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Wang Y, Xu X, Zhang A, Yang S, Li H. Role of alternative splicing in fish immunity. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109601. [PMID: 38701992 DOI: 10.1016/j.fsi.2024.109601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Alternative splicing serves as a pivotal source of complexity in the transcriptome and proteome, selectively connecting various coding elements to generate a diverse array of mRNAs. This process encodes multiple proteins with either similar or distinct functions, contributing significantly to the intricacies of cellular processes. The role of alternative splicing in mammalian immunity has been well studied. Remarkably, the immune system of fish shares substantial similarities with that of humans, and alternative splicing also emerges as a key player in the immune processes of fish. In this review, we offer an overview of alternative splicing and its associated functions in the immune processes of fish, and summarize the research progress on alternative splicing in the fish immunity. Furthermore, we review the impact of alternative splicing on the fish immune system's response to external stimuli. Finally, we present our perspectives on future directions in this field. Our aim is to provide valuable insights for the future investigations into the role of alternative splicing in immunity.
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Affiliation(s)
- Yunchao Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xinyi Xu
- Hunan Fisheries Science Institute, Changsha, 410153, China
| | - Ailong Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Shuaiqi Yang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
| | - Hongyan Li
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266003, China.
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Bai Y, Cui G, Sun X, Wei M, Liu Y, Guo J, Yang Y. Angiopoietin-Related Protein 4-Transcript 3 Increases the Proliferation, Invasion, and Migration of Hepatocellular Carcinoma Cells and Inhibits Apoptosis. DNA Cell Biol 2024; 43:175-184. [PMID: 38466955 DOI: 10.1089/dna.2023.0392] [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] [Indexed: 03/13/2024] Open
Abstract
To investigate the functional differences of angiopoietin-related protein 4 (ANGPTL4) transcripts in hepatocellular carcinoma (HCC) cells. By transfecting ANGPTL4-Transcript 1 and ANGPTL4-Transcript 3 overexpression vectors into HepG2 and Huh7 cell lines with ANGPTL4 knockdown, the effects of overexpression of two transcripts on cell viability, invasion, migration, and apoptosis were analyzed. The expression of two transcripts was compared in human liver cancer tissue, and their effects on tumor development were validated in vivo experiments in mice. Compared with control, the overexpression of ANGPTL4-Transcript 1 had no significant effect on viability, invasion, healing, and apoptosis of HepG2 and Huh7 cells. However, these two cell lines overexpressing ANGPTL4-Transcript 3 showed remarkably enhanced cell viability, invasive and healing ability, and decreased apoptosis ability. Furthermore, the mRNA level of ANGPTL4-Transcript 3 was significantly increased in human HCC tissues and promoted tumor growth compared with Transcript 1. Different transcripts of gene ANGPTL4 have distinct effects on HCC. The abnormally elevated Transcript 3 with the specific ability of promoting HCC proliferation, infiltration, and migration is expected to become a new biological marker and more precise intervention target for HCC.
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Affiliation(s)
- Yun Bai
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Guanghua Cui
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiaoke Sun
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Meiqi Wei
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yanying Liu
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jialu Guo
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yu Yang
- Department of Oncology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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Lin T, Guo J, Peng Y, Li M, Liu Y, Yu X, Wu N, Yu W. Pan-cancer transcriptomic data of ABI1 transcript variants and molecular constitutive elements identifies novel cancer metastatic and prognostic biomarkers. Cancer Biomark 2024; 39:49-62. [PMID: 37545215 PMCID: PMC10977443 DOI: 10.3233/cbm-220348] [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: 09/27/2022] [Accepted: 06/26/2023] [Indexed: 08/08/2023]
Abstract
BACKGROUND Abelson interactor 1 (ABI1) is associated with the metastasis and prognosis of many malignancies. The association between ABI1 transcript spliced variants, their molecular constitutive exons and exon-exon junctions (EEJs) in 14 cancer types and clinical outcomes remains unsolved. OBJECTIVE To identify novel cancer metastatic and prognostic biomarkers from ABI1 total mRNA, TSVs, and molecular constitutive elements. METHODS Using data from TCGA and TSVdb database, the standard median of ABI1 total mRNA, TSV, exon, and EEJ expression was used as a cut-off value. Kaplan-Meier analysis, Chi-squared test (X2) and Kendall's tau statistic were used to identify novel metastatic and prognostic biomarkers, and Cox regression analysis was performed to screen and identify independent prognostic factors. RESULTS A total of 35 ABI1-related factors were found to be closely related to the prognosis of eight candidate cancer types. A total of 14 ABI1 TSVs and molecular constitutive elements were identified as novel metastatic and prognostic biomarkers in four cancer types. A total of 13 ABI1 molecular constitutive elements were identified as independent prognostic biomarkers in six cancer types. CONCLUSIONS In this study, we identified 14 ABI1-related novel metastatic and prognostic markers and 21 independent prognostic factors in total 8 candidate cancer types.
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Affiliation(s)
- Tingru Lin
- Department of Central Laboratory and Institute of Clinical Molecular Biology, Peking University People’s Hospital, Beijing, China
- Department of Gastroenterology, Peking University People’s Hospital, Beijing, China
| | - Jingzhu Guo
- Department of Central Laboratory and Institute of Clinical Molecular Biology, Peking University People’s Hospital, Beijing, China
- Department of Pediatrics, Peking University People’s Hospital, Beijing, China
| | - Yifan Peng
- Department of Central Laboratory and Institute of Clinical Molecular Biology, Peking University People’s Hospital, Beijing, China
- Gastrointestinal Cancer Center, Unit III, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, China
| | - Mei Li
- Department of Central Laboratory and Institute of Clinical Molecular Biology, Peking University People’s Hospital, Beijing, China
| | - Yulan Liu
- Department of Gastroenterology, Peking University People’s Hospital, Beijing, China
| | - Xin Yu
- Department of Hepatobiliary Surgery, Peking University People’s Hospital, Beijing, China
| | - Na Wu
- Department of Central Laboratory and Institute of Clinical Molecular Biology, Peking University People’s Hospital, Beijing, China
| | - Weidong Yu
- Department of Central Laboratory and Institute of Clinical Molecular Biology, Peking University People’s Hospital, Beijing, China
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Yuemaierabola A, Guo J, Sun L, Yeerkenbieke B, Liu F, Ye D, Zhai X, Guo W, Cao Y. Comprehensive analysis of CPSF4-related alternative splice genes in hepatocellular carcinoma. J Cancer Res Clin Oncol 2023; 149:13955-13971. [PMID: 37542549 PMCID: PMC10590311 DOI: 10.1007/s00432-023-05178-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/11/2023] [Indexed: 08/07/2023]
Abstract
BACKGROUND An important stage in controlling gene expression is RNA alternative splicing (AS), and aberrant AS can trigger the development and spread of malignancies, including hepatocellular carcinoma (HCC). A crucial component of AS is cleavage and polyadenylation-specific factor 4 (CPSF4), a component of the CPSF complex, but it is unclear how CPSF4-related AS molecules describe immune cell infiltration in the total tumor microenvironment (TME). METHODS Using RNA-sequencing data and clinical data from TCGA-LIHC from the Cancer Genome Atlas (TCGA) database, the AS genes with differential expression were found. The univariate Cox analysis, KM analysis, and Spearman analysis were used to identify the AS genes related to prognosis. Screening of key AS genes that are highly correlated with CPSF4. Key genes were screened using Cox regression analysis and stepwise regression analysis, and prognosis prediction models and the topography of TME cell infiltration were thoroughly analyzed. RESULTS A model consisting of seven AS genes (STMN1, CLSPN, MDK, RNFT2, PRR11, RNF157, GHR) was constructed that was aimed to predict prognostic condition. The outcomes of the HCC samples in the high-risk group were considerably worse than those in the lower risk group (p < 0.0001), and different risk patient groups were formed. According to the calibration curves and the area under the ROC curve (AUC) values for survival at 1, 2, and 3 years, the clinical nomogram performs well in predicting survival in HCC patients. These values were 0.76, 0.70, and 0.69, respectively. Moreover, prognostic signature was markedly related to immune infiltration and immune checkpoint genes expression. CONCLUSION By shedding light on the function of CPSF4 and the seven AS genes in the formation and progression of HCC, this research analysis contributes to the development of more useful prognostic, diagnostic, and possibly therapeutic biomarkers.
