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Shi X, Zhang R, Liu Z, Zhao G, Guo J, Mao X, Fan B. Alternative Splicing Reveals Acute Stress Response of Litopenaeus vannamei at High Alkalinity. Mar Biotechnol (NY) 2024; 26:103-115. [PMID: 38206418 DOI: 10.1007/s10126-023-10281-w] [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] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
Alkalinity is regarded as one of the primary stressors for aquatic animals in saline-alkaline water. Alternative splicing (AS) can significantly increase the diversity of transcripts and play key roles in stress response; however, the studies on AS under alkalinity stress of crustaceans are still limited. In the present study, we devoted ourselves to the study of AS under acute alkalinity stress at control (50 mg/L) and treatment groups (350 mg/L) by RNA-seq in pacific white shrimp (Litopenaeus vannamei). We identified a total of 10,556 AS events from 4865 genes and 619 differential AS (DAS) events from 519 DAS genes in pacific white shrimp. Functional annotation showed that the DAS genes primarily involved in spliceosome. Five splicing factors (SFs), U2AF1, PUF60, CHERP, SR140 and SRSF2 were significantly up-regulated and promoted AS. Furthermore, alkalinity activated the Leukocyte transendothelial migration, mTOR signaling pathway and AMPK signaling pathway, which regulated MAPK1, EIF3B and IGFP-RP1 associated with these pathways. We also studied three SFs (HSFP1, SRSF2 and NHE-RF1), which underwent AS to form different transcript isoforms. The above results demonstrated that AS was a regulatory mechanism in pacific white shrimp in response to acute alkalinity stress. SFs played vital roles in AS of pacific white shrimp, such as HSFP1, SRSF2 and NHE-RF1. DAS genes were significantly modified in immunity of pacific white shrimp to cope with alkalinity stress. This is the first study on the response of AS to acute alkalinity stress, which provided scientific basis for AS mechanism of crustaceans response to alkalinity stress.
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Affiliation(s)
- Xiang Shi
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
| | - Ruiqi Zhang
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China.
| | - Zhe Liu
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
| | - Guiyan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
| | - Jintao Guo
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
| | - Xue Mao
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
| | - Baoyi Fan
- College of Animal Science and Technology, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Gansu Province, Lanzhou, 730070, China
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Du Y, Cao L, Wang S, Guo L, Tan L, Liu H, Feng Y, Wu W. Differences in alternative splicing and their potential underlying factors between animals and plants. J Adv Res 2023:S2090-1232(23)00354-5. [PMID: 37981087 DOI: 10.1016/j.jare.2023.11.017] [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: 05/07/2023] [Revised: 08/16/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Alternative splicing (AS), a posttranscriptional process, contributes to the complexity of transcripts from a limited number of genes in a genome, and AS is considered a great source of genetic and phenotypic diversity in eukaryotes. In animals, AS is tightly regulated during the processes of cell growth and differentiation, and its dysregulation is involved in many diseases, including cancers. Likewise, in plants, AS occurs in all stages of plant growth and development, and it seems to play important roles in the rapid reprogramming of genes in response to environmental stressors. To date, the prevalence and functional roles of AS have been extensively reviewed in animals and plants. However, AS differences between animals and plants, especially their underlying molecular mechanisms and impact factors, are anecdotal and rarely reviewed. AIM OF REVIEW This review aims to broaden our understanding of AS roles in a variety of biological processes and provide insights into the underlying mechanisms and impact factors likely leading to AS differences between animals and plants. KEY SCIENTIFIC CONCEPTS OF REVIEW We briefly summarize the roles of AS regulation in physiological and biochemical activities in animals and plants. Then, we underline the differences in the process of AS between plants and animals and especially analyze the potential impact factors, such as gene exon/intron architecture, 5'/3' untranslated regions (UTRs), spliceosome components, chromatin dynamics and transcription speeds, splicing factors [serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs)], noncoding RNAs, and environmental stimuli, which might lead to the differences. Moreover, we compare the nonsense-mediated mRNA decay (NMD)-mediated turnover of the transcripts with a premature termination codon (PTC) in animals and plants. Finally, we summarize the current AS knowledge published in animals versus plants and discuss the potential development of disease therapies and superior crops in the future.
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Affiliation(s)
- Yunfei Du
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lu Cao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lingling Tan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Hua Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Ying Feng
- Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health (SINH), Chinese Academy of Sciences (CAS), Shanghai 200032, China.
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China.
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Yan Y, Ren Y, Bao Y, Wang Y. RNA splicing alterations in lung cancer pathogenesis and therapy. Cancer Pathog Ther 2023; 1:272-283. [PMID: 38327600 PMCID: PMC10846331 DOI: 10.1016/j.cpt.2023.04.004] [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] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/25/2023] [Accepted: 04/29/2023] [Indexed: 02/09/2024]
Abstract
RNA splicing alterations are widespread and play critical roles in cancer pathogenesis and therapy. Lung cancer is highly heterogeneous and causes the most cancer-related deaths worldwide. Large-scale multi-omics studies have not only characterized the mutational landscapes but also discovered a plethora of transcriptional and post-transcriptional changes in lung cancer. Such resources have greatly facilitated the development of new diagnostic markers and therapeutic options over the past two decades. Intriguingly, altered RNA splicing has emerged as an important molecular feature and therapeutic target of lung cancer. In this review, we provide a brief overview of splicing dysregulation in lung cancer and summarize the recent progress on key splicing events and splicing factors that contribute to lung cancer pathogenesis. Moreover, we describe the general strategies targeting splicing alterations in lung cancer and highlight the potential of combining splicing modulation with currently approved therapies to combat this deadly disease. This review provides new mechanistic and therapeutic insights into splicing dysregulation in cancer.
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Affiliation(s)
- Yueren Yan
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Yunpeng Ren
- Department of Cellular and Genetic Medicine, Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yufang Bao
- Department of Cellular and Genetic Medicine, Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yongbo Wang
- Department of Cellular and Genetic Medicine, Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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Mathew V, Mei A, Giwa H, Cheong A, Chander A, Zou A, Blanton RM, Kashpur O, Cui W, Slonim D, Mahmoud T, O'Tierney-Ginn P, Mager J, Draper I, Wallingford MC. hnRNPL expression dynamics in the embryo and placenta. Gene Expr Patterns 2023; 48:119319. [PMID: 37148985 DOI: 10.1016/j.gep.2023.119319] [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: 03/07/2022] [Revised: 03/13/2023] [Accepted: 04/04/2023] [Indexed: 05/08/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein L (hnRNPL) is a conserved RNA binding protein (RBP) that plays an important role in the alternative splicing of gene transcripts, and thus in the generation of specific protein isoforms. Global deficiency in hnRNPL in mice results in preimplantation embryonic lethality at embryonic day (E) 3.5. To begin to understand the contribution of hnRNPL-regulated pathways in the normal development of the embryo and placenta, we determined hnRNPL expression profile and subcellular localization throughout development. Proteome and Western blot analyses were employed to determine hnRNPL abundance between E3.5 and E17.5. Histological analyses supported that the embryo and implantation site display distinct hnRNPL localization patterns. In the fully developed mouse placenta, nuclear hnRNPL was observed broadly in trophoblasts, whereas within the implantation site a discrete subset of cells showed hnRNPL outside the nucleus. In the first-trimester human placenta, hnRNPL was detected in the undifferentiated cytotrophoblasts, suggesting a role for this factor in trophoblast progenitors. Parallel in vitro studies utilizing Htr8 and Jeg3 cell lines confirmed expression of hnRNPL in cellular models of human trophoblasts. These studies coordinated regulation of hnRNPL during the normal developmental program in the mammalian embryo and placenta.
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Affiliation(s)
- Vineetha Mathew
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Ariel Mei
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Hamida Giwa
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Agnes Cheong
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, 01003, USA
| | - Ashmita Chander
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, 01003, USA
| | - Aaron Zou
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Robert M Blanton
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Olga Kashpur
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Wei Cui
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, 01003, USA
| | - Donna Slonim
- Department of Computer Science, Tufts University, 177 College Avenue, Medford, MA, 02155, USA
| | - Taysir Mahmoud
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Perrie O'Tierney-Ginn
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, 01003, USA
| | - Isabelle Draper
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA.
| | - Mary C Wallingford
- Mother Infant Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA; Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington St, Boston, MA, 02111, USA.
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Hazra A, Pal A, Kundu A. Alternative splicing shapes the transcriptome complexity in blackgram [Vigna mungo (L.) Hepper]. Funct Integr Genomics 2023; 23:144. [PMID: 37133618 DOI: 10.1007/s10142-023-01066-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/04/2023]
Abstract
Vigna mungo, a highly consumed crop in the pan-Asian countries, is vulnerable to several biotic and abiotic stresses. Understanding the post-transcriptional gene regulatory cascades, especially alternative splicing (AS), may underpin large-scale genetic improvements to develop stress-resilient varieties. Herein, a transcriptome based approach was undertaken to decipher the genome-wide AS landscape and splicing dynamics in order to establish the intricacies of their functional interactions in various tissues and stresses. RNA sequencing followed by high-throughput computational analyses identified 54,526 AS events involving 15,506 AS genes that generated 57,405 transcripts isoforms. Enrichment analysis revealed their involvement in diverse regulatory functions and demonstrated that transcription factors are splicing-intensive, splice variants of which are expressed differentially across tissues and environmental cues. Increased expression of a splicing regulator NHP2L1/SNU13 was found to co-occur with lower intron retention events. The host transcriptome is significantly impacted by differential isoform expression of 1172 and 765 AS genes that resulted in 1227 (46.8% up and 53.2% downregulated) and 831 (47.5% up and 52.5% downregulated) transcript isoforms under viral pathogenesis and Fe2+ stressed condition, respectively. However, genes experiencing AS operate differently from the differentially expressed genes, suggesting AS is a unique and independent mode of regulatory mechanism. Therefore, it can be inferred that AS mediates a crucial regulatory role across tissues and stressful situations and the results would provide an invaluable resource for future endeavours in V. mungo genomics.
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Affiliation(s)
- Anjan Hazra
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203, B. T. Road, Kolkata, 700108, India
- Department of Genetics, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Amita Pal
- Division of Plant Biology, Bose Institute, Kolkata, 700091, India.
| | - Anirban Kundu
- Plant Genomics and Bioinformatics Laboratory, P.G. Department of Botany, Ramakrishna Mission Vivekananda Centenary College (Autonomous), Rahara, Kolkata, 700118, India.
