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Fang F, Chen D, Basharat AR, Poulos W, Wang Q, Cibelli JB, Liu X, Sun L. Quantitative proteomics reveals the dynamic proteome landscape of zebrafish embryos during the maternal-to-zygotic transition. iScience 2024; 27:109944. [PMID: 38784018 PMCID: PMC11111832 DOI: 10.1016/j.isci.2024.109944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 08/23/2023] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Maternal-to-zygotic transition (MZT) is central to early embryogenesis. However, its underlying molecular mechanisms are still not well described. Here, we revealed the expression dynamics of 5,000 proteins across four stages of zebrafish embryos during MZT, representing one of the most systematic surveys of proteome landscape of the zebrafish embryos during MZT. Nearly 700 proteins were differentially expressed and were divided into six clusters according to their expression patterns. The proteome expression profiles accurately reflect the main events that happen during the MZT, i.e., zygotic genome activation (ZGA), clearance of maternal mRNAs, and initiation of cellular differentiation and organogenesis. MZT is modulated by many proteins at multiple levels in a collaborative fashion, i.e., transcription factors, histones, histone-modifying enzymes, RNA helicases, and P-body proteins. Significant discrepancies were discovered between zebrafish proteome and transcriptome profiles during the MZT. The proteome dynamics database will be a valuable resource for bettering our understanding of MZT.
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Affiliation(s)
- Fei Fang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Abdul Rehman Basharat
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - William Poulos
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Jose B. Cibelli
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Xiaowen Liu
- Deming Department of Medicine, School of Medicine, Tulane University, 1441 Canal Street, New Orleans, LA 70112, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
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2
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Yao G, Yu S, Hou F, Xiao Z, Li G, Ji X, Wang J. Rab3B enhances the stabilization of DDX6 to promote lung adenocarcinoma aggressiveness. Mol Med 2024; 30:75. [PMID: 38834947 PMCID: PMC11151598 DOI: 10.1186/s10020-024-00848-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 05/28/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Liver kinase B1 (LKB1) is frequently mutated in lung adenocarcinoma, and its loss contributes to tumor progression. METHODS To identify LKB1 downstream genes that promote lung adenocarcinoma aggressiveness, we performed bioinformatical analysis using publicly available datasets. RESULTS Rab3B was upregulated in LKB1-depleted lung adenocarcinoma cells and suppressed by LKB1 overexpression. CREB protein was enriched at the promoter of Rab3B in lung cancer cells. Silencing of CREB abrogated the upregulation of Rab3B upon LKB1 loss. Immunohistochemistry revealed the elevated expression of Rab3B in lung adenocarcinomas relative to adjacent normal tissues. Upregulation of Rab3B was significantly associated with lymph node metastasis, advanced tumor stage, and reduced overall survival in lung adenocarcinoma patients. Knockdown of Rab3B suppressed and overexpression of Rab3B promoted the proliferation, colony formation, and migration of lung adenocarcinoma cells in vitro. In a mouse xenograft model, Rab3B depletion restrained and Rab3B overexpression augmented the growth of lung adenocarcinoma tumors. Mechanistically, Rab3B interacted with DDX6 and enhanced its protein stability. Ectopic expression of DDX6 significantly promoted the proliferation, colony formation, and migration of lung adenocarcinoma cells. DDX6 knockdown phenocopied the effects of Rab3B depletion on lung adenocarcinoma cells. Additionally, DDX6 overexpression partially rescued the aggressive phenotype of Rab3B-depleted lung adenocarcinoma cells. CONCLUSION LKB1 deficiency promotes Rab3B upregulation via a CREB-dependent manner. Rab3B interacts with and stabilizes DDX6 protein to accelerate lung adenocarcinoma progression. The Rab3B-DDX6 axis may be potential therapeutic target for lung adenocarcinoma.
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Affiliation(s)
- Guodong Yao
- Department of Pathology, Affiliated Hospital of Qingdao University, Qingdao, 266071, Shandong Province, China
| | - Shan Yu
- Department of Pathology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Feng Hou
- Department of Pathology, Affiliated Hospital of Qingdao University, Qingdao, 266071, Shandong Province, China
| | - Zunyu Xiao
- Department of Imaging, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Guangqi Li
- Department of Pathology, Affiliated Hospital of Qingdao University, Qingdao, 266071, Shandong Province, China
| | - Xiaobin Ji
- Department of Pathology, Affiliated Hospital of Qingdao University, Qingdao, 266071, Shandong Province, China
| | - Jigang Wang
- Department of Pathology, Affiliated Hospital of Qingdao University, Qingdao, 266071, Shandong Province, China.
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3
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Deng X, Liu Z, Wang B, Ma J, Meng X. The DDX6/KIFC1 signaling axis, as regulated by YY1, contributes to the malignant behavior of pancreatic cancer. FASEB J 2024; 38:e23581. [PMID: 38551642 DOI: 10.1096/fj.202400166r] [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: 01/25/2024] [Revised: 03/07/2024] [Accepted: 03/15/2024] [Indexed: 04/02/2024]
Abstract
Human DEAD/H box RNA helicase DDX6 acts as an oncogene in several different types of cancer, where it participates in RNA processing. Nevertheless, the role of DDX6 in pancreatic cancer (PC), together with the underlying mechanism, has yet to be fully elucidated. In the present study, compared with adjacent tissues, the level of DDX6 was abnormally increased in human PC tissues, and this increased level of expression was associated with poor prognosis. Furthermore, the role of DDX6 in PC was investigated by overexpressing or silencing the DDX6 in the PC cell lines, SW1990 and PaTu-8988t. A xenograft model was established by injecting nude mice with either DDX6-overexpressing or DDX6-silenced SW1990 cells. DDX6 overexpression promoted the proliferation and cell cycle transition, inhibited the cell apoptosis of PC cells, and accelerated tumor formation, whereas DDX6 knockdown elicited the opposite effects. DDX6 exerted positive effects on PC. RNA immunoprecipitation assay showed that DDX6 bound to kinesin family member C1 (KIFC1) mRNA, which was further confirmed by RNA pull-down assay. These results suggested that DDX6 positively regulated the expression of KIFC1. KIFC1 overexpression enhanced the proliferative capability of PC cells with DDX6 knockdown and inhibited their apoptosis. By contrast, DDX6 overexpression reversed the inhibitory effect of KIFC1 silencing on tumor proliferation. Subsequently, the transcription factor Yin Yang 1 (YY1) was shown to negatively regulate DDX6 at both the mRNA and protein levels. Dual-luciferase reporter assay verified that YY1 targeted the promoter of DDX6 and inhibited its transcription. High expression levels of YY1 decreased the proliferation of PC cells and promoted cell apoptosis, although these effects were reversed by DDX6 overexpression. Taken together, YY1 may target the DDX6/KIFC1 axis, thereby negatively regulating its expression, leading to an inhibitory effect on pancreatic tumor.
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Affiliation(s)
- Xin Deng
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhen Liu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Baosheng Wang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jia Ma
- Department of Gastroenterology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xiangpeng Meng
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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4
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Perooli FM, Wilkinson KA, Pring K, Hanley JG. An essential role for the RNA helicase DDX6 in NMDA receptor-dependent gene silencing and dendritic spine shrinkage. Sci Rep 2024; 14:3066. [PMID: 38321143 PMCID: PMC10847504 DOI: 10.1038/s41598-024-53484-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/01/2024] [Indexed: 02/08/2024] Open
Abstract
MicroRNAs (miRNAs) repress translation of target mRNAs by associating with Argonaute (Ago) proteins in the RNA-induced silencing complex (RISC) to modulate protein expression. Specific miRNAs are required for NMDA receptor (NMDAR)-dependent synaptic plasticity by repressing the translation of proteins involved in dendritic spine morphogenesis. Rapid NMDAR-dependent silencing of Limk1 is essential for spine shrinkage and requires Ago2 phosphorylation at S387. Not all gene silencing events are modulated by S387 phosphorylation, and the mechanisms that govern the selection of specific mRNAs for silencing downstream of S387 phosphorylation are unknown. Here, we show that NMDAR-dependent S387 phosphorylation causes a rapid and transient increase in the association of Ago2 with Limk1, but not Apt1 mRNA. The specific increase in Limk1 mRNA binding to Ago2 requires recruitment of the helicase DDX6 to RISC. Furthermore, we show that DDX6 is required for NMDAR-dependent silencing of Limk1 via miR-134, but not Apt1 via miR-138, and is essential for NMDAR-dependent spine shrinkage. This work defines a novel mechanism for the rapid transduction of NMDAR stimulation into miRNA-mediated translational repression of specific genes to control dendritic spine morphology.
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Affiliation(s)
- Fathima M Perooli
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Kevin A Wilkinson
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Kate Pring
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Jonathan G Hanley
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK.
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5
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Xie Y, Wang Q, Yang Y, Near D, Wang H, Colon M, Nguyen C, Slattery C, Keepers B, Farber G, Wang TW, Lee SH, Shih YYI, Liu J, Qian L. Translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition. NATURE CARDIOVASCULAR RESEARCH 2023; 2:1060-1077. [PMID: 38524149 PMCID: PMC10959502 DOI: 10.1038/s44161-023-00344-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 09/06/2023] [Indexed: 03/26/2024]
Abstract
Direct reprogramming of fibroblasts into induced cardiomyocytes holds great promise for heart regeneration. Although considerable progress has been made in understanding the transcriptional and epigenetic mechanisms of iCM reprogramming, its translational regulation remains largely unexplored. Here, we characterized the translational landscape of iCM reprogramming through integrative ribosome and transcriptomic profiling, and found extensive translatome repatterning during this process. Loss of function screening for translational regulators uncovered Ybx1 as a critical barrier to iCM induction. In a mouse model of myocardial infarction, removing Ybx1 enhanced in vivo reprogramming, resulting in improved heart function and reduced scar size. Mechanistically, Ybx1 depletion de-repressed the translation of its direct targets SRF and Baf60c, both of which mediated the effect of Ybx1 depletion on iCM generation. Furthermore, removal of Ybx1 allowed single factor Tbx5-mediated iCM conversion. In summary, this study revealed a new layer of regulatory mechanism that controls cardiac reprogramming at the translational level.
