1
|
Chitluri KK, Emerson IA. The importance of protein domain mutations in cancer therapy. Heliyon 2024; 10:e27655. [PMID: 38509890 PMCID: PMC10950675 DOI: 10.1016/j.heliyon.2024.e27655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Cancer is a complex disease that is caused by multiple genetic factors. Researchers have been studying protein domain mutations to understand how they affect the progression and treatment of cancer. These mutations can significantly impact the development and spread of cancer by changing the protein structure, function, and signalling pathways. As a result, there is a growing interest in how these mutations can be used as prognostic indicators for cancer prognosis. Recent studies have shown that protein domain mutations can provide valuable information about the severity of the disease and the patient's response to treatment. They may also be used to predict the response and resistance to targeted therapy in cancer treatment. The clinical implications of protein domain mutations in cancer are significant, and they are regarded as essential biomarkers in oncology. However, additional techniques and approaches are required to characterize changes in protein domains and predict their functional effects. Machine learning and other computational tools offer promising solutions to this challenge, enabling the prediction of the impact of mutations on protein structure and function. Such predictions can aid in the clinical interpretation of genetic information. Furthermore, the development of genome editing tools like CRISPR/Cas9 has made it possible to validate the functional significance of mutants more efficiently and accurately. In conclusion, protein domain mutations hold great promise as prognostic and predictive biomarkers in cancer. Overall, considerable research is still needed to better define genetic and molecular heterogeneity and to resolve the challenges that remain, so that their full potential can be realized.
Collapse
Affiliation(s)
- Kiran Kumar Chitluri
- Bioinformatics Programming Lab, Department of Bio-Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India
| | - Isaac Arnold Emerson
- Bioinformatics Programming Lab, Department of Bio-Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India
| |
Collapse
|
2
|
Zhang Y, Lu Y, Wang N, Yang Y, Hao F, Fei X, Chen Y, Wang J. Alternative splicing-related long noncoding RNA ANRIL facilitates hepatocellular carcinoma by targeting the miR-199a-5p/SRSF1 axis and impacting Anillin. Mol Carcinog 2024. [PMID: 38411272 DOI: 10.1002/mc.23709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 01/27/2024] [Accepted: 02/12/2024] [Indexed: 02/28/2024]
Abstract
Hepatocellular carcinoma (HCC) is characterized by aberrant alternative splicing (AS), which plays an important part in the pathological process of this disease. However, available reports about genes and mechanisms involved in AS process are limited. Our previous research has identified ANRIL as a long noncoding RNA related to the AS process of HCC. Here, we investigated the exact effect and the mechanism of ANRIL on HCC progress. The ANRIL expression profile was validated using the real-time quantitative polymerase chain reaction assay. The western blot analysis and IHC assay were conducted on candidate targets, including SRSF1 and Anillin. The clinicopathological features of 97 patients were collected and analyzed. Loss-of and gain-of-function experiments were conducted. The dual-luciferase reporter assay was applied to verify the interaction between ANRIL, miR-199a-5p, and SRSF1. Anomalous upregulation of ANRIL in HCC was observed, correlating with worse clinicopathological features of HCC. HCC cell proliferation, mobility, tumorigenesis, and metastasis were impaired by depleting ANRIL. We found that ANRIL acts as a sponger of miRNA-199a-5p, resulting in an elevated level of its target protein SRSF1. The phenotypes induced by ANRIL/miR-199a-5p/SRSF1 alteration are associated with Anillin, a validated HCC promoter. ANRIL is an AS-related lncRNA promoting HCC progress by modulating the miR-199a-5p/SRSF1 axis. The downstream effector of this axis in the development of HCC is Anillin.
Collapse
Affiliation(s)
- Yifan Zhang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Yiquan Lu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Nan Wang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Yuchen Yang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Fengjie Hao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Xiaochun Fei
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Yongjun Chen
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Junqing Wang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| |
Collapse
|
3
|
Rozza R, Janoš P, Magistrato A. Assessing the Binding Mode of a Splicing Modulator Stimulating Pre-mRNA Binding to the Plastic U2AF2 Splicing Factor. J Chem Inf Model 2023; 63:7508-7517. [PMID: 37967032 DOI: 10.1021/acs.jcim.3c01204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
RNA recognition motifs (RRMs) play a pivotal role in RNA metabolism and the regulation of gene expression. Owing to their plasticity and fuzziness, targeting RRM/RNA interfaces with small molecules is a daunting challenge for drug discovery campaigns. The U2AF2 splicing factor, which recognizes the polypyrimidine (polyPy) sequence of premature messenger (pre-m)RNA, exhibits a dynamic architecture consisting of two RRMs joined by a disordered linker. An inhibitor, NSC-194308, was shown to enhance the binding of pre-mRNA to U2AF2, selectively triggering cell death in leukemia cell lines containing spliceosome mutations. The NSC-194308 binding mode remains elusive; yet, unraveling its knowledge may offer intriguing insights for effectively targeting U2AF2 and other flexible protein/protein/RNA interfaces with small molecules. To infer plausible NSC-194308 binding poses to U2AF2, here, we applied and benchmarked the performance of static and dynamic docking approaches, elucidating the molecular basis of the NSC-194308-induced pre-mRNA stabilization on U2AF2. We demonstrate that introducing dynamic effects is mandatory to assess the binding mode of the inhibitors when they target plastic and modular architectures, such as those formed by interacting RRMs. The latter are widespread across RNA binding proteins; therefore, this mechanism may be broadly applicable to discover new therapeutics aimed at selectively modulating the RNA function by targeting protein/protein/RNA interfaces.
Collapse
Affiliation(s)
- Riccardo Rozza
- National Research Council of Italy (CNR)-Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
| | - Pavel Janoš
- National Research Council of Italy (CNR)-Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy (CNR)-Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
| |
Collapse
|
4
|
Zhang J, Fang Z, Song C. Molecular characteristics and clinical implications of serine/arginine-rich splicing factors in human cancer. Aging (Albany NY) 2023; 15:13287-13311. [PMID: 38015716 DOI: 10.18632/aging.205241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/17/2023] [Indexed: 11/30/2023]
Abstract
As critical splicing regulators, serine/arginine-rich splicing factors (SRSFs) play pivotal roles in carcinogenesis. As dysregulation of SRSFs may confer potential cancer risks, targeting SRSFs could provide important insights into cancer therapy. However, a global and comprehensive pattern to elaborate the molecular characteristics, mechanisms, and clinical links of SRSFs in a wide variety of human cancer is still lacking. In this study, a systematic analysis was conducted to reveal the molecular characteristics and clinical implications of SRSFs covering more than 10000 tumour samples of 33 human cancer types. We found that SRSFs experienced prevalent genomic alterations and expression perturbations in multiple cancer types. The DNA methylation, m6A modification, and miRNA regulation of SRSFs were all cancer context-dependent. Importantly, we found that SRSFs were strongly associated with cancer immunity, and were capable of predicting response to immunotherapy. And SRSFs had colossal potential for predicting survival in multiple cancer types, including those that have received immunotherapy. Moreover, we also found that SRSFs could indicate the drug sensitivity of targeted therapy and chemotherapy. Our research highlights the significance of SRSFs in cancer occurrence and development, and provides sufficient resources for understanding the biological characteristics of SRSFs, offering a new and unique perspective for developing cancer therapeutic strategies.
Collapse
Affiliation(s)
- Jinjin Zhang
- Department of Emergency Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Zhicheng Fang
- Department of Emergency Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Congkuan Song
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| |
Collapse
|
5
|
Ning X, Fu Z, Zhang J, Gao S, Cui Z, Cong M, Guo Q, Sun X, Li J, Zhang M, Wang S. The role of alternative splicing in lung cancer. Cancer Chemother Pharmacol 2023; 92:83-95. [PMID: 37335335 DOI: 10.1007/s00280-023-04553-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/12/2023] [Indexed: 06/21/2023]
Abstract
Aberrant alternative splicing (AS) events are frequently observed in lung cancer, which can be attributed to aberrant gene AS, alterations in splicing regulatory factors, or changes in splicing regulatory mechanisms. Consequently, the dysregulation of alternative RNA splicing is the fundamental cause of lung cancer. In this review, we have summarized the pivotal role of AS in the development, progression, invasion, metastasis, angiogenesis, and drug resistance of lung cancer. Ultimately, this review emphasizes the potential of AS as biomarkers in lung cancer prognosis and diagnosis, and introduces some applications of AS isoform in the treatment of lung cancer. The comprehension of the AS may provide a glimmer of hope for the eradication of lung cancer.
Collapse
Affiliation(s)
- Xuelian Ning
- Department of Pathology, Harbin Medical University, No.157 Baojian Road, Nangang District, Harbin, 150081, China
| | - Zitong Fu
- Department of Pathology, Harbin Medical University, No.157 Baojian Road, Nangang District, Harbin, 150081, China
| | - Jing Zhang
- Department of Oncology, Chifeng Municipal Hospital, No.1 Zhaowuda Road, Chifeng, 024000, China
| | - Shuangshu Gao
- Department of Pathology, Harbin Medical University, No.157 Baojian Road, Nangang District, Harbin, 150081, China
| | - Zihan Cui
- Department of Pathology, Harbin Medical University, No.157 Baojian Road, Nangang District, Harbin, 150081, China
| | - Mingqi Cong
- Department of Pathology, Harbin Medical University, No.157 Baojian Road, Nangang District, Harbin, 150081, China
| | - Qingyu Guo
- Department of Pathology, Harbin Medical University, No.157 Baojian Road, Nangang District, Harbin, 150081, China
| | - Xixi Sun
- Department of Pathology, Harbin Medical University, No.157 Baojian Road, Nangang District, Harbin, 150081, China
| | - Jing Li
- Department of Pathology, Harbin Medical University, No.157 Baojian Road, Nangang District, Harbin, 150081, China
| | - Minghui Zhang
- Department of Oncology, Chifeng Municipal Hospital, No.1 Zhaowuda Road, Chifeng, 024000, China.
| | - Shuoshuo Wang
- Department of Pathology, Harbin Medical University, No.157 Baojian Road, Nangang District, Harbin, 150081, China.
| |
Collapse
|
6
|
Sato S, Ariga H, Maita H. Development of a Cell-Based Assay Using a Split-Luciferase Reporter for Compound Screening. Biol Pharm Bull 2023; 46:1010-1014. [PMID: 37394631 DOI: 10.1248/bpb.b23-00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Recently, the finding of recurrent mutations in the spliceosome components in cancer has indicated that the spliceosome is a potential target for cancer therapy. However, the number of small molecules known to affect the cellular spliceosome is currently limited probably because of the lack of a robust cell-based approach to identify small molecules that target the spliceosome. We have previously reported the development of a genetic reporter to detect the cellular levels of small nuclear ribonucleoproteins (snRNPs), which are subunits of the spliceosome, using a split luciferase. However, the original protocol was designed for small scale experiments and was not suitable for compound screening. Here, we found that the use of cell lysis buffer used in blue native polyacrylamide gel electrophoresis (BN-PAGE) dramatically improved the sensitivity and the robustness of the assay. Improved assay conditions were used to discover a small molecule that altered the reporter activity. Our method may be used with other cellular macromolecular complexes and may assist in the discovery of small bioactive molecules.
