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Choi S, Cho N, Kim EM, Kim KK. The role of alternative pre-mRNA splicing in cancer progression. Cancer Cell Int 2023; 23:249. [PMID: 37875914 PMCID: PMC10594706 DOI: 10.1186/s12935-023-03094-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023] Open
Abstract
Alternative pre-mRNA splicing is a critical mechanism that generates multiple mRNA from a single gene, thereby increasing the diversity of the proteome. Recent research has highlighted the significance of specific splicing isoforms in cellular processes, particularly in regulating cell numbers. In this review, we examine the current understanding of the role of alternative splicing in controlling cancer cell growth and discuss specific splicing factors and isoforms and their molecular mechanisms in cancer progression. These isoforms have been found to intricately control signaling pathways crucial for cell cycle progression, proliferation, and apoptosis. Furthermore, studies have elucidated the characteristics and functional importance of splicing factors that influence cell numbers. Abnormal expression of oncogenic splicing isoforms and splicing factors, as well as disruptions in splicing caused by genetic mutations, have been implicated in the development and progression of tumors. Collectively, these findings provide valuable insights into the complex interplay between alternative splicing and cell proliferation, thereby suggesting the potential of alternative splicing as a therapeutic target for cancer.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Eun-Mi Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea.
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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Wang Y, Li C, Gong X, Chen X, Liu C, Zhang H, Li S, Luo Y. Single-Cell Transcriptomics Reveals Splicing Features of Adult Neural Stem Cells in the Subventricular Zone. Front Cell Dev Biol 2022; 10:822934. [PMID: 35300421 PMCID: PMC8921602 DOI: 10.3389/fcell.2022.822934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/03/2022] [Indexed: 11/30/2022] Open
Abstract
The central nervous system has enormously complex cellular diversity with hundreds of distinct cell types, yet alternative splicing features in single cells of important cell types at neurogenic regions are not well understood. By employing in silico analysis, we systematically identified 3,611 alternative splicing events from 1,908 genes in 28 single-cell transcriptomic data of adult mouse ependymal and subependymal regions, and found that single-cell RNA-seq has the advantage in uncovering rare splicing isoforms compared to bulk RNA-seq at the population level. We uncovered that the simultaneous presence of multiple isoforms from the same gene in a single cell is prevalent, and quiescent stem cells, activated stem cells, and neuroblast cells exhibit high heterogeneity of splicing variants. Furthermore, we also demonstrated the existence of novel bicistronic transcripts in quiescent stem cells.
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Affiliation(s)
- Yanlu Wang
- Human Aging Research Institute and School of Life Science, Nanchang University, Nanchang, China
| | - Chun Li
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.,Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xi Gong
- Human Aging Research Institute and School of Life Science, Nanchang University, Nanchang, China
| | - Xiao Chen
- College of Architectural Engineering, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Chenming Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hailei Zhang
- Novogene Bioinformatics Technology Co., Ltd., Beijing, China
| | - Siguang Li
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuping Luo
- Human Aging Research Institute and School of Life Science, Nanchang University, Nanchang, China.,Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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Schwartz RE, Shokhirev MN, Andrade LR, Gutkind JS, Iglesias-Bartolome R, Shadel GS. Insights into epithelial cell senescence from transcriptome and secretome analysis of human oral keratinocytes. Aging (Albany NY) 2021; 13:4747-4777. [PMID: 33601339 PMCID: PMC7950289 DOI: 10.18632/aging.202658] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/21/2021] [Indexed: 01/08/2023]
Abstract
Senescent cells produce chronic inflammation that contributes to the diseases and debilities of aging. How this process is orchestrated in epithelial cells, the origin of human carcinomas, is poorly understood. We used human normal oral keratinocytes (NOKs) to elucidate senescence programs in a prototype primary mucosal epithelial cell that senesces spontaneously. While NOKs exhibit several typical facets of senescence, they also display distinct characteristics. These include expression of p21WAF1/CIP1 at early passages, making this common marker of senescence unreliable in NOKs. Transcriptome analysis by RNA-seq revealed specific commonalities with and differences from cancer cells, explicating the tumor avoidance role of senescence. Repression of DNA repair genes that correlated with downregulation of E2F1 mRNA and protein was observed for two donors; a divergent result was seen for the third. Using proteomic profiling of soluble (non-vesicular) and extracellular vesicle (EV) associated secretions, we propose additions to the senescence associated secretory phenotype, including HSP60, which localizes to the surface of EVs. Finally, EVs from senescent NOKs activate interferon pathway signaling in THP-1 monocytes in a STING-dependent manner and associate with mitochondrial and nuclear DNA. Our results highlight senescence changes in epithelial cells and how they might contribute to chronic inflammation and age-related diseases.
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Affiliation(s)
- Rachael E Schwartz
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies and University of California - San Diego, La Jolla, CA 92037, USA
| | - Maxim N Shokhirev
- Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Leonardo R Andrade
- Waitt Advanced Biophotonics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - J Silvio Gutkind
- Department of Pharmacology and Moores Cancer Center, University of California - San Diego, La Jolla, CA 92093, USA
| | - Ramiro Iglesias-Bartolome
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gerald S Shadel
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies and University of California - San Diego, La Jolla, CA 92037, USA
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