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Resistance to Molecularly Targeted Therapies in Melanoma. Cancers (Basel) 2021; 13:cancers13051115. [PMID: 33807778 PMCID: PMC7961479 DOI: 10.3390/cancers13051115] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/12/2022] Open
Abstract
Malignant melanoma is the most aggressive type of skin cancer with invasive growth patterns. In 2021, 106,110 patients are projected to be diagnosed with melanoma, out of which 7180 are expected to die. Traditional methods like surgery, radiation therapy, and chemotherapy are not effective in the treatment of metastatic and advanced melanoma. Recent approaches to treat melanoma have focused on biomarkers that play significant roles in cell growth, proliferation, migration, and survival. Several FDA-approved molecular targeted therapies such as tyrosine kinase inhibitors (TKIs) have been developed against genetic biomarkers whose overexpression is implicated in tumorigenesis. The use of targeted therapies as an alternative or supplement to immunotherapy has revolutionized the management of metastatic melanoma. Although this treatment strategy is more efficacious and less toxic in comparison to traditional therapies, targeted therapies are less effective after prolonged treatment due to acquired resistance caused by mutations and activation of alternative mechanisms in melanoma tumors. Recent studies focus on understanding the mechanisms of acquired resistance to these current therapies. Further research is needed for the development of better approaches to improve prognosis in melanoma patients. In this article, various melanoma biomarkers including BRAF, MEK, RAS, c-KIT, VEGFR, c-MET and PI3K are described, and their potential mechanisms for drug resistance are discussed.
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52
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Zhang Y, Qian J, Gu C, Yang Y. Alternative splicing and cancer: a systematic review. Signal Transduct Target Ther 2021; 6:78. [PMID: 33623018 PMCID: PMC7902610 DOI: 10.1038/s41392-021-00486-7] [Citation(s) in RCA: 169] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 01/31/2023] Open
Abstract
The abnormal regulation of alternative splicing is usually accompanied by the occurrence and development of tumors, which would produce multiple different isoforms and diversify protein expression. The aim of the present study was to conduct a systematic review in order to describe the regulatory mechanisms of alternative splicing, as well as its functions in tumor cells, from proliferation and apoptosis to invasion and metastasis, and from angiogenesis to metabolism. The abnormal splicing events contributed to tumor progression as oncogenic drivers and/or bystander factors. The alterations in splicing factors detected in tumors and other mis-splicing events (i.e., long non-coding and circular RNAs) in tumorigenesis were also included. The findings of recent therapeutic approaches targeting splicing catalysis and splicing regulatory proteins to modulate pathogenically spliced events (including tumor-specific neo-antigens for cancer immunotherapy) were introduced. The emerging RNA-based strategies for the treatment of cancer with abnormally alternative splicing isoforms were also discussed. However, further studies are still required to address the association between alternative splicing and cancer in more detail.
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Affiliation(s)
- Yuanjiao Zhang
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jinjun Qian
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chunyan Gu
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Ye Yang
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
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Liu H, Gong Z, Li K, Zhang Q, Xu Z, Xu Y. SRPK1/2 and PP1α exert opposite functions by modulating SRSF1-guided MKNK2 alternative splicing in colon adenocarcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:75. [PMID: 33602301 PMCID: PMC7893936 DOI: 10.1186/s13046-021-01877-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND The Mnk2 kinase, encoded by MKNK2 gene, plays critical roles in MAPK signaling and was involved in oncogenesis. Human MKNK2 pre-mRNA can be alternatively spliced into two splicing isoforms, the MKNK2a and MKNK2b, thus yielding Mnk2a and Mnk2b proteins with different domains. The involvement of Mnk2 alternative splicing in colon cancer has been implicated based on RNA-sequencing data from TCGA database. This study aimed at investigating the upstream modulators and clinical relevance of Mnk2 alternative splicing in colon adenocarcinoma (CAC). METHODS PCR, western blotting and immunohistochemistry (IHC) were performed to assess the expression of Mnk2 and upstream proteins in CAC. The function of Mnk2 and its regulators were demonstrated in different CAC cell lines as well as in xenograft models. Two independent cohorts of CAC patients were used to reveal the clinical significance of MKNK2 alternative splicing. RESULTS Comparing with adjacent nontumorous tissue, CAC specimen showed a decreased MKNK2a level and an increased MKNK2b level, which were correlated with KRAS mutation and tumor size. The SRSF1 (serine/arginine-rich splicing factor 1) was further confirmed to be the major splicing factor targeting MKNK2 in CAC cells. Higher expression of SRPK1/2 or decreased activity of PP1α were responsible for enhancing SRSF1 phosphorylation and nucleus translocation, subsequently resulted in a switch of MKNK2 alternative splicing. CONCLUSIONS Our data showed that phosphorylation and subcellular localization of SRSF1 were balanced by SRPK1/2 and PP1α in CAC cells. High nucleus SRSF1 promoted MKNK2 splicing into MKNK2b instead of MNK2a, consequently enhanced tumor proliferation.
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Affiliation(s)
- Hongda Liu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Zheng Gong
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Kangshuai Li
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Qun Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Zekuan Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Yunfei Xu
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, 250012, China.
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Yaron TM, Heaton BE, Levy TM, Johnson JL, Jordan TX, Cohen BM, Kerelsky A, Lin TY, Liberatore KM, Bulaon DK, Kastenhuber ER, Mercadante MN, Shobana-Ganesh K, He L, Schwartz RE, Chen S, Weinstein H, Elemento O, Piskounova E, Nilsson-Payant BE, Lee G, Trimarco JD, Burke KN, Hamele CE, Chaparian RR, Harding AT, Tata A, Zhu X, Tata PR, Smith CM, Possemato AP, Tkachev SL, Hornbeck PV, Beausoleil SA, Anand SK, Aguet F, Getz G, Davidson AD, Heesom K, Kavanagh-Williamson M, Matthews D, tenOever BR, Cantley LC, Blenis J, Heaton NS. The FDA-approved drug Alectinib compromises SARS-CoV-2 nucleocapsid phosphorylation and inhibits viral infection in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32817937 DOI: 10.1101/2020.08.14.251207] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
While vaccines are vital for preventing COVID-19 infections, it is critical to develop new therapies to treat patients who become infected. Pharmacological targeting of a host factor required for viral replication can suppress viral spread with a low probability of viral mutation leading to resistance. In particular, host kinases are highly druggable targets and a number of conserved coronavirus proteins, notably the nucleoprotein (N), require phosphorylation for full functionality. In order to understand how targeting kinases could be used to compromise viral replication, we used a combination of phosphoproteomics and bioinformatics as well as genetic and pharmacological kinase inhibition to define the enzymes important for SARS-CoV-2 N protein phosphorylation and viral replication. From these data, we propose a model whereby SRPK1/2 initiates phosphorylation of the N protein, which primes for further phosphorylation by GSK-3a/b and CK1 to achieve extensive phosphorylation of the N protein SR-rich domain. Importantly, we were able to leverage our data to identify an FDA-approved kinase inhibitor, Alectinib, that suppresses N phosphorylation by SRPK1/2 and limits SARS-CoV-2 replication. Together, these data suggest that repurposing or developing novel host-kinase directed therapies may be an efficacious strategy to prevent or treat COVID-19 and other coronavirus-mediated diseases.
