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Trink Y, Urbach A, Dekel B, Hohenstein P, Goldberger J, Kalisky T. Characterization of Alternative Splicing in High-Risk Wilms' Tumors. Int J Mol Sci 2024; 25:4520. [PMID: 38674106 PMCID: PMC11050615 DOI: 10.3390/ijms25084520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The significant heterogeneity of Wilms' tumors between different patients is thought to arise from genetic and epigenetic distortions that occur during various stages of fetal kidney development in a way that is poorly understood. To address this, we characterized the heterogeneity of alternative mRNA splicing in Wilms' tumors using a publicly available RNAseq dataset of high-risk Wilms' tumors and normal kidney samples. Through Pareto task inference and cell deconvolution, we found that the tumors and normal kidney samples are organized according to progressive stages of kidney development within a triangle-shaped region in latent space, whose vertices, or "archetypes", resemble the cap mesenchyme, the nephrogenic stroma, and epithelial tubular structures of the fetal kidney. We identified a set of genes that are alternatively spliced between tumors located in different regions of latent space and found that many of these genes are associated with the epithelial-to-mesenchymal transition (EMT) and muscle development. Using motif enrichment analysis, we identified putative splicing regulators, some of which are associated with kidney development. Our findings provide new insights into the etiology of Wilms' tumors and suggest that specific splicing mechanisms in early stages of development may contribute to tumor development in different patients.
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Affiliation(s)
- Yaron Trink
- Faculty of Engineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan 5290002, Israel; (Y.T.); (J.G.)
| | - Achia Urbach
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
| | - Benjamin Dekel
- Pediatric Stem Cell Research Institute and Division of Pediatric Nephrology, Edmond and Lily Safra Children’s Hospital, Sheba Tel-HaShomer Medical Centre, Ramat Gan 5262000, Israel
| | - Peter Hohenstein
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands;
| | - Jacob Goldberger
- Faculty of Engineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan 5290002, Israel; (Y.T.); (J.G.)
| | - Tomer Kalisky
- Faculty of Engineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, Ramat Gan 5290002, Israel; (Y.T.); (J.G.)
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2
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Moreno RY, Juetten KJ, Panina SB, Butalewicz JP, Floyd BM, Venkat Ramani MK, Marcotte EM, Brodbelt JS, Zhang YJ. Distinctive interactomes of RNA polymerase II phosphorylation during different stages of transcription. iScience 2023; 26:107581. [PMID: 37664589 PMCID: PMC10470302 DOI: 10.1016/j.isci.2023.107581] [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: 05/11/2023] [Revised: 06/28/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
During eukaryotic transcription, RNA polymerase II undergoes dynamic post-translational modifications on the C-terminal domain (CTD) of the largest subunit, generating an information-rich PTM landscape that transcriptional regulators bind. The phosphorylation of Ser5 and Ser2 of CTD heptad occurs spatiotemporally with the transcriptional stages, recruiting different transcriptional regulators to Pol II. To delineate the protein interactomes at different transcriptional stages, we reconstructed phosphorylation patterns of the CTD at Ser5 and Ser2 in vitro. Our results showed that distinct protein interactomes are recruited to RNA polymerase II at different stages of transcription by the phosphorylation of Ser2 and Ser5 of the CTD heptads. In particular, we characterized calcium homeostasis endoplasmic reticulum protein (CHERP) as a regulator bound by phospho-Ser2 heptad. Pol II association with CHERP recruits an accessory splicing complex whose loss results in broad changes in alternative splicing events. Our results shed light on the PTM-coded recruitment process that coordinates transcription.