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Affiliation(s)
- Anwaier Yuemaierabola
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Jun Guo
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Lili Sun
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Buerlan Yeerkenbieke
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Fuzhong Liu
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Dilinaer Ye
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Xiaoyi Zhai
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China
| | - Wenjia Guo
- Department of Cancer Research Institute, Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, 830011, China.
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Urumqi, 830011, China.
| | - Yan Cao
- Cancer Hospital of Xinjiang Uygur Autonomous Region (Affiliated Cancer Hospital of Xinjiang Medical University), Urumqi, 830011, China.
- Nursing School of Xinjiang Medical University, Urumqi, 830011, China.
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Temaj G, Chichiarelli S, Saha S, Telkoparan-Akillilar P, Nuhii N, Hadziselimovic R, Saso L. An intricate rewiring of cancer metabolism via alternative splicing. Biochem Pharmacol 2023; 217:115848. [PMID: 37813165 DOI: 10.1016/j.bcp.2023.115848] [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: 08/24/2023] [Revised: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
All human genes undergo alternative splicing leading to the diversity of the proteins. However, in some cases, abnormal regulation of alternative splicing can result in diseases that trigger defects in metabolism, reduced apoptosis, increased proliferation, and progression in almost all tumor types. Metabolic dysregulations and immune dysfunctions are crucial factors in cancer. In this respect, alternative splicing in tumors could be a potential target for therapeutic cancer strategies. Dysregulation of alternative splicing during mRNA maturation promotes carcinogenesis and drug resistance in many cancer types. Alternative splicing (changing the target mRNA 3'UTR binding site) can result in a protein with altered drug affinity, ultimately leading to drug resistance.. Here, we will highlight the function of various alternative splicing factors, how it regulates the reprogramming of cancer cell metabolism, and their contribution to tumor initiation and proliferation. Also, we will discuss emerging therapeutics for treating tumors via abnormal alternative splicing. Finally, we will discuss the challenges associated with these therapeutic strategies for clinical applications.
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Affiliation(s)
- Gazmend Temaj
- Faculty of Pharmacy, College UBT, 10000 Prishtina, Kosovo
| | - Silvia Chichiarelli
- Department of Biochemical Sciences "A. Rossi-Fanelli", Sapienza University of Rome, 00185 Rome, Italy.
| | - Sarmistha Saha
- Department of Biotechnology, GLA University, Mathura 00185, Uttar Pradesh, India
| | | | - Nexhibe Nuhii
- Department of Pharmacy, Faculty of Medical Sciences, State University of Tetovo, 1200 Tetovo, Macedonia
| | - Rifat Hadziselimovic
- Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", La Sapienza University, 00185 Rome, Italy.
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Li Y, Chen Z, Peng J, Yuan C, Yan S, Yang N, Li P, Kong B. The splicing factor SNRPB promotes ovarian cancer progression through regulating aberrant exon skipping of POLA1 and BRCA2. Oncogene 2023:10.1038/s41388-023-02763-x. [PMID: 37391593 DOI: 10.1038/s41388-023-02763-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 06/08/2023] [Accepted: 06/22/2023] [Indexed: 07/02/2023]
Abstract
Splicing factors play a crucial role in the initiation and development of various human cancers. SNRPB, a core spliceosome component, regulates pre-mRNA alternative splicing. However, its function and underlying mechanism in ovarian cancer remain unclear. This study identified SNRPB as a critical driver of ovarian cancer through TCGA and CPTAC database analysis. SNRPB was highly upregulated in fresh frozen ovarian cancer tissues compared with normal fallopian tubes. Immunohistochemistry revealed that SNRPB expression was increased in formalin-fixed, paraffin-embedded ovarian cancer sections and was positively correlated with a poor prognosis for ovarian cancer. Functionally, SNRPB knockdown suppressed ovarian cancer cell proliferation and invasion, and overexpression exerted opposite effects. SNRPB expression increased after cisplatin treatment, and silencing SNRPB sensitized ovarian cancer cells to cisplatin. KEGG pathway analysis revealed that the differentially expressed genes (DEGs) were mainly enriched in DNA replication and homologous recombination, and almost all DEGs related to DNA replication and homologous recombination were downregulated after SNRPB knockdown according to RNA-seq. Exon 3 skipping of the DEGs DNA polymerase alpha 1 (POLA1) and BRCA2 was induced by SNRPB silencing. Exon 3 skipping of POLA1 yielded premature termination codons and led to nonsense-mediated RNA decay (NMD); exon 3 skipping of BRCA2 led to loss of the PALB2 binding domain, which is necessary for homologous recombination, and increased ovarian cancer cell cisplatin sensitivity. POLA1 or BRCA2 knockdown partially impaired the increased malignancy of SNRPB-overexpressing ovarian cancer cells. Moreover, miR-654-5p was found to reduce SNRPB mRNA expression by directly binding to the SNRPB 3'-UTR. Overall, SNRPB was identified as an important oncogenic driver that promotes ovarian cancer progression by repressing exon 3 skipping of POLA1 and BRCA2. Thus, SNRPB is a potential treatment target and prognostic marker for ovarian cancer.
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Affiliation(s)
- Yingwei Li
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China.
- Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Ji'nan 250012, Shandong Province, China.
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China.
| | - Zhongshao Chen
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Jiali Peng
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Cunzhong Yuan
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Shi Yan
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Ning Yang
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Peng Li
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Beihua Kong
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China.
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China.
