1
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Dhawan V, Malhotra N, Singh N, Dadhwal V, Dada R. Yoga and its effect on sperm genomic integrity, gene expression, telomere length and perceived quality of life in early pregnancy loss. Sci Rep 2024; 14:11711. [PMID: 38777848 PMCID: PMC11111444 DOI: 10.1038/s41598-024-62380-w] [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: 10/04/2023] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
Achieving successful pregnancy outcomes is a delicate interplay between the maternal and the fetal counterparts. Paternal factors play a critical role in health and disease of offspring. Early pregnancy loss (EPL) is a psychologically devastating condition affecting the quality of life (QOL). Thus, it needs to be managed by a mind body integrated approach like yoga.The prospective single arm exploratory studyincluded male partners of couples experiencing recurrent pregnancy loss (RPL, n = 30), and recurrent implantation failure (RIF, n = 30) and semen samples wereassessed at the beginning and completion of yoga (6 weeks) (WHO 2010).A significant increase in the sperm concentration, motility, decrease in seminal ROS, DFI and increase in relative sperm telomere length was found at the end of yoga. The relative expression of genes critical for early embryonic developmentnormalized towards the levels of controls. WHOQOL-BREF questionnaire scores to assess QOL also showed improvement.Integration of regular practice yoga into our lifestyle may help in improving seminal redox status, genomic integrity, telomere length, normalizing gene expression and QOL, highlighting the need to use an integrated, holistic approach in management of such cases. This is pertinent for decreasing the transmission of mutation and epimutation load to the developing embryo, improving pregnancy outcomes and decreasing genetic and epigenetic disease burden in the next generation.
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Affiliation(s)
- Vidhu Dhawan
- Department of Anatomy, Laboratory of Molecular Reproduction and Genetics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Neena Malhotra
- Department of Obstetrics and Gynecology, All India Institute of Medical Sciences, New Delhi, India
| | - Neeta Singh
- Department of Obstetrics and Gynecology, All India Institute of Medical Sciences, New Delhi, India
| | - Vatsla Dadhwal
- Department of Obstetrics and Gynecology, All India Institute of Medical Sciences, New Delhi, India
| | - Rima Dada
- Department of Anatomy, Laboratory of Molecular Reproduction and Genetics, All India Institute of Medical Sciences, New Delhi, 110029, India.
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2
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Verbeeren J, Teixeira J, Garcia SMDA. The Muscleblind-like protein MBL-1 regulates microRNA expression in Caenorhabditis elegans through an evolutionarily conserved autoregulatory mechanism. PLoS Genet 2023; 19:e1011109. [PMID: 38134228 PMCID: PMC10773944 DOI: 10.1371/journal.pgen.1011109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 01/08/2024] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
The Muscleblind-like (MBNL) family is a highly conserved set of RNA-binding proteins (RBPs) that regulate RNA metabolism during the differentiation of various animal tissues. Functional insufficiency of MBNL affects muscle and central nervous system development, and contributes to the myotonic dystrophies (DM), a set of incurable multisystemic disorders. Studies on the regulation of MBNL genes are essential to provide insight into the gene regulatory networks controlled by MBNL proteins and to understand how dysregulation within these networks causes disease. In this study, we demonstrate the evolutionary conservation of an autoregulatory mechanism that governs the function of MBNL proteins by generating two distinct protein isoform types through alternative splicing. Our aim was to further our understanding of the regulatory principles that underlie this conserved feedback loop in a whole-organismal context, and to address the biological significance of the respective isoforms. Using an alternative splicing reporter, our studies show that, during development of the Caenorhabditis elegans central nervous system, the orthologous mbl-1 gene shifts production from long protein isoforms that localize to the nucleus to short isoforms that also localize to the cytoplasm. Using isoform-specific CRISPR/Cas9-generated strains, we showed that expression of short MBL-1 protein isoforms is required for healthy neuromuscular function and neurodevelopment, while expression of long MBL-1 protein isoforms is dispensable, emphasizing a key role for cytoplasmic functionalities of the MBL-1 protein. Furthermore, RNA-seq and lifespan analyses indicated that short MBL-1 isoforms are crucial regulators of miRNA expression and, in consequence, required for normal lifespan. In conclusion, this study provides support for the disruption of cytoplasmic RNA metabolism as a contributor in myotonic dystrophy and paves the way for further exploration of miRNA regulation through MBNL proteins during development and in disease models.
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Affiliation(s)
- Jens Verbeeren
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Joana Teixeira
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
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3
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Aich M, Ansari AH, Ding L, Iesmantavicius V, Paul D, Choudhary C, Maiti S, Buchholz F, Chakraborty D. TOBF1 modulates mouse embryonic stem cell fate through regulating alternative splicing of pluripotency genes. Cell Rep 2023; 42:113177. [PMID: 37751355 DOI: 10.1016/j.celrep.2023.113177] [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: 02/08/2023] [Revised: 06/28/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
Embryonic stem cells (ESCs) can undergo lineage-specific differentiation, giving rise to different cell types that constitute an organism. Although roles of transcription factors and chromatin modifiers in these cells have been described, how the alternative splicing (AS) machinery regulates their expression has not been sufficiently explored. Here, we show that the long non-coding RNA (lncRNA)-associated protein TOBF1 modulates the AS of transcripts necessary for maintaining stem cell identity in mouse ESCs. Among the genes affected is serine/arginine splicing factor 1 (SRSF1), whose AS leads to global changes in splicing and expression of a large number of downstream genes involved in the maintenance of ESC pluripotency. By overlaying information derived from TOBF1 chromatin occupancy, the distribution of its pluripotency-associated OCT-SOX binding motifs, and transcripts undergoing differential expression and AS upon its knockout, we describe local nuclear territories where these distinct events converge. Collectively, these contribute to the maintenance of mouse ESC identity.
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Affiliation(s)
- Meghali Aich
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Asgar Hussain Ansari
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Li Ding
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Vytautas Iesmantavicius
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Deepanjan Paul
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Chunaram Choudhary
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Souvik Maiti
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Debojyoti Chakraborty
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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4
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Wang L, Su X, Wang L, Luo J, Xiong Z, Leung GHD, Zhou J, Yang G, Zhai L, Zhang X, Liu Q, Lu G, Wang Y. Identification of lncRNAs associated with uterine corpus endometrial cancer prognosis based on the competing endogenous RNA network. Int J Med Sci 2023; 20:1600-1615. [PMID: 37859697 PMCID: PMC10583181 DOI: 10.7150/ijms.87430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/06/2023] [Indexed: 10/21/2023] Open
Abstract
Uterine Corpus Endometrial Carcinoma (UCEC) is one of the major malignant tumors of the female reproductive system. However, there are limitations in the currently available diagnostic approaches for UCEC. Long non-coding RNAs (lncRNAs) play important roles in regulating biological processes as competitive endogenous RNA (ceRNA) in tumors. To study the potential of lncRNAs as non-invasive diagnostic tumor markers, RNA-sequencing dataset of UCEC patients from The Cancer Genome Atlas was used to identify differentially expressed genes. A lncRNA-miRNA-mRNA ceRNA network was constructed by differentially expressed lncRNAs, miRNAs and miRNAs. Pathway enrichment and functional analysis for the mRNAs in the constructed ceRNA network provide the direction of future research for UCEC by demonstrating the most affected processes and pathways. Seven potential lncRNA biomarkers (C20orf56, LOC100144604, LOC100190940, LOC151534, LOC727677, FLJ35390, LOC158572) were validated in UCEC patients by quantitative real-time PCR. Notably, LOC100190940 and LOC158572 were identified as novel RNA molecules with unknown functions. Receiver operating characteristic (ROC) curve analysis demonstrated that the combined 7 lncRNAs had a high diagnostic value for UCEC patients with area under curve (AUC) of 0.941 (95% CI: 0.875-0.947). Our study highlights the potential of the validated 7 lncRNAs panel as diagnostic biomarkers in UCEC, providing new insights into the UCEC pathogenesis.
