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Huang C, Hsu C, Chao M, Hsu K, Lin TE, Yen S, Tu H, Pan S. In silico identification of a novel Cdc2-like kinase 2 (CLK2) inhibitor in triple negative breast cancer. Protein Sci 2024; 33:e5004. [PMID: 38723164 PMCID: PMC11081522 DOI: 10.1002/pro.5004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/29/2024] [Accepted: 04/12/2024] [Indexed: 05/13/2024]
Abstract
Dysregulation of RNA splicing processes is intricately linked to tumorigenesis in various cancers, especially breast cancer. Cdc2-like kinase 2 (CLK2), an oncogenic RNA-splicing kinase pivotal in breast cancer, plays a significant role, particularly in the context of triple-negative breast cancer (TNBC), a subtype marked by substantial medical challenges due to its low survival rates. In this study, we employed a structure-based virtual screening (SBVS) method to identify potential CLK2 inhibitors with novel chemical structures for treating TNBC. Compound 670551 emerged as a novel CLK2 inhibitor with a 50% inhibitory concentration (IC50) value of 619.7 nM. Importantly, Compound 670551 exhibited high selectivity for CLK2 over other protein kinases. Functionally, this compound significantly reduced the survival and proliferation of TNBC cells. Results from a cell-based assay demonstrated that this inhibitor led to a decrease in RNA splicing proteins, such as SRSF4 and SRSF6, resulting in cell apoptosis. In summary, we identified a novel CLK2 inhibitor as a promising potential treatment for TNBC therapy.
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Affiliation(s)
- Cheng‐Chiao Huang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipeiTaiwan
- Division of General Surgery, Department of SurgeryTaipei Medical University HospitalTaipeiTaiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
| | - Chia‐Ming Hsu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
| | - Min‐Wu Chao
- School of Medicine, College of Medicine, National Sun Yat‐sen UniversityKaohsiungTaiwan
- Institute of Biopharmaceutical Sciences, College of Medicine, National Sun Yat‐sen UniversityKaohsiungTaiwan
- The Doctoral Program of Clinical and Experimental Medicine, College of Medicine, National Sun Yat‐sen UniversityKaohsiungTaiwan
| | - Kai‐Cheng Hsu
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipeiTaiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
- Ph.D. Program in Drug Discovery and Development IndustryCollege of Pharmacy, Taipei Medical UniversityTaipeiTaiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical UniversityTaipeiTaiwan
- TMU Research Center of Drug Discovery, Taipei Medical UniversityTaipeiTaiwan
| | - Tony Eight Lin
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipeiTaiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
| | - Shih‐Chung Yen
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen)ShenzhenGuangdongChina
| | - Huang‐Ju Tu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
| | - Shiow‐Lin Pan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipeiTaiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
- Ph.D. Program in Drug Discovery and Development IndustryCollege of Pharmacy, Taipei Medical UniversityTaipeiTaiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical UniversityTaipeiTaiwan
- TMU Research Center of Drug Discovery, Taipei Medical UniversityTaipeiTaiwan
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2
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Fischer S, Lichtenthaeler C, Stepanenko A, Heyl F, Maticzka D, Kemmerer K, Klostermann M, Backofen R, Zarnack K, Weigand JE. Heterogenous nuclear ribonucleoprotein D-like controls endothelial cell functions. Biol Chem 2024; 405:229-239. [PMID: 37942876 DOI: 10.1515/hsz-2023-0254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/19/2023] [Indexed: 11/10/2023]
Abstract
HnRNPs are ubiquitously expressed RNA-binding proteins, tightly controlling posttranscriptional gene regulation. Consequently, hnRNP networks are essential for cellular homeostasis and their dysregulation is associated with cancer and other diseases. However, the physiological function of hnRNPs in non-cancerous cell systems are poorly understood. We analyzed the importance of HNRNPDL in endothelial cell functions. Knockdown of HNRNPDL led to impaired proliferation, migration and sprouting of spheroids. Transcriptome analysis identified cyclin D1 (CCND1) and tropomyosin 4 (TPM4) as targets of HNRNPDL, reflecting the phenotypic changes after knockdown. Our findings underline the importance of HNRNPDL for the homeostasis of physiological processes in endothelial cells.
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Affiliation(s)
- Sandra Fischer
- Department of Pharmacy, Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, D-35037 Marburg, Germany
| | - Chiara Lichtenthaeler
- Department of Pharmacy, Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, D-35037 Marburg, Germany
| | - Anastasiya Stepanenko
- Buchmann Institute for Molecular Life Sciences and Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Florian Heyl
- Department of Bioinformatics, University of Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany
| | - Daniel Maticzka
- Department of Bioinformatics, University of Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany
| | - Katrin Kemmerer
- Department of Pharmacy, Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, D-35037 Marburg, Germany
| | - Melina Klostermann
- Buchmann Institute for Molecular Life Sciences and Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Rolf Backofen
- Department of Bioinformatics, University of Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences and Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
| | - Julia E Weigand
- Department of Pharmacy, Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, D-35037 Marburg, Germany
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3
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Jain AP, Ghose V, Munshi S, Bhat FA, Dey G, Nanjappa V. Mass spectrometry-based proteomic analysis to characterize cisplatin induced early signaling events in head and neck squamous cell carcinoma. Mol Cell Oncol 2024; 11:2328873. [PMID: 38487372 PMCID: PMC10939151 DOI: 10.1080/23723556.2024.2328873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/06/2024] [Indexed: 03/17/2024]
Abstract
Cisplatin is the commonly used chemotherapeutic drug in treatment of various cancers. However, development of resistance towards cisplatin results in tumor recurrence. Here, we aim to understand the mechanisms of action of cisplatin and emergence of resistance to cisplatin using mass spectrometry-based proteomic approach. A panel of head and neck squamous cell carcinoma (HNSCC) cell lines were treated with cisplatin at respective IC50 for 24 h and label-free mass spectrometry analysis was carried out. Proteomic analysis of A253, FaDu, Det562 and CAL27 cell lines upon cisplatin treatment resulted in the identification of 5,060, 4,816, 4,537 and 4,142 proteins, respectively. Bioinformatics analysis of differentially regulated proteins revealed proteins implicated in DNA damage bypass pathway, translation and mRNA splicing to be enriched. Further, proteins associated with cisplatin resistance exhibited alterations following short-term cisplatin exposure. Among these, class III tubullin protein (TUBB3) was found to be upregulated in cisplatin-treated cells compared to untreated cells. Western blot analysis confirmed the elevated expression of TUBB3 in cells treated with cisplatin for 24 h, and also in cisplatin resistant HNSCC cell lines. This study delineates the early signaling events that enable HNSCC cells to counteract the cytotoxic effects of cisplatin and facilitate the development of resistance.
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Affiliation(s)
- Ankit P. Jain
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Vivek Ghose
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Srijon Munshi
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Firdous A. Bhat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Gourav Dey
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Vishalakshi Nanjappa
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education (MAHE), Manipal, India
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Zhang J, Fang Z, Song C. Molecular characteristics and clinical implications of serine/arginine-rich splicing factors in human cancer. Aging (Albany NY) 2023; 15:13287-13311. [PMID: 38015716 DOI: 10.18632/aging.205241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/17/2023] [Indexed: 11/30/2023]
Abstract
As critical splicing regulators, serine/arginine-rich splicing factors (SRSFs) play pivotal roles in carcinogenesis. As dysregulation of SRSFs may confer potential cancer risks, targeting SRSFs could provide important insights into cancer therapy. However, a global and comprehensive pattern to elaborate the molecular characteristics, mechanisms, and clinical links of SRSFs in a wide variety of human cancer is still lacking. In this study, a systematic analysis was conducted to reveal the molecular characteristics and clinical implications of SRSFs covering more than 10000 tumour samples of 33 human cancer types. We found that SRSFs experienced prevalent genomic alterations and expression perturbations in multiple cancer types. The DNA methylation, m6A modification, and miRNA regulation of SRSFs were all cancer context-dependent. Importantly, we found that SRSFs were strongly associated with cancer immunity, and were capable of predicting response to immunotherapy. And SRSFs had colossal potential for predicting survival in multiple cancer types, including those that have received immunotherapy. Moreover, we also found that SRSFs could indicate the drug sensitivity of targeted therapy and chemotherapy. Our research highlights the significance of SRSFs in cancer occurrence and development, and provides sufficient resources for understanding the biological characteristics of SRSFs, offering a new and unique perspective for developing cancer therapeutic strategies.
