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Ding W, Xiao Q, Yue Y, Chen S, She X, Pan B, Zhou L, Yin Y, Li Y, Wang S, Xu M. Deciphering alternative splicing events and their therapeutic implications in colorectal Cancer. Cell Signal 2024; 118:111134. [PMID: 38484942 DOI: 10.1016/j.cellsig.2024.111134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/28/2024] [Accepted: 03/06/2024] [Indexed: 03/17/2024]
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumors with complex molecular regulatory mechanisms. Alternative splicing (AS), a fundamental regulatory process of gene expression, plays an important role in the occurrence and development of CRC. This study analyzed AS Percent Spliced In (PSI) values from 49 pairs of CRC and normal samples in the TCGA SpliceSeq database. Using Lasso and SVM, AS features that can differentiate colorectal cancer from normal were screened. Univariate COX regression analysis identified prognosis-related AS events. A risk model was constructed and validated using machine learning, Kaplan-Meier analysis, and Decision Curve Analysis. The regulatory effect of protein arginine methyltransferase 5 (PRMT5) on poly(RC) binding protein 1 (PCBP1) was verified by immunoprecipitation experiments, and the effect of PCBP1 on the AS of Obscurin (OBSCN) was verified by PCR. Five AS events, including HNF4A.59461.AP and HNF4A.59462.AP, were identified, which can distinguish CRC from normal tissue. A machine learning model using 21 key AS events accurately predicted CRC prognosis. High-risk patients had significantly shorter survival times. PRMT5 was found to regulate PCBP1 function and then influence OBSCN AS, which may drive CRC progression. The study concluded that some AS events is significantly different in CRC and normal tissues, and some of these AS events are related to the prognosis of CRC. In addition, PRMT family-driven arginine modifications play an important role in CRC-specific AS events.
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Affiliation(s)
- Wenbo Ding
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Qianni Xiao
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Yanzhe Yue
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Shuyu Chen
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Xiangjian She
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Bei Pan
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Linpeng Zhou
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Yujuan Yin
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Youyue Li
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shukui Wang
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China; School of Basic Medicine and Clinical Pharmacy, Nanjing First Hospital, China Pharmaceutical University, Nanjing, Jiangsu, China.; Jiangsu Collaborative Innovation Center on Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, China..
| | - Mu Xu
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, China..
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Yang M, Liu J, Kim P, Zhou X. Study of prognostic splicing factors in cancer using machine learning approaches. Hum Mol Genet 2024:ddae047. [PMID: 38538560 DOI: 10.1093/hmg/ddae047] [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: 12/10/2023] [Revised: 02/11/2024] [Accepted: 03/07/2024] [Indexed: 04/12/2024] Open
Abstract
Splicing factors (SFs) are the major RNA-binding proteins (RBPs) and key molecules that regulate the splicing of mRNA molecules through binding to mRNAs. The expression of splicing factors is frequently deregulated in different cancer types, causing the generation of oncogenic proteins involved in cancer hallmarks. In this study, we investigated the genes that encode RNA-binding proteins and identified potential splicing factors that contribute to the aberrant splicing applying a random forest classification model. The result suggested 56 splicing factors were related to the prognosis of 13 cancers, two SF complexes in liver hepatocellular carcinoma, and one SF complex in esophageal carcinoma. Further systematic bioinformatics studies on these cancer prognostic splicing factors and their related alternative splicing events revealed the potential regulations in a cancer-specific manner. Our analysis found high ILF2-ILF3 expression correlates with poor prognosis in LIHC through alternative splicing. These findings emphasize the importance of SFs as potential indicators for prognosis or targets for therapeutic interventions. Their roles in cancer exhibit complexity and are contingent upon the specific context in which they operate. This recognition further underscores the need for a comprehensive understanding and exploration of the role of SFs in different types of cancer, paving the way for their potential utilization in prognostic assessments and the development of targeted therapies.
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Affiliation(s)
- Mengyuan Yang
- School of Life Sciences, Zhengzhou University, No. 100, Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Jiajia Liu
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St Suite 600, Houston, Texas 77030, United States
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St Suite 600, Houston, Texas 77030, United States
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St Suite 600, Houston, Texas 77030, United States
- McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St, Houston, Texas 77030, United States
- School of Dentistry, The University of Texas Health Science Center at Houston, 7500 Cambridge St, Houston, Texas 77054, United States
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3
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Jiang D, Zhu XL, An Y, Li YR. Clinical significance of small nuclear ribonucleoprotein U1 subunit 70 in patients with hepatocellular carcinoma. PeerJ 2024; 12:e16876. [PMID: 38500533 PMCID: PMC10946392 DOI: 10.7717/peerj.16876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 01/11/2024] [Indexed: 03/20/2024] Open
Abstract
Background & Aims Small nuclear ribonucleoprotein U1 subunit 70 (SNRNP70) as one of the components of the U1 small nuclear ribonucleoprotein (snRNP) is rarely reported in cancers. This study aims to estimate the application potential of SNRNP70 in hepatocellular carcinoma (HCC) clinical practice. Methods Based on the TCGA database and cohort of HCC patients, we investigated the expression patterns and prognostic value of SNRNP70 in HCC. Then, the combination of SNRNP70 and alpha-fetoprotein (AFP) in 278 HCC cases was analyzed. Next, western blotting and immunohistochemistry were used to detect the expression of SNRNP70 in nucleus and cytoplasm. Finally, Cell Counting Kit-8 (CCK-8) and scratch wound healing assays were used to detect the effect of SNRNP70 on the proliferation and migration of HCC cells. Results SNRNP70 was highly expressed in HCC. Its expression was increasingly high during the progression of HCC and was positively related to immune infiltration cells. Higher SNRNP70 expression indicated a poor outcome of HCC patients. In addition, nuclear SNRNP70/AFP combination could be a prognostic biomarker for overall survival and recurrence. Cell experiments confirmed that knockdown of SNRNP70 inhibited the proliferation and migration of HCC cells. Conclusion SNRNP70 may be a new biomarker for HCC progression and HCC diagnosis as well as prognosis. SNRNP70 combined with serum AFP may indicate the prognosis and recurrence status of HCC patients after operation.
