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Edenhofer FC, Térmeg A, Ohnuki M, Jocher J, Kliesmete Z, Briem E, Hellmann I, Enard W. Generation and characterization of inducible KRAB-dCas9 iPSCs from primates for cross-species CRISPRi. iScience 2024; 27:110090. [PMID: 38947524 PMCID: PMC11214527 DOI: 10.1016/j.isci.2024.110090] [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: 09/15/2023] [Revised: 03/28/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
Comparisons of molecular phenotypes across primates provide unique information to understand human biology and evolution, and single-cell RNA-seq CRISPR interference (CRISPRi) screens are a powerful approach to analyze them. Here, we generate and validate three human, three gorilla, and two cynomolgus iPS cell lines that carry a dox-inducible KRAB-dCas9 construct at the AAVS1 locus. We show that despite variable expression levels of KRAB-dCas9 among lines, comparable downregulation of target genes and comparable phenotypic effects are observed in a single-cell RNA-seq CRISPRi screen. Hence, we provide valuable resources for performing and further extending CRISPRi in human and non-human primates.
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Affiliation(s)
- Fiona C. Edenhofer
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Anita Térmeg
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Mari Ohnuki
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan
- Hakubi Center, Kyoto University, Kyoto 606-8501, Japan
| | - Jessica Jocher
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Zane Kliesmete
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Eva Briem
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany
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2
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Woo SW, Kim M, Kang D, Choe YH, Oh SJ, You AS, Lee SL, Kim J. Genome-Wide Characterization of Somatic Mutation Patterns in Cloned Dogs Reveals Implications for Neuronal Function, Tumorigenesis, and Aging. Genes (Basel) 2024; 15:801. [PMID: 38927737 PMCID: PMC11202621 DOI: 10.3390/genes15060801] [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: 04/25/2024] [Revised: 05/27/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
Studies on somatic mutations in cloned animals have revealed slight genetic variances between clones and their originals, but have yet to identify the precise effects of these differences within the organism. Somatic mutations contribute to aging and are implicated in tumor development and other age-related diseases. Thus, we compared whole genome sequencing data from an original dog with that of cloned dogs, identifying candidate somatic mutations that were disproportionately located within genes previously implicated in aging. The substitutional signature of cloning-specific somatic mutations mirrored the uniform distribution characteristic of the signature associated with human aging. Further analysis of genes revealed significant enrichment of traits associated with body size as well as the molecular mechanisms underlying neuronal function and tumorigenesis. Overall, the somatic mutations found in cloned dogs may indicate a conserved mechanism driving aging across species and a broad spectrum of pathway alterations.
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Affiliation(s)
- Seung-Wan Woo
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; (S.-W.W.); (D.K.)
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Miju Kim
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Dayeon Kang
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; (S.-W.W.); (D.K.)
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Yong-ho Choe
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (Y.-h.C.); (S.-J.O.); (S.-L.L.)
| | - Seong-Ju Oh
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (Y.-h.C.); (S.-J.O.); (S.-L.L.)
| | - Are-Sun You
- Division of Animal Diseases & Health, National Institute of Animal Science, RDA, Wanju 55365, Republic of Korea;
| | - Sung-Lim Lee
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (Y.-h.C.); (S.-J.O.); (S.-L.L.)
| | - Jaemin Kim
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; (S.-W.W.); (D.K.)
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea;
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3
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Choi Y, Choi SA, Koh EJ, Yun I, Park S, Jeon S, Kim Y, Park S, Woo D, Phi JH, Park SH, Kim DS, Kim SH, Choi JW, Lee JW, Jung TY, Bhak J, Lee S, Kim SK. Comprehensive multiomics analysis reveals distinct differences between pediatric choroid plexus papilloma and carcinoma. Acta Neuropathol Commun 2024; 12:93. [PMID: 38867333 PMCID: PMC11167863 DOI: 10.1186/s40478-024-01814-y] [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: 02/08/2024] [Accepted: 06/02/2024] [Indexed: 06/14/2024] Open
Abstract
Choroid plexus tumors (CPTs) are intraventricular tumors derived from the choroid plexus epithelium and occur frequently in children. The aim of this study was to investigate the genomic and epigenomic characteristics of CPT and identify the differences between choroid plexus papilloma (CPP) and choroid plexus carcinoma (CPC). We conducted multiomics analyses of 20 CPT patients including CPP and CPC. Multiomics analysis included whole-genome sequencing, whole-transcriptome sequencing, and methylation sequencing. Mutually exclusive TP53 and EPHA7 point mutations, coupled with the amplification of chromosome 1, were exclusively identified in CPC. In contrast, amplification of chromosome 9 was specific to CPP. Differential gene expression analysis uncovered a significant overexpression of genes related to cell cycle regulation and epithelial-mesenchymal transition pathways in CPC compared to CPP. Overexpression of genes associated with tumor metastasis and progression was observed in the CPC subgroup with leptomeningeal dissemination. Furthermore, methylation profiling unveiled hypomethylation in major repeat regions, including long interspersed nuclear elements, short interspersed nuclear elements, long terminal repeats, and retrotransposons in CPC compared to CPP, implying that the loss of epigenetic silencing of transposable elements may play a role in tumorigenesis of CPC. Finally, the differential expression of AK1, regulated by both genomic and epigenomic factors, emerged as a potential contributing factor to the histological difference of CPP against CPC. Our results suggest pronounced genomic and epigenomic disparities between CPP and CPC, providing insights into the pathogenesis of CPT at the molecular level.
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Affiliation(s)
- Yeonsong Choi
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | - Seung Ah Choi
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Eun Jung Koh
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ilsun Yun
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | - Suhyun Park
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
| | | | | | - Sangbeen Park
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Donggeon Woo
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Ji Hoon Phi
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, Republic of Korea
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Neuroscience Research Institute, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong-Seok Kim
- Department of Pediatric Neurosurgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Se Hoon Kim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Won Choi
- Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ji Won Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Tae-Young Jung
- Department of Neurosurgery, Chonnam National University Medical School and Hwasun Hospital, Hwasun, Republic of Korea
| | - Jong Bhak
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea
- Clinomics Inc., Ulsan, Republic of Korea
| | - Semin Lee
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.
- Korean Genomics Center, UNIST, Ulsan, Republic of Korea.
| | - Seung-Ki Kim
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul, Republic of Korea.
- Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.
- Neuroscience Research Institute, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Republic of Korea.
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4
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Jin SW, Seong Y, Yoon D, Kwon YS, Song H. Dissolution of ribonucleoprotein condensates by the embryonic stem cell protein L1TD1. Nucleic Acids Res 2024; 52:3310-3326. [PMID: 38165001 PMCID: PMC11014241 DOI: 10.1093/nar/gkad1244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/22/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
L1TD1 is a cytoplasmic RNA-binding protein specifically expressed in pluripotent stem cells and, unlike its mouse ortholog, is essential for the maintenance of stemness in human cells. Although L1TD1 is the only known protein-coding gene domesticated from a LINE-1 (L1) retroelement, the functional legacy of its ancestral protein, ORF1p of L1, and how it is manifested in L1TD1 are still unknown. Here, we determined RNAs associated with L1TD1 and found that, like ORF1p, L1TD1 binds L1 RNAs and localizes to high-density ribonucleoprotein (RNP) condensates. Unexpectedly, L1TD1 enhanced the translation of a subset of mRNAs enriched in the condensates. L1TD1 depletion promoted the formation of stress granules in embryonic stem cells. In HeLa cells, ectopically expressed L1TD1 facilitated the dissolution of stress granules and granules formed by pathological mutations of TDP-43 and FUS. The glutamate-rich domain and the ORF1-homology domain of L1TD1 facilitated dispersal of the RNPs and induced autophagy, respectively. These results provide insights into how L1TD1 regulates gene expression in pluripotent stem cells. We propose that the ability of L1TD1 to dissolve stress granules may provide novel opportunities for treatment of neurodegenerative diseases caused by disturbed stress granule dynamics.
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Affiliation(s)
- Sang Woo Jin
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Youngmo Seong
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Dayoung Yoon
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Young-Soo Kwon
- Department of Integrative Bioscience & Biotechnology, Sejong University, Seoul 05006, Republic of Korea
| | - Hoseok Song
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
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Chen LL, Li YQ, Kang ZH, Zhang X, Gu SY, Wang N, Shen XY. Blocking the interaction between circTNRC18 and LIN28A promotes trophoblast epithelial-mesenchymal transformation and alleviates preeclampsia. Mol Cell Endocrinol 2024; 579:112073. [PMID: 37774938 DOI: 10.1016/j.mce.2023.112073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
Abstract
Defects in migration and invasion caused by dysregulation of trophoblastic epithelial-mesenchymal transformation (EMT) play a vital role in preeclampsia (PE). We have previously shown that circTNRC18 inhibits the migration and EMT of trophoblasts; however, its role in PE remains unknown. Herein, we demonstrate that circTNRC18 interacts with an RNA-binding protein, lin-28 homolog A (LIN28A), and this interaction is enhanced in PE placental tissue. LIN28A overexpression suppresses circTNRC18-mediated inhibition of trophoblast migration, invasion, and EMT, whereas LIN28A knockdown promotes them. The intracellular distribution of LIN28A is regulated by circTNRC18, where it promotes the expression of insulin-like growth factor II by stabilizing its mRNA. circTNRC18 also promotes complex formation between GATA-binding factor 1 (GATA1) and sine oculis homeobox 1 (SIX1) by inhibiting LIN28A-GATA1 interaction. GATA1-SIX1 promotes transcription of grainyhead-like protein 2 homolog and circTNRC18-mediated regulation of cell migration and invasion. Moreover, blocking circTNRC18-LIN28A interaction with antisense nucleotides alleviates PE in a mouse model of reduced uterine perfusion pressure. Thus, targeting the circTNRC18-LIN28A regulatory axis may be a novel PE treatment method.
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Affiliation(s)
- Li-Li Chen
- Department of Obstetrics, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, PR China.
| | - Ya-Qin Li
- Department of Obstetrics, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, PR China.
| | - Zhi-Hui Kang
- Department of Obstetrics, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, PR China.
| | - Xuan Zhang
- Department of Obstetrics, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, PR China.
| | - Su-Yan Gu
- Department of Obstetrics, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, PR China.
| | - Na Wang
- Department of Obstetrics, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, PR China.
| | - Xue-Yan Shen
- Department of Obstetrics, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, PR China.
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6
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Drzymalla E, Crider KS, Wang A, Marta G, Khoury MJ, Rasooly D. Epigenome-wide association studies of prenatal maternal mental health and infant epigenetic profiles: a systematic review. Transl Psychiatry 2023; 13:377. [PMID: 38062042 PMCID: PMC10703876 DOI: 10.1038/s41398-023-02620-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 10/01/2023] [Accepted: 10/06/2023] [Indexed: 12/18/2023] Open
Abstract
Prenatal stress and poor maternal mental health are associated with adverse offspring outcomes; however, the biological mechanisms are unknown. Epigenetic modification has linked maternal health with offspring development. Epigenome-wide association studies (EWAS) have examined offspring DNA methylation profiles for association with prenatal maternal mental health to elucidate mechanisms of these complex relationships. The objective of this study is to provide a comprehensive, systematic review of EWASs of infant epigenetic profiles and prenatal maternal anxiety, depression, or depression treatment. We conducted a systematic literature search following PRISMA guidelines for EWAS studies between prenatal maternal mental health and infant epigenetics through May 22, 2023. Of 645 identified articles, 20 fulfilled inclusion criteria. We assessed replication of CpG sites among studies, conducted gene enrichment analysis, and evaluated the articles for quality and risk of bias. We found one repeated CpG site among the maternal depression studies; however, nine pairs of overlapping differentially methylatd regions were reported in at least two maternal depression studies. Gene enrichment analysis found significant pathways for maternal depression but not for any other maternal mental health category. We found evidence that these EWAS present a medium to high risk of bias. Exposure to prenatal maternal depression and anxiety or treatment for such was not consistently associated with epigenetic changes in infants in this systematic review and meta-analysis. Small sample size, potential bias due to exposure misclassification and statistical challenges are critical to address in future efforts to explore epigenetic modification as a potential mechanism by which prenatal exposure to maternal mental health disorders leads to adverse infant outcomes.