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Affiliation(s)
- Liangxiao Wang
- Department of Clinical Laboratory, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650106, Yunnan, China
| | - Xianwei Su
- Research and Development Unit, Shenzhen GenDo Medical Technology Co., Ltd., Dapeng, Shenzhen, 518000, China
| | - Liangyu Wang
- Qujing Medical College, Qujing, 655000, Yunnan, China
| | - Jianbo Luo
- Department of Clinical Laboratory, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650106, Yunnan, China
| | - Zhiqiang Xiong
- SDIVF R&D Centre, 209,12W, HKSTP, Shatin, Hong Kong, China
| | | | - Jingye Zhou
- Research and Development Unit, Shenzhen GenDo Medical Technology Co., Ltd., Dapeng, Shenzhen, 518000, China
| | - Guang Yang
- Department of Sports Medicine, Qujing First People's Hospital, 650500, Yunnan, China
| | - Li Zhai
- Department of Clinical Laboratory, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650106, Yunnan, China
| | - Xi Zhang
- Department of Clinical Laboratory, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, 650106, Yunnan, China
| | - Qiang Liu
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Gang Lu
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuming Wang
- Department of Clinical Laboratory, Yunnan Molecular Diagnostic Center, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650500, Yunnan, China
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5
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de Morree A, Rando TA. Regulation of adult stem cell quiescence and its functions in the maintenance of tissue integrity. Nat Rev Mol Cell Biol 2023; 24:334-354. [PMID: 36922629 PMCID: PMC10725182 DOI: 10.1038/s41580-022-00568-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2022] [Indexed: 03/18/2023]
Abstract
Adult stem cells are important for mammalian tissues, where they act as a cell reserve that supports normal tissue turnover and can mount a regenerative response following acute injuries. Quiescent stem cells are well established in certain tissues, such as skeletal muscle, brain, and bone marrow. The quiescent state is actively controlled and is essential for long-term maintenance of stem cell pools. In this Review, we discuss the importance of maintaining a functional pool of quiescent adult stem cells, including haematopoietic stem cells, skeletal muscle stem cells, neural stem cells, hair follicle stem cells, and mesenchymal stem cells such as fibro-adipogenic progenitors, to ensure tissue maintenance and repair. We discuss the molecular mechanisms that regulate the entry into, maintenance of, and exit from the quiescent state in mice. Recent studies revealed that quiescent stem cells have a discordance between RNA and protein levels, indicating the importance of post-transcriptional mechanisms, such as alternative polyadenylation, alternative splicing, and translation repression, in the control of stem cell quiescence. Understanding how these mechanisms guide stem cell function during homeostasis and regeneration has important implications for regenerative medicine.
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Affiliation(s)
- Antoine de Morree
- Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
| | - Thomas A Rando
- Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Tissue Regeneration, Repair, and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
- Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, USA.
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6
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Ruberto AA, Maher SP, Vantaux A, Joyner CJ, Bourke C, Balan B, Jex A, Mueller I, Witkowski B, Kyle DE. Single-cell RNA profiling of Plasmodium vivax-infected hepatocytes reveals parasite- and host- specific transcriptomic signatures and therapeutic targets. Front Cell Infect Microbiol 2022; 12:986314. [PMID: 36093191 PMCID: PMC9453201 DOI: 10.3389/fcimb.2022.986314] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/08/2022] [Indexed: 12/12/2022] Open
Abstract
The resilience of Plasmodium vivax, the most widely-distributed malaria-causing parasite in humans, is attributed to its ability to produce dormant liver forms known as hypnozoites, which can activate weeks, months, or even years after an initial mosquito bite. The factors underlying hypnozoite formation and activation are poorly understood, as is the parasite's influence on the host hepatocyte. Here, we shed light on transcriptome-wide signatures of both the parasite and the infected host cell by sequencing over 1,000 P. vivax-infected hepatocytes at single-cell resolution. We distinguish between replicating schizonts and hypnozoites at the transcriptional level, identifying key differences in transcripts encoding for RNA-binding proteins associated with cell fate. In infected hepatocytes, we show that genes associated with energy metabolism and antioxidant stress response are upregulated, and those involved in the host immune response downregulated, suggesting both schizonts and hypnozoites alter the host intracellular environment. The transcriptional markers in schizonts, hypnozoites, and infected hepatocytes revealed here pinpoint potential factors underlying dormancy and can inform therapeutic targets against P. vivax liver-stage infection.
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Affiliation(s)
- Anthony A. Ruberto
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
| | - Steven P. Maher
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
| | - Amélie Vantaux
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Chester J. Joyner
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Caitlin Bourke
- Population Health & Immunity Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Balu Balan
- Population Health & Immunity Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Aaron Jex
- Population Health & Immunity Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Ivo Mueller
- Population Health & Immunity Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Benoit Witkowski
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Dennis E. Kyle
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
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7
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Zhao C, Xie W, Zhu H, Zhao M, Liu W, Wu Z, Wang L, Zhu B, Li S, Zhou Y, Jiang X, Xu Q, Ren C. LncRNAs and their RBPs: How to influence the fate of stem cells? Stem Cell Res Ther 2022; 13:175. [PMID: 35505438 PMCID: PMC9066789 DOI: 10.1186/s13287-022-02851-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/12/2022] [Indexed: 12/12/2022] Open
Abstract
Stem cells are distinctive cells that have self-renewal potential and unique ability to differentiate into multiple functional cells. Stem cell is a frontier field of life science research and has always been a hot spot in biomedical research. Recent studies have shown that long non-coding RNAs (lncRNAs) have irreplaceable roles in stem cell self-renewal and differentiation. LncRNAs play crucial roles in stem cells through a variety of regulatory mechanisms, including the recruitment of RNA-binding proteins (RBPs) to affect the stability of their mRNAs or the expression of downstream genes. RBPs interact with different RNAs to regulate gene expression at transcriptional and post-transcriptional levels and play important roles in determining the fate of stem cells. In this review, the functions of lncRNAs and their RBPs in self-renewal and differentiation of stem cell are summarized. We focus on the four regulatory mechanisms by which lncRNAs and their RBPs are involved in epigenetic regulation, signaling pathway regulation, splicing, mRNA stability and subcellular localization and further discuss other noncoding RNAs (ncRNAs) and their RBPs in the fate of stem cells. This work provides a more comprehensive understanding of the roles of lncRNAs in determining the fate of stem cells, and a further understanding of their regulatory mechanisms will provide a theoretical basis for the development of clinical regenerative medicine.