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Affiliation(s)
| | - Kyle J. Juetten
- Department of Chemistry, University of Texas, Austin, TX, USA
| | - Svetlana B. Panina
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | | | - Brendan M. Floyd
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | | | - Edward M. Marcotte
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | | | - Y. Jessie Zhang
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
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Zhang Y, Wang X, Zhang C, Yi H. The dysregulation of lncRNAs by epigenetic factors in human pathologies. Drug Discov Today 2023; 28:103664. [PMID: 37348827 DOI: 10.1016/j.drudis.2023.103664] [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: 12/23/2022] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023]
Abstract
Dysregulation of long noncoding RNAs (lncRNAs) contributes to numerous human diseases, including cancers and autoimmune diseases (ADs). Given the importance of lncRNAs in disease initiation and progression, a deeper understanding of their complex regulatory network is required to facilitate their use as therapeutic targets for ADs. In this review, we summarize how lncRNAs are dysregulated in pathological states by epigenetic factors, including RNA-binding proteins, chemical modifications (N6-methyladenosine, 5-methylcytosine, 7-methylguanosine, adenosine-to-inosine editing, microRNA, alternative splicing, DNA methylation, and histone modification). Moreover, the roles of lncRNA epigenetic regulators in immune response and ADs are discussed, providing new insights into the complicated epigenetic factor-lncRNA network, thus, laying a theoretical foundation for future research and clinical application of lncRNAs.
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Affiliation(s)
- Yanli Zhang
- Central Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China; Key Laboratory of Organ Regeneration and Transplantation, Ministry of Education, Changchun, Jilin 130021, China; Department of Echocardiography, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Xiaocong Wang
- Department of Echocardiography, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Chen Zhang
- Colorectal and Anal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Huanfa Yi
- Central Laboratory, The First Hospital of Jilin University, Changchun, Jilin, China; Key Laboratory of Organ Regeneration and Transplantation, Ministry of Education, Changchun, Jilin 130021, China.
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Łukaszewicz-Zając M, Pączek S, Mroczko B. A Disintegrin and Metalloproteinase (ADAM) Family-Novel Biomarkers of Selected Gastrointestinal (GI) Malignancies? Cancers (Basel) 2022; 14:cancers14092307. [PMID: 35565436 PMCID: PMC9101749 DOI: 10.3390/cancers14092307] [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: 04/12/2022] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 02/06/2023] Open
Abstract
The global burden of gastrointestinal (GI) cancers is expected to increase. Therefore, it is vital that novel biomarkers useful for the early diagnosis of these malignancies are established. A growing body of data has linked secretion of proteolytic enzymes, such as metalloproteinases (MMPs), which destroy the extracellular matrix, to pathogenesis of GI tumours. A disintegrin and metalloproteinase (ADAM) proteins belong to the MMP family but have been proven to be unique due to both proteolytic and adhesive properties. Recent investigations have demonstrated that the expression of several ADAMs is upregulated in GI cancer cells. Thus, the objective of this review is to present current findings concerning the role of ADAMs in the pathogenesis of GI cancers, particularly their involvement in the development and progression of colorectal, pancreatic and gastric cancer. Furthermore, the prognostic significance of selected ADAMs in patients with GI tumours is also presented. It has been proven that ADAM8, 9, 10, 12, 15, 17 and 28 might stimulate the proliferation and invasion of GI malignancies and may be associated with unfavourable survival. In conclusion, this review confirms the role of selected ADAMs in the pathogenesis of the most common GI cancers and indicates their promising significance as potential prognostic biomarkers as well as therapeutic targets for GI malignancies. However, due to their non-specific nature, future research on ADAM biology should be performed to elucidate new strategies for the diagnosis of these common and deadly malignancies and treatment of patients with these diseases.
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Affiliation(s)
- Marta Łukaszewicz-Zając
- Department of Biochemical Diagnostics, Medical University of Bialystok, 15-269 Bialystok, Poland;
- Correspondence:
| | - Sara Pączek
- Department of Biochemical Diagnostics, University Hospital of Bialystok, 15-269 Bialystok, Poland;
| | - Barbara Mroczko
- Department of Biochemical Diagnostics, Medical University of Bialystok, 15-269 Bialystok, Poland;
- Department of Neurodegeneration Diagnostics, Medical University, 15-269 Bialystok, Poland
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5
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Cheng R, Xu Z, Luo M, Wang P, Cao H, Jin X, Zhou W, Xiao L, Jiang Q. Identification of alternative splicing-derived cancer neoantigens for mRNA vaccine development. Brief Bioinform 2022; 23:bbab553. [PMID: 35279714 DOI: 10.1093/bib/bbab553] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/15/2021] [Accepted: 12/02/2021] [Indexed: 12/17/2023] Open
Abstract
Messenger RNA (mRNA) vaccines have shown great potential for anti-tumor therapy due to the advantages in safety, efficacy and industrial production. However, it remains a challenge to identify suitable cancer neoantigens that can be targeted for mRNA vaccines. Abnormal alternative splicing occurs in a variety of tumors, which may result in the translation of abnormal transcripts into tumor-specific proteins. High-throughput technologies make it possible for systematic characterization of alternative splicing as a source of suitable target neoantigens for mRNA vaccine development. Here, we summarized difficulties and challenges for identifying alternative splicing-derived cancer neoantigens from RNA-seq data and proposed a conceptual framework for designing personalized mRNA vaccines based on alternative splicing-derived cancer neoantigens. In addition, several points were presented to spark further discussion toward improving the identification of alternative splicing-derived cancer neoantigens.