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Affiliation(s)
- Emily Drzymalla
- Division of Blood Disorders and Public Health Genomics, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Krista S Crider
- Infant Outcomes Research and Prevention Branch, Division of Birth Defects and Infant Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Arick Wang
- Infant Outcomes Research and Prevention Branch, Division of Birth Defects and Infant Disorders, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Muin J Khoury
- Division of Blood Disorders and Public Health Genomics, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Danielle Rasooly
- Division of Blood Disorders and Public Health Genomics, National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
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7
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Discovery of Novel Lin28 Inhibitors to Suppress Cancer Cell Stemness. Cancers (Basel) 2022; 14:cancers14225687. [PMID: 36428779 PMCID: PMC9688808 DOI: 10.3390/cancers14225687] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022] Open
Abstract
Lin28 is a pluripotency factor that regulates cancer cell stem-like phenotypes to promote cancer development and therapy-resistant tumor progression. It acts through its cold shock domain and zinc knuckle domain (ZKD) to interact with the Let-7 pre-microRNA and block Let-7 biosynthesis. Chemical inhibition of Lin28 from interacting with Let-7 presents a therapeutic strategy for cancer therapy. Herein, we present the computer-aided development of small molecules by in silico screening 18 million compounds from the ZINC20 library, followed by the biological validation of 163 predicted compounds to confirm 15 new Lin28 inhibitors. We report three lead compounds, Ln7, Ln15, and Ln115, that target the ZKD of both Lin28A and Lin28B isoforms and block Lin28 from binding Let-7. They restore Let-7 expression and suppress tumor oncogenes such as SOX2 in cancer cells and show strong inhibitory effects on cancer cell stem-like phenotypes. However, minimal impacts of these compounds were observed on Lin28-negative cells, confirming the on-target effects of these compounds. We conclude from this study the discovery of several new Lin28 inhibitors as promising candidate compounds that warrant further drug development into potential anticancer therapies.
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8
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Apavaloaei A, Hesnard L, Hardy MP, Benabdallah B, Ehx G, Thériault C, Laverdure JP, Durette C, Lanoix J, Courcelles M, Noronha N, Chauhan KD, Lemieux S, Beauséjour C, Bhatia M, Thibault P, Perreault C. Induced pluripotent stem cells display a distinct set of MHC I-associated peptides shared by human cancers. Cell Rep 2022; 40:111241. [PMID: 35977509 DOI: 10.1016/j.celrep.2022.111241] [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: 08/02/2021] [Revised: 06/20/2022] [Accepted: 07/27/2022] [Indexed: 11/03/2022] Open
Abstract
Previous reports showed that mouse vaccination with pluripotent stem cells (PSCs) induces durable anti-tumor immune responses via T cell recognition of some elusive oncofetal epitopes. We characterize the MHC I-associated peptide (MAP) repertoire of human induced PSCs (iPSCs) using proteogenomics. Our analyses reveal a set of 46 pluripotency-associated MAPs (paMAPs) absent from the transcriptome of normal tissues and adult stem cells but expressed in PSCs and multiple adult cancers. These paMAPs derive from coding and allegedly non-coding (48%) transcripts involved in pluripotency maintenance, and their expression in The Cancer Genome Atlas samples correlates with source gene hypomethylation and genomic aberrations common across cancer types. We find that several of these paMAPs were immunogenic. However, paMAP expression in tumors coincides with activation of pathways instrumental in immune evasion (WNT, TGF-β, and CDK4/6). We propose that currently available inhibitors of these pathways could synergize with immune targeting of paMAPs for the treatment of poorly differentiated cancers.
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Affiliation(s)
- Anca Apavaloaei
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Leslie Hesnard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Marie-Pierre Hardy
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | | | - Gregory Ehx
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Catherine Thériault
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Jean-Philippe Laverdure
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Joël Lanoix
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Mathieu Courcelles
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Nandita Noronha
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Kapil Dev Chauhan
- Faculty of Health Sciences, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Christian Beauséjour
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; Department of Pharmacology and Physiology, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Mick Bhatia
- Faculty of Health Sciences, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8N 3Z5, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Chemistry, University of Montreal, Montreal, QC H3T 1J4, Canada.
| | - Claude Perreault
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada; Department of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada.
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9
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Babaei-Abraki S, Karamali F, Nasr-Esfahani MH. The Role of Endoplasmic Reticulum and Mitochondria in Maintaining Redox Status and Glycolytic Metabolism in Pluripotent Stem Cells. Stem Cell Rev Rep 2022; 18:1789-1808. [PMID: 35141862 DOI: 10.1007/s12015-022-10338-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 10/19/2022]
Abstract
Pluripotent stem cells (PSCs), including embryonic stem cells and induced pluripotent stem cells (iPSCs), can be applicable for regenerative medicine. They strangely rely on glycolysis metabolism akin to aerobic glycolysis in cancer cells. Upon differentiation, PSCs undergo a metabolic shift from glycolysis to oxidative phosphorylation (OXPHOS). The metabolic shift depends on organelles maturation, transcriptome modification, and metabolic switching. Besides, metabolism-driven chromatin regulation is necessary for cell survival, self-renewal, proliferation, senescence, and differentiation. In this respect, mitochondria may serve as key organelle to adapt environmental changes with metabolic intermediates which are necessary for maintaining PSCs identity. The endoplasmic reticulum (ER) is another organelle whose role in cellular identity remains under-explored. The purpose of our article is to highlight the recent progress on these two organelles' role in maintaining PSCs redox status focusing on metabolism. Topics include redox status, metabolism regulation, mitochondrial dynamics, and ER stress in PSCs. They relate to the maintenance of stem cell properties and subsequent differentiation of stem cells into specific cell types.
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Affiliation(s)
- Shahnaz Babaei-Abraki
- Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.,Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Fereshteh Karamali
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
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10
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Liu S, He L, Wu J, Wu X, Xie L, Dai W, Chen L, Xie F, Liu Z. DHX9 contributes to the malignant phenotypes of colorectal cancer via activating NF-κB signaling pathway. Cell Mol Life Sci 2021; 78:8261-8281. [PMID: 34773477 PMCID: PMC11072136 DOI: 10.1007/s00018-021-04013-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/27/2021] [Accepted: 10/24/2021] [Indexed: 12/25/2022]
Abstract
Colorectal cancer (CRC) is the leading cause of cancer-related mortality worldwide, which makes it urgent to identify novel therapeutic targets for CRC treatment. In this study, DHX9 was filtered out as the prominent proliferation promoters of CRC by siRNA screening. Moreover, DHX9 was overexpressed in CRC cell lines, clinical CRC tissues and colitis-associated colorectal cancer (CAC) mouse model. The upregulation of DHX9 was positively correlated with poor prognosis in patients with CRC. Through gain- and loss-of function experiments, we found that DHX9 promoted CRC cell proliferation, colony formation, apoptosis resistance, migration and invasion in vitro. Furthermore, a xenograft mouse model and a hepatic metastasis mouse model were utilized to confirm that forced overexpression of DHX9 enhanced CRC outgrowth and metastasis in vivo, while DHX9 ablation produced the opposite effect. Mechanistically, from one aspect, DHX9 enhances p65 phosphorylation, promotes p65 nuclear translocation to facilitate NF-κB-mediated transcriptional activity. From another aspect, DHX9 interacts with p65 and RNA polymerase II (RNA Pol II) to enhance the downstream targets of NF-κB (e.g., Survivin, Snail) expression to potentiate the malignant phenotypes of CRC. Together, our results suggest that DHX9 may be a potential therapeutic target for prevention and treatment of CRC patients.
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Affiliation(s)
- Shenglan Liu
- College of Pharmacy, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Liangmei He
- Department of Gastroenterology, The First Affiliated Hospital, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Junhong Wu
- Gannan Medical University, Ganzhou, Jiangxi, China
| | - Xinqiang Wu
- Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lu Xie
- School of Basic Medicine, Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Wei Dai
- College of Pharmacy, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Lingxia Chen
- School of Basic Medicine, Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Fuhua Xie
- School of Basic Medicine, Gannan Medical University, Ganzhou, 341000, Jiangxi, China.
| | - Zhiping Liu
- School of Basic Medicine, Gannan Medical University, Ganzhou, 341000, Jiangxi, China.
- Center for Immunology, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, Jiangxi, China.
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11
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Yu NK, McClatchy DB, Diedrich JK, Romero S, Choi JH, Martínez-Bartolomé S, Delahunty CM, Muotri AR, Yates JR. Interactome analysis illustrates diverse gene regulatory processes associated with LIN28A in human iPS cell-derived neural progenitor cells. iScience 2021; 24:103321. [PMID: 34816099 PMCID: PMC8593586 DOI: 10.1016/j.isci.2021.103321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/07/2021] [Accepted: 10/19/2021] [Indexed: 12/02/2022] Open
Abstract
A single protein can be multifaceted depending on the cellular contexts and interacting molecules. LIN28A is an RNA-binding protein that governs developmental timing, cellular proliferation, differentiation, stem cell pluripotency, and metabolism. In addition to its best-known roles in microRNA biogenesis, diverse molecular roles have been recognized. In the nervous system, LIN28A is known to play critical roles in proliferation and differentiation of neural progenitor cells (NPCs). We profiled the endogenous LIN28A-interacting proteins in NPCs differentiated from human induced pluripotent stem (iPS) cells using immunoprecipitation and liquid chromatography-tandem mass spectrometry. We identified over 500 LIN28A-interacting proteins, including 156 RNA-independent interactors. Functions of these proteins span a wide range of gene regulatory processes. Prompted by the interactome data, we revealed that LIN28A may impact the subcellular distribution of its interactors and stress granule formation upon oxidative stress. Overall, our analysis opens multiple avenues for elaborating molecular roles and characteristics of LIN28A.
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Affiliation(s)
- Nam-Kyung Yu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel B. McClatchy
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jolene K. Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sarah Romero
- Department of Pediatrics/Rady Children’s Hospital San Diego, Department of Cellular & Molecular Medicine, School of Medicine, University of California, San Diego, San Diego, CA 92037, USA
| | - Jun-Hyeok Choi
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Claire M. Delahunty
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alysson R. Muotri
- Department of Pediatrics/Rady Children’s Hospital San Diego, Department of Cellular & Molecular Medicine, School of Medicine, University of California, San Diego, San Diego, CA 92037, USA
- Stem Cell Program, Center for Academic Research and Training in Anthropogeny (CARTA), Archealization Center (ArchC), Kavli Institute for Brain and Mind, La Jolla, CA 92037, USA
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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12
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Liu Y, He J, Chen R, Liu H, Chen J, Liu Y, Wang B, Guo L, Pei D, Wang J, Liu J, Chen J. AP-1 activity is a major barrier of human somatic cell reprogramming. Cell Mol Life Sci 2021; 78:5847-5863. [PMID: 34181046 PMCID: PMC11072308 DOI: 10.1007/s00018-021-03883-x] [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: 10/09/2020] [Revised: 05/09/2021] [Accepted: 06/18/2021] [Indexed: 10/21/2022]
Abstract
Human induced pluripotent stem cells (iPSCs) technology has been widely applied to cell regeneration and disease modeling. However, most mechanism of somatic reprogramming is studied on mouse system, which is not always generic in human. Consequently, the generation of human iPSCs remains inefficient. Here, we map the chromatin accessibility dynamics during the induction of human iPSCs from urine cells. Comparing to the mouse system, we found that the closing of somatic loci is much slower in human. Moreover, a conserved AP-1 motif is highly enriched among the closed loci. The introduction of AP-1 repressor, JDP2, enhances human reprogramming and facilitates the reactivation of pluripotent genes. However, ESRRB, KDM2B and SALL4, several known pluripotent factors promoting mouse somatic reprogramming fail to enhance human iPSC generation. Mechanistically, we reveal that JDP2 promotes the closing of somatic loci enriching AP-1 motifs to enhance human reprogramming. Furthermore, JDP2 can rescue reprogramming deficiency without MYC or KLF4. These results indicate AP-1 activity is a major barrier to prevent chromatin remodeling during somatic cell reprogramming.
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Affiliation(s)
- Yuting Liu
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jiangping He
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory , Guangzhou, 510005, China
| | - Ruhai Chen
- Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - He Liu
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory , Guangzhou, 510005, China
| | - Jocelyn Chen
- The Loomis Chaffee School, Windsor, CT, 06095, USA
| | - Yujian Liu
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Bo Wang
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory , Guangzhou, 510005, China
| | - Lin Guo
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory , Guangzhou, 510005, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory , Guangzhou, 510005, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jie Wang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Jing Liu
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory , Guangzhou, 510005, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory, Guangzhou Regenerative Medicine and Health GuangDong Laboratory , Guangzhou, 510005, China.
