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Li L, Jin T, Hu L, Ding J. Alternative splicing regulation and its therapeutic potential in bladder cancer. Front Oncol 2024; 14:1402350. [PMID: 39132499 PMCID: PMC11310127 DOI: 10.3389/fonc.2024.1402350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 07/05/2024] [Indexed: 08/13/2024] Open
Abstract
Bladder cancer is one of the leading causes of mortality globally. The development of bladder cancer is closely associated with alternative splicing, which regulates human gene expression and enhances the diversity of functional proteins. Alternative splicing is a distinctive feature of bladder cancer, and as such, it may hold promise as a therapeutic target. This review aims to comprehensively discuss the current knowledge of alternative splicing in the context of bladder cancer. We review the process of alternative splicing and its regulation in bladder cancer. Moreover, we emphasize the significance of abnormal alternative splicing and splicing factor irregularities during bladder cancer progression. Finally, we explore the impact of alternative splicing on bladder cancer drug resistance and the potential of alternative splicing as a therapeutic target.
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Affiliation(s)
- Lina Li
- College of Medicine, Jinhua University of Vocational Technology, Jinhua, Zhejiang, China
| | - Ting Jin
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Liang Hu
- Department of Urology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
| | - Jin Ding
- Department of Gastroenterology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang, China
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2
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Elshwekh H, Alhudiri IM, Elzagheid A, Enattah N, Abbassi Y, Abou Assali L, Marino I, Stuani C, Buratti E, Romano M. Assessing the Impact of Novel BRCA1 Exon 11 Variants on Pre-mRNA Splicing. Cells 2024; 13:824. [PMID: 38786046 PMCID: PMC11119505 DOI: 10.3390/cells13100824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Our study focused on assessing the effects of three newly identified BRCA1 exon 11 variants (c.1019T>C, c.2363T>G, and c.3192T>C) on breast cancer susceptibility. Using computational predictions and experimental splicing assays, we evaluated their potential as pathogenic mutations. Our in silico analyses suggested that the c.2363T>G and c.3192T>C variants could impact both splicing and protein function, resulting in the V340A and V788G mutations, respectively. We further examined their splicing effects using minigene assays in MCF7 and SKBR3 breast cancer cell lines. Interestingly, we found that the c.2363T>G variant significantly altered splicing patterns in MCF7 cells but not in SKBR3 cells. This finding suggests a potential influence of cellular context on the variant's effects. While attempts to correlate in silico predictions with RNA binding factors were inconclusive, this observation underscores the complexity of splicing regulation. Splicing is governed by various factors, including cellular contexts and protein interactions, making it challenging to predict outcomes accurately. Further research is needed to fully understand the functional consequences of the c.2363T>G variant in breast cancer pathogenesis. Integrating computational predictions with experimental data will provide valuable insights into the role of alternative splicing regulation in different breast cancer types and stages.
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Affiliation(s)
- Halla Elshwekh
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
- Department of Genetic Engineering, Libyan Biotechnology Research Center, Tripoli P.O. Box 30313, Libya; (I.M.A.); (A.E.); (N.E.)
| | - Inas M. Alhudiri
- Department of Genetic Engineering, Libyan Biotechnology Research Center, Tripoli P.O. Box 30313, Libya; (I.M.A.); (A.E.); (N.E.)
| | - Adam Elzagheid
- Department of Genetic Engineering, Libyan Biotechnology Research Center, Tripoli P.O. Box 30313, Libya; (I.M.A.); (A.E.); (N.E.)
| | - Nabil Enattah
- Department of Genetic Engineering, Libyan Biotechnology Research Center, Tripoli P.O. Box 30313, Libya; (I.M.A.); (A.E.); (N.E.)
| | - Yasmine Abbassi
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
| | - Lubna Abou Assali
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
| | - Ilenia Marino
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
- Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy; (H.E.); (Y.A.); (L.A.A.); (I.M.); (C.S.)
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio, 28, 34127 Trieste, Italy
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3
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Achour C, Bhattarai DP, Groza P, Román ÁC, Aguilo F. METTL3 regulates breast cancer-associated alternative splicing switches. Oncogene 2023; 42:911-925. [PMID: 36725888 PMCID: PMC10020087 DOI: 10.1038/s41388-023-02602-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 02/03/2023]
Abstract
Alternative splicing (AS) enables differential inclusion of exons from a given transcript, thereby contributing to the transcriptome and proteome diversity. Aberrant AS patterns play major roles in the development of different pathologies, including breast cancer. N6-methyladenosine (m6A), the most abundant internal modification of eukaryotic mRNA, influences tumor progression and metastasis of breast cancer, and it has been recently linked to AS regulation. Here, we identify a specific AS signature associated with breast tumorigenesis in vitro. We characterize for the first time the role of METTL3 in modulating breast cancer-associated AS programs, expanding the role of the m6A-methyltransferase in tumorigenesis. Specifically, we find that both m6A deposition in splice site boundaries and in splicing and transcription factor transcripts, such as MYC, direct AS switches of specific breast cancer-associated transcripts. Finally, we show that five of the AS events validated in vitro are associated with a poor overall survival rate for patients with breast cancer, suggesting the use of these AS events as a novel potential prognostic biomarker.
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Affiliation(s)
- Cyrinne Achour
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 87, Umeå, Sweden
| | - Devi Prasad Bhattarai
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 87, Umeå, Sweden
| | - Paula Groza
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 87, Umeå, Sweden
| | - Ángel-Carlos Román
- Department of Molecular Biology and Genetics, University of Extremadura, 06071, Badajoz, Spain.
| | - Francesca Aguilo
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden.
- Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 87, Umeå, Sweden.
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4
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Chen SX, Simpson E, Reiter JL, Liu Y. Bioinformatics detection of modulators controlling splicing factor-dependent intron retention in the human brain. Hum Mutat 2022; 43:1629-1641. [PMID: 35391504 PMCID: PMC9537345 DOI: 10.1002/humu.24379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/02/2022] [Accepted: 04/02/2022] [Indexed: 12/30/2022]
Abstract
Alternative RNA splicing is an important means of genetic control and transcriptome diversity. However, when alternative splicing events are studied independently, coordinated splicing modulated by common factors is often not recognized. As a result, the molecular mechanisms of how splicing regulators promote or repress splice site recognition in a context-dependent manner are not well understood. The functional coupling between multiple gene regulatory layers suggests that splicing is modulated by additional genetic or epigenetic components. Here, we developed a bioinformatics approach to identify causal modulators of splicing activity based on the variation of gene expression in large RNA sequencing datasets. We applied this approach in a neurological context with hundreds of dorsolateral prefrontal cortex samples. Our model is strengthened with the incorporation of genetic variants to impute gene expression in a Mendelian randomization-based approach. We identified novel modulators of the splicing factor SRSF1, including UIMC1 and the long noncoding RNA CBR3-AS1, that function over dozens of SRSF1 intron retention splicing targets. This strategy can be widely used to identify modulators of RNA-binding proteins involved in tissue-specific alternative splicing.
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Affiliation(s)
- Steven X. Chen
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
- Center for Computational Biology and BioinformaticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Ed Simpson
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
- Center for Computational Biology and BioinformaticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Jill L. Reiter
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
- Center for Computational Biology and BioinformaticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Yunlong Liu
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
- Center for Computational Biology and BioinformaticsIndiana University School of MedicineIndianapolisIndianaUSA
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5
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Chen Y, Dou Z, Chen X, Zhao D, Che T, Su W, Qu T, Zhang T, Xu C, Lei H, Li Q, Zhang H, Di C. Overexpression of splicing factor poly(rC)-binding protein 1 elicits cycle arrest, apoptosis induction, and p73 splicing in human cervical carcinoma cells. J Cancer Res Clin Oncol 2022; 148:3475-3484. [PMID: 35896897 DOI: 10.1007/s00432-022-04170-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 06/20/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE Splicing factor poly(rC)-binding protein 1 (PCBP1) is a novel tumor suppressor that is downregulated in several cancers thereby regulating tumor formation and metastasis. However, the involvement of PCBP1 in apoptosis of cancer cells and the molecular mechanism remains elusive. On this basis, we sought to investigate the role of splicing factor PCBP1 in the apoptosis in human cervical cancer cells. METHODS To investigate PCBP1 functions in vitro, we overexpressed PCBP1 in human cervical cancer cells. A series of cytological function assays were employed to study to the role of PCBP1 in cell proliferation, cell cycle arrest and apoptosis. RESULTS Overexpression of PCBP1 was found to greatly repress proliferation of HeLa cells in a time-dependent manner. It also induced a significant increase in G2/M phase arrest and apoptosis. Furthermore, overexpressed PCBP1 favored the production of long isoforms of p73, thereby inducing upregulated ratio of Bax/Bcl-2, the release of cytochrome c and the expression of caspase-3. CONCLUSION Our results revealed that PCBP1 played a vital role in p73 splicing, cycle arrest and apoptosis induction in human cervical carcinoma cells. Targeting PCBP1 may be a potential therapeutic strategy for cervical cancer therapy.
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Affiliation(s)
- Yuhong Chen
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhihui Dou
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xiaohua Chen
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Dapeng Zhao
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Tuanjie Che
- Laboratory of Precision Medicine and Translational Medicine, Suzhou Hospital Affiliated to Nanjing Medical University, Suzhou Science and Technology Town Hospital, Suzhou, 215153, China.,Key Laboratory of Functional Genomic and Molecular Diagnosis of Gansu Province, Lanzhou, 730030, China
| | - Wei Su
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Tao Qu
- Department of Biotherapy Center, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Taotao Zhang
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Caipeng Xu
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Huiweng Lei
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China.,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Qiang Li
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China. .,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China. .,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China. .,Department of Heavy Ion Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Hong Zhang
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China. .,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China. .,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China. .,Department of Heavy Ion Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.
| | - Cuixia Di
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China. .,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100039, China. .,School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China. .,Department of Heavy Ion Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.