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Affiliation(s)
- Rui Cheng
- Harbin Institute of Technology, China
| | | | - Meng Luo
- Harbin Institute of Technology, China
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Zhang Y, Yu X, Sun R, Min J, Tang X, Lin Z, Xie S, Li X, Lu S, Tian Z, Gu C, Teng L, Yang Y. Splicing factor arginine/serine‐rich 8 promotes multiple myeloma malignancy and bone lesion through alternative splicing of CACYBP and exosome‐based cellular communication. Clin Transl Med 2022; 12:e684. [PMID: 35184390 PMCID: PMC8858635 DOI: 10.1002/ctm2.684] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 12/21/2022] Open
Abstract
Background Multiple myeloma (MM) is a distinctive malignancy of plasma cell within the bone marrow (BM), of which alternative splicing factors play vital roles in the progression. Splicing factor arginine/serine‐rich 8 (SFRS8) is the exclusive factor associated with MM prognosis, however its role in MM remains undefined. Methods The analyses of 3‐(4,5)‐dimethylthiahiazo (‐z‐y1)‐3,5‐di‐ phenytetrazoliumromide (MTT) assay, immunohistochemistry, flow cytometry and xenograft model were performed to examine cell proliferation, cell cycle and apoptosis in SFRS8 overexpression or knockdown MM cells in vitro and in vivo. The SFRS8‐regulated alternative splicing events were identified by RNA immunoprecipitation sequencing (RIP‐seq) and validated by RIP‐qPCR and Co‐IP methods. Exosomes were extracted from the supernatant of myeloma cells by ultracentrifugation. Bone lesion was evaluated by TRAP staining in vitro and SCID/NOD‐TIBIA mouse model. A neon electroporation system was utilised to deliver siRNA through exosomes. The effect of siRNA‐loaded exosomes in vivo was evaluated by using a patient‐derived tumor xenograft (PDX) model and SCID/NOD‐TIBIA mouse model. Results SFRS8 was significantly upregulated in MM samples and positively associated with poor overall survival (OS) in MM patients. SFRS8 promoted MM cell proliferation in vitro and in vivo. Furthermore, calcyclin binding protein (CACYBP) was identified as the downstream target of SFRS8. Particularly, SFRS8 could reduce CACYBP isoform1 (NM_014412.3) and increase CACYBP isoform2 (NM_001007214.1) by mediating the alternative splicing of CACYBP, thereby altering the ubiquitination degradation of β‐catenin to promote MM progression. In addition, SFRS8 promoted osteoclast differentiation through exosomes in vitro and in vivo. More importantly, exosomal siRNA targeting CACYBP isoform2 inhibited tumour growth in PDX and SCID/NOD‐TIBIA mouse models. Conclusion Our findings demonstrate that targeting the SFRS8/CACYBP/β‐catenin axis may be a promising strategy for MM diagnosis and treatment.