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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13
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Chen C, Zhang M, Zhang Y. Circ_0000079 Decoys the RNA-Binding Protein FXR1 to Interrupt Formation of the FXR1/PRCKI Complex and Decline Their Mediated Cell Invasion and Drug Resistance in NSCLC. Cell Transplant 2021; 29:963689720961070. [PMID: 32951448 PMCID: PMC7784611 DOI: 10.1177/0963689720961070] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Nonsmall cell lung cancer (NSCLC) has gradually become one of the deadliest threats to human health and life worldwide. Although reports have shown that circular RNAs (circRNAs) are associated with progression and metastasis of NSCLC, the biological functions of circRNAs during these processes remain largely unknown. Our study showed that circ_0000079 (CiR79) levels were significantly downregulated in NSCLC patients, especially in cisplatin (DDP)-resistant NSCLC patients, and low circ_0000079 levels were significantly associated with poor overall survival of NSCLC patients. Then, results from Cell Counting Kit-8 (CCK-8) cell viability assay and transwell cell invasion assay in A549/DDP and H460/DDP cells transfected with pCDH-CiR79 expression vector showed that circ_0000079 overexpression significantly inhibited cell proliferation and invasion of these DDP-resistant NSCLC cells. The online bioinformatic program StarBase and RNA-binding protein immunoprecipitation predicted and demonstrated that circ_0000079 could bind with the Fragile X-Related 1 (FXR1) protein rather than with protein kinase C, iota (PRKCI), which was shown to form a complex with FXR1 to promote invasion and growth of NSCLC cells. Co-immunoprecipitation combined with Western blot assays indicated that FXR1 levels were remarkably decreased, but PRKCI levels remained unchanged in pCDH-ciR79 transfected NSCLC cells. Moreover, circ_0000079 negatively regulated FXR1/PRKCI-mediated phosphorylation of glycogen synthesis kinase 3β and activator protein 1, thus suppressing the protein level of the Snail gene, an important promoter gene regulating cancer cell growth and epithelial-mesenchymal transition. Furthermore, DDP resistance of A549/DDP and H460/DDP cells was inhibited by circ_0000079 overexpression but was restored by FXR1. Hence, our findings demonstrated that circ_0000079 might inhibit cell invasion and drug resistance in NSCLC by interrupting the formation of the FXR1/PRCKI complex by interacting with FXR1, and circ_0000079 could act as a potential biomarker and therapeutic target for NSCLC.
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Affiliation(s)
- Chen Chen
- Department of Pathology, 569063the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
| | - Min Zhang
- Department of Pathology, 569063the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
| | - Yan Zhang
- Department of Pathology, 569063the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
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14
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Dvir S, Argoetti A, Lesnik C, Roytblat M, Shriki K, Amit M, Hashimshony T, Mandel-Gutfreund Y. Uncovering the RNA-binding protein landscape in the pluripotency network of human embryonic stem cells. Cell Rep 2021; 35:109198. [PMID: 34077720 DOI: 10.1016/j.celrep.2021.109198] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
Embryonic stem cell (ESC) self-renewal and cell fate decisions are driven by a broad array of molecular signals. While transcriptional regulators have been extensively studied in human ESCs (hESCs), the extent to which RNA-binding proteins (RBPs) contribute to human pluripotency remains unclear. Here, we carry out a proteome-wide screen and identify 810 proteins that bind RNA in hESCs. We reveal that RBPs are preferentially expressed in hESCs and dynamically regulated during early stem cell differentiation. Notably, many RBPs are affected by knockdown of OCT4, a master regulator of pluripotency, several dozen of which are directly targeted by this factor. Using cross-linking and immunoprecipitation (CLIP-seq), we find that the pluripotency-associated STAT3 and OCT4 transcription factors interact with RNA in hESCs and confirm the binding of STAT3 to the conserved NORAD long-noncoding RNA. Our findings indicate that RBPs have a more widespread role in human pluripotency than previously appreciated.
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Affiliation(s)
- Shlomi Dvir
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Chen Lesnik
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | | | | | - Michal Amit
- Accellta LTD, Haifa 320003, Israel; Ephraim Katzir Department of Biotechnology Engineering, ORT Braude College, Karmiel 2161002, Israel
| | - Tamar Hashimshony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 320003, Israel; Computer Science Department, Technion - Israel Institute of Technology, Haifa 320003, Israel.
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15
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Webster NJ, Maywald RL, Benton SM, Dawson EP, Murillo OD, LaPlante EL, Milosavljevic A, Lanza DG, Heaney JD. Testicular germ cell tumors arise in the absence of sex-specific differentiation. Development 2021; 148:260592. [PMID: 33912935 DOI: 10.1242/dev.197111] [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] [Received: 09/21/2020] [Accepted: 03/22/2021] [Indexed: 01/09/2023]
Abstract
In response to signals from the embryonic testis, the germ cell intrinsic factor NANOS2 coordinates a transcriptional program necessary for the differentiation of pluripotent-like primordial germ cells toward a unipotent spermatogonial stem cell fate. Emerging evidence indicates that genetic risk factors contribute to testicular germ cell tumor initiation by disrupting sex-specific differentiation. Here, using the 129.MOLF-Chr19 mouse model of testicular teratomas and a NANOS2 reporter allele, we report that the developmental phenotypes required for tumorigenesis, including failure to enter mitotic arrest, retention of pluripotency and delayed sex-specific differentiation, were exclusive to a subpopulation of germ cells failing to express NANOS2. Single-cell RNA sequencing revealed that embryonic day 15.5 NANOS2-deficient germ cells and embryonal carcinoma cells developed a transcriptional profile enriched for MYC signaling, NODAL signaling and primed pluripotency. Moreover, lineage-tracing experiments demonstrated that embryonal carcinoma cells arose exclusively from germ cells failing to express NANOS2. Our results indicate that NANOS2 is the nexus through which several genetic risk factors influence tumor susceptibility. We propose that, in the absence of sex specification, signals native to the developing testis drive germ cell transformation.
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Affiliation(s)
- Nicholas J Webster
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rebecca L Maywald
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Susan M Benton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily P Dawson
- Department of Cell Biology, New York University, New York, NY 10003, USA
| | - Oscar D Murillo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily L LaPlante
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Denise G Lanza
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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16
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Pollini D, Loffredo R, Maniscalco F, Cardano M, Micaelli M, Bonomo I, Licata NV, Peroni D, Tomaszewska W, Rossi A, Crippa V, Dassi E, Viero G, Quattrone A, Poletti A, Conti L, Provenzani A. Multilayer and MATR3-dependent regulation of mRNAs maintains pluripotency in human induced pluripotent stem cells. iScience 2021; 24:102197. [PMID: 33733063 PMCID: PMC7940987 DOI: 10.1016/j.isci.2021.102197] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/22/2020] [Accepted: 02/11/2021] [Indexed: 10/28/2022] Open
Abstract
Matrin3 (MATR3) is a nuclear RNA/DNA-binding protein that plays pleiotropic roles in gene expression regulation by directly stabilizing target RNAs and supporting the activity of transcription factors by modulating chromatin architecture. MATR3 is involved in the differentiation of neural cells, and, here, we elucidate its critical functions in regulating pluripotent circuits in human induced pluripotent stem cells (hiPSCs). MATR3 downregulation affects hiPSCs' differentiation potential by altering key pluripotency regulators' expression levels, including OCT4, NANOG, and LIN28A by pleiotropic mechanisms. MATR3 binds to the OCT4 and YTHDF1 promoters favoring their expression. YTHDF1, in turn, binds the m6A-modified OCT4 mRNA. Furthermore, MATR3 is recruited on ribosomes and controls pluripotency regulating the translation of specific transcripts, including NANOG and LIN28A, by direct binding and favoring their stabilization. These results show that MATR3 orchestrates the pluripotency circuitry by regulating the transcription, translational efficiency, and epitranscriptome of specific transcripts.
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Affiliation(s)
- Daniele Pollini
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Rosa Loffredo
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Maniscalco
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
- Institute of Biophysics, CNR, Trento, Italy
| | - Marina Cardano
- Cell Technology Core Facility, Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Mariachiara Micaelli
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Isabelle Bonomo
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | | | - Daniele Peroni
- Mass Spectrometry Core Facility, Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Weronika Tomaszewska
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Annalisa Rossi
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Valeria Crippa
- Laboratorio di Biologia Applicata, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | | | - Alessandro Quattrone
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Angelo Poletti
- Laboratorio di Biologia Applicata, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Luciano Conti
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Alessandro Provenzani
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
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17
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Lovnicki J, Gan Y, Feng T, Li Y, Xie N, Ho CH, Lee AR, Chen X, Nappi L, Han B, Fazli L, Huang J, Gleave ME, Dong X. LIN28B promotes the development of neuroendocrine prostate cancer. J Clin Invest 2021; 130:5338-5348. [PMID: 32634132 DOI: 10.1172/jci135373] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Therapy-induced neuroendocrine prostate cancer (t-NEPC) is a highly aggressive subtype of prostate cancer with poor patient survival. Emerging evidence indicates that t-NEPC can develop when prostate adenocarcinoma cells acquire cancer stem-like cell signaling in the presence of androgen receptor inhibition, followed by redifferentiation toward neuroendocrine lineage and subsequent t-NEPC progression. Whether the stem-like signaling is controlled by the core pluripotency stem cell genes (e.g., LIN28 and SOX2) remains unknown. Here, we report that the transcription of the LIN28B isoform and SOX2 were co-upregulated in t-NEPC patient tumors, patient-derived xenografts, transgenic mice, and cell models. Immunohistochemistry validated that LIN28B and SOX2 protein expression were elevated in t-NEPC patient biopsies. Using prostate adenocarcinoma and t-NEPC cell models, we demonstrated that LIN28B induced a stem-like gene network, neuroendocrine biomarkers, and neuroendocrine cell morphology. LIN28B depletion by CRISPR inhibited t-NEPC tumorigenesis and xenograft growth. These LIN28B functions were mediated mainly through the suppression of let-7 miRNA expression, resulting in de-repression of the transcription factor HMGA2 and HMGA2-mediated SOX2 expression. This study revealed a mechanism by which t-NEPC can develop through the LIN28B/let-7/SOX2 axis that regulates a cancer cell stem-like gene network, highlighting LIN28B as a potential therapeutic target in t-NEPC.
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Affiliation(s)
- Jessica Lovnicki
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yu Gan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Urology, Xiangya Hospital, Central South University, Changsha, China
| | - Tingting Feng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Key Laboratory of Experimental Teratology, Ministry of Education, and Department of Pathology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Yinan Li
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ning Xie
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chia-Hao Ho
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ahn R Lee
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xufeng Chen
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Lucia Nappi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bo Han
- Key Laboratory of Experimental Teratology, Ministry of Education, and Department of Pathology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Ladan Fazli
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jiaoti Huang
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Martin E Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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18
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Urh K, Žlajpah M, Zidar N, Boštjančič E. Identification and Validation of New Cancer Stem Cell-Related Genes and Their Regulatory microRNAs in Colorectal Cancerogenesis. Biomedicines 2021; 9:biomedicines9020179. [PMID: 33670246 PMCID: PMC7916981 DOI: 10.3390/biomedicines9020179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/31/2021] [Accepted: 02/04/2021] [Indexed: 12/11/2022] Open
Abstract
Significant progress has been made in the last decade in our understanding of the pathogenetic mechanisms of colorectal cancer (CRC). Cancer stem cells (CSC) have gained much attention and are now believed to play a crucial role in the pathogenesis of various cancers, including CRC. In the current study, we validated gene expression of four genes related to CSC, L1TD1, SLITRK6, ST6GALNAC1 and TCEA3, identified in a previous bioinformatics analysis. Using bioinformatics, potential miRNA-target gene correlations were prioritized. In total, 70 formalin-fixed paraffin-embedded biopsy samples from 47 patients with adenoma, adenoma with early carcinoma and CRC without and with lymph node metastases were included. The expression of selected genes and microRNAs (miRNAs) was evaluated using quantitative PCR. Differential expression of all investigated genes and four of six prioritized miRNAs (hsa-miR-199a-3p, hsa-miR-335-5p, hsa-miR-425-5p, hsa-miR-1225-3p, hsa-miR-1233-3p and hsa-miR-1303) was found in at least one group of CRC cancerogenesis. L1TD1, SLITRK6, miR-1233-3p and miR-1225-3p were correlated to the level of malignancy. A negative correlation between miR-199a-3p and its predicted target SLITRK6 was observed, showing potential for further experimental validation in CRC. Our results provide further evidence that CSC-related genes and their regulatory miRNAs are involved in CRC development and progression and suggest that some them, particularly miR-199a-3p and its SLITRK6 target gene, are promising for further validation in CRC.