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Affiliation(s)
- Yifang Xie
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Qiaozi Wang
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Yuchen Yang
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
| | - David Near
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Haofei Wang
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Marazzano Colon
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Christopher Nguyen
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Conor Slattery
- EIRNA Bio Ltd, BioInnovation Centre, Food Science and Technology Building, College Road, Cork, Ireland, T12 DP07
| | - Benjamin Keepers
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599
| | - Gregory Farber
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Tzu-Wen Wang
- Departments of Neurology, University of North Carolina, Chapel Hill, NC 27599
| | - Sung-Ho Lee
- Departments of Neurology, University of North Carolina, Chapel Hill, NC 27599
| | - Yen-Yu Ian Shih
- Departments of Neurology, University of North Carolina, Chapel Hill, NC 27599
| | - Jiandong Liu
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599
| | - Li Qian
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599
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6
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Lau ESW, Zhu B, Sun MA, Ngai SM, Ge W. Proteomic analysis of zebrafish folliculogenesis identifies YB-1 (Ybx1/ybx1) as a potential gatekeeping molecule controlling early ovarian folliculogenesis. Biol Reprod 2023; 109:482-497. [PMID: 37471641 DOI: 10.1093/biolre/ioad078] [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: 01/27/2023] [Revised: 06/16/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023] Open
Abstract
As in mammals, ovarian folliculogenesis in teleosts also consists of two phases: the primary growth (PG) and secondary growth (SG) phases, which are analogous to the preantral and antral phases respectively in mammals. In this study, we performed a proteomic analysis on zebrafish follicles undergoing the PG-SG transition aiming to identify factors involved in the event. Numerous proteins showed significant changes, and the most prominent one was Y-box binding protein 1 (YB-1; Ybx1/ybx1), a transcription factor and mRNA-binding protein. YB-1 belongs to the Y-box binding protein family, which also includes the gonad-specific YB-2. Interestingly, phylogenetic analysis showed no YB-2 homolog in zebrafish. Although ybx1 mRNA was expressed in various tissues, its protein Ybx1 was primarily produced in the gonads, similar to YB-2 in other species. In the ovary, Ybx1 protein started to appear in early follicles newly emerged from the germ cell cysts, reached the highest level in late PG oocytes, but decreased precipitously when the follicles entered the SG phase. In PG follicles, Ybx1 might function as a key component of the messenger ribonucleoprotein particles (mRNPs) in association with other RNA-binding proteins. Similar to mammalian YB-1, zebrafish Ybx1 also contains functional signals that determine its intracellular localization. In conclusion, Ybx1 may play dual roles of YB-1 and YB-2 in zebrafish. In the ovary, Ybx1 binds mRNAs to stabilize them while preventing their translation. At PG-SG transition, Ybx1 is removed to release the masked mRNAs for translation into functional proteins, leading to follicle activation.
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Affiliation(s)
- Esther Shuk-Wa Lau
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong 999077, China
| | - Bo Zhu
- Department of Biomedical Sciences and Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China
| | - Ming-An Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Sai Ming Ngai
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong 999077, China
| | - Wei Ge
- Department of Biomedical Sciences and Centre of Reproduction, Development and Aging (CRDA), Faculty of Health Sciences, University of Macau, Taipa, Macau 999078, China
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7
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Takubo K, Htun PW, Ueda T, Sera Y, Iwasaki M, Koizumi M, Shiroshita K, Kobayashi H, Haraguchi M, Watanuki S, Honda ZI, Yamasaki N, Nakamura-Ishizu A, Arai F, Motoyama N, Hatta T, Natsume T, Suda T, Honda H. MBTD1 preserves adult hematopoietic stem cell pool size and function. Proc Natl Acad Sci U S A 2023; 120:e2206860120. [PMID: 37523546 PMCID: PMC10410756 DOI: 10.1073/pnas.2206860120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/28/2023] [Indexed: 08/02/2023] Open
Abstract
Mbtd1 (mbt domain containing 1) encodes a nuclear protein containing a zinc finger domain and four malignant brain tumor (MBT) repeats. We previously generated Mbtd1-deficient mice and found that MBTD1 is highly expressed in fetal hematopoietic stem cells (HSCs) and sustains the number and function of fetal HSCs. However, since Mbtd1-deficient mice die soon after birth possibly due to skeletal abnormalities, its role in adult hematopoiesis remains unclear. To address this issue, we generated Mbtd1 conditional knockout mice and analyzed adult hematopoietic tissues deficient in Mbtd1. We observed that the numbers of HSCs and progenitors increased and Mbtd1-deficient HSCs exhibited hyperactive cell cycle, resulting in a defective response to exogenous stresses. Mechanistically, we found that MBTD1 directly binds to the promoter region of FoxO3a, encoding a forkhead protein essential for HSC quiescence, and interacts with components of TIP60 chromatin remodeling complex and other proteins involved in HSC and other stem cell functions. Restoration of FOXO3a activity in Mbtd1-deficient HSCs in vivo rescued cell cycle and pool size abnormalities. These findings indicate that MBTD1 is a critical regulator for HSC pool size and function, mainly through the maintenance of cell cycle quiescence by FOXO3a.
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Affiliation(s)
- Keiyo Takubo
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo162-8655, Japan
| | - Phyo Wai Htun
- Medical Department, 7887 Healthcare Call Center, Yangon11062, Myanmar
| | - Takeshi Ueda
- Department of Biochemistry, Kindai University Faculty of Medicine,Sayama-shi, Osaka589-8511, Japan
| | - Yasuyuki Sera
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Institute of Laboratory Animals, Tokyo Women’s Medical University, Shinjuku-ku, Tokyo162-8666, Japan
| | - Masayuki Iwasaki
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Institute of Laboratory Animals, Tokyo Women’s Medical University, Shinjuku-ku, Tokyo162-8666, Japan
| | - Miho Koizumi
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Institute of Laboratory Animals, Tokyo Women’s Medical University, Shinjuku-ku, Tokyo162-8666, Japan
| | - Kohei Shiroshita
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo162-8655, Japan
| | - Hiroshi Kobayashi
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo162-8655, Japan
| | - Miho Haraguchi
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo162-8655, Japan
| | - Shintaro Watanuki
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo162-8655, Japan
| | - Zen-ichiro Honda
- Health Care Center and Graduate School of Humanities and Sciences, Institute of Environmental Science for Human Life, Ochanomizu University, Bunkyo-ku, Tokyo112-8611, Japan
| | - Norimasa Yamasaki
- Department of Molecular Oncology, Research Institute of Radiation Biology and Medicine, Hiroshima University, Minami-ku, Hiroshima734-8553, Japan
| | - Ayako Nakamura-Ishizu
- Department of Microscopic and Developmental Anatomy, Tokyo Women's Medical University, Tokyo162-8666, Japan
| | - Fumio Arai
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Science, Kyusyu University, Fukuoka812-8582, Japan
| | - Noboru Motoyama
- Department of Human Nutrition, Sugiyama Jogakuen University School of Life Studies, Nagoya464-8662, Japan
| | - Tomohisa Hatta
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo135-0064, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo135-0064, Japan
| | - Toshio Suda
- Cancer Science Institute of Singapore, National University of Singapore Center for Translational Medicine, Singapore117599, Singapore
| | - Hiroaki Honda
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Institute of Laboratory Animals, Tokyo Women’s Medical University, Shinjuku-ku, Tokyo162-8666, Japan
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8
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Kara E, McCambridge A, Proffer M, Dilts C, Pumnea B, Eshak J, Smith KA, Fielder I, Doyle DA, Ortega BM, Mukatash Y, Malik N, Mohammed AR, Govani D, Niepielko MG, Gao M. Mutational analysis of the functional motifs of the DEAD-box RNA helicase Me31B/DDX6 in Drosophila germline development. FEBS Lett 2023; 597:1848-1867. [PMID: 37235728 PMCID: PMC10389067 DOI: 10.1002/1873-3468.14668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/24/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023]
Abstract
Me31B/DDX6 is a DEAD-box family RNA helicase playing roles in post-transcriptional RNA regulation in different cell types and species. Despite the known motifs/domains of Me31B, the in vivo functions of the motifs remain unclear. Here, we used the Drosophila germline as a model and used CRISPR to mutate the key Me31B motifs/domains: helicase domain, N-terminal domain, C-terminal domain and FDF-binding motif. Then, we performed screening characterization on the mutants and report the effects of the mutations on the Drosophila germline, on processes such as fertility, oogenesis, embryo patterning, germline mRNA regulation and Me31B protein expression. The study indicates that the Me31B motifs contribute different functions to the protein and are needed for proper germline development, providing insights into the in vivo working mechanism of the helicase.
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Affiliation(s)
- Evan Kara
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | | | - Megan Proffer
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Carol Dilts
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Brooke Pumnea
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - John Eshak
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Korey A. Smith
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Isaac Fielder
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Dominique A. Doyle
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Bianca M. Ortega
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
| | - Yousif Mukatash
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Noor Malik
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | | | - Deep Govani
- Biology Department, Indiana University Northwest, Gary, IN, USA
| | - Matthew G. Niepielko
- School of Integrative Science and Technology, Kean University, Union, NJ, USA
- Biology Department, Kean University, Union, NJ, USA
| | - Ming Gao
- Biology Department, Indiana University Northwest, Gary, IN, USA
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9
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Bai Y, Gotz C, Chincarini G, Zhao Z, Slaney C, Boath J, Furic L, Angel C, Jane SM, Phillips WA, Stacker SA, Farah CS, Darido C. YBX1 integration of oncogenic PI3K/mTOR signalling regulates the fitness of malignant epithelial cells. Nat Commun 2023; 14:1591. [PMID: 36949044 PMCID: PMC10033729 DOI: 10.1038/s41467-023-37161-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
In heterogeneous head and neck cancer (HNC), subtype-specific treatment regimens are currently missing. An integrated analysis of patient HNC subtypes using single-cell sequencing and proteome profiles reveals an epithelial-mesenchymal transition (EMT) signature within the epithelial cancer-cell population. The EMT signature coincides with PI3K/mTOR inactivation in the mesenchymal subtype. Conversely, the signature is suppressed in epithelial cells of the basal subtype which exhibits hyperactive PI3K/mTOR signalling. We further identify YBX1 phosphorylation, downstream of the PI3K/mTOR pathway, restraining basal-like cancer cell proliferation. In contrast, YBX1 acts as a safeguard against the proliferation-to-invasion switch in mesenchymal-like epithelial cancer cells, and its loss accentuates partial-EMT and in vivo invasion. Interestingly, phospho-YBX1 that is mutually exclusive to partial-EMT, emerges as a prognostic marker for overall patient outcomes. These findings create a unique opportunity to sensitise mesenchymal cancer cells to PI3K/mTOR inhibitors by shifting them towards a basal-like subtype as a promising therapeutic approach against HNC.
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Affiliation(s)
- Yuchen Bai
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Carolin Gotz
- Department of Oral and Maxillofacial Surgery, Technische Universität München, Fakultät für Medizin, Klinikum rechts der Isar, Ismaningerstraße 22, 81675, Munich, Germany
- Department of Oral and Maxillofacial Surgery, Medizinische Universität Innsbruck, Anichstraße 35, 6020, Innsbruck, Austria
| | - Ginevra Chincarini
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Zixuan Zhao
- Sun Yat-sen University Cancer Center, Yuexiu District, Guangzhou, Guangdong Province, China
| | - Clare Slaney
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jarryd Boath
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Luc Furic
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Christopher Angel
- Department of Histopathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Stephen M Jane
- Department of Medicine, Central Clinical School, Monash University, 99 Commercial Road, Melbourne, VIC, 3004, Australia
| | - Wayne A Phillips
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Steven A Stacker
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Camile S Farah
- Australian Centre for Oral Oncology Research & Education; Fiona Stanley Hospital; Hollywood Private Hospital; Australian Clinical Labs, CQ University, Perth, WA, 6009, Australia
| | - Charbel Darido
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia.