Collapse
Affiliation(s)
- Satoshi Sato
- Faculty of Pharmaceutical Sciences, Hokkaido University
| | - Hiroyoshi Ariga
- Faculty of Pharmaceutical Sciences, Hokkaido University
- Graduate School of Life Science, Hokkaido University
| | - Hiroshi Maita
- Faculty of Pharmaceutical Sciences, Hokkaido University
- Graduate School of Life Science, Hokkaido University
| |
Collapse
|
7
|
Liu M, Guo J, Jia R. Emerging roles of alternative RNA splicing in oral squamous cell carcinoma. Front Oncol 2022; 12:1019750. [PMID: 36505770 PMCID: PMC9732560 DOI: 10.3389/fonc.2022.1019750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
Alternative RNA splicing (ARS) is an essential and tightly regulated cellular process of post-transcriptional regulation of pre-mRNA. It produces multiple isoforms and may encode proteins with different or even opposite functions. The dysregulated ARS of pre-mRNA contributes to the development of many cancer types, including oral squamous cell carcinoma (OSCC), and may serve as a biomarker for the diagnosis and prognosis of OSCC and an attractive therapeutic target. ARS is mainly regulated by splicing factors, whose expression is also often dysregulated in OSCC and involved in tumorigenesis. This review focuses on the expression and roles of splicing factors in OSCC, the alternative RNA splicing events associated with OSCC, and recent advances in therapeutic approaches that target ARS.
Collapse
Affiliation(s)
- Miaomiao Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jihua Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China,Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan, China,*Correspondence: Jihua Guo, ; Rong Jia,
| | - Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China,RNA Institute, Wuhan University, Wuhan, China,*Correspondence: Jihua Guo, ; Rong Jia,
| |
Collapse
|
8
|
Tang J, Xie Y, Huang J, Zhang L, Jiang W, Li Z, Bian J. A critical update on the strategies towards small molecule inhibitors targeting Serine/arginine-rich (SR) proteins and Serine/arginine-rich proteins related kinases in alternative splicing. Bioorg Med Chem 2022; 70:116921. [PMID: 35863237 DOI: 10.1016/j.bmc.2022.116921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022]
Abstract
>90% of genes in the human body undergo alternative splicing (AS) after transcription, which enriches protein species and regulates protein levels. However, there is growing evidence that various genetic isoforms resulting from dysregulated alternative splicing are prevalent in various types of cancers. Dysregulated alternative splicing leads to cancer generation and maintenance of cancer properties such as proliferation differentiation, apoptosis inhibition, invasion metastasis, and angiogenesis. Serine/arginine-rich proteins and SR protein-associated kinases mediate splice site recognition and splice complex assembly during variable splicing. Based on the impact of dysregulated alternative splicing on disease onset and progression, the search for small molecule inhibitors targeting alternative splicing is imminent. In this review, we discuss the structure and specific biological functions of SR proteins and describe the regulation of SR protein function by SR protein related kinases meticulously, which are closely related to the occurrence and development of various types of cancers. On this basis, we summarize the reported small molecule inhibitors targeting SR proteins and SR protein related kinases from the perspective of medicinal chemistry. We mainly categorize small molecule inhibitors from four aspects, including targeting SR proteins, targeting Serine/arginine-rich protein-specific kinases (SRPKs), targeting Cdc2-like kinases (CLKs) and targeting dual-specificity tyrosine-regulated kinases (DYRKs), in terms of structure, inhibition target, specific mechanism of action, biological activity, and applicable diseases. With this review, we are expected to provide a timely summary of recent advances in alternative splicing regulated by kinases and a preliminary introduction to relevant small molecule inhibitors.
Collapse
|
9
|
Maul-Newby HM, Amorello AN, Sharma T, Kim JH, Modena MS, Prichard BE, Jurica MS. A model for DHX15 mediated disassembly of A-complex spliceosomes. RNA 2022; 28:583-595. [PMID: 35046126 PMCID: PMC8925973 DOI: 10.1261/rna.078977.121] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
A critical step of pre-mRNA splicing is the recruitment of U2 snRNP to the branch point sequence of an intron. U2 snRNP conformation changes extensively during branch helix formation, and several RNA-dependent ATPases are implicated in the process. However, the molecular mechanisms involved remain to be fully dissected. We took advantage of the differential nucleotide triphosphates requirements for DExD/H-box enzymes to probe their contributions to in vitro spliceosome assembly. Both ATP and GTP hydrolysis support the formation of A-complex, indicating the activity of a DEAH-enzyme because DEAD-enzymes are selective for ATP. We immunodepleted DHX15 to assess its involvement, and although splicing efficiency decreases with reduced DHX15, A-complex accumulation incongruently increases. DHX15 depletion also results in the persistence of the atypical ATP-independent interaction between U2 snRNP and a minimal substrate that is otherwise destabilized in the presence of either ATP or GTP. These results lead us to hypothesize that DHX15 plays a quality control function in U2 snRNP's engagement with an intron. In efforts to identify the RNA target of DHX15, we determined that an extended polypyrimidine tract is not necessary for disruption of the atypical interaction between U2 snRNP and the minimal substrate. We also examined U2 snRNA by RNase H digestion and identified nucleotides in the branch binding region that become accessible with both ATP and GTP hydrolysis, again implicating a DEAH-enzyme. Together, our results demonstrate that multiple ATP-dependent rearrangements are likely involved in U2 snRNP addition to the spliceosome and that DHX15 may have an expanded role in maintaining splicing fidelity.
Collapse
Affiliation(s)
- Hannah M Maul-Newby
- Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Angela N Amorello
- Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Turvi Sharma
- Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - John H Kim
- Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Matthew S Modena
- Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Beth E Prichard
- Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Melissa S Jurica
- Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| |
Collapse
|
10
|
Osadska M, Selicky T, Kretova M, Jurcik J, Sivakova B, Cipakova I, Cipak L. The Interplay of Cohesin and RNA Processing Factors: The Impact of Their Alterations on Genome Stability. Int J Mol Sci 2022; 23:3939. [PMID: 35409298 PMCID: PMC8999970 DOI: 10.3390/ijms23073939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 12/01/2022] Open
Abstract
Cohesin, a multi-subunit protein complex, plays important roles in sister chromatid cohesion, DNA replication, chromatin organization, gene expression, transcription regulation, and the recombination or repair of DNA damage. Recently, several studies suggested that the functions of cohesin rely not only on cohesin-related protein-protein interactions, their post-translational modifications or specific DNA modifications, but that some RNA processing factors also play an important role in the regulation of cohesin functions. Therefore, the mutations and changes in the expression of cohesin subunits or alterations in the interactions between cohesin and RNA processing factors have been shown to have an impact on cohesion, the fidelity of chromosome segregation and, ultimately, on genome stability. In this review, we provide an overview of the cohesin complex and its role in chromosome segregation, highlight the causes and consequences of mutations and changes in the expression of cohesin subunits, and discuss the RNA processing factors that participate in the regulation of the processes involved in chromosome segregation. Overall, an understanding of the molecular determinants of the interplay between cohesin and RNA processing factors might help us to better understand the molecular mechanisms ensuring the integrity of the genome.
Collapse
Affiliation(s)
- Michaela Osadska
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Tomas Selicky
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Miroslava Kretova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Jan Jurcik
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Barbara Sivakova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 845 38 Bratislava, Slovakia;
| | - Ingrid Cipakova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Lubos Cipak
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| |
Collapse
|
11
|
Neil CR, Seiler MW, Reynolds DJ, Smith JJ, Vaillancourt FH, Smith PG, Agrawal AA. Reprogramming RNA processing: an emerging therapeutic landscape. Trends Pharmacol Sci 2022:S0165-6147(22)00046-3. [PMID: 35331569 DOI: 10.1016/j.tips.2022.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/13/2022]
Abstract
The production of a mature mRNA requires coordination of multiple processing steps, which ultimately control its content, localization, and stability. These steps include some of the largest macromolecular machines in the cell, which were, until recently, considered undruggable due to their biological complexity. Building from an expanded understanding of the underlying mechanisms that drive these processes, a new wave of therapeutics is seeking to target RNA processing. With a focus on impacting gene regulation at the RNA level, such modalities offer potential for sequence-specific resolution in drug design. Here, we review our current understanding of RNA-processing events and their role in gene regulation, with a focus on the therapeutic opportunities that have emerged within this landscape.
Collapse
|
12
|
Tang X, Deng Z, Ding P, Qiang W, Lu Y, Gao S, Hu Y, Yang Y, Du J, Gu C. A novel protein encoded by circHNRNPU promotes multiple myeloma progression by regulating the bone marrow microenvironment and alternative splicing. J Exp Clin Cancer Res 2022; 41:85. [PMID: 35260179 PMCID: PMC8903708 DOI: 10.1186/s13046-022-02276-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/27/2022] [Indexed: 12/11/2022]
Abstract
Backgroud Multiple myeloma (MM) is an incurable plasma cell malignancy in the bone marrow (BM), while immunoglobulin D type of MM (IgD MM) is a very rare but most severe subtype in all MM cases. Therefore, systemic study on IgD MM is purposeful to disclose the recurrent and refractory features in both IgD and other types of MM, and beneficial to the development of potent therapeutic strategy on MM. Methods Agilent SBC-ceRNA microarray chips were employed to examine 3 normal plasma cell samples (NPCs), 5 lgD MM samples and 5 lgG MM samples, respectively. Sanger sequencing, RNase R digestion and qPCR assays were used to detect the existence and expression of circHNRNPU. BaseScope™ RNA ISH assay was performed to test circHNRNPU levels in paraffin-embedded MM tissues. The protein encoded by circHNRNPU was identified by LC-MS/MS, which was named as circHNRNPU_603aa. The function of circHNRNPU_603aa on cellular proliferation and cell cycle was assessed by MTT test, colony formation assay, flow cytometry and MM xenograft mouse model in vivo. RIP-seq, RIP-PCR and WB analysis for ubiquitination were performed to explore the potential mechanism of circHNRNPU_603aa in MM. Exosomes were isolated from the culture supernatant of MM cells by ultracentrifugation and characterized by Transmission Electron Microscope and WB confirmation of exosomes markers Alix and CD9. Results CircHNRNPU was one of the top most abundant and differentially expressed circRNA in IgD MM relative to lgG and NPCs samples. Increased circHNRNPU was associated with poor outcomes in four independent MM patient cohorts. Intriguingly, MM cells secreted circHNRNPU, which encoded a protein named as circHNRNPU_603aa. Overexpressed circHNRNPU_603aa promoted MM cell proliferation in vitro and in vivo, in contrast knockdown of circHNRNPU_603aa by siRNA abrogated these effects. Due to circHNRNPU_603aa including RNA-binding RGG-box region, it regulated SKP2 exon skipping, thereby competitively inhibited c-Myc ubiquitin so as to stabilize c-Myc in MM. MM cells secreted circHNRNPU through exosomes to interfere with various cells in the BM microenvironment. Conclusion Our findings demonstrate that circHNRNPU_603aa is a promising diagnostic and therapeutic marker in both MM cells and BM niche. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02276-7.