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Differential gene expression in cisplatin-resistant and -sensitive testicular germ cell tumor cell lines. Oncotarget 2020; 11:4735-4753. [PMID: 33473258 PMCID: PMC7771712 DOI: 10.18632/oncotarget.27844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022] Open
Abstract
Testicular germ cell tumors (TGCTs) represent a well curable malignity due to their exceptional response to cisplatin (CDDP). Despite remarkable treatment results, approximately 5% of TGCT patients develop CDDP resistance and die. Exceptional curability makes TGCTs a highly valuable model system for studying the molecular mechanisms of CDDP sensitivity. Our study was aimed at revealing difference in gene expression between the CDDP-resistant and -sensitive TGCT cell lines, and hence at identifying candidate genes that could serve as potential biomarkers of CDDP response. Using gene expression array, we identified 281 genes that are differentially expressed in CDDP-resistant compared to -sensitive TGCT cell lines. The expression of 25 genes with the highest fold change was validated by RT-qPCR. Of them, DNMT3L, GAL, IGFBP2, IGFBP7, L1TD1, NANOG, NTF3, POU5F1, SOX2, WNT6, ZFP42, ID2, PCP4, SLC40A1 and TRIB3, displayed comparable expression change in gene expression array and RT-qPCR, when all CDDP-resistant TGCT cell lines were pairwise combined with all -sensitive ones. Products of the identified genes are pluripotency factors, or are involved in processes, such as cell metabolism, proliferation or migration. We propose that, after clinical validation, these genes could serve as prognostic biomarkers for early detection of CDDP response in TGCT patients.
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Pan YQ, Xing L. The Current View on the Helicase Activity of RNA Helicase A and Its Role in Gene Expression. Curr Protein Pept Sci 2020; 22:29-40. [PMID: 33143622 DOI: 10.2174/1389203721666201103084122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 08/18/2020] [Accepted: 09/09/2020] [Indexed: 11/22/2022]
Abstract
RNA helicase A (RHA) is a DExH-box helicase that plays regulatory roles in a variety of cellular processes, including transcription, translation, RNA splicing, editing, transport, and processing, microRNA genesis and maintenance of genomic stability. It is involved in virus replication, oncogenesis, and innate immune response. RHA can unwind nucleic acid duplex by nucleoside triphosphate hydrolysis. The insight into the molecular mechanism of helicase activity is fundamental to understanding the role of RHA in the cell. Herein, we reviewed the current advances on the helicase activity of RHA and its relevance to gene expression, particularly, to the genesis of circular RNA.
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Affiliation(s)
- Yuan-Qing Pan
- Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, Shanxi province, China
| | - Li Xing
- Institute of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan 030006, Shanxi province, China
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21
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Wang J, Huang J, Shi G. Retrotransposons in pluripotent stem cells. CELL REGENERATION 2020; 9:4. [PMID: 32588192 PMCID: PMC7306833 DOI: 10.1186/s13619-020-00046-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/19/2019] [Indexed: 12/18/2022]
Abstract
Transposable elements constitute about half of the mammalian genome, and can be divided into two classes: the class I (retrotransposons) and the class II (DNA transposons). A few hundred types of retrotransposons, which are dynamic and stage specific, have been annotated. The copy numbers and genomic locations are significantly varied in species. Retrotransposons are active in germ cells, early embryos and pluripotent stem cells (PSCs) correlated with low levels of DNA methylation in epigenetic regulation. Some key pluripotency transcriptional factors (such as OCT4, SOX2, and NANOG) bind retrotransposons and regulate their activities in PSCs, suggesting a vital role of retrotransposons in pluripotency maintenance and self-renewal. In response to retrotransposons transposition, cells employ a number of silencing mechanisms, such as DNA methylation and histone modification. This review summarizes expression patterns, functions, and regulation of retrotransposons in PSCs and early embryonic development.
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Affiliation(s)
- Jingwen Wang
- School of Life Sciences, SunYat-sen University, Guangzhou, 510275, P. R. China
| | - Junjiu Huang
- School of Life Sciences, SunYat-sen University, Guangzhou, 510275, P. R. China. .,Key Laboratory of Reproductive Medicine of Guangdong Province, School of Life Sciences and the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510275, China. .,Key Laboratory of Reproductive Medicine of Guangdong Province, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Guang Shi
- School of Life Sciences, SunYat-sen University, Guangzhou, 510275, P. R. China.
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Chakroborty D, Emani MR, Klén R, Böckelman C, Hagström J, Haglund C, Ristimäki A, Lahesmaa R, Elo LL. L1TD1 - a prognostic marker for colon cancer. BMC Cancer 2019; 19:727. [PMID: 31337362 PMCID: PMC6651905 DOI: 10.1186/s12885-019-5952-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/18/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Prognostic markers specific to a particular cancer type can assist in the evaluation of survival probability of patients and help clinicians to assess the available treatment modalities. METHODS Gene expression data was analyzed from three independent colon cancer microarray gene expression data sets (N = 1052). Survival analysis was performed for the three data sets, stratified by the expression level of the LINE-1 type transposase domain containing 1 (L1TD1). Correlation analysis was performed to investigate the role of the interactome of L1TD1 in colon cancer patients. RESULTS We found L1TD1 as a novel positive prognostic marker for colon cancer. Increased expression of L1TD1 associated with longer disease-free survival in all the three data sets. Our results were in contrast to a previous study on medulloblastoma, where high expression of L1TD1 was linked with poor prognosis. Notably, in medulloblastoma L1TD1 was co-expressed with its interaction partners, whereas our analysis revealed lack of co-expression of L1TD1 with its interaction partners in colon cancer. CONCLUSIONS Our results identify increased expression of L1TD1 as a prognostic marker predicting longer disease-free survival in colon cancer patients.
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Affiliation(s)
- Deepankar Chakroborty
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
| | - Maheswara Reddy Emani
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Riku Klén
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Camilla Böckelman
- Research Programs Unit, Translational Cancer Biology, University of Helsinki, Helsinki, Finland
- Department of Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jaana Hagström
- Research Programs Unit, Translational Cancer Biology, University of Helsinki, Helsinki, Finland
- Department of Pathology and Oral Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Caj Haglund
- Research Programs Unit, Translational Cancer Biology, University of Helsinki, Helsinki, Finland
- Department of Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ari Ristimäki
- Department of Pathology, HUSLAB, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Genome-Scale Biology Research program, University of Helsinki, 00290 Helsinki, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Laura L. Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
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Lu Y, Kweon SS, Tanikawa C, Jia WH, Xiang YB, Cai Q, Zeng C, Schmit SL, Shin A, Matsuo K, Jee SH, Kim DH, Kim J, Wen W, Shi J, Guo X, Li B, Wang N, Zhang B, Li X, Shin MH, Li HL, Ren Z, Oh JH, Oze I, Ahn YO, Jung KJ, Conti DV, Schumacher FR, Rennert G, Jenkins MA, Campbell PT, Hoffmeister M, Casey G, Gruber SB, Gao J, Gao YT, Pan ZZ, Kamatani Y, Zeng YX, Shu XO, Long J, Matsuda K, Zheng W. Large-Scale Genome-Wide Association Study of East Asians Identifies Loci Associated With Risk for Colorectal Cancer. Gastroenterology 2019; 156:1455-1466. [PMID: 30529582 PMCID: PMC6441622 DOI: 10.1053/j.gastro.2018.11.066] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Genome-wide association studies (GWASs) have associated approximately 50 loci with risk of colorectal cancer (CRC)-nearly one third of these loci were initially associated with CRC in studies conducted in East Asian populations. We conducted a GWAS of East Asians to identify CRC risk loci and evaluate the generalizability of findings from GWASs of European populations to Asian populations. METHODS We analyzed genetic data from 22,775 patients with CRC (cases) and 47,731 individuals without cancer (controls) from 14 studies in the Asia Colorectal Cancer Consortium. First, we performed a meta-analysis of 7 GWASs (10,625 cases and 34,595 controls) and identified 46,554 promising risk variants for replication by adding them to the Multi-Ethnic Global Array (MEGA) for genotype analysis in 6445 cases and 7175 controls. These data were analyzed, along with data from an additional 5705 cases and 5961 controls genotyped using the OncoArray. We also obtained data from 57,976 cases and 67,242 controls of European descent. Variants at identified risk loci were functionally annotated and evaluated in correlation with gene expression levels. RESULTS A meta-analyses of all samples from people of Asian descent identified 13 loci and 1 new variant at a known locus (10q24.2) associated with risk of CRC at the genome-wide significance level of P < 5 × 10-8. We did not perform experiments to replicate these associations in additional individuals of Asian ancestry. However, the lead risk variant in 6 of these loci was also significantly associated with risk of CRC in European descendants. A strong association (44%-75% increase in risk per allele) was found for 2 low-frequency variants: rs201395236 at 1q44 (minor allele frequency, 1.34%) and rs77969132 at 12p11.21 (minor allele frequency, 1.53%). For 8 of the 13 associated loci, the variants with the highest levels of significant association were located inside or near the protein-coding genes L1TD1, EFCAB2, PPP1R21, SLCO2A1, HLA-G, NOTCH4, DENND5B, and GNAS. For other intergenic loci, we provided evidence for the possible involvement of the genes ALDH7A1, PRICKLE1, KLF5, WWOX, and GLP2R. We replicated findings for 41 of 52 previously reported risk loci. CONCLUSIONS We showed that most of the risk loci previously associated with CRC risk in individuals of European descent were also associated with CRC risk in East Asians. Furthermore, we identified 13 loci significantly associated with risk for CRC in Asians. Many of these loci contained genes that regulate the immune response, Wnt signaling to β-catenin, prostaglandin E2 catabolism, and cell pluripotency and proliferation. Further analyses of these genes and their variants is warranted, particularly for the 8 loci for which the lead CRC risk variants were not replicated in persons of European descent.
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Affiliation(s)
- Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea; Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, South Korea
| | - Chizu Tanikawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - Yong-Bing Xiang
- State Key Laboratory of Oncogenes and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Chenjie Zeng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Aesun Shin
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul National University Cancer Research Institute, Seoul, Korea
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan; Department of Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Korea
| | - Dong-Hyun Kim
- Department of Social and Preventive Medicine, Hallym University College of Medicine, Okcheon-dong, Korea
| | - Jeongseon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Gyeonggi-do, South Korea
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jiajun Shi
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Nan Wang
- General Surgery Department, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Ben Zhang
- Department of Epidemiology and Biostatistics First Affiliated Hospital, Army Medical University, Shapingba District, Chongqing, China
| | - Xinxiang Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Min-Ho Shin
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Hong-Lan Li
- State Key Laboratory of Oncogenes and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zefang Ren
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jae Hwan Oh
- Center for Colorectal Cancer, National Cancer Center Hospital, National Cancer Center, Gyeonggi-do, South Korea
| | - Isao Oze
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Yoon-Ok Ahn
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Keum Ji Jung
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Korea
| | - David V Conti
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Fredrick R Schumacher
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio
| | - Gad Rennert
- Clalit Health Services National Israeli Cancer Control Center, Haifa, Israel; Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel; Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Stephen B Gruber
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California; Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jing Gao
- State Key Laboratory of Oncogenes and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yu-Tang Gao
- State Key Laboratory of Oncogenes and Related Genes and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhi-Zhong Pan
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan; Kyoto-McGill International Collaborative School in Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee.
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24
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Abstract
Research endeavors originally generated stem cell definitions for the purpose of describing normally sustainable developmental and tissue turnover processes in various species, including humans. The notion of investigating cells that possess a vague capacity of “stamm (phylum)” can be traced back to the late 19th century, mainly concentrating on cells that could produce the germline or the entire blood system. Lately, such undertakings have been recapitulated for oncogenesis, tumor growth, and cancer cell resistance to oncolytic therapies. However, due to the complexity and basic life-origin mechanisms comprising the genetic and epigenetic repertoire of the stemness in every developing or growing cell, presently there are ongoing debates regarding the biological essentials of the stem cell-like tumor initiation cells (ie, cancer stem cells; CSCs). This conceptual analysis focuses on the potential pitfalls of extrapolating that CSCs bear major traits of stemness. We propose a novel nomenclature of Tumor Survival Cells (TSCs) to further define tumor cells behaving like CSCs, based on the ruthless and detrimental features of Cancer Cell Survivology that appears fundamentally different from stem cell biology. Hence, precise academic separation of TSCs from all the stem cell-related labels applied to these unique tumor cells may help to improve scientific reasoning and strategies to decode the desperado-like survival behaviors of TSCs to eventually overcome cancer.
