostic AS events and gene expression were analyzed using the Pearson correlation coefficient. Protein‐protein interaction analysis was conducted for the prognostic AS‐related genes, and a potential regulatory network was built using Cytoscape (version 3.6.1). Meanwhile, functional enrichment analysis was conducted. A prognostic risk score model is then established based on seven hub genes (KRT222, LENG8, APOB, SLC3A1, SCD5, AQP1, and ADRA1A) that have high performance in the risk classification of KIRC patients. A total 46,415 AS events including 10,601 genes in 537 patients with KIRC were identified. In univariate Cox regression analysis, 13,362 survival associated AS events and 8,694 survival‐specific mRNAs were detected. Common 3,105 genes were screen by overlapping 13,362 survival associated AS events and 8,694 survival‐specific mRNAs. The Pearson correlation analysis suggested that 13 genes were significantly correlated with AS events (Pearson correlation coefficient >0.8 or <−0.8). Then, We conducted multivariate Cox regression analyses to select the potential prognostic AS genes. Seven genes were identified to be significantly related to OS. A prognostic model based on seven genes was constructed. The area under the ROC curve was 0.767. In the current study, a robust prognostic prediction model was constructed for KIRC patients, and the findings revealed that the AS events could act as potential prognostic biomarkers for KIRC.
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Affiliation(s)
- Jukun Song
- School Of Medicine, Guizhou University, Guiyang, Guizhou, China.,Department of Oral and Maxillofacial Surgery, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Yong Da Liu
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Guangdong Key Laboratory of Urology, Guangzhou, China
| | - Jiaming Su
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Dongbo Yuan
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Fa Sun
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
| | - Jianguo Zhu
- School Of Medicine, Guizhou University, Guiyang, Guizhou, China.,Department of Urology, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China
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Wang H, Lekbaby B, Fares N, Augustin J, Attout T, Schnuriger A, Cassard AM, Panasyuk G, Perlemuter G, Bieche I, Vacher S, Selves J, Péron JM, Bancel B, Merle P, Kremsdorf D, Hall J, Chemin I, Soussan P. Alteration of splicing factors' expression during liver disease progression: impact on hepatocellular carcinoma outcome. Hepatol Int 2019; 13:454-467. [PMID: 31140152 DOI: 10.1007/s12072-019-09950-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/29/2019] [Indexed: 12/29/2022]
Abstract
PURPOSE Trans-acting splicing factors (SF) shape the eukaryotic transcriptome by regulating alternative splicing (AS). This process is recurrently modulated in liver cancer suggesting its direct contribution to the course of liver disease. The aim of our study was to investigate the relationship between the regulation of SFs expression and liver damage. METHODS The expression profile of 10 liver-specific SF and the AS events of 7 genes associated with liver disorders was assessed by western-blotting in 6 murine models representing different stages of liver damage, from inflammation to hepatocellular carcinoma (HCC). Relevant SFs (PSF, SRSF3, and SRSF6) and target genes (INSR, SRSF3, and SLK) modulated in mice were investigated in a cohort of 179 HCC patients. RESULTS Each murine model of liver disease was characterized by a unique SF expression profile. Changes in the SF profile did not affect AS events of the selected genes despite the presence of corresponding splicing sites. In human HCC expression of SFs, including the tumor-suppressor SRSF3, and AS regulation of genes studied were frequently upregulated in tumor versus non-tumor tissues. Risk of tumor recurrence positively correlated with AS isoform of the INSR gene. In contrast, increased levels of SFs expression correlated with an extended overall survival of patients. CONCLUSIONS Dysregulation of SF expression is an early event occurring during liver injury and not just at the stage of HCC. Besides impacting on AS regulation, overexpression of SF may contribute to preserving hepatocyte homeostasis during liver pathogenesis.