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Li D, Guo J, Jia R. Epigenetic Control of Cancer Cell Proliferation and Cell Cycle Progression by HNRNPK via Promoting Exon 4 Inclusion of Histone Code Reader SPIN1. J Mol Biol 2023; 435:167993. [PMID: 36736887 DOI: 10.1016/j.jmb.2023.167993] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein K (HNRNPK, hnRNP K), a multifunctional RNA/DNA binding protein, mainly regulates transcription, translation and RNA splicing, and then plays oncogenic roles in many cancers. However, the related mechanisms remain largely unknown. Here, we found that HNRNPK can partially epigenetically regulate cancer cell proliferation via increasing transcription and exon 4-inclusion of SPIN1, an important oncogenic histone code reader. This exon 4 skipping event of SPIN1 generates a long non-coding RNA, followed by the downregulation of SPIN1 protein. SPIN1 is one of the most significantly co-expressed genes of HNRNPK in thirteen TCGA cancers. Our further studies revealed HNRNPK knockdown significantly inhibited cell growth and cell cycle progression in oral squamous cell carcinoma (OSCC) cells and promoted cell apoptosis. Overexpression of SPIN1 was able to partially rescue the growth inhibition triggered by HNRNPK knockdown. Moreover, CCND1 (Cyclin D1), a key cell cycle regulator and oncogene, epigenetically up-regulated by SPIN1, was also positively regulated by HNRNPK. In addition, we discovered that HNRNPK promoted SPIN1 exon 4 inclusion by interacting with an intronic splicing enhancer in intron 4. Collectively, our study suggests a novel epigenetic regulatory pathway of HNRNPK in OSCC, mediated by controlling the transcription activity and alternative splicing of SPIN1 gene.
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Affiliation(s)
- Di Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jihua Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China; Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
| | - Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
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Alternative ANKHD1 transcript promotes proliferation and inhibits migration in uterine corpus endometrial carcinoma. NPJ Genom Med 2022; 7:56. [PMID: 36171217 PMCID: PMC9519915 DOI: 10.1038/s41525-022-00321-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 08/08/2022] [Indexed: 11/22/2022] Open
Abstract
Alternative splicing (AS) is common in gene expression, and abnormal splicing often results in several cancers. Overall survival-associated splicing events (OS-SEs) have been used to predict prognosis in cancer. The aim of this study was to investigate the presence and function of OS-SEs in uterine corpus endometrial carcinoma (UCEC). Based on TCGA and TCGASpliceSeq databases, gene expression and the AS data of UCEC samples were retrieved. An alternate terminator of ANKHD1 transcripts named ANKHD1-BP3 was found to be significantly related to metastasis and OS in UCEC and significantly associated with HSPB1. The upregulated expression of HSPB1 induced downregulation of ANKHD1-BP3 and promoted tumor metastasis. These findings indicate that HSPB1, a splicing factor, regulates the expression of ANKHD1-BP3 to promote metastasis in UCEC.
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Wang Z, Wu Q, Liu Y, Li Q, Li J. Identification of prognostic alternative splicing signature in gastric cancer. Arch Public Health 2022; 80:145. [PMID: 35614517 PMCID: PMC9131537 DOI: 10.1186/s13690-022-00894-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 05/02/2022] [Indexed: 11/20/2022] Open
Abstract
Background Aberrant alternative splicing (AS) events could be viewed as prognostic indicators in a large number of malignancies. This study aims to identify prognostic AS events, illuminate the function of the splicing variants biomarkers and provide reliable evidence for formulating public health strategies for gastric cancer (GC) surveillance. Methods RNA-Seq data, clinical information and percent spliced in (PSI) values were available in The cancer genome atlas (TCGA) and TCGA SpliceSeq data portal. A three-step regression method was conducted to identify prognostic AS events and construct multi-AS-based signatures. The associations between prognostic AS events and splicing factors were also investigated. Results We identified a total of 1,318 survival-related AS events in GC, parent genes of which were implicated in numerous oncogenic pathways. The final prognostic signatures stratified by seven types of AS events or not stratified performed well in risk prediction for GC patients. Moreover, five signatures based on AA, AD, AT, ES and RI events function as independent prognostic indicators after multivariate adjustment of other clinical variables. Splicing network also showed marked correlation between the expression of splicing factors and PSI value of AS events in GC patients. Conclusion Our findings provide a landscape of AS events and regulatory network in GC, indicating that AS events might serve as prognostic biomarkers and therapeutic targets for GC. Supplementary Information The online version contains supplementary material available at 10.1186/s13690-022-00894-3.
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Affiliation(s)
- Zhiwu Wang
- Department of Chemoradiotherapy, Tangshan People`S Hospital, Tangshan, China
| | - Qiong Wu
- Department of Chemoradiotherapy, Tangshan People`S Hospital, Tangshan, China
| | - Yankun Liu
- The Cancer Institute, Tangshan People's Hospital, Tangshan, 063001, China
| | - Qingke Li
- The Cancer Institute, Tangshan People's Hospital, Tangshan, 063001, China
| | - Jingwu Li
- The Cancer Institute, Tangshan People's Hospital, Tangshan, 063001, China.