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6
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Yadav S, Pant D, Samaiya A, Kalra N, Gupta S, Shukla S. ERK1/2-EGR1-SRSF10 Axis Mediated Alternative Splicing Plays a Critical Role in Head and Neck Cancer. Front Cell Dev Biol 2021; 9:713661. [PMID: 34616729 PMCID: PMC8489685 DOI: 10.3389/fcell.2021.713661] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/16/2021] [Indexed: 12/21/2022] Open
Abstract
Aberrant alternative splicing is recognized to promote cancer pathogenesis, but the underlying mechanism is yet to be clear. Here, in this study, we report the frequent upregulation of SRSF10 (serine and arginine-rich splicing factor 10), a member of an expanded family of SR splicing factors, in the head and neck cancer (HNC) patients sample in comparison to paired normal tissues. We observed that SRSF10 plays a crucial role in HNC tumorigenesis by affecting the pro-death, pro-survical splice variants of BCL2L1 (BCL2 Like 1: BCLx: Apoptosis Regulator) and the two splice variants of PKM (Pyruvate kinase M), PKM1 normal isoform to PKM2 cancer-specific isoform. SRSF10 is a unique splicing factor with a similar domain organization to that of SR proteins but functions differently as it acts as a sequence-specific splicing activator in its phosphorylated form. Although a body of research studied the role of SRSF10 in the splicing process, the regulatory mechanisms underlying SRSF10 upregulation in the tumor are not very clear. In this study, we aim to dissect the pathway that regulates the SRSF10 upregulation in HNC. Our results uncover the role of transcription factor EGR1 (Early Growth Response1) in elevating the SRSF10 expression; EGR1 binds to the promoter of SRSF10 and promotes TET1 binding leading to the CpG demethylation (hydroxymethylation) in the adjacent position of the EGR1 binding motif, which thereby instigate SRSF10 expression in HNC. Interestingly we also observed that the EGR1 level is in the sink with the ERK1/2 pathway, and therefore, inhibition of the ERK1/2 pathway leads to the decreased EGR1 and SRSF10 expression level. Together, this is the first report to the best of our knowledge where we characterize the ERK 1/2-EGR1-SRSF10 axis regulating the cancer-specific splicing, which plays a critical role in HNC and could be a therapeutic target for better management of HNC patients.
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Affiliation(s)
- Sandhya Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Deepak Pant
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | | | | | - Sanjay Gupta
- Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India.,Homi Bhabha National Institute, Training School Complex, Mumbai, India
| | - Sanjeev Shukla
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
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7
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Zhao C, Yong T, Zhang Y, Xiao Y, Jin Y, Zheng C, Nirasawa T, Cai Z. Breast cancer proliferation and deterioration-associated metabolic heterogeneity changes induced by exposure of bisphenol S, a widespread replacement of bisphenol A. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125391. [PMID: 33652221 DOI: 10.1016/j.jhazmat.2021.125391] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/12/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Exposure to bisphenol A (BPA) is considered to be associated with the increased incidence of breast cancer. As a widespread replacement of BPA, the effect of bisphenol S (BPS) on breast tumor programming has not been studied. We reported that BPS exposure significantly promoted proliferation and deterioration of breast tumor by nonmonotonic dose response. The mechanisms were investigated by molecular biology and mass spectrometry-based lipidomics, proteomics and imaging. BPS exposure induced the spatially intratumor heterogeneity of morphology-driven lipids and proteins. The more significant proliferation resulted from BPS-10 (10 μg/kg body weight /day) exposure was evidenced by the variations of spatial distribution of lipids related to ceramide-sphingomyelin signaling pathway, proteins related to chromosomal stability and cell proliferation in central necrotic regions of breast tumor. In contrast, the BPS-100 exposure obviously accelerated deterioration of breast tumor by the variations of spatial distribution of proteins that were associated with the stability of nucleic acid structure in peripheral neoplastic regions. Accordingly, dysregulation of metabolism and protein function as well as DNA methylation and hypoxic tumor microenvironment could be applied to predict the possibility of tumorigenesis, proliferation and metastasis that might be caused by other bisphenol analogs.
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Affiliation(s)
- Chao Zhao
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China; Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ting Yong
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
| | - Yinbin Zhang
- Department of Oncology, The Second Affiliated Hospital of Medical College, Xi'an Jiaotong University, Shaanxi, China
| | - Yu Xiao
- Department of Breast and Thyroid Surgery, Shenzhen Second People's Hospital, Shenzhen, China
| | - Yaofeng Jin
- Department of Oncology, The Second Affiliated Hospital of Medical College, Xi'an Jiaotong University, Shaanxi, China
| | - Chang Zheng
- Department of Breast and Thyroid Surgery, Shenzhen Second People's Hospital, Shenzhen, China
| | | | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China.
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MCPIP1-mediated NFIC alternative splicing inhibits proliferation of triple-negative breast cancer via cyclin D1-Rb-E2F1 axis. Cell Death Dis 2021; 12:370. [PMID: 33824311 PMCID: PMC8024338 DOI: 10.1038/s41419-021-03661-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype with the worst prognosis and the highest metastatic and recurrence potential, which represents 15–20% of all breast cancers in Chinese females, and the 5-year overall survival rate is about 80% in Chinese women. Recently, emerging evidence suggested that aberrant alternative splicing (AS) plays a crucial role in tumorigenesis and progression. AS is generally controlled by AS-associated RNA binding proteins (RBPs). Monocyte chemotactic protein induced protein 1 (MCPIP1), a zinc finger RBP, functions as a tumor suppressor in many cancers. Here, we showed that MCPIP1 was downregulated in 80 TNBC tissues and five TNBC cell lines compared to adjacent paracancerous tissues and one human immortalized breast epithelial cell line, while its high expression levels were associated with increased overall survival in TNBC patients. We demonstrated that MCPIP1 overexpression dramatically suppressed cell cycle progression and proliferation of TNBC cells in vitro and repressed tumor growth in vivo. Mechanistically, MCPIP1 was first demonstrated to act as a splicing factor to regulate AS in TNBC cells. Furthermore, we demonstrated that MCPIP1 modulated NFIC AS to promote CTF5 synthesis, which acted as a negative regulator in TNBC cells. Subsequently, we showed that CTF5 participated in MCPIP1-mediated antiproliferative effect by transcriptionally repressing cyclin D1 expression, as well as downregulating its downstream signaling targets p-Rb and E2F1. Conclusively, our findings provided novel insights into the anti-oncogenic mechanism of MCPIP1, suggesting that MCPIP1 could serve as an alternative treatment target in TNBC.
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9
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Relevance of 2'-O-Methylation and Pseudouridylation for the Malignant Melanoma. Cancers (Basel) 2021; 13:cancers13051167. [PMID: 33803145 PMCID: PMC7963185 DOI: 10.3390/cancers13051167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/04/2021] [Indexed: 01/23/2023] Open
Abstract
Simple Summary This study investigates the expression, the histological localization, and the influence of the factors involved in 2′-O-methylation and pseudouridylation on prognostic relevant markers, proliferation markers, overall survival, molecular immune surveillance and evasion mechanisms within the malignant melanoma. Statistically significant positive correlations to the expression of markers involved in cell proliferation were observed. The upregulation of the RNA modifying factors was of prognostic relevance in this tumor disease with a negative impact on the overall survival of melanoma patients. Furthermore, the factors involved in 2′-O-methylation and pseudouridylation were statistically significant negative correlated to the expression of human leukocyte antigen class I genes as well as of components of the antigen processing machinery. Abstract The two RNA modifications 2′-O-methylation and pseudouridylation occur on several RNA species including ribosomal RNAs leading to an increased translation as well as cell proliferation associated with distinct functions. Using malignant melanoma (MM) as a model system the proteins mediating these RNA modifications were for the first time analyzed by different bioinformatics tools and public available databases regarding their expression and histological localization. Next to this, the impact of these RNA-modifying factors on prognostic relevant processes and marker genes of malignant melanoma was investigated and correlated to immune surveillance and evasion strategies. The RNA modifying factors exerted statistically significant positive correlations to the expression of genes involved in cell proliferation and were statistically significant negative correlated to the expression of human leukocyte antigen class I genes as well as of components of the antigen processing machinery in malignant melanoma. Upregulation of the RNA modifying proteins was of prognostic relevance in this tumor disease with a negative impact on the overall survival of melanoma patients. Furthermore, the expression of known oncogenic miRs, which are induced in malignant melanoma, directly correlated to the expression of factors involved in these two RNA modifications.
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10
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Gomig THB, Gontarski AM, Cavalli IJ, Souza RLRD, Lucena ACR, Batista M, Machado KC, Marchini FK, Marchi FA, Lima RS, Urban CDA, Marchi RD, Cavalli LR, Ribeiro EMDSF. Integrated analysis of label-free quantitative proteomics and bioinformatics reveal insights into signaling pathways in male breast cancer. Genet Mol Biol 2021; 44:e20190410. [PMID: 33656060 PMCID: PMC7926483 DOI: 10.1590/1678-4685-gmb-2019-0410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 01/18/2021] [Indexed: 01/04/2023] Open
Abstract
Male breast cancer (MBC) is a rare malignancy that accounts for about 1.8% of all breast cancer cases. In contrast to the high number of the “omics” studies in breast cancer in women, only recently molecular approaches have been performed in MBC research. High-throughput proteomics based methodologies are promisor strategies to characterize the MBC proteomic signatures and their association with clinico-pathological parameters. In this study, the label-free quantification-mass spectrometry and bioinformatics approaches were applied to analyze the proteomic profiling of a MBC case using the primary breast tumor and the corresponding axillary metastatic lymph nodes and adjacent non-tumor breast tissues. The differentially expressed proteins were identified in the signaling pathways of granzyme B, sirtuins, eIF2, actin cytoskeleton, eNOS, acute phase response and calcium and were connected to the upstream regulators MYC, PI3K SMARCA4 and cancer-related chemical drugs. An additional proteomic comparative analysis was performed with a primary breast tumor of a female patient and revealed an interesting set of proteins, which were mainly involved in cancer biology. Together, our data provide a relevant data source for the MBC research that can help the therapeutic strategies for its management.