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Montañés-Agudo P, Pinto YM, Creemers EE. Splicing factors in the heart: Uncovering shared and unique targets. J Mol Cell Cardiol 2023; 179:72-79. [PMID: 37059416 DOI: 10.1016/j.yjmcc.2023.04.003] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/29/2023] [Accepted: 04/09/2023] [Indexed: 04/16/2023]
Abstract
Alternative splicing generates specialized protein isoforms that allow the heart to adapt during development and disease. The recent discovery that mutations in the splicing factor RNA-binding protein 20 (RBM20) cause a severe form of familial dilated cardiomyopathy has sparked a great interest in alternative splicing in the field of cardiology. Since then, identification of splicing factors controlling alternative splicing in the heart has grown at a rapid pace. Despite the intriguing observation that a certain overlap exists between the targets of some splicing factors, an integrated and systematic analysis of their splicing networks is missing. Here, we compared the splicing networks of individual splicing factors by re-analyzing original RNA-sequencing data from eight previously published mouse models, in which a single splicing factor has been genetically deleted (i.e. HNRNPU, MBNL1/2, QKI, RBM20, RBM24, RBPMS, SRSF3, SRSF4). We show that key splicing events in Camk2d, Ryr2, Tpm1, Tpm2 and Pdlim5 require the combined action of the majority of these splicing factors. Additionally, we identified common targets and pathways among splicing factors, with the largest overlap between the splicing networks of MBNL, QKI and RBM24. We also re-analyzed a large-scale RNA-sequencing study on hearts of 128 heart failure patients. Here, we observed that MBNL1, QKI and RBM24 expression varied greatly. This variation in expression correlated with differential splicing of their downstream targets as found in mice, suggesting that aberrant splicing by MBNL1, QKI and RBM24 might contribute to the disease mechanism in heart failure.
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Affiliation(s)
- Pablo Montañés-Agudo
- Experimental Cardiology, Room K2-112, Amsterdam UMC Location University of Amsterdam, Meibergdreef 15, Amsterdam 1105AZ, the Netherlands.
| | - Yigal M Pinto
- Experimental Cardiology, Room K2-104, Amsterdam UMC, location University of Amsterdam, Meibergdreef 15, Amsterdam 1105AZ, the Netherlands.
| | - Esther E Creemers
- Experimental Cardiology, Room K2-104-2, Amsterdam UMC, Location University of Amsterdam, Meibergdreef 15, Amsterdam 1105AZ, the Netherlands.
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Zhang X, Yin X, Zhang L, Ye Z, Liang G. Identification of drug targets and prognosis projection for uterine carcinosarcoma based on alternative splicing events. Comput Biol Med 2023; 152:106346. [PMID: 36470146 DOI: 10.1016/j.compbiomed.2022.106346] [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: 09/07/2022] [Revised: 11/04/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Uterine carcinosarcoma (UCS) is an invasive variant of endometrial cancer. The complicated heterogeneity and low frequency of UCS suggest the relevant research is lack. There is an urgent need to further explore the pathogenic mechanism and identify new biomarkers of UCS from different angels to improve its diagnosis and prognosis. OBJECTIVE This study is to explore the importance of alternative splicing (AS) events in UCS, construct AS-based prognosis model and excavate key splicing factors (SFs). METHOD UCS related gene transcriptome data and AS events data were collected from The Cancer Genome Atlas (TCGA) and TCGA SpliceSeq database. The AS events related to survival were determined by Cox regression analysis, Least absolute shrinkage and selection operator (Lasso) regression analysis and optimal subset analysis. The corresponding risk score was calculated and its efficiency on prognosis was evaluated by Kaplan-Meier (K-M) survival estimate and validated by the receiver operating characteristic (ROC) curve. The prognosis model was constructed with risk score and clinic characters as independent variables to predict patients' survival. On the other hand, Kendall test was applied to inspect the correlation between the SFs and the prognosis-related AS events and a AS-SF network was constructed. Finally, the key SFs were screened through network nodes analysis and survival analysis. RESULT Seven AS events the most related to survival were detected and the risk score was obtained. K-M survival estimate and ROC curve validation suggested the risk score was effective. Then Cox model was constructed based on the risk score and a nomogram model was obtained which provided the highest prediction accuracy of 95%. Through the AS-SF network analysis, 16 SFs were screened, among which four survival-related SFs were eventually obtained. CONCLUSION The prognosis model could predict the survival rate of UCS patients by their clinical characters and AS-based risk score. And four newly discovered SFs could reveal the molecular mechanism of UCS and act as the potential drug targets and prognosis biomarkers.
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Affiliation(s)
- Xu Zhang
- School of Mathematics and Statistics, Southwest University, Chongqing, China
| | - Xiaofeng Yin
- School of Mathematics and Statistics, Southwest University, Chongqing, China
| | - Lichao Zhang
- School of Intelligent Manufacturing and Equipment, Shenzhen Institute of Information Technology, Shenzhen, China
| | - Zhiqiang Ye
- School of Elementary Education, Chongqing Normal University, Chongqing, China
| | - Guangmin Liang
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, China.
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Kashyap A, Tripathi G, Tripathi A, Rao R, Kashyap M, Bhat A, Kumar D, Rajhans A, Kumar P, Chandrashekar DS, Mahmood R, Husain A, Zayed H, Bharti AC, Kashyap MK. RNA splicing: a dual-edged sword for hepatocellular carcinoma. Med Oncol 2022; 39:173. [PMID: 35972700 DOI: 10.1007/s12032-022-01726-8] [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] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/30/2022] [Indexed: 10/15/2022]
Abstract
RNA splicing is the fundamental process that brings diversity at the transcriptome and proteome levels. The spliceosome complex regulates minor and major processes of RNA splicing. Aberrant regulation is often associated with different diseases, including diabetes, stroke, hypertension, and cancer. In the majority of cancers, dysregulated alternative RNA splicing (ARS) events directly affect tumor progression, invasiveness, and often lead to poor survival of the patients. Alike the rest of the gastrointestinal malignancies, in hepatocellular carcinoma (HCC), which alone contributes to ~ 75% of the liver cancers, a large number of ARS events have been observed, including intron retention, exon skipping, presence of alternative 3'-splice site (3'SS), and alternative 5'-splice site (5'SS). These events are reported in spliceosome and non-spliceosome complexes genes. Molecules such as MCL1, Bcl-X, and BCL2 in different isoforms can behave as anti-apoptotic or pro-apoptotic, making the spliceosome complex a dual-edged sword. The anti-apoptotic isoforms of such molecules bring in resistance to chemotherapy or cornerstone drugs. However, in contrast, multiple malignant tumors, including HCC that target the pro-apoptotic favoring isoforms/variants favor apoptotic induction and make chemotherapy effective. Herein, we discuss different splicing events, aberrations, and antisense oligonucleotides (ASOs) in modulating RNA splicing in HCC tumorigenesis with a possible therapeutic outcome.
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Abstract
Nuclear speckles are dynamic membraneless bodies located in the cell nucleus. They harbor RNAs and proteins, many of which are splicing factors, that together display complex biophysical properties dictating nuclear speckle formation and maintenance. Although these nuclear bodies were discovered decades ago, only recently has in-depth genomic analysis begun to unravel their essential functions in modulation of gene activity. Major advancements in genomic mapping techniques combined with microscopy approaches have enabled insights into the roles nuclear speckles may play in enhancing gene expression, and how gene positioning to specific nuclear landmarks can regulate gene expression and RNA processing. Some studies have drawn a link between nuclear speckles and disease. Certain maladies either involve nuclear speckles directly or dictate the localization and reorganization of many nuclear speckle factors. This is most striking during viral infection, as viruses alter the entire nuclear architecture and highjack host machinery. As discussed in this Review, nuclear speckles represent a fascinating target of study not only to reveal the links between gene positioning, genome subcompartments and gene activity, but also as a potential target for therapeutics.
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Affiliation(s)
- Gabriel P Faber
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University, Ramat Gan 5290002, Israel.,Institute of Nanotechnology , Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Shani Nadav-Eliyahu
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University, Ramat Gan 5290002, Israel.,Institute of Nanotechnology , Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences , Bar-Ilan University, Ramat Gan 5290002, Israel.,Institute of Nanotechnology , Bar-Ilan University, Ramat Gan 5290002, Israel
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Campagne S, de Vries T, Allain FHT. Probing the Interactions of Splicing Regulatory Small Molecules and Proteins with U1 snRNP Using NMR Spectroscopy. Methods Mol Biol 2022; 2537:247-262. [PMID: 35895269 DOI: 10.1007/978-1-0716-2521-7_15] [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] [Indexed: 06/15/2023]
Abstract
Alternative RNA splicing is an essential part of gene expression that not only increases the protein diversity of metazoan but also provides an additional layer of gene expression regulation. The U1 small ribonucleoparticle (U1 snRNP) plays an essential role in seeding spliceosome assembly and its binding on weak 5'-splice sites is regulated by transient interactions with splicing factors. Recent progress in allele specific splicing correction has shown the therapeutic potential offered by small molecule splicing modifiers that specifically promotes the recruitment of U1 snRNP to modulate alternative splicing and gene expression. Here, we described a method to reconstitute U1 snRNP in vitro and to study labile interactions with protein or synthetic splicing factors using solution state NMR spectroscopy. This approach allowed us to validate direct interactions between splicing regulators and U1 snRNP and could also be useful for the screening of small molecules acting on splicing regulation.
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Affiliation(s)
- Sébastien Campagne
- ARNA Laboratory, INSERM U1212, CNRS 5320, University of Bordeaux, Bordeaux, France.
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, Zurich, Switzerland.
| | - Tebbe de Vries
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Frédéric H-T Allain
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, Zurich, Switzerland.