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Affiliation(s)
- Yuanjiao Zhang
- Nanjing Hospital of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
| | - Xichao Yu
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
| | - Rongze Sun
- School of Life Science Jilin University Changchun China
| | - Jie Min
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
| | - Xiaozhu Tang
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
| | - Zigen Lin
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
| | - Siyuan Xie
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
| | - Xinying Li
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
| | - Shengfeng Lu
- Key Laboratory of A cupuncture and Medicine Research of Ministry of Education Nanjing University of Chinese Medicine Nanjing China
| | - Zhidan Tian
- Department of Pathology, Nanjing First Hospital Nanjing Medical University Nanjing China
| | - Chunyan Gu
- Nanjing Hospital of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
| | - Lesheng Teng
- School of Life Science Jilin University Changchun China
| | - Ye Yang
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
- Key Laboratory of A cupuncture and Medicine Research of Ministry of Education Nanjing University of Chinese Medicine Nanjing China
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7
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Zhang Y, Qian J, Gu C, Yang Y. Alternative splicing and cancer: a systematic review. Signal Transduct Target Ther 2021; 6:78. [PMID: 33623018 PMCID: PMC7902610 DOI: 10.1038/s41392-021-00486-7] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 01/31/2023] Open
Abstract
The abnormal regulation of alternative splicing is usually accompanied by the occurrence and development of tumors, which would produce multiple different isoforms and diversify protein expression. The aim of the present study was to conduct a systematic review in order to describe the regulatory mechanisms of alternative splicing, as well as its functions in tumor cells, from proliferation and apoptosis to invasion and metastasis, and from angiogenesis to metabolism. The abnormal splicing events contributed to tumor progression as oncogenic drivers and/or bystander factors. The alterations in splicing factors detected in tumors and other mis-splicing events (i.e., long non-coding and circular RNAs) in tumorigenesis were also included. The findings of recent therapeutic approaches targeting splicing catalysis and splicing regulatory proteins to modulate pathogenically spliced events (including tumor-specific neo-antigens for cancer immunotherapy) were introduced. The emerging RNA-based strategies for the treatment of cancer with abnormally alternative splicing isoforms were also discussed. However, further studies are still required to address the association between alternative splicing and cancer in more detail.
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Affiliation(s)
- Yuanjiao Zhang
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jinjun Qian
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chunyan Gu
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Ye Yang
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
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Ma L, Shan Y, Ma H, Elshoura I, Nafees M, Yang K, Yin W. Identification of a novel splice variant of the human musashi-1 gene. Oncol Lett 2018; 16:5441-5448. [PMID: 30250616 DOI: 10.3892/ol.2018.9300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 02/28/2018] [Indexed: 11/06/2022] Open
Abstract
Musashi-1 (Msi1) is an evolutionarily conserved RNA-binding protein that has been reported to be the key regulator in malignancies and with involvement in cancer stemness. In the present study, a novel Msi1 transcript variant generated by alternative splicing was identified and termed Msi1 variant 2. This variant was observed to be ubiquitously expressed in cancerous and non-cancerous cells compared with its wild-type variant, which is preferentially expressed in cancer cells. Notably, the expression levels of Msi1 variant 2 were inversely associated with the protein expression levels of Msi1 in various cancer cells. This naturally truncated variant contains 899 nucleotides and a skipping event of exons 3 and 4, which leads to the emergence of a premature TGA stop codon in exon 5. The present results also demonstrated that hypoxia increased the resistance of H460 cells to cisplatin by suppressing the exon 3 and 4 skipping event of Msi1. In summary, the present study identified a novel splice variant of Msi1 lacking two complete RNA recognition motifs, and revealed the role of exon 3 and 4 skipping of Msi1 pre-mRNA in regulating cisplatin resistance under hypoxia. These observations indicate that targeting Msi1 alternative splicing could represent a valuable strategy to repress Msi1 signaling in tumors overexpressing this RNA-binding protein.