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Affiliation(s)
- Cong Zhao
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medicine, Central South University, Changsha, 410008, China
| | - Wen Xie
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medicine, Central South University, Changsha, 410008, China
| | - Hecheng Zhu
- Changsha Kexin Cancer Hospital, Changsha, 410205, China
| | - Ming Zhao
- Changsha Kexin Cancer Hospital, Changsha, 410205, China
| | - Weidong Liu
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medicine, Central South University, Changsha, 410008, China
| | - Zhaoping Wu
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Lei Wang
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medicine, Central South University, Changsha, 410008, China
| | - Bin Zhu
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medicine, Central South University, Changsha, 410008, China
| | - Shasha Li
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medicine, Central South University, Changsha, 410008, China
| | - Yao Zhou
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medicine, Central South University, Changsha, 410008, China
| | - Xingjun Jiang
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China. .,Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Qiang Xu
- Department of Orthopedics, The Affiliated Zhuzhou Hospital of Xiangya Medical College, Central South University, Zhuzhou, 412007, China. .,School of Materials Science and Engineering, Central South University, Changsha, 410083, China.
| | - Caiping Ren
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China. .,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medicine, Central South University, Changsha, 410008, China.
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8
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Razmi K, Patil JG. Primordial Germ Cell Development in the Poeciliid, Gambusia holbrooki, Reveals Shared Features Between Lecithotrophs and Matrotrophs. Front Cell Dev Biol 2022; 10:793498. [PMID: 35300414 PMCID: PMC8920993 DOI: 10.3389/fcell.2022.793498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/03/2022] [Indexed: 12/02/2022] Open
Abstract
Metazoans exhibit two modes of primordial germ cell (PGC) specification that are interspersed across taxa. However, the evolutionary link between the two modes and the reproductive strategies of lecithotrophy and matrotrophy is poorly understood. As a first step to understand this, the spatio-temporal expression of teleostean germ plasm markers was investigated in Gambusia holbrooki, a poecilid with shared lecitho- and matrotrophy. A group of germ plasm components was detected in the ovum suggesting maternal inheritance mode of PGC specification. However, the strictly zygotic activation of dnd-β and nanos1 occurred relatively early, reminiscent of models with induction mode (e.g., mice). The PGC clustering, migration and colonisation patterns of G. holbrooki resembled those of zebrafish, medaka and mice at blastula, gastrula and somitogenesis, respectively—recapitulating features of advancing evolutionary nodes with progressive developmental stages. Moreover, the expression domains of PGC markers in G. holbrooki were either specific to teleost (vasa expression in developing PGCs), murine models (dnd spliced variants) or shared between the two taxa (germline and somatic expression of piwi and nanos1). Collectively, the results suggest that the reproductive developmental adaptations may reflect a transition from lecithotrophy to matrotrophy.
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Affiliation(s)
- Komeil Razmi
- Laboratory of Molecular Biology, Fisheries and Aquaculture Centre, Institute for Marine and Antarctic Studies, University of Tasmania, Taroona, TAS, Australia
| | - Jawahar G Patil
- Laboratory of Molecular Biology, Fisheries and Aquaculture Centre, Institute for Marine and Antarctic Studies, University of Tasmania, Taroona, TAS, Australia
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9
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Dvir S, Argoetti A, Lesnik C, Roytblat M, Shriki K, Amit M, Hashimshony T, Mandel-Gutfreund Y. Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells. Cell Rep 2021; 35:109198. [PMID: 34077720 DOI: 10.1016/j.celrep.2021.109198] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
Embryonic stem cell (ESC) self-renewal and cell fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carry out a proteome-wide screen and identify 810 proteins that bind RNA in hESCs. We reveal that RBPs are preferentially expressed in hESCs and dynamically regulated during early stem cell differentiation. Notably, many RBPs are affected by knockdown of OCT4, a master regulator of pluripotency, several dozen of which are directly targeted by this factor. Using cross-linking and immunoprecipitation (CLIP-seq), we find that the pluripotency-associated STAT3 and OCT4 transcription factors interact with RNA in hESCs and confirm the binding of STAT3 to the conserved NORAD long-noncoding RNA. Our findings indicate that RBPs have a more widespread role in human pluripotency than previously appreciated.
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Affiliation(s)
- Shlomi Dvir
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Chen Lesnik
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | | | | | - Michal Amit
- Accellta LTD, Haifa 320003, Israel; Ephraim Katzir Department of Biotechnology Engineering, ORT Braude College, Karmiel 2161002, Israel
| | - Tamar Hashimshony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel; Computer Science Department, Technion - Israel Institute of Technology, Haifa 320003, Israel.
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10
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Pollini D, Loffredo R, Maniscalco F, Cardano M, Micaelli M, Bonomo I, Licata NV, Peroni D, Tomaszewska W, Rossi A, Crippa V, Dassi E, Viero G, Quattrone A, Poletti A, Conti L, Provenzani A. Multilayer and MATR3-dependent regulation of mRNAs maintains pluripotency in human induced pluripotent stem cells. iScience 2021; 24:102197. [PMID: 33733063 PMCID: PMC7940987 DOI: 10.1016/j.isci.2021.102197] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/22/2020] [Accepted: 02/11/2021] [Indexed: 10/28/2022] Open
Abstract
Matrin3 (MATR3) is a nuclear RNA/DNA-binding protein that plays pleiotropic roles in gene expression regulation by directly stabilizing target RNAs and supporting the activity of transcription factors by modulating chromatin architecture. MATR3 is involved in the differentiation of neural cells, and, here, we elucidate its critical functions in regulating pluripotent circuits in human induced pluripotent stem cells (hiPSCs). MATR3 downregulation affects hiPSCs' differentiation potential by altering key pluripotency regulators' expression levels, including OCT4, NANOG, and LIN28A by pleiotropic mechanisms. MATR3 binds to the OCT4 and YTHDF1 promoters favoring their expression. YTHDF1, in turn, binds the m6A-modified OCT4 mRNA. Furthermore, MATR3 is recruited on ribosomes and controls pluripotency regulating the translation of specific transcripts, including NANOG and LIN28A, by direct binding and favoring their stabilization. These results show that MATR3 orchestrates the pluripotency circuitry by regulating the transcription, translational efficiency, and epitranscriptome of specific transcripts.
