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Cui L, Zheng Y, Xu R, Lin Y, Zheng J, Lin P, Guo B, Sun S, Zhao X. Alternative pre-mRNA splicing in stem cell function and therapeutic potential: A critical review of current evidence. Int J Biol Macromol 2024; 268:131781. [PMID: 38657924 DOI: 10.1016/j.ijbiomac.2024.131781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/23/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
Alternative splicing is a crucial regulator in stem cell biology, intricately influencing the functions of various biological macromolecules, particularly pre-mRNAs and the resultant protein isoforms. This regulatory mechanism is vital in determining stem cell pluripotency, differentiation, and proliferation. Alternative splicing's role in allowing single genes to produce multiple protein isoforms facilitates the proteomic diversity that is essential for stem cells' functional complexity. This review delves into the critical impact of alternative splicing on cellular functions, focusing on its interaction with key macromolecules and how this affects cellular behavior. We critically examine how alternative splicing modulates the function and stability of pre-mRNAs, leading to diverse protein expressions that govern stem cell characteristics, including pluripotency, self-renewal, survival, proliferation, differentiation, aging, migration, somatic reprogramming, and genomic stability. Furthermore, the review discusses the therapeutic potential of targeting alternative splicing-related pathways in disease treatment, particularly focusing on the modulation of RNA and protein interactions. We address the challenges and future prospects in this field, underscoring the need for further exploration to unravel the complex interplay between alternative splicing, RNA, proteins, and stem cell behaviors, which is crucial for advancing our understanding and therapeutic approaches in regenerative medicine and disease treatment.
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Affiliation(s)
- Li Cui
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China.
| | - Yucheng Zheng
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Rongwei Xu
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China; Hospital of Stomatology, Zunyi Medical University, Zunyi 563000, China
| | - Yunfan Lin
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Jiarong Zheng
- Department of Dentistry, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Pei Lin
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Bing Guo
- Department of Dentistry, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510080, China
| | - Shuyu Sun
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Xinyuan Zhao
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, 510280, Guangdong, China.
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Ru Y, Ma M, Zhou X, Kriti D, Cohen N, D’Souza S, Schaniel C, Motch Perrine SM, Kuo S, Pinto D, Housman G, Wu M, Holmes G, Schadt E, van Bakel H, Zhang B, Jabs EW. Transcriptomic landscape of human induced pluripotent stem cell-derived osteogenic differentiation identifies a regulatory role of KLF16. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.11.579844. [PMID: 38405902 PMCID: PMC10888757 DOI: 10.1101/2024.02.11.579844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Osteogenic differentiation is essential for bone development and metabolism, but the underlying gene regulatory networks have not been well investigated. We differentiated mesenchymal stem cells, derived from 20 human induced pluripotent stem cell lines, into preosteoblasts and osteoblasts, and performed systematic RNA-seq analyses of 60 samples for differential gene expression. We noted a highly significant correlation in expression patterns and genomic proximity among transcription factor (TF) and long noncoding RNA (lncRNA) genes. We identified TF-TF regulatory networks, regulatory roles of lncRNAs on their neighboring coding genes for TFs and splicing factors, and differential splicing of TF, lncRNA, and splicing factor genes. TF-TF regulatory and gene co-expression network analyses suggested an inhibitory role of TF KLF16 in osteogenic differentiation. We demonstrate that in vitro overexpression of human KLF16 inhibits osteogenic differentiation and mineralization, and in vivo Klf16+/- mice exhibit increased bone mineral density, trabecular number, and cortical bone area. Thus, our model system highlights the regulatory complexity of osteogenic differentiation and identifies novel osteogenic genes.