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Affiliation(s)
| | - Amanda Moletta Gontarski
- Universidade Federal do Paraná, Departamento de Genética, Programa de Pós-graduação em Genética, Curitiba, PR, Brazil
| | - Iglenir João Cavalli
- Universidade Federal do Paraná, Departamento de Genética, Programa de Pós-graduação em Genética, Curitiba, PR, Brazil
| | | | | | - Michel Batista
- Instituto Carlos Chagas, Laboratório de Genômica Funcional, Curitiba, PR, Brazil.,Fundação Oswaldo Cruz (Fiocruz), Plataforma de Espectrometria de Massas, Curitiba, PR, Brazil
| | | | - Fabricio Klerynton Marchini
- Instituto Carlos Chagas, Laboratório de Genômica Funcional, Curitiba, PR, Brazil.,Fundação Oswaldo Cruz (Fiocruz), Plataforma de Espectrometria de Massas, Curitiba, PR, Brazil
| | | | - Rubens Silveira Lima
- Hospital Nossa Senhora das Graças, Centro de Doenças da Mama, Curitiba, PR, Brazil
| | | | | | - Luciane Regina Cavalli
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, PR, Brazil.,Georgetown University, Lombardi Comprehensive Cancer Center, Washington, USA
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11
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Alvelos MI, Brüggemann M, Sutandy FXR, Juan-Mateu J, Colli ML, Busch A, Lopes M, Castela Â, Aartsma-Rus A, König J, Zarnack K, Eizirik DL. The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells. Life Sci Alliance 2021; 4:e202000825. [PMID: 33376132 PMCID: PMC7772782 DOI: 10.26508/lsa.202000825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/16/2022] Open
Abstract
In pancreatic β-cells, the expression of the splicing factor SRSF6 is regulated by GLIS3, a transcription factor encoded by a diabetes susceptibility gene. SRSF6 down-regulation promotes β-cell demise through splicing dysregulation of central genes for β-cells function and survival, but how RNAs are targeted by SRSF6 remains poorly understood. Here, we define the SRSF6 binding landscape in the human pancreatic β-cell line EndoC-βH1 by integrating individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) under basal conditions with RNA sequencing after SRSF6 knockdown. We detect thousands of SRSF6 bindings sites in coding sequences. Motif analyses suggest that SRSF6 specifically recognizes a purine-rich consensus motif consisting of GAA triplets and that the number of contiguous GAA triplets correlates with increasing binding site strength. The SRSF6 positioning determines the splicing fate. In line with its role in β-cell function, we identify SRSF6 binding sites on regulated exons in several diabetes susceptibility genes. In a proof-of-principle, the splicing of the susceptibility gene LMO7 is modulated by antisense oligonucleotides. Our present study unveils the splicing regulatory landscape of SRSF6 in immortalized human pancreatic β-cells.
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Affiliation(s)
- Maria Inês Alvelos
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Mirko Brüggemann
- Buchman Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Jonàs Juan-Mateu
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Maikel Luis Colli
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Anke Busch
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Miguel Lopes
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ângela Castela
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Julian König
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Kathi Zarnack
- Buchman Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Décio L Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
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12
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Hart V, Gautrey H, Kirby J, Tyson-Capper A. HER2 splice variants in breast cancer: investigating their impact on diagnosis and treatment outcomes. Oncotarget 2020; 11:4338-4357. [PMID: 33245725 PMCID: PMC7679030 DOI: 10.18632/oncotarget.27789] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/10/2020] [Indexed: 02/07/2023] Open
Abstract
Overexpression of the HER2 receptor occurs in approximately 20% of breast cancer patients. HER2 positivity is associated with poor prognosis and aggressive tumour phenotypes, which led to rapid progress in HER2 targeted therapeutics and diagnostic testing. Whilst these advances have greatly increased patients' chances of survival, resistance to HER2 targeted therapies, be that intrinsic or acquired, remains a problem. Different forms of the HER2 protein exist within tumours in tandem and can display altered biological activities. Interest in HER2 variants in breast cancer increased when links between resistance to anti-HER2 therapies and a particular variant, Δ16-HER2, were identified. Moreover, the P100 variant potentially reduces the efficacy of the anti-HER2 therapy trastuzumab. Another variant, Herstatin, exhibits 'auto-inhibitory' behaviour. More recently, new HER2 variants have been identified and are currently being assessed for their pro- and anti-cancer properties. It is important when directing the care of patients to consider HER2 variants collectively. This review considers HER2 variants in the context of the tumour environment where multiple variants are co-expressed at altered ratios. This study also provides an up to date account of the landscape of HER2 variants and links this to patterns of resistance against HER2 therapies and treatment plans.
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Affiliation(s)
- Vic Hart
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Hannah Gautrey
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - John Kirby
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Alison Tyson-Capper
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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13
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Yen TY, Wong R, Pizzo D, Thein M, Macher BA, Timpe LC. Over-Expression of RNA Processing, Heat Shock, and DNA Repair Proteins in Breast Tumor Compared to Normal Tissue. Proteomics 2020; 20:e2000044. [PMID: 32663359 PMCID: PMC7855622 DOI: 10.1002/pmic.202000044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/16/2020] [Indexed: 01/04/2023]
Abstract
This study identifies the main changes in protein expression in human breast tumors compared to normal breast tissue. Malignant tumors (32) and normal breast tissue samples (23), from formaldehyde-fixed, paraffin-embedded specimens are subjected to discovery proteomics using liquid chromatography/tandem mass spectrometry, with spectral counts for quantitation. The dataset contains 1406 proteins. Differential expression is measured using a method that takes advantage of estimates of the percentage of tumor on a slide. This analysis shows that the major classes of proteins over-expressed by tumors are RNA-binding, heat shock and DNA repair proteins. RNA-binding proteins, including heterogeneous nuclear ribonucleoproteins (HNRNPs), SR splice factors (SRSF) and elongation factors form the largest group. Comparison with results from another study demonstrates that the RNA-binding proteins are associated specifically with malignant transformation, rather than with cell proliferation. HNRNP and SRSF proteins help define splice sites in normal cells. Their over-expression may dysregulate splicing, which in turn has the potential to promote malignant transformation.
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Affiliation(s)
- Ten-Yang Yen
- San Francisco State University - Department of Chemistry and Biochemistry
| | - Richard Wong
- University of California San Diego - Department of Pathology
| | - Don Pizzo
- University of California San Diego - Department of Pathology
| | - Moe Thein
- San Francisco State University - Department of Chemistry and Biochemistry
| | - Bruce A. Macher
- San Francisco State University - Department of Chemistry and Biochemistry
| | - Leslie C. Timpe
- San Francisco State University - Department of Biology, 1600 Holloway Ave., San Francisco, California 94132, United States
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14
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Jasinski-Bergner S, Steven A, Seliger B. The Role of the RNA-Binding Protein Family MEX-3 in Tumorigenesis. Int J Mol Sci 2020; 21:ijms21155209. [PMID: 32717840 PMCID: PMC7432607 DOI: 10.3390/ijms21155209] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 12/16/2022] Open
Abstract
The muscle excess 3 (MEX-3) protein was first identified in Caenorhabditis elegans (C. elegans), and its respective homologues were also observed in vertebrates, including humans. It is a RNA-binding protein (RBP) with an additional ubiquitin E3 ligase function, which further acts as a post-transcriptional repressor through unknown mechanisms. In humans, MEX-3 proteins post-transcriptionally regulate a number of biological processes, including tumor immunological relevant ones. These have been shown to be involved in various diseases, including tumor diseases of distinct origins. This review provides information on the expression and function of the human MEX-3 family in healthy tissues, as well after malignant transformation. Indeed, the MEX-3 expression was shown to be deregulated in several cancers and to affect tumor biological functions, including apoptosis regulation, antigen processing, and presentation, thereby, contributing to the immune evasion of tumor cells. Furthermore, current research suggests MEX-3 proteins as putative markers for prognosis and as novel targets for the anti-cancer treatment.
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Affiliation(s)
| | | | - Barbara Seliger
- Correspondence: ; Tel.: +49-345-557-1357; Fax: +49-345-557-4055
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15
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Leung MH, Tsoi H, Gong C, Man EPS, Zona S, Yao S, Lam EWF, Khoo US. A Splice Variant of NCOR2, BQ323636.1, Confers Chemoresistance in Breast Cancer by Altering the Activity of NRF2. Cancers (Basel) 2020; 12:cancers12030533. [PMID: 32110852 PMCID: PMC7139508 DOI: 10.3390/cancers12030533] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/12/2020] [Accepted: 02/20/2020] [Indexed: 12/16/2022] Open
Abstract
Breast cancer is the most common type of female cancer. Reactive oxygen species (ROS) are vital in regulating signaling pathways that control cell survival and cell proliferation. Chemotherapeutic drugs such as anthracyclines induce cell death via ROS induction. Chemoresistance development is associated with adaptive response to oxidative stress. NRF2 is the main regulator of cytoprotective response to oxidative stress. NRF2 can enhance cell growth, antioxidant expression, and chemoresistance by providing growth advantage for malignant cells. Previously, we identified BQ323636.1 (BQ), a novel splice variant of nuclear co-repressor NCOR2, which can robustly predict tamoxifen resistance in primary breast cancer. In this study, we found that BQ was overexpressed in epirubicin-resistant cells and demonstrated that BQ overexpression could reduce the levels of epirubicin-induced ROS and confer epirubicin resistance. In vivo analysis using tissue microarray of primary breast cancer showed direct correlation between BQ expression and chemoresistance. In vitro experiments showed BQ could modulate NRF2 transcriptional activity and upregulate antioxidants. Luciferase reporter assays showed that although NCOR2 repressed the transcriptional activity of NRF2, the presence of BQ reduced this repressive activity. Co-immunoprecipitation confirmed that NCOR2 could bind to NRF2 and that this interaction was compromised by BQ overexpression, leading to increased transcriptional activity in NRF2. Our findings suggest BQ can regulate the NRF2 signaling pathway via interference with NCOR2 suppressive activity and reveals a novel role for BQ as a modulator of chemoresistance in breast cancer.
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Affiliation(s)
- Man-Hong Leung
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong; (M.-H.L.); (H.T.); (C.G.)
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Ho Tsoi
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong; (M.-H.L.); (H.T.); (C.G.)
| | - Chun Gong
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong; (M.-H.L.); (H.T.); (C.G.)