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10
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Rekad Z, Izzi V, Lamba R, Ciais D, Van Obberghen-Schilling E. The Alternative Matrisome: alternative splicing of ECM proteins in development, homeostasis and tumor progression. Matrix Biol 2022; 111:26-52. [DOI: 10.1016/j.matbio.2022.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/19/2022] [Accepted: 05/04/2022] [Indexed: 12/14/2022]
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11
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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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12
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Lei Y, Xiao J, Zhao W, Liu F, Sui Y, Wang K, Liu Y. Myc pathway-guided alternative splicing events predict the overall survival of lung squamous cell carcinoma. ALL LIFE 2022. [DOI: 10.1080/26895293.2022.2043449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Youming Lei
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Jian Xiao
- Department of Cardiothoracic Surgery, Changzheng Hospital, Naval Medical University, Shanghai, People’s Republic of China
| | - Wei Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Fanghao Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
| | - Yi Sui
- Department of IVD Medical Marketing, 3D Medicine Inc., Shanghai, People’s Republic of China
| | - Kun Wang
- Department of Thoracic Surgery, Anning First People’s Hospital (Kunming Fourth People’s Hospital), Seventh Affiliated Hospital of Dali University, Kunming, People’s Republic of China
| | - Yinqiang Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, People’s Republic of China
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13
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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: 28] [Impact Index Per Article: 14.0] [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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14
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Chen B, Deng T, Deng L, Yu H, He B, Chen K, Zheng C, Wang D, Wang Y, Chen G. Identification of tumour immune microenvironment-related alternative splicing events for the prognostication of pancreatic adenocarcinoma. BMC Cancer 2021; 21:1211. [PMID: 34772375 PMCID: PMC8590242 DOI: 10.1186/s12885-021-08962-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/01/2021] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Pancreatic adenocarcinoma (PAAD) is characterized by low antitumour immune cell infiltration in an immunosuppressive microenvironment. This study aimed to systematically explore the impact on prognostic alternative splicing events (ASs) of tumour immune microenvironment (TIME) in PAAD. METHODS The ESTIMATE algorithm was implemented to compute the stromal/immune-related scores of each PAAD patient, followed by Kaplan-Meier (KM) survival analysis of patients with different scores grouped by X-tile software. TIME-related differentially expressed ASs (DEASs) were determined and evaluated through functional annotation analysis. In addition, Cox analyses were implemented to construct a TIME-related signature and an AS clinical nomogram. Moreover, comprehensive analyses, including gene set enrichment analysis (GSEA), immune infiltration, immune checkpoint gene expression, and tumour mutation were performed between the two risk groups to understand the potential mechanisms. Finally, Cytoscape was implemented to illuminate the AS-splicing factor (SF) regulatory network. RESULTS A total of 437 TIME-related DEASs significantly related to PAAD tumorigenesis and the formation of the TIME were identified. Additionally, a robust TIME-related prognostic signature based on seven DEASs was generated, and an AS clinical nomogram combining the signature and four clinical predictors also exhibited prominent discrimination by ROC (0.762 ~ 0.804) and calibration curves. More importantly, the fractions of CD8 T cells, regulatory T cells and activated memory CD4 T cells were lower, and the expression of four immune checkpoints-PD-L1, CD47, CD276, and PVR-was obviously higher in high-risk patients. Finally, functional analysis and tumour mutations revealed that aberrant immune signatures and activated carcinogenic pathways in high-risk patients may be the cause of the poor prognosis. CONCLUSION We extracted a list of DEASs associated with the TIME through the ESTIMATE algorithm and constructed a prognostic signature on the basis of seven DEASs to predict the prognosis of PAAD patients, which may guide advanced decision-making for personalized precision intervention.
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Affiliation(s)
- Bo Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Tuo Deng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Liming Deng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Haitao Yu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Bangjie He
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kaiyu Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chongming Zheng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Daojie Wang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yi Wang
- Division of Preventive Medicine, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China.
| | - Gang Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China. .,Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
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15
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Wu T, Wang W, Wang Y, Yao M, Du L, Zhang X, Huang Y, Wang J, Yu H, Bian X. Comprehensive analysis of alternative splicing profiling reveals novel events associated with prognosis and the infiltration of immune cells in prostate cancer. Transl Androl Urol 2021; 10:3056-3068. [PMID: 34430408 PMCID: PMC8350246 DOI: 10.21037/tau-21-585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/16/2021] [Indexed: 11/17/2022] Open
Abstract
Background Alternative splicing (AS) is believed to play a vital role in tumor development. Therefore, comprehensive investigation of AS and its biological function in prostate cancer (PCa) is crucial. Methods The AS profiling of 489 patients with PCa was obtained from The Cancer Genome Atlas (TCGA) SpliceSeq database. Bioinformatics tools were used to describe splicing associations and build prognostic models. Unsupervised clustering of the determined prognostic AS events and the relationship with immune characteristics were also explored. Results In total, 20,723 AS events were detected and 2,805 were identified in PCa. In the regulatory networks, the data suggested a significant correlation between splicing factor (SF) expression and AS events. To stratify the progression risk of PCa patients, prognostic models were constructed using splicing patterns. Six AS events were screened out as independent prognostic factors for progression-free survival. Based on the gene features, we constructed the combined prognostic predictors model, and the receiver operating characteristic (ROC) curve for this model reached a high area under the ROC curve (AUC) of 0.729793, indicating a favorable ability to predict patient outcomes. Through unsupervised clustering analysis, the correlations between AS-based clusters and prognosis as well as immune characteristics were revealed. The correlation analysis on TIMER revealed the relationship between gene expression and immune cell infiltration. Conclusions This in-depth genome-wide analysis of the AS profiling in PCa revealed unique AS events associated with cancer progression and the infiltration of immune cells, with potential for predicting outcomes and therapeutic responses.
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Affiliation(s)
- Tianqi Wu
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Radiotherapy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wenfeng Wang
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yanhao Wang
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Mengfei Yao
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Leilei Du
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xingming Zhang
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yongqiang Huang
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jianhua Wang
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,School of Medicine, Anhui University of Science & Technology, Huainan, China
| | - Hongbo Yu
- Department of Urology, Affiliated Mingji Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaojie Bian
- Shanghai Urological Cancer Institute, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
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16
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Huang R, Zheng Z, Xian S, Zhang J, Jia J, Song D, Yan P, Yin H, Hu P, Zhu X, Huang Z, Meng T, Zhang J. Identification of prognostic and bone metastatic alternative splicing signatures in bladder cancer. Bioengineered 2021; 12:5289-5304. [PMID: 34402716 PMCID: PMC8806927 DOI: 10.1080/21655979.2021.1964252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bladder cancer (BLCA), originating from the epithelium of the urinary bladder, was the second most common malignancy in the urinary system with a high metastasis rate and poor post-metastasis prognosis. Alternative splicing events (ASEs) were regarded as important markers of tumor progression and prognosis, however, their roles in bladder cancer bone metastasis have not been recognized. In this study, we constructed a predictive model based on ASEs and explored the molecular mechanism of ASEs in BLCA bone metastasis, based on data from the Cancer Genome Atlas (TCGA) and TCGASpliceSeq databases. We proposed the hypothesis that the splicing events of ITGB4 was regulated by the splicing factor JUP, and this regulation might play a key role in BLCA bone metastasis through the glycosphingolipid biosynthesis ganglio series pathway.