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Affiliation(s)
- Jinjin Zhang
- Department of Emergency Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Zhicheng Fang
- Department of Emergency Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Congkuan Song
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
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5
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Sun Y, Liu X, Wu Z, Wang X, Zhang Y, Yan W, You Y. SRSF4 Confers Temozolomide Resistance of Glioma via Accelerating Double Strand Break Repair. J Mol Neurosci 2023; 73:259-268. [PMID: 37014544 DOI: 10.1007/s12031-023-02115-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/23/2023] [Indexed: 04/05/2023]
Abstract
Temozolomide (TMZ)-based chemotherapy plays a central part in glioma treatment. However, prominent resistance to TMZ is a major change by now. In this study, expression and prognosis of SRSF4 were analyzed using multiple public datasets. Therapeutic efficacy against TMZ resistance was determined by assessing colony formation, flow cytometry, and western blot assays. Bio-informational analysis, immunofluorescence (IF), and western blot assays were performed to evaluate double strand break repair. An orthotopic xenograft model was used to exam the functional role of SRSF4. Here, we found that SRSF4 expression was associated with histological grade, IDH1 status, 1p/19q codeletion, molecular subtype, tumor recurrence, and poor prognosis. SRSF4 promotes TMZ resistance through positively regulating MDC1, thereby accelerating double strand break repair. Targeting SRSF4 could significantly improve chemosensitivity. Taken together, our collective findings highlight an important role of SRSF4 in the regulation of TMZ resistance by modulation of double strand break repair.
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Affiliation(s)
- Yi Sun
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Xingdong Liu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Zhiqiang Wu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Xiefeng Wang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Yong Zhang
- Department of Neurosurgery, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, Jiangsu, China.
| | - Wei Yan
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China.
| | - Yongping You
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, China.
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Lemaitre F, Chakrama F, O’Grady T, Peulen O, Rademaker G, Deward A, Chabot B, Piette J, Colige A, Lambert C, Dequiedt F, Habraken Y. The transcription factor c-Jun inhibits RBM39 to reprogram pre-mRNA splicing during genotoxic stress. Nucleic Acids Res 2022; 50:12768-12789. [PMID: 36477312 PMCID: PMC9825188 DOI: 10.1093/nar/gkac1130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 10/31/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022] Open
Abstract
Genotoxic agents, that are used in cancer therapy, elicit the reprogramming of the transcriptome of cancer cells. These changes reflect the cellular response to stress and underlie some of the mechanisms leading to drug resistance. Here, we profiled genome-wide changes in pre-mRNA splicing induced by cisplatin in breast cancer cells. Among the set of cisplatin-induced alternative splicing events we focused on COASY, a gene encoding a mitochondrial enzyme involved in coenzyme A biosynthesis. Treatment with cisplatin induces the production of a short isoform of COASY lacking exons 4 and 5, whose depletion impedes mitochondrial function and decreases sensitivity to cisplatin. We identified RBM39 as a major effector of the cisplatin-induced effect on COASY splicing. RBM39 also controls a genome-wide set of alternative splicing events partially overlapping with the cisplatin-mediated ones. Unexpectedly, inactivation of RBM39 in response to cisplatin involves its interaction with the AP-1 family transcription factor c-Jun that prevents RBM39 binding to pre-mRNA. Our findings therefore uncover a novel cisplatin-induced interaction between a splicing regulator and a transcription factor that has a global impact on alternative splicing and contributes to drug resistance.
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Affiliation(s)
| | | | - Tina O’Grady
- Laboratory of Gene Expression and Cancer, GIGA-Molecular Biology of Diseases, B34, University of Liège, Liège 4000, Belgium
| | - Olivier Peulen
- Metastasis Research Laboratory, GIGA-Cancer, B23, University of Liège, Liège 4000, Belgium
| | - Gilles Rademaker
- Metastasis Research Laboratory, GIGA-Cancer, B23, University of Liège, Liège 4000, Belgium
| | - Adeline Deward
- Laboratory of Virology and Immunology, GIGA-Molecular Biology of Diseases, B34, University of Liège, Liège 4000, Belgium
| | - Benoit Chabot
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences. Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jacques Piette
- Laboratory of Virology and Immunology, GIGA-Molecular Biology of Diseases, B34, University of Liège, Liège 4000, Belgium
| | - Alain Colige
- Laboratory of Connective Tissues Biology, GIGA-Cancer, B23, University of Liège, Liège 4000, Belgium
| | - Charles Lambert
- Laboratory of Connective Tissues Biology, GIGA-Cancer, B23, University of Liège, Liège 4000, Belgium
| | - Franck Dequiedt
- Correspondence may also be addressed to Franck Dequiedt. Tel: +32 366 9028;
| | - Yvette Habraken
- To whom correspondence should be addressed. Tel: +32 4 366 2447; Fax: +32 4 366 4198;
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7
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Metformin Treatment Modulates Long Non-Coding RNA Isoforms Expression in Human Cells. Noncoding RNA 2022; 8:ncrna8050068. [PMID: 36287120 PMCID: PMC9607547 DOI: 10.3390/ncrna8050068] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) undergo splicing and have multiple transcribed isoforms. Nevertheless, for lncRNAs, as well as for mRNA, measurements of expression are routinely performed only at the gene level. Metformin is the first-line oral therapy for type 2 diabetes mellitus and other metabolic diseases. However, its mechanism of action remains not thoroughly explained. Transcriptomic analyses using metformin in different cell types reveal that only protein-coding genes are considered. We aimed to characterize lncRNA isoforms that were differentially affected by metformin treatment on multiple human cell types (three cancer, two non-cancer) and to provide insights into the lncRNA regulation by this drug. We selected six series to perform a differential expression (DE) isoform analysis. We also inferred the biological roles for lncRNA DE isoforms using in silico tools. We found the same isoform of an lncRNA (AC016831.6-205) highly expressed in all six metformin series, which has a second exon putatively coding for a peptide with relevance to the drug action. Moreover, the other two lncRNA isoforms (ZBED5-AS1-207 and AC125807.2-201) may also behave as cis-regulatory elements to the expression of transcripts in their vicinity. Our results strongly reinforce the importance of considering DE isoforms of lncRNA for understanding metformin mechanisms at the molecular level.
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Chunlin K, Feng D, Peirong W. Research on the Enhancement Mechanism of Dihydromyricetin on the Inhibitory Role of Cisplatin Towards Breast Cancer Cell Activity. J BIOMATER TISS ENG 2022. [DOI: 10.1166/jbt.2022.2980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Objective: The purpose of our study was to evaluate Enhancement Mechanism of Dihydromyricetin (DMY) on the Inhibitory Role of Cisplatin Towards Breast Cancer Cell Activity. Materials and Methods: The MCF-7 were divided into NC, DMY, Cis and DMY+Cis groups. Using relative
methods (MTT, TUNEL, Transwell, flow cytometry and wound healing) to evaluate MCF-7 cell biological activities including cell viability, apoptosis, invasion cell number and wound healing rate. The relative proteins expressions including FOXO-1, Noxa, Bim, Cyto C, Caspase-3, Caspase-9 and Apaf-1
were evaluated by WB assay. Results: MCF-7 cell viability, invasion cell number and wound healing rates were significantly depressed and apoptosis rate were significantly increased in DMY, Cis and DMY+Cis groups (P < 0.01, respectively). Compared with Cis group, cell viability,
invasion cell number and wound healing rates were significantly depressed and apoptosis rate were significantly increased in DMY+Cis group (P < 0.05, respectively). Conclusion: Dihydromyricetin can effectively enhance the inhibitory effect of cisplatin on breast cancer cells.