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Kato K, Udagawa R, Hayashi Y, Maki M, Yanagida M, Higashiura S, Yagishita R, Shimamoto H, Kimura K. SF3B14 is involved in the centrosome regulation trough splicing of TUBGCP6 pre-mRNA. Biochem Biophys Res Commun 2021; 588:133-9. [PMID: 34954520 DOI: 10.1016/j.bbrc.2021.12.059] [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: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 11/20/2022]
Abstract
Splicing precursor messenger RNA (pre-mRNA) is a critical step to produce physiologically functional protein. Splicing failure not only gives rise to dysfunctional proteins but also generates abnormal protein function, which causes several diseases. Several pre-mRNA splicing factors are reported to regulate mitosis directly at mitotic structures and/or indirectly through controlling the pre-mRNA splicing for mitotic proteins. In this study, we described the mitotic functions of SF3B14, a component of the spliceosomal U2 small nuclear ribonucleoprotein (snRNP), which we identified as a candidate involved in mitosis based on the large-scale RNA interference (RNAi) screen of the nucleolar proteome database. We observed that SF3B14 depletion caused prolonged mitosis and several mitotic defects, such as monopolar spindle and chromosome misalignment during metaphase. Although SF3B14 was found in the nucleolar proteome database, our immunofluorescent stainings demonstrated that SF3B14 was predominantly localized in the nucleoplasm and excluded from the nucleolus during interphase. In addition, SF3B14 did not colocalize with specific mitotic structures during mitosis, which is not in line with its direct mitotic function. Notably, we found that the SF3B14 depletion reduced protein levels of TUBGCP6, required for centrosome regulation, and increased the unspliced/spliced ratio of its mRNA. Taken together, we propose that the pre-mRNA of TUBGCP6 is one of the targets for SF3B14 splicing through which SF3B14 controls mitotic chromosome behavior.
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Zhao YJ, Wu LY, Pang JS, Liao W, Chen YJ, He Y, Yang H. Integrated multi-omics analysis of the clinical relevance and potential regulatory mechanisms of splicing factors in hepatocellular carcinoma. Bioengineered 2021; 12:3978-3992. [PMID: 34288818 PMCID: PMC8806902 DOI: 10.1080/21655979.2021.1948949] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/23/2021] [Indexed: 01/04/2023] Open
Abstract
Splicing factors (SFs) have been increasingly documented to perturb the genome of cancers. However, little is known about the alterations of SFs in hepatocellular carcinoma (HCC). This study comprehensively delineated the genomic and epigenomic characteristics of 404 SFs in HCC based on the multi-omics data from the Cancer Genome Atlas database. The analysis revealed several clinically relevant SFs that could be effective biomarkers for monitoring the onset and prognosis of HCC (such as, HSPB1, DDX39A, and NELFE, which were the three most significant clinically relevant SFs). Functional enrichment analysis of these indicators showed the enrichment of pathways related to splicing and mRNA processes. Furthermore, the study found that SF copy number variation is common in HCC and could be a typical characteristic of hepato-carcinogenesis; the complex expression regulation of SFs was significantly affected by copy number variant and methylation. Several SFs with significant mutation patterns were identified (such as, RNF213, SF3B1, SPEN, NOVA1, and EEF1A1), and the potential regulatory network of SFs was constructed to identify their potential mechanisms for regulating clinically relevant alternative splicing events. Therefore, this study established a foundation to uncover the broad molecular spectrum of SFs for future functional and therapeutic studies of HCC.
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Affiliation(s)
- Yu-jia Zhao
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Lin-Yong Wu
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Jin-shu Pang
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Wei Liao
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Yu-ji Chen
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Yun He
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
| | - Hong Yang
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, P. R. China
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13
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Zhang D, Zou D, Deng Y, Yang L. Systematic analysis of the relationship between ovarian cancer prognosis and alternative splicing. J Ovarian Res 2021; 14:120. [PMID: 34526089 PMCID: PMC8442315 DOI: 10.1186/s13048-021-00866-1] [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: 05/02/2021] [Accepted: 06/30/2021] [Indexed: 11/10/2022] Open
Abstract
Background Ovarian cancer(OC) is the gynecological tumor with the highest mortality rate, effective biomarkers are of great significance in improving its prognosis. In recent years, there have been many studies on alternative splicing (AS) events, and the role of AS events in tumor has become a focus of attention. Methods Data were downloaded from the TCGA database and Univariate Cox regression analysis was performed to determine AS events associated with OC prognosis.Eight prognostic models of OC were constructed in R package, and the accuracy of the models were evaluated by the time-dependent receiver operating characteristic (ROC) curves.Eight types of survival curves were drawn to evaluate the differences between the high and low risk groups.Independent prognostic factors of OC were analyzed by single factor independent analysis and multi-factor independent prognostic analysis.Again, Univariate Cox regression analysis was used to analyze the relationship between splicing factors(SF) and AS events, and Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) enrichment analysis were performed on OS-related SFs to understand the pathways. Results Univariate Cox regression analysis showed that among the 15,278 genes, there were 31,286 overall survival (OS) related AS events, among which 1524 AS events were significantly correlated with OS. The area under the time-dependent receiver operating characteristic curve (AUC) of AT and ME were the largest and the RI was the smallest,which were 0.757 and 0.68 respectively. The constructed models have good value for the prognosis assessment of OC patients. Among the eight survival curves, AP was the most significant difference between the high and low risk groups, with a P value of 1.61e − 1.The results of single factor independent analysis and multi-factor independent prognostic analysis showed that risk score calculated by the model and age could be used as independent risk factors.According to univariate COX regression analysis,109 SFs were correlated with AS events and adjusted in two ways: positive and negative. Conclusions SFs and AS events can directly or indirectly affect the prognosis of OC patients. It is very important to find effective prognostic markers to improve the survival rate of OC. Supplementary Information The online version contains supplementary material available at 10.1186/s13048-021-00866-1.
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Affiliation(s)
- Di Zhang
- Department of Gynaecology, the 2nd Afliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Dan Zou
- Department of Gynaecology, the 2nd Afliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Yue Deng
- Department of Gynaecology, the 2nd Afliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Lihua Yang
- Department of Gynaecology, the 2nd Afliated Hospital of Kunming Medical University, Kunming, Yunnan, China.
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14
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Al Abo M, Hyslop T, Qin X, Owzar K, George DJ, Patierno SR, Freedman JA. Differential alternative RNA splicing and transcription events between tumors from African American and White patients in The Cancer Genome Atlas. Genomics 2021; 113:1234-1246. [PMID: 33705884 DOI: 10.1016/j.ygeno.2021.02.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 10/09/2020] [Revised: 01/15/2021] [Accepted: 02/01/2021] [Indexed: 11/26/2022]
Abstract
Individuals of African ancestry suffer disproportionally from higher incidence, aggressiveness, and mortality for particular cancers. This disparity likely results from an interplay among differences in multiple determinants of health, including differences in tumor biology. We used The Cancer Genome Atlas (TCGA) SpliceSeq and TCGA aggregate expression datasets and identified differential alternative RNA splicing and transcription events (ARS/T) in cancers between self-identified African American (AA) and White (W) patients. We found that retained intron events were enriched among race-related ARS/T. In addition, on average, 12% of the most highly ranked race-related ARS/T overlapped between any two analyzed cancers. Moreover, the genes undergoing race-related ARS/T functioned in cancer-promoting pathways, and a number of race-related ARS/T were associated with patient survival. We built a web-application, CanSplice, to mine genomic datasets by self-identified race. The race-related targets have the potential to aid in the development of new biomarkers and therapeutics to mitigate cancer disparity.
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Affiliation(s)
- Muthana Al Abo
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Terry Hyslop
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Xiaodi Qin
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kouros Owzar
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Daniel J George
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Medicine, Division of Medical Oncology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Steven R Patierno
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Medicine, Division of Medical Oncology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jennifer A Freedman
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA; Department of Medicine, Division of Medical Oncology, Duke University School of Medicine, Durham, NC, 27710, USA.
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15
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Abstract
Alternative splicing (AS) plays a critical role in enhancing proteome complexity in higher eukaryotes. Almost all the multi intron-containing genes undergo AS in humans. Splicing mainly occurs co-transcriptionally, where RNA polymerase II (RNA pol II) plays a crucial role in coordinating transcription and pre-mRNA splicing. Aberrant AS leads to non-functional proteins causative in various pathophysiological conditions such as cancers, neurodegenerative diseases, and muscular dystrophies. Transcription and pre-mRNA splicing are deeply interconnected and can influence each other's functions. Several studies evinced that specific promoters employed by RNA pol II dictate the RNA processing decisions. Promoter-specific recruitment of certain transcriptional factors or transcriptional coactivators influences splicing, and the extent to which these factors affect splicing has not been discussed in detail. Here, in this review, various DNA-binding proteins and their influence on promoter-specific AS are extensively discussed. Besides, this review highlights how the promoter-specific epigenetic changes might regulate AS.
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16
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Koedoot E, van Steijn E, Vermeer M, González-Prieto R, Vertegaal ACO, Martens JWM, Le Dévédec SE, van de Water B. Splicing factors control triple-negative breast cancer cell mitosis through SUN2 interaction and sororin intron retention. J Exp Clin Cancer Res 2021; 40:82. [PMID: 33648524 PMCID: PMC7919097 DOI: 10.1186/s13046-021-01863-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 10/29/2020] [Accepted: 02/01/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited therapeutic opportunities. Recently, splicing factors have gained attention as potential targets for cancer treatment. Here we systematically evaluated the role of RNA splicing factors in TNBC cell proliferation. METHODS In this study, we performed an RNAi screen targeting 244 individual splicing factors to systematically evaluate their role in TNBC cell proliferation. For top candidates, mechanistic insight was gained using amongst others western blot, PCR, FACS, molecular imaging and cloning. Pulldown followed by mass spectrometry were used to determine protein-protein interactions and patient-derived RNA sequencing data was used relate splicing factor expression levels to proliferation markers. RESULTS We identified nine splicing factors, including SNRPD2, SNRPD3 and NHP2L1, of which depletion inhibited proliferation in two TNBC cell lines by deregulation of sister chromatid cohesion (SCC) via increased sororin intron 1 retention and down-regulation of SMC1, MAU2 and ESPL1. Protein-protein interaction analysis of SNRPD2, SNRPD3 and NHP2L1 identified that seven out of the nine identified splicing factors belong to the same spliceosome complex including novel component SUN2 that was also critical for efficient sororin splicing. Finally, sororin transcript levels are highly correlated to various proliferation markers in BC patients. CONCLUSION We systematically determined splicing factors that control proliferation of breast cancer cells through a mechanism that involves effective sororin splicing and thereby appropriate sister chromatid cohesion. Moreover, we identified SUN2 as an important new spliceosome complex interacting protein that is critical in this process. We anticipate that deregulating sororin levels through targeting of the relevant splicing factors might be a potential strategy to treat TNBC.