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Ellen PS Man
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong; (M.-H.L.); (H.T.); (C.G.)
| | - Stefania Zona
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Shang Yao
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Eric W.-F. Lam
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
- Correspondence: (E.W.-F.L.); (U.-S.K.); Tel.: +44-7594-2810 (E.W.-F.L.); +852-22552664 (U.-S.K.); Fax: +852-2218-5205 (U.-S.K.)
| | - Ui-Soon Khoo
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong; (M.-H.L.); (H.T.); (C.G.)
- Correspondence: (E.W.-F.L.); (U.-S.K.); Tel.: +44-7594-2810 (E.W.-F.L.); +852-22552664 (U.-S.K.); Fax: +852-2218-5205 (U.-S.K.)
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16
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Rong MH, Zhu ZH, Guan Y, Li MW, Zheng JS, Huang YQ, Wei DM, Li YM, Wu XJ, Bu HP, Peng HL, Wei XL, Li GS, Li MX, Chen MH, Huang SN. Identification of prognostic splicing factors and exploration of their potential regulatory mechanisms in pancreatic adenocarcinoma. PeerJ 2020; 8:e8380. [PMID: 32095320 PMCID: PMC7020824 DOI: 10.7717/peerj.8380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 12/10/2019] [Indexed: 12/24/2022] Open
Abstract
Pancreatic adenocarcinoma (PAAD), the most common subtype of pancreatic cancer, is a highly lethal disease. In this study, we integrated the expression profiles of splicing factors (SFs) of PAAD from RNA-sequencing data to provide a comprehensive view of the clinical significance of SFs. A prognostic index (PI) based on SFs was developed using the least absolute shrinkage and selection operator (LASSO) COX analysis. The PI exhibited excellent performance in predicting the status of overall survival of PAAD patients. We also used the percent spliced in (PSI) value obtained from SpliceSeq software to quantify different types of alternative splicing (AS). The prognostic value of AS events was explored using univariate COX and LASSO COX analyses; AS-based PIs were also proposed. The integration of prognosis-associated SFs and AS events suggested the potential regulatory mechanisms of splicing processes in PAAD. This study defined the markedly clinical significance of SFs and provided novel insight into their potential regulatory mechanisms.
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Affiliation(s)
- Min-Hua Rong
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Zhan-Hui Zhu
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Ying Guan
- Affiliated Cancer Hospital, Guangxi Medical University, Department of Radiotherapy, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Mei-Wei Li
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Jia-Shuo Zheng
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Yue-Qi Huang
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Dan-Ming Wei
- First Affiliated Hospital, Guangxi Medical University, Department of Pathology, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Ying-Mei Li
- First Affiliated Hospital, Guangxi Medical University, Department of Pathology, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Xiao-Ju Wu
- First Affiliated Hospital, Guangxi Medical University, Department of Pathology, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Hui-Ping Bu
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Hui-Liu Peng
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Xiao-Lin Wei
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Guo-Sheng Li
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Ming-Xuan Li
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Ming-Hui Chen
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Su-Ning Huang
- Affiliated Cancer Hospital, Guangxi Medical University, Department of Radiotherapy, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
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17
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Yang Q, Zhao J, Zhang W, Chen D, Wang Y. Aberrant alternative splicing in breast cancer. J Mol Cell Biol 2019; 11:920-929. [PMID: 31065692 PMCID: PMC6884705 DOI: 10.1093/jmcb/mjz033] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 02/19/2019] [Accepted: 03/03/2019] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing is critical for human gene expression regulation, which plays a determined role in expanding the diversity of functional proteins. Importantly, alternative splicing is a hallmark of cancer and a potential target for cancer therapeutics. Based on the statistical data, breast cancer is one of the top leading causes of cancer-related deaths in women worldwide. Strikingly, alternative splicing is closely associated with breast cancer development. Here, we seek to provide a general review of the relationship between alternative splicing and breast cancer. We introduce the process of alternative splicing and its regulatory role in cancers. In addition, we highlight the functions of aberrant alternative splicing and mutations of splicing factors in breast cancer progression. Moreover, we discuss the role of alternative splicing in cancer drug resistance and the potential of being targets for cancer therapeutics.
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Affiliation(s)
- Quan Yang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Jinyao Zhao
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Wenjing Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Dan Chen
- Department of Pathology, First Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Yang Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
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18
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DeLigio JT, Stevens SC, Nazario-Muñoz GS, MacKnight HP, Doe KK, Chalfant CE, Park MA. Serine/Arginine-Rich Splicing Factor 3 Modulates the Alternative Splicing of Cytoplasmic Polyadenylation Element Binding Protein 2. Mol Cancer Res 2019; 17:1920-1930. [PMID: 31138601 PMCID: PMC6726571 DOI: 10.1158/1541-7786.mcr-18-1291] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/17/2019] [Accepted: 05/21/2019] [Indexed: 02/06/2023]
Abstract
Triple negative breast cancer (TNBC) has an unusually low 5-year survival rate linked to higher metastatic rates. Our laboratory recently delineated a role for the alternative RNA splicing (AS) of cytoplasmic polyadenylation element binding protein 2 (CPEB2), via inclusion/exclusion of exon 4, in the metastasis of TNBC. In these studies, the mechanism governing the inclusion/exclusion of exon 4 was examined. Specifically, the RNA trans-factor, SRSF3, was found to be explicitly associated with CPEB2 exon 4. A SRSF3 consensus sequence was identified in exon 4, and mutation of this sequence abolished the association of SRSF3. The expression of SRSF3 was upregulated in TNBC cells upon the acquisition of anoikis resistance correlating with a reduction in the CPEB2A/B ratio. Importantly, downregulation of SRSF3 in these cells by siRNA induced the exclusion of exon 4 in cells increasing the ratio of CPEB2A (exon 4 excluded) to CPEB2B (exon 4 included). Downregulation of SRSF3 also reversed the CPEB2A/B ratio of a wild-type CPEB2 exon 4 minigene and endogenous CPEB2 pre-mRNA, but not a mutant CPEB2 minigene with the SRSF3 RNA cis-element ablated. SRSF3 downregulation ablated the anoikis resistance of TNBC cells, which was "rescued" by ectopic expression of CPEB2B. Finally, analysis of The Cancer Genome Atlas database showed a positive relationship between SRSF3 expression and lower CPEB2A/B ratios in aggressive breast cancers. IMPLICATIONS: These findings demonstrate that SRSF3 modulates CPEB2 AS to induce the expression of the CPEB2B isoform that drives TNBC phenotypes correlating with aggressive human breast cancer. VISUAL OVERVIEW: http://mcr.aacrjournals.org/content/molcanres/17/9/1920/F1.large.jpg.
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Affiliation(s)
- James T DeLigio
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University (VCU), Richmond Virginia
| | - Shaun C Stevens
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida
| | - Gina S Nazario-Muñoz
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida
| | - H Patrick MacKnight
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University (VCU), Richmond Virginia
| | - Keli K Doe
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University (VCU), Richmond Virginia
| | - Charles E Chalfant
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University (VCU), Richmond Virginia.
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida
- VCU Massey Cancer Center, Cancer Cell Signaling Program, VCU, Richmond Virginia
- Research Service, Hunter Holmes McGuire Veterans Administration Medical Center, Richmond, Virginia
- VCU Institute of Molecular Medicine, Richmond, Virginia
- VCU Johnson Center for Critical Care and Pulmonary Research, Richmond, Virginia
- Research Service, James A. Haley Veterans Hospital, Tampa, Florida
- The Moffitt Cancer Center, Tampa, Florida
| | - Margaret A Park
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University (VCU), Richmond Virginia.
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida
- VCU Massey Cancer Center, Cancer Cell Signaling Program, VCU, Richmond Virginia
- VCU Johnson Center for Critical Care and Pulmonary Research, Richmond, Virginia
- Research Service, James A. Haley Veterans Hospital, Tampa, Florida
- The Moffitt Cancer Center, Tampa, Florida
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19
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Kouyama Y, Masuda T, Fujii A, Ogawa Y, Sato K, Tobo T, Wakiyama H, Yoshikawa Y, Noda M, Tsuruda Y, Kuroda Y, Eguchi H, Ishida F, Kudo SE, Mimori K. Oncogenic splicing abnormalities induced by DEAD-Box Helicase 56 amplification in colorectal cancer. Cancer Sci 2019; 110:3132-3144. [PMID: 31390121 PMCID: PMC6778637 DOI: 10.1111/cas.14163] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing, regulated by DEAD‐Box Helicase (DDX) families, plays an important role in cancer. However, the relationship between the DDX family and cancer has not been fully elucidated. In the present study, we identified a candidate oncogene DDX56 on Ch.7p by a bioinformatics approach using The Cancer Genome Atlas (TCGA) dataset of colorectal cancer (CRC). DDX56 expression was measured by RT‐qPCR and immunochemical staining in 108 CRC patients. Clinicopathological and survival analyses were carried out using three CRC datasets. Biological roles of DDX56 were explored by gene set enrichment analysis (GSEA), and cell proliferation in vitro and in vivo, cell cycle assays, and using DDX56‐knockdown or overexpressed CRC cells. RNA sequencing was carried out to elucidate the effect of DDX56 on mRNA splicing. We found that DDX56 expression was positively correlated with the amplification of DDX56 and was upregulated in CRC cells. High DDX56 expression was associated with lymphatic invasion and distant metastasis and was an independent poor prognostic factor. In vitro analysis, in vivo analysis and GSEA showed that DDX56 promoted proliferation ability through regulating the cell cycle. DDX56 knockdown reduced intron retention and tumor suppressor WEE1 expression, which functions as a G2‐M DNA damage checkpoint. We have identified DDX56 as a novel oncogene and prognostic biomarker of CRC that promotes alternative splicing of WEE1.