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Affiliation(s)
- Ke Chunlin
- The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
| | - Dong Feng
- The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
| | - Wang Peirong
- The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China
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Murphy AJ, Li AH, Li P, Sun H. Therapeutic Targeting of Alternative Splicing: A New Frontier in Cancer Treatment. Front Oncol 2022; 12:868664. [PMID: 35463320 PMCID: PMC9027816 DOI: 10.3389/fonc.2022.868664] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/11/2022] [Indexed: 01/05/2023] Open
Abstract
The ability for cells to harness alternative splicing enables them to diversify their proteome in order to carry out complex biological functions and adapt to external and internal stimuli. The spliceosome is the multiprotein-RNA complex charged with the intricate task of alternative splicing. Aberrant splicing can arise from abnormal spliceosomes or splicing factors and drive cancer development and progression. This review will provide an overview of the alternative splicing process and aberrant splicing in cancer, with a focus on serine/arginine-rich (SR) proteins and their recently reported roles in cancer development and progression and beyond. Recent mapping of the spliceosome, its associated splicing factors, and their relationship to cancer have opened the door to novel therapeutic approaches that capitalize on the widespread influence of alternative splicing. We conclude by discussing small molecule inhibitors of the spliceosome that have been identified in an evolving era of cancer treatment.
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Affiliation(s)
- Anthony J. Murphy
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, United States
| | - Alex H. Li
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, United States
| | - Peichao Li
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hong Sun
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, United States
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Genomic Mapping of Splicing-Related Genes Identify Amplifications in LSM1, CLNS1A, and ILF2 in Luminal Breast Cancer. Cancers (Basel) 2021; 13:cancers13164118. [PMID: 34439272 PMCID: PMC8391113 DOI: 10.3390/cancers13164118] [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: 07/19/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 01/04/2023] Open
Abstract
Simple Summary The alternative splicing (AS) process is highly relevant, affecting most of the hallmarks of cancer, such as proliferation, angiogenesis, and metastasis. Our study evaluated alterations in 304 splicing-related genes and their prognosis value in breast cancer patients. Amplifications in CLNS1A, LSM1, and ILF2 genes in luminal patients were significantly associated with poor outcome. Downregulation of these genes in luminal cell lines showed an antiproliferative effect. Pharmacological modulation of transcription and RNA regulation is key for the optimal development of therapeutic strategies against key proteins. Administration of a BET inhibitor and BET-PROTAC reduced the expression of these identified genes and displayed a significant antiproliferative effect on these cell models. In conclusion, we describe novel splicing genes amplified in luminal breast tumors that are associated with detrimental prognosis and can be modulated pharmacologically. It opens the door for further studies confirming the effect of these genes in patients treated with BET inhibitors. Abstract Alternative splicing is an essential biological process, which increases the diversity and complexity of the human transcriptome. In our study, 304 splicing pathway-related genes were evaluated in tumors from breast cancer patients (TCGA dataset). A high number of alterations were detected, including mutations and copy number alterations (CNAs), although mutations were less frequently present compared with CNAs. In the four molecular subtypes, 14 common splice genes showed high level amplification in >5% of patients. Certain genes were only amplified in specific breast cancer subtypes. Most altered genes in each molecular subtype clustered to a few chromosomal regions. In the Luminal subtype, amplifications of LSM1, CLNS1A, and ILF2 showed a strong significant association with prognosis. An even more robust association with OS and RFS was observed when expression of these three genes was combined. Inhibition of LSM1, CLNS1A, and ILF2, using siRNA in MCF7 and T47D cells, showed a decrease in cell proliferation. The mRNA expression of these genes was reduced by treatment with BET inhibitors, a family of epigenetic modulators. We map the presence of splicing-related genes in breast cancer, describing three novel genes, LSM1, CLNS1A, and ILF2, that have an oncogenic role and can be modulated with BET inhibitors.
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11
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Rovira-Clavé X, Jiang S, Bai Y, Zhu B, Barlow G, Bhate S, Coskun AF, Han G, Ho CMK, Hitzman C, Chen SY, Bava FA, Nolan GP. Subcellular localization of biomolecules and drug distribution by high-definition ion beam imaging. Nat Commun 2021; 12:4628. [PMID: 34330905 PMCID: PMC8324837 DOI: 10.1038/s41467-021-24822-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 06/02/2021] [Indexed: 12/03/2022] Open
Abstract
Simultaneous visualization of the relationship between multiple biomolecules and their ligands or small molecules at the nanometer scale in cells will enable greater understanding of how biological processes operate. We present here high-definition multiplex ion beam imaging (HD-MIBI), a secondary ion mass spectrometry approach capable of high-parameter imaging in 3D of targeted biological entities and exogenously added structurally-unmodified small molecules. With this technology, the atomic constituents of the biomolecules themselves can be used in our system as the “tag” and we demonstrate measurements down to ~30 nm lateral resolution. We correlated the subcellular localization of the chemotherapy drug cisplatin simultaneously with five subnuclear structures. Cisplatin was preferentially enriched in nuclear speckles and excluded from closed-chromatin regions, indicative of a role for cisplatin in active regions of chromatin. Unexpectedly, cells surviving multi-drug treatment with cisplatin and the BET inhibitor JQ1 demonstrated near total cisplatin exclusion from the nucleus, suggesting that selective subcellular drug relocalization may modulate resistance to this important chemotherapeutic treatment. Multiplexed high-resolution imaging techniques, such as HD-MIBI, will enable studies of biomolecules and drug distributions in biologically relevant subcellular microenvironments by visualizing the processes themselves in concert, rather than inferring mechanism through surrogate analyses. Multiplexed ion beam imaging can provide subcellular localisation information but with limited resolution. Here the authors report an ion beam imaging method with nanoscale resolution which they use to assess the subcellular distribution of cisplatin.
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Affiliation(s)
- Xavier Rovira-Clavé
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sizun Jiang
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yunhao Bai
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Graham Barlow
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Salil Bhate
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Ahmet F Coskun
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Guojun Han
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Chin-Min Kimmy Ho
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA.,Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chuck Hitzman
- Stanford Nano Shared Facility, Stanford University, Stanford, CA, USA
| | - Shih-Yu Chen
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Felice-Alessio Bava
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA. .,Department of Pathology, Stanford University, Stanford, CA, USA.
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12
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Monroe JD, Moolani SA, Irihamye EN, Speed JS, Gibert Y, Smith ME. RNA-Seq Analysis of Cisplatin and the Monofunctional Platinum(II) Complex, Phenanthriplatin, in A549 Non-Small Cell Lung Cancer and IMR90 Lung Fibroblast Cell Lines. Cells 2020; 9:cells9122637. [PMID: 33302475 PMCID: PMC7764052 DOI: 10.3390/cells9122637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Abstract
Phenanthriplatin is a new monofunctional platinum(II) complex that binds only one strand of DNA and acts by blocking gene transcription, but its effect on gene regulation has not been characterized relative to the traditional platinum-based complex, cisplatin. A549 non-small cell lung cancer and IMR90 lung fibroblast cells were treated with cisplatin, phenanthriplatin, or a control and then their RNA transcripts were subjected to next generation sequencing analysis. DESeq2 and CuffDiff2 were used to identify up- and downregulated genes and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases were used to identify pathways and functions. We found that phenanthriplatin may regulate the genes GPRC5a, TFF1, and TNFRSF10D, which act through p53 to control apoptosis, differently or to a greater extent than cisplatin, and that it, unlike cisplatin, could upregulate ATP5MD, a gene which signals through the Wnt/β catenin pathway. Furthermore, phenanthriplatin caused unique or enhanced effects compared to cisplatin on genes regulating the cytoskeleton, cell migration, and proliferation, e.g., AGAP1, DIAPH2, GDF15, and THSD1 (p < 0.05; q < 0.05). Phenanthriplatin may modulate some oncogenes differently than cisplatin potentially leading to improved clinical outcome, but this monofunctional complex should be carefully matched with cancer gene data to be successfully applied in chemotherapy.