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Affiliation(s)
- Esmee Koedoot
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Eline van Steijn
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marjolein Vermeer
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Román González-Prieto
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - John W M Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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17
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Xie X, Zheng X, Xie T, Cai J, Yao Y. Identification of prognostic alternative splicing signatures in uveal melanoma. Int Ophthalmol 2021; 41:1347-1362. [PMID: 33479809 DOI: 10.1007/s10792-021-01699-z] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 01/08/2021] [Indexed: 10/25/2022]
Abstract
PURPOSE Alternative splicing (AS) events were reportedly associated with the development of multiple cancers. The study was designed to provide a comprehensive analysis of AS events and explore their potential prognostic value in uveal melanoma (UM). METHODS The prognostic AS events, identified based on the data of 80 UM patients obtained from The Cancer Genome Atlas, were further screened and analyzed for construction of prognostic signatures by using LASSO regression and multivariate Cox model. Kaplan-Meier survival analysis was used to evaluate the prognostic value. The AS events-related functional pathways were explored by gene set enrichment analysis (GSEA). The difference between two subgroups in terms of treatment options was investigated. The regulatory network between prognostic AS events and splicing factors (SFs) was then constructed. RESULTS A total of 1014 AS events were identified as prognostic AS events. Five prognostic AS events were involved in the construction of prognostic signatures, including AKAP2/87175/AP, RGMA/32575/ES, DNASE1L1/90581/ES, BIN1/55198/ES and ERCC2/50430/AT. UM patients were then divided into two subgroups. Prognostic AS signatures had an excellent performance in predicting the survival of UM patients, with an area under curve (AUC) of 0.962. GSEA results suggested several splicing-associated mechanisms, including cellular metabolic process and apoptosis. Low-risk subgroup could be more sensitive to drugs. A higher expression of immune checkpoint genes was observed in high-risk group than in low-risk group. SFs-AS regulatory network also revealed significant association between AS events and SFs. CONCLUSIONS Aberrant AS events in UM patients might serve as prognostic predictors.
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Affiliation(s)
- Xinyi Xie
- Department of Ophthalmology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Qing Yang Road 299, Wuxi, Jiangsu, 214023, China
| | - Xinhua Zheng
- Department of Ophthalmology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Qing Yang Road 299, Wuxi, Jiangsu, 214023, China
| | - Tianhua Xie
- Department of Ophthalmology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Qing Yang Road 299, Wuxi, Jiangsu, 214023, China
| | - Jiping Cai
- Department of Ophthalmology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Qing Yang Road 299, Wuxi, Jiangsu, 214023, China
| | - Yong Yao
- Department of Ophthalmology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Qing Yang Road 299, Wuxi, Jiangsu, 214023, China.
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18
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Abstract
Quantification of alternative splicing to detect the abundance of differentially spliced isoforms of a gene in total RNA can be accomplished via RT-PCR using both quantitative real-time and semiquantitative PCR methods. These methods require careful PCR primer design to ensure specific detection of particular splice isoforms. We will also describe analysis of alternative splicing using a splicing "minigene" in mammalian cell tissue culture to facilitate investigation of the regulation of alternative splicing of a particular exon of interest.
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Affiliation(s)
- Samuel E Harvey
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jingyi Lyu
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chonghui Cheng
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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19
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Abstract
N6-methyladenosine (m6A) is the most prevalent posttranscriptional modification in eukaryotes and plays a pivotal role in various biological processes. A knowledge base with the systematic collection and curation of context specific transcriptome-wide methylations is critical for elucidating their biological functions as well as for developing bioinformatics tools. In this chapter, we present a comprehensive platform MeT-DB V2.0 for elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome. Met-DB V2.0 database contains context specific m6A peaks and single-base sites predicted from 185 samples for 7 species from 26 independent studies. Moreover, it is also integrated with a new database for targets of m6A readers, erasers and writers and expanded with more collections of functional data. The Met-DB V2.0 web interface and genome browser provide more friendly, powerful, and informative ways to query and visualize the data. More importantly, MeT-DB V2.0 offers for the first time a series of tools specifically designed for understanding m6A functions. The MeT-DB V2.0 web server is freely available at: http://compgenomics.utsa.edu/MeTDB and www.xjtlu.edu.cn/metdb2 .
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Affiliation(s)
- Hui Liu
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu, China
| | - Jiani Ma
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu, China
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Lin Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, Jiangsu, China.
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20
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Du JX, Zhu GQ, Cai JL, Wang B, Luo YH, Chen C, Cai CZ, Zhang SJ, Zhou J, Fan J, Zhu W, Dai Z. Splicing factors: Insights into their regulatory network in alternative splicing in cancer. Cancer Lett 2020; 501:83-104. [PMID: 33309781 DOI: 10.1016/j.canlet.2020.11.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/18/2022]
Abstract
More than 95% of all human genes are alternatively spliced after transcription, which enriches the diversity of proteins and regulates transcript and/or protein levels. The splicing isoforms produced from the same gene can manifest distinctly, even exerting opposite effects. Mounting evidence indicates that the alternative splicing (AS) mechanism is ubiquitous in various cancers and drives the generation and maintenance of various hallmarks of cancer, such as enhanced proliferation, inhibited apoptosis, invasion and metastasis, and angiogenesis. Splicing factors (SFs) play pivotal roles in the recognition of splice sites and the assembly of spliceosomes during AS. In this review, we mainly discuss the similarities and differences of SF domains, the details of SF function in AS, the effect of SF-driven pathological AS on different hallmarks of cancer, and the main drivers of SF expression level and subcellular localization. In addition, we briefly introduce the application prospects of targeted therapeutic strategies, including small-molecule inhibitors, siRNAs and splice-switching oligonucleotides (SSOs), from three perspectives (drivers, SFs and pathological AS). Finally, we share our insights into the potential direction of research on SF-centric AS-related regulatory networks.
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Affiliation(s)
- Jun-Xian Du
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Gui-Qi Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia-Liang Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Biao Wang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Yi-Hong Luo
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cong Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Cheng-Zhe Cai
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Si-Jia Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Jian Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China
| | - Wei Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
| | - Zhi Dai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China; Key Laboratory of Carcinogenesis and Cancer Invasion, Fudan University, Ministry of Education, Shanghai, 200032, China.
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21
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Jakubauskienė E, Vilys L, Pečiulienė I, Kanopka A. The role of hypoxia on Alzheimer's disease-related APP and Tau mRNA formation. Gene 2020; 766:145146. [PMID: 32941952 DOI: 10.1016/j.gene.2020.145146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 05/24/2020] [Revised: 08/24/2020] [Accepted: 09/09/2020] [Indexed: 12/26/2022]
Abstract
The removal of introns from mRNA precursors (pre-mRNAs) is an essential step in eukaryotic gene expression. The splicing machinery heavily contributes to biological complexity and especially to the ability of cells to adapt to altered cellular conditions. Hypoxia also plays a key role in the pathophysiology of many diseases, including Alzheimer's disease (AD). In the presented study, we have examined the influence of cellular hypoxia on mRNA splice variant formation from Alzheimer's disease-related Tau and APP genes in brain cells. We have shown that the hypoxic microenvironment influenced the formation of Tau mRNA splice variants, but had no effect on APP mRNA splice variant formation. Additionally, our presented results indicate that splicing factor SRSF1 but not SRSF5 alters the formation of Tau cellular mRNA splice variants in hypoxic cells. Obtained results have also shown that hypoxic brain cells possess enhanced CLK1-4 kinase mRNA levels. This study underlines that cellular hypoxia can influence disease development through changing pre-mRNA splicing.
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Affiliation(s)
| | - Laurynas Vilys
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Inga Pečiulienė
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania
| | - Arvydas Kanopka
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.
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22
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More DA, Kumar A. SRSF3: Newly discovered functions and roles in human health and diseases. Eur J Cell Biol 2020; 99:151099. [PMID: 32800280 DOI: 10.1016/j.ejcb.2020.151099] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 04/29/2020] [Revised: 06/15/2020] [Accepted: 06/29/2020] [Indexed: 12/21/2022] Open
Abstract
The serine/arginine rich proteins (SR proteins) are members of a family of RNA binding proteins involved in regulating various features of RNA metabolism, including pre-mRNA constitutive and alternative splicing. In humans, a total of 12 SR splicing factors (SRSFs) namely SRSF1-SRSF12 have been reported. SRSF3, the smallest member of the SR family and the focus of this review, regulates critical steps in mRNA metabolism and has been shown to have mRNA-independent functions as well. Recent studies on SRSF3 have uncovered its role in a wide array of complex biological processes. We have also reviewed the involvement of SRSF3 in disease conditions like cancer, ageing, neurological and cardiac disorders. Finally, we have discussed in detail the autoregulation of SRSF3 and its implications in cancer and commented on the potential of SRSF3 as a therapeutic target, especially in the context of cancer.
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Affiliation(s)
- Dhanashree Anil More
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Arun Kumar
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India.
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23
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Ding Y, Feng G, Yang M. Prognostic role of alternative splicing events in head and neck squamous cell carcinoma. Cancer Cell Int 2020; 20:168. [PMID: 32467664 PMCID: PMC7227031 DOI: 10.1186/s12935-020-01249-0] [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: 01/31/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
Background Aberrant alternative splicing (AS) is implicated in biological processes of cancer. This study aims to reveal prognostic AS events and signatures that may serve as prognostic predictors for head and neck squamous cell carcinoma (HNSCC). Methods Prognostic AS events in HNSCC were identified by univariate COX analysis. Prognostic signatures comprising prognostic AS events were constructed for prognosis prediction in patients with HNSCC. The correlation between the percent spliced in (PSI) values of AS events and the expression of splicing factors (SFs) was analyzed by Pearson correlation analysis. Gene functional annotation analysis was performed to reveal pathways in which prognostic AS is enriched. Results A total of 27,611 AS events in 15,873 genes were observed, and there were 3433 AS events in 2624 genes significantly associated with overall survival (OS) for HNSCC. Moreover, we found that AS prognostic signatures could accurately predict HNSCC prognosis. SF-AS regulatory networks were constructed according to the correlation between PSI values of AS events and the expression levels of SFs. Conclusions Our study identified prognostic AS events and signatures. Furthermore, it established SF-AS networks in HNSCC that were valuable in predicting the prognosis of patients with HNSCC and elucidating the regulatory mechanisms underlying AS in HNSCC.