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Affiliation(s)
- Runzhi Huang
- Key Laboratory Of Spine And Spinal Cord Injury Repair And Regeneration Tongji University, Ministry Of Education, Shanghai, China.,Division Of Spine, Department Of Orthopedics, Tongji Hospital Affiliated To Tongji University School Of Medicine, Shanghai, China
| | - Zixuan Zheng
- Tongji University School Of Medicine (Shanghai Pulmonary Hospital), Shanghai, China
| | - Shuyuan Xian
- Key Laboratory Of Spine And Spinal Cord Injury Repair And Regeneration Tongji University, Ministry Of Education, Shanghai, China.,Division Of Spine, Department Of Orthopedics, Tongji Hospital Affiliated To Tongji University School Of Medicine, Shanghai, China
| | - Jiayao Zhang
- School Of Mathematical Sciences Of Tongji University, Shanghai, China
| | - Jingyi Jia
- Tongji University School Of Medicine (Shanghai Pulmonary Hospital), Shanghai, China
| | - Dianwen Song
- Department Of Orthopedics, Shanghai General Hospital, School Of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Penghui Yan
- Department Of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huabin Yin
- Department Of Orthopedics, Shanghai General Hospital, School Of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Peng Hu
- Department Of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaolong Zhu
- Department Of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zongqiang Huang
- Department Of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tong Meng
- Department Of Orthopedics, Shanghai General Hospital, School Of Medicine, Shanghai Jiaotong University, Shanghai, China.,Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School Of Medicine, Shanghai, China
| | - Jie Zhang
- Key Laboratory Of Spine And Spinal Cord Injury Repair And Regeneration Tongji University, Ministry Of Education, Shanghai, China.,Division Of Spine, Department Of Orthopedics, Tongji Hospital Affiliated To Tongji University School Of Medicine, Shanghai, China
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17
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Mehterov N, Kazakova M, Sbirkov Y, Vladimirov B, Belev N, Yaneva G, Todorova K, Hayrabedyan S, Sarafian V. Alternative RNA Splicing-The Trojan Horse of Cancer Cells in Chemotherapy. Genes (Basel) 2021; 12:genes12071085. [PMID: 34356101 PMCID: PMC8306420 DOI: 10.3390/genes12071085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Almost all transcribed human genes undergo alternative RNA splicing, which increases the diversity of the coding and non-coding cellular landscape. The resultant gene products might have distinctly different and, in some cases, even opposite functions. Therefore, the abnormal regulation of alternative splicing plays a crucial role in malignant transformation, development, and progression, a fact supported by the distinct splicing profiles identified in both healthy and tumor cells. Drug resistance, resulting in treatment failure, still remains a major challenge for current cancer therapy. Furthermore, tumor cells often take advantage of aberrant RNA splicing to overcome the toxicity of the administered chemotherapeutic agents. Thus, deciphering the alternative RNA splicing variants in tumor cells would provide opportunities for designing novel therapeutics combating cancer more efficiently. In the present review, we provide a comprehensive outline of the recent findings in alternative splicing in the most common neoplasms, including lung, breast, prostate, head and neck, glioma, colon, and blood malignancies. Molecular mechanisms developed by cancer cells to promote oncogenesis as well as to evade anticancer drug treatment and the subsequent chemotherapy failure are also discussed. Taken together, these findings offer novel opportunities for future studies and the development of targeted therapy for cancer-specific splicing variants.
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Affiliation(s)
- Nikolay Mehterov
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
| | - Maria Kazakova
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
| | - Yordan Sbirkov
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
| | - Boyan Vladimirov
- Department of Maxillofacial Surgery, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria;
| | - Nikolay Belev
- Medical Simulation and Training Center, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria;
| | - Galina Yaneva
- Department of Biology, Faculty of Pharmacy, Medical University of Varna, 9002 Varna, Bulgaria;
| | - Krassimira Todorova
- Laboratory of Reproductive OMICs Technologies, Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (K.T.); (S.H.)
| | - Soren Hayrabedyan
- Laboratory of Reproductive OMICs Technologies, Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (K.T.); (S.H.)
| | - Victoria Sarafian
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
- Correspondence: ; Tel.: +359-882-512-952
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18
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Identification of survival-related alternative splicing signatures in acute myeloid leukemia. Biosci Rep 2021; 41:229155. [PMID: 34212178 PMCID: PMC8292762 DOI: 10.1042/bsr20204037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 06/11/2021] [Accepted: 06/30/2021] [Indexed: 01/25/2023] Open
Abstract
Aberrant RNA alternative splicing (AS) variants play critical roles in tumorigenesis and prognosis in human cancers. Here, we conducted a comprehensive profiling of aberrant AS events in acute myeloid leukemia (AML). RNA AS profile, including seven AS types, and the percent spliced in (PSI) value for each patient were generated by SpliceSeq using RNA-seq data from TCGA. Univariate followed by multivariate Cox regression analysis were used to identify survival-related AS events and develop the AS signatures. A nomogram was developed, and its predictive efficacy was assessed. About 27,892 AS events and 3,178 events were associated with overall survival (OS) after strict filtering. Parent genes of survival-associated AS events were mainly enriched in leukemia-associated processes including chromatin modification, autophagy, and T-cell receptor signaling pathway. The 10 AS signature based on seven types of AS events showed better efficacy in predicting OS of patients than those built on a single AS event type. The area under curve (AUC) value of the 10 AS signature for 3-year OS was 0.91. Gene set enrichment analysis (GSEA) confirmed that these survival-related AS events contribute to AML progression. Moreover, the nomogram showed good predictive performance for patient's prognosis. Finally, the correlation network of AS variants with splicing factor genes found potential important regulatory genes in AML. The present study presented a systematic analysis of survival-related AS events and developed AS signatures for predicting the patient’s survival. Further studies are needed to validate the signatures in independent AML cohorts and might provide a promising perspective for developing therapeutic targets.
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19
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Fish L, Khoroshkin M, Navickas A, Garcia K, Culbertson B, Hänisch B, Zhang S, Nguyen HCB, Soto LM, Dermit M, Mardakheh FK, Molina H, Alarcón C, Najafabadi HS, Goodarzi H. A prometastatic splicing program regulated by SNRPA1 interactions with structured RNA elements. Science 2021; 372:eabc7531. [PMID: 33986153 PMCID: PMC8238114 DOI: 10.1126/science.abc7531] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 04/01/2021] [Indexed: 12/14/2022]
Abstract
Aberrant alternative splicing is a hallmark of cancer, yet the underlying regulatory programs that control this process remain largely unknown. Here, we report a systematic effort to decipher the RNA structural code that shapes pathological splicing during breast cancer metastasis. We discovered a previously unknown structural splicing enhancer that is enriched near cassette exons with increased inclusion in highly metastatic cells. We show that the spliceosomal protein small nuclear ribonucleoprotein polypeptide A' (SNRPA1) interacts with these enhancers to promote cassette exon inclusion. This interaction enhances metastatic lung colonization and cancer cell invasion, in part through SNRPA1-mediated regulation of PLEC alternative splicing, which can be counteracted by splicing modulating morpholinos. Our findings establish a noncanonical regulatory role for SNRPA1 as a prometastatic splicing enhancer in breast cancer.
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Affiliation(s)
- Lisa Fish
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Matvei Khoroshkin
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Albertas Navickas
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kristle Garcia
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bruce Culbertson
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Benjamin Hänisch
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steven Zhang
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hoang C B Nguyen
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Larisa M Soto
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Maria Dermit
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Faraz K Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Henrik Molina
- Proteome Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Claudio Alarcón
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Hamed S Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
- McGill Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
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20
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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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Su Z, Huang D. Alternative Splicing of Pre-mRNA in the Control of Immune Activity. Genes (Basel) 2021; 12:genes12040574. [PMID: 33921058 PMCID: PMC8071365 DOI: 10.3390/genes12040574] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023] Open
Abstract
The human immune response is a complex process that responds to numerous exogenous antigens in preventing infection by microorganisms, as well as to endogenous components in the surveillance of tumors and autoimmune diseases, and a great number of molecules are necessary to carry the functional complexity of immune activity. Alternative splicing of pre-mRNA plays an important role in immune cell development and regulation of immune activity through yielding diverse transcriptional isoforms to supplement the function of limited genes associated with the immune reaction. In addition, multiple factors have been identified as being involved in the control of alternative splicing at the cis, trans, or co-transcriptional level, and the aberrant splicing of RNA leads to the abnormal modulation of immune activity in infections, immune diseases, and tumors. In this review, we summarize the recent discoveries on the generation of immune-associated alternative splice variants, clinical disorders, and possible regulatory mechanisms. We also discuss the immune responses to the neoantigens produced by alternative splicing, and finally, we issue some alternative splicing and immunity correlated questions based on our knowledge.