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Affiliation(s)
- Lin Ma
- State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, Jiangsu 210046, P.R. China
| | - Yating Shan
- State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, Jiangsu 210046, P.R. China
| | - Heliang Ma
- Department of Radiology, Jinan Central Hospital, Jinan, Shandong 250013, P.R. China
| | - Ihab Elshoura
- State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, Jiangsu 210046, P.R. China
| | - Muhammad Nafees
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210046, P.R. China
| | - Kaiyong Yang
- State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, Jiangsu 210046, P.R. China
| | - Wu Yin
- State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, Jiangsu 210046, P.R. China
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Mthembu NN, Mbita Z, Hull R, Dlamini Z. Abnormalities in alternative splicing of angiogenesis-related genes and their role in HIV-related cancers. HIV AIDS-RESEARCH AND PALLIATIVE CARE 2017; 9:77-93. [PMID: 28694706 PMCID: PMC5490432 DOI: 10.2147/hiv.s124911] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alternative splicing of mRNA leads to an increase in proteome biodiversity by allowing the generation of multiple mRNAs, coding for multiple protein isoforms of various structural and functional properties from a single primary pre-mRNA transcript. The protein isoforms produced are tightly regulated in normal development but are mostly deregulated in various cancers. In HIV-infected individuals with AIDS, there is an increase in aberrant alternative splicing, resulting in an increase in HIV/AIDS-related cancers, such as Kaposi’s sarcoma, non-Hodgkin’s lymphoma, and cervical cancer. This aberrant splicing leads to abnormal production of protein and is caused by mutations in cis-acting elements or trans-acting factors in angiogenesis-related genes. Restoring the normal regulation of alternative splicing of angiogenic genes would alter the expression of protein isoforms and may confer normal cell physiology in patients with these cancers. This review highlights the abnormalities in alternative splicing of angiogenesis-related genes and their implication in HIV/AIDS-related cancers. This allows us to gain an insight into the pathogenesis of HIV/AIDS-related cancer and in turn elucidate the therapeutic potential of alternatively spliced genes in HIV/AIDS-related malignancies.
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Affiliation(s)
| | - Zukile Mbita
- Department of Biochemistry, Microbiology and Biotechnology, University of Limpopo, Sovenga, South Africa
| | - Rodney Hull
- Research, Innovation and Engagements, Mangosuthu University of Technology, Durban
| | - Zodwa Dlamini
- Research, Innovation and Engagements, Mangosuthu University of Technology, Durban
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Liu R, Liu T, Wei W, Guo K, Yang N, Tian S, Zhu J, Liu Y, Zhou W, Yang H. Novel interacting proteins identified by tandem affinity purification coupled to nano LC–MS/MS interact with ribosomal S6 protein kinase 4 (RSK4) and its variant protein (RSK4m). Int J Biol Macromol 2017; 96:421-428. [DOI: 10.1016/j.ijbiomac.2016.12.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 12/05/2016] [Accepted: 12/12/2016] [Indexed: 12/16/2022]
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Kozlov AP. Expression of evolutionarily novel genes in tumors. Infect Agent Cancer 2016; 11:34. [PMID: 27437030 PMCID: PMC4949931 DOI: 10.1186/s13027-016-0077-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/18/2016] [Indexed: 01/29/2023] Open
Abstract
The evolutionarily novel genes originated through different molecular mechanisms are expressed in tumors. Sometimes the expression of evolutionarily novel genes in tumors is highly specific. Moreover positive selection of many human tumor-related genes in primate lineage suggests their involvement in the origin of new functions beneficial to organisms. It is suggested to consider the expression of evolutionarily young or novel genes in tumors as a new biological phenomenon, a phenomenon of TSEEN (tumor specifically expressed, evolutionarily novel) genes.
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Affiliation(s)
- A. P. Kozlov
- The Biomedical Center and Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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12
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Hong Y, Kim WJ, Bang CY, Lee JC, Oh YM. Identification of Alternative Splicing and Fusion Transcripts in Non-Small Cell Lung Cancer by RNA Sequencing. Tuberc Respir Dis (Seoul) 2016; 79:85-90. [PMID: 27066085 PMCID: PMC4823188 DOI: 10.4046/trd.2016.79.2.85] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 11/04/2015] [Accepted: 12/14/2015] [Indexed: 12/22/2022] Open
Abstract
Background Lung cancer is the most common cause of cancer related death. Alterations in gene sequence, structure, and expression have an important role in the pathogenesis of lung cancer. Fusion genes and alternative splicing of cancer-related genes have the potential to be oncogenic. In the current study, we performed RNA-sequencing (RNA-seq) to investigate potential fusion genes and alternative splicing in non-small cell lung cancer. Methods RNA was isolated from lung tissues obtained from 86 subjects with lung cancer. The RNA samples from lung cancer and normal tissues were processed with RNA-seq using the HiSeq 2000 system. Fusion genes were evaluated using Defuse and ChimeraScan. Candidate fusion transcripts were validated by Sanger sequencing. Alternative splicing was analyzed using multivariate analysis of transcript sequencing and validated using quantitative real time polymerase chain reaction. Results RNA-seq data identified oncogenic fusion genes EML4-ALK and SLC34A2-ROS1 in three of 86 normal-cancer paired samples. Nine distinct fusion transcripts were selected using DeFuse and ChimeraScan; of which, four fusion transcripts were validated by Sanger sequencing. In 33 squamous cell carcinoma, 29 tumor specific skipped exon events and six mutually exclusive exon events were identified. ITGB4 and PYCR1 were top genes that showed significant tumor specific splice variants. Conclusion In conclusion, RNA-seq data identified novel potential fusion transcripts and splice variants. Further evaluation of their functional significance in the pathogenesis of lung cancer is required.