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Affiliation(s)
- Dong Jiang
- Department of Ultrasound, Eastern Hepatobiliary Surgery Hospital, The Third Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Xia-Ling Zhu
- Department of Ultrasound, Eastern Hepatobiliary Surgery Hospital, The Third Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Yan An
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi-ran Li
- Department of Intensive Care Medicine, Eastern Hepatobiliary Surgery Hospital, The Third Affiliated Hospital of Naval Medical University, Shanghai, China
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Maltseva D, Tonevitsky A. RNA-binding proteins regulating the CD44 alternative splicing. Front Mol Biosci 2023; 10:1326148. [PMID: 38106992 PMCID: PMC10722200 DOI: 10.3389/fmolb.2023.1326148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 11/15/2023] [Indexed: 12/19/2023] Open
Abstract
Alternative splicing is often deregulated in cancer, and cancer-specific isoform switches are part of the oncogenic transformation of cells. Accumulating evidence indicates that isoforms of the multifunctional cell-surface glycoprotein CD44 play different roles in cancer cells as compared to normal cells. In particular, the shift of CD44 isoforms is required for epithelial to mesenchymal transition (EMT) and is crucial for the maintenance of pluripotency in normal human cells and the acquisition of cancer stem cells phenotype for malignant cells. The growing and seemingly promising use of splicing inhibitors for treating cancer and other pathologies gives hope for the prospect of using such an approach to regulate CD44 alternative splicing. This review integrates current knowledge about regulating CD44 alternative splicing by RNA-binding proteins.
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Affiliation(s)
- Diana Maltseva
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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5
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Badia-I-Mompel P, Wessels L, Müller-Dott S, Trimbour R, Ramirez Flores RO, Argelaguet R, Saez-Rodriguez J. Gene regulatory network inference in the era of single-cell multi-omics. Nat Rev Genet 2023; 24:739-754. [PMID: 37365273 DOI: 10.1038/s41576-023-00618-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2023] [Indexed: 06/28/2023]
Abstract
The interplay between chromatin, transcription factors and genes generates complex regulatory circuits that can be represented as gene regulatory networks (GRNs). The study of GRNs is useful to understand how cellular identity is established, maintained and disrupted in disease. GRNs can be inferred from experimental data - historically, bulk omics data - and/or from the literature. The advent of single-cell multi-omics technologies has led to the development of novel computational methods that leverage genomic, transcriptomic and chromatin accessibility information to infer GRNs at an unprecedented resolution. Here, we review the key principles of inferring GRNs that encompass transcription factor-gene interactions from transcriptomics and chromatin accessibility data. We focus on the comparison and classification of methods that use single-cell multimodal data. We highlight challenges in GRN inference, in particular with respect to benchmarking, and potential further developments using additional data modalities.
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Affiliation(s)
- Pau Badia-I-Mompel
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Lorna Wessels
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience, Medical Faculty, MannHeim Heidelberg University, Mannheim, Germany
| | - Sophia Müller-Dott
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Rémi Trimbour
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Machine Learning for Integrative Genomics Group, Paris, France
| | - Ricardo O Ramirez Flores
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | | | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany.
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Zhang Q, Cao L, Song H, Lin K, Pang E. MkcDBGAS: a reference-free approach to identify comprehensive alternative splicing events in a transcriptome. Brief Bioinform 2023; 24:bbad367. [PMID: 37833843 PMCID: PMC10576019 DOI: 10.1093/bib/bbad367] [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: 07/21/2023] [Revised: 08/31/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Alternative splicing (AS) is an essential post-transcriptional mechanism that regulates many biological processes. However, identifying comprehensive types of AS events without guidance from a reference genome is still a challenge. Here, we proposed a novel method, MkcDBGAS, to identify all seven types of AS events using transcriptome alone, without a reference genome. MkcDBGAS, modeled by full-length transcripts of human and Arabidopsis thaliana, consists of three modules. In the first module, MkcDBGAS, for the first time, uses a colored de Bruijn graph with dynamic- and mixed- kmers to identify bubbles generated by AS with precision higher than 98.17% and detect AS types overlooked by other tools. In the second module, to further classify types of AS, MkcDBGAS added the motifs of exons to construct the feature matrix followed by the XGBoost-based classifier with the accuracy of classification greater than 93.40%, which outperformed other widely used machine learning models and the state-of-the-art methods. Highly scalable, MkcDBGAS performed well when applied to Iso-Seq data of Amborella and transcriptome of mouse. In the third module, MkcDBGAS provides the analysis of differential splicing across multiple biological conditions when RNA-sequencing data is available. MkcDBGAS is the first accurate and scalable method for detecting all seven types of AS events using the transcriptome alone, which will greatly empower the studies of AS in a wider field.