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Affiliation(s)
- Zhongjing Su
- Department of Histology and Embryology, Shantou University Medical College, No. 22, Xinling Road, Shantou 515041, China
- Correspondence: (Z.S.); (D.H.)
| | - Dongyang Huang
- Department of Cell Biology, Shantou University Medical College, No. 22, Xinling Road, Shantou 515041, China
- Correspondence: (Z.S.); (D.H.)
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22
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Xu Z, Wei J, Qin F, Sun Y, Xiang W, Yuan L, Qin J, Deng K, Zheng T, Li S. Hypoxia-associated alternative splicing signature in lung adenocarcinoma. Epigenomics 2020; 13:47-63. [PMID: 33336585 DOI: 10.2217/epi-2020-0399] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim: To establish a signature based on hypoxia-related alternative splicing (AS) events for lung adenocarcinoma. Materials & methods: The least absolute shrinkage and selection operator Cox approach was used to construct a prognostic model. A nomogram that integrates the final AS predictor and stage was created. The network of the key AS events and splicing factors was created. Results: We created a prognostic signature of 11 AS events. Moreover, a nomogram that constitutes the pathological stage and risk was exhibited to be greatly effective in estimating the survival likelihood of lung adenocarcinoma patients. Conclusion: Herein we developed the first-ever signature based on hypoxia-related AS events with both prognostic predictive power and diagnostic efficacy.
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Affiliation(s)
- Zhanyu Xu
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Jiangbo Wei
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Fanglu Qin
- Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Yu Sun
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Weiwei Xiang
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Liqiang Yuan
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Junqi Qin
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Kun Deng
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Tiaozhan Zheng
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
| | - Shikang Li
- Department of Thoracic & Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, PR China
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23
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Wang Y, Wang Z, Zhao B, Chen W, Wang Y, Ma W. Development of a nomogram for prognostic prediction of lower-grade glioma based on alternative splicing signatures. Cancer Med 2020; 9:9266-9281. [PMID: 33047900 PMCID: PMC7774734 DOI: 10.1002/cam4.3530] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/17/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The prognosis of lower-grade glioma (LGG) differs from that of other grades gliomas. Although lots of studies on the prognostic biomarkers of LGG have been reported, few have significant clinical impact. Alternative splicing (AS) events can affect cell function by splicing precursor mRNA. Therefore, a prognostic model for LGG based on AS events are important to establish. METHODS RNA sequencing, clinical, and AS event data of 510 LGG patients from the TCGA database were downloaded. Univariate Cox regression analysis was used to screen out prognostic-related AS events and LASSO regression and multivariate Cox regression were used to establish prognostic risk scores for patients in the training set (n = 340). After validation, a nomogram model was established based on the AS signature and clinical information, which was able to predict 1-, 3-, and 5-year survival rates. Finally, considering the regulatory effect of splicing factors (SFs) on AS events, an AS-SF regulatory network was analyzed. RESULTS The most common AS event was exon skipping and the least was mutually exclusive exons. All the seven AS events were related to the prognosis of LGG patients, regardless of whether they were separated or considered as a whole event (integrated AS event), and the integrated AS event had the most significant correlation. After further inclusion of clinical indicators, eight factors were screened out: age, new event, KPS, WHO grade, treatment, integrated AS signature, IDH1 and TP53 mutation status, and a nomogram model was established. The study also constructed an AS-SF regulatory network. CONCLUSION The AS events and clinical factors that can predict the prognosis of LGG patients were screened, and a prognostic prediction model was established. The results of this study can play an important role in clinical work to better evaluate the prognosis of patients and impact treatment options.
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Affiliation(s)
- Yaning Wang
- Departments of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zihao Wang
- Departments of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Binghao Zhao
- Departments of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenlin Chen
- Departments of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Wang
- Departments of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenbin Ma
- Departments of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Makhafola TJ, Mbele M, Yacqub-Usman K, Hendren A, Haigh DB, Blackley Z, Meyer M, Mongan NP, Bates DO, Dlamini Z. Apoptosis in Cancer Cells Is Induced by Alternative Splicing of hnRNPA2/B1 Through Splicing of Bcl-x, a Mechanism that Can Be Stimulated by an Extract of the South African Medicinal Plant, Cotyledon orbiculata. Front Oncol 2020; 10:547392. [PMID: 33163396 PMCID: PMC7580256 DOI: 10.3389/fonc.2020.547392] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/21/2020] [Indexed: 01/09/2023] Open
Abstract
Alternative splicing is deregulated in cancer and alternatively spliced products can be linked to cancer hallmarks. Targeting alternative splicing could offer novel effective cancer treatments. We investigated the effects of the crude extract of a South African medicinal plant, Cotyledon orbiculata, on cell survival of colon (HCT116) and esophageal (OE33 and KYSE70) cancer cell lines. Using RNASeq, we discovered that the extract interfered with mRNA regulatory pathways. The extract caused hnRNPA2B1 to splice from the hnRNPB1 to the hnRNPA2 isoform, resulting in a switch in the BCL2L1 gene from Bcl-xL to Bcl-xS causing activation of caspase-3-cleavage and apoptosis. Similar splicing effects were induced by the known anti-cancer splicing modulator pladienolide B. Knockdown of hnRNPB1 using siRNA resulted in decreased cell viability and increased caspase-3-cleavage, and over-expression of hnRNPB1 prevented the effect of C. orbiculata extract on apoptosis and cell survival. The effect of the hnRNPA2/B1 splicing switch by the C. orbiculata extract increased hnRNPA2B1 binding to Bcl-xl/s, BCL2, MDM2, cMYC, CD44, CDK6, and cJUN mRNA. These findings suggest that apoptosis in HCT116, OE33, and KYSE cancer cells is controlled by switched splicing of hnRNPA2B1 and BCL2L1, providing evidence that hnRNPB1 regulates apoptosis. Inhibiting this splicing could have therapeutic potential for colon and esophageal cancers. Targeting hnRNPA2B1 splicing in colon cancer regulates splicing of BCL2L1 to induce apoptosis. This approach could be a useful therapeutic strategy to induce apoptosis and restrain cancer cell proliferation and tumor progression. Here, we found that the extract of Cotyledon orbiculata, a South African medicinal plant, had an anti-proliferative effect in cancer cells, mediated by apoptosis induced by alternative splicing of hnRNPA2B1 and BCL2L1.