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Affiliation(s)
- Yuta Kouyama
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan.,Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Takaaki Masuda
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Atsushi Fujii
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Yushi Ogawa
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Kuniaki Sato
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Taro Tobo
- Department of Clinical Laboratory Medicine, Kyushu University Beppu Hospital, Oita, Japan
| | - Hiroaki Wakiyama
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | | | - Miwa Noda
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Yusuke Tsuruda
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Yousuke Kuroda
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Hidetoshi Eguchi
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
| | - Fumio Ishida
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Shin-Ei Kudo
- Digestive Disease Center, Showa University Northern Yokohama Hospital, Yokohama, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Oita, Japan
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20
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Meng X, Yang S, Zhang J, Yu H. Contribution of alternative splicing to breast cancer metastasis. JOURNAL OF CANCER METASTASIS AND TREATMENT 2019; 5:21. [PMID: 31737791 PMCID: PMC6857724 DOI: 10.20517/2394-4722.2018.96] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Alternative splicing is a major contributor to transcriptome and proteome diversity in eukaryotes. Comparing to normal samples, about 30% more alternative splicing events were recently identified in 32 cancer types included in The Cancer Genome Atlas database. Some alternative splicing isoforms and their encoded proteins contribute to specific cancer hallmarks. In this review, we will discuss recent progress regarding the contributions of alternative splicing to breast cancer metastasis. We plan to dissect the role of MTDH, CD44 and their interaction with other mRNA splicing factors. We believe an in-depth understanding of the mechanism underlying the contribution of splicing to breast cancer metastasis will provide novel strategies to the management of breast cancer.
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Affiliation(s)
- Xiangbing Meng
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Shujie Yang
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Jun Zhang
- Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Division of Hematology, Oncology and Blood & Marrow Transplantation, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Huimin Yu
- Department of Obstetrics and Gynecology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Department of Pathogenic Biology, Shenzhen University School of medicine, Shenzhen 518060, China
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21
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Robinson TJ, Freedman JA, Al Abo M, Deveaux AE, LaCroix B, Patierno BM, George DJ, Patierno SR. Alternative RNA Splicing as a Potential Major Source of Untapped Molecular Targets in Precision Oncology and Cancer Disparities. Clin Cancer Res 2019; 25:2963-2968. [PMID: 30755441 PMCID: PMC6653604 DOI: 10.1158/1078-0432.ccr-18-2445] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 09/18/2018] [Accepted: 01/29/2019] [Indexed: 12/12/2022]
Abstract
Studies of alternative RNA splicing (ARS) have the potential to provide an abundance of novel targets for development of new biomarkers and therapeutics in oncology, which will be necessary to improve outcomes for patients with cancer and mitigate cancer disparities. ARS, a key step in gene expression enabling individual genes to encode multiple proteins, is emerging as a major driver of abnormal phenotypic heterogeneity. Recent studies have begun to identify RNA splicing-related genetic and genomic variation in tumors, oncogenes dysregulated by ARS, RNA splice variants driving race-related cancer aggressiveness and drug response, spliceosome-dependent transformation, and RNA splicing-related immunogenic epitopes in cancer. In addition, recent studies have begun to identify and test, preclinically and clinically, approaches to modulate and exploit ARS for therapeutic application, including splice-switching oligonucleotides, small molecules targeting RNA splicing or RNA splice variants, and combination regimens with immunotherapies. Although ARS data hold such promise for precision oncology, inclusion of studies of ARS in translational and clinical cancer research remains limited. Technologic developments in sequencing and bioinformatics are being routinely incorporated into clinical oncology that permit investigation of clinically relevant ARS events, yet ARS remains largely overlooked either because of a lack of awareness within the clinical oncology community or perceived barriers to the technical complexity of analyzing ARS. This perspective aims to increase such awareness, propose immediate opportunities to improve identification and analysis of ARS, and call for bioinformaticians and cancer researchers to work together to address the urgent need to incorporate ARS into cancer biology and precision oncology.
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Affiliation(s)
| | - Jennifer A Freedman
- Department of Medicine, Division of Medical Oncology, Duke University Medical Center, Durham, North Carolina
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
| | - Muthana Al Abo
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
| | - April E Deveaux
- Department of Medicine, Division of Medical Oncology, Duke University Medical Center, Durham, North Carolina
| | - Bonnie LaCroix
- Department of Medicine, Division of Medical Oncology, Duke University Medical Center, Durham, North Carolina
| | - Brendon M Patierno
- Department of Medicine, Division of Medical Oncology, Duke University Medical Center, Durham, North Carolina
| | - Daniel J George
- Department of Medicine, Division of Medical Oncology, Duke University Medical Center, Durham, North Carolina
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
| | - Steven R Patierno
- Department of Medicine, Division of Medical Oncology, Duke University Medical Center, Durham, North Carolina.
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
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22
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Gökmen-Polar Y, Neelamraju Y, Goswami CP, Gu Y, Gu X, Nallamothu G, Vieth E, Janga SC, Ryan M, Badve SS. Splicing factor ESRP1 controls ER-positive breast cancer by altering metabolic pathways. EMBO Rep 2019; 20:embr.201846078. [PMID: 30665944 DOI: 10.15252/embr.201846078] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 12/04/2018] [Accepted: 12/11/2018] [Indexed: 12/12/2022] Open
Abstract
The epithelial splicing regulatory proteins 1 and 2 (ESRP1 and ESRP2) control the epithelial-to-mesenchymal transition (EMT) splicing program in cancer. However, their role in breast cancer recurrence is unclear. In this study, we report that high levels of ESRP1, but not ESRP2, are associated with poor prognosis in estrogen receptor positive (ER+) breast tumors. Knockdown of ESRP1 in endocrine-resistant breast cancer models decreases growth significantly and alters the EMT splicing signature, which we confirm using TCGA SpliceSeq data of ER+ BRCA tumors. However, these changes are not accompanied by the development of a mesenchymal phenotype or a change in key EMT-transcription factors. In tamoxifen-resistant cells, knockdown of ESRP1 affects lipid metabolism and oxidoreductase processes, resulting in the decreased expression of fatty acid synthase (FASN), stearoyl-CoA desaturase 1 (SCD1), and phosphoglycerate dehydrogenase (PHGDH) at both the mRNA and protein levels. Furthermore, ESRP1 knockdown increases the basal respiration and spare respiration capacity. This study reports a novel role for ESRP1 that could form the basis for the prevention of tamoxifen resistance in ER+ breast cancer.
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Affiliation(s)
- Yesim Gökmen-Polar
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Chirayu P Goswami
- Department of Bioinformatics, Thomas Jefferson University Hospitals, Philadelphia, PA, USA
| | - Yuan Gu
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Xiaoping Gu
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Gouthami Nallamothu
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Edyta Vieth
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sarath C Janga
- Department of BioHealth Informatics, School of Informatics and Computing, IUPUI, Indianapolis, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.,Centre for Computational Biology and Bioinformatics Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michael Ryan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,In Silico Solutions, Falls Church, VA, USA
| | - Sunil S Badve
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA .,Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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23
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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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24
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Huang ZG, He RQ, Mo ZN. Prognostic value and potential function of splicing events in prostate adenocarcinoma. Int J Oncol 2018; 53:2473-2487. [PMID: 30221674 PMCID: PMC6203144 DOI: 10.3892/ijo.2018.4563] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/09/2018] [Indexed: 12/21/2022] Open
Abstract
Prostate adenocarcinoma (PRAD) is one of the most common types of malignancy in males and at present, effective prognostic indicators are limited. The development of PRAD has been associated with abnormalities in alternative splicing (AS), a requisite biological process of gene expression in eukaryotic cells; however, the prognostic value of AS products and splicing events remains to be elucidated. In the present study, the data of splicing events and the clinical information of PRAD patients were obtained from The Cancer Genome Atlas (TCGA)SpliceSeq and TCGA databases, respectively. A prognostic index (PI) was generated from disease-free survival-associated splicing events (DFS-SEs), which were identified by univariate/multivariate Cox regression analysis. A total of 6,909 DFS-SEs were identified in PRAD. The corresponding genes for the DFS-SEs were significantly enriched in mitochondria and their associated pathways according to Gene Ontology annotation and in the pathways of fatty acid metabolism, oxidative phosphorylation and Huntington's disease according to a Kyoto Encyclopedia of Genes and Genomes pathway analysis. The PI for mutually exclusive exons had the greatest ability to predict the probability of five-year disease-free survival of patients with PRAD, with an area under the time-dependent receiver-operating characteristic curve of 0.7606. Patients with PRAD, when divided into a 'low' and a 'high' group based on their median PI for exon skip values, exhibited a marked difference in disease-free survival (low vs. high, 3,588.45±250.51 vs. 1,531.08±136.50 days; P=7.43×10−9). A correlation network between DFS-SEs of splicing factors and non-splicing factors was constructed to determine the potential mechanisms in PRAD, which included the potential regulatory interaction between the splicing event of splicing factor RNA binding motif protein 5-alternate terminator (AT)-64957 and the splicing event of non-splicing factor heterochromatin protein 1 binding protein 3-AT-939. In conclusion, the PIs derived from DFS-SEs are valuable prognostic factors for patients with PRAD, and the function of splicing events in PRAD deserves further exploration.
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Affiliation(s)
- Zhi-Guang Huang
- Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Rong-Quan He
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Zeng-Nan Mo
- Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
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25
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Abstract
Breast cancer is known to be a heterogeneous disease driven by a large repertoire of molecular abnormalities, which contribute to its diverse clinical behaviour. Despite the success of targeted therapy approaches for breast cancer patient management, there is still a lack of the molecular understanding of aggressive forms of the disease and clinical management of these patients remains difficult. The advent of high-throughput sequencing technologies has paved the way for a more complete understanding of the molecular make-up of the breast cancer genome. As such, it is becoming apparent that disruption of canonical splicing within breast cancer governs its clinical progression. In this review, we discuss the role of dysregulation of spliceosomal component genes and associated factors in the progression of breast cancer, their role in therapy resistance and the use of quantitative isoform expression as potential prognostic and predictive biomarkers with a particular focus on oestrogen receptor-positive breast cancer.