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Affiliation(s)
- Daniele Pollini
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Rosa Loffredo
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Maniscalco
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
- Institute of Biophysics, CNR, Trento, Italy
| | - Marina Cardano
- Cell Technology Core Facility, Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Mariachiara Micaelli
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Isabelle Bonomo
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | | | - Daniele Peroni
- Mass Spectrometry Core Facility, Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Weronika Tomaszewska
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Annalisa Rossi
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Valeria Crippa
- Laboratorio di Biologia Applicata, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | | | - Alessandro Quattrone
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Angelo Poletti
- Laboratorio di Biologia Applicata, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Luciano Conti
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Alessandro Provenzani
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
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11
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Hou L, Wei Y, Lin Y, Wang X, Lai Y, Yin M, Chen Y, Guo X, Wu S, Zhu Y, Yuan J, Tariq M, Li N, Sun H, Wang H, Zhang X, Chen J, Bao X, Jauch R. Concurrent binding to DNA and RNA facilitates the pluripotency reprogramming activity of Sox2. Nucleic Acids Res 2020; 48:3869-3887. [PMID: 32016422 PMCID: PMC7144947 DOI: 10.1093/nar/gkaa067] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 01/16/2020] [Accepted: 01/22/2020] [Indexed: 02/03/2023] Open
Abstract
Some transcription factors that specifically bind double-stranded DNA appear to also function as RNA-binding proteins. Here, we demonstrate that the transcription factor Sox2 is able to directly bind RNA in vitro as well as in mouse and human cells. Sox2 targets RNA via a 60-amino-acid RNA binding motif (RBM) positioned C-terminally of the DNA binding high mobility group (HMG) box. Sox2 can associate with RNA and DNA simultaneously to form ternary RNA/Sox2/DNA complexes. Deletion of the RBM does not affect selection of target genes but mitigates binding to pluripotency related transcripts, switches exon usage and impairs the reprogramming of somatic cells to a pluripotent state. Our findings designate Sox2 as a multi-functional factor that associates with RNA whilst binding to cognate DNA sequences, suggesting that it may co-transcriptionally regulate RNA metabolism during somatic cell reprogramming.
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Affiliation(s)
- Linlin Hou
- Department of Biochemistry, Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangzhou/Shenzhen, China.,CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yuanjie Wei
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yingying Lin
- Department of Biochemistry, Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangzhou/Shenzhen, China.,Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiwei Wang
- Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yiwei Lai
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Menghui Yin
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China
| | - Yanpu Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Xiangpeng Guo
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Senbin Wu
- Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | | | - Jie Yuan
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Muqddas Tariq
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Na Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaofei Zhang
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,CAS Key Laboratory of Regenerative Biology, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xichen Bao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Ralf Jauch
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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12
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Wu KJ. The role of miRNA biogenesis and DDX17 in tumorigenesis and cancer stemness. Biomed J 2020; 43:107-114. [PMID: 32513392 PMCID: PMC7283569 DOI: 10.1016/j.bj.2020.03.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 03/03/2020] [Accepted: 03/09/2020] [Indexed: 12/18/2022] Open
Abstract
Cancer stemness represents one of the major mechanisms that predispose patients to tumor aggressiveness, metastasis, and treatment resistance. MicroRNA biogenesis is an important process controlling miRNA processing and maturation. Deregulation of miRNA biogenesis can lead to tumorigenesis and cancer stemness. DDX17 is a co-factor of the miRNA microprocessor. Misregulation of DDX17 can be associated with cancer stemness. K63-linked polyubiquitination of DDX17 presents a concerted mechanism of decreased synthesis of stemness-inhibiting miRNAs and increased transcriptional activation of stemness-related gene expression. K63-linked polyubiquitination of HAUSP serves as a scaffold to anchor HIF-1α, CBP, the mediator complex, and the super-elongation complex to enhance HIF-1α-induced gene transcription. Recent progress in RNA modifications shows that RNA N6-methyladenosine (m6A) modification is a crucial mechanism to regulate RNA levels. M6A modification of miRNAs can also be linked to tumorigenesis and cancer stemness. Overall, miRNA biogenesis and K63-linked polyubiquitination of DDX17 play an important role in the induction of cancer stemness. Delineation of the mechanisms and identification of suitable targets may provide new therapeutic options for treatment-resistant cancers.
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Affiliation(s)
- Kou-Juey Wu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan; Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan, Taiwan.
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13
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Li D, Kishta MS, Wang J. Regulation of pluripotency and reprogramming by RNA binding proteins. Curr Top Dev Biol 2020; 138:113-138. [PMID: 32220295 DOI: 10.1016/bs.ctdb.2020.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Embryonic stem cells have the capacities of self-renewal and pluripotency. Pluripotency establishment (somatic cell reprogramming), maintenance, and execution (differentiation) require orchestrated regulatory mechanisms of a cell's molecular machinery, including signaling pathways, epigenetics, transcription, translation, and protein degradation. RNA binding proteins (RBPs) take part in every process of RNA regulation and recent studies began to address their important functions in the regulation of pluripotency and reprogramming. Here, we discuss the roles of RBPs in key regulatory steps in the control of pluripotency and reprogramming. Among RNA binding proteins are a group of RNA helicases that are responsible for RNA structure remodeling with important functional implications. We highlight the largest family of RNA helicases, DDX (DEAD-box) helicase family and our current understanding of their functions specifically in the regulation of pluripotency and reprogramming.
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Affiliation(s)
- Dan Li
- Department of Cell, Developmental and Regenerative Biology; The Black Family Stem Cell Institute; Icahn School of Medicine at Mount Sinai, New York, NY, United States; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Mohamed S Kishta
- Hormones Department, Medical Research Division, National Research Centre, Cairo, Egypt; Stem Cell Lab., Center of Excellence for Advanced Sciences, National Research Centre, Cairo, Egypt; Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY, United States
| | - Jianlong Wang
- Department of Cell, Developmental and Regenerative Biology; The Black Family Stem Cell Institute; Icahn School of Medicine at Mount Sinai, New York, NY, United States; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY, United States.
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14
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Modic M, Cacchiarelli D, Ten Berge D. Integrative biology studies in pluripotent stem cells. Stem Cell Res 2019; 42:101686. [PMID: 31887610 DOI: 10.1016/j.scr.2019.101686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Miha Modic
- The Francis Crick Institute, London NW1 1AT, UK; Department for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK.
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy; Department of Translational Medicine, University of Naples "Federico II", Naples, Italy.
| | - Derk Ten Berge
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Postbus 2040, 3000 CA Rotterdam, The Netherlands.