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Affiliation(s)
- Jerry D. Monroe
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS 39216, USA; (J.D.M.); (Y.G.)
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101-1080, USA; (S.A.M.); (E.N.I.)
| | - Satya A. Moolani
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101-1080, USA; (S.A.M.); (E.N.I.)
- Program in Cognitive Science, Case Western Reserve University, Cleveland, OH 44106-7063, USA
| | - Elvin N. Irihamye
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101-1080, USA; (S.A.M.); (E.N.I.)
- Program in Neuroscience, Indiana University Bloomington, Bloomington, IN 47405-2204, USA
| | - Joshua S. Speed
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA;
| | - Yann Gibert
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS 39216, USA; (J.D.M.); (Y.G.)
| | - Michael E. Smith
- Department of Biology, Western Kentucky University, Bowling Green, KY 42101-1080, USA; (S.A.M.); (E.N.I.)
- Correspondence:
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13
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Pellarin I, Belletti B, Baldassarre G. RNA splicing alteration in the response to platinum chemotherapy in ovarian cancer: A possible biomarker and therapeutic target. Med Res Rev 2020; 41:586-615. [PMID: 33058230 DOI: 10.1002/med.21741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/09/2020] [Accepted: 10/02/2020] [Indexed: 12/18/2022]
Abstract
Since its discovery, alternative splicing has been recognized as a powerful way for a cell to amplify the genetic information and for a living organism to adapt, evolve, and survive. We now know that a very high number of genes are regulated by alternative splicing and that alterations of splicing have been observed in different types of human diseases, including cancer. Here, we review the accumulating knowledge that links the regulation of alternative splicing to the response to chemotherapy, focusing our attention on ovarian cancer and platinum-based treatments. Moreover, we discuss how expanding information could be exploited to identify new possible biomarkers of platinum response, to better select patients, and/or to design new therapies able to overcome platinum resistance.
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Affiliation(s)
- Ilenia Pellarin
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, Aviano, Italy
| | - Barbara Belletti
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, Aviano, Italy
| | - Gustavo Baldassarre
- Molecular Oncology Unit, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, Aviano, Italy
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14
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Fergany AAM, Tatarskiy VV. RNA Splicing: Basic Aspects Underlie Antitumor Targeting. Recent Pat Anticancer Drug Discov 2020; 15:293-305. [PMID: 32900350 DOI: 10.2174/1574892815666200908122402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/15/2020] [Accepted: 07/29/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND RNA splicing, a fundamental step in gene expression, is aimed at intron removal and ordering of exons to form the protein's reading frame. OBJECTIVE This review is focused on the role of RNA splicing in cancer biology; the splicing abnormalities that lead to tumor progression emerge as targets for therapeutic intervention. METHODS We discuss the role of aberrant mRNA splicing in carcinogenesis and drug response. RESULTS AND CONCLUSION Pharmacological modulation of RNA splicing sets the stage for treatment approaches in situations where mRNA splicing is a clinically meaningful mechanism of the disease.
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Affiliation(s)
- Alzahraa A M Fergany
- Department of Occupational and Environmental Health, Graduate School of Pharmaceutical Science, Tokyo University of Science, Chiba, Japan
| | - Victor V Tatarskiy
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russian Federation
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15
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Zheng X, Peng Q, Wang L, Zhang X, Huang L, Wang J, Qin Z. Serine/arginine-rich splicing factors: the bridge linking alternative splicing and cancer. Int J Biol Sci 2020; 16:2442-2453. [PMID: 32760211 PMCID: PMC7378643 DOI: 10.7150/ijbs.46751] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/22/2020] [Indexed: 01/08/2023] Open
Abstract
The serine/arginine-rich splicing factors (SRs) belong to the serine arginine-rich protein family, which plays an extremely important role in the splicing process of precursor RNA. The SRs recognize the splicing elements on precursor RNA, then recruit and assemble spliceosome to promote or inhibit the occurrence of splicing events. In tumors, aberrant expression of SRs causes abnormal splicing of RNA, contributing to proliferation, migration and apoptosis resistance of tumor cells. Here, we reviewed the vital role of SRs in various tumors and discussed the promise of analyzing mRNA alternative splicing events in tumor. Further, we highlight the challenges and discussed the perspectives for the identification of new potential targets for cancer therapy via SRs family members.
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Affiliation(s)
- Xiang Zheng
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541001, China
| | - Qiu Peng
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, 410008, China
| | - Lujuan Wang
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, 410008, China
| | - Xuemei Zhang
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541001, China
| | - Lili Huang
- Laboratory of Genetics and Metabolism, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region; Guangxi Birth Defects Research and Prevention Institute, Nanning, Guangxi, 530003, China
| | - Jia Wang
- Department of Immunology, Changzhi Medical College, Changzhi, Shanxi, 046000 China
| | - Zailong Qin
- Laboratory of Genetics and Metabolism, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region; Guangxi Birth Defects Research and Prevention Institute, Nanning, Guangxi, 530003, China
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16
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Pellarin I, Dall'Acqua A, Gambelli A, Pellizzari I, D'Andrea S, Sonego M, Lorenzon I, Schiappacassi M, Belletti B, Baldassarre G. Splicing factor proline- and glutamine-rich (SFPQ) protein regulates platinum response in ovarian cancer-modulating SRSF2 activity. Oncogene 2020; 39:4390-4403. [PMID: 32332923 PMCID: PMC7253352 DOI: 10.1038/s41388-020-1292-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 03/23/2020] [Accepted: 03/31/2020] [Indexed: 11/09/2022]
Abstract
In epithelial ovarian cancer (EOC), response to platinum (PT)-based chemotherapy dictates subsequent treatments and predicts patients' prognosis. Alternative splicing is often deregulated in human cancers and can be altered by chemotherapy. Whether and how changes in alternative splicing regulation could impact on the response of EOC to PT-based chemotherapy is still not clarified. We identified the splicing factor proline and glutamine rich (SFPQ) as a critical mediator of response to PT in an unbiased functional genomic screening in EOC cells and, using a large cohort of primary and recurrent EOC samples, we observed that it is frequently overexpressed in recurrent PT-treated samples and that its overexpression correlates with PT resistance. At mechanistic level, we show that, under PT treatment, SFPQ, in complex with p54nrb, binds and regulates the activity of the splicing factor SRSF2. SFPQ/p54nrb complex decreases SRSF2 binding to caspase-9 RNA, favoring the expression of its alternative spliced antiapoptotic form. As a consequence, SFPQ/p54nrb protects cells from PT-induced death, eventually contributing to chemoresistance. Overall, our work unveils a previously unreported SFPQ/p54nrb/SRSF2 pathway that in EOC cells plays a central role in regulating alternative splicing and PT-induced apoptosis and that could result in the design of new possible ways of intervention to overcome PT resistance.
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Affiliation(s)
- Ilenia Pellarin
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Alessandra Dall'Acqua
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Alice Gambelli
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Ilenia Pellizzari
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Sara D'Andrea
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Maura Sonego
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Ilaria Lorenzon
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Monica Schiappacassi
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Barbara Belletti
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy
| | - Gustavo Baldassarre
- Division of Molecular Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, National Cancer Institute, 33081, Aviano, PN, Italy.
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17
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Roles of Splicing Factors in Hormone-Related Cancer Progression. Int J Mol Sci 2020; 21:ijms21051551. [PMID: 32106418 PMCID: PMC7084890 DOI: 10.3390/ijms21051551] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 02/20/2020] [Indexed: 12/19/2022] Open
Abstract
Splicing of mRNA precursor (pre-mRNA) is a mechanism to generate multiple mRNA isoforms from a single pre-mRNA, and it plays an essential role in a variety of biological phenomena and diseases such as cancers. Previous studies have demonstrated that cancer-specific splicing events are involved in various aspects of cancers such as proliferation, migration and response to hormones, suggesting that splicing-targeting therapy can be promising as a new strategy for cancer treatment. In this review, we focus on the splicing regulation by RNA-binding proteins including Drosophila behavior/human splicing (DBHS) family proteins, serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) in hormone-related cancers, such as breast and prostate cancers.