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Affiliation(s)
- Quanbao Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lei Cao
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Hongtao Song
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Kui Lin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Erli Pang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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7
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Zhang H, Tian J, Ren S, Han B, Tian R, Zuo X, Liu H, Wang Z, Cui Y, Liu L, Guo H, Zhang F, Niu R. Comprehensively analysis of splicing factors to construct prognosis prediction classifier in prostate cancer. J Cell Mol Med 2023; 27:2684-2700. [PMID: 37559353 PMCID: PMC10494302 DOI: 10.1111/jcmm.17849] [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: 04/08/2023] [Revised: 07/02/2023] [Accepted: 07/05/2023] [Indexed: 08/11/2023] Open
Abstract
Splicing factors (SFs) are proteins that control the alternative splicing (AS) of RNAs, which have been recognized as new cancer hallmarks. Their dysregulation has been found to be involved in many biological processes of cancer, such as carcinogenesis, proliferation, metastasis and senescence. Dysregulation of SFs has been demonstrated to contribute to the progression of prostate cancer (PCa). However, a comprehensive analysis of the prognosis value of SFs in PCa is limited. In this work, we systematically analysed 393 SFs to deeply characterize the expression patterns, clinical relevance and biological functions of SFs in PCa. We identified 53 survival-related SFs that can stratify PCa into two de nove molecular subtypes with distinct mRNA expression and AS-event expression patterns and displayed significant differences in pathway activity and clinical outcomes. An SF-based classifier was established using LASSO-COX regression with six key SFs (BCAS1, LSM3, DHX16, NOVA2, RBM47 and SNRPN), which showed promising prognosis-prediction performance with a receiver operating characteristic (ROC) >0.700 in both the training and testing datasets, as well as in three external PCa cohorts (DKFZ, GSE70769 and GSE21035). CRISPR/CAS9 screening data and cell-level functional analysis suggested that LSM3 and DHX16 are essential factors for the proliferation and cell cycle progression in PCa cells. This study proposes that SFs and AS events are potential multidimensional biomarkers for the diagnosis, prognosis and treatment of PCa.
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Affiliation(s)
- He Zhang
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Jianfei Tian
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Sixin Ren
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Baoai Han
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Ruinan Tian
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Xiaoyan Zuo
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Hui Liu
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Zhiyong Wang
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Yanfen Cui
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Liming Liu
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Hui Guo
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Fei Zhang
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
| | - Ruifang Niu
- Public LaboratoryTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for CancerTianjinChina
- Key Laboratory of Cancer Prevention and TherapyTianjinChina
- Tianjin's Clinical Research Center for CancerTianjinChina
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8
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Arancio W, Sciaraffa N, Coronnello C. MBS: a genome browser annotation track for high-confident microRNA binding sites in whole human transcriptome. Database (Oxford) 2023; 2023:7146264. [PMID: 37114805 PMCID: PMC10141451 DOI: 10.1093/database/baad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/15/2023] [Accepted: 03/07/2023] [Indexed: 04/29/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding ribonucleic acids (RNAs) that play a role in many regulatory pathways in eukaryotes. They usually exert their functions by binding mature messenger RNAs. The prediction of the binding targets of the endogenous miRNAs is crucial to unravel the processes they are involved in. In this work, we performed an extensive miRNA binding sites (MBS) prediction over all the annotated transcript sequences and made them available through an UCSC track. MBS annotation track allows to study and visualize the human miRNA binding sites transcriptome-wide in a genome browser, together with any other available information the user is interested in. In the creation of the database that underlies the MBS track, three consolidated algorithms of miRNA binding prediction have been used: PITA, miRanda and TargetScan, and information about the binding sites predicted by all of them has been collected. MBS track displays high-confident miRNA binding sites for the whole length of each human transcript, both coding and non-coding ones. Each annotation can redirect to a web page with the details of the miRNA binding and the involved transcripts. MBS can be easily applied to retrieve specific information such as the effects of alternative splicing on miRNA binding or when a specific miRNA binds an exon-exon junction in the mature RNA. Overall, MBS will be of great help for studying and visualizing, in a user-friendly mode, the predicted miRNA binding sites on all the transcripts arising from a gene or a region of interest. Database URL https://datasharingada.fondazionerimed.com:8080/MBS.
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Affiliation(s)
- Walter Arancio
- Institute for Biomedical Research and Innovation (IRIB), National Research Council (CNR), via Ugo la Malfa, 153, Palermo 90133, Italy
| | - Nicolina Sciaraffa
- Advanced Data Analysis Group, Ri.MED Foundation, via Bandiera, 11, Palermo 90133, Italy
| | - Claudia Coronnello
- Advanced Data Analysis Group, Ri.MED Foundation, via Bandiera, 11, Palermo 90133, Italy
- National Center for Gene Therapy and Drugs based on RNA Technology, via Bandiera, 11, Palermo 90133, Italy
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9
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Ivanova OM, Anufrieva KS, Kazakova AN, Malyants IK, Shnaider PV, Lukina MM, Shender VO. Non-canonical functions of spliceosome components in cancer progression. Cell Death Dis 2023; 14:77. [PMID: 36732501 PMCID: PMC9895063 DOI: 10.1038/s41419-022-05470-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 02/04/2023]
Abstract
Dysregulation of pre-mRNA splicing is a common hallmark of cancer cells and it is associated with altered expression, localization, and mutations of the components of the splicing machinery. In the last few years, it has been elucidated that spliceosome components can also influence cellular processes in a splicing-independent manner. Here, we analyze open source data to understand the effect of the knockdown of splicing factors in human cells on the expression and splicing of genes relevant to cell proliferation, migration, cell cycle regulation, DNA repair, and cell death. We supplement this information with a comprehensive literature review of non-canonical functions of splicing factors linked to cancer progression. We also specifically discuss the involvement of splicing factors in intercellular communication and known autoregulatory mechanisms in restoring their levels in cells. Finally, we discuss strategies to target components of the spliceosome machinery that are promising for anticancer therapy. Altogether, this review greatly expands understanding of the role of spliceosome proteins in cancer progression.
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Affiliation(s)
- Olga M Ivanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Institute for Regenerative Medicine, Sechenov University, Moscow, 119991, Russian Federation.
| | - Ksenia S Anufrieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Anastasia N Kazakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701, Russian Federation
| | - Irina K Malyants
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Chemical-Pharmaceutical Technologies and Biomedical Drugs, Mendeleev University of Chemical Technology of Russia, Moscow, 125047, Russian Federation
| | - Polina V Shnaider
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Maria M Lukina
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Victoria O Shender
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation.