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Affiliation(s)
- Ying Ru
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Meng Ma
- Mount Sinai Genomics, Sema4, Stamford, CT, 06902, USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Divya Kriti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ninette Cohen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Present address: Division of Cytogenetics and Molecular Pathology, Zucker School of Medicine at Hofstra/Northwell, Northwell Health Laboratories, Lake Success, NY, 11030, USA
| | - Sunita D’Souza
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Present address: St Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Christoph Schaniel
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Medicine, Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Susan M. Motch Perrine
- Department of Anthropology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Sharon Kuo
- Department of Anthropology, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biomedical Sciences, University of Minnesota, Duluth, MN, 55812, USA
| | - Dalila Pinto
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Genevieve Housman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Meng Wu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, 55905
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905
| | - Greg Holmes
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Eric Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, 55905
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905
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Li W, Zeng W, Jin X, Xu H, Fang X, Ma Z, Cao G, Li R, Ma L. High-Altitude Stress Orchestrates mRNA Expression and Alternative Splicing of Ovarian Follicle Development Genes in Tibetan Sheep. Animals (Basel) 2022; 12:2812. [PMID: 36290198 PMCID: PMC9597790 DOI: 10.3390/ani12202812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/14/2022] [Accepted: 10/14/2022] [Indexed: 10/01/2023] Open
Abstract
High-altitude stress threatens the survival rate of Tibetan sheep and reduces their fertility. However, the molecular basis of this phenomenon remains elusive. Here, we used RNA-seq to elucidate the transcriptome dynamics of high-altitude stress in Tibetan sheep ovaries. In total, 104 genes were characterized as high-altitude stress-related differentially expressed genes (DEGs). In addition, 36 DEGs contributed to ovarian follicle development, and 28 of them were downregulated under high-altitude stress. In particular, high-altitude stress significantly suppressed the expression of two ovarian lymphatic system marker genes: LYVE1 and ADAMTS-1. Network analysis revealed that luteinizing hormone (LH)/follicle-stimulating hormone (FSH) signaling-related genes, such as EGR1, FKBP5, DUSP1, and FOS, were central regulators in the DEG network, and these genes were also suppressed under high-altitude stress. As a post-transcriptional regulation mechanism, alternative splicing (AS) is ubiquitous in Tibetan sheep. High-altitude stress induced 917 differentially alternative splicing (DAS) events. High-altitude stress modulated DAS in an AS-type-specific manner: suppressing skipped exon events but increasing retained intron events. C2H2-type zinc finger transcription factors and RNA processing factors were mainly enriched in DAS. These findings revealed high-altitude stress repressed ovarian development by suppressing the gene expression of LH/FSH hormone signaling genes and inducing intron retention of C2H2-type zinc finger transcription factors.
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Affiliation(s)
- Wenhao Li
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China
| | - Weike Zeng
- College of Forestry, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiayang Jin
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China
| | - Huiming Xu
- College of Forestry, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xingyan Fang
- College of Forestry, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhijie Ma
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China
| | - Gangjian Cao
- College of Forestry, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ruizhe Li
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China
| | - Liuyin Ma
- College of Forestry, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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The Biological and Clinical Consequences of RNA Splicing Factor U2AF1 Mutation in Myeloid Malignancies. Cancers (Basel) 2022; 14:cancers14184406. [PMID: 36139566 PMCID: PMC9496927 DOI: 10.3390/cancers14184406] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/04/2022] [Accepted: 09/06/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary U2 small nuclear RNA auxiliary factor 1 (U2AF1) is one of the most important RNA splicing genes involved in regulating the alternative splicing of pre-mRNA. U2AF1 mutation is a genetic driver event in the initiation of myelodysplastic syndromes (MDSs) and frequently occurs in myeloid malignancies. U2AF1 mutation can severely impair hematopoiesis, drive tumor progression, adversely affect disease prognosis, and promote leukemic transformation. This review summarizes the biological and clinical implications of the oncogenic role of U2AF1 mutation in myeloid tumors. Our work provides important and comprehensive insights into the development of the U2AF1 mutation as a novel prognostic biomarker and therapeutic target for myeloid malignancies. Abstract Mutations of spliceosome genes have been frequently identified in myeloid malignancies with the large-scale application of advanced sequencing technology. U2 small nuclear RNA auxiliary factor 1 (U2AF1), an essential component of U2AF heterodimer, plays a pivotal role in the pre-mRNA splicing processes to generate functional mRNAs. Over the past few decades, the mutation landscape of U2AF1 (most frequently involved S34 and Q157 hotspots) has been drawn in multiple cancers, particularly in myeloid malignancies. As a recognized early driver of myelodysplastic syndromes (MDSs), U2AF1 mutates most frequently in MDS, followed by acute myeloid leukemia (AML) and myeloproliferative neoplasms (MPNs). Here, for the first time, we summarize the research progress of U2AF1 mutations in myeloid malignancies, including the correlations between U2AF1 mutations with clinical and genetic characteristics, prognosis, and the leukemic transformation of patients. We also summarize the adverse effects of U2AF1 mutations on hematopoietic function, and the alterations in downstream alternative gene splicing and biological pathways, thus providing comprehensive insights into the roles of U2AF1 mutations in the myeloid malignancy pathogenesis. U2AF1 mutations are expected to be potential novel molecular markers for myeloid malignancies, especially for risk stratification, prognosis assessment, and a therapeutic target of MDS patients.
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