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Affiliation(s)
- Hualin Wang
- INSERM U1135, Centre d'immunologie et de maladie infectieuse, 91 boulevard de l'Hôpital, 75013, Paris, France.,Sorbonne Université, Paris, France
| | - Bouchra Lekbaby
- INSERM U1135, Centre d'immunologie et de maladie infectieuse, 91 boulevard de l'Hôpital, 75013, Paris, France.,Sorbonne Université, Paris, France
| | - Nadim Fares
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052, CNRS 5286, Lyon Cedex 03, France
| | - Jeremy Augustin
- INSERM U1135, Centre d'immunologie et de maladie infectieuse, 91 boulevard de l'Hôpital, 75013, Paris, France.,Sorbonne Université, Paris, France
| | - Tarik Attout
- INSERM U1135, Centre d'immunologie et de maladie infectieuse, 91 boulevard de l'Hôpital, 75013, Paris, France.,Sorbonne Université, Paris, France
| | - Aurelie Schnuriger
- INSERM U1135, Centre d'immunologie et de maladie infectieuse, 91 boulevard de l'Hôpital, 75013, Paris, France.,Sorbonne Université, Paris, France.,Département de Virologie, Hôpitaux Est Parisien, Paris, France
| | - Anne-Marie Cassard
- Faculté de médecine Paris-Sud, Université Paris-Sud, 94270, Kremlin-Bicêtre, France
| | - Ganna Panasyuk
- Institut Necker-Enfants Malades, Université Paris Descartes, Paris, France.,INSERM U1151/CNRS Unité Mixte de Recherche (UMR) 8253, Paris, France
| | - Gabriel Perlemuter
- Faculté de médecine Paris-Sud, Université Paris-Sud, 94270, Kremlin-Bicêtre, France.,AP-HP, Hôpital Antoine Béclère, Service d'hépato-gastroentérologie, 92140, Clamart, France
| | | | | | - Janick Selves
- Institut Universitaire de Cancérologie de Toulouse Oncopole, Université Paul Sabatier, Toulouse, France
| | - Jean-Marie Péron
- Institut Universitaire de Cancérologie de Toulouse Oncopole, Université Paul Sabatier, Toulouse, France
| | - Brigitte Bancel
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052, CNRS 5286, Lyon Cedex 03, France
| | - Philippe Merle
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052, CNRS 5286, Lyon Cedex 03, France
| | - Dina Kremsdorf
- INSERM U1135, Centre d'immunologie et de maladie infectieuse, 91 boulevard de l'Hôpital, 75013, Paris, France.,Sorbonne Université, Paris, France
| | - Janet Hall
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052, CNRS 5286, Lyon Cedex 03, France
| | - Isabelle Chemin
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052, CNRS 5286, Lyon Cedex 03, France
| | - Patrick Soussan
- INSERM U1135, Centre d'immunologie et de maladie infectieuse, 91 boulevard de l'Hôpital, 75013, Paris, France. .,Sorbonne Université, Paris, France. .,Département de Virologie, Hôpitaux Est Parisien, Paris, France.
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Zhu GQ, Zhou YJ, Qiu LX, Wang B, Yang Y, Liao WT, Luo YH, Shi YH, Zhou J, Fan J, Dai Z. Prognostic alternative mRNA splicing signature in hepatocellular carcinoma: a study based on large-scale sequencing data. Carcinogenesis 2019; 40:1077-1085. [PMID: 31099827 DOI: 10.1093/carcin/bgz073] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 04/01/2019] [Accepted: 04/10/2019] [Indexed: 02/05/2023] Open
Abstract
Most genes are alternatively spliced and increasing number of evidences show that alternative splicing (AS) is modified and related to tumor progression. Systematic profiles of AS signature in hepatocellular carcinoma (HCC) is absent and urgently needed. Here, differentially spliced AS transcripts between HCC and non-HCC tissues were compared, prognosis-associated AS events by using univariate Cox regression analysis were selected. Our gene functional enrichment analysis demonstrated the potential pathways enriched by survival-associated AS. Prognostic AS signatures were then constructed for HCC prognosis prediction by Lasso regression model. We also analyzed splicing factors (SFs) regulating underlying mechanisms by Pearson correlation and then built corresponding regulatory networks. In addition, we explored the performance of AS signature in the mutated HCC samples. Genome-wide AS events in 377 HCC patients from TCGA were profiled. Among 34 163 AS events in 8985 genes, 3950 AS events in 2403 genes associated with overall survival (OS) significantly for HCC were detected. In addition, computational algorithm results showed that metabolic and ribosome pathways may be the potential molecular mechanisms regulating the poor prognosis. More importantly, survival-associated AS signatures revealed high performance in predicting HCC prognosis. The area under curve for AS signature was 0.806 in all HCC and 0.944 in TP53 mutated HCC samples at 2000 days of OS. We submitted prognostic SFs to build the AS regulatory network, from which we found prognostic AS events were significantly enriched in metabolism-related pathways. A robust AS signature for HCC patients and revealed the regulatory splicing networks contributing to the potential significantly enriched metabolism-related pathways.
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Affiliation(s)
- Gui-Qi Zhu
- Liver Cancer Institute, Zhongshan Hospital.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Yu-Jie Zhou
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Renji Hospital, School of Medicine, Shanghai Institute of Digestive Disease, Shanghai Jiao Tong University, Shanghai, China
| | - Li-Xin Qiu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Biao Wang
- Liver Cancer Institute, Zhongshan Hospital.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Yi Yang
- Liver Cancer Institute, Zhongshan Hospital.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Wei-Ting Liao
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yi-Hong Luo
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ying-Hong Shi
- Liver Cancer Institute, Zhongshan Hospital.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Jian Zhou
- Liver Cancer Institute, Zhongshan Hospital.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Zhi Dai
- Liver Cancer Institute, Zhongshan Hospital.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
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