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Xi Y, Abuduxiku M, Qu M. GRN knockdown regulates the expression and alternative splicing of genes associated with aphasia-related diseases in PC12 cells. Brain Res 2024; 1840:149031. [PMID: 38823507 DOI: 10.1016/j.brainres.2024.149031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/15/2024] [Accepted: 05/25/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Prior research has shown that granulin precursor (GRN, also termed PGRN) is closely linked to aphasia. However, there has been little research on the mechanism of action of GRN in post-stroke aphasia (PSA). METHODS In this study, RT-qPCR was used to identify variations in gene expression, while RNA sequencing (RNA-seq) was utilized to acquire transcriptional profiles. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were employed for bioinformatics analysis. RESULTS GRN was considerably more active in PSA subjects. After silencing the GRN, 197 transcripts had differential expression, and 237 alternative splicing events (ASEs) were substantially affected. The analysis of differentially expressed genes (DEGs) using GO and KEGG approaches showed that these genes have various molecular functions and are significantly enriched in metabolic signaling pathways. Regarding Alternative Splicing (AS), the GO and KEGG analyses revealed numerous functional genes involved in transcription and metabolism. CONCLUSIONS The knockdown of GRN has been shown to be associated with alterations in transcription, metabolism, and ASEs, potentially impacting transcriptional and metabolic pathways through its involvement in AS. Furthermore, GRN knockdown is associated with nervous system disease-related gene transcription and AS processes, as well as its involvement in G protein-coupled receptor (GPCR) and wingless/integrated (Wnt) signaling pathways, which impact the initiation and resolution of PSA.
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Affiliation(s)
- Yanling Xi
- Department of Rehabilitation Medicine, Shanghai Pudong New Area Guangming Hospital of Traditional Chinese Medicine, China
| | - Munire Abuduxiku
- Department of Rehabilitation Medicine, The Affiliated Hospital of Traditional Chinese Medicine of Xinjiang Medical University, China
| | - Mei Qu
- Department of Rehabilitation Medicine, Shanghai Pudong New Area Guangming Hospital of Traditional Chinese Medicine, China.
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2
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Lambourne L, Mattioli K, Santoso C, Sheynkman G, Inukai S, Kaundal B, Berenson A, Spirohn-Fitzgerald K, Bhattacharjee A, Rothman E, Shrestha S, Laval F, Yang Z, Bisht D, Sewell JA, Li G, Prasad A, Phanor S, Lane R, Campbell DM, Hunt T, Balcha D, Gebbia M, Twizere JC, Hao T, Frankish A, Riback JA, Salomonis N, Calderwood MA, Hill DE, Sahni N, Vidal M, Bulyk ML, Fuxman Bass JI. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584681. [PMID: 38617209 PMCID: PMC11014633 DOI: 10.1101/2024.03.12.584681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Most human Transcription factors (TFs) genes encode multiple protein isoforms differing in DNA binding domains, effector domains, or other protein regions. The global extent to which this results in functional differences between isoforms remains unknown. Here, we systematically compared 693 isoforms of 246 TF genes, assessing DNA binding, protein binding, transcriptional activation, subcellular localization, and condensate formation. Relative to reference isoforms, two-thirds of alternative TF isoforms exhibit differences in one or more molecular activities, which often could not be predicted from sequence. We observed two primary categories of alternative TF isoforms: "rewirers" and "negative regulators", both of which were associated with differentiation and cancer. Our results support a model wherein the relative expression levels of, and interactions involving, TF isoforms add an understudied layer of complexity to gene regulatory networks, demonstrating the importance of isoform-aware characterization of TF functions and providing a rich resource for further studies.
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Affiliation(s)
- Luke Lambourne
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kaia Mattioli
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Clarissa Santoso
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Gloria Sheynkman
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sachi Inukai
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Babita Kaundal
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna Berenson
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA
| | - Kerstin Spirohn-Fitzgerald
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anukana Bhattacharjee
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Elisabeth Rothman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Florent Laval
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Zhipeng Yang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Deepa Bisht
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared A Sewell
- Department of Biology, Boston University, Boston, MA, USA
| | - Guangyuan Li
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anisa Prasad
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Harvard College, Cambridge MA, USA
| | - Sabrina Phanor
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ryan Lane
- Department of Biology, Boston University, Boston, MA, USA
| | | | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dawit Balcha
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marinella Gebbia
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Jean-Claude Twizere
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adam Frankish
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Josh A Riback
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Juan I Fuxman Bass
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA
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de Jong GW, Adams KL. Subgenome-dominant expression and alternative splicing in response to Sclerotinia infection in polyploid Brassica napus and progenitors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:142-158. [PMID: 36710652 DOI: 10.1111/tpj.16127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Polyploidy has played an extensive role in the evolution of flowering plants. Allopolyploids, with subgenomes containing duplicated gene pairs called homeologs, can show rapid transcriptome changes including novel alternative splicing (AS) patterns. The extent to which abiotic stress modulates AS of homeologs is a nascent topic in polyploidy research. We subjected both resynthesized and natural lines of polyploid Brassica napus, along with the progenitors Brassica rapa and Brassica oleracea, to infection with the fungal pathogen Sclerotinia sclerotiorum. RNA-sequencing analyses revealed widespread divergence between polyploid subgenomes in both gene expression and AS patterns. Resynthesized B. napus displayed significantly more A and C subgenome biased homeologs under pathogen infection than during uninfected growth. Differential AS (DAS) in response to infection was highest in natural B. napus (12 709 DAS events) and lower in resynthesized B. napus (8863 DAS events). Natural B. napus had more upregulated events and fewer downregulated events. There was a global expression bias towards the B. oleracea-derived (C) subgenome in both resynthesized and natural B. napus, enhanced by widespread non-parental downregulation of the B. rapa-derived (A) homeolog. In the resynthesized B. napus, this resulted in a disproportionate C subgenome contribution to the pathogen defense response, characterized by biases in both transcript expression levels and the proportion of induced genes. Our results elucidate the complex ways in which Sclerotinia infection affects expression and AS of homeologous genes in resynthesized and natural B. napus.