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Affiliation(s)
- Tshepiso Jan Makhafola
- SA-Medical Research Council (MRC)/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Faculty of Health Sciences, Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria, South Africa.,Division of Cancer and Stem Cells, Centre for Cancer Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Mzwandile Mbele
- SA-Medical Research Council (MRC)/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Faculty of Health Sciences, Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria, South Africa.,Division of Cancer and Stem Cells, Centre for Cancer Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Kiren Yacqub-Usman
- Division of Cancer and Stem Cells, Centre for Cancer Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Amy Hendren
- Division of Cancer and Stem Cells, Centre for Cancer Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Daisy Belle Haigh
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Zoe Blackley
- Division of Cancer and Stem Cells, Centre for Cancer Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Mervin Meyer
- Biolabels Unit, Department of Biotechnology, Department of Science and Technology (DST)/Mintek Nanotechnology Innovation Centre (NIC), University of the Western Cape, Bellville, South Africa
| | - Nigel Patrick Mongan
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - David Owen Bates
- Division of Cancer and Stem Cells, Centre for Cancer Sciences, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Zodwa Dlamini
- SA-Medical Research Council (MRC)/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers Extramural Unit, Faculty of Health Sciences, Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria, South Africa
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25
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Huang J, Sachdeva M, Xu E, Robinson TJ, Luo L, Ma Y, Williams NT, Lopez O, Cervia LD, Yuan F, Qin X, Zhang D, Owzar K, Gokgoz N, Seto A, Okada T, Singer S, Andrulis IL, Wunder JS, Lazar AJ, Rubin BP, Pipho K, Mello SS, Giudice J, Kirsch DG. The Long Noncoding RNA NEAT1 Promotes Sarcoma Metastasis by Regulating RNA Splicing Pathways. Mol Cancer Res 2020; 18:1534-1544. [PMID: 32561656 PMCID: PMC7541426 DOI: 10.1158/1541-7786.mcr-19-1170] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/09/2020] [Accepted: 06/15/2020] [Indexed: 11/16/2022]
Abstract
Soft-tissue sarcomas (STS) are rare malignancies showing lineage differentiation toward diverse mesenchymal tissues. Half of all high-grade STSs develop lung metastasis with a median survival of 15 months. Here, we used a genetically engineered mouse model that mimics undifferentiated pleomorphic sarcoma (UPS) to study the molecular mechanisms driving metastasis. High-grade sarcomas were generated with Cre recombinase technology using mice with conditional mutations in Kras and Trp53 (KP) genes. After amputation of the limb bearing the primary tumor, mice were followed for the development of lung metastasis. Using RNA-sequencing of matched primary KP tumors and lung metastases, we found that the long noncoding RNA (lncRNA) Nuclear Enriched Abundant Transcript 1 (Neat1) is significantly upregulated in lung metastases. Furthermore, NEAT1 RNA ISH of human UPS showed that NEAT1 is upregulated within a subset of lung metastases compared with paired primary UPS. Remarkably, CRISPR/Cas9-mediated knockout of Neat1 suppressed the ability of KP tumor cells to colonize the lungs. To gain insight into the underlying mechanisms by which the lncRNA Neat1 promotes sarcoma metastasis, we pulled down Neat1 RNA and used mass spectrometry to identify interacting proteins. Interestingly, most Neat1 interacting proteins are involved in RNA splicing regulation. In particular, KH-Type Splicing Regulatory Protein (KHSRP) interacts with Neat1 and is associated with poor prognosis of human STS. Moreover, depletion of KHSRP suppressed the ability of KP tumor cells to colonize the lungs. Collectively, these results suggest that Neat1 and its interacting proteins, which regulate RNA splicing, are involved in mediating sarcoma metastasis. IMPLICATIONS: Understanding that lncRNA NEAT1 promotes sarcoma metastasis, at least in part, through interacting with the RNA splicing regulator KHSRP may translate into new therapeutic approaches for sarcoma.
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Affiliation(s)
- Jianguo Huang
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Mohit Sachdeva
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Eric Xu
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Timothy J Robinson
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Nerissa T Williams
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Omar Lopez
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina
| | - Lisa D Cervia
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Fan Yuan
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Xiaodi Qin
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
| | - Dadong Zhang
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
| | - Kouros Owzar
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Department of Biostatistics & Bioinformatics, Duke University, Durham, North Carolina
| | - Nalan Gokgoz
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Andrew Seto
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Tomoyo Okada
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samuel Singer
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Jay S Wunder
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- University of Toronto Musculoskeletal Oncology Unit, and Department of Surgery, University of Toronto, Toronto, Canada
| | - Alexander J Lazar
- Departments of Pathology, Genomic Medicine, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Brian P Rubin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Krista Pipho
- University of Rochester Medical Center, Rochester, New York
| | | | - Jimena Giudice
- Department of Cell Biology and Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- McAllister Heart Institute, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - David G Kirsch
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina.
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina
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26
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Hu C, Wang Y, Liu C, Shen R, Chen B, Sun K, Rao H, Ye L, Ye J, Tian S. Systematic Profiling of Alternative Splicing for Sarcoma Patients Reveals Novel Prognostic Biomarkers Associated with Tumor Microenvironment and Immune Cells. Med Sci Monit 2020; 26:e924126. [PMID: 32683393 PMCID: PMC7388651 DOI: 10.12659/msm.924126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Alternative splicing (AS) events is a novel biomarker of tumor prognosis, but the role of AS events in sarcoma patients remains unclear. Material/Methods RNA-seq and clinicopathologic data of the sarcoma cohort were extracted from the TCGA database and data on AS events were downloaded from the TCGASpliceSeq database. Univariate Cox analysis, LASSO regression analysis, and multivariate Cox analysis were performed to determine the overall survival (OS)- and disease-free survival (DFS)-related AS events. Two nomograms were developed based on the independent variables, and subgroup analysis was performed. The area under the curve (AUC), calibration curve, and decision curve analysis (DCA) were used to evaluate the nomograms. Then, we used the CIBERSORT and ESTIMATE package to determine the immune cell proportion and tumor microenvironment (TME) score, respectively. The associations between AS events-based clusters and TME and immune cells were studied. Results We identified 1945 and 1831 AS events as OS- and DFS-related AS events, respectively. Two nomograms based on the AS events and clinical data were established and the AUCs of nomograms ranged from 0.807 to 0.894. The calibration curve and DCA showed excellent performance of nomograms. In addition, the results indicated the distinct relationships between AS events-based clusters and OS, DFS, immune score, stromal score, and 10 immune cells. Conclusions Our study indicated that AS events are novel prognostic biomarkers for sarcoma patients that may be associated with the TME and immune cells.