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18
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Global Analysis of Alternative Splicing Difference in Peripheral Immune Organs between Tongcheng Pigs and Large White Pigs Artificially Infected with PRRSV In Vivo. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4045204. [PMID: 32083129 PMCID: PMC7011390 DOI: 10.1155/2020/4045204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/13/2019] [Indexed: 11/17/2022]
Abstract
Alternative splicing (AS) plays a significant role in regulating gene expression at the transcriptional level in eukaryotes. Flexibility and diversity of transcriptome and proteome can be significantly increased through alternative splicing of genes. In the present study, transcriptome data of peripheral immune organs including spleen and inguinal lymph nodes (ILN) were used to identify AS difference between PRRSV-resistant Tongcheng (TC) pigs and PRRSV-susceptible Large White (LW) pigs artificially infected with porcine reproductive and respiratory syndrome virus (PRRSV) in vivo. The results showed that PRRSV infection induced global alternative splicing events (ASEs) with different modes. Among them, 373 genes and 595 genes in the spleen and ILN of TC pigs, while 458 genes and 560 genes in the spleen and ILN of LW pigs had significantly differential ASEs. Alternative splicing was subject to tissue-specific and lineage-specific regulation in response to PRRSV infection. Enriched GO terms and pathways showed that genes with differential ASEs played important roles in transcriptional regulation, immune response, metabolism, and apoptosis. Furthermore, a splicing factor associated with apoptosis, SRSF4, was significantly upregulated in LW pigs. Functional analysis on apoptosis associated genes was validated by RT-PCR and DNA sequencing. These findings revealed different response to PRRSV between PRRSV-resistant TC pigs and PRRSV-susceptible LW pigs at the level of alternative splicing, suggesting the potential relationship between AS and disease resistance to PRRSV.
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19
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Molecular Insights into miRNA-Driven Resistance to 5-Fluorouracil and Oxaliplatin Chemotherapy: miR-23b Modulates the Epithelial–Mesenchymal Transition of Colorectal Cancer Cells. J Clin Med 2019; 8:jcm8122115. [PMID: 31810268 PMCID: PMC6947029 DOI: 10.3390/jcm8122115] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 02/07/2023] Open
Abstract
Although treatment of colorectal cancer with 5-florouracil and oxaliplatin is widely used, it is frequently followed by a relapse. Therefore, there is an urgent need for profound understanding of chemotherapy resistance mechanisms as well as the profiling of predictive markers for individualized treatment. In this study, we identified the changes in 14 miRNAs in 5-fluouracil and 40 miRNAs in oxaliplatin-resistant cell lines by miRNA sequencing. The decrease in miR-224-5p expression in the 5-fluorouracil-resistant cells correlated with drug insensitivity due to its overexpression-induced drug-dependent apoptosis. On the other hand, the miR-23b/27b/24-1 cluster was overexpressed in oxaliplatin-resistant cells. The knockout of miR-23b led to the partial restoration of oxaliplatin susceptibility, showing the essential role of miR-23b in the development of drug resistance by this cluster. Proteomic analysis identified target genes of miR-23b and showed that endothelial–mesenchymal transition (EMT) was implicated in oxaliplatin insensibility. Data revealed that EMT markers, such as vimentin and SNAI2, were expressed moderately higher in the oxaliplatin-resistant cells and their expression increased further in the less drug-resistant cells, which had miR-23b knockout. This establishes that the balance of EMT contributes to the drug resistance, showing the importance of the miR-23b-mediated fine-tuning of EMT in oxaliplatin-resistant cancer cells.
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20
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Idris M, Harmston N, Petretto E, Madan B, Virshup DM. Broad regulation of gene isoform expression by Wnt signaling in cancer. RNA (NEW YORK, N.Y.) 2019; 25:1696-1713. [PMID: 31506381 PMCID: PMC6859862 DOI: 10.1261/rna.071506.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/06/2019] [Indexed: 05/08/2023]
Abstract
Differential gene isoform expression is a ubiquitous mechanism to enhance proteome diversity and maintain cell homeostasis. Mechanisms such as splicing that drive gene isoform variability are highly dynamic and responsive to changes in cell signaling pathways. Wnt/β-catenin signaling has profound effects on cell activity and cell fate and is known to modify several splicing events by altering the expression of individual splicing factors. However, a global assessment of how extensively Wnt signaling regulates splicing and other mechanisms that determine mRNA isoform composition in cancer is lacking. We used deep time-resolved RNA-seq in two independent in vivo Wnt-addicted tumor models during treatment with the potent Wnt inhibitor ETC-159 and examined Wnt regulated splicing events and splicing regulators. We found 1025 genes that underwent Wnt regulated variable exon usage leading to isoform expression changes. This was accompanied by extensive Wnt regulated changes in the expression of splicing regulators. Many of these Wnt regulated events were conserved in multiple human cancers, and many were linked to previously defined cancer-associated splicing quantitative trait loci. This suggests that the Wnt regulated splicing events are components of fundamental oncogenic processes. These findings demonstrate the wide-ranging effects of Wnt signaling on the isoform composition of the cell and provides an extensive resource of expression changes of splicing regulators and gene isoforms regulated by Wnt signaling.
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Affiliation(s)
- Muhammad Idris
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
| | - Nathan Harmston
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
- Centre for Computational Biology and Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857
- Science Division, Yale-NUS College, Singapore, 138527
| | - Enrico Petretto
- Centre for Computational Biology and Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857
| | - Babita Madan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
| | - David M Virshup
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, 169857
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina 27705, USA
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21
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Splicing regulatory factors in breast cancer hallmarks and disease progression. Oncotarget 2019; 10:6021-6037. [PMID: 31666932 PMCID: PMC6800274 DOI: 10.18632/oncotarget.27215] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/29/2019] [Indexed: 12/31/2022] Open
Abstract
By regulating transcript isoform expression levels, alternative splicing provides an additional layer of protein control. Recent studies show evidence that cancer cells use different splicing events to fulfill their requirements in order to develop, progress and metastasize. However, there has been less attention for the role of the complex catalyzing the complicated multistep splicing reaction: the spliceosome. The spliceosome consists of multiple sub-complexes in total comprising 244 proteins or splice factors and 5 associated RNA molecules. Here we discuss the role of splice factors in the oncogenic processes tumors cells need to fulfill their oncogenic properties (the so-called the hallmarks of cancer). Despite the fact that splice factors have been investigated only recently, they seem to play a prominent role in already five hallmarks of cancer: angiogenesis, resisting cell death, sustaining proliferation, deregulating cellular energetics and invasion and metastasis formation by affecting major signaling pathways such as epithelial-to-mesenchymal transition, the Warburg effect, DNA damage response and hormone receptor dependent proliferation. Moreover, we could relate expression of representative genes of four other hallmarks (enabling replicative mortality, genomic instability, avoiding immune destruction and evading growth suppression) to splice factor levels in human breast cancer tumors, suggesting that also these hallmarks could be regulated by splice factors. Since many splice factors are involved in multiple hallmarks of cancer, inhibiting splice factors might provide a new layer of oncogenic control and a powerful method to combat breast cancer progression.