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Affiliation(s)
- Grant W de Jong
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Keith L Adams
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
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Goslin K, Finocchio A, Wellmer F. Floral Homeotic Factors: A Question of Specificity. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12051128. [PMID: 36903987 PMCID: PMC10004826 DOI: 10.3390/plants12051128] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 05/27/2023]
Abstract
MADS-domain transcription factors are involved in the control of a multitude of processes in eukaryotes, and in plants, they play particularly important roles during reproductive development. Among the members of this large family of regulatory proteins are the floral organ identity factors, which specify the identities of the different types of floral organs in a combinatorial manner. Much has been learned over the past three decades about the function of these master regulators. For example, it has been shown that they have similar DNA-binding activities and that their genome-wide binding patterns exhibit large overlaps. At the same time, it appears that only a minority of binding events lead to changes in gene expression and that the different floral organ identity factors have distinct sets of target genes. Thus, binding of these transcription factors to the promoters of target genes alone may not be sufficient for their regulation. How these master regulators achieve specificity in a developmental context is currently not well understood. Here, we review what is known about their activities and highlight open questions that need to be addressed to gain more detailed insights into the molecular mechanisms underlying their functions. We discuss evidence for the involvement of cofactors as well as the results from studies on transcription factors in animals that may be instructive for a better understanding of how the floral organ identity factors achieve regulatory specificity.
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DAZAP1 overexpression promotes growth of HCC cell lines: a primary study using CEUS. Clin Transl Oncol 2022; 24:1168-1176. [PMID: 35091997 DOI: 10.1007/s12094-021-02758-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/08/2021] [Indexed: 10/19/2022]
Abstract
PURPOSE Hepatocellular carcinoma (HCC) is one of the most common types of hepatic carcinoma. The overall prognosis is poor. DAZAP1, a regulator of alternative splicing (AS) events, may participate in tumor growth. METHODS We collected 105 HCC patients and tissue samples from the Department of Hepatological Surgery in the Second Affiliated Hospital of Qiqihar Medical University. TCGA datasets were downloaded and operated using the R project. DAZAP1 expressions were examined by quantitative RT-PCR and western blotting. CCK8 assay was used to investigate the cell proliferation, and transwell assay was employed to examine the ability of migration and invasion in vitro. Contrast-enhanced ultrasound (CEUS) was used to evaluate images and parameters of the tumor. RESULTS DAZAP1 is highly expressed in the tissue samples of HCC. The peak intensity (PI) and area under the curve (AUC) of the tumor is higher than that of liver parenchyma, and correlated with high DAZAP1 expression. Parameters of CEUS in the tumor are correlated with TNM stage, tumor size, and vascularity. High DAZAP1 expression correlates with a shorter survival time and advanced histologic grade (G3-G4). Bioinformatical analysis revealed that downregulation of DAZAP1 identified differentiated expressed genes (DEGs) involved in the tumor growth process. CONCLUSIONS DAZAP1 is highly expressed in hepatic carcinoma and related to the blood flow, and high DAZAP1 expression predicts poor prognosis. DAZAP1 may promote liver carcinoma cell proliferation, migration, and invasion of HEPG2 cells. CEUS parameters are related to the high DAZAP1 expression, and will help to differentiate the HCC tumor.
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ABA Mediates Plant Development and Abiotic Stress via Alternative Splicing. Int J Mol Sci 2022; 23:ijms23073796. [PMID: 35409156 PMCID: PMC8998868 DOI: 10.3390/ijms23073796] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/25/2022] [Accepted: 03/27/2022] [Indexed: 02/01/2023] Open
Abstract
Alternative splicing (AS) exists in eukaryotes to increase the complexity and adaptability of systems under biophysiological conditions by increasing transcriptional and protein diversity. As a classic hormone, abscisic acid (ABA) can effectively control plant growth, improve stress resistance, and promote dormancy. At the transcriptional level, ABA helps plants respond to the outside world by regulating transcription factors through signal transduction pathways to regulate gene expression. However, at the post-transcriptional level, the mechanism by which ABA can regulate plant biological processes by mediating alternative splicing is not well understood. Therefore, this paper briefly introduces the mechanism of ABA-induced alternative splicing and the role of ABA mediating AS in plant response to the environment and its own growth.