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10
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Pedraza-Arevalo S, Alors-Pérez E, Blázquez-Encinas R, Herrera-Martínez AD, Jiménez-Vacas JM, Fuentes-Fayos AC, Reyes Ó, Ventura S, Sánchez-Sánchez R, Ortega-Salas R, Serrano-Blanch R, Gálvez-Moreno MA, Gahete MD, Ibáñez-Costa A, Luque RM, Castaño JP. Spliceosomic dysregulation unveils NOVA1 as a candidate actionable therapeutic target in pancreatic neuroendocrine tumors. Transl Res 2023; 251:63-73. [PMID: 35882361 DOI: 10.1016/j.trsl.2022.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 02/09/2023]
Abstract
Dysregulation of the splicing machinery is emerging as a hallmark in cancer due to its association with multiple dysfunctions in tumor cells. Inappropriate function of this machinery can generate tumor-driving splicing variants and trigger oncogenic actions. However, its role in pancreatic neuroendocrine tumors (PanNETs) is poorly defined. In this study we aimed to characterize the expression pattern of a set of splicing machinery components in PanNETs, and their relationship with aggressiveness features. A qPCR-based array was first deployed to determine the expression levels of components of the major (n = 13) and minor spliceosome (n = 4) and associated splicing factors (n = 27), using a microfluidic technology in 20 PanNETs and non-tumoral adjacent samples. Subsequently, in vivo and in vitro models were applied to explore the pathophysiological role of NOVA1. Expression analysis revealed that a substantial proportion of splicing machinery components was altered in tumors. Notably, key splicing factors were overexpressed in PanNETs samples, wherein their levels correlated with clinical and malignancy features. Using in vivo and in vitro assays, we demonstrate that one of those altered factors, NOVA1, is tightly related to cell proliferation, alters pivotal signaling pathways and interferes with responsiveness to drug treatment in PanNETs, suggesting a role for this factor in the aggressiveness of these tumors and its suitability as therapeutic target. Altogether, our results unveil a severe alteration of the splicing machinery in PanNETs and identify the putative relevance of NOVA1 in tumor development/progression, which could provide novel avenues to develop diagnostic biomarkers and therapeutic tools for this pathology.
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Affiliation(s)
- Sergio Pedraza-Arevalo
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain
| | - Emilia Alors-Pérez
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain
| | - Ricardo Blázquez-Encinas
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain
| | - Aura D Herrera-Martínez
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Endocrinology and Nutrition Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Juan M Jiménez-Vacas
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain
| | - Antonio C Fuentes-Fayos
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain
| | - Óscar Reyes
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Computer Sciences, University of Córdoba, Córdoba, Spain
| | - Sebastián Ventura
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Computer Sciences, University of Córdoba, Córdoba, Spain
| | - Rafael Sánchez-Sánchez
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Pathology Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Rosa Ortega-Salas
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Pathology Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Raquel Serrano-Blanch
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Medical Oncology Service, Reina Sofia University Hospital, Córdoba, Spain
| | - María A Gálvez-Moreno
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Endocrinology and Nutrition Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Manuel D Gahete
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain
| | - Alejandro Ibáñez-Costa
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain.
| | - Raúl M Luque
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain.
| | - Justo P Castaño
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain; Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain; CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain; Reina Sofia University Hospital, Córdoba, Spain.
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11
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The VEGF/VEGFR Axis Revisited: Implications for Cancer Therapy. Int J Mol Sci 2022; 23:ijms232415585. [PMID: 36555234 PMCID: PMC9779738 DOI: 10.3390/ijms232415585] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
The vascular endothelial growth factor (VEGF)/vascular endothelial growth factor receptor (VEGFR) axis is indispensable in the process of angiogenesis and has been implicated as a key driver of tumor vascularization. Consequently, several strategies that target VEGF and its cognate receptors, VEGFR-1 and VEGFR-2, have been designed to treat cancer. While therapies targeting full-length VEGF have resulted in an improvement in both overall survival and progression-free survival in various cancers, these benefits have been modest. In addition, the inhibition of VEGFRs is associated with undesirable off-target effects. Moreover, VEGF splice variants that modulate sprouting and non-sprouting angiogenesis have been identified in recent years. Cues within the tumor microenvironment determine the expression patterns of these variants. Noteworthy is that the mechanisms of action of these variants challenge the established norm of VEGF signaling. Furthermore, the aberrant expression of some of these variants has been observed in several cancers. Herein, developments in the understanding of the VEGF/VEGFR axis and the splice products of these molecules, as well as the environmental cues that regulate these variants are reviewed. Furthermore, strategies that incorporate the targeting of VEGF variants to enhance the effectiveness of antiangiogenic therapies in the clinical setting are discussed.
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12
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Liu Z, Liu X, Liu F, Zhao H, Zhang Y, Wang Y, Ma Y, Wang F, Zhang W, Petinrin OO, Yao Z, Liang J, He Q, Feng D, Wang L, Wong KC. The comprehensive and systematic identification of BLCA-specific SF-regulated, survival-related AS events. Gene 2022; 835:146657. [PMID: 35710083 DOI: 10.1016/j.gene.2022.146657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/27/2022] [Accepted: 06/02/2022] [Indexed: 12/23/2022]
Abstract
Bladder urothelial carcinoma (BLCA) is a complex disease with high morbidity and mortality. Changes in alternative splicing (AS) and splicing factor (SF) can affect gene expression, thus playing an essential role in tumorigenesis. This study downloaded 412 patients' clinical information and 433 samples of transcriptome profiling data from TCGA. And we collected 48 AS signatures from SpliceSeq. LASSO and Cox analyses were used for identifying survival-related AS events in BLCA. Finally, 1,645 OS-related AS events in 1,129 genes were validated by Kaplan-Meier (KM) survival analysis, ROC analysis, risk curve analysis, and independent prognostic analysis. Finally, our survey provides an AS-SF regulation network consisting of five SFs and 46 AS events. In the end, we profiled genes that AS occurred in pan-cancer and five SFs' expression in tumor and normal samples in BLCA. We selected CLIP-seq data for validation the interaction regulated by RBP. Our study paves the way for potential therapeutic targets of BLCA.