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Affiliation(s)
- Yang D Teng
- 1 Department of Physical Medicine and Rehabilitation, Harvard Medical School and Spaulding Rehabilitation Hospital Network, Brigham and Women's Hospital, and Massachusetts General Hospital , Boston, Massachusetts.,2 Department of Neurosurgery, Harvard Medical School , Boston, Massachusetts.,3 Division of SCI Research, VA Boston Healthcare System , Boston, Massachusetts
| | - Lei Wang
- 1 Department of Physical Medicine and Rehabilitation, Harvard Medical School and Spaulding Rehabilitation Hospital Network, Brigham and Women's Hospital, and Massachusetts General Hospital , Boston, Massachusetts.,2 Department of Neurosurgery, Harvard Medical School , Boston, Massachusetts.,3 Division of SCI Research, VA Boston Healthcare System , Boston, Massachusetts
| | - Serdar Kabatas
- 1 Department of Physical Medicine and Rehabilitation, Harvard Medical School and Spaulding Rehabilitation Hospital Network, Brigham and Women's Hospital, and Massachusetts General Hospital , Boston, Massachusetts.,2 Department of Neurosurgery, Harvard Medical School , Boston, Massachusetts.,3 Division of SCI Research, VA Boston Healthcare System , Boston, Massachusetts
| | - Henning Ulrich
- 4 Departamento de Bioquímica, Instituto de Química , Universidade de São Paulo, São Paulo, Brazil
| | - Ross D Zafonte
- 1 Department of Physical Medicine and Rehabilitation, Harvard Medical School and Spaulding Rehabilitation Hospital Network, Brigham and Women's Hospital, and Massachusetts General Hospital , Boston, Massachusetts
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Bioinformatics Analysis Reveals Most Prominent Gene Candidates to Distinguish Colorectal Adenoma from Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2018; 2018:9416515. [PMID: 30175151 PMCID: PMC6106857 DOI: 10.1155/2018/9416515] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/30/2018] [Indexed: 12/18/2022]
Abstract
Colorectal cancer (CRC) is one of the leading causes of death by cancer worldwide. Bowel cancer screening programs enable us to detect early lesions and improve the prognosis of patients with CRC. However, they also generate a significant number of problematic polyps, e.g., adenomas with epithelial misplacement (pseudoinvasion) which can mimic early adenocarcinoma. Therefore, biomarkers that would enable us to distinguish between adenoma with epithelial misplacement (pseudoinvasion) and adenoma with early adenocarcinomas (true invasion) are needed. We hypothesized that the former are genetically similar to adenoma and the latter to adenocarcinoma and we used bioinformatics approach to search for candidate genes that might be potentially used to distinguish between the two lesions. We used publicly available data from Gene Expression Omnibus database and we analyzed gene expression profiles of 252 samples of normal mucosa, colorectal adenoma, and carcinoma. In total, we analyzed 122 colorectal adenomas, 59 colorectal carcinomas, and 62 normal mucosa samples. We have identified 16 genes with differential expression in carcinoma compared to adenoma: COL12A1, COL1A2, COL3A1, DCN, PLAU, SPARC, SPON2, SPP1, SULF1, FADS1, G0S2, EPHA4, KIAA1324, L1TD1, PCKS1, and C11orf96. In conclusion, our in silico analysis revealed 16 candidate genes with different expression patterns in adenoma compared to carcinoma, which might be used to discriminate between these two lesions.
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26
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Narad P, Anand L, Gupta R, Sengupta A. Construction of Discrete Model of Human Pluripotency in Predicting Lineage-Specific Outcomes and Targeted Knockdowns of Essential Genes. Sci Rep 2018; 8:11031. [PMID: 30038409 PMCID: PMC6056480 DOI: 10.1038/s41598-018-29480-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 07/06/2018] [Indexed: 01/08/2023] Open
Abstract
A network consisting of 45 core genes was developed for the genes/proteins responsible for loss/gain of function in human pluripotent stem cells. The nodes were included on the basis of literature curation. The initial network topology was further refined by constructing an inferred Boolean model from time-series RNA-seq expression data. The final Boolean network was obtained by integration of the initial topology and the inferred topology into a refined model termed as the integrated model. Expression levels were observed to be bi-modular for most of the genes involved in the mechanism of human pluripotency. Thus, single and combinatorial perturbations/knockdowns were executed using an in silico approach. The model perturbations were validated with literature studies. A number of outcomes are predicted using the knockdowns of the core pluripotency circuit and we are able to establish the minimum requirement for maintenance of pluripotency in human. The network model is able to predict lineage-specific outcomes and targeted knockdowns of essential genes involved in human pluripotency which are challenging to perform due to ethical constraints surrounding human embryonic stem cells.
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Affiliation(s)
- Priyanka Narad
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, India.
| | - Lakshay Anand
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, India
| | - Romasha Gupta
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, India
| | - Abhishek Sengupta
- Amity Institute of Biotechnology, Amity University, Uttar Pradesh, India
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27
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Lund RJ, Rahkonen N, Malonzo M, Kauko L, Emani MR, Kivinen V, Närvä E, Kemppainen E, Laiho A, Skottman H, Hovatta O, Rasool O, Nykter M, Lähdesmäki H, Lahesmaa R. RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA + and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells. Stem Cell Reports 2018; 8:1442-1454. [PMID: 28494942 PMCID: PMC5425787 DOI: 10.1016/j.stemcr.2017.04.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 04/13/2017] [Accepted: 04/13/2017] [Indexed: 11/17/2022] Open
Abstract
POLR3G is expressed at high levels in human pluripotent stem cells (hPSCs) and is required for maintenance of stem cell state through mechanisms not known in detail. To explore how POLR3G regulates stem cell state, we carried out deep-sequencing analysis of polyA+ and smallRNA transcriptomes present in hPSCs and regulated in POLR3G-dependent manner. Our data reveal that POLR3G regulates a specific subset of the hPSC transcriptome, including multiple transcript types, such as protein-coding genes, long intervening non-coding RNAs, microRNAs and small nucleolar RNAs, and affects RNA splicing. The primary function of POLR3G is in the maintenance rather than repression of transcription. The majority of POLR3G polyA+ transcriptome is regulated during differentiation, and the key pluripotency factors bind to the promoters of at least 30% of the POLR3G-regulated transcripts. Among the direct targets of POLR3G, POLG is potentially important in sustaining stem cell status in a POLR3G-dependent manner.
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Affiliation(s)
- Riikka J Lund
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland.
| | - Nelly Rahkonen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Maia Malonzo
- Department of Computer Science, Aalto University, Espoo 02150, Finland
| | - Leni Kauko
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Maheswara Reddy Emani
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Virpi Kivinen
- Faculty of Medicine and Life Sciences, BioMediTech, University of Tampere, Tampere 33014, Finland
| | - Elisa Närvä
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Esko Kemppainen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Asta Laiho
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Heli Skottman
- Faculty of Medicine and Life Sciences, BioMediTech, University of Tampere, Tampere 33014, Finland
| | - Outi Hovatta
- Department CLINTEC, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm 171 77, Sweden
| | - Omid Rasool
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Matti Nykter
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland; Faculty of Medicine and Life Sciences, BioMediTech, University of Tampere, Tampere 33014, Finland
| | - Harri Lähdesmäki
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland; Department of Computer Science, Aalto University, Espoo 02150, Finland
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku 20520, Finland
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28
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Lee T, Pelletier J. The biology of DHX9 and its potential as a therapeutic target. Oncotarget 2018; 7:42716-42739. [PMID: 27034008 PMCID: PMC5173168 DOI: 10.18632/oncotarget.8446] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/16/2016] [Indexed: 12/25/2022] Open
Abstract
DHX9 is member of the DExD/H-box family of helicases with a “DEIH” sequence at its eponymous DExH-box motif. Initially purified from human and bovine cells and identified as a homologue of the Drosophila Maleless (MLE) protein, it is an NTP-dependent helicase consisting of a conserved helicase core domain, two double-stranded RNA-binding domains at the N-terminus, and a nuclear transport domain and a single-stranded DNA-binding RGG-box at the C-terminus. With an ability to unwind DNA and RNA duplexes, as well as more complex nucleic acid structures, DHX9 appears to play a central role in many cellular processes. Its functions include regulation of DNA replication, transcription, translation, microRNA biogenesis, RNA processing and transport, and maintenance of genomic stability. Because of its central role in gene regulation and RNA metabolism, there are growing implications for DHX9 in human diseases and their treatment. This review will provide an overview of the structure, biochemistry, and biology of DHX9, its role in cancer and other human diseases, and the possibility of targeting DHX9 in chemotherapy.
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Affiliation(s)
- Teresa Lee
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Department of Oncology, McGill University, Montreal, Quebec, Canada.,Department of Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada
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29
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Hong S. RNA Binding Protein as an Emerging Therapeutic Target for Cancer Prevention and Treatment. J Cancer Prev 2017; 22:203-210. [PMID: 29302577 PMCID: PMC5751837 DOI: 10.15430/jcp.2017.22.4.203] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/17/2017] [Accepted: 11/21/2017] [Indexed: 12/13/2022] Open
Abstract
After transcription, RNAs are always associated with RNA binding proteins (RBPs) to perform biological activities. RBPs can interact with target RNAs in sequence- and structure-dependent manner through their unique RNA binding domains. In development and progression of carcinogenesis, RBPs are aberrantly dysregulated in many human cancers with various mechanisms, such as genetic alteration, epigenetic change, noncoding RNA-mediated regulation, and post-translational modifications. Upon deregulation in cancers, RBPs influence every step in the development and progression of cancer, including sustained cell proliferation, evasion of apoptosis, avoiding immune surveillance, inducing angiogenesis, and activating metastasis. To develop therapeutic strategies targeting RBPs, RNA interference-based oligonucleotides or small molecule inhibitors have been screened based on reduced RBP-RNA interaction and changed level of target RNAs. Identification of binding RNAs with high-throughput techniques and integral analysis of multiple datasets will help us develop new therapeutic drugs or prognostic biomarkers for human cancers.
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Affiliation(s)
- Suntaek Hong
- Department of Biochemistry, College of Medicine, Gachon University, Incheon, Korea
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30
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Effects of oxidative and thermal stresses on stress granule formation in human induced pluripotent stem cells. PLoS One 2017; 12:e0182059. [PMID: 28746394 PMCID: PMC5528897 DOI: 10.1371/journal.pone.0182059] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/11/2017] [Indexed: 12/14/2022] Open
Abstract
Stress Granules (SGs) are dynamic ribonucleoprotein aggregates, which have been observed in cells subjected to environmental stresses, such as oxidative stress and heat shock (HS). Although pluripotent stem cells (PSCs) are highly sensitive to oxidative stress, the role of SGs in regulating PSC self-renewal and differentiation has not been fully elucidated. Here we found that sodium arsenite (SA) and HS, but not hydrogen peroxide (H2O2), induce SG formation in human induced (hi) PSCs. Particularly, we found that these granules contain the well-known SG proteins (G3BP, TIAR, eIF4E, eIF4A, eIF3B, eIF4G, and PABP), were found in juxtaposition to processing bodies (PBs), and were disassembled after the removal of the stress. Moreover, we showed that SA and HS, but not H2O2, promote eIF2α phosphorylation in hiPSCs forming SGs. Analysis of pluripotent protein expression showed that HS significantly reduced all tested markers (OCT4, SOX2, NANOG, KLF4, L1TD1, and LIN28A), while SA selectively reduced the expression levels of NANOG and L1TD1. Finally, in addition to LIN28A and L1TD1, we identified DPPA5 (pluripotent protein marker) as a novel component of SGs. Collectively, these results provide new insights into the molecular cues of hiPSCs responses to environmental insults.
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31
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Chen Q, Hu G. Post-transcriptional regulation of the pluripotent state. Curr Opin Genet Dev 2017; 46:15-23. [PMID: 28654825 DOI: 10.1016/j.gde.2017.06.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/17/2017] [Accepted: 06/08/2017] [Indexed: 12/20/2022]
Abstract
Pluripotency describes the developmental capacity to give rise to all cell types in the adult body. A comprehensive understanding of the molecular mechanisms that regulate pluripotency is important for both basic and translational research. While earlier studies mostly focused on signaling pathways, transcriptional regulation, and epigenetic modifications, recent investigations showed that RNA binding proteins, RNA processing machineries, and regulatory RNA molecules also play essential roles. Here, we provide a concise review on the latest findings and developments in post-transcriptional regulation of the pluripotent state.
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Affiliation(s)
- Qing Chen
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, NC, United States.