Collapse
Affiliation(s)
- Xiaozhu Tang
- Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing, China.,School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhendong Deng
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Pinggang Ding
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wanting Qiang
- Department of Hematology, Myeloma & Lymphoma Center, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yue Lu
- Department of Radiotherapy, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Shengyao Gao
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ye Hu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ye Yang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Juan Du
- Department of Hematology, Myeloma & Lymphoma Center, Changzheng Hospital, Naval Medical University, Shanghai, China.
| | - Chunyan Gu
- Nanjing Hospital of Chinese Medicine affiliated to Nanjing University of Chinese Medicine, Nanjing, China. .,School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| |
Collapse
|
13
|
Guo C, Li H, Pan N, Xu S, Zeng Q, Zhou B, Wang J. Identification of prognostic signature with seven LncRNAs for papillary thyroid carcinoma. Adv Med Sci 2022; 67:103-13. [PMID: 35121283 DOI: 10.1016/j.advms.2021.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/15/2021] [Accepted: 11/01/2021] [Indexed: 12/24/2022]
Abstract
PURPOSE With the increasing incidence of thyroid cancer (TC), the prognostic risk assessment of thyroid cancer has been becoming more and more important. The aim of this study was to screen TC-related biomarkers and identify key multi-long non coding RNA (lncRNA) signature for prognostic risk assessment of papillary TC. MATERIAL AND METHODS The lncRNAs differentially expressed between TC tissue and adjacent normal tissue was identified by R language. Bioinformatics analysis was applied to screen the lncRNAs significantly associated with prognosis in TC patients and build the multi-lncRNA signature. The lncRNAs were annotated by co-expression and enrichment analysis to demonstrate the underlying mechanism of their effect on prognosis. RESULTS 285 up-regulated and 174 down-regulated differently expressed lncRNAs were identified. Based on seven signature lncRNAs (AL591846.2, AC253536.3, AC004112.1, LINC00900, AC008555.1, TNRC6C-AS1, LINC01736) a prognostic risk assessment model was built. The model can segregate the patients into the high-risk and low-risk groups (P value <0.0001, CI: 0.02∼0.14). ROC analysis revealed that the area under the curve reached 0.86, indicating that this model had an excellent sensitivity and specificity. Also, the model could act as an independent prognostic indication (HR = 2.90, P value = 0.0094 with multivariate analysis). Annotation results further supported and enriched our understanding of the seven signature lncRNAs. Importantly, expression levels of three of the seven lncRNAs were confirmed in Gene Expression Omnibus (GEO) data. CONCLUSIONS This study has provided a promising method for the prognostic risk assessment in patients with TC.
Collapse
|
14
|
Zhang Y, Yu X, Sun R, Min J, Tang X, Lin Z, Xie S, Li X, Lu S, Tian Z, Gu C, Teng L, Yang Y. Splicing factor arginine/serine‐rich 8 promotes multiple myeloma malignancy and bone lesion through alternative splicing of CACYBP and exosome‐based cellular communication. Clin Transl Med 2022; 12:e684. [PMID: 35184390 PMCID: PMC8858635 DOI: 10.1002/ctm2.684] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 12/21/2022] Open
Abstract
Background Multiple myeloma (MM) is a distinctive malignancy of plasma cell within the bone marrow (BM), of which alternative splicing factors play vital roles in the progression. Splicing factor arginine/serine‐rich 8 (SFRS8) is the exclusive factor associated with MM prognosis, however its role in MM remains undefined. Methods The analyses of 3‐(4,5)‐dimethylthiahiazo (‐z‐y1)‐3,5‐di‐ phenytetrazoliumromide (MTT) assay, immunohistochemistry, flow cytometry and xenograft model were performed to examine cell proliferation, cell cycle and apoptosis in SFRS8 overexpression or knockdown MM cells in vitro and in vivo. The SFRS8‐regulated alternative splicing events were identified by RNA immunoprecipitation sequencing (RIP‐seq) and validated by RIP‐qPCR and Co‐IP methods. Exosomes were extracted from the supernatant of myeloma cells by ultracentrifugation. Bone lesion was evaluated by TRAP staining in vitro and SCID/NOD‐TIBIA mouse model. A neon electroporation system was utilised to deliver siRNA through exosomes. The effect of siRNA‐loaded exosomes in vivo was evaluated by using a patient‐derived tumor xenograft (PDX) model and SCID/NOD‐TIBIA mouse model. Results SFRS8 was significantly upregulated in MM samples and positively associated with poor overall survival (OS) in MM patients. SFRS8 promoted MM cell proliferation in vitro and in vivo. Furthermore, calcyclin binding protein (CACYBP) was identified as the downstream target of SFRS8. Particularly, SFRS8 could reduce CACYBP isoform1 (NM_014412.3) and increase CACYBP isoform2 (NM_001007214.1) by mediating the alternative splicing of CACYBP, thereby altering the ubiquitination degradation of β‐catenin to promote MM progression. In addition, SFRS8 promoted osteoclast differentiation through exosomes in vitro and in vivo. More importantly, exosomal siRNA targeting CACYBP isoform2 inhibited tumour growth in PDX and SCID/NOD‐TIBIA mouse models. Conclusion Our findings demonstrate that targeting the SFRS8/CACYBP/β‐catenin axis may be a promising strategy for MM diagnosis and treatment.
Collapse
Affiliation(s)
- Yuanjiao Zhang
- Nanjing Hospital of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
| | - Xichao Yu
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
| | - Rongze Sun
- School of Life Science Jilin University Changchun China
| | - Jie Min
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
| | - Xiaozhu Tang
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
| | - Zigen Lin
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
| | - Siyuan Xie
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
| | - Xinying Li
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
| | - Shengfeng Lu
- Key Laboratory of A cupuncture and Medicine Research of Ministry of Education Nanjing University of Chinese Medicine Nanjing China
| | - Zhidan Tian
- Department of Pathology, Nanjing First Hospital Nanjing Medical University Nanjing China
| | - Chunyan Gu
- Nanjing Hospital of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
| | - Lesheng Teng
- School of Life Science Jilin University Changchun China
| | - Ye Yang
- School of Medicine & Holistic Integrative Medicine Nanjing University of Chinese Medicine Nanjing China
- Key Laboratory of A cupuncture and Medicine Research of Ministry of Education Nanjing University of Chinese Medicine Nanjing China
| |
Collapse
|
15
|
Cao J, Zhang R, Zhang Y, Wang Y. Combined screening analysis of aberrantly methylated-differentially expressed genes and pathways in hepatocellular carcinoma. J Gastrointest Oncol 2022; 13:311-325. [PMID: 35284134 PMCID: PMC8899745 DOI: 10.21037/jgo-21-866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/30/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Methylation plays an important role in hepatocellular carcinoma (HCC) by altering the expression of key genes. The aim of this study was to screen the aberrantly methylated-differentially expressed genes (DEGs) in HCC and elucidate their underlying molecular mechanism. METHODS Gene expression microarrays (GSE101685) and gene methylation microarrays (GSE44909) were selected. DEGs and differentially methylated genes (DMGs) were screened. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using the Database for Annotation, Visualization, and Integrated discovery (DAVID). The Search Tool for the Retrieval of Interacting Genes (STRING) database was used to analyze the functional protein-protein interaction (PPI) network. Molecular Complex Detection (MCODE) analysis was performed using the Cytoscape software. Hub genes were verified in The Cancer Genome Atlas (TCGA) database. RESULTS A total of 80 hypomethylation-high expression genes (Hypo-HGs) were identified. Pathway enrichment analysis showed DNA replication, cell cycle, viral carcinogenesis, and the spliceosome. The top 5 hub genes were minichromosome maintenance complex component 3 (MCM3), checkpoint kinase 1 (CHEK1), kinesin family member 11 (KIF11), PDZ binding kinase (PBK), and Rac GTPase activating protein 1 (RACGAP1). In addition, 189 hypermethylation-low expression genes (Hyper-LGs) were identified. Pathway enrichment analysis indicated enrichment in metabolic pathways, drug metabolism-other enzymes, and chemical carcinogenesis. The top 5 hub genes were leukocyte immunoglobulin like receptor B2 (LILRB2), formyl peptide receptor 1 (FPR1), S100 calcium binding protein A9 (S100A9), S100 calcium binding protein A8 (S100A8), and myeloid cell nuclear differentiation antigen (MNDA). The methylation status and mRNA expression of MCM3, CHEK1, KIF11, PBK, and S100A9 were consistent in the TCGA database and significantly correlated with the prognosis of patients. CONCLUSIONS Combined screening of aberrantly methylated-DEGs based on bioinformatic analysis may provide new clues for elucidating the epigenetic mechanism in HCC. Hub genes, including MCM3, CHEK1, KIF11, PBK, and S100A9, may serve as biomarkers for the precise diagnosis of HCC.
Collapse
Affiliation(s)
- Jisen Cao
- Department of Hepatobiliary Surgery, The Third Central Hospital of Tianjin, Tianjin, China
| | - Ruiqiang Zhang
- Department of Orthopedics, General Hospital of Tianjin Medical University, Tianjin, China
| | - Ye Zhang
- Department of Hepatobiliary Surgery, The Third Central Hospital of Tianjin, Tianjin, China
| | - Yijun Wang
- Department of Hepatobiliary Surgery, The Third Central Hospital of Tianjin, Tianjin, China
| |
Collapse
|
16
|
Spinello A, Borišek J, Malcovati L, Magistrato A. Investigating the Molecular Mechanism of H3B-8800: A Splicing Modulator Inducing Preferential Lethality in Spliceosome-Mutant Cancers. Int J Mol Sci 2021; 22:ijms222011222. [PMID: 34681880 PMCID: PMC8540225 DOI: 10.3390/ijms222011222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022] Open
Abstract
The SF3B1 protein, part of the SF3b complex, recognizes the intron branch point sequence of precursor messenger RNA (pre-mRNA), thus contributing to splicing fidelity. SF3B1 is frequently mutated in cancer and is the target of distinct families of splicing modulators (SMs). Among these, H3B-8800 is of particular interest, as it induces preferential lethality in cancer cells bearing the frequent and highly pathogenic K700E SF3B1 mutation. Despite the potential of H3B-8800 to treat myeloid leukemia and other cancer types hallmarked by SF3B1 mutations, the molecular mechanism underlying its preferential lethality towards spliceosome-mutant cancer cells remains elusive. Here, microsecond-long all-atom simulations addressed the binding/dissociation mechanism of H3B-8800 to wild type and K700E SF3B1-containing SF3b (K700ESB3b) complexes at the atomic level, unlocking that the K700E mutation little affects the thermodynamics and kinetic traits of H3B-8800 binding. This supports the hypothesis that the selectivity of H3B-8800 towards mutant cancer cells is unrelated to its preferential targeting of K700ESB3b. Nevertheless, this set of simulations discloses that the K700E mutation and H3B-8800 binding affect the overall SF3b internal motion, which in turn may influence the way SF3b interacts with other spliceosome components. Finally, we unveil the existence of a putative druggable SF3b pocket in the vicinity of K700E that could be harnessed in future rational drug-discovery efforts to specifically target mutant SF3b.