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Affiliation(s)
- Zhe Liu
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Xudong Liu
- School of Medicine, Chongqing University, Chongqing 400044, China; Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Fang Liu
- CYGNUS BIOSCIENCES (Beijing), Beijing 100176, China
| | - Hui Zhao
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310058, China
| | - Yu Zhang
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Yafan Wang
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Ying Ma
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China
| | - Fuzhou Wang
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Weitong Zhang
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | | | - Zhongyu Yao
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Jingbo Liang
- Department of Biomedical of Science, City University of Hong Kong, Hong Kong, China
| | - Qian He
- Department of Biomedical of Science, City University of Hong Kong, Hong Kong, China
| | - Dayun Feng
- Department of Neurosurgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710038, China.
| | - Lei Wang
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China; College of Medicine, Xinyang Normal University, Xinyang 464000, China.
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong, China.
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13
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Ye F, Liang Y, Cheng Z, Liu Y, Hu J, Li W, Chen X, Gao J, Jiang H. Immunological Characteristics of Alternative Splicing Profiles Related to Prognosis in Bladder Cancer. Front Immunol 2022; 13:911902. [PMID: 35769470 PMCID: PMC9234272 DOI: 10.3389/fimmu.2022.911902] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/20/2022] [Indexed: 11/20/2022] Open
Abstract
Several studies have found that pathological imbalance of alterative splicing (AS) events is associated with cancer susceptibility. carcinogenicity. Nevertheless, the relationship between heritable variation in AS events and carcinogenicity has not been extensively explored. Here, we downloaded AS event signatures, transcriptome profiles, and matched clinical information from The Cancer Genome Atlas (TCGA) database, identified the prognostic AS-related events via conducting the univariate Cox regression algorism. Subsequently, the prognostic AS-related events were further reduced by the least absolute shrinkage and selection operator (LASSO) logistic regression model, and employed for constructing the risk model. Single-sample (ssGSEA), ESTIMATE, and the CIBERSORT algorithms were conducted to evaluate tumor microenvironment status. CCK8, cell culture scratch, transwell invasion assays and flow cytometry were conducted to confirm the reliability of the model. We found 2751 prognostic-related AS events, and constructed a risk model with seven prognostic-related AS events. Compared with high-risk score patients, the overall survival rate of the patients with low-risk score was remarkably longer. Besides, we further found that risk score was also closely related to alterations in immune cell infiltration and immunotherapeutic molecules, indicating its potential as an observation of immune infiltration and clinical response to immunotherapy. In addition, the downstream target gene (DYM) could be a promising prognostic factor for bladder cancer. Our investigation provided an indispensable reference for ulteriorly exploring the role of AS events in the tumor microenvironment and immunotherapy efficiency, and rendered personalized prognosis monitoring for bladder cancer.
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Affiliation(s)
- Fangdie Ye
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yingchun Liang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhang Cheng
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yufei Liu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jimeng Hu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Weijian Li
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinan Chen
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiahao Gao
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
| | - Haowen Jiang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
- *Correspondence: Haowen Jiang,
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14
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Wang X, Pei J, Xiong L, Guo S, Cao M, Kang Y, Bao P, Wu X, Chu M, Liang C, Yan P, Guo X. Identification of the TSSK4 Alternative Spliceosomes and Analysis of the Function of the TSSK4 Protein in Yak (Bos grunniens). Animals (Basel) 2022; 12:ani12111380. [PMID: 35681843 PMCID: PMC9179852 DOI: 10.3390/ani12111380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/17/2022] [Accepted: 05/25/2022] [Indexed: 02/04/2023] Open
Abstract
In mammals, the testis-specific serine/threonine kinase (TSSK) is essential for spermatogenesis and male fertility. TSSK4 belongs to the family of the testis-specific serine/threonine-protein kinase (TSSK), with a crucial role in spermatogenesis. This study aimed to analyze the variable spliceosome of the TSSK4 gene in the yak for understanding the regulatory function of the TSSK4 spliceosome in yak testis development using PCR amplification and cloning techniques. The GST pull-down was used for pulling down the protein interacting with TSSK4, and then the protein interacting with TSSK4 was identified using LC–MS/MS. The results of the PCR amplification demonstrated multiple bands of the TSSK4 gene in the yak. The cloning and sequencing yielded a total of six alternative spliceosomes, which included only two alternative spliceosomes before sexual maturity and four alternative spliceosomes after sexual maturity. The sub-cells of the alternative spliceosomes were found to localize in the nucleus before sexual maturity and in the cytoplasm after sexual maturity. The LC–MS/MS analysis of the alternative spliceosome with the highest expression after sexual maturity yielded a total of 223 interacting proteins. The enrichment analysis of the 223 interacting proteins revealed these proteins participate in biological processes, cell composition, and molecular functions. The KEGG analysis indicated that the TSSK4-interacting protein participates in the estrogen signaling pathways, tight junctions, endoplasmic reticulum protein processing, and other signaling pathways. This study cloned the six alternative spliceosomes of the TSSK4 gene laying the foundation for studying the function of each spliceosome in the future.