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Affiliation(s)
- Yanni Ding
- Department of Breast Surgery, Shaan Xi Provincial Tumor Hospital, Xi'an City, Shaan Xi Province 710000 China
| | - Guang Feng
- 2The Third Department of Burns and Plastic Surgery and Center of Wound Repair, The Fourth Medical Center of PLA General Hospital, Beijing, 100048 China
| | - Min Yang
- Department of Breast Surgery, Shaan Xi Provincial Tumor Hospital, Xi'an City, Shaan Xi Province 710000 China
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24
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Abstract
Pre-mRNA splicing is the removal of introns and ligation of exons to form mature mRNAs, and it provides a critical mechanism by which eukaryotic cells can regulate their gene expression. Strikingly, more than 90% of protein-encoding transcripts are alternatively spliced, through exon inclusion/skipping, differential use of 5' or 3' alternative splice sites, intron retention or selection of an alternative promoter, thereby drastically increasing protein diversity. Splicing is altered in various pathological conditions, including cancers. In the last decade, high-throughput transcriptomic analyses have identified thousands of splice variants in cancers, which can distinguish between tumoral and normal tissues as well as identify tumor types, subtypes and clinical stages. These abnormal or aberrantly expressed splice variants, found in all cancer hallmarks, can result from mutations in splice sites, deregulated expression or even somatic mutations of components of the spliceosome machinery. Therefore, and based on these recent observations, a new anti-cancer strategy of targeting the spliceosome machinery with small molecules has emerged; however, the potential for these therapies is still a matter of great debate. Notably, more preclinical studies are needed to clarify which splicing patterns are mainly affected by these compounds, which cancer patients could be the most eligible for these treatments and whether using these spliceosome inhibitors alone or in combination with chemotherapies or targeted therapies would provide better therapeutic benefits. In this commentary, I will discuss all of these aspects.
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Affiliation(s)
- Beatrice Eymin
- INSERM U1209, CNRS UMR5309, Institute For Advanced Biosciences, 38000 Grenoble, France; Université Grenoble Alpes, 38000 Grenoble, France.
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25
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Lee BP, Smith M, Buffenstein R, Harries LW. Negligible senescence in naked mole rats may be a consequence of well-maintained splicing regulation. GeroScience 2020; 42:633-651. [PMID: 31927681 PMCID: PMC7205774 DOI: 10.1007/s11357-019-00150-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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: 11/22/2019] [Accepted: 12/27/2019] [Indexed: 02/07/2023] Open
Abstract
Naked mole-rats (NMRs) have amongst the longest lifespans relative to body size of any known, non-volant mammalian species. They also display an enhanced stress resistance phenotype, negligible senescence and very rarely are they burdened with chronic age-related diseases. Alternative splicing (AS) dysregulation is emerging as a potential driver of senescence and ageing. We hypothesised that the expression of splicing factors, important regulators of patterns of AS, may differ in NMRs when compared to other species with relatively shorter lifespans. We designed assays specific to NMR splicing regulatory factors and also to a panel of pre-selected brain-expressed genes known to demonstrate senescence-related alterations in AS in other species, and measured age-related changes in the transcript expression levels of these using embryonic and neonatal developmental stages through to extreme old age in NMR brain samples. We also compared splicing factor expression in both young mouse and NMR spleen and brain samples. Both NMR tissues showed approximately double the expression levels observed in tissues from similarly sized mice. Furthermore, contrary to observations in other species, following a brief period of labile expression in early life stages, adult NMR splicing factors and patterns of AS for functionally relevant brain genes remained remarkably stable for at least two decades. These findings are consistent with a model whereby the conservation of splicing regulation and stable patterns of AS may contribute to better molecular stress responses and the avoidance of senescence in NMRs, contributing to their exceptional lifespan and prolonged healthspan.
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Affiliation(s)
- B P Lee
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | - M Smith
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA
| | - R Buffenstein
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA.
| | - L W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK.
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26
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Rong MH, Zhu ZH, Guan Y, Li MW, Zheng JS, Huang YQ, Wei DM, Li YM, Wu XJ, Bu HP, Peng HL, Wei XL, Li GS, Li MX, Chen MH, Huang SN. Identification of prognostic splicing factors and exploration of their potential regulatory mechanisms in pancreatic adenocarcinoma. PeerJ 2020; 8:e8380. [PMID: 32095320 PMCID: PMC7020824 DOI: 10.7717/peerj.8380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [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: 06/04/2019] [Accepted: 12/10/2019] [Indexed: 12/24/2022] Open
Abstract
Pancreatic adenocarcinoma (PAAD), the most common subtype of pancreatic cancer, is a highly lethal disease. In this study, we integrated the expression profiles of splicing factors (SFs) of PAAD from RNA-sequencing data to provide a comprehensive view of the clinical significance of SFs. A prognostic index (PI) based on SFs was developed using the least absolute shrinkage and selection operator (LASSO) COX analysis. The PI exhibited excellent performance in predicting the status of overall survival of PAAD patients. We also used the percent spliced in (PSI) value obtained from SpliceSeq software to quantify different types of alternative splicing (AS). The prognostic value of AS events was explored using univariate COX and LASSO COX analyses; AS-based PIs were also proposed. The integration of prognosis-associated SFs and AS events suggested the potential regulatory mechanisms of splicing processes in PAAD. This study defined the markedly clinical significance of SFs and provided novel insight into their potential regulatory mechanisms.
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Affiliation(s)
- Min-Hua Rong
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Zhan-Hui Zhu
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Ying Guan
- Affiliated Cancer Hospital, Guangxi Medical University, Department of Radiotherapy, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Mei-Wei Li
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Jia-Shuo Zheng
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Yue-Qi Huang
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Dan-Ming Wei
- First Affiliated Hospital, Guangxi Medical University, Department of Pathology, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Ying-Mei Li
- First Affiliated Hospital, Guangxi Medical University, Department of Pathology, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Xiao-Ju Wu
- First Affiliated Hospital, Guangxi Medical University, Department of Pathology, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Hui-Ping Bu
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Hui-Liu Peng
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Xiao-Lin Wei
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Guo-Sheng Li
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Ming-Xuan Li
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Ming-Hui Chen
- Affiliated Cancer Hospital, Guangxi Medical University, Research Department, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
| | - Su-Ning Huang
- Affiliated Cancer Hospital, Guangxi Medical University, Department of Radiotherapy, Nanning, Guangxi Zhuang Autonomous Region, P.R. China
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27
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Hamieh A, Nandrot EF. Retinal Pigment Epithelial Cells: The Unveiled Component in the Etiology of Prpf Splicing Factor-Associated Retinitis Pigmentosa. Adv Exp Med Biol 2020; 1185:227-231. [PMID: 31884616 DOI: 10.1007/978-3-030-27378-1_37] [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] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pre-mRNA splicing is a critical step in RNA processing in all eukaryotic cells. It consists of introns removal and requires the assembly of a large RNA-protein complex called the spliceosome. This complex of small nuclear ribonucleoproteins is associated with accessory proteins from the pre-mRNA processing factor (PRPF) family. Mutations in different splicing factor-encoding genes were identified in retinitis pigmentosa (RP) patients. A surprising feature of these ubiquitous factors is that the outcome of their alteration is restricted to the retina. Because of their high metabolic demand, most studies focused on photoreceptors dysfunction and associated degeneration. However, cells from the retinal pigment epithelium (RPE) are also crucial to maintaining retinal homeostasis and photoreceptor function. Moreover, mutations in RPE-specific genes are associated with some RP cases. Indeed, we identified major RPE defects in Prpf31-mutant mice: circadian rhythms of both photoreceptor outer segments (POS) phagocytosis and retinal adhesion were attenuated or lost, leading to ultrastructural anomalies and vacuoles. Taken together, our published and ongoing data suggest that (1) similar molecular events take place in human and mouse cells and (2) these functional defects generate various stress processes.
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Affiliation(s)
- Abdallah Hamieh
- Therapeutics Department, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Emeline F Nandrot
- Therapeutics Department, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.
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28
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Song H, Wang L, Chen D, Li F. The Function of Pre-mRNA Alternative Splicing in Mammal Spermatogenesis. Int J Biol Sci 2020; 16:38-48. [PMID: 31892844 PMCID: PMC6930371 DOI: 10.7150/ijbs.34422] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [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: 02/26/2019] [Accepted: 09/20/2019] [Indexed: 01/05/2023] Open
Abstract
Alternative pre-mRNA splicing plays important roles in co-transcriptional and post-transcriptional regulation of gene expression functioned during many developmental processes, such as spermatogenesis. The studies focusing on alternative splicing on spermatogenesis supported the notion that the development of testis is regulated by a higher level of alternative splicing than other tissues. Here, we aim to review the mechanisms underlying alternative splicing, particularly the splicing variants functioned in the process of spermatogenesis and the male infertility. There are five points regarding the alternative splicing including ⅰ) a brief introduction of alternative pre-mRNA splicing; ⅱ) the alternative splicing events in spermatogenesis-associated genes enriched in different stages of spermatogenesis; ⅲ) the mechanisms of alternative splicing regulation, such as splicing factors and m6A demethylation; ⅳ) the splice site recognition and alternative splicing, including the production and degradation of abnormal transcripts caused by gene variations and nonsense-mediated mRNA decay, respectively; ⅴ) abnormal alternative splicing correlated with male infertility. Taking together, this review highlights the impacts of alternative splicing and splicing variants in mammal spermatogenesis and provides new insights of the potential application of the alternative splicing into the therapy of male infertility.
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Affiliation(s)
- Huibin Song
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ling Wang
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Dake Chen
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Fenge Li
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, PR China
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29
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Yang X, Huang WT, He RQ, Ma J, Lin P, Xie ZC, Ma FC, Chen G. Determining the prognostic significance of alternative splicing events in soft tissue sarcoma using data from The Cancer Genome Atlas. J Transl Med 2019; 17:283. [PMID: 31443718 PMCID: PMC6708253 DOI: 10.1186/s12967-019-2029-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 03/09/2019] [Accepted: 08/18/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Surgery, adjuvant chemotherapy, and radiotherapy are the primary treatment options for soft tissue sarcomas (STSs). However, identifying ways to improve the prognosis of patients with STS remains a considerable challenge. Evidence shows that the dysregulation of alternative splicing (AS) events is involved in tumor pathogenesis and progression. The present study objective was to identify survival-associated AS events that could serve as prognostic biomarkers and potentially serve as tumor-selective STS drug targets. METHODS STS-specific 'percent spliced in' (PSI) values for splicing events in 206 STS samples were downloaded from The Cancer Genome Atlas SpliceSeq® database. Prognostic analyses were performed on seven types of AS events to determine their prognostic value in STS patients, for which prediction models were constructed with the risk score formula [Formula: see text]. Prediction models were also constructed to determine the prognostic value of AS events, and Spearman's rank correlation coefficients were calculated to determine the degree of correlation between splicing factor expression and the PSI values. RESULTS A total 10,439 events were found to significantly correlate with patient survival rates. The area under the time-dependent receiver operating characteristic curve for the prognostic predictor of STS overall survival was 0.826. Notably, the splicing events of certain STS key genes were significantly associated with STS 2-year overall survival in the present study, including exon skip (ES) events in MDM2 and EWSR1, alternate terminator events in CDKN2A and HMGA2 for dedifferentiated liposarcoma, ES in MDM2 and alternate promoter events in CDKN2A for leiomyosarcoma, and ES in EWSR1 for undifferentiated pleomorphic sarcoma. Moreover, splicing correlation networks between AS events and splicing factors revealed that almost all of the AS events showed negatively correlations with the expression of splicing factors. CONCLUSION An in-depth analysis of alternative RNA splicing could provide new insights into the mechanisms of STS oncogenesis and the potential for novel approaches to this type of cancer therapy.