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22
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Phoomak C, Park D, Silsirivanit A, Sawanyawisuth K, Vaeteewoottacharn K, Detarya M, Wongkham C, Lebrilla CB, Wongkham S. O-GlcNAc-induced nuclear translocation of hnRNP-K is associated with progression and metastasis of cholangiocarcinoma. Mol Oncol 2019; 13:338-357. [PMID: 30444036 PMCID: PMC6360360 DOI: 10.1002/1878-0261.12406] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/06/2018] [Accepted: 11/03/2018] [Indexed: 12/31/2022] Open
Abstract
O‐GlcNAcylation is a key post‐translational modification that modifies the functions of proteins. Associations between O‐GlcNAcylation, shorter survival of cholangiocarcinoma (CCA) patients, and increased migration/invasion of CCA cell lines have been reported. However, the specific O‐GlcNAcylated proteins (OGPs) that participate in promotion of CCA progression are poorly understood. OGPs were isolated from human CCA cell lines, KKU‐213 and KKU‐214, using a click chemistry‐based enzymatic labeling system, identified using LC‐MS/MS, and searched against an OGP database. From the proteomic analysis, a total of 21 OGPs related to cancer progression were identified, of which 12 have not been previously reported. Among these, hnRNP‐K, a multifaceted RNA‐ and DNA‐binding protein known as a pre‐mRNA‐binding protein, was one of the most abundantly expressed, suggesting its involvement in CCA progression. O‐GlcNAcylation of hnRNP‐K was further verified by anti‐OGP/anti‐hnRNP‐K immunoprecipitations and sWGA pull‐down assays. The perpetuation of CCA by hnRNP‐K was evaluated using siRNA, which revealed modulation of cyclin D1, XIAP, EMT markers, and MMP2 and MMP7 expression. In native CCA cells, hnRNP‐K was primarily localized in the nucleus; however, when O‐GlcNAcylation was suppressed, hnRNP‐K was retained in the cytoplasm. These data signify an association between nuclear accumulation of hnRNP‐K and the migratory capabilities of CCA cells. In human CCA tissues, expression of nuclear hnRNP‐K was positively correlated with high O‐GlcNAcylation levels, metastatic stage, and shorter survival of CCA patients. This study demonstrates the significance of O‐GlcNAcylation on the nuclear translocation of hnRNP‐K and its impact on the progression of CCA.
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Affiliation(s)
- Chatchai Phoomak
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Thailand
| | - Dayoung Park
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Department of Chemistry, University of California, Davis, CA, USA
| | - Atit Silsirivanit
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Thailand.,Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Thailand
| | - Kanlayanee Sawanyawisuth
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Thailand
| | - Kulthida Vaeteewoottacharn
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Thailand.,Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Thailand
| | - Marutpong Detarya
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Thailand
| | - Chaisiri Wongkham
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Thailand
| | | | - Sopit Wongkham
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Thailand.,Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Thailand
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23
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Liu S, Shao Y, Wang Q, Zhai Y, Li X. Genotoxic stress causes the accumulation of DNA-dependent protein kinase catalytic subunit phosphorylated at serine 2056 at nuclear speckles and alters pre-mRNA alternative splicing. FEBS Open Bio 2018; 9:304-314. [PMID: 30761255 PMCID: PMC6356181 DOI: 10.1002/2211-5463.12569] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 11/25/2018] [Accepted: 12/05/2018] [Indexed: 01/28/2023] Open
Abstract
RNA splicing has emerged as a critical player in the DNA damage response (DDR). However, the underlying mechanism(s) by which pre‐mRNA splicing is coordinately regulated by genotoxic stress has remained largely unclear. Here, we show that a DDR factor, DNA‐dependent protein kinase (DNA‐PK), participates in the modulation of pre‐mRNA splicing in the presence of DNA double‐strand break (DSB)‐induced genotoxic stress. Through indirect immunostaining, we made the surprising discovery that DNA‐PK catalytic subunits (DNA‐PKcs) autophosphorylated at serine 2056 (S2056) accumulate at nuclear speckles (dynamic nuclear structures that are enriched with splicing factors), following their dissociation from DSB lesions. Inactivation of DNA‐PKcs, either using a small molecule inhibitor or by RNA interference, alters alternative splicing of a set of pre‐mRNAs in A549 cells treated with the topoisomerase II inhibitor mitoxantrone, indicative of an involvement of DNA‐PKcs in modulating pre‐mRNA splicing following genotoxic stress. These findings indicate a novel physical and functional connection between the DNA damage response and pre‐mRNA splicing, and enhance our understanding of how mRNA splicing is involved in the cellular response to DSB lesions.
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Affiliation(s)
- Shuang Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development College of Life Sciences Beijing Normal University China
| | - Yuan Shao
- Beijing Key Laboratory of DNA Damage Response College of Life Sciences Capital Normal University China
| | - Qi Wang
- Beijing Key Laboratory of DNA Damage Response College of Life Sciences Capital Normal University China
| | - Yonggong Zhai
- Beijing Key Laboratory of Gene Resource and Molecular Development College of Life Sciences Beijing Normal University China
| | - Xialu Li
- Beijing Key Laboratory of DNA Damage Response College of Life Sciences Capital Normal University China
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24
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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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Urbanski L, Leclair N, Anczuków O. Alternative-splicing defects in cancer: Splicing regulators and their downstream targets, guiding the way to novel cancer therapeutics. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1476. [PMID: 29693319 PMCID: PMC6002934 DOI: 10.1002/wrna.1476] [Citation(s) in RCA: 221] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 12/14/2022]
Abstract
Defects in alternative splicing are frequently found in human tumors and result either from mutations in splicing-regulatory elements of specific cancer genes or from changes in the regulatory splicing machinery. RNA splicing regulators have emerged as a new class of oncoproteins and tumor suppressors, and contribute to disease progression by modulating RNA isoforms involved in the hallmark cancer pathways. Thus, dysregulation of alternative RNA splicing is fundamental to cancer and provides a potentially rich source of novel therapeutic targets. Here, we review the alterations in splicing regulatory factors detected in human tumors, as well as the resulting alternatively spliced isoforms that impact cancer hallmarks, and discuss how they contribute to disease pathogenesis. RNA splicing is a highly regulated process and, as such, the regulators are themselves tightly regulated. Differential transcriptional and posttranscriptional regulation of splicing factors modulates their levels and activities in tumor cells. Furthermore, the composition of the tumor microenvironment can also influence which isoforms are expressed in a given cell type and impact drug responses. Finally, we summarize current efforts in targeting alternative splicing, including global splicing inhibition using small molecules blocking the spliceosome or splicing-factor-modifying enzymes, as well as splice-switching RNA-based therapeutics to modulate cancer-specific splicing isoforms. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Anufrieva KS, Shender VО, Arapidi GP, Pavlyukov MS, Shakhparonov MI, Shnaider PV, Butenko IO, Lagarkova MA, Govorun VM. Therapy-induced stress response is associated with downregulation of pre-mRNA splicing in cancer cells. Genome Med 2018; 10:49. [PMID: 29950180 PMCID: PMC6020472 DOI: 10.1186/s13073-018-0557-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 06/07/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Abnormal pre-mRNA splicing regulation is common in cancer, but the effects of chemotherapy on this process remain unclear. METHODS To evaluate the effect of chemotherapy on slicing regulation, we performed meta-analyses of previously published transcriptomic, proteomic, phosphoproteomic, and secretome datasets. Our findings were verified by LC-MS/MS, western blotting, immunofluorescence, and FACS analyses of multiple cancer cell lines treated with cisplatin and pladienolide B. RESULTS Our results revealed that different types of chemotherapy lead to similar changes in alternative splicing by inducing intron retention in multiple genes. To determine the mechanism underlying this effect, we analyzed gene expression in 101 cell lines affected by ɣ-irradiation, hypoxia, and 10 various chemotherapeutic drugs. Strikingly, оnly genes involved in the cell cycle and pre-mRNA splicing regulation were changed in a similar manner in all 335 tested samples regardless of stress stimuli. We revealed significant downregulation of gene expression levels in these two pathways, which could be explained by the observed decrease in splicing efficiency and global intron retention. We showed that the levels of active spliceosomal proteins might be further post-translationally decreased by phosphorylation and export into the extracellular space. To further explore these bioinformatics findings, we performed proteomic analysis of cisplatin-treated ovarian cancer cells. Finally, we demonstrated that the splicing inhibitor pladienolide B impairs the cellular response to DNA damage and significantly increases the sensitivity of cancer cells to chemotherapy. CONCLUSIONS Decreased splicing efficiency and global intron retention is a novel stress response mechanism that may promote survival of malignant cells following therapy. We found that this mechanism can be inhibited by pladienolide B, which significantly increases the sensitivity of cancer cells to cisplatin which makes it a good candidate drug for improving the efficiency of cancer therapy.
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Affiliation(s)
- Ksenia S Anufrieva
- Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia.