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Du JX, Zhu GQ, Cai JL, Wang B, Luo YH, Chen C, Cai CZ, Zhang SJ, Zhou J, Fan J, Zhu W, Dai Z. Splicing factors: Insights into their regulatory network in alternative splicing in cancer. Cancer Lett 2020; 501:83-104. [PMID: 33309781 DOI: 10.1016/j.canlet.2020.11.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/18/2022]
Abstract
More than 95% of all human genes are alternatively spliced after transcription, which enriches the diversity of proteins and regulates transcript and/or protein levels. The splicing isoforms produced from the same gene can manifest distinctly, even exerting opposite effects. Mounting evidence indicates that the alternative splicing (AS) mechanism is ubiquitous in various cancers and drives the generation and maintenance of various hallmarks of cancer, such as enhanced proliferation, inhibited apoptosis, invasion and metastasis, and angiogenesis. Splicing factors (SFs) play pivotal roles in the recognition of splice sites and the assembly of spliceosomes during AS. In this review, we mainly discuss the similarities and differences of SF domains, the details of SF function in AS, the effect of SF-driven pathological AS on different hallmarks of cancer, and the main drivers of SF expression level and subcellular localization. In addition, we briefly introduce the application prospects of targeted therapeutic strategies, including small-molecule inhibitors, siRNAs and splice-switching oligonucleotides (SSOs), from three perspectives (drivers, SFs and pathological AS). Finally, we share our insights into the potential direction of research on SF-centric AS-related regulatory networks.
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Affiliation(s)
- Jun-Xian Du
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Gui-Qi Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia-Liang Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Biao Wang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Yi-Hong Luo
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cong Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cheng-Zhe Cai
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Si-Jia Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Jian Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Wei Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
| | - Zhi Dai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China.
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Di Matteo A, Belloni E, Pradella D, Cappelletto A, Volf N, Zacchigna S, Ghigna C. Alternative splicing in endothelial cells: novel therapeutic opportunities in cancer angiogenesis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:275. [PMID: 33287867 PMCID: PMC7720527 DOI: 10.1186/s13046-020-01753-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/26/2020] [Indexed: 02/07/2023]
Abstract
Alternative splicing (AS) is a pervasive molecular process generating multiple protein isoforms, from a single gene. It plays fundamental roles during development, differentiation and maintenance of tissue homeostasis, while aberrant AS is considered a hallmark of multiple diseases, including cancer. Cancer-restricted AS isoforms represent either predictive biomarkers for diagnosis/prognosis or targets for anti-cancer therapies. Here, we discuss the contribution of AS regulation in cancer angiogenesis, a complex process supporting disease development and progression. We consider AS programs acting in a specific and non-redundant manner to influence morphological and functional changes involved in cancer angiogenesis. In particular, we describe relevant AS variants or splicing regulators controlling either secreted or membrane-bound angiogenic factors, which may represent attractive targets for therapeutic interventions in human cancer.
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Affiliation(s)
- Anna Di Matteo
- Istituto di Genetica Molecolare, "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100, Pavia, Italy
| | - Elisa Belloni
- Istituto di Genetica Molecolare, "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100, Pavia, Italy
| | - Davide Pradella
- Istituto di Genetica Molecolare, "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100, Pavia, Italy
| | - Ambra Cappelletto
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149, Trieste, Italy
| | - Nina Volf
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149, Trieste, Italy
| | - Serena Zacchigna
- Cardiovascular Biology Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149, Trieste, Italy. .,Department of Medical, Surgical and Health Sciences, University of Trieste, 34149, Trieste, Italy.
| | - Claudia Ghigna
- Istituto di Genetica Molecolare, "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100, Pavia, Italy.
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57
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Bustos F, Segarra-Fas A, Nardocci G, Cassidy A, Antico O, Davidson L, Brandenburg L, Macartney TJ, Toth R, Hastie CJ, Moran J, Gourlay R, Varghese J, Soares RF, Montecino M, Findlay GM. Functional Diversification of SRSF Protein Kinase to Control Ubiquitin-Dependent Neurodevelopmental Signaling. Dev Cell 2020; 55:629-647.e7. [PMID: 33080171 PMCID: PMC7725506 DOI: 10.1016/j.devcel.2020.09.025] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 08/17/2020] [Accepted: 09/25/2020] [Indexed: 02/06/2023]
Abstract
Conserved protein kinases with core cellular functions have been frequently redeployed during metazoan evolution to regulate specialized developmental processes. The Ser/Arg (SR)-rich splicing factor (SRSF) protein kinase (SRPK), which is implicated in splicing regulation, is one such conserved eukaryotic kinase. Surprisingly, we show that SRPK has acquired the capacity to control a neurodevelopmental ubiquitin signaling pathway. In mammalian embryonic stem cells and cultured neurons, SRPK phosphorylates Ser-Arg motifs in RNF12/RLIM, a key developmental E3 ubiquitin ligase that is mutated in an intellectual disability syndrome. Processive phosphorylation by SRPK stimulates RNF12-dependent ubiquitylation of nuclear transcription factor substrates, thereby acting to restrain a neural gene expression program that is aberrantly expressed in intellectual disability. SRPK family genes are also mutated in intellectual disability disorders, and patient-derived SRPK point mutations impair RNF12 phosphorylation. Our data reveal unappreciated functional diversification of SRPK to regulate ubiquitin signaling that ensures correct regulation of neurodevelopmental gene expression.
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Affiliation(s)
- Francisco Bustos
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, the University of Dundee, Dundee DD1 5EH, UK
| | - Anna Segarra-Fas
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, the University of Dundee, Dundee DD1 5EH, UK
| | - Gino Nardocci
- Institute of Biomedical Sciences and FONDAP Center for Genome Regulation, Universidad Andrés Bello, Santiago, Chile
| | - Andrew Cassidy
- Tayside Centre for Genomic Analysis, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Odetta Antico
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, the University of Dundee, Dundee DD1 5EH, UK
| | - Lindsay Davidson
- School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Lennart Brandenburg
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, the University of Dundee, Dundee DD1 5EH, UK
| | - Thomas J Macartney
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, the University of Dundee, Dundee DD1 5EH, UK
| | - Rachel Toth
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, the University of Dundee, Dundee DD1 5EH, UK
| | - C James Hastie
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, the University of Dundee, Dundee DD1 5EH, UK
| | - Jennifer Moran
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, the University of Dundee, Dundee DD1 5EH, UK
| | - Robert Gourlay
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, the University of Dundee, Dundee DD1 5EH, UK
| | - Joby Varghese
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, the University of Dundee, Dundee DD1 5EH, UK
| | - Renata F Soares
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, the University of Dundee, Dundee DD1 5EH, UK
| | - Martin Montecino
- Institute of Biomedical Sciences and FONDAP Center for Genome Regulation, Universidad Andrés Bello, Santiago, Chile
| | - Greg M Findlay
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, the University of Dundee, Dundee DD1 5EH, UK.
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Abstract
In the first decade of targeted covalent inhibition, scientists have successfully reversed the previous trend that had impeded the use of covalent inhibition in drug development. Successes in the clinic, mainly in the field of kinase inhibitors, are existing proof that safe covalent inhibitors can be designed and employed to develop effective treatments. The case of KRASG12C covalent inhibitors entering clinical trials in 2019 has been among the hottest topics discussed in drug discovery, raising expectations for the future of the field. In this perspective, an overview of the milestones hit with targeted covalent inhibitors, as well as the promise and the needs of current research, are presented. While recent results have confirmed the potential that was foreseen, many questions remain unexplored in this branch of precision medicine.