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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10
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Shih CY, Chen YC, Lin HY, Chu CY. RNA Helicase DDX6 Regulates A-to-I Editing and Neuronal Differentiation in Human Cells. Int J Mol Sci 2023; 24:ijms24043197. [PMID: 36834609 PMCID: PMC9965400 DOI: 10.3390/ijms24043197] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/24/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
The DEAD-box proteins, one family of RNA-binding proteins (RBPs), participate in post-transcriptional regulation of gene expression with multiple aspects. Among them, DDX6 is an essential component of the cytoplasmic RNA processing body (P-body) and is involved in translational repression, miRNA-meditated gene silencing, and RNA decay. In addition to the cytoplasmic function, DDX6 is also present in the nucleus, but the nuclear function remains unknown. To decipher the potential role of DDX6 in the nucleus, we performed mass spectrometry analysis of immunoprecipitated DDX6 from a HeLa nuclear extract. We found that adenosine deaminases that act on RNA 1 (ADAR1) interact with DDX6 in the nucleus. Utilizing our newly developed dual-fluorescence reporter assay, we elucidated the DDX6 function as negative regulators in cellular ADAR1p110 and ADAR2. In addition, depletion of DDX6 and ADARs results in the opposite effect on facilitation of RA-induced differentiation of neuronal lineage cells. Our data suggest the impact of DDX6 in regulation of the cellular RNA editing level, thus contributing to differentiation in the neuronal cell model.
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Affiliation(s)
- Chia-Yu Shih
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Yun-Chi Chen
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Heng-Yi Lin
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chia-Ying Chu
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
- Center for Systems Biology, National Taiwan University, Taipei 10617, Taiwan
- Correspondence: ; Tel.: +886-2-33669876
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11
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Nisa KU, Tarfeen N, Humaira, Wani S, Nisa Q, Ali S, Wali AF. Proteomic approaches in the study of cancers. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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12
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Cancer proteomics, current status, challenges, and future outlook. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00011-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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13
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Yu T, Wu F, Jia Y, Zhang X, Qi X, Jin Z, Hao T, Zhao J, Liu Z, Wang C, Niu M, Yue Q, Li M, Liu Y. RNA N 6-methyladenosine modification mediates downregulation of NR4A1 to facilitate malignancy of cervical cancer. Cell Biosci 2022; 12:207. [PMID: 36566195 DOI: 10.1186/s13578-022-00937-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/05/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND N6-methyladenosine is the most abundant eukaryotic mRNA modification and alters a wide range of cellular processes in cancer. Therefore, defining the molecular details are critical for understanding the regulatory mechanism of m6A modification. RESULTS We found that METTL3, a core m6A methyltransferase component, is upregulated and functions as an oncogene in cervical cancer. Mechanistically, METTL3 induces the degradation of m6A-modified transcripts of NR4A1 though YTHDF2-DDX6 pathway. In addition, NR4A1 overexpression attenuates the malignant progression through recruiting the LSD1/HDAC1/CoREST transcriptional repression complex to AKT1 promoter. CONCLUSIONS Our findings reveal that m6A regulates cervical cancer cellular progression through manipulating NR4A1 pathway.
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Affiliation(s)
- Tao Yu
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
| | - Fuxia Wu
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Yan Jia
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Xue Zhang
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Xiaozhen Qi
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Zeyuan Jin
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Tongxin Hao
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Jianing Zhao
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Ziyu Liu
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Chaokun Wang
- Department of Integrative Chinese and Western Medicine, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Minmin Niu
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Qin Yue
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Min Li
- Department of Pathogen Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Yankun Liu
- Department of Molecular Diagnosis, Tangshan People's Hospital, Tangshan, 063001, China.
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14
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Li D, Yang J, Malik V, Huang Y, Huang X, Zhou H, Wang J. An RNAi screen of RNA helicases identifies eIF4A3 as a regulator of embryonic stem cell identity. Nucleic Acids Res 2022; 50:12462-12479. [PMID: 36416264 PMCID: PMC9757061 DOI: 10.1093/nar/gkac1084] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022] Open
Abstract
RNA helicases are involved in multiple steps of RNA metabolism to direct their roles in gene expression, yet their functions in pluripotency control remain largely unexplored. Starting from an RNA interference (RNAi) screen of RNA helicases, we identified that eIF4A3, a DEAD-box (Ddx) helicase component of the exon junction complex (EJC), is essential for the maintenance of embryonic stem cells (ESCs). Mechanistically, we show that eIF4A3 post-transcriptionally controls the pluripotency-related cell cycle regulators and that its depletion causes the loss of pluripotency via cell cycle dysregulation. Specifically, eIF4A3 is required for the efficient nuclear export of Ccnb1 mRNA, which encodes Cyclin B1, a key component of the pluripotency-promoting pathway during the cell cycle progression of ESCs. Our results reveal a previously unappreciated role for eIF4A3 and its associated EJC in maintaining stem cell pluripotency through post-transcriptional control of the cell cycle.
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Affiliation(s)
- Dan Li
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Cell, Developmental and Regenerative Biology; The Black Family Stem Cell Institute; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jihong Yang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vikas Malik
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yuting Huang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Xin Huang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hongwei Zhou
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development and Stem Cell Therapies, Columbia Stem Cell Initiative, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
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15
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Yu J, Wang W, Yang J, Zhang Y, Gong X, Luo H, Cao N, Xu Z, Tian M, Yang P, Mei Q, Chen Z, Li Z, Li C, Duan X, Lyu QR, Gao C, Zhang B, Wang Y, Wu G, Zeng C. LncRNA PSR Regulates Vascular Remodeling Through Encoding a Novel Protein Arteridin. Circ Res 2022; 131:768-787. [PMID: 36134578 PMCID: PMC9588624 DOI: 10.1161/circresaha.122.321080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 09/06/2022] [Indexed: 01/26/2023]
Abstract
RATIONALE Vascular smooth muscle cells (VSMCs) phenotype switch from contractile to proliferative phenotype is a pathological hallmark in various cardiovascular diseases. Recently, a subset of long noncoding RNAs was identified to produce functional polypeptides. However, the functional impact and regulatory mechanisms of long noncoding RNAs in VSMCs phenotype switching remain to be fully elucidated. OBJECTIVES To illustrate the biological function and mechanism of a VSMC-enriched long noncoding RNA and its encoded peptide in VSMC phenotype switching and vascular remodeling. RESULTS We identified a VSMC-enriched transcript encoded by a previously uncharacterized gene, which we called phenotype switching regulator (PSR), which was markedly upregulated during vascular remodeling. Although PSR was annotated as a long noncoding RNA, we demonstrated that the lncPSR (PSR transcript) also encoded a protein, which we named arteridin. In VSMCs, both arteridin and lncPSR were necessary and sufficient to induce phenotype switching. Mechanistically, arteridin and lncPSR regulate downstream genes by directly interacting with a transcription factor YBX1 (Y-box binding protein 1) and modulating its nuclear translocation and chromatin targeting. Intriguingly, the PSR transcription was also robustly induced by arteridin. More importantly, the loss of PSR gene or arteridin protein significantly attenuated the vascular remodeling induced by carotid arterial injury. In addition, VSMC-specific inhibition of lncPSR using adeno-associated virus attenuated Ang II (angiotensin II)-induced hypertensive vascular remodeling. CONCLUSIONS PSR is a VSMC-enriched gene, and its transcript IncPSR and encoded protein (arteridin) coordinately regulate transcriptional reprogramming through a shared interacting partner, YBX1. This is a previously uncharacterized regulatory circuit in VSMC phenotype switching during vascular remodeling, with lncPSR/arteridin as potential therapeutic targets for the treatment of VSMC phenotype switching-related vascular remodeling.
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Affiliation(s)
- Junyi Yu
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Wei Wang
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Jining Yang
- Research Center for Nutrition and Food Safety, Chongqing Key Laboratory of Nutrition and Food Safety, Institute of Military Preventive Medicine, The Third Military Medical University, Chongqing, P.R. China
| | - Ye Zhang
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Xue Gong
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Hao Luo
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Nian Cao
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Zaicheng Xu
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Miao Tian
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Peili Yang
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Qiao Mei
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Zhi Chen
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Zhuxin Li
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Chuanwei Li
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Xudong Duan
- Cardiovascular Research Center of Chongqing College, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Chongqing, P. R. China
| | - Qing Rex Lyu
- Cardiovascular Research Center of Chongqing College, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Chongqing, P. R. China
| | - Chen Gao
- Department of Pharmacology & Systems Physiology, University of Cincinnati College of Medicine, OH, USA
| | - Bing Zhang
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yibin Wang
- Signature Program in Cardiovascular and Metabolic Diseases, Duke-NUS School of Medicine, Singapore
| | - Gengze Wu
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Chunyu Zeng
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
- Cardiovascular Research Center of Chongqing College, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Chongqing, P. R. China
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China
- Heart Center of Fujian Province, Union Hospital, Fujian Medical University, Fuzhou, P.R. China
- Department of Cardiology, Chongqing General Hospital, Chongqing, P. R. China
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, P.R. China
- Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing
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16
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Kim J, Muraoka M, Okada H, Toyoda A, Ajima R, Saga Y. The RNA helicase DDX6 controls early mouse embryogenesis by repressing aberrant inhibition of BMP signaling through miRNA-mediated gene silencing. PLoS Genet 2022; 18:e1009967. [PMID: 36197846 PMCID: PMC9534413 DOI: 10.1371/journal.pgen.1009967] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Abstract
The evolutionarily conserved RNA helicase DDX6 is a central player in post-transcriptional regulation, but its role during embryogenesis remains elusive. We here show that DDX6 enables proper cell lineage specification from pluripotent cells by analyzing Ddx6 knockout (KO) mouse embryos and employing an in vitro epiblast-like cell (EpiLC) induction system. Our study unveils that DDX6 is an important BMP signaling regulator. Deletion of Ddx6 causes the aberrant upregulation of the negative regulators of BMP signaling, which is accompanied by enhanced expression of Nodal and related genes. Ddx6 KO pluripotent cells acquire higher pluripotency with a strong inclination toward neural lineage commitment. During gastrulation, abnormally expanded Nodal and Eomes expression in the primitive streak likely promotes endoderm cell fate specification while inhibiting mesoderm differentiation. We also genetically dissected major DDX6 pathways by generating Dgcr8, Dcp2, and Eif4enif1 KO models in addition to Ddx6 KO. We found that the miRNA pathway mutant Dgcr8 KO phenocopies Ddx6 KO, indicating that DDX6 mostly works along with the miRNA pathway during early development, whereas its P-body-related functions are dispensable. Therefore, we conclude that DDX6 prevents aberrant upregulation of BMP signaling inhibitors by participating in miRNA-mediated gene silencing processes. Overall, this study delineates how DDX6 affects the development of the three primary germ layers during early mouse embryogenesis and the underlying mechanism of DDX6 function.