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15
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Di Stefano B, Luo EC, Haggerty C, Aigner S, Charlton J, Brumbaugh J, Ji F, Rabano Jiménez I, Clowers KJ, Huebner AJ, Clement K, Lipchina I, de Kort MAC, Anselmo A, Pulice J, Gerli MFM, Gu H, Gygi SP, Sadreyev RI, Meissner A, Yeo GW, Hochedlinger K. The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. Cell Stem Cell 2019; 25:622-638.e13. [PMID: 31588046 DOI: 10.1016/j.stem.2019.08.018] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/19/2019] [Accepted: 08/29/2019] [Indexed: 01/02/2023]
Abstract
Post-transcriptional mechanisms have the potential to influence complex changes in gene expression, yet their role in cell fate transitions remains largely unexplored. Here, we show that suppression of the RNA helicase DDX6 endows human and mouse primed embryonic stem cells (ESCs) with a differentiation-resistant, "hyper-pluripotent" state, which readily reprograms to a naive state resembling the preimplantation embryo. We further demonstrate that DDX6 plays a key role in adult progenitors where it controls the balance between self-renewal and differentiation in a context-dependent manner. Mechanistically, DDX6 mediates the translational suppression of target mRNAs in P-bodies. Upon loss of DDX6 activity, P-bodies dissolve and release mRNAs encoding fate-instructive transcription and chromatin factors that re-enter the ribosome pool. Increased translation of these targets impacts cell fate by rewiring the enhancer, heterochromatin, and DNA methylation landscapes of undifferentiated cell types. Collectively, our data establish a link between P-body homeostasis, chromatin organization, and stem cell potency.
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Affiliation(s)
- Bruno Di Stefano
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - En-Ching Luo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Chuck Haggerty
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Jocelyn Charlton
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Justin Brumbaugh
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Inés Rabano Jiménez
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Katie J Clowers
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Aaron J Huebner
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - Kendell Clement
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Inna Lipchina
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - Marit A C de Kort
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - Anthony Anselmo
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - John Pulice
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - Mattia F M Gerli
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Hongcang Gu
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Alexander Meissner
- Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92093, USA.
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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16
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Dhawan V, Kumar M, Deka D, Malhotra N, Dadhwal V, Singh N, Dada R. Meditation & yoga: Impact on oxidative DNA damage & dysregulated sperm transcripts in male partners of couples with recurrent pregnancy loss. Indian J Med Res 2019; 148:S134-S139. [PMID: 30964091 PMCID: PMC6469372 DOI: 10.4103/ijmr.ijmr_1988_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background & objectives Recurrent pregnancy loss (RPL) is one of the devastating complications of pregnancy and current focus lies in addressing the management of paternal factors. Dysregulation in selective transcripts delivered to oocyte at fertilization can result in pregnancy losses and adversely affect embryogenesis. The objective of this study was to assess the effect of yoga-based lifestyle intervention (YBLI) on seminal oxidative stress (OS), DNA damage and spermatozoal transcript levels. Methods The present study was a part of a prospective ongoing exploratory study and 30 male partners of couples with RPL were included from August 2016 to June 2017. Semen samples were obtained at baseline and at the end of YBLI (21 days). Gene expression analysis was performed by quantitative polymerase chain reaction on spermatozoal FOXG1, SOX3, OGG1, PARP1, RPS6, RBM9, RPS17 and RPL29. The levels of seminal OS and sperm DNA damage was assessed by measuring levels of reactive oxygen species (ROS) by chemiluminescence and DNA fragmentation index (DFI) by sperm chromatin structure assay. Results SOX3, OGG1 and PARP1 were observed to be upregulated, while FOXG1, RPS6, RBM9, RPS17 and RPL29 showed downregulation. A significant reduction in ROS levels, an increase in sperm motility, sperm count (done twice) and a decrease in DFI was seen after YBLI. Interpretation & conclusions Adopting YBLI may help in a significant decline in oxidative DNA damage and normalization of sperm transcript levels. This may not only improve pregnancy outcomes but also improve the health trajectory of the offspring.
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Affiliation(s)
- Vidhu Dhawan
- Department of Anatomy, Laboratory of Molecular Reproduction & Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Manoj Kumar
- Department of Anatomy, Laboratory of Molecular Reproduction & Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Dipika Deka
- Department of Obstetrics & Gynaecology, All India Institute of Medical Sciences, New Delhi, India
| | - Neena Malhotra
- Department of Obstetrics & Gynaecology, All India Institute of Medical Sciences, New Delhi, India
| | - Vatsla Dadhwal
- Department of Obstetrics & Gynaecology, All India Institute of Medical Sciences, New Delhi, India
| | - Neeta Singh
- Department of Obstetrics & Gynaecology, All India Institute of Medical Sciences, New Delhi, India
| | - Rima Dada
- Department of Anatomy, Laboratory of Molecular Reproduction & Genetics, All India Institute of Medical Sciences, New Delhi, India
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17
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Caines R, Cochrane A, Kelaini S, Vila-Gonzalez M, Yang C, Eleftheriadou M, Moez A, Stitt AW, Zeng L, Grieve DJ, Margariti A. The RNA-binding protein QKI controls alternative splicing in vascular cells, producing an effective model for therapy. J Cell Sci 2019; 132:jcs.230276. [PMID: 31331967 DOI: 10.1242/jcs.230276] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/10/2019] [Indexed: 12/31/2022] Open
Abstract
Dysfunction of endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) leads to ischaemia, the central pathology of cardiovascular disease. Stem cell technology will revolutionise regenerative medicine, but a need remains to understand key mechanisms of vascular differentiation. RNA-binding proteins have emerged as novel post-transcriptional regulators of alternative splicing and we have previously shown that the RNA-binding protein Quaking (QKI) plays roles in EC differentiation. In this study, we decipher the role of the alternative splicing isoform Quaking 6 (QKI-6) to induce VSMC differentiation from induced pluripotent stem cells (iPSCs). PDGF-BB stimulation induced QKI-6, which bound to HDAC7 intron 1 via the QKI-binding motif, promoting HDAC7 splicing and iPS-VSMC differentiation. Overexpression of QKI-6 transcriptionally activated SM22 (also known as TAGLN), while QKI-6 knockdown diminished differentiation capability. VSMCs overexpressing QKI-6 demonstrated greater contractile ability, and upon combination with iPS-ECs-overexpressing the alternative splicing isoform Quaking 5 (QKI-5), exhibited higher angiogenic potential in vivo than control cells alone. This study demonstrates that QKI-6 is critical for modulation of HDAC7 splicing, regulating phenotypically and functionally robust iPS-VSMCs. These findings also highlight that the QKI isoforms hold key roles in alternative splicing, giving rise to cells which can be used in vascular therapy or for disease modelling.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Rachel Caines
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL
| | - Amy Cochrane
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL
| | - Sophia Kelaini
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL
| | - Marta Vila-Gonzalez
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL
| | - Chunbo Yang
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL
| | - Magdalini Eleftheriadou
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL
| | - Arya Moez
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL
| | - Alan W Stitt
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL
| | - Lingfang Zeng
- Cardiovascular Division, King's College London, London SE5 9NU, UK
| | - David J Grieve
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL
| | - Andriana Margariti
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL
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18
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Chiabotto G, Gai C, Deregibus MC, Camussi G. Salivary Extracellular Vesicle-Associated exRNA as Cancer Biomarker. Cancers (Basel) 2019; 11:cancers11070891. [PMID: 31247906 PMCID: PMC6679099 DOI: 10.3390/cancers11070891] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/11/2019] [Accepted: 06/22/2019] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles (EVs) secreted in biological fluids contain several transcripts of the cell of origin, which may modify the functions and phenotype of proximal and distant cells. Cancer-derived EVs may promote a favorable microenvironment for cancer growth and invasion by acting on stroma and endothelial cells and may favor metastasis formation. The transcripts contained in cancer EVs may be exploited as biomarkers. Protein and extracellular RNA (exRNA) profiling in patient bio-fluids, such as blood and urine, was performed to identify molecular features with potential diagnostic and prognostic values. EVs are concentrated in saliva, and salivary EVs are particularly enriched in exRNAs. Several studies were focused on salivary EVs for the detection of biomarkers either of non-oral or oral cancers. The present paper provides an overview of the available studies on the diagnostic potential of exRNA profiling in salivary EVs.