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59
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Chandra A, Ananda H, Singh N, Qamar I. Identification of a novel and potent small molecule inhibitor of SRPK1: mechanism of dual inhibition of SRPK1 for the inhibition of cancer progression. Aging (Albany NY) 2020; 13:163-180. [PMID: 33291073 PMCID: PMC7835025 DOI: 10.18632/aging.202301] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/19/2020] [Indexed: 01/05/2023]
Abstract
Protein kinases are the family of attractive enzyme targets for drug design with relevance to cancer biology. Serine arginine protein kinase 1 (SRPK1) is responsible for the phosphorylation of serine/arginine (SR)-rich proteins. Alternative Splicing Factor/Splicing Factor 2 (ASF/SF2) involved in mRNA editing. ASF/SF2 is over expressed in many cancers and plays crucial roles in the cell survival. Phosphorylation of ASF/SF2 is decisive for its functions in cancer. In search of potential anticancer therapeutic agents for attenuating phosphorylation of ASF/SF2, we have explored specific and potential inhibitors of SRPK1 from natural and drug like compounds databases using in-silico methods. Compound ZINC02154892 (C02) was found to be the most potent inhibitor for SRPK1. In-vitro molecular and cell biology studies have shown C02 as a potent and specific inhibitor of phosphorylation of ASF/SF2 and cell survival in leukemic cell line. Structural analysis of SRPK1 with compound C02 revealed a unique pattern of binding targeting ATP binding site along with inhibiting recruitment of ASF/SF2 by SRPK1. The possibilities of compound C02 to be used as a lead compound paving way for the development of potent and specific inhibitors of SRPK1 for designing of novel potential anticancer inhibitor is inferred from the current studies.
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Affiliation(s)
- Anshuman Chandra
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Hanumappa Ananda
- Department of Clinical Embryology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
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Bessa C, Matos P, Jordan P, Gonçalves V. Alternative Splicing: Expanding the Landscape of Cancer Biomarkers and Therapeutics. Int J Mol Sci 2020; 21:ijms21239032. [PMID: 33261131 PMCID: PMC7729450 DOI: 10.3390/ijms21239032] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing (AS) is a critical post-transcriptional regulatory mechanism used by more than 95% of transcribed human genes and responsible for structural transcript variation and proteome diversity. In the past decade, genome-wide transcriptome sequencing has revealed that AS is tightly regulated in a tissue- and developmental stage-specific manner, and also frequently dysregulated in multiple human cancer types. It is currently recognized that splicing defects, including genetic alterations in the spliced gene, altered expression of both core components or regulators of the precursor messenger RNA (pre-mRNA) splicing machinery, or both, are major drivers of tumorigenesis. Hence, in this review we provide an overview of our current understanding of splicing alterations in cancer, and emphasize the need to further explore the cancer-specific splicing programs in order to obtain new insights in oncology. Furthermore, we also discuss the recent advances in the identification of dysregulated splicing signatures on a genome-wide scale and their potential use as biomarkers. Finally, we highlight the therapeutic opportunities arising from dysregulated splicing and summarize the current approaches to therapeutically target AS in cancer.
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Affiliation(s)
- Cláudia Bessa
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (C.B.); (P.M.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Paulo Matos
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (C.B.); (P.M.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Peter Jordan
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (C.B.); (P.M.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
- Correspondence: (P.J.); (V.G.); Tel.: +351-217-519-380 (P.J.)
| | - Vânia Gonçalves
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (C.B.); (P.M.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
- Correspondence: (P.J.); (V.G.); Tel.: +351-217-519-380 (P.J.)
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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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62
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Sciarrillo R, Wojtuszkiewicz A, Assaraf YG, Jansen G, Kaspers GJL, Giovannetti E, Cloos J. The role of alternative splicing in cancer: From oncogenesis to drug resistance. Drug Resist Updat 2020; 53:100728. [PMID: 33070093 DOI: 10.1016/j.drup.2020.100728] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 12/15/2022]
Abstract
Alternative splicing is a tightly regulated process whereby non-coding sequences of pre-mRNA are removed and protein-coding segments are assembled in diverse combinations, ultimately giving rise to proteins with distinct or even opposing functions. In the past decade, whole genome/transcriptome sequencing studies revealed the high complexity of splicing regulation, which occurs co-transcriptionally and is influenced by chromatin status and mRNA modifications. Consequently, splicing profiles of both healthy and malignant cells display high diversity and alternative splicing was shown to be widely deregulated in multiple cancer types. In particular, mutations in pre-mRNA regulatory sequences, splicing regulators and chromatin modifiers, as well as differential expression of splicing factors are important contributors to cancer pathogenesis. It has become clear that these aberrations contribute to many facets of cancer, including oncogenic transformation, cancer progression, response to anticancer drug treatment as well as resistance to therapy. In this respect, alternative splicing was shown to perturb the expression a broad spectrum of relevant genes involved in drug uptake/metabolism (i.e. SLC29A1, dCK, FPGS, and TP), activation of nuclear receptor pathways (i.e. GR, AR), regulation of apoptosis (i.e. MCL1, BCL-X, and FAS) and modulation of response to immunotherapy (CD19). Furthermore, aberrant splicing constitutes an important source of novel cancer biomarkers and the spliceosome machinery represents an attractive target for a novel and rapidly expanding class of therapeutic agents. Small molecule inhibitors targeting SF3B1 or splice factor kinases were highly cytotoxic against a wide range of cancer models, including drug-resistant cells. Importantly, these effects are enhanced in specific cancer subsets, such as splicing factor-mutated and c-MYC-driven tumors. Furthermore, pre-clinical studies report synergistic effects of spliceosome modulators in combination with conventional antitumor agents. These strategies based on the use of low dose splicing modulators could shift the therapeutic window towards decreased toxicity in healthy tissues. Here we provide an extensive overview of the latest findings in the field of regulation of splicing in cancer, including molecular mechanisms by which cancer cells harness alternative splicing to drive oncogenesis and evade anticancer drug treatment as well as splicing-based vulnerabilities that can provide novel treatment opportunities. Furthermore, we discuss current challenges arising from genome-wide detection and prediction methods of aberrant splicing, as well as unravelling functional relevance of the plethora of cancer-related splicing alterations.
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Affiliation(s)
- Rocco Sciarrillo
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Department of Pediatric Oncology, Emma's Children's Hospital, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Anna Wojtuszkiewicz
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Gerrit Jansen
- Amsterdam Immunology and Rheumatology Center, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Gertjan J L Kaspers
- Department of Pediatric Oncology, Emma's Children's Hospital, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands; Fondazione Pisana per la Scienza, Pisa, Italy
| | - Jacqueline Cloos
- Department of Hematology, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, Netherlands.
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Caccamo D, Currò M, Ientile R, Verderio EAM, Scala A, Mazzaglia A, Pennisi R, Musarra-Pizzo M, Zagami R, Neri G, Rosmini C, Potara M, Focsan M, Astilean S, Piperno A, Sciortino MT. Intracellular Fate and Impact on Gene Expression of Doxorubicin/Cyclodextrin-Graphene Nanomaterials at Sub-Toxic Concentration. Int J Mol Sci 2020; 21:ijms21144891. [PMID: 32664456 PMCID: PMC7402311 DOI: 10.3390/ijms21144891] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022] Open
Abstract
The graphene road in nanomedicine still seems very long and winding because the current knowledge about graphene/cell interactions and the safety issues are not yet sufficiently clarified. Specifically, the impact of graphene exposure on gene expression is a largely unexplored concern. Herein, we investigated the intracellular fate of graphene (G) decorated with cyclodextrins (CD) and loaded with doxorubicin (DOX) and the modulation of genes involved in cancer-associated canonical pathways. Intracellular fate of GCD@DOX, tracked by FLIM, Raman mapping and fluorescence microscopy, evidenced the efficient cellular uptake of GCD@DOX and the presence of DOX in the nucleus, without graphene carrier. The NanoString nCounter™ platform provided evidence for 34 (out of 700) differentially expressed cancer-related genes in HEp-2 cells treated with GCD@DOX (25 µg/mL) compared with untreated cells. Cells treated with GCD alone (25 µg/mL) showed modification for 16 genes. Overall, 14 common genes were differentially expressed in both GCD and GCD@DOX treated cells and 4 of these genes with an opposite trend. The modification of cancer related genes also at sub-cytotoxic G concentration should be taken in consideration for the rational design of safe and effective G-based drug/gene delivery systems. The reliable advantages provided by NanoString® technology, such as sensibility and the direct RNA measurements, could be the cornerstone in this field.