Collapse
Affiliation(s)
- Angelo Spinello
- National Research Council of Italy, Institute of Materials Foundry (CNR-IOM) c/o SISSA, Via Bonomea 265, 34136 Trieste, Italy;
| | - Jure Borišek
- National Institute of Chemistry, Theory Department, Hajdrihova 19, 1000 Ljubljana, Slovenia;
| | - Luca Malcovati
- Department of Hematology, IRCCS S. Matteo Hospital Foundation, 27100 Pavia, Italy;
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
| | - Alessandra Magistrato
- National Research Council of Italy, Institute of Materials Foundry (CNR-IOM) c/o SISSA, Via Bonomea 265, 34136 Trieste, Italy;
- Correspondence:
| |
Collapse
|
17
|
Abstract
In this issue of Cell Chemical Biology, Chatrikhi et al. (2021) identify a small molecule that enhances U2AF2 association with RNA to block pre-mRNA splicing during early stages of spliceosome assembly. This provides a mechanism of splicing inhibition and a molecular tool for elucidating intron recognition and spliceosome assembly.
Collapse
Affiliation(s)
- Sierra L Love
- Department of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA; Graduate Training Program in Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aaron A Hoskins
- Graduate Training Program in Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| |
Collapse
|
18
|
Cheng C, Liu L, Bao Y, Yi J, Quan W, Xue Y, Sun L, Zhang Y. SUVA: splicing site usage variation analysis from RNA-seq data reveals highly conserved complex splicing biomarkers in liver cancer. RNA Biol 2021; 18:157-171. [PMID: 34152934 DOI: 10.1080/15476286.2021.1940037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Most of the current alternative splicing (AS) analysis tools are powerless to analyse complex splicing. To address this, we developed SUVA (Splice sites Usage Variation Analysis) that decomposes complex splicing events into five types of splice junction pairs. By analysing real and simulated data, SUVA showed higher sensitivity and accuracy in detecting AS events than the compared methods. Notably, SUVA detected extensive complex AS events and screened out 69 highly conserved and dominant AS events associated with cancer. The cancer-associated complex AS events in FN1 and the co-regulated RNA-binding proteins were significantly correlated with patient survival.
Collapse
Affiliation(s)
- Chao Cheng
- ABLife BioBigData Institute, Wuhan, Hubei China.,Center for Genome Analysis, ABLife Inc., Wuhan, Hubei China
| | - Lei Liu
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun China
| | - Yongli Bao
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun China
| | - Jingwen Yi
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun China
| | - Weili Quan
- ABLife BioBigData Institute, Wuhan, Hubei China
| | - Yaqiang Xue
- ABLife BioBigData Institute, Wuhan, Hubei China
| | - Luguo Sun
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun China
| | - Yi Zhang
- ABLife BioBigData Institute, Wuhan, Hubei China.,Center for Genome Analysis, ABLife Inc., Wuhan, Hubei China
| |
Collapse
|
19
|
El Marabti E, Abdel-Wahab O. Therapeutic Modulation of RNA Splicing in Malignant and Non-Malignant Disease. Trends Mol Med 2021; 27:643-659. [PMID: 33994320 DOI: 10.1016/j.molmed.2021.04.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 01/24/2023]
Abstract
RNA splicing is the enzymatic process by which non-protein coding sequences are removed from RNA to produce mature protein-coding mRNA. Splicing is thereby a major mediator of proteome diversity as well as a dynamic regulator of gene expression. Genetic alterations disrupting splicing of individual genes or altering the function of splicing factors contribute to a wide range of human genetic diseases as well as cancer. These observations have resulted in the development of therapies based on oligonucleotides that bind to RNA sequences and modulate splicing for therapeutic benefit. In parallel, small molecules that bind to splicing factors to alter their function or modify RNA processing of individual transcripts are being pursued for monogenic disorders as well as for cancer.
Collapse
Affiliation(s)
- Ettaib El Marabti
- Clinical Transplant Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| |
Collapse
|
20
|
Dlamini Z, Alaouna M, Mbatha S, Bhayat A, Mabongo M, Chatziioannou A, Hull R. Genetic Drivers of Head and Neck Squamous Cell Carcinoma: Aberrant Splicing Events, Mutational Burden, HPV Infection and Future Targets. Genes (Basel) 2021; 12:422. [PMID: 33804181 DOI: 10.3390/genes12030422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/16/2021] [Accepted: 03/11/2021] [Indexed: 12/15/2022] Open
Abstract
Head and neck cancers include cancers that originate from a variety of locations. These include the mouth, nasal cavity, throat, sinuses, and salivary glands. These cancers are the sixth most diagnosed cancers worldwide. Due to the tissues they arise from, they are collectively named head and neck squamous cell carcinomas (HNSCC). The most important risk factors for head and neck cancers are infection with human papillomavirus (HPV), tobacco use and alcohol consumption. The genetic basis behind the development and progression of HNSCC includes aberrant non-coding RNA levels. However, one of the most important differences between healthy tissue and HNSCC tissue is changes in the alternative splicing of genes that play a vital role in processes that can be described as the hallmarks of cancer. These changes in the expression profile of alternately spliced mRNA give rise to various protein isoforms. These protein isoforms, alternate methylation of proteins, and changes in the transcription of non-coding RNAs (ncRNA) can be used as diagnostic or prognostic markers and as targets for the development of new therapeutic agents. This review aims to describe changes in alternative splicing and ncRNA patterns that contribute to the development and progression of HNSCC. It will also review the use of the changes in gene expression as biomarkers or as the basis for the development of new therapies.
Collapse
|
21
|
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.
Collapse
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.
| |
Collapse
|
22
|
Choi HY, Jo H, Zhao X, Hoadley KA, Newman S, Holt J, Hayward MC, Love MI, Marron JS, Hayes DN. SCISSOR: a framework for identifying structural changes in RNA transcripts. Nat Commun 2021; 12:286. [PMID: 33436599 PMCID: PMC7804101 DOI: 10.1038/s41467-020-20593-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/02/2020] [Indexed: 02/08/2023] Open
Abstract
High-throughput sequencing protocols such as RNA-seq have made it possible to interrogate the sequence, structure and abundance of RNA transcripts at higher resolution than previous microarray and other molecular techniques. While many computational tools have been proposed for identifying mRNA variation through differential splicing/alternative exon usage, challenges in its analysis remain. Here, we propose a framework for unbiased and robust discovery of aberrant RNA transcript structures using short read sequencing data based on shape changes in an RNA-seq coverage profile. Shape changes in selecting sample outliers in RNA-seq, SCISSOR, is a series of procedures for transforming and normalizing base-level RNA sequencing coverage data in a transcript independent manner, followed by a statistical framework for its analysis ( https://github.com/hyochoi/SCISSOR ). The resulting high dimensional object is amenable to unsupervised screening of structural alterations across RNA-seq cohorts with nearly no assumption on the mutational mechanisms underlying abnormalities. This enables SCISSOR to independently recapture known variants such as splice site mutations in tumor suppressor genes as well as novel variants that are previously unrecognized or difficult to identify by any existing methods including recurrent alternate transcription start sites and recurrent complex deletions in 3' UTRs.
Collapse
Affiliation(s)
- Hyo Young Choi
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- UTHSC Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heejoon Jo
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- UTHSC Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Xiaobei Zhao
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- UTHSC Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Katherine A Hoadley
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Scott Newman
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeremiah Holt
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Michele C Hayward
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - J S Marron
- Department of Statistics and Operations Research, University of North Carolina, Chapel Hill, NC, USA
| | - D Neil Hayes
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA.
- UTHSC Center for Cancer Research, University of Tennessee Health Science Center, Memphis, TN, USA.
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| |
Collapse
|
23
|
Abstract
In this chapter, the essential role of the SF3b multi-protein complex will be discussed in the context of the overall spliceosome. SF3b is critical during spliceosome assembly for recognition of the branch point (BP) adenosine and, by de facto, selection of the 3' splice site. This complex is highly dynamic, undergoing significant conformational changes upon loading of the branch duplex RNA and in its relative positioning during spliceosomal remodeling from the A, pre-B, B, Bact and B* complexes. Ultimately, during the spliceosome activation phase, SF3b must be displaced to unmask the branch point adenosine for the first splicing reaction to occur. In certain cancers, such as the hematological malignancies CML, CLL and MDS, the SF3b subunit SF3B1 is frequently mutated. Recent studies suggest these mutations lead to inappropriate branch point selection and mis-splicing events that appear to be drivers of disease. Finally, the SF3b complex is the target for at least three different classes of natural product-based inhibitors. These inhibitors bind in the BP adenosine-binding pocket and demonstrate a pre-mRNA competitive mechanism of action resulting in either intron retention or exon skipping. These compounds are extremely useful as chemical probes to isolate and characterize early stages of spliceosome assembly. They are also being explored preclinically and clinically as possible agents for hematological cancers.
Collapse
|
24
|
Abstract
While the processing of mRNA is essential for gene expression, recent findings have highlighted that RNA processing is systematically altered in cancer. Mutations in RNA splicing factor genes and the shortening of 3' untranslated regions are widely observed. Moreover, evidence is accumulating that other types of RNAs, including circular RNAs, can contribute to tumorigenesis. In this Review, we highlight how altered processing or activity of coding and non-coding RNAs contributes to cancer. We introduce the regulation of gene expression by coding and non-coding RNA and discuss both established roles (microRNAs and long non-coding RNAs) and emerging roles (selective mRNA processing and circular RNAs) for RNAs, highlighting the potential mechanisms by which these RNA subtypes contribute to cancer. The widespread alteration of coding and non-coding RNA demonstrates that altered RNA biogenesis contributes to multiple hallmarks of cancer.
Collapse
Affiliation(s)
- Gregory J Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia.
- Department of Medicine, University of Adelaide, Adelaide, SA, Australia.