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia.
- Systems Biology Lab, Moscow Institute of Physics and Technology (State University), Moscow, Region, 141701, Russia.
| | - Victoria О Shender
- Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia.
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia.
| | - Georgij P Arapidi
- Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
- Systems Biology Lab, Moscow Institute of Physics and Technology (State University), Moscow, Region, 141701, Russia
| | - Marat S Pavlyukov
- Laboratory of Membrane Bioenergetics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Michail I Shakhparonov
- Laboratory of Membrane Bioenergetics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Polina V Shnaider
- Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Ivan O Butenko
- Laboratory of Proteomic Analysis, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Maria A Lagarkova
- Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Vadim M Govorun
- Laboratory of Proteomics, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
- Laboratory of Proteomic Analysis, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
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Physiological and Pathological Function of Serine/Arginine-Rich Splicing Factor 4 and Related Diseases. BIOMED RESEARCH INTERNATIONAL 2018; 2018:3819719. [PMID: 29789787 PMCID: PMC5896335 DOI: 10.1155/2018/3819719] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/03/2018] [Accepted: 01/17/2018] [Indexed: 01/06/2023]
Abstract
Serine/arginine-rich splicing factors (SRSFs) have one or two RNA recognition motifs in the N terminal and a serine/arginine-enriched domain in the C terminal. SRSFs are essential components of spliceosomes and are involved in alternative splicing, spliceosome assembly, mRNA export, and nonsense-mediated mRNA decay. The maintenance of cellular and tissue homeostasis relies on accurate alternative splicing, and various patterns of abnormal alternative splicing can cause different diseases. SRSF4 is associated with many physiological and pathological processes and has applications in the diagnosis and prognosis of specific diseases. In this review, we discuss knowledge of SRSF4 in physiological and pathological processes and highlight the applications of SRSF4 in the regulation of gene expression and associated diseases.
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28
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Selection of internal references for qRT-PCR assays of human hepatocellular carcinoma cell lines. Biosci Rep 2017; 37:BSR20171281. [PMID: 29180379 PMCID: PMC5741833 DOI: 10.1042/bsr20171281] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/13/2022] Open
Abstract
Selecting internal references is important for normalizing the loading quantity of samples in quantitative reverse-transcription PCR (qRT-PCR). In the present study, a systematic evaluation of reference genes among nine hepatocellular carcinoma (HCC) cell lines was conducted. After screening the microarray assay data of ten HCC cell lines, 19 candidate reference genes were preselected and then evaluated by qRT-PCR, together with ACTB, GAPDH, HPRT1 and TUBB The expression evenness of these candidate genes was evaluated using RefFinder. The stabilities of the reference genes were further evaluated under different experimental perturbations in Huh-7 and MHCC-97L, and the applicability of the reference genes was assessed by measuring the mRNA expression of CCND1, CCND3, CDK4 and CDK6 under sorafenib treatment in Huh-7. Results showed that TFG and SFRS4 are among the most reliable reference genes, and ACTB ranks third and acts quite well as a classical choice, whereas GAPDH, HPRT1 and TUBB are not proper reference genes in qRT-PCR assays among the HCC cell lines. SFRS4, YWHAB, SFRS4 and CNPY3 are the most stable reference genes of the MHCC-97L under the perturbations of chemotherapy, oxidative stress, starvation and hypoxia respectively, whereas YWHAB is the most stable one of Huh-7 under all perturbations. GAPDH is recommended as a reference gene under chemotherapy perturbations. YWHAB and UBE2B, TMED2 and TSFM, and GAPDH and TSFM are the two best reference genes under oxidative stress, starvation and hypoxia perturbations respectively. TSFM is stable in both cell lines across all the perturbations.
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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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Lambert CA, Garbacki N, Colige AC. Chemotherapy induces alternative transcription and splicing: Facts and hopes for cancer treatment. Int J Biochem Cell Biol 2017; 91:84-97. [DOI: 10.1016/j.biocel.2017.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 04/04/2017] [Accepted: 04/15/2017] [Indexed: 01/14/2023]
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31
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Bjørklund SS, Panda A, Kumar S, Seiler M, Robinson D, Gheeya J, Yao M, Alnæs GIG, Toppmeyer D, Riis M, Naume B, Børresen-Dale AL, Kristensen VN, Ganesan S, Bhanot G. Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma. Sci Rep 2017; 7:5568. [PMID: 28717182 PMCID: PMC5514065 DOI: 10.1038/s41598-017-05537-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 06/05/2017] [Indexed: 12/11/2022] Open
Abstract
Cancer cells can have different patterns of exon usage of individual genes when compared to normal tissue, suggesting that alternative splicing may play a role in shaping the tumor phenotype. The discovery and identification of gene variants has increased dramatically with the introduction of RNA-sequencing technology, which enables whole transcriptome analysis of known, as well as novel isoforms. Here we report alternative splicing and transcriptional events among subtypes of invasive ductal carcinoma in The Cancer Genome Atlas (TCGA) Breast Invasive Carcinoma (BRCA) cohort. Alternative exon usage was widespread, and although common events were shared among three subtypes, ER+ HER2−, ER− HER2−, and HER2+, many events on the exon level were subtype specific. Additional RNA-seq analysis was carried out in an independent cohort of 43 ER+ HER2− and ER− HER2− primary breast tumors, confirming many of the exon events identified in the TCGA cohort. Alternative splicing and transcriptional events detected in five genes, MYO6, EPB41L1, TPD52, IQCG, and ACOX2 were validated by qRT-PCR in a third cohort of 40 ER+ HER2− and ER− HER2− patients, showing that these events were truly subtype specific.
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Affiliation(s)
- Sunniva Stordal Bjørklund
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA.,Department of Cancer Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo, 0310, Norway.,The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, P.O box 1171, Blindern, 0318, Oslo, Norway
| | - Anshuman Panda
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA.,Department of Physics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Surendra Kumar
- Department of Cancer Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo, 0310, Norway.,The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, P.O box 1171, Blindern, 0318, Oslo, Norway.,Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Akershus University hospital, Division of Medicine, 1476, Lørenskog, Norway
| | - Michael Seiler
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA.,BioMaPS Institute, Rutgers University, Piscataway, NJ, 08854, USA
| | - Doug Robinson
- BioMaPS Institute, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jinesh Gheeya
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA
| | - Ming Yao
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA
| | - Grethe I Grenaker Alnæs
- Department of Cancer Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo, 0310, Norway
| | - Deborah Toppmeyer
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA
| | - Margit Riis
- Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Akershus University hospital, Division of Medicine, 1476, Lørenskog, Norway.,Department of Surgery, Akershus University Hospital, 1478, Lørenskog, Norway.,Department of Breast and Endocrine Surgery, Oslo University Hospital, Ullevål, 0450, Oslo, Norway
| | - Bjørn Naume
- Department of Oncology, Oslo University Hospital, Radiumhospitalet, Oslo, Norway
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo, 0310, Norway.,The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, P.O box 1171, Blindern, 0318, Oslo, Norway
| | - Vessela N Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo, 0310, Norway.,The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, P.O box 1171, Blindern, 0318, Oslo, Norway.,Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Akershus University hospital, Division of Medicine, 1476, Lørenskog, Norway
| | - Shridar Ganesan
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA.
| | - Gyan Bhanot
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA. .,Department of Physics, Rutgers University, Piscataway, NJ, 08854, USA. .,Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, NJ, 08854, USA.