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Affiliation(s)
- Yoonki Hong
- Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
| | - Woo Jin Kim
- Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
| | - Chi Young Bang
- Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
| | - Jae Cheol Lee
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Yeon-Mok Oh
- Department of Pulmonary and Critical Care Medicine and Clinical Research Center for Chronic Obstructive Airway Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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13
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Li Z, Li Q, Han L, Tian N, Liang Q, Li Y, Zhao X, Du C, Tian Y. Pro-apoptotic effects of splice-switching oligonucleotides targeting Bcl-x pre-mRNA in human glioma cell lines. Oncol Rep 2015; 35:1013-9. [PMID: 26718027 DOI: 10.3892/or.2015.4465] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 10/26/2015] [Indexed: 11/06/2022] Open
Abstract
Alternative splicing is a near-ubiquitous phenomenon with important roles in human diseases, including cancers. Splice-switching oligonucleotides (SSOs) have emerged as a class of antisense therapeutics that modulate alternative splicing by hybridizing to the pre-mRNA splice site. The Bcl-x gene is alternatively spliced to express anti‑apoptotic Bcl-xL and pro-apoptotic Bcl-xS. Bcl-xL expression is upregulated in many cancers and is considered a general mechanism by which cancer cells evade apoptosis. By redirecting Bcl-x pre-mRNA splicing from Bcl-xL to Bcl-xS, SSO exerted pro-apoptotic and chemosensitizing effects in various cancer cell lines. In this study, we investigated the effects of SSO targeting Bcl-x pre-mRNA in human glioma cell lines. First, we performed reverse transcription-polymerase chain reaction (RT-PCR) and western blotting to determine the mRNA and protein expression levels of Bcl-xL in glioma cell lines (U87 and U251) and a normal human astrocyte cell line (HA1800). Then, the Bcl-x SSO was designed to bind to the downstream 5' alternative splice site of exon 2 in Bcl-x pre-mRNA and was modified using 2'-O-methoxyethyl-phosphorothioate. An oligonucleotide targeting aberrantly spliced human β-globin intron was used as a negative control. The SSOs were delivered with a cationic lipid into glioma and astrocyte cell lines. The antitumor effects of the SSOs were assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assays and flow cytometry, and the switch in production from Bcl-xL to Bcl-xS was analyzed by RT-PCR and western blotting. Bcl-xL mRNA and protein were highly expressed in both glioma cell lines. The Bcl-x SSO modified Bcl-x pre-mRNA splicing and had pro-apoptotic effects on the glioma cell lines. By contrast, the lipid alone and the control SSO did not affect Bcl-xL expression or induce apoptosis. Our study demonstrated the antitumor activity of an SSO that targets Bcl-x pre-mRNA splicing in glioma cell lines. Bcl-x SSO may be a potential strategy for treating gliomas.