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7
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Zhang B, Yao K, Cheng C. A network-based integration for understanding racial disparity in prostate cancer. Transl Oncol 2022; 17:101327. [PMID: 34998235 PMCID: PMC8738961 DOI: 10.1016/j.tranon.2021.101327] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/24/2022] Open
Abstract
Compared to Caucasians (CAs), African Americans (AAs) have a higher rate of incidence and mortality in prostate cancer and are prone to be diagnosed at later stages. To understand this racial disparity, molecular features of different types, including gene expression, DNA methylation and other genomic alterations, have been compared between tumor samples from the two races, but led to different disparity associated genes (DAGs). In this study, we applied a network-based algorithm to integrate a comprehensive set of genomic datasets and identified 130 core DAGs. Out of these genes, 78 were not identified by any individual dataset but prioritized and selected through network propagation. We found DAGs were highly enriched in several critical prostate cancer-related signaling transduction and cell cycle pathways and were more likely to be associated with patient prognosis in prostate cancer. Furthermore, DAGs were over-represented in prostate cancer risk genes identified from previous genome wide association studies. We also found DAGs were enriched in kinase and transcription factor encoding genes. Interestingly, for many of these prioritized kinases their association with racial disparity did not manifest from the original genomic/transcriptomic data but was reflected by their differential phosphorylation levels between AA and CA prostate tumor samples. Similarly, the disparity relevance of some transcription factors was not reflected at the mRNA or protein expression level, but at the activity level as demonstrated by their differential ability in regulating target gene expression. Our integrative analysis provided new candidate targets for improving prostate cancer treatment and addressing the racial disparity problem.
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Affiliation(s)
- Baoyi Zhang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX 77030, United States
| | - Kevin Yao
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, United States; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, United States; Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX 77030, United States.
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8
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Zhang H, Lu X, Huang G, Hua M, Zhang W, Wang T, Huang L, Wang Z, Chen Q, Li J, Yang Q, Yang G. A genomic mutation spectrum of collecting duct carcinoma in the Chinese population. BMC Med Genomics 2022; 15:1. [PMID: 34980126 PMCID: PMC8722201 DOI: 10.1186/s12920-021-01143-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/01/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Renal collecting duct carcinoma (CDC) is a rare and lethal subtype of renal cell carcinoma (RCC). The genomic profile of the Chinese population with CDC remains unclear. In addition, clinical treatments are contradictory. In this study, we aimed to identify the genomic mutation spectrum of CDC in the Chinese population. METHODS Whole-exome sequencing was performed using the Illumina Novaseq™ 6000 platform. MuTect2 detects single-nucleotide variants (SNVs) and small scale insertions/deletions (INDELs). The identified mutations were annotated with ANNOVAR and validated by Sanger sequencing. Control-FREEC was used to detect copy number variation (CNV), and GISTIC was applied to detect frequently mutated altered regions. These data were compared with associated The Cancer Genome Atlas cohorts. RESULTS Ten normal-matched CDC patients were included. The mean tumour mutation burden was 1.37 Mut/Mb. Six new recurrent somatic mutated genes were identified, including RBM14, MTUS1, GAK, DST, RNF213 and XIRP2 (20% and 2 of 10, respectively), and validated by Sanger sequencing. In terms of common mutated genes, SETD2 was altered in both CDC and other RCC subtypes but not in bladder urothelial carcinoma (BLCA); CDKN2A was a driver gene in both CDC (SNV: 10%, 1 of 10) and BLCA but not in other RCC subtypes. Next, 29 amplifications and 6 deletions of recurrent focal somatic CNVs were identified by GISTIC2.0, which displayed differences from kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP) and BLCA cohorts. Of note, CDKN2A (CNV alteration: 30%, 3 of 10) and CDKN2A-AS1 were the only overlapping genes of these four cohorts. Importantly, the CDKN2A mutation in our cohort differed from previous studies in urinary carcinomas. Moreover, CDKN2A-altered cases had significantly worse overall survival than wild-type cases in both KIRC and KIRP cohorts. In addition, the most frequently altered genomic pathway of our CDC cohort was the CDKN2A-mediated p53/RB1 pathway. CONCLUSIONS Our study offers the first genomic spectrum of the Chinese population with CDC, which differs from that of the Western population. The altered CDKN2A-mediated p53/RB1 pathway might provide new insight into potential therapeutic targets for CDC patients.