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Affiliation(s)
- Xia Yang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Wen-Ting Huang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Rong-Quan He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jie Ma
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Peng Lin
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Zu-Cheng Xie
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Fu-Chao Ma
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
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30
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Perrone B, La Cognata V, Sprovieri T, Ungaro C, Conforti FL, Andò S, Cavallaro S. Alternative Splicing of ALS Genes: Misregulation and Potential Therapies. Cell Mol Neurobiol 2019; 40:1-14. [PMID: 31385134 DOI: 10.1007/s10571-019-00717-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 04/09/2019] [Accepted: 07/31/2019] [Indexed: 12/12/2022]
Abstract
Neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA), Parkinson's, Alzheimer's, and Huntington's disease affect a rapidly increasing population worldwide. Although common pathogenic mechanisms have been identified (e.g., protein aggregation or dysfunction, immune response alteration and axonal degeneration), the molecular events underlying timing, dosage, expression, and location of RNA molecules are still not fully elucidated. In particular, the alternative splicing (AS) mechanism is a crucial player in RNA processing and represents a fundamental determinant for brain development, as well as for the physiological functions of neuronal circuits. Although in recent years our knowledge of AS events has increased substantially, deciphering the molecular interconnections between splicing and ALS remains a complex task and still requires considerable efforts. In the present review, we will summarize the current scientific evidence outlining the involvement of AS in the pathogenic processes of ALS. We will also focus on recent insights concerning the tuning of splicing mechanisms by epigenomic and epi-transcriptomic regulation, providing an overview of the available genomic technologies to investigate AS drivers on a genome-wide scale, even at a single-cell level resolution. In the future, gene therapy strategies and RNA-based technologies may be utilized to intercept or modulate the splicing mechanism and produce beneficial effects against ALS.
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Affiliation(s)
- Benedetta Perrone
- Institute for Biomedical Research and Innovation, National Research Council, Mangone, Cosenza, Italy
| | - Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council, Catania, Italy
| | - Teresa Sprovieri
- Institute for Biomedical Research and Innovation, National Research Council, Mangone, Cosenza, Italy
| | - Carmine Ungaro
- Institute for Biomedical Research and Innovation, National Research Council, Mangone, Cosenza, Italy
| | - Francesca Luisa Conforti
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, Cosenza, Italy
| | - Sebastiano Andò
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, Cosenza, Italy.,Centro Sanitario, University of Calabria, Arcavacata di Rende, Cosenza, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council, Catania, Italy.
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31
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Lee BP, Pilling LC, Bandinelli S, Ferrucci L, Melzer D, Harries LW. The transcript expression levels of HNRNPM, HNRNPA0 and AKAP17A splicing factors may be predictively associated with ageing phenotypes in human peripheral blood. Biogerontology 2019; 20:649-663. [PMID: 31292793 PMCID: PMC6733819 DOI: 10.1007/s10522-019-09819-0] [Citation(s) in RCA: 10] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/24/2019] [Indexed: 12/18/2022]
Abstract
Dysregulation of splicing factor expression is emerging as a driver of human ageing; levels of transcripts encoding splicing regulators have previously been implicated in ageing and cellular senescence both in vitro and in vivo. We measured the expression levels of an a priori panel of 20 age- or senescence-associated splicing factors by qRT-PCR in peripheral blood samples from the InCHIANTI Study of Aging, and assessed longitudinal relationships with human ageing phenotypes (cognitive decline and physical ability) using multivariate linear regression. AKAP17A, HNRNPA0 and HNRNPM transcript levels were all predictively associated with severe decline in MMSE score (p = 0.007, 0.001 and 0.008 respectively). Further analyses also found expression of these genes was associated with a performance decline in two other cognitive measures; the Trail Making Test and the Purdue Pegboard Test. AKAP17A was nominally associated with a decline in mean hand-grip strength (p = 0.023), and further analyses found nominal associations with two other physical ability measures; the Epidemiologic Studies of the Elderly-Short Physical Performance Battery and calculated speed (m/s) during a timed 400 m fast walking test. These data add weight to the hypothesis that splicing dyregulation may contribute to the development of some ageing phenotypes in the human population.
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Affiliation(s)
- Benjamin P Lee
- Institute of Biomedical and Clinical Sciences, University of Exeter College of Medicine and Health, RILD Building, RD&E NHSFT Campus, Barrack Rd, Exeter, EX2 5DW, UK
| | - Luke C Pilling
- Epidemiology and Public Health, University of Exeter College of Medicine and Health, RILD Building, RD&E NHSFT Campus, Barrack Rd, Exeter, EX2 5DW, UK
| | | | - Luigi Ferrucci
- National Institute on Aging, Clinical Research Branch, Harbor Hospital, Baltimore, MD, 21225, USA
| | - David Melzer
- Epidemiology and Public Health, University of Exeter College of Medicine and Health, RILD Building, RD&E NHSFT Campus, Barrack Rd, Exeter, EX2 5DW, UK
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter College of Medicine and Health, RILD Building, RD&E NHSFT Campus, Barrack Rd, Exeter, EX2 5DW, UK.
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32
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Wang H, Lekbaby B, Fares N, Augustin J, Attout T, Schnuriger A, Cassard AM, Panasyuk G, Perlemuter G, Bieche I, Vacher S, Selves J, Péron JM, Bancel B, Merle P, Kremsdorf D, Hall J, Chemin I, Soussan P. Alteration of splicing factors' expression during liver disease progression: impact on hepatocellular carcinoma outcome. Hepatol Int 2019; 13:454-467. [PMID: 31140152 DOI: 10.1007/s12072-019-09950-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 12/12/2018] [Accepted: 04/29/2019] [Indexed: 12/29/2022]
Abstract
PURPOSE Trans-acting splicing factors (SF) shape the eukaryotic transcriptome by regulating alternative splicing (AS). This process is recurrently modulated in liver cancer suggesting its direct contribution to the course of liver disease. The aim of our study was to investigate the relationship between the regulation of SFs expression and liver damage. METHODS The expression profile of 10 liver-specific SF and the AS events of 7 genes associated with liver disorders was assessed by western-blotting in 6 murine models representing different stages of liver damage, from inflammation to hepatocellular carcinoma (HCC). Relevant SFs (PSF, SRSF3, and SRSF6) and target genes (INSR, SRSF3, and SLK) modulated in mice were investigated in a cohort of 179 HCC patients. RESULTS Each murine model of liver disease was characterized by a unique SF expression profile. Changes in the SF profile did not affect AS events of the selected genes despite the presence of corresponding splicing sites. In human HCC expression of SFs, including the tumor-suppressor SRSF3, and AS regulation of genes studied were frequently upregulated in tumor versus non-tumor tissues. Risk of tumor recurrence positively correlated with AS isoform of the INSR gene. In contrast, increased levels of SFs expression correlated with an extended overall survival of patients. CONCLUSIONS Dysregulation of SF expression is an early event occurring during liver injury and not just at the stage of HCC. Besides impacting on AS regulation, overexpression of SF may contribute to preserving hepatocyte homeostasis during liver pathogenesis.
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Affiliation(s)
- Hualin Wang
- INSERM U1135, Centre d'immunologie et de maladie infectieuse, 91 boulevard de l'Hôpital, 75013, Paris, France.,Sorbonne Université, Paris, France
| | - Bouchra Lekbaby
- INSERM U1135, Centre d'immunologie et de maladie infectieuse, 91 boulevard de l'Hôpital, 75013, Paris, France.,Sorbonne Université, Paris, France
| | - Nadim Fares
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052, CNRS 5286, Lyon Cedex 03, France
| | - Jeremy Augustin
- INSERM U1135, Centre d'immunologie et de maladie infectieuse, 91 boulevard de l'Hôpital, 75013, Paris, France.,Sorbonne Université, Paris, France
| | - Tarik Attout
- INSERM U1135, Centre d'immunologie et de maladie infectieuse, 91 boulevard de l'Hôpital, 75013, Paris, France.,Sorbonne Université, Paris, France
| | - Aurelie Schnuriger
- INSERM U1135, Centre d'immunologie et de maladie infectieuse, 91 boulevard de l'Hôpital, 75013, Paris, France.,Sorbonne Université, Paris, France.,Département de Virologie, Hôpitaux Est Parisien, Paris, France
| | - Anne-Marie Cassard
- Faculté de médecine Paris-Sud, Université Paris-Sud, 94270, Kremlin-Bicêtre, France
| | - Ganna Panasyuk
- Institut Necker-Enfants Malades, Université Paris Descartes, Paris, France.,INSERM U1151/CNRS Unité Mixte de Recherche (UMR) 8253, Paris, France
| | - Gabriel Perlemuter
- Faculté de médecine Paris-Sud, Université Paris-Sud, 94270, Kremlin-Bicêtre, France.,AP-HP, Hôpital Antoine Béclère, Service d'hépato-gastroentérologie, 92140, Clamart, France
| | | | | | - Janick Selves
- Institut Universitaire de Cancérologie de Toulouse Oncopole, Université Paul Sabatier, Toulouse, France
| | - Jean-Marie Péron
- Institut Universitaire de Cancérologie de Toulouse Oncopole, Université Paul Sabatier, Toulouse, France
| | - Brigitte Bancel
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052, CNRS 5286, Lyon Cedex 03, France
| | - Philippe Merle
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052, CNRS 5286, Lyon Cedex 03, France
| | - Dina Kremsdorf
- INSERM U1135, Centre d'immunologie et de maladie infectieuse, 91 boulevard de l'Hôpital, 75013, Paris, France.,Sorbonne Université, Paris, France
| | - Janet Hall
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052, CNRS 5286, Lyon Cedex 03, France
| | - Isabelle Chemin
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052, CNRS 5286, Lyon Cedex 03, France
| | - Patrick Soussan
- INSERM U1135, Centre d'immunologie et de maladie infectieuse, 91 boulevard de l'Hôpital, 75013, Paris, France. .,Sorbonne Université, Paris, France. .,Département de Virologie, Hôpitaux Est Parisien, Paris, France.