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Affiliation(s)
- Zhaohui Li
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130031, P.R. China
| | - Qingwei Li
- Department of Neurosurgery, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150036, P.R. China
| | - Liang Han
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130031, P.R. China
| | - Nan Tian
- Department of Cell Biology, College of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Qianlei Liang
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130031, P.R. China
| | - Yanzhe Li
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130031, P.R. China
| | - Xingli Zhao
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130031, P.R. China
| | - Chao Du
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130031, P.R. China
| | - Yu Tian
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130031, P.R. China
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14
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Sveen A, Kilpinen S, Ruusulehto A, Lothe RA, Skotheim RI. Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes. Oncogene 2015; 35:2413-27. [PMID: 26300000 DOI: 10.1038/onc.2015.318] [Citation(s) in RCA: 333] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/22/2015] [Accepted: 07/22/2015] [Indexed: 02/07/2023]
Abstract
Alternative splicing is a widespread process contributing to structural transcript variation and proteome diversity. In cancer, the splicing process is commonly disrupted, resulting in both functional and non-functional end-products. Cancer-specific splicing events are known to contribute to disease progression; however, the dysregulated splicing patterns found on a genome-wide scale have until recently been less well-studied. In this review, we provide an overview of aberrant RNA splicing and its regulation in cancer. We then focus on the executors of the splicing process. Based on a comprehensive catalog of splicing factor encoding genes and analyses of available gene expression and somatic mutation data, we identify cancer-associated patterns of dysregulation. Splicing factor genes are shown to be significantly differentially expressed between cancer and corresponding normal samples, and to have reduced inter-individual expression variation in cancer. Furthermore, we identify enrichment of predicted cancer-critical genes among the splicing factors. In addition to previously described oncogenic splicing factor genes, we propose 24 novel cancer-critical splicing factors predicted from somatic mutations.
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Affiliation(s)
- A Sveen
- Department of Molecular Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | | | - R A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - R I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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15
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LI ZHAOHUI, TIAN YU, TIAN NAN, ZHAO XINGLI, DU CHAO, HAN LIANG, ZHANG HAISHAN. Aberrant alternative splicing pattern of ADAR2 downregulates adenosine-to-inosine editing in glioma. Oncol Rep 2015; 33:2845-52. [DOI: 10.3892/or.2015.3907] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/20/2015] [Indexed: 11/05/2022] Open
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16
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Wang Y, Liu J, Huang BO, Xu YM, Li J, Huang LF, Lin J, Zhang J, Min QH, Yang WM, Wang XZ. Mechanism of alternative splicing and its regulation. Biomed Rep 2014; 3:152-158. [PMID: 25798239 DOI: 10.3892/br.2014.407] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 12/10/2014] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing of precursor mRNA is an essential mechanism to increase the complexity of gene expression, and it plays an important role in cellular differentiation and organism development. Regulation of alternative splicing is a complicated process in which numerous interacting components are at work, including cis-acting elements and trans-acting factors, and is further guided by the functional coupling between transcription and splicing. Additional molecular features, such as chromatin structure, RNA structure and alternative transcription initiation or alternative transcription termination, collaborate with these basic components to generate the protein diversity due to alternative splicing. All these factors contributing to this one fundamental biological process add up to a mechanism that is critical to the proper functioning of cells. Any corruption of the process may lead to disruption of normal cellular function and the eventuality of disease. Cancer is one of those diseases, where alternative splicing may be the basis for the identification of novel diagnostic and prognostic biomarkers, as well as new strategies for therapy. Thus, an in-depth understanding of alternative splicing regulation has the potential not only to elucidate fundamental biological principles, but to provide solutions for various diseases.
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Affiliation(s)
- Yan Wang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Jing Liu
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - B O Huang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Yan-Mei Xu
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Jing Li
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Lin-Feng Huang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Jin Lin
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Jing Zhang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Qing-Hua Min
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Wei-Ming Yang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
| | - Xiao-Zhong Wang
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, P.R. China
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17
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Roy B, Haupt LM, Griffiths LR. Review: Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity. Curr Genomics 2013; 14:182-94. [PMID: 24179441 PMCID: PMC3664468 DOI: 10.2174/1389202911314030004] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 02/08/2013] [Accepted: 02/25/2013] [Indexed: 12/22/2022] Open
Abstract
Prior to the completion of the human genome project, the human genome was thought to have a greater number of genes as it seemed structurally and functionally more complex than other simpler organisms. This along with the belief of “one gene, one protein”, were demonstrated to be incorrect. The inequality in the ratio of gene to protein formation gave rise to the theory of alternative splicing (AS). AS is a mechanism by which one gene gives rise to multiple protein products. Numerous databases and online bioinformatic tools are available for the detection and analysis of AS. Bioinformatics provides an important approach to study mRNA and protein diversity by various tools such as expressed sequence tag (EST) sequences obtained from completely processed mRNA. Microarrays and deep sequencing approaches also aid in the detection of splicing events. Initially it was postulated that AS occurred only in about 5% of all genes but was later found to be more abundant. Using bioinformatic approaches, the level of AS in human genes was found to be fairly high with 35-59% of genes having at least one AS form. Our ability to determine and predict AS is important as disorders in splicing patterns may lead to abnormal splice variants resulting in genetic diseases. In addition, the diversity of proteins produced by AS poses a challenge for successful drug discovery and therefore a greater understanding of AS would be beneficial.