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Affiliation(s)
- Jessica Kim
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masafumi Muraoka
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | - Hajime Okada
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Rieko Ajima
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
- * E-mail: (RA); (YS)
| | - Yumiko Saga
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Mammalian Development Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Japan
- * E-mail: (RA); (YS)
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17
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Jia R, Lin J, You J, Li S, Shan G, Huang C. The DEAD-box helicase Hlc regulates basal transcription and chromatin opening of stress-responsive genes. Nucleic Acids Res 2022; 50:9175-9189. [PMID: 35950495 PMCID: PMC9458421 DOI: 10.1093/nar/gkac684] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/17/2022] [Accepted: 07/28/2022] [Indexed: 12/24/2022] Open
Abstract
Stress-responsive genes are lowly transcribed under normal conditions and robustly induced in response to stress. The significant difference between basal and induced transcription indicates that the general transcriptional machinery requires a mechanism to distinguish each transcription state. However, what factors specifically function in basal transcription remains poorly understood. Using a classic model stress-responsive gene (Drosophila MtnA), we found that knockdown of the DEAD-box helicase Hlc resulted in a significant transcription attenuation of MtnA under normal, but not stressed, conditions. Mechanistically, Hlc directly binds to the MtnA locus to maintain the accessibility of chromatin near the transcriptional start site, which allows the recruitment of RNA polymerase II and subsequent MtnA transcription. Using RNA-seq, we then identified plenty of additional stress-responsive genes whose basal transcription was reduced upon knockdown of Hlc. Taken together, these data suggest that Hlc-mediated basal transcription regulation is an essential and widespread mechanism for precise control of stress-responsive genes.
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Affiliation(s)
| | | | | | - Shi Li
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ge Shan
- School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chuan Huang
- To whom correspondence should be addressed. Tel: +86 19956025374;
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18
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Malone TJ, Kaczmarek LK. The role of altered translation in intellectual disability and epilepsy. Prog Neurobiol 2022; 213:102267. [PMID: 35364140 PMCID: PMC10583652 DOI: 10.1016/j.pneurobio.2022.102267] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/18/2022] [Accepted: 03/24/2022] [Indexed: 11/29/2022]
Abstract
A very high proportion of cases of intellectual disability are genetic in origin and are associated with the occurrence of epileptic seizures during childhood. These two disorders together effect more than 5% of the world's population. One feature linking the two diseases is that learning and memory require the synthesis of new synaptic components and ion channels, while maintenance of overall excitability also requires synthesis of similar proteins in response to altered neuronal stimulation. Many of these disorders result from mutations in proteins that regulate mRNA processing, translation initiation, translation elongation, mRNA stability or upstream translation modulators. One theme that emerges on reviewing this field is that mutations in proteins that regulate changes in translation following neuronal stimulation are more likely to result in epilepsy with intellectual disability than general translation regulators with no known role in activity-dependent changes. This is consistent with the notion that activity-dependent translation in neurons differs from that in other cells types in that the changes in local cellular composition, morphology and connectivity that occur generally in response to stimuli are directly coupled to local synaptic activity and persist for months or years after the original stimulus.
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Affiliation(s)
- Taylor J Malone
- Departments of Pharmacology, and of Cellular & Molecular Physiology, Yale University, 333 Cedar Street B-309, New Haven, CT 06520, USA
| | - Leonard K Kaczmarek
- Departments of Pharmacology, and of Cellular & Molecular Physiology, Yale University, 333 Cedar Street B-309, New Haven, CT 06520, USA.
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19
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Bauer KE, Bargenda N, Schieweck R, Illig C, Segura I, Harner M, Kiebler MA. RNA supply drives physiological granule assembly in neurons. Nat Commun 2022; 13:2781. [PMID: 35589693 DOI: 10.1038/s41467-022-30067-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 04/11/2022] [Indexed: 11/09/2022] Open
Abstract
Membraneless cytoplasmic condensates of mRNAs and proteins, known as RNA granules, play pivotal roles in the regulation of mRNA fate. Their maintenance fine-tunes time and location of protein expression, affecting many cellular processes, which require complex protein distribution. Here, we report that RNA granules-monitored by DEAD-Box helicase 6 (DDX6)-disassemble during neuronal maturation both in cell culture and in vivo. This process requires neuronal function, as synaptic inhibition results in reversible granule assembly. Importantly, granule assembly is dependent on the RNA-binding protein Staufen2, known for its role in RNA localization. Altering the levels of free cytoplasmic mRNA reveals that RNA availability facilitates DDX6 granule formation. Specifically depleting RNA from DDX6 granules confirms RNA as an important driver of granule formation. Moreover, RNA is required for DDX6 granule assembly upon synaptic inhibition. Together, this data demonstrates how RNA supply favors RNA granule assembly, which not only impacts subcellular RNA localization but also translation-dependent synaptic plasticity, learning, and memory.
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Affiliation(s)
- Karl E Bauer
- BioMedical Center, Dept. Cell Biology and Anatomy, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Niklas Bargenda
- BioMedical Center, Dept. Cell Biology and Anatomy, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Rico Schieweck
- BioMedical Center, Dept. Cell Biology and Anatomy, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Christin Illig
- BioMedical Center, Dept. Cell Biology and Anatomy, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Inmaculada Segura
- BioMedical Center, Dept. Cell Biology and Anatomy, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany.,Max Planck Institute for Biological Intelligence (in foundation), Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Max Harner
- BioMedical Center, Dept. Cell Biology and Anatomy, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Michael A Kiebler
- BioMedical Center, Dept. Cell Biology and Anatomy, Medical Faculty, Ludwig Maximilians University, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany.
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20
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Li J, Tiwari M, Chen Y, Luanpitpong S, Sen GL. CDK12 Is Necessary to Promote Epidermal Differentiation Through Transcription Elongation. Stem Cells 2022; 40:435-445. [PMID: 35325240 PMCID: PMC9199850 DOI: 10.1093/stmcls/sxac002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/17/2021] [Indexed: 01/30/2023]
Abstract
Proper differentiation of the epidermis is essential to prevent water loss and to protect the body from the outside environment. Perturbations in this process can lead to a variety of skin diseases that impacts 1 in 5 people. While transcription factors that control epidermal differentiation have been well characterized, other aspects of transcription control such as elongation are poorly understood. Here we show that of the two cyclin-dependent kinases (CDK12 and CDK13), that are known to regulate transcription elongation, only CDK12 is necessary for epidermal differentiation. Depletion of CDK12 led to loss of differentiation gene expression and absence of skin barrier formation in regenerated human epidermis. CDK12 binds to genes that code for differentiation promoting transcription factors (GRHL3, KLF4, and OVOL1) and is necessary for their elongation. CDK12 is necessary for elongation by promoting Ser2 phosphorylation on the C-terminal domain of RNA polymerase II and the stabilization of binding of the elongation factor SPT6 to target genes. Our results suggest that control of transcription elongation by CDK12 plays a prominent role in adult cell fate decisions.
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Affiliation(s)
- Jingting Li
- Institute of Precision Medicine, Department of Burns, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Manisha Tiwari
- Department of Dermatology and Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Yifang Chen
- Department of Dermatology and Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Sudjit Luanpitpong
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok, Thailand
| | - George L Sen
- Department of Dermatology and Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
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21
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Shannon JL, Corcoran DL, Murray JC, Ziegler SF, MacLeod AS, Zhang JY. Thymic stromal lymphopoietin controls hair growth. Stem Cell Reports 2022; 17:649-663. [PMID: 35216683 PMCID: PMC9039851 DOI: 10.1016/j.stemcr.2022.01.017] [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: 02/17/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/17/2022] Open
Abstract
Skin tissue regeneration after injury involves the production and integration of signals by stem cells residing in hair follicles (HFSCs). Much remains unknown about how specific wound-derived factors modulate stem cell contribution to hair growth. We demonstrate that thymic stromal lymphopoietin (TSLP) is produced in response to skin injury and during the anagen phase of the hair cycle. Intradermal injection of TSLP promoted wound-induced hair growth (WIHG), whereas neutralizing TSLP receptor (TSLPR) inhibited WIHG. Using flow cytometry and fluorescent immunostaining, we found that TSLP promoted proliferation of transit-amplifying cells. Lgr5CreER-mediated deletion of Tslpr in HFSCs inhibited both wound-induced and exogenous TSLP-induced hair growth. Our data highlight a novel function for TSLP in regulation of hair follicle activity during homeostasis and wound healing.
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Affiliation(s)
- Jessica L Shannon
- Department of Dermatology, Duke University, P.O. Box 103052, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA
| | - David L Corcoran
- Genomic and Computational Biology, Duke University, Durham, NC 27705, USA
| | - John C Murray
- Department of Dermatology, Duke University, P.O. Box 103052, Durham, NC 27710, USA
| | - Steven F Ziegler
- Benaroya Research Institute, Seattle, WA 98101, USA; Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Amanda S MacLeod
- Department of Dermatology, Duke University, P.O. Box 103052, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
| | - Jennifer Y Zhang
- Department of Dermatology, Duke University, P.O. Box 103052, Durham, NC 27710, USA; Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA.
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22
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Buddika K, Huang YT, Ariyapala IS, Butrum-Griffith A, Norrell SA, O'Connor AM, Patel VK, Rector SA, Slovan M, Sokolowski M, Kato Y, Nakamura A, Sokol NS. Coordinated repression of pro-differentiation genes via P-bodies and transcription maintains Drosophila intestinal stem cell identity. Curr Biol 2022; 32:386-397.e6. [PMID: 34875230 PMCID: PMC8792327 DOI: 10.1016/j.cub.2021.11.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 09/17/2021] [Accepted: 11/11/2021] [Indexed: 01/26/2023]
Abstract
The role of processing bodies (P-bodies), key sites of post-transcriptional control, in adult stem cells remains poorly understood. Here, we report that adult Drosophila intestinal stem cells, but not surrounding differentiated cells such as absorptive enterocytes (ECs), harbor P-bodies that contain Drosophila orthologs of mammalian P-body components DDX6, EDC3, EDC4, and LSM14A/B. A targeted RNAi screen in intestinal progenitor cells identified 39 previously known and 64 novel P-body regulators, including Patr-1, a gene necessary for P-body assembly. Loss of Patr-1-dependent P-bodies leads to a loss of stem cells that is associated with inappropriate expression of EC-fate gene nubbin. Transcriptomic analysis of progenitor cells identifies a cadre of such weakly transcribed pro-differentiation transcripts that are elevated after P-body loss. Altogether, this study identifies a P-body-dependent repression activity that coordinates with known transcriptional repression programs to maintain a population of in vivo stem cells in a state primed for differentiation.
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Affiliation(s)
- Kasun Buddika
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Yi-Ting Huang
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | | | - Sam A Norrell
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Alex M O'Connor
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Viraj K Patel
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Samuel A Rector
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Mark Slovan
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | - Yasuko Kato
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Akira Nakamura
- Department of Germline Development, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Kumamoto 860-0811, Japan
| | - Nicholas S Sokol
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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23
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Castelli LM, Benson BC, Huang WP, Lin YH, Hautbergue GM. RNA Helicases in Microsatellite Repeat Expansion Disorders and Neurodegeneration. Front Genet 2022; 13:886563. [PMID: 35646086 PMCID: PMC9133428 DOI: 10.3389/fgene.2022.886563] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
Short repeated sequences of 3-6 nucleotides are causing a growing number of over 50 microsatellite expansion disorders, which mainly present with neurodegenerative features. Although considered rare diseases in relation to the relatively low number of cases, these primarily adult-onset conditions, often debilitating and fatal in absence of a cure, collectively pose a large burden on healthcare systems in an ageing world population. The pathological mechanisms driving disease onset are complex implicating several non-exclusive mechanisms of neuronal injury linked to RNA and protein toxic gain- and loss- of functions. Adding to the complexity of pathogenesis, microsatellite repeat expansions are polymorphic and found in coding as well as in non-coding regions of genes. They form secondary and tertiary structures involving G-quadruplexes and atypical helices in repeated GC-rich sequences. Unwinding of these structures by RNA helicases plays multiple roles in the expression of genes including repeat-associated non-AUG (RAN) translation of polymeric-repeat proteins with aggregating and cytotoxic properties. Here, we will briefly review the pathogenic mechanisms mediated by microsatellite repeat expansions prior to focus on the RNA helicases eIF4A, DDX3X and DHX36 which act as modifiers of RAN translation in C9ORF72-linked amyotrophic lateral sclerosis/frontotemporal dementia (C9ORF72-ALS/FTD) and Fragile X-associated tremor/ataxia syndrome (FXTAS). We will further review the RNA helicases DDX5/17, DHX9, Dicer and UPF1 which play additional roles in the dysregulation of RNA metabolism in repeat expansion disorders. In addition, we will contrast these with the roles of other RNA helicases such as DDX19/20, senataxin and others which have been associated with neurodegeneration independently of microsatellite repeat expansions. Finally, we will discuss the challenges and potential opportunities that are associated with the targeting of RNA helicases for the development of future therapeutic approaches.