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, NC, United States.
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32
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Zhai L, Wang C, Chen Y, Zhou S, Li L. Rbm46 regulates mouse embryonic stem cell differentiation by targeting β-Catenin mRNA for degradation. PLoS One 2017; 12:e0172420. [PMID: 28212427 PMCID: PMC5315375 DOI: 10.1371/journal.pone.0172420] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 02/03/2017] [Indexed: 12/01/2022] Open
Abstract
Embryonic stem cells (ESCs) are pluripotent cells and have the capability for differentiation into any of the three embryonic germ layers. The Wnt/β-Catenin pathway has been shown to play an essential role in ESC differentiation regulation. Activation of β-Catenin by post-translational modification has been extensively studied. However, mechanism(s) of post-transcriptional regulation of β-Catenin are not well defined. In this study, we report an RNA recognition motif-containing protein (RNA binding motif protein 46, RBM46) which regulates the degradation of β-Catenin mRNA. Our results show that Rbm46 is distributed primarily in the cytoplasm of mouse ESCs (mESCs) and is elevated during the process of ESC differentiation. In addition, overexpression of Rbm46 results in differentiation of mESCs into trophectoderm, while knock-down of Rbm46 leads to mESC differentiation into endoderm. β-Catenin, a key effector in the Wnt pathway which has been reported to play a significant role in the regulation of ESC differentiation, is post-transcriptionally regulated by Rbm46. Our study reveals Rbm46 plays a novel role in the regulation of ESC differentiation.
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Affiliation(s)
- Lei Zhai
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Peking University Stem Cell Research Center, China National Center for International Research, Peking University Health Science Center, Beijing, China
- * E-mail: (LZ); (LL)
| | - Chenchen Wang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Peking University Stem Cell Research Center, China National Center for International Research, Peking University Health Science Center, Beijing, China
| | - Yuanfan Chen
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Peking University Stem Cell Research Center, China National Center for International Research, Peking University Health Science Center, Beijing, China
| | - Shixin Zhou
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Peking University Stem Cell Research Center, China National Center for International Research, Peking University Health Science Center, Beijing, China
| | - Lingsong Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Peking University Stem Cell Research Center, China National Center for International Research, Peking University Health Science Center, Beijing, China
- SARI Center for Stem Cell and Nanomedicine, Shanghai Advanced Research Institute, University of Chinese Academy of Sciences, Shanghai, China
- * E-mail: (LZ); (LL)
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33
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Cao S, Sun R, Wang W, Meng X, Zhang Y, Zhang N, Yang S. RNA helicase DHX9 may be a therapeutic target in lung cancer and inhibited by enoxacin. Am J Transl Res 2017; 9:674-682. [PMID: 28337295 PMCID: PMC5340702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 01/17/2017] [Indexed: 06/06/2023]
Abstract
RNA helicase DHX9 is a member of human RNA enzymes. Previous studies have reported that DHX9 is highly expressed in various types of malignant tumor. However, its role in the progression of lung cancer remains to be fully clarified. The present study aims to investigate the oncogenic role of DHX9 in serum, tissues and lung cancer cell lines in vitro. We used RNA interference to downregulate DHX9 expression in A549 cells using a small interfering RNA lentiviral vector. Subsequently, enoxacin was used to inhibit cell proliferation, and this effect was detected using MTT. The results showed that DHX9 was overexpressed in the serum and tissues of lung cancer, especially in small cell lung cancer. Though enoxacin suppressed the proliferation of NSCLC cells, the inhibition effect was diminished when DHX9 was knocked down. In conclusion, the present study provided evidence suggesting that DHX9 was overexpressed in lung cancer and may contribute to the growth of lung cancer, and enoxacin may inhibit the proliferation based on DHX9. Thus DHX9 may be used as a diagnostic marker and a potential therapeutic target for the treatment of NSCLC.
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Affiliation(s)
- Shiguang Cao
- Department of Respiratory, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, China
- Department of Nuclear Medicine, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, China
| | - Ruiying Sun
- Department of Respiratory, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, China
| | - Wei Wang
- Department of Respiratory, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, China
| | - Xia Meng
- Department of Respiratory, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, China
| | - Yuping Zhang
- Department of Respiratory, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, China
| | - Na Zhang
- Department of Respiratory, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, China
| | - Shuanying Yang
- Department of Respiratory, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, China
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34
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Cai W, Xiong Chen Z, Rane G, Satendra Singh S, Choo Z, Wang C, Yuan Y, Zea Tan T, Arfuso F, Yap CT, Pongor LS, Yang H, Lee MB, Cher Goh B, Sethi G, Benoukraf T, Tergaonkar V, Prem Kumar A. Wanted DEAD/H or Alive: Helicases Winding Up in Cancers. J Natl Cancer Inst 2017; 109:2957323. [PMID: 28122908 DOI: 10.1093/jnci/djw278] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/08/2016] [Accepted: 10/20/2016] [Indexed: 12/23/2022] Open
Abstract
Cancer is one of the most studied areas of human biology over the past century. Despite having attracted much attention, hype, and investments, the search to find a cure for cancer remains an uphill battle. Recent discoveries that challenged the central dogma of molecular biology not only further increase the complexity but also demonstrate how various types of noncoding RNAs such as microRNA and long noncoding RNA, as well as their related processes such as RNA editing, are important in regulating gene expression. Parallel to this aspect, an increasing number of reports have focused on a family of proteins known as DEAD/H-box helicases involved in RNA metabolism, regulation of long and short noncoding RNAs, and novel roles as "editing helicases" and their association with cancers. This review summarizes recent findings on the roles of RNA helicases in various cancers, which are broadly classified into adult solid tumors, childhood solid tumors, leukemia, and cancer stem cells. The potential small molecule inhibitors of helicases and their therapeutic value are also discussed. In addition, analyzing next-generation sequencing data obtained from public portals and reviewing existing literature, we provide new insights on the potential of DEAD/H-box helicases to act as pharmacological drug targets in cancers.
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Affiliation(s)
- Wanpei Cai
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Zhi Xiong Chen
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Grishma Rane
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Shikha Satendra Singh
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Zhang'e Choo
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Chao Wang
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Yi Yuan
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Tuan Zea Tan
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Frank Arfuso
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Celestial T Yap
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Lorinc S Pongor
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Henry Yang
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Martin B Lee
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Boon Cher Goh
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Gautam Sethi
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Touati Benoukraf
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Vinay Tergaonkar
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
| | - Alan Prem Kumar
- Affiliations of authors: Cancer Science Institute of Singapore, National University of Singapore, Singapore (WC, GR, SSS, CW, YY, TZT, HY, BCG, TB, APK); Departments of Pharmacology (WC, GR, SSS, CW, BCG, GS, APK), Physiology (ZXC, ZC, CTY), and Biochemistry (VT), Yong Loo Lin School of Medicine, National University of Singapore, Singapore; KK Women's and Children's Hospital, Singapore (ZXC); Stem Cell and Cancer Biology Laboratory (FA), School of Biomedical Sciences (GS, APK), Curtin Health Innovation Research Institute, Curtin Medical School (APK), Curtin University, Perth, WA, Australia; National University Cancer Institute, National University Health System, Singapore (CTY, BCG, APK); 2 Department of Pediatrics, Semmelweis University, Budapest, Hungary (LSP); MTA TTK Lendület Cancer Biomarker Research Group, Research Centre for Natural Sciences, Budapest, Hungary (LSP); Department of Renal Medicine (MBL) and Department of Haematology-Oncology (BCG), National University Health System, Singapore; Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore (VT); Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia (VT); Department of Biological Sciences, University of North Texas, Denton, TX (APK)
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35
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Altenberger C, Heller G, Ziegler B, Tomasich E, Marhold M, Topakian T, Müllauer L, Heffeter P, Lang G, End-Pfützenreuter A, Döme B, Arns BM, Klepetko W, Zielinski CC, Zöchbauer-Müller S. SPAG6 and L1TD1 are transcriptionally regulated by DNA methylation in non-small cell lung cancers. Mol Cancer 2017; 16:1. [PMID: 28093071 PMCID: PMC5240214 DOI: 10.1186/s12943-016-0568-5] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/07/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND DNA methylation regulates together with other epigenetic mechanisms the transcriptional activity of genes and is involved in the pathogenesis of malignant diseases including lung cancer. In non-small cell lung cancer (NSCLC) various tumor suppressor genes are already known to be tumor-specifically methylated. However, from the vast majority of a large number of genes which were identified to be tumor-specifically methylated, tumor-specific methylation was unknown so far. Thus, the major aim of this study was to investigate in detail the mechanism(s) responsible for transcriptional regulation of the genes SPAG6 and L1TD1 in NSCLCs. METHODS We analysed publically available RNA-sequencing data and performed gene expression analyses by RT-PCR. DNA methylation analyses were done by methylation-sensitive high-resolution melt analyses and bisulfite genomic sequencing. We additionally investigated protein expression using immunohistochemistry. Cell culture experiments included tumor cell growth, proliferation, viability as well as colony formation assays. Moreover, we performed xenograft experiments using immunodeficient mice. RESULTS We observed frequent downregulation of SPAG6 and L1TD1 mRNA expression in primary tumor (TU) samples compared to corresponding non-malignant lung tissue (NL) samples of NSCLC patients. We furthermore observed re-expression of both genes after treatment with epigenetically active drugs in most NSCLC cell lines with downregulated SPAG6 and L1TD1 mRNA expression. Frequent tumor-specific DNA methylation of SPAG6 and L1TD1 was detected when we analysed TU and corresponding NL samples of NSCLC patients. ROC curve analyses demonstrated that methylation of both genes is able to distinguish between TU and NL samples of these patients. Immunohistochemistry revealed a close association between SPAG6/L1TD1 methylation and downregulated protein expression of these genes. Moreover, by performing functional assays we observed reduced cell growth, proliferation and viability of pCMV6-L1TD1 transfected NSCLC cells. In addition, reduced volumes of tumors derived from pCMV6-L1TD1 compared to pCMV6-ENTRY transfected NCI-H1975 cells were seen in a xenograft tumor model. CONCLUSIONS Overall, our results demonstrate that SPAG6 and L1TD1 are tumor-specifically methylated in NSCLCs and that DNA methylation is involved in the transcriptional regulation of these genes. Moreover, in vitro as well as in vivo experiments revealed tumor-cell growth suppressing properties of L1TD1 in NSCLC cells.
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MESH Headings
- Animals
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/pathology
- Cell Line, Tumor
- Cell Proliferation
- Cell Survival/genetics
- DNA Methylation
- Databases, Genetic
- Disease Models, Animal
- Gene Expression Regulation, Neoplastic
- Gene Silencing
- Heterografts
- High-Throughput Nucleotide Sequencing
- Humans
- Immunohistochemistry
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Mice
- Microtubule Proteins/genetics
- Microtubule Proteins/metabolism
- Polymorphism, Single Nucleotide
- Proteins/genetics
- Proteins/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Deletion
- Transcription, Genetic
- Tumor Burden
- Tumor Stem Cell Assay
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Affiliation(s)
- Corinna Altenberger
- Department of Medicine I, Clinical Division of Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Gerwin Heller
- Department of Medicine I, Clinical Division of Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Barbara Ziegler
- Department of Medicine I, Clinical Division of Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Erwin Tomasich
- Department of Medicine I, Clinical Division of Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Maximilian Marhold
- Department of Medicine I, Clinical Division of Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Thais Topakian
- Department of Medicine I, Clinical Division of Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Leonhard Müllauer
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Petra Heffeter
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Vienna, Austria
| | - György Lang
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Division of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary
| | - Adelheid End-Pfützenreuter
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Division of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Balazs Döme
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Division of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
- Department of Thoracic Oncology and Tumor Biology, National Koranyi Institute of Pulmonology, Budapest, Hungary
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary
| | - Britt-Madeleine Arns
- Department of Respiratory and Critical Care Medicine and Ludwig Boltzmann Institute for COPD, Otto-Wagner Hospital, Vienna, Austria
| | - Walter Klepetko
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Division of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Christoph C Zielinski
- Department of Medicine I, Clinical Division of Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Sabine Zöchbauer-Müller
- Department of Medicine I, Clinical Division of Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.