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Affiliation(s)
- Huaru Zhang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China
- Department of Urology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Xiaojun Lu
- Department of Urology, the First Affiliated Hospital, Naval Military Medical University, Shanghai, 200433, China
| | - Gang Huang
- Department of Urology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Meimian Hua
- Department of Urology, the First Affiliated Hospital, Naval Military Medical University, Shanghai, 200433, China
| | - Wenhui Zhang
- Department of Urology, the First Affiliated Hospital, Naval Military Medical University, Shanghai, 200433, China
| | - Tao Wang
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Liqun Huang
- Department of Urology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Ziwei Wang
- Department of Urology, the First Affiliated Hospital, Naval Military Medical University, Shanghai, 200433, China
| | - Qing Chen
- Department of Urology, the First Affiliated Hospital, Naval Military Medical University, Shanghai, 200433, China
| | - Jing Li
- Department of Bioinformatics, Center for Translational Medicine, Second Military Medical University, Shanghai, 200433, China.
| | - Qing Yang
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200011, China.
| | - Guosheng Yang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China.
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, 510317, China.
- Department of Urology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China.
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Abstract
Alternative splicing enables higher eukaryotes to expand mRNA diversity from a finite number of genes through highly combinatorial splice site selection mechanisms that are influenced by the sequence of competing splice sites, cis-regulatory elements binding trans-acting factors, the length of exons and introns harbouring alternative splice sites and RNA secondary structures at putative splice junctions. To test the hypothesis that the intron definition or exon definition modes of splice site recognition direct the selection of alternative splice patterns, we created a database of alternative splice site usage (ALTssDB). When alternative splice sites are embedded within short introns (intron definition), the 5' and 3' splice sites closest to each other across the intron preferentially pair, consistent with previous observations. However, when alternative splice sites are embedded within large flanking introns (exon definition), the 5' and 3' splice sites closest to each other across the exon are preferentially selected. Thus, alternative splicing decisions are influenced by the intron and exon definition modes of splice site recognition. The results demonstrate that the spliceosome pairs splice sites that are closest in proximity within the unit of initial splice site selection.
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Affiliation(s)
- Francisco Carranza
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, USA
| | - Hossein Shenasa
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, USA
| | - Klemens J Hertel
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California, USA
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TF-RBP-AS Triplet Analysis Reveals the Mechanisms of Aberrant Alternative Splicing Events in Kidney Cancer: Implications for Their Possible Clinical Use as Prognostic and Therapeutic Biomarkers. Int J Mol Sci 2021; 22:ijms22168789. [PMID: 34445498 PMCID: PMC8395830 DOI: 10.3390/ijms22168789] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/30/2021] [Accepted: 08/11/2021] [Indexed: 12/17/2022] Open
Abstract
Aberrant alternative splicing (AS) is increasingly linked to cancer; however, how AS contributes to cancer development still remains largely unknown. AS events (ASEs) are largely regulated by RNA-binding proteins (RBPs) whose ability can be modulated by a variety of genetic and epigenetic mechanisms. In this study, we used a computational framework to investigate the roles of transcription factors (TFs) on regulating RBP-AS interactions. A total of 6519 TF–RBP–AS triplets were identified, including 290 TFs, 175 RBPs, and 16 ASEs from TCGA–KIRC RNA sequencing data. TF function categories were defined according to correlation changes between RBP expression and their targeted ASEs. The results suggested that most TFs affected multiple targets, and six different classes of TF-mediated transcriptional dysregulations were identified. Then, regulatory networks were constructed for TF–RBP–AS triplets. Further pathway-enrichment analysis showed that these TFs and RBPs involved in triplets were enriched in a variety of pathways that were associated with cancer development and progression. Survival analysis showed that some triplets were highly associated with survival rates. These findings demonstrated that the integration of TFs into alternative splicing regulatory networks can help us in understanding the roles of alternative splicing in cancer.
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11
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Cheng C, Liu L, Bao Y, Yi J, Quan W, Xue Y, Sun L, Zhang Y. SUVA: splicing site usage variation analysis from RNA-seq data reveals highly conserved complex splicing biomarkers in liver cancer. RNA Biol 2021; 18:157-171. [PMID: 34152934 DOI: 10.1080/15476286.2021.1940037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Most of the current alternative splicing (AS) analysis tools are powerless to analyse complex splicing. To address this, we developed SUVA (Splice sites Usage Variation Analysis) that decomposes complex splicing events into five types of splice junction pairs. By analysing real and simulated data, SUVA showed higher sensitivity and accuracy in detecting AS events than the compared methods. Notably, SUVA detected extensive complex AS events and screened out 69 highly conserved and dominant AS events associated with cancer. The cancer-associated complex AS events in FN1 and the co-regulated RNA-binding proteins were significantly correlated with patient survival.