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Affiliation(s)
- Daniela Caccamo
- Department of Biomedical Sciences, Dental Sciences and Morpho-Functional Imaging, Polyclinic Hospital University, 98125 Messina, Italy; (D.C.); (M.C.); (R.I.)
| | - Monica Currò
- Department of Biomedical Sciences, Dental Sciences and Morpho-Functional Imaging, Polyclinic Hospital University, 98125 Messina, Italy; (D.C.); (M.C.); (R.I.)
| | - Riccardo Ientile
- Department of Biomedical Sciences, Dental Sciences and Morpho-Functional Imaging, Polyclinic Hospital University, 98125 Messina, Italy; (D.C.); (M.C.); (R.I.)
| | - Elisabetta AM Verderio
- School of Science and Technology, Centre for Health, Ageing and Understanding of Disease, Nottingham Trent University, Nottingham NG11 8NS, UK;
| | - Angela Scala
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (R.P.); (M.M.P.); (G.N.); (C.R.)
| | - Antonino Mazzaglia
- CNR-Istituto per lo Studio dei Materiali Nanostrutturati (CNR-ISMN), Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.M.); (R.Z.)
| | - Rosamaria Pennisi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (R.P.); (M.M.P.); (G.N.); (C.R.)
- Department of Innate Immunology, Shenzhen International Institute for Biomedical Research, 140 Jinye Ave, Building A10, Life Science Park, Dapeng New District, Shenzhen 518119, China
| | - Maria Musarra-Pizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (R.P.); (M.M.P.); (G.N.); (C.R.)
| | - Roberto Zagami
- CNR-Istituto per lo Studio dei Materiali Nanostrutturati (CNR-ISMN), Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.M.); (R.Z.)
| | - Giulia Neri
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (R.P.); (M.M.P.); (G.N.); (C.R.)
| | - Consolato Rosmini
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (R.P.); (M.M.P.); (G.N.); (C.R.)
| | - Monica Potara
- Nanobiophotonics and Laser Microspectroscopy Center, Interdisciplinary Research Institute in Bio-Nano-Sciences, Babes-Bolyai University, T. Laurian Str. 42, 400271 Cluj-Napoca, Romania; (M.P.); (M.F.); (S.A.)
| | - Monica Focsan
- Nanobiophotonics and Laser Microspectroscopy Center, Interdisciplinary Research Institute in Bio-Nano-Sciences, Babes-Bolyai University, T. Laurian Str. 42, 400271 Cluj-Napoca, Romania; (M.P.); (M.F.); (S.A.)
| | - Simion Astilean
- Nanobiophotonics and Laser Microspectroscopy Center, Interdisciplinary Research Institute in Bio-Nano-Sciences, Babes-Bolyai University, T. Laurian Str. 42, 400271 Cluj-Napoca, Romania; (M.P.); (M.F.); (S.A.)
- Department of Biomolecular Physics, Faculty of Physics, Babes-Bolyai University, M Kogalniceanu Str. 1, 400084 Cluj-Napoca, Romania
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (R.P.); (M.M.P.); (G.N.); (C.R.)
- Correspondence: (A.P.); (M.T.S.); Tel.: +39-090-6765173 (A.P.); +39-090-6765217 (M.T.S.)
| | - Maria Teresa Sciortino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d’Alcontres 31, 98166 Messina, Italy; (A.S.); (R.P.); (M.M.P.); (G.N.); (C.R.)
- Correspondence: (A.P.); (M.T.S.); Tel.: +39-090-6765173 (A.P.); +39-090-6765217 (M.T.S.)
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64
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Cascarina SM, Ross ED. A proposed role for the SARS-CoV-2 nucleocapsid protein in the formation and regulation of biomolecular condensates. FASEB J 2020; 34:9832-9842. [PMID: 32562316 PMCID: PMC7323129 DOI: 10.1096/fj.202001351] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 05/31/2020] [Indexed: 02/06/2023]
Abstract
To date, the recently discovered SARS‐CoV‐2 virus has afflicted >6.9 million people worldwide and disrupted the global economy. Development of effective vaccines or treatments for SARS‐CoV‐2 infection will be aided by a molecular‐level understanding of SARS‐CoV‐2 proteins and their interactions with host cell proteins. The SARS‐CoV‐2 nucleocapsid (N) protein is highly homologous to the N protein of SARS‐CoV, which is essential for viral RNA replication and packaging into new virions. Emerging models indicate that nucleocapsid proteins of other viruses can form biomolecular condensates to spatiotemporally regulate N protein localization and function. Our bioinformatic analyses, in combination with pre‐existing experimental evidence, suggest that the SARS‐CoV‐2 N protein is capable of forming or regulating biomolecular condensates in vivo by interaction with RNA and key host cell proteins. We discuss multiple models, whereby the N protein of SARS‐CoV‐2 may harness this activity to regulate viral life cycle and host cell response to viral infection.
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Affiliation(s)
- Sean M Cascarina
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Eric D Ross
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
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65
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Teng M, Ficarro SB, Yoon H, Che J, Zhou J, Fischer ES, Marto JA, Zhang T, Gray NS. Rationally Designed Covalent BCL6 Inhibitor That Targets a Tyrosine Residue in the Homodimer Interface. ACS Med Chem Lett 2020; 11:1269-1273. [PMID: 32551010 DOI: 10.1021/acsmedchemlett.0c00111] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/03/2020] [Indexed: 12/29/2022] Open
Abstract
B-cell lymphoma 6 (BCL6) is a transcriptional repressor frequently deregulated in lymphoid malignancies. BCL6 engages with number of corepressors, and these protein-protein interactions are being explored as a strategy for drug development. Here, we report the development of an irreversible BCL6 inhibitor TMX-2164 that uses a sulfonyl fluoride to covalently react with the hydroxyl group of Tyrosine 58 located in the lateral groove. TMX-2164 exhibits significantly improved inhibitory activity compared to that of its reversible parental compound and displays sustained target engagement and antiproliferative activity in cells. TMX-2164 therefore represents an example of a tyrosine-directed covalent inhibitor of BCL6 which demonstrates advantages relative to reversible targeting.