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Affiliation(s)
- Abigail Read
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer Research, London, UK
- Division of Molecular PathologyThe Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer Research, London, UK
- Division of Molecular PathologyThe Institute of Cancer Research, London, UK
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26
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Abstract
Cancer metastasis is defined as the dissemination of malignant cells from the primary tumor site, leading to colonization of distant organs and the establishment of a secondary tumor. Metastasis is frequently associated with chemoresistance and is the major cause of cancer-related mortality. Metastatic cells need to acquire the ability to resist to stresses provided by different environments, such as reactive oxygen species, shear stress, hemodynamic forces, stromal composition, and immune responses, to colonize other tissues. Hence, only a small population of cells has a metastasis-initiating potential. Several studies have revealed the misregulation of transcriptional variants during cancer progression, and many splice events can be used to distinguish between normal and tumoral tissue. These variants, which are abnormally expressed in malignant cells, contribute to an adaptive response of tumor cells and the success of the metastatic cascade, promoting an anomalous cell cycle, cellular adhesion, resistance to death, cell survival, migration and invasion. Understanding the different aspects of splicing regulation and the influence of transcriptional variants that control metastatic cells is critical for the development of therapeutic strategies. In this review, we describe how transcriptional variants contribute to metastatic competence and discuss how targeting specific isoforms may be a promising therapeutic strategy.
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Affiliation(s)
- Joice De Faria Poloni
- a Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul, Departamento de Biologia Molecular e Biotecnologia , Universidade Federal do Rio Grande do Sul , Porto Alegre , RS , Brazil
| | - Diego Bonatto
- a Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul, Departamento de Biologia Molecular e Biotecnologia , Universidade Federal do Rio Grande do Sul , Porto Alegre , RS , Brazil
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27
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Ohe K, Miyajima S, Tanaka T, Hamaguchi Y, Harada Y, Horita Y, Beppu Y, Ito F, Yamasaki T, Terai H, Mori M, Murata Y, Tanabe M, Abe I, Ashida K, Kobayashi K, Enjoji M, Nomiyama T, Yanase T, Harada N, Utsumi T, Mayeda A. HMGA1a Induces Alternative Splicing of the Estrogen Receptor-α lpha Gene by Trapping U1 snRNP to an Upstream Pseudo-5' Splice Site. Front Mol Biosci 2018; 5:52. [PMID: 29938207 PMCID: PMC6002489 DOI: 10.3389/fmolb.2018.00052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/22/2018] [Indexed: 12/31/2022] Open
Abstract
Objectives: The high-mobility group A protein 1a (HMGA1a) protein is known as a transcription factor that binds to DNA, but recent studies have shown it exerts novel functions through RNA-binding. We were prompted to decipher the mechanism of HMGA1a-induced alternative splicing of the estrogen receptor alpha (ERα) that we recently reported would alter tamoxifen sensitivity in MCF-7 TAMR1 cells. Methods: Endogenous expression of full length ERα66 and its isoform ERα46 were evaluated in MCF-7 breast cancer cells by transient expression of HMGA1a and an RNA decoy (2′-O-methylated RNA of the HMGA1a RNA-binding site) that binds to HMGA1a. RNA-binding of HMGA1a was checked by RNA-EMSA. In vitro splicing assay was performed to check the direct involvement of HMGA1a in splicing regulation. RNA-EMSA assay in the presence of purified U1 snRNP was performed with psoralen UV crosslinking to check complex formation of HMGA1a-U1 snRNP at the upstream pseudo-5′ splice site of exon 1. Results: HMGA1a induced exon skipping of a shortened exon 1 of ERα in in vitro splicing assays that was blocked by the HMGA1a RNA decoy and sequence-specific RNA-binding was confirmed by RNA-EMSA. RNA-EMSA combined with psoralen UV crosslinking showed that HMGA1a trapped purified U1 snRNP at the upstream pseudo-5′ splice site. Conclusions: Regulation of ERα alternative splicing by an HMGA1a-trapped U1 snRNP complex at the upstream 5′ splice site of exon 1 offers novel insight on 5′ splice site regulation by U1 snRNP as well as a promising target in breast cancer therapy where alternative splicing of ERα is involved.
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Affiliation(s)
- Kenji Ohe
- Department of Pharmacotherapeutics, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, Japan
| | - Shinsuke Miyajima
- Department of Breast Surgery, Fujita Health University, Toyoake, Japan
| | - Tomoko Tanaka
- Department of Endocrinology and Diabetes Mellitus, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Yuriko Hamaguchi
- Department of Endocrinology and Diabetes Mellitus, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Yoshihiro Harada
- Department of Pharmacotherapeutics, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, Japan
| | - Yuta Horita
- Department of Pharmacotherapeutics, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, Japan
| | - Yuki Beppu
- Department of Pharmacotherapeutics, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, Japan
| | - Fumiaki Ito
- Department of Pharmacotherapeutics, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, Japan
| | - Takafumi Yamasaki
- Department of Pharmacotherapeutics, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, Japan
| | - Hiroki Terai
- Department of Pharmacotherapeutics, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, Japan
| | - Masayoshi Mori
- Department of Pharmacotherapeutics, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, Japan
| | - Yusuke Murata
- Department of Pharmacotherapeutics, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, Japan
| | - Makito Tanabe
- Department of Endocrinology and Diabetes Mellitus, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Ichiro Abe
- Department of Endocrinology and Diabetes Mellitus, Fukuoka University Chikushi Hospital, Chikushino, Japan
| | - Kenji Ashida
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kunihisa Kobayashi
- Department of Endocrinology and Diabetes Mellitus, Fukuoka University Chikushi Hospital, Chikushino, Japan
| | - Munechika Enjoji
- Department of Pharmacotherapeutics, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, Japan
| | - Takashi Nomiyama
- Department of Endocrinology and Diabetes Mellitus, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Toshihiko Yanase
- Department of Endocrinology and Diabetes Mellitus, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Nobuhiro Harada
- Department of Biochemistry, Fujita Health University, Toyoake, Japan
| | - Toshiaki Utsumi
- Department of Breast Surgery, Fujita Health University, Toyoake, Japan
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
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28
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Alternative splicing and cancer metastasis: prognostic and therapeutic applications. Clin Exp Metastasis 2018; 35:393-402. [PMID: 29845349 DOI: 10.1007/s10585-018-9905-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/22/2018] [Indexed: 12/12/2022]
Abstract
Metastatic cells exhibit an extraordinary phenotypic plasticity, not only in adapting to unfamiliar microenvironments but also in surviving aggressive treatments and immune responses. A major source of phenotypic variability is alternative splicing (AS) of the pre-messenger RNA. This process is catalyzed by one of the most complex pieces of cellular molecular regulatory events, the spliceosome, which is composed of ribonucleoproteins and polypeptides termed spliceosome factors. With strong evidence indicating that AS affects nearly all genes encoded by the human genome, aberrant AS programs have a significant impact on cancer cell development and progression. In this review, we present insights about the genomic and epigenomic factors affecting AS, summarize the most recent findings linking aberrant AS to metastatic progression, and highlight potential prognostic and therapeutic applications.
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29
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Alternative Splicing in Breast Cancer and the Potential Development of Therapeutic Tools. Genes (Basel) 2017; 8:genes8100217. [PMID: 28981467 PMCID: PMC5664086 DOI: 10.3390/genes8100217] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 08/22/2017] [Accepted: 08/22/2017] [Indexed: 12/19/2022] Open
Abstract
Alternative splicing is a key molecular mechanism now considered as a hallmark of cancer that has been associated with the expression of distinct isoforms during the onset and progression of the disease. The leading cause of cancer-related deaths in women worldwide is breast cancer, and even when the role of alternative splicing in this type of cancer has been established, the function of this mechanism in breast cancer biology is not completely decoded. In order to gain a comprehensive view of the role of alternative splicing in breast cancer biology and development, we summarize here recent findings regarding alternative splicing events that have been well documented for breast cancer evolution, considering its prognostic and therapeutic value. Moreover, we analyze how the response to endocrine and chemical therapies could be affected due to alternative splicing and differential expression of variant isoforms. With all this knowledge, it becomes clear that targeting alternative splicing represents an innovative approach for breast cancer therapeutics and the information derived from current studies could guide clinical decisions with a direct impact in the clinical advances for breast cancer patients nowadays.
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30
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Sheng J, Zhao J, Xu Q, Wang L, Zhang W, Zhang Y. Bioinformatics analysis of SRSF1-controlled gene networks in colorectal cancer. Oncol Lett 2017; 14:5393-5399. [PMID: 29113173 PMCID: PMC5656040 DOI: 10.3892/ol.2017.6900] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/15/2017] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer is the third most common type of cancer and the fourth leading cause of cancer-associated mortality worldwide. Serine/arginine-rich splicing factor 1 (SRSF1) is a well-characterized oncogenic factor that promotes tumorigenesis by controlling a number of alternative splicing events. However, there is limited network analysis, from a global aspect, to study the effect of SRSF1 on colorectal cancer. In the present study, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of available gene regulation data from The Cancer Genome Atlas database revealed the enriched functions and signaling pathways of SRSF1. Subsequently, Oncomine analysis was performed, which demonstrated that SRSF1 was upregulated in a number of types of colon cancer. From overlapping the analysis of 2,678 SRSF1-related genes and 3,625 colorectal cancer genes in GeneCards, 468 genes were identified as SRSF1-related colorectal cancer genes. The GO results revealed that these overlapped genes were primarily enriched in metabolic processes, response to DNA damage, regulation of the cell cycle and a number of additional biological processes. KEGG pathway analysis revealed that SRSF1-related colorectal cancer genes were associated with the cell cycle, deregulated signaling pathways associated with cancer progression and colorectal cancer signaling pathways. In addition, the Search Tool for the Retrieval of Interacting Genes/Proteins database and Cytoscape analysis demonstrated that 468 SRSF1-related colorectal cancer genes exhibit potential interaction networks in which these genes were enriched in DNA metabolic processes, cell cycle regulation and regulation of apoptosis. The results of the present study suggested that SRSF1 exhibited an increased degree of interaction with key molecules, including NUF2 NDC80 kinetochore complex component, kinesin family member 2C, structural maintenance of chromosomes 3, ATM serine/threonine kinase, BRCA1 DNA repair associated, protein kinase DNA-activated catalytic polypeptide, heat shock protein 90 alpha family class A member 1, ras homolog family member A, and phosphatase and tensin homolog. Collectively, the bioinformatics analysis of the present study indicated that SRSF1 may have key functions in the progression and development of colorectal cancer.