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia.
| | - Vihandha O Wickramasinghe
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
| |
Collapse
|
25
|
Zhang S, Bao Y, Shen X, Pan Y, Sun Y, Xiao M, Chen K, Wei H, Zuo J, Saffen D, Zong WX, Sun Y, Wang Z, Wang Y. RNA binding motif protein 10 suppresses lung cancer progression by controlling alternative splicing of eukaryotic translation initiation factor 4H. EBioMedicine 2020; 61:103067. [PMID: 33130397 PMCID: PMC7585942 DOI: 10.1016/j.ebiom.2020.103067] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 12/25/2022] Open
Abstract
Background RNA splicing defects are emerging molecular hallmarks of cancer. The gene encoding splicing factor RNA binding motif protein 10 (RBM10) has been found frequently mutated in various types of cancer, particularly lung adenocarcinoma (LUAD), but how RBM10 affects cancer pathogenesis remains to be determined. Moreover, the functional roles and clinical significance of RBM10 mutation-associated splicing events in LUAD are largely unknown. Methods RBM10 mutations and their functional impacts were examined in LUAD patients from a Chinese patient cohort and The Cancer Genome Atlas (TCGA). Alternative splicing (AS) changes induced by RBM10 mutations in LUAD were identified by RNA sequencing and correlated with patient survival. Functions of RBM10 and the splice variants of eukaryotic translation initiation factor 4H containing or lacking exon 5 (EIF4H-L and EIF4H-S respectively) in LUAD development and progression were examined by cellular phenotypic assays and xenograft tumour formation. Findings RBM10 mutations in LUAD generally lead to loss-of-function and cause extensive alterations in splicing events that can serve as prognostic predictors. RBM10 suppresses LUADprogression largely by regulating alternative splicing of EIF4H exon 5. Loss of RBM10 in LUAD enhances the expression of EIF4H-L in LUAD. EIF4H-L, but not EIF4H-S, is critical for LUAD cell proliferation, survival and tumourigenesis. Interpretation Our study demonstrates a new molecular mechanism underlying RBM10 suppressive functions in lung cancer and the therapeutic value of RBM10-regulated AS events, providing important mechanistic and translational insights into splicing defects in cancer.
Collapse
Affiliation(s)
- Sirui Zhang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yufang Bao
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xianfeng Shen
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yunjian Pan
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yue Sun
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Man Xiao
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Kexuan Chen
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Huanhuan Wei
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ji Zuo
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - David Saffen
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Wei-Xing Zong
- Department of Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Yihua Sun
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yongbo Wang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
| |
Collapse
|
26
|
Murai A, Ebara S, Sasaki S, Ohashi T, Miyazaki T, Nomura T, Araki S. Synergistic apoptotic effects in cancer cells by the combination of CLK and Bcl-2 family inhibitors. PLoS One 2020; 15:e0240718. [PMID: 33064779 DOI: 10.1371/journal.pone.0240718] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 10/01/2020] [Indexed: 02/03/2023] Open
Abstract
Emerging evidence indicates that alternative splicing plays a critical role in cancer progression through abnormal expression or mutation of splicing factors. Small-molecule splicing modulators have recently attracted considerable attention as a novel class of cancer therapeutics. CDC-like kinases (CLKs) are central to exon recognition in mRNA splicing and CLK inhibitors exhibit anti-tumour activities. Most importantly, molecular mechanism-based combination strategies for cancer therapy must be considered. However, it remains unclear whether CLK inhibitors modulate expression and splicing of apoptosis-related genes, and whether CLK inhibitors enhance cytotoxicity in combination with apoptosis inducers. Here we report an appropriate mechanism-based drug combination approach. Unexpectedly, we found that the CLK inhibitor T3 rapidly induced apoptosis in A2780 cells and G2/M cell cycle arrest in HCT116 cells. Regardless of the different phenotypes of the two cancer cell types, T3 decreased the levels of anti-apoptotic proteins (cIAP1, cIAP2, XIAP, cFLIP and Mcl-1) for a short period of exposure and altered the splicing of the anti-apoptotic MCL1L and CFLAR isoform in A2780 and HCT116 cells. In contrast, other members of the Bcl-2 family (i.e., Bcl-xL and Bcl-2) were resistant to T3-induced expression and splicing modulation. T3 and a Bcl-xL/Bcl-2 inhibitor synergistically induced apoptosis. Taken together, the use of a CLK inhibitor is a novel therapeutic approach to sensitise cancer cells to Bcl-xL/Bcl-2 inhibitors.
Collapse
|
27
|
Meissl K, Simonović N, Amenitsch L, Witalisz-Siepracka A, Klein K, Lassnig C, Puga A, Vogl C, Poelzl A, Bosmann M, Dohnal A, Sexl V, Müller M, Strobl B. STAT1 Isoforms Differentially Regulate NK Cell Maturation and Anti-tumor Activity. Front Immunol 2020; 11:2189. [PMID: 33042133 PMCID: PMC7519029 DOI: 10.3389/fimmu.2020.02189] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/11/2020] [Indexed: 12/18/2022] Open
Abstract
Natural killer (NK) cells are important components of the innate immune defense against infections and cancers. Signal transducer and activator of transcription 1 (STAT1) is a transcription factor that is essential for NK cell maturation and NK cell-dependent tumor surveillance. Two alternatively spliced isoforms of STAT1 exist: a full-length STAT1α and a C-terminally truncated STAT1β isoform. Aberrant splicing is frequently observed in cancer cells and several anti-cancer drugs interfere with the cellular splicing machinery. To investigate whether NK cell-mediated tumor surveillance is affected by a switch in STAT1 splicing, we made use of knock-in mice expressing either only the STAT1α (Stat1α/α) or the STAT1β (Stat1β/β ) isoform. NK cells from Stat1α/α mice matured normally and controlled transplanted tumor cells as efficiently as NK cells from wild-type mice. In contrast, NK cells from Stat1β/β mice showed impaired maturation and effector functions, albeit less severe than NK cells from mice that completely lack STAT1 (Stat1-/- ). Mechanistically, we show that NK cell maturation requires the presence of STAT1α in the niche rather than in NK cells themselves and that NK cell maturation depends on IFNγ signaling under homeostatic conditions. The impaired NK cell maturation in Stat1β/β mice was paralleled by decreased IL-15 receptor alpha (IL-15Rα) surface levels on dendritic cells, macrophages and monocytes. Treatment of Stat1β/β mice with exogenous IL-15/IL-15Rα complexes rescued NK cell maturation but not their effector functions. Collectively, our findings provide evidence that STAT1 isoforms are not functionally redundant in regulating NK cell activity and that the absence of STAT1α severely impairs, but does not abolish, NK cell-dependent tumor surveillance.
Collapse
Affiliation(s)
- Katrin Meissl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Natalija Simonović
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Lena Amenitsch
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Agnieszka Witalisz-Siepracka
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Klara Klein
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Caroline Lassnig
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
- Biomodels Austria, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ana Puga
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Claus Vogl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Andrea Poelzl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Markus Bosmann
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, United States
- Center for Thrombosis and Hemostasis, University Medical Center Mainz, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Alexander Dohnal
- Tumor Immunology, St. Anna Kinderkrebsforschung, Children’s Cancer Research Institute, Vienna, Austria
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
- Biomodels Austria, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Birgit Strobl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| |
Collapse
|
28
|
Fergany AAM, Tatarskiy VV. RNA Splicing: Basic Aspects Underlie Antitumor Targeting. Recent Pat Anticancer Drug Discov 2020; 15:293-305. [PMID: 32900350 DOI: 10.2174/1574892815666200908122402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/15/2020] [Accepted: 07/29/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND RNA splicing, a fundamental step in gene expression, is aimed at intron removal and ordering of exons to form the protein's reading frame. OBJECTIVE This review is focused on the role of RNA splicing in cancer biology; the splicing abnormalities that lead to tumor progression emerge as targets for therapeutic intervention. METHODS We discuss the role of aberrant mRNA splicing in carcinogenesis and drug response. RESULTS AND CONCLUSION Pharmacological modulation of RNA splicing sets the stage for treatment approaches in situations where mRNA splicing is a clinically meaningful mechanism of the disease.
Collapse
Affiliation(s)
- Alzahraa A M Fergany
- Department of Occupational and Environmental Health, Graduate School of Pharmaceutical Science, Tokyo University of Science, Chiba, Japan
| | - Victor V Tatarskiy
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russian Federation
| |
Collapse
|
29
|
Hou HA, Tien HF. Genomic landscape in acute myeloid leukemia and its implications in risk classification and targeted therapies. J Biomed Sci 2020; 27:81. [PMID: 32690020 PMCID: PMC7372828 DOI: 10.1186/s12929-020-00674-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/14/2020] [Indexed: 02/08/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous hematologic malignancy in terms of clinical features, underlying pathogenesis and treatment outcomes. Recent advances in genomic techniques have unraveled the molecular complexity of AML leukemogenesis, which in turn have led to refinement of risk stratification and personalized therapeutic strategies for patients with AML. Incorporation of prognostic and druggable genetic biomarkers into clinical practice to guide patient-specific treatment is going to be the mainstay in AML therapeutics. Since 2017 there has been an explosion of novel treatment options to tailor personalized therapy for AML patients. In the past 3 years, the U.S. Food and Drug Administration approved a total of eight drugs for the treatment of AML; most specifically target certain gene mutations, biological pathways, or surface antigen. These novel agents are especially beneficial for older patients or those with comorbidities, in whom the treatment choice is limited and the clinical outcome is very poor. How to balance efficacy and toxicity to further improve patient outcome is clinically relevant. In this review article, we give an overview of the most relevant genetic markers in AML with special focus on the therapeutic implications of these aberrations.
Collapse
Affiliation(s)
- Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan
| | - Hwei-Fang Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan.
| |
Collapse
|
30
|
Zheng X, Peng Q, Wang L, Zhang X, Huang L, Wang J, Qin Z. Serine/arginine-rich splicing factors: the bridge linking alternative splicing and cancer. Int J Biol Sci 2020; 16:2442-2453. [PMID: 32760211 PMCID: PMC7378643 DOI: 10.7150/ijbs.46751] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/22/2020] [Indexed: 01/08/2023] Open
Abstract
The serine/arginine-rich splicing factors (SRs) belong to the serine arginine-rich protein family, which plays an extremely important role in the splicing process of precursor RNA. The SRs recognize the splicing elements on precursor RNA, then recruit and assemble spliceosome to promote or inhibit the occurrence of splicing events. In tumors, aberrant expression of SRs causes abnormal splicing of RNA, contributing to proliferation, migration and apoptosis resistance of tumor cells. Here, we reviewed the vital role of SRs in various tumors and discussed the promise of analyzing mRNA alternative splicing events in tumor. Further, we highlight the challenges and discussed the perspectives for the identification of new potential targets for cancer therapy via SRs family members.