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Affiliation(s)
- Mingxing Teng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Scott B. Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Oncologic Pathology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
| | - Hojong Yoon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jing Zhou
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jarrod A. Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Oncologic Pathology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Nathanael S. Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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66
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Combined SRPK and AKT pharmacological inhibition is synergistic in T-cell acute lymphoblastic leukemia cells. Toxicol In Vitro 2020; 65:104777. [DOI: 10.1016/j.tiv.2020.104777] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/13/2020] [Accepted: 01/17/2020] [Indexed: 12/13/2022]
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67
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Rahman MA, Nasrin F, Bhattacharjee S, Nandi S. Hallmarks of Splicing Defects in Cancer: Clinical Applications in the Era of Personalized Medicine. Cancers (Basel) 2020; 12:cancers12061381. [PMID: 32481522 PMCID: PMC7352608 DOI: 10.3390/cancers12061381] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/25/2020] [Accepted: 05/25/2020] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing promotes proteome diversity by using limited number of genes, a key control point of gene expression. Splicing is carried out by large macromolecular machineries, called spliceosome, composed of small RNAs and proteins. Alternative splicing is regulated by splicing regulatory cis-elements in RNA and trans-acting splicing factors that are often tightly regulated in a tissue-specific and developmental stage-specific manner. The biogenesis of ribonucleoprotein (RNP) complexes is strictly regulated to ensure that correct complements of RNA and proteins are coordinated in the right cell at the right time to support physiological functions. Any perturbations that impair formation of functional spliceosomes by disrupting the cis-elements, or by compromising RNA-binding or function of trans-factors can be deleterious to cells and result in pathological consequences. The recent discovery of oncogenic mutations in splicing factors, and growing evidence of the perturbed splicing in multiple types of cancer, underscores RNA processing defects as a critical driver of oncogenesis. These findings have resulted in a growing interest in targeting RNA splicing as a therapeutic approach for cancer treatment. This review summarizes our current understanding of splicing alterations in cancer, recent therapeutic efforts targeting splicing defects in cancer, and future potentials to develop novel cancer therapies.
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68
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Wang C, Zhou Z, Subhramanyam CS, Cao Q, Heng ZSL, Liu W, Fu X, Hu Q. SRPK1 acetylation modulates alternative splicing to regulate cisplatin resistance in breast cancer cells. Commun Biol 2020; 3:268. [PMID: 32461560 PMCID: PMC7253463 DOI: 10.1038/s42003-020-0983-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 05/04/2020] [Indexed: 12/22/2022] Open
Abstract
Cisplatin and other platinum-based compounds are frequently used to treat breast cancer, but their utility is severely compromised by drug resistance. Many genes dictating drug responsiveness are subject to pre-mRNA alternative splicing which is regulated by key kinases such as the serine-arginine protein kinase 1 (SRPK1). However, its contribution to drug resistance remains controversial. In this study, we have identified that Tip60-mediated acetylation of SRPK1 is closely associated with chemotherapy sensitivity. In breast cancer cells, cisplatin induced SRPK1 acetylation but in the corresponding resistant cells, it reduced acetylation yet increased phosphorylation and kinase activity of SRPK1, favouring the splicing of some anti-apoptotic variants. Significantly, the cisplatin-resistant cells could be re-sensitized by enhancing SRPK1 acetylation or inhibiting its kinase activity. Hence, our study reveals a key role of SRPK1 in the development of cisplatin resistance in breast cancer cells and suggests a potential therapeutic avenue for overcoming chemotherapy resistance. Wang et al. find that the therapeutic agent cisplatin has opposite effect on acetylation of serine-arginine protein kinase 1 (SRPK1) in cisplatin-resistant versus – sensitive breast cancer cells. Inhibiting SRPK1 activity or enhancing its acetylation re-sensitises cells to cisplatin, suggesting a potential strategy to treat cancers resistant to platinum-based therapy.
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Affiliation(s)
- Cheng Wang
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 4 Medical Drive, Singapore, Singapore, 117594
| | - Zhihong Zhou
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, Singapore, 117593
| | | | - Qiong Cao
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 4 Medical Drive, Singapore, Singapore, 117594
| | - Zealyn Shi Lin Heng
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 4 Medical Drive, Singapore, Singapore, 117594
| | - Wen Liu
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiang'an South Road, Xiamen, Fujian, 361102, China
| | - Xiangdong Fu
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0651, USA
| | - Qidong Hu
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, 4 Medical Drive, Singapore, Singapore, 117594.
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69
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Eymin B. Targeting the spliceosome machinery: A new therapeutic axis in cancer? Biochem Pharmacol 2020; 189:114039. [PMID: 32417188 DOI: 10.1016/j.bcp.2020.114039] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/12/2020] [Indexed: 02/06/2023]
Abstract
Pre-mRNA splicing is the removal of introns and ligation of exons to form mature mRNAs, and it provides a critical mechanism by which eukaryotic cells can regulate their gene expression. Strikingly, more than 90% of protein-encoding transcripts are alternatively spliced, through exon inclusion/skipping, differential use of 5' or 3' alternative splice sites, intron retention or selection of an alternative promoter, thereby drastically increasing protein diversity. Splicing is altered in various pathological conditions, including cancers. In the last decade, high-throughput transcriptomic analyses have identified thousands of splice variants in cancers, which can distinguish between tumoral and normal tissues as well as identify tumor types, subtypes and clinical stages. These abnormal or aberrantly expressed splice variants, found in all cancer hallmarks, can result from mutations in splice sites, deregulated expression or even somatic mutations of components of the spliceosome machinery. Therefore, and based on these recent observations, a new anti-cancer strategy of targeting the spliceosome machinery with small molecules has emerged; however, the potential for these therapies is still a matter of great debate. Notably, more preclinical studies are needed to clarify which splicing patterns are mainly affected by these compounds, which cancer patients could be the most eligible for these treatments and whether using these spliceosome inhibitors alone or in combination with chemotherapies or targeted therapies would provide better therapeutic benefits. In this commentary, I will discuss all of these aspects.
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Affiliation(s)
- Beatrice Eymin
- INSERM U1209, CNRS UMR5309, Institute For Advanced Biosciences, 38000 Grenoble, France; Université Grenoble Alpes, 38000 Grenoble, France.
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70
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Roles and mechanisms of alternative splicing in cancer - implications for care. Nat Rev Clin Oncol 2020; 17:457-474. [PMID: 32303702 DOI: 10.1038/s41571-020-0350-x] [Citation(s) in RCA: 379] [Impact Index Per Article: 94.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2020] [Indexed: 12/14/2022]
Abstract
Removal of introns from messenger RNA precursors (pre-mRNA splicing) is an essential step for the expression of most eukaryotic genes. Alternative splicing enables the regulated generation of multiple mRNA and protein products from a single gene. Cancer cells have general as well as cancer type-specific and subtype-specific alterations in the splicing process that can have prognostic value and contribute to every hallmark of cancer progression, including cancer immune responses. These splicing alterations are often linked to the occurrence of cancer driver mutations in genes encoding either core components or regulators of the splicing machinery. Of therapeutic relevance, the transcriptomic landscape of cancer cells makes them particularly vulnerable to pharmacological inhibition of splicing. Small-molecule splicing modulators are currently in clinical trials and, in addition to splice site-switching antisense oligonucleotides, offer the promise of novel and personalized approaches to cancer treatment.
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71
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Boer RE, Torrey ZR, Schneekloth JS. Chemical Modulation of Pre-mRNA Splicing in Mammalian Systems. ACS Chem Biol 2020; 15:808-818. [PMID: 32191432 DOI: 10.1021/acschembio.0c00001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
RNA splicing is a key component of gene expression and proteomic diversity in humans. The spliceosome assembles on and processes individual nascent pre-mRNA transcripts into distinct mature mRNAs that can code for different proteins. Splicing programs can be affected by somatic mutations and changes in response to exogenous stimuli. Importantly, alterations in splicing can be direct drivers of diseases including cancers. This Review describes recent advances and the potential for targeting and controlling pre-mRNA splicing in humans with small molecules, ranging from targeting spliceosomal proteins to direct targeting of individual RNA transcripts.