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Affiliation(s)
- Junxiu Sheng
- Department of Oncology, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China.,Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Jinyao Zhao
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Qiuhong Xu
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Linlin Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Wenjing Zhang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Yang Zhang
- Department of Oncology, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China
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31
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Bondy-Chorney E, Baldwin RM, Didillon A, Chabot B, Jasmin BJ, Côté J. RNA binding protein RALY promotes Protein Arginine Methyltransferase 1 alternatively spliced isoform v2 relative expression and metastatic potential in breast cancer cells. Int J Biochem Cell Biol 2017; 91:124-135. [PMID: 28733251 DOI: 10.1016/j.biocel.2017.07.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 07/09/2017] [Accepted: 07/15/2017] [Indexed: 01/24/2023]
Abstract
Aberrant expression of Protein Arginine Methyltransferases (PRMTs) has been observed in several cancer types, including breast cancer. We previously reported that the PRMT1v2 isoform, which is generated through inclusion of alternative exon 2, is overexpressed in breast cancer cells and promotes their invasiveness. However, the precise mechanism by which expression of this isoform is controlled and how it is dysregulated in breast cancer remains unknown. Using a custom RNA interference-based screen, we identified several RNA binding proteins (RBP) which, when knocked down, altered the relative abundance of the alternatively spliced PRMT1v2 isoform. Amongst the top hits were SNW Domain containing 1 (SNW1) and RBP-associated with lethal yellow mutation (RALY), which both associated with the PRMT1 pre-mRNA and upon depletion caused an increase or decrease in the relative abundance of PRMT1v2 isoform mRNA and protein. Most importantly, a significant decrease in invasion was observed upon RALY knockdown in aggressive breast cancer cells, consistent with targeting PRMT1v2 directly, and this effect was rescued by the exogenous re-expression of PRMT1v2. We show that SNW1 expression is decreased, while RALY expression is increased in breast cancer cells and tumours, which correlates with decreased patient survival. This work revealed crucial insight into the mechanisms regulating the expression of the PRMT1 alternatively spliced isoform v2 and its dysregulation in breast cancer. It also provides proof-of-concept support for the development of therapeutic strategies where regulators of PRMT1 exon 2 alternative splicing are targeted as an approach to selectively reduce PRMT1v2 levels and metastasis in breast cancer.
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Affiliation(s)
- Emma Bondy-Chorney
- Department of Cellular and Molecular Medicine, University of Ottawa, Centre for Neuromuscular Disease, Ottawa, Ontario, K1H 8L1, Canada
| | - R Mitchell Baldwin
- Department of Cellular and Molecular Medicine, University of Ottawa, Centre for Neuromuscular Disease, Ottawa, Ontario, K1H 8L1, Canada
| | - Andréanne Didillon
- Department of Cellular and Molecular Medicine, University of Ottawa, Centre for Neuromuscular Disease, Ottawa, Ontario, K1H 8L1, Canada
| | - Benoît Chabot
- Département de microbiologie et d'infectiologie, Faculté de Médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1 K 2R1, Canada
| | - Bernard J Jasmin
- Department of Cellular and Molecular Medicine, University of Ottawa, Centre for Neuromuscular Disease, Ottawa, Ontario, K1H 8L1, Canada
| | - Jocelyn Côté
- Department of Cellular and Molecular Medicine, University of Ottawa, Centre for Neuromuscular Disease, Ottawa, Ontario, K1H 8L1, Canada.
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Fujita T, Higashitsuji H, Higashitsuji H, Liu Y, Itoh K, Sakurai T, Kojima T, Kandori S, Nishiyama H, Fukumoto M, Fukumoto M, Shibasaki K, Fujita J. TRPV4-dependent induction of a novel mammalian cold-inducible protein SRSF5 as well as CIRP and RBM3. Sci Rep 2017; 7:2295. [PMID: 28536481 PMCID: PMC5442135 DOI: 10.1038/s41598-017-02473-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/11/2017] [Indexed: 02/06/2023] Open
Abstract
Cold-inducible RNA-binding protein (CIRP) and RNA-binding motif protein 3 (RBM3) are two evolutionarily conserved RNA-binding proteins that are structurally related to hnRNPs and upregulated in response to moderately low temperatures in mammalian cells. Although contributions of splicing efficiency, the gene promoters activated upon mild hypothermia and the transcription factor Sp1 to induction of CIRP have been reported, precise mechanisms by which hypothermia and other stresses induce the expression of mammalian cold-inducible proteins (CIPs) are poorly understood. By screening the serine/arginine-rich splicing factors (SRSFs), we report that the transcript and protein levels of SRSF5 were increased in mammalian cells cultured at 32 °C. Expression of SRSF5 as well as CIRP and RBM3 were also induced by DNA damage, hypoxia, cycloheximide and hypotonicity. Immunohistochemical studies demonstrated that SRSF5 was constitutively expressed in male germ cells and the level was decreased in human testicular germ cell tumors. SRSF5 facilitated production of p19 H-RAS, and increased sensitivity to doxorubicin in human U-2 OS cells. Induction of CIPs was dependent on transient receptor potential vanilloid 4 (TRPV4) channel protein, but seemed independent of its ion channel activity. These findings indicate a previously unappreciated role for the TRP protein in linking environmental stress to splicing.
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Affiliation(s)
- Takanori Fujita
- Department of Clinical Molecular Biology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8507, Japan.,School of Economics, Nagoya University, Nagoya, Nagoya, 464-8601, Japan
| | - Hiroaki Higashitsuji
- Department of Clinical Molecular Biology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8507, Japan
| | - Hisako Higashitsuji
- Department of Clinical Molecular Biology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8507, Japan
| | - Yu Liu
- Department of Clinical Molecular Biology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8507, Japan
| | - Katsuhiko Itoh
- Department of Clinical Molecular Biology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8507, Japan
| | - Toshiharu Sakurai
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Takahiro Kojima
- Department of Urology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Shuya Kandori
- Department of Urology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Hiroyuki Nishiyama
- Department of Urology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
| | - Motoi Fukumoto
- Department of Pathology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Manabu Fukumoto
- Department of Pathology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, 980-8575, Japan.,Department of Molecular Pathology, Tokyo Medical University, Shinjuku-ku, Tokyo, 160-8402, Japan
| | - Koji Shibasaki
- Department of Molecular and Cellular Neurobiology, Gunma University Graduate School of Medicine, Maebashi, Gunma, 371-8511, Japan
| | - Jun Fujita
- Department of Clinical Molecular Biology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, 606-8507, Japan. .,Department of Rehabilitation Medicine, Biwako-Chuo Hospital, Otsu, Shiga, 520-0834, Japan.
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Kwok J, O'Shea M, Hume DA, Lengeling A. Jmjd6, a JmjC Dioxygenase with Many Interaction Partners and Pleiotropic Functions. Front Genet 2017; 8:32. [PMID: 28360925 PMCID: PMC5352680 DOI: 10.3389/fgene.2017.00032] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/27/2017] [Indexed: 12/20/2022] Open
Abstract
Lysyl hydroxylation and arginyl demethylation are post-translational events that are important for many cellular processes. The jumonji domain containing protein 6 (JMJD6) has been reported to catalyze both lysyl hydroxylation and arginyl demethylation on diverse protein substrates. It also interacts directly with RNA. This review summarizes knowledge of JMJD6 functions that have emerged in the last 15 years and considers how a single Jumonji C (JmjC) domain-containing enzyme can target so many different substrates. New links and synergies between the three main proposed functions of Jmjd6 in histone demethylation, promoter proximal pause release of polymerase II and RNA splicing are discussed. The physiological context of the described molecular functions is considered and recently described novel roles for JMJD6 in cancer and immune biology are reviewed. The increased knowledge of JMJD6 functions has wider implications for our general understanding of the JmjC protein family of which JMJD6 is a member.
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Affiliation(s)
- Janice Kwok
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
| | - Marie O'Shea
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
| | - David A Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
| | - Andreas Lengeling
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
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Shirali S, Barari A, Hosseini SA, Khodadi E. Effects of Six Weeks Endurance Training and Aloe Vera Supplementation on COX-2 and VEGF Levels in Mice with Breast Cancer. Asian Pac J Cancer Prev 2017; 18:31-36. [PMID: 28240006 PMCID: PMC5563116 DOI: 10.22034/apjcp.2017.18.1.31] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The aim of this study was to determine effects of six weeks endurance training and Aloe Vera supplementation on
COX-2 and VEGF levels in mice with breast cancer. For this purpose, 35 rats were randomly divided into 5 groups:
control (healthy) and 4 cancer groups: control (cancer only), training, Aloe Vera and Aloe Vera + training. Breast
cancer tumors were generated in mice by implantind. The training program comprised six weeks of swimming training
accomplished in three sessions per week. Training time started with 10 minutes on the first day and increased to 60
minutes in the second week and the water flow rate was increased from 7 to 15 liters per minute at a constant rate. Aloe
Vera extract at a dose of 300 mg/kg BW was administrated to rats by intraperitoneal injection. At the end of the study
period, rats were anesthetized and blood samples were taken. Significant differences were concluded at p<0.05 with
Kolmogorov-Smirnov and Tukey tests to analyze the data. The results showed significant increase in levels of serum.
COX-2 and VEGF levels in the cancer group compared with the healthy group. Administration of Aloe Vera extract
caused significant decrease in the COX-2 level in the cancer group. Also, in the training (swimming exercise) and
Aloe Vera + training cancer groups, we observed significant decrease in the VEGF level as compared to controls. Our
results suggest that Aloe Vera and training inhibit the COX pathway and cause decrease production of prostaglandin
E2. Hence administration of Aloe Vera in combination with endurance training might synergistically improve the host
milieu in mice bearing breast cancers.
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Affiliation(s)
- Saeed Shirali
- Research Center of Thalassemia and Hemoglobinopathy, Department of Laboratory Sciences, School of Paramedical Sciences, Ayatollah Amoli Branch, Islamic Azad University, Amol,Student Research Committee, Ayatollah Amoli Branch, Islamic Azad University, Amol.