Collapse
Affiliation(s)
- Xiang Zheng
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541001, China
| | - Qiu Peng
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, 410008, China
| | - Lujuan Wang
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, 410008, China
| | - Xuemei Zhang
- Department of Pathology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541001, China
| | - Lili Huang
- Laboratory of Genetics and Metabolism, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region; Guangxi Birth Defects Research and Prevention Institute, Nanning, Guangxi, 530003, China
| | - Jia Wang
- Department of Immunology, Changzhi Medical College, Changzhi, Shanxi, 046000 China
| | - Zailong Qin
- Laboratory of Genetics and Metabolism, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region; Guangxi Birth Defects Research and Prevention Institute, Nanning, Guangxi, 530003, China
| |
Collapse
|
31
|
Zuo S, Li X, Bao W, Li S. Pre-mRNA processing factor 3 enhances the progression of keratinocyte-derived cutaneous squamous cell carcinoma by regulating the JAK2/STAT3 pathway. Sci Rep 2020; 10:8863. [PMID: 32483193 PMCID: PMC7264194 DOI: 10.1038/s41598-020-65928-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/12/2020] [Indexed: 12/24/2022] Open
Abstract
The precise role of pre-mRNA processing factors (PRPs) in human tumorigenesis has not been yet explored. The object of the present study was to explore the effects of PRP3 in a common metastatic skin cancer, keratinocyte-derived cutaneous squamous cell carcinoma (cSCCs). RT-qPCR and western blotting were conducted to measure the expression levels of PRP3 in various cSCC cell lines and cSCC tissues. A benign epidermal keratinocyte cell line was transfected with a eukaryotic expression plasmid to overexpress PRP3. In addition, the endogenous expression level of PRP3 in cSCC cells was silenced using a short hairpin RNA method, and the role of PRP3 on cell proliferation and migration was examined by Cell Counting Kit-8, colony formation, wound healing assay and Transwell assays following knockdown in cSCC cells, and overexpression in keratinovcyte cells. Elevated levels of PRP3 mRNA and protein were noted in cSCC cell lines or cSCC tissues compared with actinic keratosis (AK) or benign epidermal keratinocyte cell line, respectively. Upregulation of PRP3 expression was found to be associated with poor clinical outcomes in patients with cSCCs. The upregulation of PRP3 promoted cell viability, metastasis and the activity of the JAK2/STAT3 pathway in epidermal keratinocyte cells. Interestingly, loss of PRP3 had no obvious impact on cell viability and migration in benign epidermal keratinocyte cells. Functionally, the inhibition of the JAK2/STAT3 pathway reversed the increased cell viability and migration of cSCC cells induced by PRP3. Taken together, the present observations indicated that PRP3 served as a tumor active factor in cSCCs by targeting the JAK2/STAT3 pathway. Moreover, it is implied that impeding the PRP3 activity may selectively constrain cancer cell growth and migration with limited effect on normal skin cells.
Collapse
Affiliation(s)
- Siyao Zuo
- Department of Dermatology and Venereology, The First Hospital of Jilin University, Changchun, China
| | - Xin Li
- Department of Infectious Disease, The First Hospital of Jilin University, Changchun, China
| | - Wanguo Bao
- Department of Infectious Disease, The First Hospital of Jilin University, Changchun, China.
| | - Shanshan Li
- Department of Dermatology and Venereology, The First Hospital of Jilin University, Changchun, China.
| |
Collapse
|
32
|
Wang S, Wang M, Wang B, Chen J, Cheng X, Sun X. Pre-mRNA Processing Factor 8 Accelerates the Progression of Hepatocellular Carcinoma by Regulating the PI3K/Akt Pathway. Onco Targets Ther 2020; 13:4717-4730. [PMID: 32547101 PMCID: PMC7263830 DOI: 10.2147/ott.s241214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/02/2020] [Indexed: 12/22/2022] Open
Abstract
Background The specific function of pre-mRNA processing factors (Prps) in human malignancies has not been yet investigated. The aim of the present study was to determine the impacts of Prp8 in a common human malignancy, hepatocellular carcinoma (HCC). Materials and Methods RT-qPCR and Western blotting were performed to measure the expression levels of Prp8 in various HCC cell lines and HCC tissues. A hepatic astrocyte line was transfected with a eukaryotic expression plasmid to overexpress Prp8. In addition, the endogenous expression level of Prp8 in HCC cells was silenced using a short hairpin RNA method, and the role of Prp8 on cell proliferation and migration was examined by Cell Counting Kit-8, wound healing assay and Transwell assays following knockdown in HCC cells, and overexpression in astrocytes. Results Upregulation of Prp8 expression was found to be associated with poor clinical outcomes in patients with HCC. The upregulation of Prp8 promoted cell viability, metastasis and the activity of the PI3K/Akt pathway in hepatic astrocytes cells and HCC cells. Interestingly, loss of Prp8 had no obvious impact on cell viability and migration in hepatic astrocytes, but significantly inhibit the cell malignancy of HCC cells. Functionally, the inhibition of the PI3K/Akt pathway reversed the increased cell viability and migration of HCC cells induced by Prp8 via inhibiting EMT process. Conclusion Collectively, the present results suggested that Prp8 served as a tumor promoter in HCC by targeting and regulating the PI3K/Akt pathway.
Collapse
Affiliation(s)
- Shouhan Wang
- Department of Hepatopancreatobiliary Surgery, Cancer Hospital of Jilin Province, Changchun, People's Republic of China
| | - Min Wang
- Department of Pathology, Cancer Hospital of Jilin Province, Changchun, People's Republic of China
| | - Bin Wang
- Department of Hepatopancreatobiliary Surgery, Cancer Hospital of Jilin Province, Changchun, People's Republic of China
| | - Jiaqi Chen
- Department of Hepatopancreatobiliary Surgery, Cancer Hospital of Jilin Province, Changchun, People's Republic of China
| | - Xianbin Cheng
- Department of Hepatopancreatobiliary Surgery, Cancer Hospital of Jilin Province, Changchun, People's Republic of China
| | - Xiaodan Sun
- Department of 2nd Gynecologic Oncology Surgery, Cancer Hospital of Jilin Province, Changchun, People's Republic of China
| |
Collapse
|
33
|
Takeiwa T, Mitobe Y, Ikeda K, Horie-Inoue K, Inoue S. Roles of Splicing Factors in Hormone-Related Cancer Progression. Int J Mol Sci 2020; 21:E1551. [PMID: 32106418 DOI: 10.3390/ijms21051551] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 02/20/2020] [Indexed: 12/19/2022] Open
Abstract
Splicing of mRNA precursor (pre-mRNA) is a mechanism to generate multiple mRNA isoforms from a single pre-mRNA, and it plays an essential role in a variety of biological phenomena and diseases such as cancers. Previous studies have demonstrated that cancer-specific splicing events are involved in various aspects of cancers such as proliferation, migration and response to hormones, suggesting that splicing-targeting therapy can be promising as a new strategy for cancer treatment. In this review, we focus on the splicing regulation by RNA-binding proteins including Drosophila behavior/human splicing (DBHS) family proteins, serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) in hormone-related cancers, such as breast and prostate cancers.
Collapse
|
34
|
Wang Y, Bao Y, Zhang S, Wang Z. Splicing dysregulation in cancer: from mechanistic understanding to a new class of therapeutic targets. Sci China Life Sci 2020; 63:469-484. [PMID: 32086672 DOI: 10.1007/s11427-019-1605-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022]
Abstract
RNA splicing dysregulation is widespread in cancer. Accumulating evidence demonstrates that splicing defects resulting from splicing dysregulation play critical roles in cancer pathogenesis and can serve as new biomarkers and therapeutic targets for cancer intervention. These findings have greatly deepened the mechanistic understandings of the regulation of alternative splicing in cancer cells, leading to rapidly growing interests in targeting cancer-related splicing defects as new therapies. Here we summarize the current research progress on splicing dysregulation in cancer and highlight the strategies available or under development for targeting RNA splicing defects in cancer.
Collapse
Affiliation(s)
- Yongbo Wang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Yufang Bao
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Sirui Zhang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| |
Collapse
|
35
|
Wu Z, Liu J, Sun R, Chen D, Wang K, Cao C, Xu X. A Novel Prognostic Index Based on Alternative Splicing in Papillary Renal Cell Carcinoma. Front Genet 2020; 10:1333. [PMID: 32063918 PMCID: PMC6999693 DOI: 10.3389/fgene.2019.01333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 12/05/2019] [Indexed: 01/08/2023] Open
Abstract
Background Papillary renal cell carcinoma (pRCC) is a heterogeneous multifocal or isolated tumor with an invasive phenotype. Previous studies presented that alternative splicing, as a crucial posttranscriptional regulator in gene expression, is associated with tumorigenesis. However, the association between alternative splicing and pRCC has not been clarified Methods The RNA sequencing data and clinical information were downloaded from The Cancer Genome Atlas database and mRNA splicing profiles from TCGASpliceSeq. The percent spliced in data of alternative splicing merged with survival information was firstly calculated by univariate Cox regression analysis to screen for survival‐associated alternative splicing events, and survival‐associated alternative splicing events were then analyzed by Gene Ontology categories using Kyoto Encyclopedia of Genes and Genomes. Meanwhile, the least absolute shrinkage and selection operator Cox analysis and multivariate Cox analysis were performed to calculate the prognostic index for each alternative splicing type. In addition, clinical factors were introduced to assess the performance of prognostic index. Results A total of 4,084 candidate survival-associated alternative splicing events in 2,558 genes were screened out. Patients were divided into the low-risk group and the high-risk group based on the median prognostic index value. The Kaplan-Meier survival analysis (p < 0.05) and receiver operating characteristics curves (AUC>0.9) indicated that prognostic index was effective and stable for predicting the prognosis of pRCC patients. Furthermore, a regulatory network was constructed incorporating alternative splicing events and survival-associated splicing factors. Conclusion Our study provides new insights into the mechanism of alternative splicing events in tumorigenesis and their clinical potential for pRCC.
Collapse
Affiliation(s)
- Zhipeng Wu
- Department of Urology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rui Sun
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Dongming Chen
- Department of Urology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Kai Wang
- Department of Urology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Changchun Cao
- Department of Urology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| | - Xianlin Xu
- Department of Urology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, China
| |
Collapse
|
36
|
Abstract
The relationship between inflammation and cancer has been long recognized by the medical and scientific community. In the last decades, it has returned to the forefront of clinical oncology since a wealth of knowledge has been gathered about the cells, cytokines and physiological processes that are central to both inflammation and cancer. It is now robustly established that chronic inflammation can induce certain cancers but also that solid tumors, in turn, can initiate and perpetuate local inflammatory processes that foster tumor growth and dissemination. Inflammation is the hallmark of the innate immune response to tissue damage or infection, but also mediates the activation, expansion and recruitment to the tissues of cells and antibodies of the adaptive immune system. The functional integration of both components of the immune response is crucial to identify and subdue tumor development, progression and dissemination. When this tight control goes awry, altered cells can avoid the immune surveillance and even subvert the innate immunity to promote their full oncogenic transformation. In this chapter, we make a general overview of the most recent data linking the inflammatory process to cancer. We start with the overall inflammatory cues and processes that influence the relationship between tumor and the microenvironment that surrounds it and follow the ever-increasing complexity of processes that end up producing subtle changes in the splicing of certain genes to ascertain survival advantage to cancer cells.