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Affiliation(s)
- Giulia Chiabotto
- Department of Medical Sciences, University of Torino, Torino 10126, Italy.
| | - Chiara Gai
- Department of Medical Sciences, University of Torino, Torino 10126, Italy.
| | - Maria Chiara Deregibus
- i3T Business Incubator and Technology Transfer, University of Torino, Torino 10126, Italy.
| | - Giovanni Camussi
- Department of Medical Sciences, University of Torino, Torino 10126, Italy.
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19
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Kao SH, Cheng WC, Wang YT, Wu HT, Yeh HY, Chen YJ, Tsai MH, Wu KJ. Regulation of miRNA Biogenesis and Histone Modification by K63-Polyubiquitinated DDX17 Controls Cancer Stem-like Features. Cancer Res 2019; 79:2549-2563. [PMID: 30877109 DOI: 10.1158/0008-5472.can-18-2376] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/17/2019] [Accepted: 03/12/2019] [Indexed: 11/16/2022]
Abstract
Markers of cancer stemness predispose patients to tumor aggressiveness, drug and immunotherapy resistance, relapse, and metastasis. DDX17 is a cofactor of the Drosha-DGCR8 complex in miRNA biogenesis and transcriptional coactivator and has been associated with cancer stem-like properties. However, the precise mechanism by which DDX17 controls cancer stem-like features remains elusive. Here, we show that the E3 ligase HectH9 mediated K63-polyubiquitination of DDX17 under hypoxia to control stem-like properties and tumor-initiating capabilities. Polyubiquitinated DDX17 disassociated from the Drosha-DGCR8 complex, leading to decreased biogenesis of anti-stemness miRNAs. Increased association of polyubiquitinated DDX17 with p300-YAP resulted in histone 3 lysine 56 (H3K56) acetylation proximal to stemness-related genes and their subsequent transcriptional activation. High expression of HectH9 and six stemness-related genes (BMI1, SOX2, OCT4, NANOG, NOTCH1, and NOTCH2) predicted poor survival in patients with head and neck squamous cell carcinoma and lung adenocarcinoma. Our findings demonstrate that concerted regulation of miRNA biogenesis and histone modifications through posttranslational modification of DDX17 underlies many cancer stem-like features. Inhibition of DDX17 ubiquitination may serve as a new therapeutic venue for cancer treatment. SIGNIFICANCE: Hypoxia-induced polyubiquitination of DDX17 controls its dissociation from the pri-miRNA-Drosha-DCGR8 complex to reduce anti-stemness miRNA biogenesis and association with YAP and p300 to enhance transcription of stemness-related genes.
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Affiliation(s)
- Shih-Han Kao
- Research Center for Tumor Medical Science, China Medical University, Taichung, Taiwan.,Drug Development Center, China Medical University, Taichung, Taiwan
| | - Wei-Chung Cheng
- Research Center for Tumor Medical Science, China Medical University, Taichung, Taiwan.,Drug Development Center, China Medical University, Taichung, Taiwan.,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Yi-Ting Wang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Han-Tsang Wu
- Department of Cell and Tissue Engineering, Changhua Christian Hospital, Changhua City, Taiwan
| | - Han-Yu Yeh
- Research Center for Tumor Medical Science, China Medical University, Taichung, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Ming-Hsui Tsai
- Department of Otolaryngology, China Medical University Hospital, Taichung, Taiwan
| | - Kou-Juey Wu
- Research Center for Tumor Medical Science, China Medical University, Taichung, Taiwan. .,Drug Development Center, China Medical University, Taichung, Taiwan.,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.,Institute of New Drug Development, China Medical University, Taichung, Taiwan.,Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.,Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.,Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
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20
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Lloret-Llinares M, Karadoulama E, Chen Y, Wojenski LA, Villafano GJ, Bornholdt J, Andersson R, Core L, Sandelin A, Jensen TH. The RNA exosome contributes to gene expression regulation during stem cell differentiation. Nucleic Acids Res 2018; 46:11502-11513. [PMID: 30212902 PMCID: PMC6265456 DOI: 10.1093/nar/gky817] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/29/2018] [Accepted: 09/09/2018] [Indexed: 12/27/2022] Open
Abstract
Gene expression programs change during cellular transitions. It is well established that a network of transcription factors and chromatin modifiers regulate RNA levels during embryonic stem cell (ESC) differentiation, but the full impact of post-transcriptional processes remains elusive. While cytoplasmic RNA turnover mechanisms have been implicated in differentiation, the contribution of nuclear RNA decay has not been investigated. Here, we differentiate mouse ESCs, depleted for the ribonucleolytic RNA exosome, into embryoid bodies to determine to which degree RNA abundance in the two states can be attributed to changes in transcription versus RNA decay by the exosome. As a general observation, we find that exosome depletion mainly leads to the stabilization of RNAs from lowly transcribed loci, including several protein-coding genes. Depletion of the nuclear exosome cofactor RBM7 leads to similar effects. In particular, transcripts that are differentially expressed between states tend to be more exosome sensitive in the state where expression is low. We conclude that the RNA exosome contributes to down-regulation of transcripts with disparate expression, often in conjunction with transcriptional down-regulation.
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Affiliation(s)
| | - Evdoxia Karadoulama
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Denmark
| | - Yun Chen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Denmark
| | - Luke A Wojenski
- Department of Molecular and Cell Biology, Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Geno J Villafano
- Department of Molecular and Cell Biology, Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Jette Bornholdt
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Denmark
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Denmark
| | - Leighton Core
- Department of Molecular and Cell Biology, Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Denmark
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21
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Dhawan V, Kumar M, Deka D, Malhotra N, Singh N, Dadhwal V, Dada R. Paternal factors and embryonic development: Role in recurrent pregnancy loss. Andrologia 2018; 51:e13171. [PMID: 30324700 DOI: 10.1111/and.13171] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/18/2018] [Accepted: 08/27/2018] [Indexed: 12/29/2022] Open
Abstract
The events occurring at the maternal-foetal interface define a successful pregnancy but the current paradigm has shifted towards assessing the contribution of spermatozoa for embryogenesis. Spermatozoa with defective DNA integrity may fertilise the oocyte but affect subsequent embryonic development. The present case-control study was conducted in male partners of couples experiencing recurrent pregnancy loss (RPL) to assess the gene expression of spermatozoal FOXG1, SOX3, OGG1, PARP1, RPS6, RBM9, RPS17 and RPL29. This was correlated with reactive oxygen species (ROS) levels and DNA Fragmentation Index (DFI). Semen samples were obtained from 60 cases and 30 fertile controls. Gene expression was done by qPCR analysis, and relative quantification was calculated by the 2-ΔΔCt method. Chemiluminescence and the sperm chromatin structure assay were used to measure the ROS and DFI levels respectively. FOXG1, OGG1, RPS6 and RBM9 were seen to be upregulated, while SOX3 and PARP1 were downregulated. Relative expression of SOX3, OGG1, RPS6 and RPS17 showed a significant difference between patients and controls (p < 0.05). RPL patients were seen to have high ROS (>27.8; p = 0.001) and DFI (>30.7; p < 0.0001) with respect to controls. Sperm transcript dysregulation and oxidative DNA damage can be "carried over" after implantation, thus affecting embryogenesis and health of the future progeny.