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Affiliation(s)
- Chuan Hu
- Department of Joint Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Yuanhe Wang
- Department of Joint Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Chuan Liu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, Liaoning, China (mainland)
| | - Rui Shen
- Department of Joint Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Bo Chen
- Wenzhou Medical University, Wenzhou, Zhejiang, China (mainland)
| | - Kang Sun
- Department of Joint Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
| | - Huili Rao
- Sir Run Run Shaw Hospital, Zhejiang University, School of Medicine, Hangzhou, Zhejiang, China (mainland)
| | - Lin Ye
- Wenzhou Medical University, Wenzhou, Zhejiang, China (mainland)
| | - Jianjun Ye
- Wenzhou Medical University, Wenzhou, Zhejiang, China (mainland)
| | - Shaoqi Tian
- Department of Joint Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China (mainland)
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27
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Li Z, Chen X, Wei M, Liu G, Tian Y, Zhang X, Zhu G, Chen C, Liu J, Wang T, Lin G, Wang J, Cai G, Lv Y. Systemic Analysis of RNA Alternative Splicing Signals Related to the Prognosis for Head and Neck Squamous Cell Carcinoma. Front Oncol 2020; 10:87. [PMID: 32117741 PMCID: PMC7025462 DOI: 10.3389/fonc.2020.00087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 01/16/2020] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing (AS) is an important mechanism that is responsible for the production of protein diversity. An increasing body of evidence has suggested that out-of-control AS is closely related to the genesis and development of cancer. Systematic analysis of genome-wide AS in head and neck squamous cell carcinoma (HNSCC) has not yet been carried out, and consideration of this topic remains at the preliminary stage and requires further investigation. In this study, systemic bioinformatic analysis was carried out on the genome-wide AS events of 555 clinical HNSCC samples from the TCGA database. Firstly, we statistically analyzed the distributions of seven AS event types in HNSCC samples. Then, through univariate survival analysis, we observed the relationship between AS and the prognosis of the disease and found that 437 intersections of AS events were significantly related to overall survival. Among them, 335 cross-genes showed a high degree of consistency in the genes associated with overall survival and recurrence. The overall survival was significantly related to AS events. Besides, the frequency of overall survival-related ES events was evidently reduced, while the AP and the AT events were increased. In addition, AT events accounted for the largest proportion. Further, multiple regression model analysis proved that AS could become a new classification method for HNSCC, and KEGG enrichment analysis proved that most genes and proteins interacting with AS events had different biological functions and were associated with a variety of diseases. Finally, through the selection of characteristic HNSCC genes and the construction of a prognostic model, seven cross-genes related to survival and recurrence were screened out, and these characteristic genes were verified by multivariate survival model analysis so as to classify the prognosis at different splicing times and gene expression levels. These results have laid a solid foundation for our further research and play a decisive role in showing the correlation of AS with the prognosis of HNSCC.
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Affiliation(s)
- Zhexuan Li
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xun Chen
- Department of Stomatology, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - Ming Wei
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Guancheng Liu
- Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Yongquan Tian
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xin Zhang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Gangcai Zhu
- Department of Otolaryngology Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Changhan Chen
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Jiangyi Liu
- Quanzhou Disease Prevention and Control Center, Quanzhou, China
| | - Tiansheng Wang
- Department of Otolaryngology Head and Neck Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Gongbiao Lin
- Department of Otolaryngology Head and Neck Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - Juncheng Wang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Gengming Cai
- Department of Otolaryngology Head and Neck Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - Yunxia Lv
- Department of Thyroid Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Uncovering the signaling landscape controlling breast cancer cell migration identifies novel metastasis driver genes. Nat Commun 2019; 10:2983. [PMID: 31278301 PMCID: PMC6611796 DOI: 10.1038/s41467-019-11020-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/06/2019] [Indexed: 12/18/2022] Open
Abstract
Ttriple-negative breast cancer (TNBC) is an aggressive and highly metastatic breast cancer subtype. Enhanced TNBC cell motility is a prerequisite of TNBC cell dissemination. Here, we apply an imaging-based RNAi phenotypic cell migration screen using two highly motile TNBC cell lines (Hs578T and MDA-MB-231) to provide a repository of signaling determinants that functionally drive TNBC cell motility. We have screened ~4,200 target genes individually and discovered 133 and 113 migratory modulators of Hs578T and MDA-MB-231, respectively, which are linked to signaling networks predictive for breast cancer progression. The splicing factors PRPF4B and BUD31 and the transcription factor BPTF are essential for cancer cell migration, amplified in human primary breast tumors and associated with metastasis-free survival. Depletion of PRPF4B, BUD31 and BPTF causes primarily down regulation of genes involved in focal adhesion and ECM-interaction pathways. PRPF4B is essential for TNBC metastasis formation in vivo, making PRPF4B a candidate for further drug development. Triple-negative breast cancers (TNBC) have enhanced migratory behaviour. Here, the authors perform a phenotypic imaging-based RNAi screen to identify several genes associated with regulation of migratory phenotypes and show that one of the regulators, PRPF4B, mediates metastasis in TNBC in mice.
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29
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Caruso JA, Carruthers NJ, Thibodeau B, Geddes TJ, Dombkowski AA, Stemmer PM. Global Signaling Profiling in a Human Model of Tumorigenic Progression Indicates a Role for Alternative RNA Splicing in Cellular Reprogramming. Int J Mol Sci 2018; 19:ijms19102847. [PMID: 30241319 PMCID: PMC6213538 DOI: 10.3390/ijms19102847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 12/13/2022] Open
Abstract
Intracellular signaling is controlled to a large extent by the phosphorylation status of proteins. To determine how human breast cells can be reprogrammed during tumorigenic progression, we profiled cell lines in the MCF10A lineage by phosphoproteomic analyses. A large cluster of proteins involved in RNA splicing were hypophosphorylated as cells progressed to a hyperplastic state, and then hyperphosphorylated after progression to a fully metastatic phenotype. A comprehensive transcriptomic approach was used to determine whether alterations in splicing factor phosphorylation status would be reflected in changes in mRNA splicing. Results indicated that the degree of mRNA splicing trended with the degree of tumorigenicity of the 4 cell lines tested. That is, highly metastatic cell cultures had the greatest number of genes with splice variants, and these genes had greater fluctuations in expression intensities. Genes with high splicing indices were mapped against gene ontology terms to determine whether they have known roles in cancer. This group showed highly significant associations for angiogenesis, cytokine-mediated signaling, cell migration, programmed cell death and epithelial cell differentiation. In summary, data from global profiling of a human model of breast cancer development suggest that therapeutics should be developed which target signaling pathways that regulate RNA splicing.
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Affiliation(s)
- Joseph A Caruso
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA.
| | - Nicholas J Carruthers
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA.
| | - Bryan Thibodeau
- Beaumont BioBank and Molecular Core Laboratory, Royal Oak, MI 48073, USA.
| | - Timothy J Geddes
- Beaumont BioBank and Molecular Core Laboratory, Royal Oak, MI 48073, USA.
| | - Alan A Dombkowski
- Department of Pediatrics, Wayne State University, Detroit, MI 48201, USA.
| | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA.
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