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Affiliation(s)
- Lydia M Castelli
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Bridget C Benson
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Wan-Ping Huang
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Ya-Hui Lin
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield, United Kingdom.,Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom.,Healthy Lifespan Institute (HELSI), University of Sheffield, Sheffield, United Kingdom
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24
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Kwon YW, Jo HS, Bae S, Seo Y, Song P, Song M, Yoon JH. Application of Proteomics in Cancer: Recent Trends and Approaches for Biomarkers Discovery. Front Med (Lausanne) 2021; 8:747333. [PMID: 34631760 PMCID: PMC8492935 DOI: 10.3389/fmed.2021.747333] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022] Open
Abstract
Proteomics has become an important field in molecular sciences, as it provides valuable information on the identity, expression levels, and modification of proteins. For example, cancer proteomics unraveled key information in mechanistic studies on tumor growth and metastasis, which has contributed to the identification of clinically applicable biomarkers as well as therapeutic targets. Several cancer proteome databases have been established and are being shared worldwide. Importantly, the integration of proteomics studies with other omics is providing extensive data related to molecular mechanisms and target modulators. These data may be analyzed and processed through bioinformatic pipelines to obtain useful information. The purpose of this review is to provide an overview of cancer proteomics and recent advances in proteomic techniques. In particular, we aim to offer insights into current proteomics studies of brain cancer, in which proteomic applications are in a relatively early stage. This review covers applications of proteomics from the discovery of biomarkers to the characterization of molecular mechanisms through advances in technology. Moreover, it addresses global trends in proteomics approaches for translational research. As a core method in translational research, the continued development of this field is expected to provide valuable information at a scale beyond that previously seen.
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Affiliation(s)
- Yang Woo Kwon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Han-Seul Jo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Sungwon Bae
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Youngsuk Seo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Parkyong Song
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, South Korea
| | - Minseok Song
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Jong Hyuk Yoon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
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25
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Saba JA, Liakath-Ali K, Green R, Watt FM. Translational control of stem cell function. Nat Rev Mol Cell Biol 2021; 22:671-690. [PMID: 34272502 DOI: 10.1038/s41580-021-00386-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 12/22/2022]
Abstract
Stem cells are characterized by their ability to self-renew and differentiate into many different cell types. Research has focused primarily on how these processes are regulated at a transcriptional level. However, recent studies have indicated that stem cell behaviour is strongly coupled to the regulation of protein synthesis by the ribosome. In this Review, we discuss how different translation mechanisms control the function of adult and embryonic stem cells. Stem cells are characterized by low global translation rates despite high levels of ribosome biogenesis. The maintenance of pluripotency, the commitment to a specific cell fate and the switch to cell differentiation depend on the tight regulation of protein synthesis and ribosome biogenesis. Translation regulatory mechanisms that impact on stem cell function include mTOR signalling, ribosome levels, and mRNA and tRNA features and amounts. Understanding these mechanisms important for stem cell self-renewal and differentiation may also guide our understanding of cancer grade and metastasis.
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Affiliation(s)
- James A Saba
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kifayathullah Liakath-Ali
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Fiona M Watt
- King's College London Centre for Stem Cells and Regenerative Medicine, Guy's Hospital, London, UK.
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26
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Li J, Chen Y, Tiwari M, Bansal V, Sen GL. Regulation of integrin and extracellular matrix genes by HNRNPL is necessary for epidermal renewal. PLoS Biol 2021; 19:e3001378. [PMID: 34543262 PMCID: PMC8452081 DOI: 10.1371/journal.pbio.3001378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/30/2021] [Indexed: 01/05/2023] Open
Abstract
Stratified epithelia such as the epidermis require coordinated regulation of stem and progenitor cell proliferation, survival, and differentiation to maintain homeostasis. Integrin-mediated anchorage of the basal layer stem cells of the epidermis to the underlying dermis through extracellular matrix (ECM) proteins is crucial for this process. It is currently unknown how the expression of these integrins and ECM genes are regulated. Here, we show that the RNA-binding protein (RBP) heterogeneous nuclear ribonucleoprotein L (HNRNPL) binds to these genes on chromatin to promote their expression. HNRNPL recruits RNA polymerase II (Pol II) to integrin/ECM genes and is required for stabilizing Pol II transcription through those genes. In the absence of HNRNPL, the basal layer of the epidermis where the stem cells reside prematurely differentiates and detaches from the underlying dermis due to diminished integrin/ECM expression. Our results demonstrate a critical role for RBPs on chromatin to maintain stem and progenitor cell fate by dictating the expression of specific classes of genes.
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Affiliation(s)
- Jingting Li
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yifang Chen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, California, United States of America
| | - Manisha Tiwari
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, California, United States of America
| | - Varun Bansal
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, California, United States of America
| | - George L. Sen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, California, United States of America
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27
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Babarinde IA, Ma G, Li Y, Deng B, Luo Z, Liu H, Abdul MM, Ward C, Chen M, Fu X, Shi L, Duttlinger M, He J, Sun L, Li W, Zhuang Q, Tong G, Frampton J, Cazier JB, Chen J, Jauch R, Esteban MA, Hutchins AP. Transposable element sequence fragments incorporated into coding and noncoding transcripts modulate the transcriptome of human pluripotent stem cells. Nucleic Acids Res 2021; 49:9132-9153. [PMID: 34390351 PMCID: PMC8450112 DOI: 10.1093/nar/gkab710] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) occupy nearly 40% of mammalian genomes and, whilst most are fragmentary and no longer capable of transposition, they can nevertheless contribute to cell function. TEs within genes transcribed by RNA polymerase II can be copied as parts of primary transcripts; however, their full contribution to mature transcript sequences remains unresolved. Here, using long and short read (LR and SR) RNA sequencing data, we show that 26% of coding and 65% of noncoding transcripts in human pluripotent stem cells (hPSCs) contain TE-derived sequences. Different TE families are incorporated into RNAs in unique patterns, with consequences to transcript structure and function. The presence of TE sequences within a transcript is correlated with TE-type specific changes in its subcellular distribution, alterations in steady-state levels and half-life, and differential association with RNA Binding Proteins (RBPs). We identify hPSC-specific incorporation of endogenous retroviruses (ERVs) and LINE:L1 into protein-coding mRNAs, which generate TE sequence-derived peptides. Finally, single cell RNA-seq reveals that hPSCs express ERV-containing transcripts, whilst differentiating subpopulations lack ERVs and express SINE and LINE-containing transcripts. Overall, our comprehensive analysis demonstrates that the incorporation of TE sequences into the RNAs of hPSCs is more widespread and has a greater impact than previously appreciated.
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Affiliation(s)
- Isaac A Babarinde
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Gang Ma
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuhao Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Boping Deng
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Zhiwei Luo
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Hao Liu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Mazid Md Abdul
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Carl Ward
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Minchun Chen
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiuling Fu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Liyang Shi
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Martha Duttlinger
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiangping He
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Li Sun
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wenjuan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Qiang Zhuang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guoqing Tong
- Center for Reproductive Medicine, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200120, China
| | - Jon Frampton
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Jean-Baptiste Cazier
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK.,Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | - Jiekai Chen
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China.,Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Miguel A Esteban
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Andrew P Hutchins
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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28
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Zhang R, Cheng M, Liu B, Yuan M, Chen D, Wang Y, Wu Z. DEAD-Box Helicase DDX6 Facilitated RIG-I-Mediated Type-I Interferon Response to EV71 Infection. Front Cell Infect Microbiol 2021; 11:725392. [PMID: 34485180 PMCID: PMC8414799 DOI: 10.3389/fcimb.2021.725392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/28/2021] [Indexed: 12/24/2022] Open
Abstract
Previous studies have shown that DEAD (Glu-Asp-Ala-Glu)-box RNA helicases play important roles in viral infection, either as cytosolic sensors of pathogenic molecules or as essential host factors against viral infection. In the current study, we found that DDX6, an RNA helicase belonging to the DEAD-box family of helicase, exhibited anti-Enterovirus 71 activity through augmenting RIG-I-mediated type-I IFN response. Moreover, DDX6 binds viral RNA to form an RNA-protein complex to positively regulate the RIG-I-mediated interferon response; however, EV71 has evolved a strategy to antagonize the antiviral effect of DDX6 by proteolytic degradation of the molecule through its non-structural protein 2A, a virus-encoded protease.
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Affiliation(s)
- Rui Zhang
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
| | - Min Cheng
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
| | - Bingxin Liu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
| | - Meng Yuan
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
| | - Deyan Chen
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
| | - Yujiong Wang
- School of Life Sciences, Ningxia University, Yinchuan, China
| | - Zhiwei Wu
- Center for Public Health Research, Medical School, Nanjing University, Nanjing, China
- School of Life Sciences, Ningxia University, Yinchuan, China
- Medical School and Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, China
- State Key Lab of Analytical Chemistry for Life Science, Nanjing University, Nanjing, China
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29
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Specific Interaction of DDX6 with an RNA Hairpin in the 3' UTR of the Dengue Virus Genome Mediates G 1 Phase Arrest. J Virol 2021; 95:e0051021. [PMID: 34132569 DOI: 10.1128/jvi.00510-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The extent to which viral genomic RNAs interact with host factors and contribute to host response and disease pathogenesis is not well known. Here, we report that the human RNA helicase DDX6 specifically binds to the viral most conserved RNA hairpin in the A3 element in the dengue 3' UTR, with nanomolar affinities. DDX6 CLIP confirmed the interaction in HuH-7 cells infected by dengue virus serotype 2. This interaction requires three conserved residues-Lys307, Lys367, and Arg369-as well as the unstructured extension in the C-terminal domain of DDX6. Interestingly, alanine substitution of these three basic residues resulted in RNA-independent ATPase activity, suggesting a mechanism by which RNA-binding and ATPase activities are coupled in DEAD box helicases. Furthermore, we applied a cross-omics gene enrichment approach to suggest that DDX6 is functionally related to cell cycle regulation and viral pathogenicity. Indeed, infected cells exhibited cell cycle arrest in G1 phase and a decrease in the early S phase. Exogenous expression of intact DDX6, but not A3-binding-deficient mutants, alleviated these effects by rescue of the DNA preinitiation complex expression. Disruption of the DDX6-binding site was found in dengue and Zika live-attenuated vaccine strains. Our results suggested that dengue virus has evolved an RNA aptamer against DDX6 to alter host cell states and defined DDX6 as a new regulator of G1/S transition. IMPORTANCE Dengue virus (DENV) is transmitted by mosquitoes to humans, infecting 390 million individuals per year globally. About 20% of infected patients shows a spectrum of clinical manifestation, ranging from a mild flu-like syndrome, to dengue fever, to life-threatening severe dengue diseases, including dengue hemorrhagic fever and dengue shock syndrome. There is currently no specific treatment for dengue diseases, and the molecular mechanism underlying dengue pathogenesis remains poorly understood. In this study, we combined biochemical, bioinformatics, high-content analysis and RNA sequencing approaches to characterize a highly conserved interface of the RNA genome of DENV with a human factor named DDX6 in infected cells. The significance of our research is in identifying the mechanism for a viral strategy to alter host cell fates, which conceivably allows us to generate a model for live-attenuated vaccine and the design of new therapeutic reagent for dengue diseases.