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Affiliation(s)
- Chao Cheng
- ABLife BioBigData Institute, Wuhan, Hubei China.,Center for Genome Analysis, ABLife Inc., Wuhan, Hubei China
| | - Lei Liu
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun China
| | - Yongli Bao
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun China
| | - Jingwen Yi
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun China
| | - Weili Quan
- ABLife BioBigData Institute, Wuhan, Hubei China
| | - Yaqiang Xue
- ABLife BioBigData Institute, Wuhan, Hubei China
| | - Luguo Sun
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun China
| | - Yi Zhang
- ABLife BioBigData Institute, Wuhan, Hubei China.,Center for Genome Analysis, ABLife Inc., Wuhan, Hubei China
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12
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Madhavan BK, Han Z, Singh B, Bordt N, Kaymak S, Bandapalli OR, Kihm L, Shahzad K, Isermann B, Herzig S, Nawroth P, Kumar V. Elevated Expression of the RAGE Variant- V in SCLC Mitigates the Effect of Chemotherapeutic Drugs. Cancers (Basel) 2021; 13:cancers13112843. [PMID: 34200336 PMCID: PMC8201239 DOI: 10.3390/cancers13112843] [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: 04/19/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Radiomimetic drugs induce extensive genotoxic insults to their target cells. Irreparable DNA damage leaves cells with the choice between a program leading to cell death or senescence, but not DNA repair. Among the challenges of an advanced stage of small cell lung carcinoma (SCLC), the resistance to radiomimetic drugs is the most prominent one. In SCLC, the initial chemotherapeutic treatment primes cell to modify their DNA repair and cell cycle regulatory systems, using alternative but highly efficient forms of DNA repair and auxiliary factors. This modulated system now bypasses several regulatory controls. Thus, at this stage, cells become resistant to any beneficial effects of chemotherapeutic drugs. In the present study, we observed that variant-V of the receptor for advanced glycation end-products (RAGE) is abundantly expressed in advancing and metastasizing SCLC. Therefore, it may serve as a potential target for specific therapeutic interventions directed to SCLC. Abstract Small cell lung carcinoma (SCLC) is a highly aggressive malignancy with a very high mortality rate. A prominent part of this is because these carcinomas are refractory to chemotherapies, such as etoposide or cisplatin, making effective treatment almost impossible. Here, we report that elevated expression of the RAGE variant-V in SCLC promotes homology-directed DNA DSBs repair when challenged with anti-cancer drugs. This variant exclusively localizes to the nucleus, interacts with members of the double-strand break (DSB) repair machinery and thus promotes the recruitment of DSBs repair factors at the site of damage. Increased expression of this variant thus, promotes timely DNA repair. Congruently, the tumor cells expressing high levels of variant-V can tolerate chemotherapeutic drug treatment better than the RAGE depleted cells. Our findings reveal a yet undisclosed role of the RAGE variant-V in the homology-directed DNA repair. This variant thus can be a potential target to be considered for future therapeutic approaches in advanced SSLC.
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Affiliation(s)
- Bindhu K. Madhavan
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, 69120 Heidelberg, Germany; (B.K.M.); (Z.H.); (B.S.); (N.B.); (S.K.); (L.K.); (P.N.)
| | - Zhe Han
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, 69120 Heidelberg, Germany; (B.K.M.); (Z.H.); (B.S.); (N.B.); (S.K.); (L.K.); (P.N.)
| | - Bishal Singh
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, 69120 Heidelberg, Germany; (B.K.M.); (Z.H.); (B.S.); (N.B.); (S.K.); (L.K.); (P.N.)
| | - Nico Bordt
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, 69120 Heidelberg, Germany; (B.K.M.); (Z.H.); (B.S.); (N.B.); (S.K.); (L.K.); (P.N.)
| | - Serap Kaymak
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, 69120 Heidelberg, Germany; (B.K.M.); (Z.H.); (B.S.); (N.B.); (S.K.); (L.K.); (P.N.)
| | - Obul Reddy Bandapalli
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany;
- Medical Faculty, Heidelberg University, 69117 Heidelberg, Germany
| | - Lars Kihm
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, 69120 Heidelberg, Germany; (B.K.M.); (Z.H.); (B.S.); (N.B.); (S.K.); (L.K.); (P.N.)
| | - Khurrum Shahzad
- Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, 04103 Leipzig, Germany; (K.S.); (B.I.)
| | - Berend Isermann
- Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, 04103 Leipzig, Germany; (K.S.); (B.I.)
| | - Stephan Herzig
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany;
- Molecular Metabolic Control, Technical University Munich, 80333 Munich, Germany
- Helmholtz Center Munich, Institute for Diabetes and Cancer, D-85764 Neuherberg, Germany
- Joint Heidelberg-IDC Translational Diabetes Programm, Helmholtz-Zentrum, 69120 Heidelberg, Germany
| | - Peter Nawroth
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, 69120 Heidelberg, Germany; (B.K.M.); (Z.H.); (B.S.); (N.B.); (S.K.); (L.K.); (P.N.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany;
- Joint Heidelberg-IDC Translational Diabetes Programm, Helmholtz-Zentrum, 69120 Heidelberg, Germany
| | - Varun Kumar
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, 69120 Heidelberg, Germany; (B.K.M.); (Z.H.); (B.S.); (N.B.); (S.K.); (L.K.); (P.N.)