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32
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Yang J, Wu Y, Wang X, Xu L, Zhao X, Yang Y. Chemoresistance is associated with overexpression of HAX-1, inhibition of which resensitizes drug-resistant breast cancer cells to chemotherapy. Tumour Biol 2017; 39:1010428317692228. [PMID: 28347249 DOI: 10.1177/1010428317692228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Acquired resistance to standard chemotherapy is the common and critical limitation for cancer therapy. Hematopoietic cell-specific protein 1-associated protein X-1 (HAX-1) has been reported to be upregulated in numerous cancers. However, the role of HAX-1 in oncotherapy remains unclear. In this study, we established MDA-MB-231 cell lines which were resistant to cisplatin (MDA-MB-231/CR) or doxorubicin (MDA-MB-231/DR) to study the chemoresistance in breast cancer. As a result, the HAX-1 which is an apoptosis-associated protein was observed to be overexpressed in both MDA-MB-231/CR and MDA-MB-231/DR compared with the routine MDA-MB-231 cells. Moreover, knockdown of HAX-1 via RNA interference decreased IC50 level of cisplatin by 70.91% in MDA-MB-231/CR cells, and the IC50 level of doxorubicin was decreased by 76.46% in MDA-MB-231/DR cells when the HAX-1 was downregulated. Additionally, we found that the knockdown of HAX-1 induced the release of cytochrome C from mitochondria, resulting in the activation of caspases. Taken together, our study indicates that the overexpression of HAX-1 is essential in the development of chemoresistance in breast cancer. Furthermore, we identify that HAX-1 may become the target for cancer therapy.
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Affiliation(s)
- Ji Yang
- 1 Department of Geriatrics, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yue Wu
- 1 Department of Geriatrics, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiao Wang
- 2 Oncology Department, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Liqian Xu
- 1 Department of Geriatrics, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaohong Zhao
- 1 Department of Geriatrics, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yunmei Yang
- 1 Department of Geriatrics, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Kędzierska H, Piekiełko-Witkowska A. Splicing factors of SR and hnRNP families as regulators of apoptosis in cancer. Cancer Lett 2017; 396:53-65. [PMID: 28315432 DOI: 10.1016/j.canlet.2017.03.013] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/08/2017] [Accepted: 03/08/2017] [Indexed: 12/19/2022]
Abstract
SR and hnRNP proteins were initially discovered as regulators of alternative splicing: the process of controlled removal of introns and selective joining of exons through which multiple transcripts and, subsequently, proteins can be expressed from a single gene. Alternative splicing affects genes involved in all crucial cellular processes, including apoptosis. During cancerogenesis impaired apoptotic control facilitates survival of cells bearing molecular aberrations, contributing to their unrestricted proliferation and chemoresistance. Apparently, SR and hnRNP proteins regulate all levels of expression of apoptotic genes, including transcription initiation and elongation, alternative splicing, mRNA stability, translation, and protein degradation. The frequently disturbed expressions of SR/hnRNP proteins in cancers lead to impaired functioning of target apoptotic genes, including regulators of the extrinsic (Fas, caspase-8, caspase-2, c-FLIP) and the intrinsic pathway (Apaf-1, caspase-9, ICAD), genes encoding Bcl-2 proteins, IAPs, and p53 tumor suppressor. Prototypical members of SR/hnRNP families, SRSF1 and hnRNP A1, promote synthesis of anti-apoptotic splice variants of Bcl-x and Mcl-1, which results in attenuation of programmed cell death in breast cancer and chronic myeloid leukemia. SR/hnRNP proteins significantly affect responses to chemotherapy, acting as mediators or modulators of drug-induced apoptosis. Aberrant expression of SRSF1 and hnRNP K can interfere with tumor responses to chemotherapy in pancreatic and liver cancers. Currently, a number of splicing factor inhibitors is being tested in pre-clinical and clinical trials. In this review we discuss recent findings on the role of SR and hnRNP proteins in apoptotic control in cancer cells as well as their significance in anticancer treatments.
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Affiliation(s)
- Hanna Kędzierska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Agnieszka Piekiełko-Witkowska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland.
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Hendricks C, Dubail J, Brohée L, Delforge Y, Colige A, Deroanne C. A Novel Physiological Glycosaminoglycan-Deficient Splice Variant of Neuropilin-1 Is Anti-Tumorigenic In Vitro and In Vivo. PLoS One 2016; 11:e0165153. [PMID: 27798666 PMCID: PMC5087894 DOI: 10.1371/journal.pone.0165153] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/09/2016] [Indexed: 01/13/2023] Open
Abstract
Neuropilin-1 (NRP1) is a transmembrane protein acting as a co-receptor for several growth factors and interacting with other proteins such as integrins and plexins/semaphorins. It is involved in axonal development, angiogenesis and cancer progression. Its primary mRNA is subjected to alternative splicing mechanisms generating different isoforms, some of which lack the transmembrane domain and display antagonist properties to NRP1 full size (FS). NRP1 is further post-translationally modified by the addition of glycosaminoglycans (GAG) side chains through an O-glycosylation site at serine612. Here, we characterized a novel splice variant which has never been investigated, NRP1-Δ7, differing from the NRP1-FS by a deletion of 7 amino acids occurring two residues downstream of the O-glycosylation site. This short sequence contains two aspartic residues critical for efficient glycosylation. As expected, the high molecular weight products appearing as a smear in SDS-PAGE and reflecting the presence of GAG in NRP1-FS were undetectable in the NRP1-Δ7 protein. NRP1-Δ7 mRNA was found expressed at an appreciable level, between 10 and 30% of the total NRP1, by various cells lines and tissues from human and murine origin. To investigate the biological properties of this isoform, we generated prostatic (PC3) and breast (MDA-MB-231) cancer cells able to express recombinant NRP1-FS or NRP1-Δ7 in a doxycycline-inducible manner. Cells with increased expression of NRP1-Δ7 were characterized in vitro by a significant reduction of proliferation, migration and anchorage-independent growth, while NRP1-FS had the expected opposite “pro-tumoral” effects. Upon VEGF-A165 treatment, a lower internalization rate was observed for NRP1-Δ7 than for NRP1-FS. Finally, we showed that NRP1-Δ7 inhibited growth of prostatic tumors and their vascularization in vivo. This report identifies NRP1-Δ7 as a splice variant displaying anti-tumorigenic properties in vitro and in vivo, emphasizing the need to consider this isoform in future studies.
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Affiliation(s)
- Céline Hendricks
- Laboratory of Connective Tissues Biology, Tour de Pathologie, GIGA-Cancer, University of Liège, Sart-Tilman, Belgium
| | - Johanne Dubail
- Laboratory of Connective Tissues Biology, Tour de Pathologie, GIGA-Cancer, University of Liège, Sart-Tilman, Belgium
| | - Laura Brohée
- Laboratory of Connective Tissues Biology, Tour de Pathologie, GIGA-Cancer, University of Liège, Sart-Tilman, Belgium
| | - Yves Delforge
- Laboratory of Connective Tissues Biology, Tour de Pathologie, GIGA-Cancer, University of Liège, Sart-Tilman, Belgium
| | - Alain Colige
- Laboratory of Connective Tissues Biology, Tour de Pathologie, GIGA-Cancer, University of Liège, Sart-Tilman, Belgium
- * E-mail: (AC)
| | - Christophe Deroanne
- Laboratory of Connective Tissues Biology, Tour de Pathologie, GIGA-Cancer, University of Liège, Sart-Tilman, Belgium
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Shkreta L, Chabot B. The RNA Splicing Response to DNA Damage. Biomolecules 2015; 5:2935-77. [PMID: 26529031 PMCID: PMC4693264 DOI: 10.3390/biom5042935] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/20/2015] [Accepted: 10/16/2015] [Indexed: 12/29/2022] Open
Abstract
The number of factors known to participate in the DNA damage response (DDR) has expanded considerably in recent years to include splicing and alternative splicing factors. While the binding of splicing proteins and ribonucleoprotein complexes to nascent transcripts prevents genomic instability by deterring the formation of RNA/DNA duplexes, splicing factors are also recruited to, or removed from, sites of DNA damage. The first steps of the DDR promote the post-translational modification of splicing factors to affect their localization and activity, while more downstream DDR events alter their expression. Although descriptions of molecular mechanisms remain limited, an emerging trend is that DNA damage disrupts the coupling of constitutive and alternative splicing with the transcription of genes involved in DNA repair, cell-cycle control and apoptosis. A better understanding of how changes in splice site selection are integrated into the DDR may provide new avenues to combat cancer and delay aging.
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Affiliation(s)
- Lulzim Shkreta
- Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
| | - Benoit Chabot
- Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
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