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30
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Maeda R, Kami D, Shikuma A, Suzuki Y, Taya T, Matoba S, Gojo S. RNA decay in processing bodies is indispensable for adipogenesis. Cell Death Dis 2021; 12:285. [PMID: 33731683 PMCID: PMC7969960 DOI: 10.1038/s41419-021-03537-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 12/19/2022]
Abstract
The RNA decay pathway plays key regulatory roles in cell identities and differentiation processes. Although adipogenesis is transcriptionally and epigenetically regulated and has been thoroughly investigated, how RNA metabolism that contributes to the stability of phenotype-shaping transcriptomes participates in differentiation remains elusive. In this study, we investigated Ddx6, an essential component of processing bodies (PBs) that executes RNA decay and translational repression in the cytoplasm and participates in the cellular transition of reprogramming. Upon adipogenic induction, Ddx6 dynamically accumulated to form PBs with a binding partner, 4E-T, at the early phase prior to emergence of intracellular lipid droplets. In contrast, preadipocytes with Ddx6 knockout (KO) or 4E-T knockdown (KD) failed to generate PBs, resulting in significant suppression of adipogenesis. Transcription factors related to preadipocytes and negative regulators of adipogenesis that were not expressed under adipogenic stimulation were maintained in Ddx6-KO and 4E-T-KD preadipocytes under adipogenic induction. Elimination of Dlk1, a major negative regulator of adipogenesis, in 3T3L1 Ddx6-KO cells did not restore adipogenic differentiation capacity to any extent. Similar to murine cells, human primary mesenchymal stem cells, which can differentiate into adipocytes upon stimulation with adipogenic cocktails, required DDX6 to maturate into adipocytes. Therefore, RNA decay of the entire parental transcriptome, rather than removal of a strong negative regulator, could be indispensable for adipogenesis.
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Affiliation(s)
- Ryotaro Maeda
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Daisuke Kami
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Akira Shikuma
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yosuke Suzuki
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Toshihiko Taya
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoaki Matoba
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoshi Gojo
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan.
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31
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Sergeeva O, Zatsepin T. RNA Helicases as Shadow Modulators of Cell Cycle Progression. Int J Mol Sci 2021; 22:2984. [PMID: 33804185 PMCID: PMC8001981 DOI: 10.3390/ijms22062984] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/06/2021] [Accepted: 03/10/2021] [Indexed: 02/07/2023] Open
Abstract
The progress of the cell cycle is directly regulated by modulation of cyclins and cyclin-dependent kinases. However, many proteins that control DNA replication, RNA transcription and the synthesis and degradation of proteins can manage the activity or levels of master cell cycle regulators. Among them, RNA helicases are key participants in RNA metabolism involved in the global or specific tuning of cell cycle regulators at the level of transcription and translation. Several RNA helicases have been recently evaluated as promising therapeutic targets, including eIF4A, DDX3 and DDX5. However, targeting RNA helicases can result in side effects due to the influence on the cell cycle. In this review, we discuss direct and indirect participation of RNA helicases in the regulation of the cell cycle in order to draw attention to downstream events that may occur after suppression or inhibition of RNA helicases.
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Affiliation(s)
- Olga Sergeeva
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30b1, 121205 Moscow, Russia;
| | - Timofei Zatsepin
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30b1, 121205 Moscow, Russia;
- Department of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russia
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32
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Bearss JJ, Padi SK, Singh N, Cardo-Vila M, Song JH, Mouneimne G, Fernandes N, Li Y, Harter MR, Gard JM, Cress AE, Peti W, Nelson AD, Buchan JR, Kraft AS, Okumura K. EDC3 phosphorylation regulates growth and invasion through controlling P-body formation and dynamics. EMBO Rep 2021; 22:e50835. [PMID: 33586867 DOI: 10.15252/embr.202050835] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 12/20/2020] [Accepted: 01/13/2021] [Indexed: 12/18/2022] Open
Abstract
Regulation of mRNA stability and translation plays a critical role in determining protein abundance within cells. Processing bodies (P-bodies) are critical regulators of these processes. Here, we report that the Pim1 and 3 protein kinases bind to the P-body protein enhancer of mRNA decapping 3 (EDC3) and phosphorylate EDC3 on serine (S)161, thereby modifying P-body assembly. EDC3 phosphorylation is highly elevated in many tumor types, is reduced upon treatment of cells with kinase inhibitors, and blocks the localization of EDC3 to P-bodies. Prostate cancer cells harboring an EDC3 S161A mutation show markedly decreased growth, migration, and invasion in tissue culture and in xenograft models. Consistent with these phenotypic changes, the expression of integrin β1 and α6 mRNA and protein is reduced in these mutated cells. These results demonstrate that EDC3 phosphorylation regulates multiple cancer-relevant functions and suggest that modulation of P-body activity may represent a new paradigm for cancer treatment.
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Affiliation(s)
- Jeremiah J Bearss
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA
| | - Sathish Kr Padi
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA.,Department of Molecular Biology and Biophysics, UConn Health Center, Farmington, CT, USA
| | - Neha Singh
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA
| | - Marina Cardo-Vila
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA.,Department of Otolaryngology-Head and Neck Surgery, University of Arizona, Tucson, AZ, USA
| | - Jin H Song
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA.,Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Ghassan Mouneimne
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Nikita Fernandes
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Yang Li
- Department of Molecular Biology and Biophysics, UConn Health Center, Farmington, CT, USA.,Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Matthew R Harter
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Jaime Mc Gard
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA
| | - Anne E Cress
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA.,Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Wolfgang Peti
- Department of Molecular Biology and Biophysics, UConn Health Center, Farmington, CT, USA.,Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | | | - J Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Andrew S Kraft
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA.,Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Koichi Okumura
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ, USA.,Department of Physiology, University of Arizona, Tucson, AZ, USA
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Li J, Xu X, Tiwari M, Chen Y, Fuller M, Bansal V, Tamayo P, Das S, Ghosh P, Sen GL. SPT6 promotes epidermal differentiation and blockade of an intestinal-like phenotype through control of transcriptional elongation. Nat Commun 2021; 12:784. [PMID: 33542242 PMCID: PMC7862286 DOI: 10.1038/s41467-021-21067-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
In adult tissue, stem and progenitor cells must tightly regulate the balance between proliferation and differentiation to sustain homeostasis. How this exquisite balance is achieved is an area of active investigation. Here, we show that epidermal genes, including ~30% of induced differentiation genes already contain stalled Pol II at the promoters in epidermal stem and progenitor cells which is then released into productive transcription elongation upon differentiation. Central to this process are SPT6 and PAF1 which are necessary for the elongation of these differentiation genes. Upon SPT6 or PAF1 depletion there is a loss of human skin differentiation and stratification. Unexpectedly, loss of SPT6 also causes the spontaneous transdifferentiation of epidermal cells into an intestinal-like phenotype due to the stalled transcription of the master regulator of epidermal fate P63. Our findings suggest that control of transcription elongation through SPT6 plays a prominent role in adult somatic tissue differentiation and the inhibition of alternative cell fate choices.
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Affiliation(s)
- Jingting Li
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Xiaojun Xu
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Manisha Tiwari
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Yifang Chen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Mackenzie Fuller
- Departments of Medicine and Cellular and Molecular Medicine, HUMANOID Center of Research Excellence, University of California, San Diego, La Jolla, CA, USA
- Department of Pathology, HUMANOID Center of Research Excellence, University of California, San Diego, La Jolla, CA, USA
| | - Varun Bansal
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA
| | - Pablo Tamayo
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
- Division of Medical Genetics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Soumita Das
- Department of Pathology, HUMANOID Center of Research Excellence, University of California, San Diego, La Jolla, CA, USA
| | - Pradipta Ghosh
- Departments of Medicine and Cellular and Molecular Medicine, HUMANOID Center of Research Excellence, University of California, San Diego, La Jolla, CA, USA
| | - George L Sen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.
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Epidermal progenitors suppress GRHL3-mediated differentiation through intronic polyadenylation promoted by CPSF-HNRNPA3 collaboration. Nat Commun 2021; 12:448. [PMID: 33469008 PMCID: PMC7815847 DOI: 10.1038/s41467-020-20674-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 12/11/2020] [Indexed: 01/29/2023] Open
Abstract
In self-renewing somatic tissue such as skin epidermis, terminal differentiation genes must be suppressed in progenitors to sustain regenerative capacity. Here we show that hundreds of intronic polyadenylation (IpA) sites are differentially used during keratinocyte differentiation, which is accompanied by downregulation of the Cleavage and Polyadenylation Specificity Factor (CPSF) complex. Sustained CPSF expression in undifferentiated keratinocytes requires the contribution from the transcription factor MYC. In keratinocytes cultured in undifferentiation condition, CSPF knockdown induces premature differentiation and partially affects dynamically used IpA sites. These sites include an IpA site located in the first intron of the differentiation activator GRHL3. CRISPR knockout of GRHL3 IpA increased full-length GRHL3 mRNA expression. Using a targeted genetic screen, we identify that HNRNPA3 interacts with CPSF and enhances GRHL3 IpA. Our data suggest a model where the interaction between CPSF and RNA-binding proteins, such as HNRNPA3, promotes site-specific IpA and suppresses premature differentiation in progenitors.
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35
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Kanakamani S, Suresh PS, Venkatesh T. Regulation of processing bodies: From viruses to cancer epigenetic machinery. Cell Biol Int 2020; 45:708-719. [PMID: 33325125 DOI: 10.1002/cbin.11527] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/17/2020] [Accepted: 12/13/2020] [Indexed: 11/08/2022]
Abstract
Processing bodies (PBs) are 100-300 nm cytoplasmic messenger ribonucleoprotein particle (mRNP) granules that regulate eukaryotic gene expression. These cytoplasmic compartments harbor messenger RNAs (mRNAs) and several proteins involved in mRNA decay, microRNA silencing, nonsense-mediated mRNA decay, and splicing. Though membrane-less, PB structures are maintained by RNA-protein and protein-protein interactions. PB proteins have intrinsically disordered regions and low complexity domains, which account for its liquid to liquid phase separation. In addition to being dynamic and actively involved in the exchange of materials with other mRNPs and organelles, they undergo changes on various cellular cues and environmental stresses, including viral infections. Interestingly, several PB proteins are individually implicated in cancer development, and no study has addressed the effects on PB dynamics after epigenetic modifications of cancer-associated PB genes. In the current review, we summarize modulations undergone by P bodies or P body components upon viral infections. Furthermore, we discuss the selective and widely investigated PB proteins that undergo methylation changes in cancer and their potential as biomarkers.