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany;
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, 69117 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-56-6960
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13
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Chandra A, Ananda H, Singh N, Qamar I. Identification of a novel and potent small molecule inhibitor of SRPK1: mechanism of dual inhibition of SRPK1 for the inhibition of cancer progression. Aging (Albany NY) 2020; 13:163-180. [PMID: 33291073 PMCID: PMC7835025 DOI: 10.18632/aging.202301] [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: 05/21/2020] [Accepted: 08/19/2020] [Indexed: 01/05/2023]
Abstract
Protein kinases are the family of attractive enzyme targets for drug design with relevance to cancer biology. Serine arginine protein kinase 1 (SRPK1) is responsible for the phosphorylation of serine/arginine (SR)-rich proteins. Alternative Splicing Factor/Splicing Factor 2 (ASF/SF2) involved in mRNA editing. ASF/SF2 is over expressed in many cancers and plays crucial roles in the cell survival. Phosphorylation of ASF/SF2 is decisive for its functions in cancer. In search of potential anticancer therapeutic agents for attenuating phosphorylation of ASF/SF2, we have explored specific and potential inhibitors of SRPK1 from natural and drug like compounds databases using in-silico methods. Compound ZINC02154892 (C02) was found to be the most potent inhibitor for SRPK1. In-vitro molecular and cell biology studies have shown C02 as a potent and specific inhibitor of phosphorylation of ASF/SF2 and cell survival in leukemic cell line. Structural analysis of SRPK1 with compound C02 revealed a unique pattern of binding targeting ATP binding site along with inhibiting recruitment of ASF/SF2 by SRPK1. The possibilities of compound C02 to be used as a lead compound paving way for the development of potent and specific inhibitors of SRPK1 for designing of novel potential anticancer inhibitor is inferred from the current studies.
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Affiliation(s)
- Anshuman Chandra
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Hanumappa Ananda
- Department of Clinical Embryology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
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14
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Mei C, Song PY, Zhang W, Zhou HH, Li X, Liu ZQ. Aberrant RNA Splicing Events Driven by Mutations of RNA-Binding Proteins as Indicators for Skin Cutaneous Melanoma Prognosis. Front Oncol 2020; 10:568469. [PMID: 33178596 PMCID: PMC7593665 DOI: 10.3389/fonc.2020.568469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/14/2020] [Indexed: 12/29/2022] Open
Abstract
The worldwide incidence of skin cutaneous melanoma (SKCM) is increasing at a more rapid rate than other tumors. Aberrant alternative splicing (AS) is found to be common in cancer; however, how this process contributes to cancer prognosis still remains largely unknown. Mutations in RNA-binding proteins (RBPs) may trigger great changes in the splicing process. In this study, we comprehensively analyzed DNA and RNA sequencing data and clinical information of SKCM patients, together with widespread changes in splicing patterns induced by RBP mutations. We screened mRNA expression-related and prognosis-related mutations in RBPs and investigated the potential affections of RBP mutations on splicing patterns. Mutations in 853 RBPs were demonstrated to be correlated with splicing aberrations (p < 0.01). Functional enrichment analysis revealed that these alternative splicing events (ASEs) may participate in tumor progress by regulating the modification process, cell-cycle checkpoint, metabolic pathways, MAPK signaling, PI3K-Akt signaling, and other important pathways in cancer. We also constructed a prediction model based on overall survival-related AS events (OS-ASEs) affected by RBP mutations, which exhibited a good predict efficiency with the area under the curve of 0.989. Our work highlights the importance of RBP mutations in splicing alterations and provides effective biomarkers for prediction of prognosis of SKCM.
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Affiliation(s)
- Chao Mei
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Key Laboratory of Biological Nanotechnology of National Health Commission, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Pei-Yuan Song
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Key Laboratory of Biological Nanotechnology of National Health Commission, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Wei Zhang
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Key Laboratory of Biological Nanotechnology of National Health Commission, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Key Laboratory of Biological Nanotechnology of National Health Commission, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Xi Li
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Key Laboratory of Biological Nanotechnology of National Health Commission, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Key Laboratory of Biological Nanotechnology of National Health Commission, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Engineering Research Center for Applied Technology of Pharmacogenomics of Ministry of Education, Institute of Clinical Pharmacology, Central South University, Changsha, China
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15
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A Genetic Screen for Human Genes Suppressing FUS Induced Toxicity in Yeast. G3-GENES GENOMES GENETICS 2020; 10:1843-1852. [PMID: 32276960 PMCID: PMC7263679 DOI: 10.1534/g3.120.401164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
FUS is a nucleic acid binding protein that, when mutated, cause a subset of familial amyotrophic lateral sclerosis (ALS). Expression of FUS in yeast recapitulates several pathological features of the disease-causing mutant proteins, including nuclear to cytoplasmic translocation, formation of cytoplasmic inclusions, and cytotoxicity. Genetic screens using the yeast model of FUS have identified yeast genes and their corresponding human homologs suppressing FUS induced toxicity in yeast, neurons and animal models. To expand the search for human suppressor genes of FUS induced toxicity, we carried out a genome-scale genetic screen using a newly constructed library containing 13570 human genes cloned in an inducible yeast-expression vector. Through multiple rounds of verification, we found 37 human genes that, when overexpressed, suppress FUS induced toxicity in yeast. Human genes with DNA or RNA binding functions are overrepresented among the identified suppressor genes, supporting that perturbations of RNA metabolism is a key underlying mechanism of FUS toxicity.