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Affiliation(s)
- Xingdong Wang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (J.P.); (L.X.); (S.G.); (M.C.); (Y.K.); (P.B.); (X.W.); (M.C.); (C.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (J.P.); (L.X.); (S.G.); (M.C.); (Y.K.); (P.B.); (X.W.); (M.C.); (C.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Lin Xiong
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (J.P.); (L.X.); (S.G.); (M.C.); (Y.K.); (P.B.); (X.W.); (M.C.); (C.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Shaoke Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (J.P.); (L.X.); (S.G.); (M.C.); (Y.K.); (P.B.); (X.W.); (M.C.); (C.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Mengli Cao
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (J.P.); (L.X.); (S.G.); (M.C.); (Y.K.); (P.B.); (X.W.); (M.C.); (C.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yandong Kang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (J.P.); (L.X.); (S.G.); (M.C.); (Y.K.); (P.B.); (X.W.); (M.C.); (C.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (J.P.); (L.X.); (S.G.); (M.C.); (Y.K.); (P.B.); (X.W.); (M.C.); (C.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (J.P.); (L.X.); (S.G.); (M.C.); (Y.K.); (P.B.); (X.W.); (M.C.); (C.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (J.P.); (L.X.); (S.G.); (M.C.); (Y.K.); (P.B.); (X.W.); (M.C.); (C.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (J.P.); (L.X.); (S.G.); (M.C.); (Y.K.); (P.B.); (X.W.); (M.C.); (C.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (J.P.); (L.X.); (S.G.); (M.C.); (Y.K.); (P.B.); (X.W.); (M.C.); (C.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (J.P.); (L.X.); (S.G.); (M.C.); (Y.K.); (P.B.); (X.W.); (M.C.); (C.L.); (P.Y.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Correspondence: ; Tel.: +86-1899-3037-854
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15
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Malhan D, Basti A, Relógio A. Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes. NPJ Syst Biol Appl 2022; 8:17. [PMID: 35552415 PMCID: PMC9098426 DOI: 10.1038/s41540-022-00225-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/04/2022] [Indexed: 12/13/2022] Open
Abstract
Emerging evidence points towards a regulatory role of the circadian clock in alternative splicing (AS). Whether alterations in core-clock components may contribute to differential AS events is largely unknown. To address this, we carried out a computational analysis on recently generated time-series RNA-seq datasets from three core-clock knockout (KO) genes (ARNTL, NR1D1, PER2) and WT of a colorectal cancer (CRC) cell line, and time-series RNA-seq datasets for additional CRC and Hodgkin’s lymphoma (HL) cells, murine WT, Arntl KO, and Nr1d1/2 KO, and murine SCN WT tissue. The deletion of individual core-clock genes resulted in the loss of circadian expression in crucial spliceosome components such as SF3A1 (in ARNTLKO), SNW1 (in NR1D1KO), and HNRNPC (in PER2KO), which led to a differential pattern of KO-specific AS events. All HCT116KO cells showed a rhythmicity loss of a crucial spliceosome gene U2AF1, which was also not rhythmic in higher progression stage CRC and HL cancer cells. AS analysis revealed an increase in alternative first exon events specific to PER2 and NR1D1 KO in HCT116 cells, and a KO-specific change in expression and rhythmicity pattern of AS transcripts related to cancer hallmarks genes including FGFR2 in HCT116_ARNTLKO, CD44 in HCT116_NR1D1KO, and MET in HCT116_PER2KO. KO-specific changes in rhythmic properties of known spliced variants of these genes (e.g. FGFR2 IIIb/FGFR2 IIIc) correlated with epithelial-mesenchymal-transition signalling. Altogether, our bioinformatic analysis highlights a role for the circadian clock in the regulation of AS, and reveals a potential impact of clock disruption in aberrant splicing in cancer hallmark genes.
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Affiliation(s)
- Deeksha Malhan
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany
| | - Alireza Basti
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany. .,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany. .,Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany.
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16
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Ye Z, Bing A, Zhao S, Yi S, Zhan X. Comprehensive analysis of spliceosome genes and their mutants across 27 cancer types in 9070 patients: clinically relevant outcomes in the context of 3P medicine. EPMA J 2022; 13:335-350. [DOI: 10.1007/s13167-022-00279-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/25/2022] [Indexed: 12/19/2022]
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17
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Yang Y, Yuan H, Yang Q, Cai Y, Ren Y, Li Y, Gao C, Zhao S. Post-transcriptional regulation through alternative splicing in the lungs of Tibetan pigs under hypoxia. Gene 2022; 819:146268. [PMID: 35124151 DOI: 10.1016/j.gene.2022.146268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/22/2022] [Accepted: 01/28/2022] [Indexed: 11/15/2022]
Abstract
In multicellular organisms, alternative splicing (AS) is central to the regulation of multiple biological processes. To further elucidate the adaptive strategy of AS in the lungs of Tibetan pigs in response to hypoxia, we identified and analyzed five basic AS types and 59,930 AS events in 18,179 genes. We found that approximately 65.10% of the total expressed genes underwent AS in the lungs of Tibetan pigs at a high altitude (TH). The frequencies of AS events were similar among the different groups (5.06-5.30 events in each gene on average). Skipped exons (SEs) were the predominant type of AS event, followed by mutually exclusive exons (MXEs), alternative 3' splice sites (A3SSs) and alternative 5' splice sites (A5SSs). Retained introns (RIs), the remaining type of AS event, showed lower frequencies. Further comparison analysis of differentially expressed genes (DEGs) and differentially spliced genes (DSGs) identified 2,209 differential splicing events in the above 18,000 expressed genes, including 918 increased and 1,291 decreased splicing events between the TH and Tibetan pigs at a low altitude (TL) groups. We identified 227 hypoxia-related genes involved in lung development that were differentially regulated through AS. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis clearly identified many DEGs and DSGs at high or low altitude. Seven pathways in the top 20 enriched KEGG terms overlapped for the DEGs and DSGs, including the chemokine signaling pathway, B cell receptor signaling pathway, and cytokine-cytokine receptor interaction, which exert many immunoregulatory and inflammatory actions critical to the lung under hypoxia. Twelve pathways overlapped in hypoxic DEGs and DSGs and included antigen processing, presentation and biosynthesis. GO analysis of the DEGs and DSGs among the four groups showed that numerous GO terms were enriched in the biological category, and the proportion of genes with downregulated expression was greater among 227 hypoxic genes than that of all genes. The results suggest that AS plays an essential role in the regulation of gene expression during hypoxia and that numerous genes involved in lung development are differentially regulated through AS.