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Silipo M, Gautrey H, Satam S, Lennard T, Tyson-Capper A. How is Herstatin, a tumor suppressor splice variant of the oncogene HER2, regulated? RNA Biol 2016; 14:536-543. [PMID: 27935425 DOI: 10.1080/15476286.2016.1267074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The human epidermal growth factor receptor 2 (HER2)/receptor tyrosine-protein kinasebB-2 (ERBB2) is overexpressed in 20-30% of breast tumors leading to faster growing and more aggressive tumors. Alternative splicing generates a functionally distinct HER2 variant called Herstatin, which is produced by the inclusion of intron 8. Herstatin acts as a tumor suppressor by effectively blocking HER2 activity and cell proliferation, while promoting apoptosis. In the present study we investigated HER2 pre-mRNA regulatory sequences and splicing factors which regulate the alternative splicing of Herstatin. A Herstatin minigene, comprising exon 8/intron 8/exon 9 of HER2 was generated and subsequent in vitro splicing assays revealed that RNA secondary structure and somatic mutations did not impact on inclusion of intron 8. However, using RNase-assisted RNA chromatography, followed by mass spectrometry, we identified six RNA-binding proteins (splicing factors) that bind to RNA sequences surrounding exon 8/intron 8 and intron 8/exon 9 boundaries; these included hnRNP I, H1, D, A2/B1 and hnRNPA1 plus the SR protein SRSF1. Specifically, overexpression of hnRNP A1 significantly increased retention of intron 8 resulting in higher levels of Herstatin in SKBR3 breast cancer cells whereas SRSF1 only had a marginal effect in decreasing Herstatin but increased exogenous HER2 levels under these experimental conditions. In conclusion, we have identified the first splicing factors and regulatory sequences that are involved in the production of Herstatin.
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Affiliation(s)
- Marco Silipo
- a Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University , Newcastle , UK
| | - Hannah Gautrey
- a Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University , Newcastle , UK
| | - Swapna Satam
- a Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University , Newcastle , UK
| | - Thomas Lennard
- b Northern Institute for Cancer Research, Faculty of Medical Sciences, Newcastle University , Newcastle , UK
| | - Alison Tyson-Capper
- a Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University , Newcastle , UK
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Luz FAC, Brígido PC, Moraes AS, Silva MJB. Aberrant Splicing in Cancer: Mediators of Malignant Progression through an Imperfect Splice Program Shift. Oncology 2016; 92:3-13. [PMID: 27794578 DOI: 10.1159/000450650] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/30/2016] [Indexed: 01/07/2023]
Abstract
Although the efforts to understand the genetic basis of cancer allowed advances in diagnosis and therapy, little is known about other molecular bases. Splicing is a key event in gene expression, controlling the excision of introns decoded inside genes and being responsible for 80% of the proteome amplification through events of alternative splicing. Growing data from the last decade point to deregulation of splicing events as crucial in carcinogenesis and tumor progression. Several alterations in splicing events were observed in cancer, caused by either missexpression of or detrimental mutations in some splicing factors, and appear to be critical in carcinogenesis and key events during tumor progression. Notwithstanding, it is difficult to determine whether it is a cause or consequence of cancer and/or tumorigenesis. Most reviews focus on the generated isoforms of deregulated splicing pattern, while others mainly summarize deregulated splicing factors observed in cancer. In this review, events associated with carcinogenesis and tumor progression mainly, and epithelial-to-mesenchymal transition, which is also implicated in alternative splicing regulation, will be progressively discussed in the light of a new perspective, suggesting that splicing deregulation mediates cell reprogramming in tumor progression by an imperfect shift of the splice program.
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Affiliation(s)
- Felipe Andrés Cordero Luz
- Laboratório de Osteoimunologia e Imunologia dos Tumores, Instituto de Ciências Biomédicas (ICBIM), Universidade Federal de Uberlândia (UFU), Uberlândia, Brazil
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Leo F, Bartels S, Mägel L, Framke T, Büsche G, Jonigk D, Christgen M, Lehmann U, Kreipe H. Prognostic factors in the myoepithelial-like spindle cell type of metaplastic breast cancer. Virchows Arch 2016; 469:191-201. [PMID: 27220763 PMCID: PMC4978764 DOI: 10.1007/s00428-016-1950-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 04/04/2016] [Accepted: 04/27/2016] [Indexed: 11/28/2022]
Abstract
Metaplastic breast carcinoma (MBC) comprises a heterogeneous group of tumors with difficult to predict biological behavior. A subset of MBC, characterized by spindle-shaped tumor cells with a myoepithelial-like immunophenotype, was entered into a retrospective study (n = 42, median follow-up time 43 months). Molecular parameters (DNA sequences of mutation hot spots in AKT1, ALK, APC, BRAF, CDH1, CTNNB1, EGFR, ERBB2, FBXW7, FGFR2, FOXL2, GNAQ, GNAS, KIT, KRAS, MAP2K1, MET, MSH6, NRAS, PDGFRA, PIK3CA, PTEN, SF3B1, SMAD4, SRC, SRSF2, STK11, TP53, and U2AF1; copy numbers for EGFR, c-myc, FGFR, PLAG, c-met) were assessed. None of the patients had axillary lymph node involvement. In 13 cases, local recurrence developed after surgery (30.9 %). Distant metastasis occurred in seven patients (17 %; four after local recurrence). The most frequent genetic alteration was PIK3CA mutation (50 % of cases). None of the pathological parameters (size, grade, stage, Ki-67 labeling index) was significantly associated with disease-free survival (DFS) or overall survival (OS). PIK3CA mutation, especially the H1047R type, tended to adversely affect OS. Type of resection (mastectomy vs. breast-conserving therapy, width of margins) or adjuvant radiotherapy had no influence on DFS or OS, whereas in the group treated with radio-/chemotherapy, no local recurrence or metastasis and no death occurred. We conclude that the spindle cell type of MBC with myoepithelial features exhibits a higher frequency of PIK3CA mutation than other types of metaplastic or basal-like breast cancer and may benefit from combined radio-/chemotherapy. Classical pathological parameters are not helpful in identifying the high-risk tumors among this subgroup of MBC.
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Affiliation(s)
- Fabian Leo
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Stephan Bartels
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Lavinia Mägel
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Theodor Framke
- Institute of Biometry, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Guntram Büsche
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Danny Jonigk
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Matthias Christgen
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Ulrich Lehmann
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Hans Kreipe
- Institute of Pathology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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Inoue K, Fry EA. Aberrant Splicing of Estrogen Receptor, HER2, and CD44 Genes in Breast Cancer. GENETICS & EPIGENETICS 2015; 7:19-32. [PMID: 26692764 PMCID: PMC4669075 DOI: 10.4137/geg.s35500] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 11/01/2015] [Accepted: 11/03/2015] [Indexed: 12/12/2022]
Abstract
Breast cancer (BC) is the most common cause of cancer-related death among women under the age of 50 years. Established biomarkers, such as hormone receptors (estrogen receptor [ER]/progesterone receptor) and human epidermal growth factor receptor 2 (HER2), play significant roles in the selection of patients for endocrine and trastuzumab therapies. However, the initial treatment response is often followed by tumor relapse with intrinsic resistance to the first-line therapy, so it has been expected to identify novel molecular markers to improve the survival and quality of life of patients. Alternative splicing of pre-messenger RNAs is a ubiquitous and flexible mechanism for the control of gene expression in mammalian cells. It provides cells with the opportunity to create protein isoforms with different, even opposing, functions from a single genomic locus. Aberrant alternative splicing is very common in cancer where emerging tumor cells take advantage of this flexibility to produce proteins that promote cell growth and survival. While a number of splicing alterations have been reported in human cancers, we focus on aberrant splicing of ER, HER2, and CD44 genes from the viewpoint of BC development. ERα36, a splice variant from the ER1 locus, governs nongenomic membrane signaling pathways triggered by estrogen and confers 4-hydroxytamoxifen resistance in BC therapy. The alternative spliced isoform of HER2 lacking exon 20 (Δ16HER2) has been reported in human BC; this isoform is associated with transforming ability than the wild-type HER2 and recapitulates the phenotypes of endocrine therapy-resistant BC. Although both CD44 splice isoforms (CD44s, CD44v) play essential roles in BC development, CD44v is more associated with those with favorable prognosis, such as luminal A subtype, while CD44s is linked to those with poor prognosis, such as HER2 or basal cell subtypes that are often metastatic. Hence, the detection of splice variants from these loci will provide keys to understand the pathogenesis, predict the prognosis, and choose specific therapies for BC.
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Affiliation(s)
- Kazushi Inoue
- Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Elizabeth A. Fry
- Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, NC, USA
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Sveen A, Kilpinen S, Ruusulehto A, Lothe RA, Skotheim RI. Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes. Oncogene 2015; 35:2413-27. [PMID: 26300000 DOI: 10.1038/onc.2015.318] [Citation(s) in RCA: 333] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/22/2015] [Accepted: 07/22/2015] [Indexed: 02/07/2023]
Abstract
Alternative splicing is a widespread process contributing to structural transcript variation and proteome diversity. In cancer, the splicing process is commonly disrupted, resulting in both functional and non-functional end-products. Cancer-specific splicing events are known to contribute to disease progression; however, the dysregulated splicing patterns found on a genome-wide scale have until recently been less well-studied. In this review, we provide an overview of aberrant RNA splicing and its regulation in cancer. We then focus on the executors of the splicing process. Based on a comprehensive catalog of splicing factor encoding genes and analyses of available gene expression and somatic mutation data, we identify cancer-associated patterns of dysregulation. Splicing factor genes are shown to be significantly differentially expressed between cancer and corresponding normal samples, and to have reduced inter-individual expression variation in cancer. Furthermore, we identify enrichment of predicted cancer-critical genes among the splicing factors. In addition to previously described oncogenic splicing factor genes, we propose 24 novel cancer-critical splicing factors predicted from somatic mutations.
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Affiliation(s)
- A Sveen
- Department of Molecular Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | | | - R A Lothe
- Department of Molecular Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - R I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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