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16
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Wang Y, Chen SX, Rao X, Liu Y. Modulator-Dependent RBPs Changes Alternative Splicing Outcomes in Kidney Cancer. Front Genet 2020; 11:265. [PMID: 32273884 PMCID: PMC7113372 DOI: 10.3389/fgene.2020.00265] [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: 01/20/2020] [Accepted: 03/05/2020] [Indexed: 12/19/2022] Open
Abstract
Alternative splicing alterations can contribute to human disease. The ability of an RNA-binding protein to regulate alternative splicing outcomes can be modulated by a variety of genetic and epigenetic mechanisms. In this study, we use a computational framework to investigate the roles of certain genes, termed modulators, on changing RBPs' effect on splicing regulation. A total of 1,040,254 modulator-mediated RBP-splicing interactions were identified, including 137 RBPs, 4,309 splicing events and 2,905 modulator candidates from TCGA-KIRC RNA sequencing data. Modulators function categories were defined according to the correlation changes between RBPs expression and their targets splicing outcomes. QKI, as one of the RBPs influencing the most splicing events, attracted our attention in this study: 2,014 changing triplets were identified, including 1,101 modulators and 187 splicing events. Pathway enrichment analysis showed that QKI splicing targets were enriched in tight junction pathway, endocytosis and MAPK signaling pathways, all of which are highly associated with cancer development and progression. This is the first instance of a comprehensive study on how alternative splicing outcomes changes are associated with different expression level of certain proteins, even though they were regulated by the same RBP. Our work may provide a novel view on understanding alternative splicing mechanisms in kidney cancer.
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Affiliation(s)
- Yang Wang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.,State Key Laboratory of Biocatalysts and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Steven X Chen
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Xi Rao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
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17
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Gao L, He RQ, Huang ZG, Dang YW, Gu YY, Yan HB, Li SH, Chen G. Genome-wide Analysis of the Alternative Splicing Profiles Revealed Novel Prognostic Index for Kidney Renal Cell Clear Cell Carcinoma. J Cancer 2020; 11:1542-1554. [PMID: 32047561 PMCID: PMC6995393 DOI: 10.7150/jca.36998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 12/13/2019] [Indexed: 11/21/2022] Open
Abstract
Alternative splicing (AS) is a major mechanism that greatly enhanced the diversity of proteome. Mounting evidence demonstrated that aberration of AS are important steps for the initiation and progression of human cancers. Here, we comprehensively investigated the association between whole landscape of AS profiles and the survival outcome of renal cell carcinoma (RCC) patients using RNA-seq data from TCGA SpliceSeq. Because of the limited number size of deaths in kidney chromophobe renal cell carcinoma (KICH) and papillary renal cell carcinoma (KIRP) TCGA cohorts, we only conducted survival analysis in kidney clear renal cell carcinoma (KIRC). We further constructed prognostic index (PI) based on prognosis-related AS events and built correlation network for splicing factors and prognosis-related AS events. According to the results, a total of 5351 AS events in 3522 genes were significantly correlated with the overall survival (OS) of kidney clear cell renal cell carcinoma (KIRC) patients. Seven of the PI models exhibited preferable prognosis-predicting capacity for KIRC with PI-ALL reaching the highest area under curve value of 0.875. The splicing regulatory network between splicing factors and prognosis-related AS events depicted a tangled web of relationships between them. One of the splicing factors: KHDRBS3 was validated by immunohistochemistry to be down-regulated in KIRC tissues. In conclusion, the powerful efficiency of risk stratification of PI models indicated the potential of AS signature as promising prognostic markers for KIRC and the splicing regulation network provided possible genetic mechanism of KIRC.