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Affiliation(s)
- Bishakha Roy
- Genomics Research Centre, Griffith Health Institute, Griffith University Gold Coast, Queensland 4222, Australia
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18
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Dudek AM, Grotenhuis AJ, Vermeulen SH, Kiemeney LALM, Verhaegh GW. Urinary bladder cancer susceptibility markers. What do we know about functional mechanisms? Int J Mol Sci 2013; 14:12346-66. [PMID: 23752272 PMCID: PMC3709789 DOI: 10.3390/ijms140612346] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 05/23/2013] [Accepted: 05/30/2013] [Indexed: 12/24/2022] Open
Abstract
Genome-wide association studies (GWAS) have been successful in the identification of the several urinary bladder cancer (UBC) susceptibility loci, pointing towards novel genes involved in tumor development. Despite that, functional characterization of the identified variants remains challenging, as they mostly map to poorly understood, non-coding regions. Recently, two of the UBC risk variants (PSCA and UGT1A) were confirmed to have functional consequences. They were shown to modify bladder cancer risk by influencing gene expression in an allele-specific manner. Although the role of the other UBC risk variants is unknown, it can be hypothesized-based on studies from different cancer types-that they influence cancer susceptibility by alterations in regulatory networks. The insight into UBC heritability gained through GWAS and further functional studies can impact on cancer prevention and screening, as well as on the development of new biomarkers and future personalized therapies.
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Affiliation(s)
- Aleksandra M. Dudek
- Department of Urology, Radboud University Medical Centre, Geert Grooteplein 16, Nijmegen 6525 GA, The Netherlands; E-Mails: (L.A.L.M.K.); (G.W.V.)
- Department for Health Evidence, Radboud University Medical Centre, Geert Grooteplein 21, Nijmegen 6525 EZ, The Netherlands; E-Mails: (A.J.G.); (S.H.V.)
- Nijmegen Centre for Molecular Life Sciences, Geert Grooteplein 28, Nijmegen 6525 GA, The Netherlands
| | - Anne J. Grotenhuis
- Department for Health Evidence, Radboud University Medical Centre, Geert Grooteplein 21, Nijmegen 6525 EZ, The Netherlands; E-Mails: (A.J.G.); (S.H.V.)
- Nijmegen Centre for Evidence Based Practice, Geert Grooteplein 21, Nijmegen 6525 GA, The Netherlands
| | - Sita H. Vermeulen
- Department for Health Evidence, Radboud University Medical Centre, Geert Grooteplein 21, Nijmegen 6525 EZ, The Netherlands; E-Mails: (A.J.G.); (S.H.V.)
- Nijmegen Centre for Evidence Based Practice, Geert Grooteplein 21, Nijmegen 6525 GA, The Netherlands
| | - Lambertus A. L. M. Kiemeney
- Department of Urology, Radboud University Medical Centre, Geert Grooteplein 16, Nijmegen 6525 GA, The Netherlands; E-Mails: (L.A.L.M.K.); (G.W.V.)
- Department for Health Evidence, Radboud University Medical Centre, Geert Grooteplein 21, Nijmegen 6525 EZ, The Netherlands; E-Mails: (A.J.G.); (S.H.V.)
- Nijmegen Centre for Evidence Based Practice, Geert Grooteplein 21, Nijmegen 6525 GA, The Netherlands
| | - Gerald W. Verhaegh
- Department of Urology, Radboud University Medical Centre, Geert Grooteplein 16, Nijmegen 6525 GA, The Netherlands; E-Mails: (L.A.L.M.K.); (G.W.V.)
- Nijmegen Centre for Molecular Life Sciences, Geert Grooteplein 28, Nijmegen 6525 GA, The Netherlands
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