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Affiliation(s)
- Robert E. Boer
- Chemical Biology Laboratory, National Cancer Institute, Frederick Maryland 21702, United States
| | - Zachary R. Torrey
- Chemical Biology Laboratory, National Cancer Institute, Frederick Maryland 21702, United States
| | - John S. Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick Maryland 21702, United States
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72
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Gou LT, Lim DH, Ma W, Aubol BE, Hao Y, Wang X, Zhao J, Liang Z, Shao C, Zhang X, Meng F, Li H, Zhang X, Xu R, Li D, Rosenfeld MG, Mellon PL, Adams JA, Liu MF, Fu XD. Initiation of Parental Genome Reprogramming in Fertilized Oocyte by Splicing Kinase SRPK1-Catalyzed Protamine Phosphorylation. Cell 2020; 180:1212-1227.e14. [PMID: 32169215 DOI: 10.1016/j.cell.2020.02.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 12/04/2019] [Accepted: 02/07/2020] [Indexed: 01/15/2023]
Abstract
The paternal genome undergoes a massive exchange of histone with protamine for compaction into sperm during spermiogenesis. Upon fertilization, this process is potently reversed, which is essential for parental genome reprogramming and subsequent activation; however, it remains poorly understood how this fundamental process is initiated and regulated. Here, we report that the previously characterized splicing kinase SRPK1 initiates this life-beginning event by catalyzing site-specific phosphorylation of protamine, thereby triggering protamine-to-histone exchange in the fertilized oocyte. Interestingly, protamine undergoes a DNA-dependent phase transition to gel-like condensates and SRPK1-mediated phosphorylation likely helps open up such structures to enhance protamine dismissal by nucleoplasmin (NPM2) and enable the recruitment of HIRA for H3.3 deposition. Remarkably, genome-wide assay for transposase-accessible chromatin sequencing (ATAC-seq) analysis reveals that selective chromatin accessibility in both sperm and MII oocytes is largely erased in early pronuclei in a protamine phosphorylation-dependent manner, suggesting that SRPK1-catalyzed phosphorylation initiates a highly synchronized reorganization program in both parental genomes.
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Affiliation(s)
- Lan-Tao Gou
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Do-Hwan Lim
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wubin Ma
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brandon E Aubol
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yajing Hao
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xin Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jun Zhao
- Transgenic and Knockout Mouse Core, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhengyu Liang
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Changwei Shao
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xuan Zhang
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Fan Meng
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hairi Li
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xiaorong Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ruiming Xu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dangsheng Li
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Pamela L Mellon
- Transgenic and Knockout Mouse Core, University of California, San Diego, La Jolla, CA 92093, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joseph A Adams
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mo-Fang Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences-University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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73
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Jones LH, Kelly JW. Structure-based design and analysis of SuFEx chemical probes. RSC Med Chem 2020; 11:10-17. [PMID: 33479601 DOI: 10.1039/c9md00542k] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 12/16/2019] [Indexed: 12/11/2022] Open
Abstract
The discerning reactivity of sulfur(vi)-fluoride exchange (SuFEx) chemistry has enabled the context-specific labeling of protein binding sites by chemical probes that incorporate these versatile warheads. Emerging information from protein-probe structures and proteomic mapping experiments is helping advance our understanding of the protein microenvironment that dictates the reactivity of targetable amino acid residues. This review explores these new findings that should influence the future rational design of SuFEx probes for a multitude of applications in chemical biology and drug discovery.
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Affiliation(s)
- Lyn H Jones
- Center for Protein Degradation , Dana-Farber Cancer Institute , 360 Longwood Avenue , Boston , MA 02215 , USA .
| | - Jeffery W Kelly
- Departments of Chemistry and Molecular Medicine , The Scripps Research Institute , La Jolla , CA , USA
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74
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Abdeldayem A, Raouf YS, Constantinescu SN, Moriggl R, Gunning PT. Advances in covalent kinase inhibitors. Chem Soc Rev 2020; 49:2617-2687. [DOI: 10.1039/c9cs00720b] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This comprehensive review details recent advances, challenges and innovations in covalent kinase inhibition within a 10 year period (2007–2018).
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Affiliation(s)
- Ayah Abdeldayem
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | - Yasir S. Raouf
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | | | - Richard Moriggl
- Institute of Animal Breeding and Genetics
- University of Veterinary Medicine
- 1210 Vienna
- Austria
| | - Patrick T. Gunning
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
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75
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Nikas IP, Themistocleous SC, Paschou SA, Tsamis KI, Ryu HS. Serine-Arginine Protein Kinase 1 (SRPK1) as a Prognostic Factor and Potential Therapeutic Target in Cancer: Current Evidence and Future Perspectives. Cells 2019; 9:cells9010019. [PMID: 31861708 PMCID: PMC7017105 DOI: 10.3390/cells9010019] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 02/06/2023] Open
Abstract
Cancer, a heterogeneous disease composed of tumor cells and microenvironment, is driven by deregulated processes such as increased proliferation, invasion, metastasis, angiogenesis, and evasion of apoptosis. Alternative splicing, a mechanism led by splicing factors, is implicated in carcinogenesis by affecting any of the processes above. Accumulating evidence suggests that serine-arginine protein kinase 1 (SRPK1), an enzyme that phosphorylates splicing factors rich in serine/arginine domains, has a prognostic and potential predictive role in various cancers. Its upregulation is correlated with higher tumor staging, grading, and shorter survival. SRPK1 is also highly expressed in the premalignant changes of some cancers, showing a potential role in the early steps of carcinogenesis. Of interest, its downregulation in preclinical models has mostly been tumor-suppressive and affected diverse processes heterogeneously, depending on the oncogenic context. In addition, targeting SRPK1 has enhanced sensitivity to platinum-based chemotherapy in some cancers. Lastly, its aberrant function has been noted not only in cancer cells but also in the endothelial cells of the microenvironment. Although the aforementioned evidence seems promising, more studies are needed to reinforce the use of SRPK1 inhibitors in clinical trials.
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Affiliation(s)
- Ilias P. Nikas
- School of Medicine, European University Cyprus, 2404 Nicosia, Cyprus; (S.C.T.); (S.A.P.); (K.I.T.)
- Correspondence: ; Tel.: +357-22559633
| | - Sophie C. Themistocleous
- School of Medicine, European University Cyprus, 2404 Nicosia, Cyprus; (S.C.T.); (S.A.P.); (K.I.T.)
| | - Stavroula A. Paschou
- School of Medicine, European University Cyprus, 2404 Nicosia, Cyprus; (S.C.T.); (S.A.P.); (K.I.T.)
- Division of Endocrinology and Diabetes, “Aghia Sophia” Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Konstantinos I. Tsamis
- School of Medicine, European University Cyprus, 2404 Nicosia, Cyprus; (S.C.T.); (S.A.P.); (K.I.T.)