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Affiliation(s)
- Li Gao
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Rong-Quan He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Zhi-Guang Huang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Yi-Wu Dang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Yong-Yao Gu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Hai-Biao Yan
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Sheng-Hua Li
- Department of Urology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
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18
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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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19
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Liu Z, Li W, Pang Y, Zhou Z, Liu S, Cheng K, Qin Q, Jia Y, Liu S. SF3B4 is regulated by microRNA-133b and promotes cell proliferation and metastasis in hepatocellular carcinoma. EBioMedicine 2018; 38:57-68. [PMID: 30391496 PMCID: PMC6306498 DOI: 10.1016/j.ebiom.2018.10.067] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 10/26/2018] [Accepted: 10/26/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Splicing factor 3b subunit 4 (SF3B4) is a splicing factor and potential oncogene in hepatocellular carcinoma (HCC); however, its regulatory mechanism is yet unclear. We aimed to determine the role of SF3B4 in HCC and the underlying mechanism. METHODS To investigate the association between alternative splicing events and miRNAs, putative miRNAs were screened using TargetScan. Expression levels of and prognostic information for SF3B4 and miRNAs were determined based on public genomic data and clinical samples. Then, we examined the possible roles of SF3B4 and miRNA-133b in HCC cells and a xenograft mouse model. Pearson correlation analysis and in vitro experiments verified SF3B4 as a miRNA-133b target. Protein levels of key targets from the SF3B4 signaling pathway were estimated using western blotting. FINDINGS The expression of SF3B4 was upregulated in HCC tissues and cell lines whereas, the expression of miRNA-133b was downregulated. MiRNA-133b negatively regulated the expression of SF3B4. Effects of SF3B4 overexpression were partially abolished by miRNA-133b mimics, confirming that SF3B4 is a target of miRNA-133b. Moreover, molecules associated with SF3B4, including KLF4, KIP1, and SNAI2, were also modulated by miRNA-133b. INTERPRETATION SF3B4 plays a crucial role in HCC and is negatively regulated by miRNA-133b. The miRNA-133b/ SF3B4 axis may serve as a new therapeutic target for HCC treatment. FUND: China National Funds for Distinguished Young Scientists (No.81425019), the State Key Program of National Natural Science Foundation of China (No.81730076), Shanghai Science and Technology Committee Program (No.18XD1405300) and Specially-Appointed Professor Fund of Shanghai (GZ2015009). China National Funds for National Natural Science Fund (No.81672899).
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Affiliation(s)
- Zhiyong Liu
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Wei Li
- Department of General Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Yanan Pang
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Zaixin Zhou
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Shupeng Liu
- Clinical Trial Center, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Kai Cheng
- Clinical Trial Center, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Qin Qin
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Yin Jia
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Shanrong Liu
- Department of Laboratory Diagnostics, Changhai Hospital, Second Military Medical University, Shanghai 200433, China.
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20
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Li J, Wang Y, Meng X, Liang H. Modulation of transcriptional activity in brain lower grade glioma by alternative splicing. PeerJ 2018; 6:e4686. [PMID: 29780667 PMCID: PMC5957051 DOI: 10.7717/peerj.4686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/10/2018] [Indexed: 01/14/2023] Open
Abstract
Proteins that modify the activity of transcription factors (TFs) are often called modulators and play a vital role in gene transcriptional regulation. Alternative splicing is a critical step of gene processing, and differentially spliced isoforms may have different functions. Alternative splicing can modulate gene function by adding or removing certain protein domains and thereby influence the activity of a protein. The objective of this study is to investigate the role of alternative splicing in modulating the transcriptional regulation in brain lower grade glioma (LGG), especially transcription factor ELK1, which is closely related to various disorders, including Alzheimer’s disease and Down syndrome. The results showed that changes in the exon inclusion ratio of proteins APP and STK16 are associated with changes in the expression correlation between ELK1 and its targets. In addition, the structural features of the two modulators are strongly associated with the pathological impact of exon inclusion. The results of our analysis suggest that alternatively spliced proteins have different functions in modifying transcription factors and can thereby induce the dysregulation of multiple genes.
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Affiliation(s)
- Jin Li
- College of Automation, Harbin Engineering University, Harbin, Heilongjiang, China
| | - Yang Wang
- College of Automation, Harbin Engineering University, Harbin, Heilongjiang, China
| | - Xianglian Meng
- College of Automation, Harbin Engineering University, Harbin, Heilongjiang, China
| | - Hong Liang
- College of Automation, Harbin Engineering University, Harbin, Heilongjiang, China
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21
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Zheng WJ, Ruan J, Xu H, Zhao Z, Liu Z. The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: putting systems biology to work. BMC SYSTEMS BIOLOGY 2017; 11:88. [PMID: 28984194 PMCID: PMC5629615 DOI: 10.1186/s12918-017-0461-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Between December 8–10, 2016, the International Conference on Intelligent Biology and Medicine (ICIBM 2016) was held in Houston, Texas, USA. The conference included eight scientific sessions, four tutorials, one poster session, four highlighted talks and four keynotes that covered topics in 3D genome structure analysis and visualization, next generation sequencing analysis, computational drug discovery, medical informatics, cancer genomics and systems biology. Systems biology has been a main theme in ICIBM 2016, with exciting advances were presented in many areas of systems biology. Here, we selected seven high quality papers to be published in BMC Systems Biology.
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Affiliation(s)
- W Jim Zheng
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Jianhua Ruan
- Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Hua Xu
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Zhangdong Liu
- The Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX, 77030, USA
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