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36
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He C, Sidoli S, Warneford-Thomson R, Tatomer DC, Wilusz JE, Garcia BA, Bonasio R. High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells. Mol Cell 2016; 64:416-430. [PMID: 27768875 PMCID: PMC5222606 DOI: 10.1016/j.molcel.2016.09.034] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/30/2016] [Accepted: 09/23/2016] [Indexed: 12/21/2022]
Abstract
Interactions between noncoding RNAs and chromatin proteins play important roles in gene regulation, but the molecular details of most of these interactions are unknown. Using protein-RNA photocrosslinking and mass spectrometry on embryonic stem cell nuclei, we identified and mapped, at peptide resolution, the RNA-binding regions in ∼800 known and previously unknown RNA-binding proteins, many of which are transcriptional regulators and chromatin modifiers. In addition to known RNA-binding motifs, we detected several protein domains previously unknown to function in RNA recognition, as well as non-annotated and/or disordered regions, suggesting that many functional protein-RNA contacts remain unexplored. We identified RNA-binding regions in several chromatin regulators, including TET2, and validated their ability to bind RNA. Thus, proteomic identification of RNA-binding regions (RBR-ID) is a powerful tool to map protein-RNA interactions and will allow rational design of mutants to dissect their function at a mechanistic level.
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Affiliation(s)
- Chongsheng He
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simone Sidoli
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert Warneford-Thomson
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Deirdre C Tatomer
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Roberto Bonasio
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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37
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Abstract
Retrotransposons have generated about 40 % of the human genome. This review examines the strategies the cell has evolved to coexist with these genomic "parasites", focussing on the non-long terminal repeat retrotransposons of humans and mice. Some of the restriction factors for retrotransposition, including the APOBECs, MOV10, RNASEL, SAMHD1, TREX1, and ZAP, also limit replication of retroviruses, including HIV, and are part of the intrinsic immune system of the cell. Many of these proteins act in the cytoplasm to degrade retroelement RNA or inhibit its translation. Some factors act in the nucleus and involve DNA repair enzymes or epigenetic processes of DNA methylation and histone modification. RISC and piRNA pathway proteins protect the germline. Retrotransposon control is relaxed in some cell types, such as neurons in the brain, stem cells, and in certain types of disease and cancer, with implications for human health and disease. This review also considers potential pitfalls in interpreting retrotransposon-related data, as well as issues to consider for future research.
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Affiliation(s)
- John L. Goodier
- McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA 212051
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38
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Rangasamy D, Lenka N, Ohms S, Dahlstrom JE, Blackburn AC, Board PG. Activation of LINE-1 Retrotransposon Increases the Risk of Epithelial-Mesenchymal Transition and Metastasis in Epithelial Cancer. Curr Mol Med 2016; 15:588-97. [PMID: 26321759 PMCID: PMC5384359 DOI: 10.2174/1566524015666150831130827] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 07/31/2015] [Accepted: 08/27/2015] [Indexed: 12/12/2022]
Abstract
Epithelial cancers comprise 80-90% of human cancers. During the process of cancer progression, cells lose their epithelial characteristics and acquire stem-like mesenchymal features that are resistant to chemotherapy. This process, termed the epithelial-mesenchymal transition (EMT), plays a critical role in the development of metastases. Because of the unique migratory and invasive properties of cells undergoing the EMT, therapeutic control of the EMT offers great hope and new opportunities for treating cancer. In recent years, a plethora of genes and noncoding RNAs, including miRNAs, have been linked to the EMT and the acquisition of stem cell-like properties. Despite these advances, questions remain unanswered about the molecular processes underlying such a cellular transition. In this article, we discuss how expression of the normally repressed LINE-1 (or L1) retrotransposons activates the process of EMT and the development of metastases. L1 is rarely expressed in differentiated stem cells or adult somatic tissues. However, its expression is widespread in almost all epithelial cancers and in stem cells in their undifferentiated state, suggesting a link between L1 activity and the proliferative and metastatic behaviour of cancer cells. We present an overview of L1 activity in cancer cells including how genes involved in proliferation, invasive and metastasis are modulated by L1 expression. The role of L1 in the differential expression of the let-7 family of miRNAs (that regulate genes involved in the EMT and metastasis) is also discussed. We also summarize recent novel insights into the role of the L1-encoded reverse transcriptase enzyme in epithelial cell plasticity that suggest it might be a potential therapeutic target that could reverse the EMT and the metastasis-associated stem cell-like properties of cancer cells.
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Affiliation(s)
- D Rangasamy
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia.
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39
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Shapiro JA. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process. BIOLOGY 2016; 5:E27. [PMID: 27338490 PMCID: PMC4929541 DOI: 10.3390/biology5020027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/20/2016] [Accepted: 06/02/2016] [Indexed: 01/15/2023]
Abstract
The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read-Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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40
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Expression of Genes Related to Germ Cell Lineage and Pluripotency in Single Cells and Colonies of Human Adult Germ Stem Cells. Stem Cells Int 2015; 2016:8582526. [PMID: 26649052 PMCID: PMC4655073 DOI: 10.1155/2016/8582526] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/09/2015] [Accepted: 02/11/2015] [Indexed: 01/06/2023] Open
Abstract
The aim of this study was to elucidate the molecular status of single human adult germ stem cells (haGSCs) and haGSC colonies, which spontaneously developed from the CD49f MACS and matrix- (collagen−/laminin+ binding-) selected fraction of enriched spermatogonia. Single-cell transcriptional profiling by Fluidigm BioMark system of a long-term cultured haGSCs cluster in comparison to human embryonic stem cells (hESCs) and human fibroblasts (hFibs) revealed that haGSCs showed a characteristic germ- and pluripotency-associated gene expression profile with some similarities to hESCs and with a significant distinction from somatic hFibs. Genome-wide comparisons with microarray analysis confirmed that different haGSC colonies exhibited gene expression heterogeneity with more or less pluripotency. The results of this study confirm that haGSCs are adult stem cells with a specific molecular gene expression profile in vitro, related but not identical to true pluripotent stem cells. Under ES-cell conditions haGSC colonies could be selected and maintained in a partial pluripotent state at the molecular level, which may be related to their cell plasticity and potential to differentiate into cells of all germ layers.
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41
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Witte S, Bradley A, Enright AJ, Muljo SA. High-density P300 enhancers control cell state transitions. BMC Genomics 2015; 16:903. [PMID: 26546038 PMCID: PMC4636788 DOI: 10.1186/s12864-015-1905-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 09/08/2015] [Indexed: 12/11/2022] Open
Abstract
Background Transcriptional enhancers are frequently bound by a set of transcription factors that collaborate to activate lineage-specific gene expression. Recently, it was appreciated that a subset of enhancers comprise extended clusters dubbed stretch- or super-enhancers (SEs). These SEs are located near key cell identity genes, and enriched for non-coding genetic variations associated with disease. Previously, SEs have been defined as having the highest density of Med1, Brd4 or H3K27ac by ChIP-seq. The histone acetyltransferase P300 has been used as a marker of enhancers, but little is known about its binding to SEs. Results We establish that P300 marks a similar SE repertoire in embryonic stem cells as previously reported using Med1 and H3K27ac. We also exemplify a role for SEs in mouse T helper cell fate decision. Similarly, upon activation of macrophages by bacterial endotoxin, we found that many SE-associated genes encode inflammatory proteins that are strongly up-regulated. These SEs arise from small, low-density enhancers in unstimulated macrophages. We also identified expression quantitative trait loci (eQTL) in human monocytes that lie within such SEs. In macrophages and Th17 cells, inflammatory SEs can be perturbed either genetically or pharmacologically thus revealing new avenues to target inflammation. Conclusions Our findings support the notion that P300-marked SEs can help identify key nodes of transcriptional control during cell fate decisions. The SE landscape changes drastically during cell differentiation and cell activation. As these processes are crucial in immune responses, SEs may be useful in revealing novel targets for treating inflammatory diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1905-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Steven Witte
- Integrative Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. .,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | - Allan Bradley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | - Anton J Enright
- EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | - Stefan A Muljo
- Integrative Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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Transposable elements at the center of the crossroads between embryogenesis, embryonic stem cells, reprogramming, and long non-coding RNAs. Sci Bull (Beijing) 2015; 60:1722-1733. [PMID: 26543668 PMCID: PMC4624819 DOI: 10.1007/s11434-015-0905-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 09/18/2015] [Indexed: 12/19/2022]
Abstract
Transposable elements (TEs) are mobile genomic sequences of DNA capable of autonomous and non-autonomous duplication. TEs have been highly successful, and nearly half of the human genome now consists of various families of TEs. Originally thought to be non-functional, these elements have been co-opted by animal genomes to perform a variety of physiological functions ranging from TE-derived proteins acting directly in normal biological functions, to innovations in transcription factor logic and influence on epigenetic control of gene expression. During embryonic development, when the genome is epigenetically reprogrammed and DNA-demethylated, TEs are released from repression and show embryonic stage-specific expression, and in human and mouse embryos, intact TE-derived endogenous viral particles can even be detected. A similar process occurs during the reprogramming of somatic cells to pluripotent cells: When the somatic DNA is demethylated, TEs are released from repression. In embryonic stem cells (ESCs), where DNA is hypomethylated, an elaborate system of epigenetic control is employed to suppress TEs, a system that often overlaps with normal epigenetic control of ESC gene expression. Finally, many long non-coding RNAs (lncRNAs) involved in normal ESC function and those assisting or impairing reprogramming contain multiple TEs in their RNA. These TEs may act as regulatory units to recruit RNA-binding proteins and epigenetic modifiers. This review covers how TEs are interlinked with the epigenetic machinery and lncRNAs, and how these links influence each other to modulate aspects of ESCs, embryogenesis, and somatic cell reprogramming.
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43
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MeSiC: A Model-Based Method for Estimating 5 mC Levels at Single-CpG Resolution from MeDIP-seq. Sci Rep 2015; 5:14699. [PMID: 26424089 PMCID: PMC4589794 DOI: 10.1038/srep14699] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 09/07/2015] [Indexed: 01/03/2023] Open
Abstract
As the fifth base in mammalian genome, 5-methylcytosine (5 mC) is essential for many biological processes including normal development and disease. Methylated DNA immunoprecipitation sequencing (MeDIP-seq), which uses anti-5 mC antibodies to enrich for methylated fraction of the genome, is widely used to investigate methylome at a resolution of 100–500 bp. Considering the CpG density-dependent bias and limited resolution of MeDIP-seq, we developed a Random Forest Regression (RFR) model method, MeSiC, to estimate DNA methylation levels at single-base resolution. MeSiC integrated MeDIP-seq signals of CpG sites and their surrounding neighbors as well as genomic features to construct genomic element-dependent RFR models. In the H1 cell line, a high correlation was observed between MeSiC predictions and actual 5 mC levels. Meanwhile, MeSiC enabled to calibrate CpG density-dependent bias of MeDIP-seq signals. Importantly, we found that MeSiC models constructed in the H1 cell line could be used to accurately predict DNA methylation levels for other cell types. Comparisons with methylCRF and MEDIPS showed that MeSiC achieved comparable and even better performance. These demonstrate that MeSiC can provide accurate estimations of 5 mC levels at single-CpG resolution using MeDIP-seq data alone.
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Santos MCT, Silva PBG, Rodini CO, Furukawa G, Marco Antonio DS, Zanotto-Filho A, Moreira JCF, Okamoto OK. Embryonic Stem Cell-Related Protein L1TD1 Is Required for Cell Viability, Neurosphere Formation, and Chemoresistance in Medulloblastoma. Stem Cells Dev 2015; 24:2700-8. [PMID: 26159230 DOI: 10.1089/scd.2015.0052] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Misexpression of stem cell-related genes may occur in some cancer cells, influencing patient's prognosis. This is the case of medulloblastoma, a common and clinically challenging malignant tumor of the central nervous system, where expression of the pluripotency factor, OCT4, is correlated with poor survival. A downstream target of OCT4, L1TD1 (LINE-1 type transposase domain-containing protein 1 family member), encodes a novel embryonic stem cell (ESC)-related protein involved in pluripotency and self-renewal of ESCs. L1TD1 is still poorly characterized and its expression pattern and function in cancer cells are virtually unknown. Although normally restricted to non-neoplastic undifferentiated cells and germ cells, we found that high L1TD1 expression also occurs in medulloblastoma cells, reaching levels similar to those found in ESCs, and is correlated with poor prognosis. Conversely to what is reported during normal cell differentiation, when differentiated cells remain healthy, despite L1TD1 downregulation, depletion of L1TD1 protein levels by targeted gene silencing significantly reduced medulloblastoma cell viability, inhibiting cell proliferation and inducing apoptosis. More strikingly, L1TD1 depletion downregulated expression of the neural stem cell markers, CD133 and Nestin, inhibited neurosphere generation capability, and sensitized medulloblastoma cells to temozolomide and cisplatin, two chemotherapeutic agents of clinical relevance in medulloblastoma treatment. Our findings provide insights about the contribution of pluripotency-related genes to a more aggressive tumor phenotype through their involvement in the acquisition of stem-like properties by cancer cells and point out L1TD1 as a potential therapeutic target in malignant brain tumors.