- Neurosurgical Institute, Medical School, University of Ioannina, 45500 Ioannina, Greece
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, 03080 Seoul, Korea;
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76
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Prattapong P, Ngernsombat C, Aimjongjun S, Janvilisri T. CRISPR/Cas9-mediated double knockout of SRPK1 and SRPK2 in a nasopharyngeal carcinoma cell line. Cancer Rep (Hoboken) 2019; 3:e1224. [PMID: 32671994 DOI: 10.1002/cnr2.1224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/22/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Serine-arginine protein kinase (SRPK) is a regulator of alternative splicing events via phosphorylation of splicing factor proteins. Oncogenic roles of SRPK1 and SRPK2 have been reported in various types of cancer. To date, only SRPK1/2 specific inhibitors and small interfering RNA (siRNA) have been used for halting their function momentarily; however, there is no attempt to generate SRPK1/2 stable knockout cancer cells as a tool to investigate their roles in tumorigenesis. AIM Our objective is therefore to establish a nasopharyngeal carcinoma (NPC) cell line with stable SRPK1 or SRPK2 knockout and SRPK1/2 double knockout as a model to investigate their potential roles in NPC. METHODS AND RESULTS CNE1 was selected as a representative of NPC cell lines to create single and double knockout of SRPK1/2 proteins. SRPK1/2 KO plasmid with cas9, green fluorescent protein (GFP), and gRNA expression was cotransfected with SRPK1/2 homology-directed repair (HDR) plasmid containing puromycin resistance, red fluorescent protein (RFP), and 5' and 3' arm sequence for homologous recombination to CNE1 cells. The transfected CNE1 cells with GFP and RFP expression were sorted through fluorescence-activated cell sorting for further treatment with puromycin containing medium. This step generated stable single knockout of SRPK1 and SRPK2. The SRPK2 knockout NPC cells were used as a precursor for double knockout generation via transfection with Cre plasmid for excision of inserted material to generate puromycin-sensitive SRPK2 knockout clone. The puromycin-sensitive SRPK2 knockout cells were transfected with SRPK1 KO/HDR plasmid and treated with puromycin-containing medium. The puromycin-resistant cells of SRPK1/2 stable double knockout were expanded, and the corresponding protein expression was confirmed by western immunoblotting analysis. CONCLUSION Single and double knockout of SRPK1/2 were established using clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated 9 (Cas9) system in an NPC cell line as a model for investigation of their splicing mechanism in NPC.
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Affiliation(s)
- Pongphol Prattapong
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Chawalit Ngernsombat
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sathid Aimjongjun
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
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77
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Recent Advances in Selective and Irreversible Covalent Ligand Development and Validation. Cell Chem Biol 2019; 26:1486-1500. [PMID: 31631011 DOI: 10.1016/j.chembiol.2019.09.012] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/06/2019] [Accepted: 09/26/2019] [Indexed: 12/20/2022]
Abstract
Some of the most widely used drugs, such as aspirin and penicillin, are covalent drugs. Covalent binding can improve potency, selectivity, and duration of the effects, but the intrinsic reactivity represents a potential liability and may result in idiosyncratic toxicity. For decades, the cons were believed to outweigh the pros, and covalent targeting was deprioritized in drug discovery. Recently, several covalent inhibitors have been approved for cancer treatment, thus rebooting the field. In this review, we briefly reflect on the history of selective covalent targeting, and provide a comprehensive overview of emerging developments from a chemical biology stand-point. Our discussion will reflect on efforts to validate irreversible covalent ligands, expand the scope of targets, and discover new ligands and warheads. We conclude with a brief commentary of remaining limitations and emerging opportunities in selective covalent targeting.
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78
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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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79
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Desterro J, Bak-Gordon P, Carmo-Fonseca M. Targeting mRNA processing as an anticancer strategy. Nat Rev Drug Discov 2019; 19:112-129. [PMID: 31554928 DOI: 10.1038/s41573-019-0042-3] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2019] [Indexed: 12/19/2022]
Abstract
Discoveries in the past decade have highlighted the potential of mRNA as a therapeutic target for cancer. Specifically, RNA sequencing revealed that, in addition to gene mutations, alterations in mRNA can contribute to the initiation and progression of cancer. Indeed, precursor mRNA processing, which includes the removal of introns by splicing and the formation of 3' ends by cleavage and polyadenylation, is frequently altered in tumours. These alterations result in numerous cancer-specific mRNAs that generate altered levels of normal proteins or proteins with new functions, leading to the activation of oncogenes or the inactivation of tumour-suppressor genes. Abnormally spliced and polyadenylated mRNAs are also associated with resistance to cancer treatment and, unexpectedly, certain cancers are highly sensitive to the pharmacological inhibition of splicing. This Review summarizes recent progress in our understanding of how splicing and polyadenylation are altered in cancer and highlights how this knowledge has been translated for drug discovery, resulting in the production of small molecules and oligonucleotides that modulate the spliceosome and are in clinical trials for the treatment of cancer.
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Affiliation(s)
- Joana Desterro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Instituto Português de Oncologia de Lisboa, Serviço de Hematologia, Lisboa, Portugal
| | - Pedro Bak-Gordon
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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80
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Huang YM, Wang SM, Leng J, Moku B, Zhao C, Alharbi NS, Qin HL. Converting (E)-(Hetero)arylethanesulfonyl Fluorides to (Z)-(Hetero)arylethanesulfonyl Fluorides Under Light Irradiation. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900799] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yu-Mei Huang
- State Key Laboratory of Silicate Materials for Architectures; and; School of Chemistry, Chemical Engineering and Life Science; Wuhan University of Technology; 430070 Wuhan Hubei Province People's Republic of China
| | - Shi-Meng Wang
- State Key Laboratory of Silicate Materials for Architectures; and; School of Chemistry, Chemical Engineering and Life Science; Wuhan University of Technology; 430070 Wuhan Hubei Province People's Republic of China
| | - Jing Leng
- State Key Laboratory of Silicate Materials for Architectures; and; School of Chemistry, Chemical Engineering and Life Science; Wuhan University of Technology; 430070 Wuhan Hubei Province People's Republic of China
| | - Balakrishna Moku
- State Key Laboratory of Silicate Materials for Architectures; and; School of Chemistry, Chemical Engineering and Life Science; Wuhan University of Technology; 430070 Wuhan Hubei Province People's Republic of China
| | - Chuang Zhao
- State Key Laboratory of Silicate Materials for Architectures; and; School of Chemistry, Chemical Engineering and Life Science; Wuhan University of Technology; 430070 Wuhan Hubei Province People's Republic of China
| | - Njud S. Alharbi
- Biotechnology Research group; Department of Biological Sciences; Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
| | - Hua-Li Qin
- State Key Laboratory of Silicate Materials for Architectures; and; School of Chemistry, Chemical Engineering and Life Science; Wuhan University of Technology; 430070 Wuhan Hubei Province People's Republic of China
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81
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Bowler E, Oltean S. Alternative Splicing in Angiogenesis. Int J Mol Sci 2019; 20:E2067. [PMID: 31027366 PMCID: PMC6540211 DOI: 10.3390/ijms20092067] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/15/2019] [Accepted: 04/23/2019] [Indexed: 12/12/2022] Open
Abstract
Alternative splicing of pre-mRNA allows the generation of multiple splice isoforms from a given gene, which can have distinct functions. In fact, splice isoforms can have opposing functions and there are many instances whereby a splice isoform acts as an inhibitor of canonical isoform function, thereby adding an additional layer of regulation to important processes. Angiogenesis is an important process that is governed by alternative splicing mechanisms. This review focuses on the alternative spliced isoforms of key genes that are involved in the angiogenesis process; VEGF-A, VEGFR1, VEGFR2, NRP-1, FGFRs, Vasohibin-1, Vasohibin-2, HIF-1α, Angiopoietin-1 and Angiopoietin-2.
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Affiliation(s)
- Elizabeth Bowler
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and Health, University of Exeter, Exeter EX4 4PY, UK.
| | - Sebastian Oltean
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and Health, University of Exeter, Exeter EX4 4PY, UK.