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Affiliation(s)
- Vidhu Dhawan
- Department of Anatomy, Laboratory of Molecular Reproduction & Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Manoj Kumar
- Department of Anatomy, Laboratory of Molecular Reproduction & Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Dipika Deka
- Department of Obstetrics & Gynaecology, All India Institute of Medical Sciences, New Delhi, India
| | - Neena Malhotra
- Department of Obstetrics & Gynaecology, All India Institute of Medical Sciences, New Delhi, India
| | - Neeta Singh
- Department of Obstetrics & Gynaecology, All India Institute of Medical Sciences, New Delhi, India
| | - Vatsla Dadhwal
- Department of Obstetrics & Gynaecology, All India Institute of Medical Sciences, New Delhi, India
| | - Rima Dada
- Department of Anatomy, Laboratory of Molecular Reproduction & Genetics, All India Institute of Medical Sciences, New Delhi, India
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22
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Abstract
The role of RNA binding proteins (RBPs) during nuclear reprogramming is poorly characterized. In this issue of Cell Stem Cell,Li et al. (2017) show that DEAD-box RBP DDX5 acts as a reprogramming roadblock and give important mechanistic insights into the establishment of pluripotency by characterizing the intricate downstream events.
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23
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Chen Q, Hu G. Post-transcriptional regulation of the pluripotent state. Curr Opin Genet Dev 2017; 46:15-23. [PMID: 28654825 DOI: 10.1016/j.gde.2017.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/17/2017] [Accepted: 06/08/2017] [Indexed: 12/20/2022]
Abstract
Pluripotency describes the developmental capacity to give rise to all cell types in the adult body. A comprehensive understanding of the molecular mechanisms that regulate pluripotency is important for both basic and translational research. While earlier studies mostly focused on signaling pathways, transcriptional regulation, and epigenetic modifications, recent investigations showed that RNA binding proteins, RNA processing machineries, and regulatory RNA molecules also play essential roles. Here, we provide a concise review on the latest findings and developments in post-transcriptional regulation of the pluripotent state.
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Affiliation(s)
- Qing Chen
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, NC, United States.
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, NC, United States.
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24
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Li H, Lai P, Jia J, Song Y, Xia Q, Huang K, He N, Ping W, Chen J, Yang Z, Li J, Yao M, Dong X, Zhao J, Hou C, Esteban MA, Gao S, Pei D, Hutchins AP, Yao H. RNA Helicase DDX5 Inhibits Reprogramming to Pluripotency by miRNA-Based Repression of RYBP and its PRC1-Dependent and -Independent Functions. Cell Stem Cell 2017; 20:462-477.e6. [PMID: 28111200 DOI: 10.1016/j.stem.2016.12.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 08/08/2016] [Accepted: 12/02/2016] [Indexed: 12/24/2022]
Abstract
RNA-binding proteins (RBPs), in addition to their functions in cellular homeostasis, play important roles in lineage specification and maintaining cellular identity. Despite their diverse and essential functions, which touch on nearly all aspects of RNA metabolism, the roles of RBPs in somatic cell reprogramming are poorly understood. Here we show that the DEAD-box RBP DDX5 inhibits reprogramming by repressing the expression and function of the non-canonical polycomb complex 1 (PRC1) subunit RYBP. Disrupting Ddx5 expression improves the efficiency of iPSC generation and impedes processing of miR-125b, leading to Rybp upregulation and suppression of lineage-specific genes via RYBP-dependent ubiquitination of H2AK119. Furthermore, RYBP is required for PRC1-independent recruitment of OCT4 to the promoter of Kdm2b, a histone demethylase gene that promotes reprogramming by reactivating endogenous pluripotency genes. Together, these results reveal important functions of DDX5 in regulating reprogramming and highlight the importance of a Ddx5-miR125b-Rybp axis in controlling cell fate.
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Affiliation(s)
- Huanhuan Li
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; GZMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou 511436, China
| | - Ping Lai
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jinping Jia
- Laboratory of Translational Genomics, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yawei Song
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Qing Xia
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Kaimeng Huang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Na He
- Department of Biology, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Wangfang Ping
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jiayu Chen
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhongzhou Yang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jiao Li
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Mingze Yao
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiaotao Dong
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jicheng Zhao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunhui Hou
- Department of Biology, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Miguel A Esteban
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Shaorong Gao
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Andrew P Hutchins
- Department of Biology, Southern University of Science and Technology of China, Shenzhen 518055, China
| | - Hongjie Yao
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CAS Center for Excellence in Molecular Cell Science, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
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25
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Loiselle JJ, Roy JG, Sutherland LC. RBM5 reduces small cell lung cancer growth, increases cisplatin sensitivity and regulates key transformation-associated pathways. Heliyon 2016; 2:e00204. [PMID: 27957556 PMCID: PMC5133678 DOI: 10.1016/j.heliyon.2016.e00204] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/07/2016] [Accepted: 11/22/2016] [Indexed: 12/21/2022] Open
Abstract
Small cell lung cancer (SCLC) is the most aggressive type of lung cancer, with almost 95% of patients succumbing to the disease. Although RBM5, a tumor suppressor gene, is downregulated in the majority of lung cancers, its role in SCLC is unknown. Using the GLC20 SCLC cell line, which has a homozygous deletion encompassing the RBM5 gene locus, we established stable RBM5 expressing sublines and investigated the effects of RBM5 re-expression. Transcriptome and target identification studies determined that RBM5 directly regulates the cell cycle and apoptosis in SCLC cells, as well as significantly downregulates other important transformation-associated pathways such as angiogenesis and cell adhesion. RNA sequencing of paired non-tumor and tumor SCLC patient specimens showed decreased RBM5 expression in the tumors, and expression alterations in the majority of the same pathways that were altered in the GLC20 cells and sublines. Functional studies confirmed RBM5 expression slows SCLC cell line growth, and increases sensitivity to the chemotherapy drug cisplatin. Overall, our work demonstrates the importance of RBM5 expression to the non-transformed state of lung cells and the consequences of its deletion to SCLC development and progression.