Collapse
Affiliation(s)
- Ana Luísa Silva
- Serviço de Endocrinologia, Diabetes e Metabolismo do CHLN-Hospital Santa Maria, Lisbon, Portugal
- ISAMB-Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Márcia Faria
- Serviço de Endocrinologia, Diabetes e Metabolismo do CHLN-Hospital Santa Maria, Lisbon, Portugal
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Lisbon, Portugal
| | - Paulo Matos
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Lisbon, Portugal
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal
| |
Collapse
|
37
|
Dong X, Chen R. Understanding aberrant RNA splicing to facilitate cancer diagnosis and therapy. Oncogene 2019; 39:2231-2242. [PMID: 31819165 DOI: 10.1038/s41388-019-1138-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 12/31/2022]
Abstract
Almost all genes in normal cells undergo alternative RNA splicing to generate a greater extent of diversification of gene products for normal cellular functions. RNA splicing is tightly regulated and closely interplays with genetic and epigenetic machinery. While DNA polymorphism and somatic mutations modulate alternative splicing patterns, RNA splicing also controls genomic stability, chromatin organization, and transcriptome. Tumor cells, in turn, often take advantage of aberrant RNA splicing to develop, grow and progress into therapy-resistant tumors. Understanding alternative RNA splicing in tumor cells would, therefore, provide us opportunities to gain further insights into tumor biology, identify diagnostic or prognosis biomarkers, as well as to design effective therapeutic means to control tumor progression. Here, we provide an overview of RNA splicing mechanisms and use prostate cancer as an example to review recent advancements in our understanding of RNA splicing in cancer progression and therapy resistance. We also discuss emerging diagnostic and therapeutic potentials of RNA splicing events or RNA splicing factors.
Collapse
Affiliation(s)
- Xuesen Dong
- Department of Urologic Sciences, Faculty of Medicine, The University of British Columbia, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada. .,The Vancouver Prostate Centre, Vancouver General Hospital, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada.
| | - Ruiqi Chen
- Faculty of Medicine, University of Toronto, 27 King's College Circle 8, Toronto, ON, M5S 1A1, Canada
| |
Collapse
|
38
|
Abstract
The U2 small nuclear ribonucleoprotein (snRNP) is an essential component of the spliceosome, the cellular machine responsible for removing introns from precursor mRNAs (pre-mRNAs) in all eukaryotes. U2 is an extraordinarily dynamic splicing factor and the most frequently mutated in cancers. Cryo-electron microscopy (cryo-EM) has transformed our structural and functional understanding of the role of U2 in splicing. In this review, we synthesize these and other data with respect to a view of U2 as an assembly of interconnected functional modules. These modules are organized by the U2 small nuclear RNA (snRNA) for roles in spliceosome assembly, intron substrate recognition, and protein scaffolding. We describe new discoveries regarding the structure of U2 components and how the snRNP undergoes numerous conformational and compositional changes during splicing. We specifically highlight large scale movements of U2 modules as the spliceosome creates and rearranges its active site. U2 serves as a compelling example for how cellular machines can exploit the modular organization and structural plasticity of an RNP.
Collapse
Affiliation(s)
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
39
|
Maji D, Grossfield A, Kielkopf CL. Structures of SF3b1 reveal a dynamic Achilles heel of spliceosome assembly: Implications for cancer-associated abnormalities and drug discovery. Biochim Biophys Acta Gene Regul Mech 2019; 1862:194440. [PMID: 31707043 DOI: 10.1016/j.bbagrm.2019.194440] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 09/30/2019] [Indexed: 12/11/2022]
Abstract
The pre-mRNA splicing factor SF3b1 exhibits recurrent mutations among hematologic malignancies and cancers, and consequently is a major therapeutic target of clinically-advanced spliceosome inhibitors. In this review, we highlight and rigorously analyze emerging views of SF3b1 conformational transitions, including the human SF3b particle either in isolation or bound to spliceosome inhibitors, and human or yeast spliceosome assemblies. Among spliceosome states characterized to date, an SF3b1 α-helical superhelix significantly closes to surround a U2 small nuclear RNA duplex with the pre-mRNA branch point sequence. The SF3b1 torus is locally unwound at an active site adenosine, whereas protein cofactors appear to stabilize overall closure in the spliceosome. Network analyses demonstrates that the natural SF3b1 dynamics mimic its conformational change in the spliceosome, raising the possibility of conformational selection underpinning spliceosome assembly. These dynamic SF3b1 conformations have consequences for gatekeeping of spliceosome assembly and therapeutic targeting of its cancer-associated dysfunction.
Collapse
|
40
|
Borišek J, Saltalamacchia A, Gallì A, Palermo G, Molteni E, Malcovati L, Magistrato A. Disclosing the Impact of Carcinogenic SF3b Mutations on Pre-mRNA Recognition Via All-Atom Simulations. Biomolecules 2019; 9:E633. [PMID: 31640290 DOI: 10.3390/biom9100633] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/15/2019] [Accepted: 10/17/2019] [Indexed: 02/07/2023] Open
Abstract
The spliceosome accurately promotes precursor messenger-RNA splicing by recognizing specific noncoding intronic tracts including the branch point sequence (BPS) and the 3'-splice-site (3'SS). Mutations of Hsh155 (yeast)/SF3B1 (human), which is a protein of the SF3b factor involved in BPS recognition and induces altered BPS binding and 3'SS selection, lead to mis-spliced mRNA transcripts. Although these mutations recur in hematologic malignancies, the mechanism by which they change gene expression remains unclear. In this study, multi-microsecond-long molecular-dynamics simulations of eighth distinct ∼700,000 atom models of the spliceosome Bact complex, and gene sequencing of SF3B1, disclose that these carcinogenic isoforms destabilize intron binding and/or affect the functional dynamics of Hsh155/SF3B1 only when binding non-consensus BPSs, as opposed to the non-pathogenic variants newly annotated here. This pinpoints a cross-talk between the distal Hsh155 mutation and BPS recognition sites. Our outcomes unprecedentedly contribute to elucidating the principles of pre-mRNA recognition, which provides critical insights on the mechanism underlying constitutive/alternative/aberrant splicing.
Collapse
|
41
|
Huang X, Liu J, Mo X, Liu H, Wei C, Huang L, Chen J, Tian C, Meng Y, Wu G, Xie W, P.C. FJ, Liu Z, Tang W. Systematic profiling of alternative splicing events and splicing factors in left- and right-sided colon cancer. Aging (Albany NY) 2019; 11:8270-8293. [PMID: 31586988 PMCID: PMC6814588 DOI: 10.18632/aging.102319] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 09/21/2019] [Indexed: 02/07/2023]
Abstract
Left- and right-sided colon cancer (LC and RC) differ substantially in their molecular characteristics and prognoses, and are thus treated using different strategies. We systematically analyzed alternative splicing (AS) events and splicing factors in LC and RC. RNA-seq data were used for genome-wide profiling of AS events that could distinguish LC from RC. The Exon Skip splicing pattern was more common in RC, while the Retained Intron pattern was more common in LC. The AS events that were upregulated in RC were enriched for genes in the axon guidance pathway, while those that were upregulated in LC were enriched for genes in immune-related pathways. Prognostic models based on differentially expressed AS events were built, and a prognostic signature based on these AS events performed well for risk stratification in colon cancer patients. A correlation network of differentially expressed AS events and differentially expressed splicing factors was constructed, and RBM25 was identified as the hub gene in the network. In conclusion, large differences in AS events may contribute to the phenotypic differences between LC and RC. The differentially expressed AS events reported herein could be used as biomarkers and treatment targets for colon cancer.
Collapse
Affiliation(s)
- Xiaoliang Huang
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
| | - Jungang Liu
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
| | - Xianwei Mo
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
| | - Haizhou Liu
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
| | - Chunyin Wei
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
| | - Lingxu Huang
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
| | - Jianhong Chen
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
| | - Chao Tian
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
| | - Yongsheng Meng
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
| | - Guo Wu
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
| | - Weishun Xie
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
| | - Franco Jeen P.C.
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
| | - Zujun Liu
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
| | - Weizhong Tang
- Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
- Guangxi Clinical Research Center for Colorectal Cancer, Nanning 530021, Guangxi Zhuang Autonomous Region, The People’s Republic of China
| |
Collapse
|
42
|
Borišek J, Saltalamacchia A, Spinello A, Magistrato A. Exploiting Cryo-EM Structural Information and All-Atom Simulations To Decrypt the Molecular Mechanism of Splicing Modulators. J Chem Inf Model 2019; 60:2510-2521. [DOI: 10.1021/acs.jcim.9b00635] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jure Borišek
- National Research Council (CNR)-IOM c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Andrea Saltalamacchia
- International School for Advanced studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Angelo Spinello
- National Research Council (CNR)-IOM c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council (CNR)-IOM c/o International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste, Italy
| |
Collapse
|
43
|
Taladriz-Sender A, Campbell E, Burley GA. Splice-switching small molecules: A new therapeutic approach to modulate gene expression. Methods 2019; 167:134-142. [PMID: 31203161 DOI: 10.1016/j.ymeth.2019.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 12/12/2022] Open
Abstract
Manipulating alternative RNA splicing events with small molecules is emerging as a viable mechanism for the development of therapeutics. A salient challenge in the field is understanding the molecular determinants defining the selectivity of splice-switching events and their mechanisms of action. In this review, the current state-of-the-art in splice-switching small molecules is described. Three examples of splice-switching small molecules are presented, and the differences in their modes of action compared.
Collapse
Affiliation(s)
- Andrea Taladriz-Sender
- Department of Pure and Applied Chemistry, University of Strathclyde. Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Emma Campbell
- Department of Pure and Applied Chemistry, University of Strathclyde. Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde. Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom.
| |
Collapse
|
44
|
Tam AS, Stirling PC. Splicing, genome stability and disease: splice like your genome depends on it! Curr Genet 2019; 65:905-912. [PMID: 30953124 DOI: 10.1007/s00294-019-00964-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 12/21/2022]
Abstract
The spliceosome has been implicated in genome maintenance for decades. Recently, a surge in discoveries in cancer has suggested that the oncogenic mechanism of spliceosomal defects may involve defective genome stability. The action of the core spliceosome prevents R-loop accumulation, and regulates the expression of genome stability factors. At the same time, specific spliceosomal components have non-canonical functions in genome maintenance. Here we review these different models, highlighting their discovery in different model systems, and describing their potential impact on human disease states.