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Affiliation(s)
- Yanan Yang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Haonan Yuan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Qiaoli Yang
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yuan Cai
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yue Ren
- Academy of Agriculture and Animal Husbandry Sciences, Institute of Animal Husbandry and Veterinary Medicine, Lhasa, Xizang, China
| | - Yongqing Li
- Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Shengguo Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, China.
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18
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Li H, Huang J, Zhang J, Gao Y, Han B, Sun D. Identification of Alternative Splicing Events Associated with Paratuberculosis in Dairy Cattle Using Multi-Tissue RNA Sequencing Data. Genes (Basel) 2022; 13:genes13030497. [PMID: 35328051 PMCID: PMC8948961 DOI: 10.3390/genes13030497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 01/18/2023] Open
Abstract
Paratuberculosis is a major endemic disease caused by Mycobacterium avium subspecies paratuberculosis (MAP) infection and leads to huge economic loss in the dairy sector worldwide. Alternative splicing (AS) events, playing indispensable regulatory roles in many protein functions and biological pathways, are shown to be associated with complex traits and diseases. In this study, by integrating the RNA sequencing (RNA-seq) data of 24 samples from three tissues (peripheral blood, jejunum and salivary gland) of Holstein cows, we obtained 2,706,541,696 uniquely mapped reads in total that represented 12,870 expressed genes, and detected 4285 differentially expressed genes (DEGs) between MAP-infected and healthy cows (p < 0.05). Of them, 92 differentially expressed splicing factors (DESFs) were included. Further, 119, 150 and 68 differential alternative splicing (DAS) events between MAP-infected and healthy cows were identified in peripheral blood, jejunum and salivary glands, respectively. Of note, six DAS events were highly and significantly correlated with the DESFs (R2 > 0.9; p < 0.01), and their corresponding genes (COPI coat complex subunit gamma 2gene (COPG2), kinesin family member 2C gene (KIF2C), exocyst complex component 7 (EXOC7), Rab9 effector protein with kelch motifs gene (RABEPK), deoxyribonuclease 1 gene (DNASE1) and early endosome antigen 1gene (EEA1)) were significantly enriched in immune response such as vesicle-mediated transport, regulation of acute inflammatory response and tuberculosis through gene ontology (GO) and KEGG analysis. KS test showed that the DAS events in the EXOC7 and KIF2C genes indeed displayed differences between MAP-infected cows and healthy cows. The DAS in EXOC7 might produce a new protein sequence with lack of 23 amino acids, and the DAS in KIF2C induced a stop codon of premature occurrence and resulted in a lack of functional domain. In summary, this study identified the DAS events and corresponding genes related to MAP-infection base on the RNA-seq data from multiple tissues of Holstein cows, providing novel insights into the regulatory mechanisms underpinning paratuberculosis in dairy cattle.
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19
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Peng Q, Zhou Y, Oyang L, Wu N, Tang Y, Su M, Luo X, Wang Y, Sheng X, Ma J, Liao Q. Impacts and mechanisms of alternative mRNA splicing in cancer metabolism, immune response, and therapeutics. Mol Ther 2022; 30:1018-1035. [PMID: 34793975 PMCID: PMC8899522 DOI: 10.1016/j.ymthe.2021.11.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/29/2021] [Accepted: 11/11/2021] [Indexed: 02/08/2023] Open
Abstract
Alternative pre-mRNA splicing (AS) provides the potential to produce diversity at RNA and protein levels. Disruptions in the regulation of pre-mRNA splicing can lead to diseases. With the development of transcriptome and genome sequencing technology, increasing diseases have been identified to be associated with abnormal splicing of mRNAs. In tumors, abnormal alternative splicing frequently plays critical roles in cancer pathogenesis and may be considered as new biomarkers and therapeutic targets for cancer intervention. Metabolic abnormalities and immune disorders are important hallmarks of cancer. AS produces multiple different isoforms and diversifies protein expression, which is utilized by the immune and metabolic reprogramming systems to expand gene functions. The abnormal splicing events contributed to tumor progression, partially due to effects on immune response and metabolic reprogramming. Herein, we reviewed the vital role of alternative splicing in regulating cancer metabolism and immune response. We discussed how alternative splicing regulates metabolic reprogramming of cancer cells and antitumor immune response, and the possible strategies to targeting alternative splicing pathways or splicing-regulated metabolic pathway in the context of anticancer immunotherapy. Further, we highlighted the challenges and discuss the perspectives for RNA-based strategies for the treatment of cancer with abnormally alternative splicing isoforms.
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Affiliation(s)
- Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China,Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China,Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Min Su
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Xia Luo
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Ying Wang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Xiaowu Sheng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Jian Ma
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China; Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China.