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Affiliation(s)
- Márcia Cristina Teixeira Santos
- 1 Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
| | - Patrícia Benites Gonçalves Silva
- 1 Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
| | - Carolina Oliveira Rodini
- 1 Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
| | - Gabriela Furukawa
- 1 Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
| | - David Santos Marco Antonio
- 1 Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
| | - Alfeu Zanotto-Filho
- 2 Department of Biochemistry, Oxidative Stress Research Center, Federal University of Rio Grande do Sul , Porto Alegre, Brazil
| | - José C F Moreira
- 2 Department of Biochemistry, Oxidative Stress Research Center, Federal University of Rio Grande do Sul , Porto Alegre, Brazil
| | - Oswaldo Keith Okamoto
- 1 Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo , São Paulo, Brazil
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Robbez-Masson L, Rowe HM. Retrotransposons shape species-specific embryonic stem cell gene expression. Retrovirology 2015; 12:45. [PMID: 26021318 PMCID: PMC4448215 DOI: 10.1186/s12977-015-0173-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/07/2015] [Indexed: 01/20/2023] Open
Abstract
Over half of our genome is composed of retrotransposons, which are mobile elements that can readily amplify their copy number by replicating through an RNA intermediate. Most of these elements are no longer mobile but still contain regulatory sequences that can serve as promoters, enhancers or repressors for cellular genes. Despite dominating our genetic content, little is known about the precise functions of retrotransposons, which include both endogenous retroviruses (ERVs) and non-LTR elements like long interspersed nuclear element 1 (LINE-1). However, a few recent cutting-edge publications have illustrated how retrotransposons shape species-specific stem cell gene expression by two opposing mechanisms, involving their recruitment of stem cell-enriched transcription factors (TFs): firstly, they can activate expression of genes linked to naïve pluripotency, and secondly, they can induce repression of proximal genes. The paradox that different retrotransposons are active or silent in embryonic stem cells (ESCs) can be explained by differences between retrotransposon families, between individual copies within the same family, and between subpopulations of ESCs. Since they have coevolved with their host genomes, some of them have been co-opted to perform species-specific beneficial functions, while others have been implicated in genetic disease. In this review, we will discuss retrotransposon functions in ESCs, focusing on recent mechanistic advances of how HERV-H has been adopted to preserve human naïve pluripotency and how particular LINE-1, SVA and ERV family members recruit species-specific transcriptional repressors. This review highlights the fine balance between activation and repression of retrotransposons that exists to harness their ability to drive evolution, while minimizing the risk they pose to genome integrity.
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Affiliation(s)
- Luisa Robbez-Masson
- Division of Infection and Immunity, Medical Research Council Centre for Medical Molecular Virology, University College London, 90 Gower Street, London, WC1E 6BT, UK.
| | - Helen M Rowe
- Division of Infection and Immunity, Medical Research Council Centre for Medical Molecular Virology, University College London, 90 Gower Street, London, WC1E 6BT, UK.
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Zhao B, Zhang WD, Duan YL, Lu YQ, Cun YX, Li CH, Guo K, Nie WH, Li L, Zhang R, Zheng P. Filia Is an ESC-Specific Regulator of DNA Damage Response and Safeguards Genomic Stability. Cell Stem Cell 2015; 16:684-98. [PMID: 25936915 DOI: 10.1016/j.stem.2015.03.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 02/16/2015] [Accepted: 03/22/2015] [Indexed: 12/20/2022]
Abstract
Pluripotent stem cells (PSCs) hold great promise in cell-based therapy, but the genomic instability seen in culture hampers their full application. A greater understanding of the factors that regulate genomic stability in PSCs could help address this issue. Here we describe the identification of Filia as a specific regulator of genomic stability in mouse embryonic stem cells (ESCs). Filia expression is induced by genotoxic stress. Filia promotes centrosome integrity and regulates the DNA damage response (DDR) through multiple pathways, including DDR signaling, cell-cycle checkpoints and damage repair, ESC differentiation, and apoptosis. Filia depletion causes ESC genomic instability, induces resistance to apoptosis, and promotes malignant transformation. As part of its role in DDR, Filia interacts with PARP1 and stimulates its enzymatic activity. Filia also constitutively resides on centrosomes and translocates to DNA damage sites and mitochondria, consistent with its multifaceted roles in regulating centrosome integrity, damage repair, and apoptosis.
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Affiliation(s)
- Bo Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wei-Dao Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Ying-Liang Duan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yong-Qing Lu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yi-Xian Cun
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Chao-Hui Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Kun Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Wen-Hui Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Lei Li
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rugang Zhang
- Gene Expression and Regulation Program, The Wistar Institute Cancer Center, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
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Abstract
The transcription factor OCT4 is an established diagnostic marker for central nervous system (CNS) germinoma. However, no data are available to date concerning the expression of its downstream target undifferentiated embryonic cell transcription factor 1 (UTF1) in CNS germ cell tumours. We examined 21 CNS germinomas and two mixed CNS germ cell tumours for UTF1 and the post-transcriptional regulator LIN28 immunohistochemical expression. We compared the profile to established diagnostic germinoma markers and to the expression in six testicular and four metastatic germ cell tumours as well as 150 CNS tumours of various backgrounds. We found UTF1 expression in 23 of 23 and LIN28 in 20 of 23 CNS germ cell tumours. The established germinoma markers cKIT (23/23), OCT4 (21/23) and placental alkaline phosphatase (PLAP) (19/21) were also frequently expressed in our cohort. In terms of signal intensity and frequency, UTF1 showed similar results as cKIT but staining was superior to OCT4, PLAP and LIN28. OCT4 was absent in all CNS metastases and haemangioblastomas, while UTF1 was weakly observed in two metastases.With a sensitivity of 100% and a specificity of 97% in the detection of CNS germinomas, UTF1 serves as a new reliable alternative in the diagnostic setting of CNS germ cell tumours.
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Unique gene expression profile of the proliferating Xenopus tadpole tail blastema cells deciphered by RNA-sequencing analysis. PLoS One 2015; 10:e0111655. [PMID: 25775398 PMCID: PMC4361676 DOI: 10.1371/journal.pone.0111655] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 10/05/2014] [Indexed: 12/19/2022] Open
Abstract
Organ regenerative ability depends on the animal species and the developmental stage. The molecular bases for variable organ regenerative ability, however, remain unknown. Previous studies have identified genes preferentially expressed in the blastema tissues in various animals, but transcriptome analysis of the isolated proliferating blastema cells has not yet been reported. In the present study, we used RNA-sequencing analysis to analyze the gene expression profile of isolated proliferating blastema cells of regenerating Xenopus laevis tadpole tails. We used flow cytometry to isolate proliferating cells, and non-proliferating blastema cells, from regenerating tadpole tails as well as proliferating tail bud cells from tail bud embryos, the latter two of which were used as control cells, based on their DNA content. Among the 28 candidate genes identified by RNA-sequencing analysis, quantitative reverse transcription-polymerase chain reaction identified 10 genes whose expression was enriched in regenerating tadpole tails compared with non-regenerating tadpole tails or tails from the tail bud embryos. Among them, whole mount in situ hybridization revealed that chromosome segregation 1-like and interleukin 11 were expressed in the broad area of the tail blastema, while brevican, lysyl oxidase, and keratin 18 were mainly expressed in the notochord bud in regenerating tails. We further combined whole mount in situ hybridization with immunohistochemistry for the incorporated 5-bromo-2-deoxyuridine to confirm that keratin 18 and interleukin 11 were expressed in the proliferating tail blastema cells. Based on the proposed functions of their homologs in other animal species, these genes might have roles in the extracellular matrix formation in the notochord bud (brevican and lysyl oxidase), cell proliferation (chromosome segregation 1-like and keratin 18), and in the maintenance of the differentiation ability of proliferating blastema cells (interleukin 11) in regenerating tadpole tails.
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The L1TD1 protein interactome reveals the importance of post-transcriptional regulation in human pluripotency. Stem Cell Reports 2015; 4:519-28. [PMID: 25702638 PMCID: PMC4376047 DOI: 10.1016/j.stemcr.2015.01.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 01/16/2015] [Accepted: 01/16/2015] [Indexed: 11/24/2022] Open
Abstract
The RNA-binding protein L1TD1 is one of the most specific and abundant proteins in pluripotent stem cells and is essential for the maintenance of pluripotency in human cells. Here, we identify the protein interaction network of L1TD1 in human embryonic stem cells (hESCs) and provide insights into the interactome network constructed in human pluripotent cells. Our data reveal that L1TD1 has an important role in RNA splicing, translation, protein traffic, and degradation. L1TD1 interacts with multiple stem-cell-specific proteins, many of which are still uncharacterized in the context of development. Further, we show that L1TD1 is a part of the pluripotency interactome network of OCT4, SOX2, and NANOG, bridging nuclear and cytoplasmic regulation and highlighting the importance of RNA biology in pluripotency. A protein interactome is constructed in human embryonic stem cells L1TD1 interacts with U2af1 and Srsf3, which are vital for somatic cell reprogramming L1TD1 is involved in the high proteasome activity of pluripotent cells L1TD1 connects uncharacterized factors to the OCT4, SOX2, and NANOG network
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Moniot B, Ujjan S, Champagne J, Hirai H, Aritake K, Nagata K, Dubois E, Nidelet S, Nakamura M, Urade Y, Poulat F, Boizet-Bonhoure B. Prostaglandin D2 acts through the Dp2 receptor to influence male germ cell differentiation in the foetal mouse testis. Development 2014; 141:3561-71. [DOI: 10.1242/dev.103408] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Through intercellular signalling, the somatic compartment of the foetal testis is able to program primordial germ cells to undergo spermatogenesis. Fibroblast growth factor 9 and several members of the transforming growth factor β superfamily are involved in this process in the foetal testis, counteracting the induction of meiosis by retinoic acid and activating germinal mitotic arrest. Here, using in vitro and in vivo approaches, we show that prostaglandin D2 (PGD2), which is produced through both L-Pgds and H-Pgds enzymatic activities in the somatic and germ cell compartments of the foetal testis, plays a role in mitotic arrest in male germ cells by activating the expression and nuclear localization of the CDK inhibitor p21Cip1 and by repressing pluripotency markers. We show that PGD2 acts through its Dp2 receptor, at least in part through direct effects in germ cells, and contributes to the proper differentiation of male germ cells through the upregulation of the master gene Nanos2. Our data identify PGD2 signalling as an early pathway that acts in both paracrine and autocrine manners, and contributes to the differentiation of germ cells in the foetal testis.
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Affiliation(s)
- Brigitte Moniot
- Genetic and Development department, Institute of Human Genetics, CNRS UPR1142, Montpellier 34094, Cedex 05, France
| | - Safdar Ujjan
- Genetic and Development department, Institute of Human Genetics, CNRS UPR1142, Montpellier 34094, Cedex 05, France
| | - Julien Champagne
- Genetic and Development department, Institute of Human Genetics, CNRS UPR1142, Montpellier 34094, Cedex 05, France
| | - Hiroyuki Hirai
- Department of Advanced Technology and Development, BML, Matoba, Kawagoe, Saitama 350-1101, Japan
| | - Kosuke Aritake
- Department of Molecular Behavioral Biology, Osaka Bioscience Institute, Osaka 565-0874, Japan
| | - Kinya Nagata
- Department of Advanced Technology and Development, BML, Matoba, Kawagoe, Saitama 350-1101, Japan
| | - Emeric Dubois
- Plateforme MGX, Functional Genomic Institute, CNRS UMR 5203 – INSERM U 661, Montpellier 34094, Cedex 05, France
| | - Sabine Nidelet
- Plateforme MGX, Functional Genomic Institute, CNRS UMR 5203 – INSERM U 661, Montpellier 34094, Cedex 05, France
| | - Masataka Nakamura
- Human Gene Sciences Center, Tokyo Medical and Dental University, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yoshihiro Urade
- Department of Molecular Behavioral Biology, Osaka Bioscience Institute, Osaka 565-0874, Japan
| | - Francis Poulat
- Genetic and Development department, Institute of Human Genetics, CNRS UPR1142, Montpellier 34094, Cedex 05, France
| | - Brigitte Boizet-Bonhoure
- Genetic and Development department, Institute of Human Genetics, CNRS UPR1142, Montpellier 34094, Cedex 05, France
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