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Affiliation(s)
- Julie J. Loiselle
- Biomolecular Sciences Program, Laurentian University, Sudbury, ON P3E 2C6, Canada
| | - Justin G. Roy
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON P3E 2C6, Canada
| | - Leslie C. Sutherland
- Biomolecular Sciences Program, Laurentian University, Sudbury, ON P3E 2C6, Canada
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON P3E 2C6, Canada
- Health Sciences North Research Institute (HSNRI), 41 Ramsey Lake Road, Sudbury, ON P3E 5J1, Canada
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26
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Ladd AN. New Insights Into the Role of RNA-Binding Proteins in the Regulation of Heart Development. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:125-85. [PMID: 27017008 DOI: 10.1016/bs.ircmb.2015.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The regulation of gene expression during development takes place both at the transcriptional and posttranscriptional levels. RNA-binding proteins (RBPs) regulate pre-mRNA processing, mRNA localization, stability, and translation. Many RBPs are expressed in the heart and have been implicated in heart development, function, or disease. This chapter will review the current knowledge about RBPs in the developing heart, focusing on those that regulate posttranscriptional gene expression. The involvement of RBPs at each stage of heart development will be considered in turn, including the establishment of specific cardiac cell types and formation of the primitive heart tube, cardiac morphogenesis, and postnatal maturation and aging. The contributions of RBPs to cardiac birth defects and heart disease will also be considered in these contexts. Finally, the interplay between RBPs and other regulatory factors in the developing heart, such as transcription factors and miRNAs, will be discussed.
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Affiliation(s)
- A N Ladd
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States of America.
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27
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The Poly(C) Binding Protein Pcbp2 and Its Retrotransposed Derivative Pcbp1 Are Independently Essential to Mouse Development. Mol Cell Biol 2015; 36:304-19. [PMID: 26527618 DOI: 10.1128/mcb.00936-15] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 10/28/2015] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins participate in a complex array of posttranscriptional controls essential to cell type specification and somatic development. Despite their detailed biochemical characterizations, the degree to which each RNA-binding protein impacts mammalian embryonic development remains incompletely defined, and the level of functional redundancy among subsets of these proteins remains open to question. The poly(C) binding proteins, PCBPs (αCPs and hnRNP E proteins), are encoded by a highly conserved and broadly expressed gene family. The two major Pcbp isoforms, Pcbp2 and Pcbp1, are robustly expressed in a wide range of tissues and exert both nuclear and cytoplasmic controls over gene expression. Here, we report that Pcbp1-null embryos are rendered nonviable in the peri-implantation stage. In contrast, Pcbp2-null embryos undergo normal development until midgestation (12.5 to 13.5 days postcoitum), at which time they undergo a dramatic loss in viability associated with combined cardiovascular and hematopoietic abnormalities. Mice heterozygous for either Pcbp1 or Pcbp2 null alleles display a mild and nondisruptive defect in initial postpartum weight gain. These data reveal that Pcbp1 and Pcbp2 are individually essential for mouse embryonic development and have distinct impacts on embryonic viability and that Pcpb2 has a nonredundant in vivo role in hematopoiesis. These data further provide direct evidence that Pcbp1, a retrotransposed derivative of Pcpb2, has evolved an essential function(s) in the mammalian genome.
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28
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Heterogeneous nuclear ribonucleoprotein A1 post-transcriptionally regulates Drp1 expression in neuroblastoma cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1423-31. [PMID: 26518267 PMCID: PMC4655839 DOI: 10.1016/j.bbagrm.2015.10.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/04/2015] [Accepted: 10/23/2015] [Indexed: 12/22/2022]
Abstract
Excessive mitochondrial fission is associated with the pathogenesis of neurodegenerative diseases. Dynamin-related protein 1 (Drp1) possesses specific fission activity in the mitochondria and peroxisomes. Various post-translational modifications of Drp1 are known to modulate complex mitochondrial dynamics. However, the post-transcriptional regulation of Drp1 remains poorly understood. Here, we show that the heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) regulates Drp1 expression at the post-transcriptional level. hnRNP A1 directly interacts with Drp1 mRNA at its 3′UTR region, and enhances translation potential without affecting mRNA stability. Down-regulation of hnRNP A1 induces mitochondrial elongation by reducing Drp1 expression. Moreover, depletion of hnRNP A1 suppresses 3-NP-mediated mitochondrial fission and dysfunction. In contrast, over-expression of hnRNP A1 promotes mitochondrial fragmentation by increasing Drp1 expression. Additionally, hnRNP A1 significantly exacerbates 3-NP-induced mitochondrial dysfunction and cell death in neuroblastoma cells. Interestingly, treatment with 3-NP induces subcellular translocation of hnRNP A1 from the nucleus to the cytoplasm, which accelerates the increase in Drp1 expression in hnRNP A1 over-expressing cells. Collectively, our findings suggest that hnRNP A1 controls mitochondrial dynamics by post-transcriptional regulation of Drp1. hnRNP A1 increases Drp1 expression through the interaction with 3′UTR of Drp1 mRNA. Down-regulation of hnRNP A1 increases mitochondrial elongation by reducing drp1 expression. Down-regulation of hnRNPA1 inhibits 3-NP-mediated mitochondrial dysfunction. Over-expression of hnRNP A1 potentiates 3-NP-mediated mitochondrial dysfunction and cell death. Treatment of 3-NP promotes translocation of hnRNP A1 to the cytoplasm and enhances Drp1 expression.
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29
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Quesenberry PJ, Aliotta J, Deregibus MC, Camussi G. Role of extracellular RNA-carrying vesicles in cell differentiation and reprogramming. Stem Cell Res Ther 2015; 6:153. [PMID: 26334526 PMCID: PMC4558901 DOI: 10.1186/s13287-015-0150-x] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Growing evidence suggests that transcriptional regulators and secreted RNA molecules encapsulated within membrane vesicles modify the phenotype of target cells. Membrane vesicles, actively released by cells, represent a mechanism of intercellular communication that is conserved evolutionarily and involves the transfer of molecules able to induce epigenetic changes in recipient cells. Extracellular vesicles, which include exosomes and microvesicles, carry proteins, bioactive lipids, and nucleic acids, which are protected from enzyme degradation. These vesicles can transfer signals capable of altering cell function and/or reprogramming targeted cells. In the present review we focus on the extracellular vesicle-induced epigenetic changes in recipient cells that may lead to phenotypic and functional modifications. The relevance of these phenomena in stem cell biology and tissue repair is discussed.
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Affiliation(s)
- Peter J Quesenberry
- Department of Medicine, Warren Alpert Medical School of Brown University, Box G-A1, Providence, RI, 02912, USA.
| | - Jason Aliotta
- Department of Medicine, Warren Alpert Medical School of Brown University, Box G-A1, Providence, RI, 02912, USA
| | - Maria Chiara Deregibus
- Translational Center for Regenerative Medicine, University of Torino/Fresenius Medical Care, via Nizza 52, 10126, Torino, Italy
- Department of Medical Sciences, University of Torino, Corso Dogliotti 14, 10126, Torino, Italy
| | - Giovanni Camussi
- Department of Medical Sciences, University of Torino, Corso Dogliotti 14, 10126, Torino, Italy.
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