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20
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Xiao D, Kim HJ, Pang I, Yang P. Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities. Bioinformatics 2022; 38:1956-1963. [PMID: 35015814 PMCID: PMC9113330 DOI: 10.1093/bioinformatics/btac015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/21/2021] [Accepted: 01/06/2022] [Indexed: 11/29/2022] Open
Abstract
Motivation The advance of mass spectrometry-based technologies enabled the profiling of the phosphoproteomes of a multitude of cell and tissue types. However, current research primarily focused on investigating the phosphorylation dynamics in specific cell types and experimental conditions, whereas the phosphorylation events that are common across cell/tissue types and stable regardless of experimental conditions are, so far, mostly ignored. Results Here, we developed a statistical framework to identify the stable phosphoproteome across 53 human phosphoproteomics datasets, covering 40 cell/tissue types and 194 conditions/treatments. We demonstrate that the stably phosphorylated sites (SPSs) identified from our statistical framework are evolutionarily conserved, functionally important and enriched in a range of core signaling and gene pathways. Particularly, we show that SPSs are highly enriched in the RNA splicing pathway, an essential cellular process in mammalian cells, and frequently disrupted by cancer mutations, suggesting a link between the dysregulation of RNA splicing and cancer development through mutations on SPSs. Availability and implementation The source code for data analysis in this study is available from Github repository https://github.com/PYangLab/SPSs under the open-source license of GPL-3. The data used in this study are publicly available (see Section 2.8). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Di Xiao
- Computational Systems Biology Group
| | - Hani Jieun Kim
- Computational Systems Biology Group.,Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia
| | - Ignatius Pang
- Bioinformatics Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Pengyi Yang
- Computational Systems Biology Group.,Charles Perkins Centre, School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia
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21
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Du JX, Luo YH, Zhang SJ, Wang B, Chen C, Zhu GQ, Zhu P, Cai CZ, Wan JL, Cai JL, Chen SP, Dai Z, Zhu W. Splicing factor SRSF1 promotes breast cancer progression via oncogenic splice switching of PTPMT1. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:171. [PMID: 33992102 PMCID: PMC8122567 DOI: 10.1186/s13046-021-01978-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/09/2021] [Indexed: 02/08/2023]
Abstract
Background Intensive evidence has highlighted the effect of aberrant alternative splicing (AS) events on cancer progression when triggered by dysregulation of the SR protein family. Nonetheless, the underlying mechanism in breast cancer (BRCA) remains elusive. Here we sought to explore the molecular function of SRSF1 and identify the key AS events regulated by SRSF1 in BRCA. Methods We conducted a comprehensive analysis of the expression and clinical correlation of SRSF1 in BRCA based on the TCGA dataset, Metabric database and clinical tissue samples. Functional analysis of SRSF1 in BRCA was conducted in vitro and in vivo. SRSF1-mediated AS events and their binding motifs were identified by RNA-seq, RNA immunoprecipitation-PCR (RIP-PCR) and in vivo crosslinking followed by immunoprecipitation (CLIP), which was further validated by the minigene reporter assay. PTPMT1 exon 3 (E3) AS was identified to partially mediate the oncogenic role of SRSF1 by the P-AKT/C-MYC axis. Finally, the expression and clinical significance of these AS events were validated in clinical samples and using the TCGA database. Results SRSF1 expression was consistently upregulated in BRCA samples, positively associated with tumor grade and the Ki-67 index, and correlated with poor prognosis in a hormone receptor-positive (HR+) cohort, which facilitated proliferation, cell migration and inhibited apoptosis in vitro and in vivo. We identified SRSF1-mediated AS events and discovered the SRSF1 binding motif in the regulation of splice switching of PTPMT1. Furthermore, PTPMT1 splice switching was regulated by SRSF1 by binding directly to its motif in E3 which partially mediated the oncogenic role of SRSF1 by the AKT/C-MYC axis. Additionally, PTPMT1 splice switching was validated in tissue samples of BRCA patients and using the TCGA database. The high-risk group, identified by AS of PTPMT1 and expression of SRSF1, possessed poorer prognosis in the stage I/II TCGA BRCA cohort. Conclusions SRSF1 exerts oncogenic roles in BRCA partially by regulating the AS of PTPMT1, which could be a therapeutic target candidate in BRCA and a prognostic factor in HR+ BRCA patient. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01978-8.
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Affiliation(s)
- Jun-Xian Du
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yi-Hong Luo
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Si-Jia Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Biao Wang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Cong Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Gui-Qi Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Ping Zhu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, No. 130 Dongan Road, Shanghai, 200032, China
| | - Cheng-Zhe Cai
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jing-Lei Wan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia-Liang Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Shi-Ping Chen
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Zhi Dai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China.
| | - Wei Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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22
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Hu J, Cai D, Zhao Z, Zhong GC, Gong J. Suppression of Heterogeneous Nuclear Ribonucleoprotein C Inhibit Hepatocellular Carcinoma Proliferation, Migration, and Invasion via Ras/MAPK Signaling Pathway. Front Oncol 2021; 11:659676. [PMID: 33937074 PMCID: PMC8087488 DOI: 10.3389/fonc.2021.659676] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/30/2021] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC), the most common malignant tumor, has high fatality and recurrence rates. Accumulating evidence shows that heterogeneous nuclear ribonucleoprotein C (HNRNPC), which is mainly involved in RNA splicing, export, and translation, promotes progression and metastasis of multiple tumor types; however, the effects of HNRNPC in HCC are unknown. In the present study, high levels of HNRNPC were detected in tumor tissues compared with para-tumor tissues by immunohistochemical and western blot assays. Furthermore, Cox proportional hazards regression models, the Kaplan–Meier method, and clinicopathologic features analysis showed that HNRNPC was not only an independent prognostic factor for both overall and disease-free survival in HCC but also a predictor of large tumor size and advanced tumor stage. Functional experiments revealed that silencing of HNRNPC not only led to arrest of more HCC cells at G0/G1 phase to inhibit their proliferation, but also suppressed EMT process to block their invasion, and migration in vitro; this was related to the Ras/MAPK signaling pathway. In addition, blocking of HCC cell proliferation regulated by HNRNPC silencing was observed in vivo. Finally, rescue tests showed that after recovery of Ras/MAPK signaling pathway activity by treatment with Ras agonists, the proliferation, migration, and invasion suppression of Huh-7 and Hep 3B cell lines caused by HNRNPC knockdown was partially reversed. Taken together, these results indicate that HNRNPC knockdown inhibits HCC cell proliferation, migration and invasion, in part via the Ras/MAPK signaling pathway. Thus, HNRNPC may have an important role in the progression of HCC and represents a promising biomarker for evaluation of prognosis and a potential therapeutic target in HCC patients.
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Affiliation(s)
- Jiejun Hu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dong Cai
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhibo Zhao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guo-Chao Zhong
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jianping Gong
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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