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82
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Ray S, Murkin AS. New Electrophiles and Strategies for Mechanism-Based and Targeted Covalent Inhibitor Design. Biochemistry 2019; 58:5234-5244. [PMID: 30990686 DOI: 10.1021/acs.biochem.9b00293] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Covalent inhibitors are experiencing a growing resurgence in drug design and are an increasingly useful tool in molecular biology. The ability to attach inhibitors to their targets by a covalent linkage offers pharmacodynamic and pharmacokinetic advantages, but this can also be a liability if undesired off-target reactions are not mitigated. The discovery of new electrophilic groups that react selectively with specific amino acid residues is therefore highly desirable in the design of targeted covalent inhibitors (TCIs). Additionally, the ability to control the reactivity through exploitation of the target enzyme's machinery, as in mechanism-based inhibitors (MBIs), greatly benefits from the discovery of new strategies. This Perspective showcases recent advances in electrophile development and their application in TCIs and MBIs, exhibiting high selectivity for their targets.
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Affiliation(s)
- Sneha Ray
- Department of Chemistry , University at Buffalo, The State University of New York , Buffalo , New York 14260-3000 , United States
| | - Andrew S Murkin
- Department of Chemistry , University at Buffalo, The State University of New York , Buffalo , New York 14260-3000 , United States
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83
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Gehringer M, Laufer SA. Emerging and Re-Emerging Warheads for Targeted Covalent Inhibitors: Applications in Medicinal Chemistry and Chemical Biology. J Med Chem 2019; 62:5673-5724. [PMID: 30565923 DOI: 10.1021/acs.jmedchem.8b01153] [Citation(s) in RCA: 378] [Impact Index Per Article: 75.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Targeted covalent inhibitors (TCIs) are designed to bind poorly conserved amino acids by means of reactive groups, the so-called warheads. Currently, targeting noncatalytic cysteine residues with acrylamides and other α,β-unsaturated carbonyl compounds is the predominant strategy in TCI development. The recent ascent of covalent drugs has stimulated considerable efforts to characterize alternative warheads for the covalent-reversible and irreversible engagement of noncatalytic cysteine residues as well as other amino acids. This Perspective article provides an overview of warheads-beyond α,β-unsaturated amides-recently used in the design of targeted covalent ligands. Promising reactive groups that have not yet demonstrated their utility in TCI development are also highlighted. Special emphasis is placed on the discussion of reactivity and of case studies illustrating applications in medicinal chemistry and chemical biology.
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Affiliation(s)
- Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry , Eberhard Karls University Tübingen , Auf der Morgenstelle 8 , 72076 Tübingen , Germany
| | - Stefan A Laufer
- Department of Pharmaceutical/Medicinal Chemistry , Eberhard Karls University Tübingen , Auf der Morgenstelle 8 , 72076 Tübingen , Germany
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84
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Patel M, Sachidanandan M, Adnan M. Serine arginine protein kinase 1 (SRPK1): a moonlighting protein with theranostic ability in cancer prevention. Mol Biol Rep 2018; 46:1487-1497. [PMID: 30535769 DOI: 10.1007/s11033-018-4545-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/30/2018] [Indexed: 12/15/2022]
Abstract
Serine/arginine protein kinase 1 (SRPK1); a versatile functional moonlighting protein involved in varied cellular activities comprised of cell cycle progression, innate immune response, chromatin reorganization, negative and positive regulation of viral genome replication, protein amino acid phosphorylation, regulation of numerous mRNA-processing pathways, germ cell development as well as inflammation due to acquaintances with many transcription factors and signaling pathways. Several diseases including cancer have been associated with dysregulation of SRPK1. The function of SRPK1 in cancer is contradictory and inexplicable because it acts as both tumor suppressor and promoter based on the type of cell and locale. Over expression of SRPK1 including its role has been recently narrated and associated with several cancers, which includes, lung, glioma, prostate and breast via dysregulated signals from the Akt/eIF4E/HIF-1/VEGF, Erk or MAPK, PI3K/AKT/mTOR, TGF-β, and Wnt/β-catenin signaling pathways. Therefore, SRPK1 has occurred as a promising and possible curative target in cancer. In recent years, few natural and synthetic SRPK1 inhibitors have been discovered. This review emphasizes and highlights the complicated connections between SRPK1 and oncogenic signaling circuits together with the possibility of aiming SRPK1 in the treatment of cancer.
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Affiliation(s)
- Mitesh Patel
- Department of Biosciences, Bapalal Vaidya Botanical Research Centre, Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - Manojkumar Sachidanandan
- Department of Oral Radiology, College of Dentistry, University of Hail, P O Box 2440, Hail, Saudi Arabia
| | - Mohd Adnan
- Department of Biology, Faculty of Science, University of Hail, P O Box 2440, Hail, Saudi Arabia.
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85
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Antimetastatic effect of the pharmacological inhibition of serine/arginine-rich protein kinases (SRPK) in murine melanoma. Toxicol Appl Pharmacol 2018; 356:214-223. [DOI: 10.1016/j.taap.2018.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/14/2018] [Accepted: 08/17/2018] [Indexed: 02/06/2023]
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86
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Foulkes DM, Byrne DP, Yeung W, Shrestha S, Bailey FP, Ferries S, Eyers CE, Keeshan K, Wells C, Drewry DH, Zuercher WJ, Kannan N, Eyers PA. Covalent inhibitors of EGFR family protein kinases induce degradation of human Tribbles 2 (TRIB2) pseudokinase in cancer cells. Sci Signal 2018; 11:11/549/eaat7951. [PMID: 30254057 DOI: 10.1126/scisignal.aat7951] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A major challenge associated with biochemical and cellular analysis of pseudokinases is a lack of target-validated small-molecule compounds with which to probe function. Tribbles 2 (TRIB2) is a cancer-associated pseudokinase with a diverse interactome, including the canonical AKT signaling module. There is substantial evidence that human TRIB2 promotes survival and drug resistance in solid tumors and blood cancers and therefore is of interest as a therapeutic target. The unusual TRIB2 pseudokinase domain contains a unique cysteine-rich C-helix and interacts with a conserved peptide motif in its own carboxyl-terminal tail, which also supports its interaction with E3 ubiquitin ligases. We found that TRIB2 is a target of previously described small-molecule protein kinase inhibitors, which were originally designed to inhibit the canonical kinase domains of epidermal growth factor receptor tyrosine kinase family members. Using a thermal shift assay, we discovered TRIB2-binding compounds within the Published Kinase Inhibitor Set (PKIS) and used a drug repurposing approach to classify compounds that either stabilized or destabilized TRIB2 in vitro. TRIB2 destabilizing agents, including the covalent drug afatinib, led to rapid TRIB2 degradation in human AML cancer cells, eliciting tractable effects on signaling and survival. Our data reveal new drug leads for the development of TRIB2-degrading compounds, which will also be invaluable for unraveling the cellular mechanisms of TRIB2-based signaling. Our study highlights that small molecule-induced protein down-regulation through drug "off-targets" might be relevant for other inhibitors that serendipitously target pseudokinases.
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Affiliation(s)
- Daniel M Foulkes
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Dominic P Byrne
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Wayland Yeung
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Safal Shrestha
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Fiona P Bailey
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Samantha Ferries
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.,Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Claire E Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.,Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Karen Keeshan
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Scotland, UK
| | - Carrow Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William J Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natarajan Kannan
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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87
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Affiliation(s)
- Praveen K. Chinthakindi
- Department of Medicinal Chemistry; Drug Design and Discovery; Uppsala University; Box 574 SE-75123 Uppsala Sweden
| | - Per I. Arvidsson
- Catalysis and Peptide Research Unit; University of KwaZulu Natal; Durban South Africa
- Science for Life Laboratory, Drug Discovery and Development Platform and Division of Translational Medicine and Chemical Biology; Department of Medical Biochemistry and Biophysics; Karolinska Institutet; Stockholm Sweden
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