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Affiliation(s)
- Sunmathy Kanakamani
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Kasargod, India
| | - Padmanaban S Suresh
- Department of Biotechnology, National Institute of Technology Calicut, Calicut, India
| | - Thejaswini Venkatesh
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Kasargod, India
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36
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Ling J, Sckaff M, Tiwari M, Chen Y, Li J, Jones J, Sen GL. RAS-mediated suppression of PAR3 and its effects on SCC initiation and tissue architecture occur independently of hyperplasia. J Cell Sci 2020; 133:jcs.249102. [PMID: 33172988 DOI: 10.1242/jcs.249102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Abstract
Proper epithelial development and homeostasis depends on strict control of oriented cell division. Current evidence shows that this process is regulated by intrinsic polarity factors and external spatial cues. Owing to the lack of an appropriate model system that can recapitulate the architecture of the skin, deregulation of spindle orientation in human epithelial carcinoma has never been investigated. Here, using an inducible model of human squamous cell carcinoma (SCC), we demonstrate that RAS-dependent suppression of PAR3 (encoded by PARD3) accelerates epithelial disorganization during early tumorigenesis. Diminished PAR3 led to loss of E-cadherin-mediated cell adhesion, which in turn contributed to misoriented cell division. Pharmacological inhibition of the MAPK pathway downstream of RAS activation reversed the defects in PAR3 expression, E-cadherin-mediated cell adhesion and mitotic spindle orientation. Thus, temporal analysis of human neoplasia provides a powerful approach to study cellular and molecular transformations during early oncogenesis, which allowed identification of PAR3 as a critical regulator of tissue architecture during initial human SCC development.
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Affiliation(s)
- Ji Ling
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093-0869, USA
| | - Maria Sckaff
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093-0869, USA
| | - Manisha Tiwari
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093-0869, USA
| | - Yifang Chen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093-0869, USA
| | - Jingting Li
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093-0869, USA
| | - Jackson Jones
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093-0869, USA
| | - George L Sen
- Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92093-0869, USA
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37
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Flora P, Ezhkova E. Regulatory mechanisms governing epidermal stem cell function during development and homeostasis. Development 2020; 147:147/22/dev194100. [PMID: 33191273 DOI: 10.1242/dev.194100] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cell divisions and cell-fate decisions require stringent regulation for proper tissue development and homeostasis. The mammalian epidermis is a highly organized tissue structure that is sustained by epidermal stem cells (ESCs) that balance self-renewal and cell-fate decisions to establish a protective barrier, while replacing dying cells during homeostasis and in response to injury. Extensive work over past decades has provided insights into the regulatory mechanisms that control ESC specification, self-renewal and maintenance during different stages of the lifetime of an organism. In this Review, we discuss recent findings that have furthered our understanding of key regulatory features that allow ESCs to establish a functional barrier during development and to maintain tissue homeostasis in adults.
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Affiliation(s)
- Pooja Flora
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Elena Ezhkova
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
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Xue X, Huang J, Yu K, Chen X, He Y, Qi D, Wu Y. YB-1 transferred by gastric cancer exosomes promotes angiogenesis via enhancing the expression of angiogenic factors in vascular endothelial cells. BMC Cancer 2020; 20:996. [PMID: 33054752 PMCID: PMC7557103 DOI: 10.1186/s12885-020-07509-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/07/2020] [Indexed: 12/31/2022] Open
Abstract
Background Angiogenesis is important for the progression of gastric cancer (GC). Y-box binding protein 1 (YB-1) predicts advanced disease and indicates neovasculature formation in GC tissues, while the related mechanisms remain elusive. Exosomes mediate intercellular communications via transferring various molecules including proteins, lipids, mRNAs, and microRNAs, while the cargos of GC exosomes and the related mechanisms in GC angiogenesis were rarely reported except for several microRNAs. Methods In this study, human umbilical vein endothelial cells (HUVECs) were, respectively, treated by the exosomes isolated from the YB-1 transfected and the control SGC-7901 cells (SGC-7901-OE-Exo and SGC-7901-NC-Exo), and their apoptosis, proliferation, migration, invasion, and angiogenesis were, sequentially, compared. The levels of angiogenic factors including VEGF, Ang-1, MMP-9 and IL-8 in the exosome-treated HUVECs and the GC-derived exosomes were, separately, detected using PCR and Western blotting as well as RNA sequencing assays. Results We observed the consistent level of YB-1 in the exosomes and their originated GC cells, and the internalization of exosomes into HUVECs. Comparing with SGC-7901-NC-Exo, SGC-7901-OE-Exo significantly inhibited the apoptosis but promoted the proliferation, migration, invasion, and angiogenesis of HUVECs, within which the increased mRNA and protein levels of VEGF, Ang-1, MMP-9 and IL-8 were demonstrated. Meanwhile, mRNA levels of VEGF, Ang-1, MMP-9 and IL-8 showed no significant difference between SGC-7901-NC-Exo and SGC-7901-OE-Exo, although statistically higher mRNA of YB-1 was detected in the SGC-7901-OE-Exo. Conclusions Our findings illustrate YB-1 as the key component of exosome to promote GC angiogenesis by upregulating specific angiogenic factors in the exosome-treated endothelial cells but not in the exosomes themselves.
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Affiliation(s)
- Xiaoxia Xue
- Science Experiment Center, China Medical University, 77 Puhe Road, Shenyang North New Area, Liaoning, 110122, Shenyang, China
| | - Jin Huang
- Department of Radiation Therapy, The First Hospital, China Medical University, 518 Chuangxin Road, Hunnan District, Shenyang, 110167, Liaoning, China
| | - Kai Yu
- Department of General Practice, The First Hospital, China Medical University, 155 South Nanjing Street, Heping District, Shenyang, 110001, Liaoning, China
| | - Xinyue Chen
- Department of General Practice, The First Hospital, China Medical University, 155 South Nanjing Street, Heping District, Shenyang, 110001, Liaoning, China
| | - Yini He
- Department of General Practice, The First Hospital, China Medical University, 155 South Nanjing Street, Heping District, Shenyang, 110001, Liaoning, China
| | - Dianjun Qi
- Department of General Practice, The First Hospital, China Medical University, 155 South Nanjing Street, Heping District, Shenyang, 110001, Liaoning, China
| | - Ying Wu
- Department of General Practice, The First Hospital, China Medical University, 155 South Nanjing Street, Heping District, Shenyang, 110001, Liaoning, China.
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Tian Y, Zeng Z, Li X, Wang Y, Chen R, Mattijssen S, Gaidamakov S, Wu Y, Maraia RJ, Peng W, Zhu J. Transcriptome-wide stability analysis uncovers LARP4-mediated NFκB1 mRNA stabilization during T cell activation. Nucleic Acids Res 2020; 48:8724-8739. [PMID: 32735645 PMCID: PMC7470963 DOI: 10.1093/nar/gkaa643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 06/30/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023] Open
Abstract
T cell activation is a well-established model for studying cellular responses to exogenous stimulation. Motivated by our previous finding that intron retention (IR) could lead to transcript instability, in this study, we performed BruChase-Seq to experimentally monitor the expression dynamics of nascent transcripts in resting and activated CD4+ T cells. Computational modeling was then applied to quantify the stability of spliced and intron-retained transcripts on a genome-wide scale. Beyond substantiating that intron-retained transcripts were considerably less stable than spliced transcripts, we found a global stabilization of spliced mRNAs upon T cell activation, although the stability of intron-retained transcripts remained relatively constant. In addition, we identified that La-related protein 4 (LARP4), an RNA-binding protein (RBP) known to enhance mRNA stability, was involved in T cell activation-dependent mRNA stabilization. Knocking out Larp4 in mice destabilized Nfκb1 mRNAs and reduced secretion of interleukin-2 (IL2) and interferon-gamma (IFNγ), two factors critical for T cell proliferation and function. We propose that coordination between splicing regulation and mRNA stability may provide a novel paradigm to control spatiotemporal gene expression during T cell activation.
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Affiliation(s)
- Yi Tian
- Department of Physics, George Washington University, Washington, DC 20052, USA
- Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Zhouhao Zeng
- Department of Physics, George Washington University, Washington, DC 20052, USA
| | - Xiang Li
- Department of Physics, George Washington University, Washington, DC 20052, USA
| | - Yiyin Wang
- Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Runsen Chen
- Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Cardiothoracic Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Sandy Mattijssen
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Sergei Gaidamakov
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Yuzhang Wu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Richard J Maraia
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Weiqun Peng
- Department of Physics, George Washington University, Washington, DC 20052, USA
| | - Jun Zhu
- Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Wang J, Liu J, Ye M, Liu F, Wu S, Huang J, Shi G. Ddx56 maintains proliferation of mouse embryonic stem cells via ribosome assembly and interaction with the Oct4/Sox2 complex. Stem Cell Res Ther 2020; 11:314. [PMID: 32703285 PMCID: PMC7376950 DOI: 10.1186/s13287-020-01800-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/07/2020] [Accepted: 07/01/2020] [Indexed: 12/17/2022] Open
Abstract
Background Embryonic stem cells (ESCs) are important source of clinical stem cells for therapy, so dissecting the functional gene regulatory network involved in their self-renewal and proliferation is an urgent task. We previously reported that Ddx56 interacts with the core transcriptional factor Oct4 by mass spectrometry analysis in ESCs. However, the exact function of Ddx56 in ESCs remains unclear. Methods We investigated the role of Ddx56 in mouse ESCs (mESCs) through both gain- and loss-of-function strategies. The effect of Ddx56 on mESCs was determined based on morphological changes, involvement in the network of pluripotency markers (Nanog, Oct4, Sox2), and altered lineage marker expression. In addition, the role of Ddx56 in mESCs was evaluated by polysome fractionation, qRT-PCR, and co-immunoprecipitation (co-IP). Finally, RNA sequencing was applied to explore potential network regulation by Ddx56 in mESCs. Result We found that Ddx56 participated in ribosome assembly, as knockout or RNAi knockdown of Ddx56 led to ribosome dysfunction and cell lethality. Surprisingly, exogenous expression of C-terminal domain truncated Ddx56 (Ddx56 ΔC-ter) did not affect ribosome assembly, but decreased mESC proliferation by downregulation of proliferation-related genes and cell cycle changing. In terms of mechanism, Ddx56 interacted with the Oct4 and Sox2 complex by binding to Sox2, whereas Ddx56 ΔC-ter showed weaker interaction with Sox2 and led to retardation of mESC proliferation. Conclusions Ddx56 maintains ESC proliferation by conventional regulation of ribosome assembly and interaction with the Oct4 and Sox2 complex.