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Chauhan K, Kalam H, Dutt R, Kumar D. RNA Splicing: A New Paradigm in Host-Pathogen Interactions. J Mol Biol 2019; 431:1565-1575. [PMID: 30857970 DOI: 10.1016/j.jmb.2019.03.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [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: 08/22/2018] [Revised: 02/26/2019] [Accepted: 03/02/2019] [Indexed: 12/21/2022]
Abstract
RNA splicing brings diversity to the eukaryotic proteome. Different spliced variants of a gene may differ in their structure, function, localization, and stability influencing protein stoichiometry and physiological outcomes. Alternate spliced variants of different genes are known to associate with various chronic pathologies including cancer. Emerging evidence suggests precise regulation of splicing as fundamental to normal well-being. In this context, infection-induced alternative splicing has emerged as a new pivot of host function, which pathogenic microbes can alter-directly or indirectly-to tweak the host immune responses against the pathogen. The implications of these findings are vast, and although not explored much in the case of pathogenic infections, we present here examples from splicing mediated regulation of immune responses across a variety of conditions and explore how this fascinating finding brings a new paradigm to host-pathogen interactions.
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Affiliation(s)
- Komal Chauhan
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Haroon Kalam
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ravi Dutt
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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34
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Boudreault S, Armero VES, Scott MS, Perreault JP, Bisaillon M. The Epstein-Barr virus EBNA1 protein modulates the alternative splicing of cellular genes. Virol J 2019; 16:29. [PMID: 30832682 PMCID: PMC6399920 DOI: 10.1186/s12985-019-1137-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 11/22/2018] [Accepted: 02/25/2019] [Indexed: 12/13/2022] Open
Abstract
Background Alternative splicing (AS) is an important mRNA maturation step that allows increased variability and diversity of proteins in eukaryotes. AS is dysregulated in numerous diseases, and its implication in the carcinogenic process is well known. However, progress in understanding how oncogenic viruses modulate splicing, and how this modulation is involved in viral oncogenicity has been limited. Epstein-Barr virus (EBV) is involved in various cancers, and its EBNA1 oncoprotein is the only viral protein expressed in all EBV malignancies. Methods In the present study, the ability of EBNA1 to modulate the AS of cellular genes was assessed using a high-throughput RT-PCR approach to examine AS in 1238 cancer-associated genes. RNA immunoprecipitation coupled to RNA sequencing (RIP-Seq) assays were also performed to identify cellular mRNAs bound by EBNA1. Results Upon EBNA1 expression, we detected modifications to the AS profiles of 89 genes involved in cancer. Moreover, we show that EBNA1 modulates the expression levels of various splicing factors such as hnRNPA1, FOX-2, and SF1. Finally, RNA immunoprecipitation coupled to RIP-Seq assays demonstrate that EBNA1 immunoprecipitates specific cellular mRNAs, but not the ones that are spliced differently in EBNA1-expressing cells. Conclusion The EBNA1 protein can modulate the AS profiles of numerous cellular genes. Interestingly, this modulation protein does not require the RNA binding activity of EBNA1. Overall, these findings underline the novel role of EBNA1 as a cellular splicing modulator. Electronic supplementary material The online version of this article (10.1186/s12985-019-1137-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simon Boudreault
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Victoria E S Armero
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Michelle S Scott
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Jean-Pierre Perreault
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada
| | - Martin Bisaillon
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4K8, Canada.
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Lin P, He RQ, Ma FC, Liang L, He Y, Yang H, Dang YW, Chen G. Systematic Analysis of Survival-Associated Alternative Splicing Signatures in Gastrointestinal Pan-Adenocarcinomas. EBioMedicine 2018; 34:46-60. [PMID: 30131306 PMCID: PMC6116578 DOI: 10.1016/j.ebiom.2018.07.040] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [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: 05/29/2018] [Revised: 07/29/2018] [Accepted: 07/31/2018] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Gastrointestinal pan-adenocarcinomas, which mainly include adenocarcinomas of the esophagus, stomach, colon, and rectum, place a heavy burden on society owing to their poor prognoses. Since aberrant alternative splicing (AS) are starting to be considered as efficacious signatures for tumor prognosis predicting and therapeutic targets, systematic analysis of AS events is urgent. METHODS Prognosis-related AS events were selected by using univariate COX regression analysis. Gene functional enrichment analysis revealed the pathways enriched by prognosis-related AS. Then, prognostic signatures based on AS events were developed for prognosis prediction. Potential mechanism to regulate splicing events by splicing factors was analyzed via Pearson correlation and regulatory networks were constructed. FINDINGS A total of 967, 918, 674, and 406 AS events were identified as prognosis-related AS events in esophagus, stomach, colon, and rectum adenocarcinomas, respectively. Survival-associated AS events were distinguishing in the four subtypes of adenocarcinoma. Furthermore, computational algorithm results indicated that perturbation of ribosome and ubiquitin-mediated proteolysis pathways were the potential molecular mechanisms corresponding to inferior prognoses. Most notably, several prognostic signatures based on AS events displayed moderate performance in prognosis predicting. The area under curve values of the time-dependent receiver operating characteristic were 0.961, 0.871, 0.870, and 0.890 in esophagus, stomach, colon, and rectum adenocarcinomas. Survival-associated splicing factors were submitted to construct the AS regulatory network, which could be an underlying mechanism of AS events. INTERPRETATION AS may could be ideal indiactors in the prognosis of gastrointestinal pan-adenocarcinomas. Exploring interesting splicing regulatory networks is conducive to solve the puzzles of AS.
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Affiliation(s)
- Peng Lin
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Rong-Quan He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Fu-Chao Ma
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Liang Liang
- Department of General Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Yun He
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Hong Yang
- Department of Medical Ultrasonics, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Yi-Wu Dang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China.
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El-Athman R, Fuhr L, Relógio A. A Systems-Level Analysis Reveals Circadian Regulation of Splicing in Colorectal Cancer. EBioMedicine 2018; 33:68-81. [PMID: 29936137 PMCID: PMC6085510 DOI: 10.1016/j.ebiom.2018.06.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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: 04/27/2018] [Revised: 05/28/2018] [Accepted: 06/11/2018] [Indexed: 12/26/2022] Open
Abstract
Accumulating evidence points to a significant role of the circadian clock in the regulation of splicing in various organisms, including mammals. Both dysregulated circadian rhythms and aberrant pre-mRNA splicing are frequently implicated in human disease, in particular in cancer. To investigate the role of the circadian clock in the regulation of splicing in a cancer progression context at the systems-level, we conducted a genome-wide analysis and compared the rhythmic transcriptional profiles of colon carcinoma cell lines SW480 and SW620, derived from primary and metastatic sites of the same patient, respectively. We identified spliceosome components and splicing factors with cell-specific circadian expression patterns including SRSF1, HNRNPLL, ESRP1, and RBM 8A, as well as altered alternative splicing events and circadian alternative splicing patterns of output genes (e.g., VEGFA, NCAM1, FGFR2, CD44) in our cellular model. Our data reveals a remarkable interplay between the circadian clock and pre-mRNA splicing with putative consequences in tumor progression and metastasis.
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Affiliation(s)
- Rukeia El-Athman
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany; Medical Department of Hematology, Oncology, and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany
| | - Luise Fuhr
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany; Medical Department of Hematology, Oncology, and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany; Medical Department of Hematology, Oncology, and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany.
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37
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Adamopoulos PG, Raptis GD, Kontos CK, Scorilas A. Discovery and expression analysis of novel transcripts of the human SR-related CTD-associated factor 1 (SCAF1) gene in human cancer cells using Next-Generation Sequencing. Gene 2018; 670:155-165. [PMID: 29787824 DOI: 10.1016/j.gene.2018.05.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 03/16/2018] [Accepted: 05/13/2018] [Indexed: 02/07/2023]
Abstract
The human SR-related CTD associated factor 1 (SCAF1) gene is a new member of the human SR (Ser/Arg-rich) superfamily of pre-mRNA splicing factors, which has been discovered and cloned by members of our lab. SCAF1 interacts with the CTD domain of the RNA polymerase II polypeptide A and is firmly involved in pre-mRNA splicing. Although it was found to be expressed widely in multiple human tissues, its mRNA levels vary a lot. The significant relation of SCAF1 with cancer has been confirmed by many studies, since SCAF1 mRNA transcript was found to be overexpressed in breast and ovarian tumors, confirming its significant prognostic value as a cancer biomarker in both these human malignancies. In this study, we describe the discovery and cloning of fifteen novel transcripts of the human SCAF1 gene (SCAF1 v.2 - v.16), using nested PCR and NGS technology. In detail, extensive bioinformatic analysis revealed that these novel SCAF1 splice variants comprise a total of nine novel alternative splicing events between the annotated exons of the gene, thus producing seven novel SCAF1 transcripts with open-reading frames, which are predicted to encode novel SCAF1 isoforms and eight novel SCAF1 transcripts with premature termination codons that are likely long non-coding RNAs. Additionally, a novel 3' UTR was discovered and cloned using nested 3' RACE and was validated with Sanger sequencing. In order to validate the NGS findings as well as to investigate the expression profile of each novel transcript, RT-PCR experiments were carried out with the use of variant-specific primers. Since SCAF1 is implicated in many human malignancies, qualifying as a potential biomarker, the quantification of the presented novel transcripts in human samples may have clinical applications in different types of cancer.
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Affiliation(s)
- Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios D Raptis
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, Greece.
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Abstract
Quantification of alternative splicing to detect the abundance of differentially spliced isoforms of a gene in total RNA can be accomplished via RT-PCR using both quantitative real-time and semi-quantitative PCR methods. These methods require careful PCR primer design to ensure specific detection of particular splice isoforms. We also describe analysis of alternative splicing using a splicing "minigene" in mammalian cell tissue culture to facilitate investigation of the regulation of alternative splicing of a particular exon of interest.