Collapse
Affiliation(s)
- Annie S Tam
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Peter C Stirling
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
45
|
Angiolini F, Belloni E, Giordano M, Campioni M, Forneris F, Paronetto MP, Lupia M, Brandas C, Pradella D, Di Matteo A, Giampietro C, Jodice G, Luise C, Bertalot G, Freddi S, Malinverno M, Irimia M, Moulton JD, Summerton J, Chiapparino A, Ghilardi C, Giavazzi R, Nyqvist D, Gabellini D, Dejana E, Cavallaro U, Ghigna C. A novel L1CAM isoform with angiogenic activity generated by NOVA2-mediated alternative splicing. eLife 2019; 8:44305. [PMID: 30829570 PMCID: PMC6398979 DOI: 10.7554/elife.44305] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/08/2019] [Indexed: 12/13/2022] Open
Abstract
The biological players involved in angiogenesis are only partially defined. Here, we report that endothelial cells (ECs) express a novel isoform of the cell-surface adhesion molecule L1CAM, termed L1-ΔTM. The splicing factor NOVA2, which binds directly to L1CAM pre-mRNA, is necessary and sufficient for the skipping of L1CAM transmembrane domain in ECs, leading to the release of soluble L1-ΔTM. The latter exerts high angiogenic function through both autocrine and paracrine activities. Mechanistically, L1-ΔTM-induced angiogenesis requires fibroblast growth factor receptor-1 signaling, implying a crosstalk between the two molecules. NOVA2 and L1-ΔTM are overexpressed in the vasculature of ovarian cancer, where L1-ΔTM levels correlate with tumor vascularization, supporting the involvement of NOVA2-mediated L1-ΔTM production in tumor angiogenesis. Finally, high NOVA2 expression is associated with poor outcome in ovarian cancer patients. Our results point to L1-ΔTM as a novel, EC-derived angiogenic factor which may represent a target for innovative antiangiogenic therapies. Growing tumors stimulate the formation of new blood vessels to supply the oxygen and nutrients the cancerous cells need to stay alive. Stopping tumors from forming the blood vessels could therefore help us to treat cancer. To do so, we need to understand how different proteins control when and how blood vessels develop. Cells make proteins by first ‘transcribing’ genes to form RNA molecules. In many cases, the RNA then goes through a process called alternative splicing. Proteins known as splicing factors cut out different segments of the RNA molecule and stick together the remaining segments to form templates for protein production. This enables a single gene to produce many different variants of a protein. Angiolini, Belloni, Giordano et al. have now studied mouse and human versions of the cells that line the blood vessels grown by tumors. This revealed that a splicing factor called NOVA2 targets a protein called L1CAM, which is normally responsible for gluing adjacent cells together. Angiolini et al. found that NOVA2 splices L1CAM into a form not seen before. Instead of remaining anchored to cell surfaces, the newly identified form of L1CAM is released into the blood circulation, where it stimulates new blood vessels to grow. Samples taken from the blood vessels of human ovarian tumors showed high levels of both NOVA2 and the modified form of L1CAM, while blood vessels in healthy tissue contain no, or very low levels of both proteins. Therefore, if the new form of L1CAM can be detected in the blood, it could be used to help cancer diagnosis, and to indicate which patients would benefit from treatments that restrict the growth of blood vessels in tumors. Further work is now needed to explore these possibilities.
Collapse
Affiliation(s)
- Francesca Angiolini
- Unit of Gynecological Oncology Research, Program of Gynecological Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Elisa Belloni
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Marco Giordano
- Unit of Gynecological Oncology Research, Program of Gynecological Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Matteo Campioni
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Federico Forneris
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, Università degli Studi di Roma "Foro Italico", Rome, Italy
| | - Michela Lupia
- Unit of Gynecological Oncology Research, Program of Gynecological Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Chiara Brandas
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Davide Pradella
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy.,Università degli Studi di Pavia, Pavia, Italy
| | - Anna Di Matteo
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | | | - Giovanna Jodice
- Molecular Medicine Program, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Chiara Luise
- Molecular Medicine Program, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Giovanni Bertalot
- Molecular Medicine Program, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Stefano Freddi
- Molecular Medicine Program, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Manuel Irimia
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | | | | | - Antonella Chiapparino
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Carmen Ghilardi
- Laboratory of Biology and Treatment of Metastasis, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Raffaella Giavazzi
- Laboratory of Biology and Treatment of Metastasis, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Daniel Nyqvist
- Division of Vascular Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Davide Gabellini
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elisabetta Dejana
- FIRC Institute of Molecular Oncology, Milan, Italy.,Rudbeck Laboratory and Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ugo Cavallaro
- Unit of Gynecological Oncology Research, Program of Gynecological Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Claudia Ghigna
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| |
Collapse
|
46
|
Aird D, Teng T, Huang CL, Pazolli E, Banka D, Cheung-Ong K, Eifert C, Furman C, Wu ZJ, Seiler M, Buonamici S, Fekkes P, Karr C, Palacino J, Park E, Smith PG, Yu L, Mizui Y, Warmuth M, Chicas A, Corson L, Zhu P. Sensitivity to splicing modulation of BCL2 family genes defines cancer therapeutic strategies for splicing modulators. Nat Commun 2019; 10:137. [PMID: 30635584 DOI: 10.1038/s41467-018-08150-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/18/2018] [Indexed: 11/24/2022] Open
Abstract
Dysregulation of RNA splicing by spliceosome mutations or in cancer genes is increasingly recognized as a hallmark of cancer. Small molecule splicing modulators have been introduced into clinical trials to treat solid tumors or leukemia bearing recurrent spliceosome mutations. Nevertheless, further investigation of the molecular mechanisms that may enlighten therapeutic strategies for splicing modulators is highly desired. Here, using unbiased functional approaches, we report that the sensitivity to splicing modulation of the anti-apoptotic BCL2 family genes is a key mechanism underlying preferential cytotoxicity induced by the SF3b-targeting splicing modulator E7107. While BCL2A1, BCL2L2 and MCL1 are prone to splicing perturbation, BCL2L1 exhibits resistance to E7107-induced splicing modulation. Consequently, E7107 selectively induces apoptosis in BCL2A1-dependent melanoma cells and MCL1-dependent NSCLC cells. Furthermore, combination of BCLxL (BCL2L1-encoded) inhibitors and E7107 remarkably enhances cytotoxicity in cancer cells. These findings inform mechanism-based approaches to the future clinical development of splicing modulators in cancer treatment. Small molecule modulators of RNA splicing have therapeutic potential in tumours bearing spliceosome mutations. Here, the authors identify BCL2 genes have differential sensitivities to SF3b-targeting splicing modulators and combination of SF3b-targeting splicing modulators and BCLxL inhibition induces synergistic cytotoxicity in cancer cells.
Collapse
|
47
|
Abstract
Alternative splicing, the process of removing introns and joining exons of pre-mRNA, is critical for growth, development, tissue homeostasis, and species diversity. Dysregulation of alternative splicing can initiate and drive disease. Aberrant alternative splicing has been shown to promote the "hallmarks of cancer" in both hematological and solid cancers. Of interest, recent work has focused on the role of alternative splicing in prostate cancer and prostate cancer health disparities. We will provide a review of prostate cancer health disparities involving the African American population, alternative RNA splicing, and alternative splicing in prostate cancer. Lastly, we will summarize our work on differential alternative splicing in prostate cancer disparities and its implications for disparate health outcomes and therapeutic targets.
Collapse
Affiliation(s)
- Jacqueline Olender
- Department of Pharmacology and Physiology, GW Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Norman H Lee
- Department of Pharmacology and Physiology, GW Cancer Center, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
| |
Collapse
|
48
|
Sciarrillo R, Wojtuszkiewicz A, El Hassouni B, Funel N, Gandellini P, Lagerweij T, Buonamici S, Blijlevens M, Zeeuw van der Laan EA, Zaffaroni N, Deraco M, Kusamura S, Würdinger T, Peters GJ, Molthoff CFM, Jansen G, Kaspers GJL, Cloos J, Giovannetti E. Splicing modulation as novel therapeutic strategy against diffuse malignant peritoneal mesothelioma. EBioMedicine 2019; 39:215-25. [PMID: 30581150 DOI: 10.1016/j.ebiom.2018.12.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 12/29/2022] Open
Abstract
Introduction Therapeutic options for diffuse malignant peritoneal mesothelioma (DMPM) are limited to surgery and locoregional chemotherapy. Despite improvements in survival rates, patients eventually succumb to disease progression. We investigated splicing deregulation both as molecular prognostic factor and potential novel target in DMPM, while we tested modulators of SF3b complex for antitumor activity. Methods Tissue-microarrays of 64 DMPM specimens were subjected to immunohistochemical assessment of SF3B1 expression and correlation to clinical outcome. Two primary cell cultures were used for gene expression profiling and in vitro screening of SF3b modulators. Drug-induced splicing alterations affecting downstream cellular pathways were detected through RNA sequencing. Ultimately, we established bioluminescent orthotopic mouse models to test the efficacy of splicing modulation in vivo. Results Spliceosomal genes are differentially upregulated in DMPM cells compared to normal tissues and high expression of SF3B1 correlated with poor clinical outcome in univariate and multivariate analysis. SF3b modulators (Pladienolide-B, E7107, Meayamycin-B) showed potent cytotoxic activity in vitro with IC50 values in the low nanomolar range. Differential splicing analysis of Pladienolide-B-treated cells revealed abundant alterations of transcripts involved in cell cycle, apoptosis and other oncogenic pathways. This was validated by RT-PCR and functional assays. E7107 demonstrated remarkable in vivo antitumor efficacy, with significant improvement of survival rates compared to vehicle-treated controls. Conclusions SF3B1 emerged as a novel potential prognostic factor in DMPM. Splicing modulators markedly impair cancer cell viability, resulting also in potent antitumor activity in vivo. Our data designate splicing as a promising therapeutic target in DMPM.
Collapse
|
49
|
Abstract
RNA splicing, the enzymatic process of removing segments of premature RNA to produce mature RNA, is a key mediator of proteome diversity and regulator of gene expression. Increased systematic sequencing of the genome and transcriptome of cancers has identified a variety of means by which RNA splicing is altered in cancer relative to normal cells. These findings, in combination with the discovery of recurrent change-of-function mutations in splicing factors in a variety of cancers, suggest that alterations in splicing are drivers of tumorigenesis. Greater characterization of altered splicing in cancer parallels increasing efforts to pharmacologically perturb splicing and early-phase clinical development of small molecules that disrupt splicing in patients with cancer. Here we review recent studies of global changes in splicing in cancer, splicing regulation of mitogenic pathways critical in cancer transformation, and efforts to therapeutically target splicing in cancer.
Collapse
Affiliation(s)
- Luisa Escobar-Hoyos
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Cornell Medical College, New York, NY 10065, USA.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| |
Collapse
|
50
|
Abstract
More than 95% of the 20,000 to 25,000 transcribed human genes undergo alternative RNA splicing, which increases the diversity of the proteome. Isoforms derived from the same gene can have distinct and, in some cases, opposing functions. Accumulating evidence suggests that aberrant RNA splicing is a common and driving event in cancer development and progression. Moreover, aberrant splicing events conferring drug/therapy resistance in cancer is far more common than previously envisioned. In this review, aberrant splicing events in cancer-associated genes, namely BCL2L1, FAS, HRAS, CD44, Cyclin D1, CASP2, TMPRSS2-ERG, FGFR2, VEGF, AR and KLF6, will be discussed. Also highlighted are the functional consequences of aberrant splice variants (BCR-Abl35INS, BIM-γ, IK6, p61 BRAF V600E, CD19-∆2, AR-V7 and PIK3CD-S) in promoting resistance to cancer targeted therapy or immunotherapy. To overcome drug resistance, we discuss opportunities for developing novel strategies to specifically target the aberrant splice variants or splicing machinery that generates the splice variants. Therapeutic approaches include the development of splice variant-specific siRNAs, splice switching antisense oligonucleotides, and small molecule inhibitors targeting splicing factors, splicing factor kinases or the aberrant oncogenic protein isoforms.
Collapse
Affiliation(s)
- Bi-Dar Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA.
| | - Norman H Lee
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, GW Cancer Center, Washington, DC 20037, USA.
| |
Collapse
|