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Affiliation(s)
- Jingwen Wang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jiahui Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Miaoman Ye
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Feng Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Su Wu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.,Key Laboratory of Reproductive Medicine of Guangdong Province, The First Affiliated Hospital and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Guang Shi
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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Y-Box Binding Proteins in mRNP Assembly, Translation, and Stability Control. Biomolecules 2020; 10:biom10040591. [PMID: 32290447 PMCID: PMC7226217 DOI: 10.3390/biom10040591] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022] Open
Abstract
Y-box binding proteins (YB proteins) are DNA/RNA-binding proteins belonging to a large family of proteins with the cold shock domain. Functionally, these proteins are known to be the most diverse, although the literature hardly offers any molecular mechanisms governing their activities in the cell, tissue, or the whole organism. This review describes the involvement of YB proteins in RNA-dependent processes, such as mRNA packaging into mRNPs, mRNA translation, and mRNA stabilization. In addition, recent data on the structural peculiarities of YB proteins underlying their interactions with nucleic acids are discussed.
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DDX6 Helicase Behavior and Protein Partners in Human Adipose Tissue-Derived Stem Cells during Early Adipogenesis and Osteogenesis. Int J Mol Sci 2020; 21:ijms21072607. [PMID: 32283676 PMCID: PMC7177724 DOI: 10.3390/ijms21072607] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/20/2022] Open
Abstract
DDX6 helicase is an RNA-binding protein involved in different aspects of gene expression regulation. The roles played by DDX6 depend on the complexes associated with it. Here, for the first time, we characterize the protein complexes associated with DDX6 in human adipose tissue-derived stem cells (hASCs) and analyze the dynamics of this helicase under different conditions of translational activity and differentiation. The results obtained demonstrated that the DDX6 helicase is associated with proteins involved in the control of mRNA localization, translation and metabolism in hASCs. DDX6 complexes may also assemble into more complex structures, such as RNA-dependent granules, the abundance and composition of which change upon inhibited translational activity. This finding supports the supposition that DDX6 is possibly involved in the regulation of the mRNA life cycle in hASCs. Although there was no significant variation in the protein composition of these complexes during early adipogenic or osteogenic induction, there was a change in the distribution pattern of DDX6: the number of DDX6 granules per cell was reduced during adipogenesis and was enhanced during osteogenesis.
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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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Todorova K, Mandinova A. Novel approaches for managing aged skin and nonmelanoma skin cancer. Adv Drug Deliv Rev 2020; 153:18-27. [PMID: 32526451 DOI: 10.1016/j.addr.2020.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 05/30/2020] [Accepted: 06/04/2020] [Indexed: 12/29/2022]
Abstract
The process of aging influences every bodily organ and tissue, and those with rapid epithelial cell turnover, are particularly affected. The most visible of these, however, is the skin (including the epidermis), the largest human organ that provides a barrier to external insults, structure to the body and its movements, facilitates thermoregulation, harbors immune cells, and incorporates sensory neurons (including mechanoreceptors, nociceptors, and thermoreceptors). Skin aging has traditionally been categorized into intrinsic and extrinsic, with the latter nearly exclusively restricted to "photoaging," (i.e., aging due to exposure to solar or artificial ultraviolet radiation). However, both intrinsic and extrinsic aging share similar causes, including oxidative damage, telomere shortening, and mitochondrial senescence. Also, like other malignancies, the risk of malignant and nonmalignant lesions increases with age. Herein, we review the most recent findings in skin aging and nonmelanoma skin cancer, including addition to traditional and developing therapies.
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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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HNRNPK maintains epidermal progenitor function through transcription of proliferation genes and degrading differentiation promoting mRNAs. Nat Commun 2019; 10:4198. [PMID: 31519929 PMCID: PMC6744489 DOI: 10.1038/s41467-019-12238-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 08/16/2019] [Indexed: 01/08/2023] Open
Abstract
Maintenance of high-turnover tissues such as the epidermis requires a balance between stem cell proliferation and differentiation. The molecular mechanisms governing this process are an area of investigation. Here we show that HNRNPK, a multifunctional protein, is necessary to prevent premature differentiation and sustains the proliferative capacity of epidermal stem and progenitor cells. To prevent premature differentiation of progenitor cells, HNRNPK is necessary for DDX6 to bind a subset of mRNAs that code for transcription factors that promote differentiation. Upon binding, these mRNAs such as GRHL3, KLF4, and ZNF750 are degraded through the mRNA degradation pathway, which prevents premature differentiation. To sustain the proliferative capacity of the epidermis, HNRNPK is necessary for RNA Polymerase II binding to proliferation/self-renewal genes such as MYC, CYR61, FGFBP1, EGFR, and cyclins to promote their expression. Our study establishes a prominent role for HNRNPK in maintaining adult tissue self-renewal through both transcriptional and post-transcriptional mechanisms. Maintenance of high turnover in tissues such as epidermis requires balance between proliferation and differentiation. Here the authors show that HNRNPK promotes RNA Polymerase II binding to proliferation and self-renewal genes as well as degradation of differentiation promoting mRNAs together with DDX6 in epidermis.
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Peter D, Ruscica V, Bawankar P, Weber R, Helms S, Valkov E, Igreja C, Izaurralde E. Molecular basis for GIGYF-Me31B complex assembly in 4EHP-mediated translational repression. Genes Dev 2019; 33:1355-1360. [PMID: 31439631 PMCID: PMC6771390 DOI: 10.1101/gad.329219.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/18/2019] [Indexed: 11/24/2022]
Abstract
In this study, Peter et al. provide new insights into how GIGYF proteins function together with DDX6 in the regulation of mRNA expression. They used structural analysis, in vivo expression analysis, and biochemical assays to show that GIGYF contains a motif that is necessary and sufficient for direct interaction with Me31B/DDX6, and their findings advance our understanding of the mechanism and assembly of the 4EHP–GIGYF–DDX6 repressor complex. GIGYF (Grb10-interacting GYF [glycine–tyrosine–phenylalanine domain]) proteins coordinate with 4EHP (eIF4E [eukaryotic initiation factor 4E] homologous protein), the DEAD (Asp–Glu–Ala–Asp)-box helicase Me31B/DDX6, and mRNA-binding proteins to elicit transcript-specific repression. However, the underlying molecular mechanism remains unclear. Here, we report that GIGYF contains a motif necessary and sufficient for direct interaction with Me31B/DDX6. A 2.4 Å crystal structure of the GIGYF–Me31B complex reveals that this motif arranges into a coil connected to a β hairpin on binding to conserved hydrophobic patches on the Me31B RecA2 domain. Structure-guided mutants indicate that 4EHP–GIGYF–DDX6 complex assembly is required for tristetraprolin-mediated down-regulation of an AU-rich mRNA, thus revealing the molecular principles of translational repression.
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Affiliation(s)
- Daniel Peter
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany.,European Molecular Biology Laboratory, 38042 Grenoble Cedex 9, France
| | - Vincenzo Ruscica
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Praveen Bawankar
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany.,Institute of Molecular Biology, 55128 Mainz, Germany
| | - Ramona Weber
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Sigrun Helms
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Eugene Valkov
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Cátia Igreja
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
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Li Z, Zhou M, Cai Z, Liu H, Zhong W, Hao Q, Cheng D, Hu X, Hou J, Xu P, Xue Y, Zhou Y, Xu T. RNA-binding protein DDX1 is responsible for fatty acid-mediated repression of insulin translation. Nucleic Acids Res 2019; 46:12052-12066. [PMID: 30295850 PMCID: PMC6294501 DOI: 10.1093/nar/gky867] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 09/14/2018] [Indexed: 01/13/2023] Open
Abstract
The molecular mechanism in pancreatic β cells underlying hyperlipidemia and insulin insufficiency remains unclear. Here, we find that the fatty acid-induced decrease in insulin levels occurs due to a decrease in insulin translation. Since regulation at the translational level is generally mediated through RNA-binding proteins, using RNA antisense purification coupled with mass spectrometry, we identify a novel insulin mRNA-binding protein, namely, DDX1, that is sensitive to palmitate treatment. Notably, the knockdown or overexpression of DDX1 affects insulin translation, and the knockdown of DDX1 eliminates the palmitate-induced repression of insulin translation. Molecular mechanism studies show that palmitate treatment causes DDX1 phosphorylation at S295 and dissociates DDX1 from insulin mRNA, thereby leading to the suppression of insulin translation. In addition, DDX1 may interact with the translation initiation factors eIF3A and eIF4B to regulate translation. In high-fat diet mice, the inhibition of insulin translation happens at an early prediabetic stage before the elevation of glucose levels. We speculate that the DDX1-mediated repression of insulin translation worsens the situation of insulin resistance and contributes to the elevation of blood glucose levels in obese animals.
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Affiliation(s)
- Zonghong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China.,Jilin Province Key Laboratory on Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Maoge Zhou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhaokui Cai
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongyang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen Zhong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Hao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Dongwan Cheng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Xihao Hu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Junjie Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingyong Xu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yifa Zhou
- Jilin Province Key Laboratory on Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Tao Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
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Casaos J, Gorelick NL, Huq S, Choi J, Xia Y, Serra R, Felder R, Lott T, Kast RE, Suk I, Brem H, Tyler B, Skuli N. The Use of Ribavirin as an Anticancer Therapeutic: Will It Go Viral? Mol Cancer Ther 2019; 18:1185-1194. [DOI: 10.1158/1535-7163.mct-18-0666] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/25/2019] [Accepted: 05/08/2019] [Indexed: 11/16/2022]
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50
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Huan W, Zhang J, Li Y, Zhi K. Involvement of DHX9/YB-1 complex induced alternative splicing of Krüppel-like factor 5 mRNA in phenotypic transformation of vascular smooth muscle cells. Am J Physiol Cell Physiol 2019; 317:C262-C269. [PMID: 31116584 DOI: 10.1152/ajpcell.00067.2019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Phenotypic transformation of vascular smooth muscle cells is a key phenomenon in the development of aortic dissection disease. However, the molecular mechanisms underlying this phenomenon have not been fully understood. We used β-BAPN combined with ANG II treatment to establish a disease model of acute aortic dissection (AAD) in mice. We first examined the gene expression profile of aortic tissue in mice with AAD using a gene chip, followed by confirmation of DExH-box helicase 9 (DHX9) expression using RT-PCR, Western blot, and immunofluorescence analysis. We further developed vascular smooth muscle cell-specific DHX9 conditional knockout mice and conducted differential and functional analysis of gene expression and alternative splicing in mouse vascular smooth muscle cells. Finally, we examined the involvement of DHX9 in Krüppel-like factor 5 (KLF5) mRNA alternative splicing. Our study reported a significant decrease in the expression of DHX9 in the vascular smooth muscle cells (VSMCs) of mice with AAD. The smooth muscle cell-specific knockout of DHX9 exacerbated the development of AAD and altered the transcriptional level expression of many smooth muscle cell phenotype-related genes. Finally, we reported that DHX9 may induce alternative splicing of KLF5 mRNA by bridging YB-1. These results together suggested a new pathogenic mechanism underlying the development of AAD, and future research of this mechanism may help identify effective therapeutic intervention for AAD.
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Affiliation(s)
- Wei Huan
- Department of Vascular Surgery, Changzheng Hospital, The Second Military Medical University, Shanghai, China
| | - Jing Zhang
- Department of Cardiovascular Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yingke Li
- Department of Anesthesiology, Changzheng Hospital, The Second Military Medical University, Shanghai, China
| | - Kangkang Zhi
- Department of Vascular Surgery, Changzheng Hospital, The Second Military Medical University, Shanghai, China
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