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Affiliation(s)
- Samuel E Harvey
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Chonghui Cheng
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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Simpson CG, Fuller J, Calixto CPG, McNicol J, Booth C, Brown JWS, Staiger D. Monitoring Alternative Splicing Changes in Arabidopsis Circadian Clock Genes. Methods Mol Biol 2016; 1398:119-32. [PMID: 26867620 DOI: 10.1007/978-1-4939-3356-3_11] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Posttranscriptional control makes an important contribution to circadian regulation of gene expression. In higher plants, alternative splicing is particularly prevalent upon abiotic and biotic stress and in the circadian system. Here we describe in detail a high-resolution reverse transcription-PCR based panel (HR RT-PCR) to monitor alternative splicing events. The use of the panel allows the quantification of changes in the proportion of splice isoforms between different samples, e.g., different time points, different tissues, genotypes, ecotypes, or treatments.
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Affiliation(s)
- Craig G Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, Scotland, UK.
| | - John Fuller
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, Scotland, UK
| | - Cristiane P G Calixto
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Dundee, DD2 5DA, UK
| | - Jim McNicol
- Biomathematics and Statistics Scotland, Invergowrie, DD2 5DA, Scotland, UK
| | - Clare Booth
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, Scotland, UK
| | - John W S Brown
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, Scotland, UK.,Division of Plant Sciences, University of Dundee at The James Hutton Institute, Dundee, DD2 5DA, UK
| | - Dorothee Staiger
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Universitaetsstrasse 25, Bielefeld, D-33615, Germany
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40
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Schimmer BP, Cordova M. Corticotropin (ACTH) regulates alternative RNA splicing in Y1 mouse adrenocortical tumor cells. Mol Cell Endocrinol 2015; 408:5-11. [PMID: 25281401 DOI: 10.1016/j.mce.2014.09.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/18/2014] [Accepted: 09/24/2014] [Indexed: 10/24/2022]
Abstract
The stimulatory effect of ACTH on gene expression is well documented and is thought to be a major mechanism by which ACTH maintains the functional and structural integrity of the gland. Previously, we showed that ACTH regulates the accumulation of over 1200 transcripts in Y1 adrenal cells, including a cluster with functions in alternative splicing of RNA. On this basis, we postulated that some of the effects of ACTH on the transcription landscape of Y1 cells are mediated by alternative splicing. In this study, we demonstrate that ACTH regulates the alternative splicing of four transcripts - Gnas, Cd151, Dab2 and Tia1. Inasmuch as alternative splicing potentially affects transcripts from more than two-thirds of the mouse genome, we suggest that these findings are representative of a genome-wide effect of ACTH that impacts on the mRNA and protein composition of the adrenal cortex.
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Valdés J, Nozaki T, Sato E, Chiba Y, Nakada-Tsukui K, Villegas-Sepúlveda N, Winkler R, Azuara-Liceaga E, Mendoza-Figueroa MS, Watanabe N, Santos HJ, Saito-Nakano Y, Galindo-Rosales JM. Proteomic analysis of Entamoeba histolytica in vivo assembled pre-mRNA splicing complexes. J Proteomics 2014; 111:30-45. [PMID: 25109466 DOI: 10.1016/j.jprot.2014.07.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [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: 01/23/2014] [Revised: 06/27/2014] [Accepted: 07/23/2014] [Indexed: 10/24/2022]
Abstract
UNLABELLED The genome of the human intestinal parasite Entamoeba histolytica contains nearly 3000 introns and bioinformatic predictions indicate that major and minor spliceosomes occur in Entamoeba. However, except for the U2-, U4-, U5- and U6 snRNAs, no other splicing factor has been cloned and characterized. Here, we HA-tagged cloned the snRNP component U1A and assessed its expression and nuclear localization. Because the snRNP-free U1A form interacts with polyadenylate-binding protein, HA-U1A immunoprecipitates could identify early and late splicing complexes. Avoiding Entamoeba's endonucleases and ensuring the precipitation of RNA-binding proteins, parasite cultures were UV cross-linked prior to nuclear fraction immunoprecipitations with HA antibodies, and precipitates were subjected to tandem mass spectrometry (MS/MS) analyses. To discriminate their nuclear roles (chromatin-, co-transcriptional-, splicing-related), MS/MS analyses were carried out with proteins eluted with MS2-GST-sepharose from nuclear extracts of an MS2 aptamer-tagged Rabx13 intron amoeba transformant. Thus, we probed thirty-six Entamoeba proteins corresponding to 32 cognate splicing-specific factors, including 13 DExH/D helicases required for all stages of splicing, and 12 different splicing-related helicases were identified also. Furthermore 50 additional proteins, possibly involved in co-transcriptional processes were identified, revealing the complexity of co-transcriptional splicing in Entamoeba. Some of these later factors were not previously found in splicing complex analyses. BIOLOGICAL SIGNIFICANCE Numerous facts about the splicing of the nearly 3000 introns of the Entamoeba genome have not been unraveled, particularly the splicing factors and their activities. Considering that many of such introns are located in metabolic genes, the knowledge of the splicing cues has the potential to be used to attack or control the parasite. We have found numerous new splicing-related factors which could have therapeutic benefit. We also detected all the DExH/A RNA helicases involved in splicing and splicing proofreading control. Still, Entamoeba is very inefficient in splicing fidelity, thus we may have found a possible model system to study these processes.
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Affiliation(s)
- Jesús Valdés
- Departament of Biochemistry, CINVESTAV, México D.F., Mexico.
| | - Tomoyoshi Nozaki
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Emi Sato
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoko Chiba
- University of Tsukuba, Graduate School of Life and Environmental Sciences, Tsukuba, Japan
| | - Kumiko Nakada-Tsukui
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Robert Winkler
- Department of Biotechnology and Biochemistry, CINVESTAV Unidad Irapuato, Irapuato, Guanajuato, Mexico
| | | | | | - Natsuki Watanabe
- University of Tsukuba, Graduate School of Life and Environmental Sciences, Tsukuba, Japan
| | - Herbert J Santos
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan; University of Tsukuba, Graduate School of Life and Environmental Sciences, Tsukuba, Japan; Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - Yumiko Saito-Nakano
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
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Biamonti G, Catillo M, Pignataro D, Montecucco A, Ghigna C. The alternative splicing side of cancer. Semin Cell Dev Biol 2014; 32:30-6. [PMID: 24657195 DOI: 10.1016/j.semcdb.2014.03.016] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [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: 02/06/2014] [Accepted: 03/11/2014] [Indexed: 12/22/2022]
Abstract
Alternative splicing emerges as a potent and pervasive mechanism of gene expression regulation that expands the coding capacity of the genome and forms an intermediate layer of regulation between transcriptional and post-translational networks. Indeed, alternative splicing occupies a pivotal position in developmental programs and in the cell response to external and internal stimuli. Not surprisingly, therefore, its deregulation frequently leads to human disease. In this review we provide an updated overview of the impact of alternative splicing on tumorigenesis. Moreover, we discuss the intricacy of the reciprocal interactions between alternative splicing programs and signal transduction pathways, which appear to be crucially linked to cancer progression in response to the tumor microenvironment. Finally, we focus on the recently described interplay between splicing and chromatin organization which is expected to shed new lights into gene expression regulation in normal and cancer cells.
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Affiliation(s)
- Giuseppe Biamonti
- Istituto di Genetica Molecolare - CNR, Via Abbiategrasso 207, 27011 Pavia, Italy.
| | - Morena Catillo
- Istituto di Genetica Molecolare - CNR, Via Abbiategrasso 207, 27011 Pavia, Italy
| | - Daniela Pignataro
- Istituto di Genetica Molecolare - CNR, Via Abbiategrasso 207, 27011 Pavia, Italy
| | | | - Claudia Ghigna
- Istituto di Genetica Molecolare - CNR, Via Abbiategrasso 207, 27011 Pavia, Italy
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Wang Y, Wang Z. Systematical identification of splicing regulatory cis-elements and cognate trans-factors. Methods 2014; 65:350-8. [PMID: 23974071 PMCID: PMC3932149 DOI: 10.1016/j.ymeth.2013.08.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [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: 05/17/2013] [Revised: 08/09/2013] [Accepted: 08/12/2013] [Indexed: 01/22/2023] Open
Abstract
The majority of human genes undergo alternative splicing to generate multiple isoforms with distinct functions. This process is generally controlled by cis-acting splicing regulatory elements (SREs) that recruit trans-acting factors to promote or inhibit the use of nearby splice sites. The growing interest in understanding the regulatory rules of splicing necessitates the systematic identification of these SREs and their cognate protein factors using experimental and computational approaches. Here we describe a strategy to identify and analyze both cis-acting SREs and trans-acting splicing factors. This strategy involves a cell-based screen to identify SREs from a random sequences library and a modified RNA affinity purification approach to unbiasedly identify the splicing factors. These methods can be adopted to identify splicing enhancers or silencers in both exons and introns, and can be extended to different cultured cells. The resulting SREs and splicing factors can be further analyzed with a series of computational and experimental approaches. This approach will help us to collect a molecular part-list for splicing regulation, providing a rich data source that enables a better understanding of the "splicing code".
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Affiliation(s)
- Yang Wang
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, United States.
| | - Zefeng Wang
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, United States.
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Abstract
Pre-mRNA splicing is an essential step in the process of gene expression in eukaryotes and consists of the removal of introns and the linking of exons to generate mature mRNAs. This is a highly regulated mechanism that allows the alternative usage of exons, the retention of intronic sequences and the generation of exonic sequences of variable length. Most human genes undergo splicing events, and disruptions of this process have been associated with a variety of diseases, including cancer. Hepatocellular carcinoma (HCC) is a molecularly heterogeneous type of tumor that usually develops in a cirrhotic liver. Alterations in pre-mRNA splicing of some genes have been observed in liver cancer, and although still scarce, the available data suggest that splicing defects may have a role in hepatocarcinogenesis. Here we briefly review the general mechanisms that regulate pre-mRNA splicing, and discuss some examples that illustrate how this process is impaired in liver tumorigenesis, and may contribute to HCC development. We believe that a more thorough examination of pre-mRNA splicing is still needed to accurately draw the molecular portrait of liver cancer. This will surely contribute to a better understanding of the disease and to the development of new effective therapies.
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