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Saatci O, Alam R, Huynh-Dam KT, Isik A, Uner M, Belder N, Ersan PG, Tokat UM, Ulukan B, Cetin M, Calisir K, Gedik ME, Bal H, Sener Sahin O, Riazalhosseini Y, Thieffry D, Gautheret D, Ogretmen B, Aksoy S, Uner A, Akyol A, Sahin O. Targeting LINC00152 activates cAMP/Ca 2+/ferroptosis axis and overcomes tamoxifen resistance in ER+ breast cancer. Cell Death Dis 2024; 15:418. [PMID: 38879508 PMCID: PMC11180193 DOI: 10.1038/s41419-024-06814-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/19/2024]
Abstract
Tamoxifen has been the mainstay therapy to treat early, locally advanced, and metastatic estrogen receptor-positive (ER + ) breast cancer, constituting around 75% of all cases. However, the emergence of resistance is common, necessitating the identification of novel therapeutic targets. Here, we demonstrated that long-noncoding RNA LINC00152 confers tamoxifen resistance by blocking tamoxifen-induced ferroptosis, an iron-mediated cell death. Mechanistically, inhibiting LINC00152 reduces the mRNA stability of phosphodiesterase 4D (PDE4D), leading to activation of the cAMP/PKA/CREB axis and increased expression of the TRPC1 Ca2+ channel. This causes cytosolic Ca2+ overload and generation of reactive oxygen species (ROS) that is, on the one hand, accompanied by downregulation of FTH1, a member of the iron sequestration unit, thus increasing intracellular Fe2+ levels; and on the other hand, inhibition of the peroxidase activity upon reduced GPX4 and xCT levels, in part by cAMP/CREB. These ultimately restore tamoxifen-dependent lipid peroxidation and ferroptotic cell death which are reversed upon chelating Ca2+ or overexpressing GPX4 or xCT. Overexpressing PDE4D reverses LINC00152 inhibition-mediated tamoxifen sensitization by de-activating the cAMP/Ca2+/ferroptosis axis. Importantly, high LINC00152 expression is significantly correlated with high PDE4D/low ferroptosis and worse survival in multiple cohorts of tamoxifen- or tamoxifen-containing endocrine therapy-treated ER+ breast cancer patients. Overall, we identified LINC00152 inhibition as a novel mechanism of tamoxifen sensitization via restoring tamoxifen-dependent ferroptosis upon destabilizing PDE4D, increasing cAMP and Ca2+ levels, thus leading to ROS generation and lipid peroxidation. Our findings reveal LINC00152 and its effectors as actionable therapeutic targets to improve clinical outcome in refractory ER+ breast cancer.
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Affiliation(s)
- Ozge Saatci
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Rashedul Alam
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Kim-Tuyen Huynh-Dam
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Aynur Isik
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, Turkey
| | - Meral Uner
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, Turkey
| | - Nevin Belder
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, 06800, Turkey
| | - Pelin Gulizar Ersan
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, 06800, Turkey
| | - Unal Metin Tokat
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, 06800, Turkey
| | - Burge Ulukan
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Metin Cetin
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Kubra Calisir
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Mustafa Emre Gedik
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Hilal Bal
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, 06800, Turkey
| | - Ozlem Sener Sahin
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Yasser Riazalhosseini
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Quebec, Canada
| | - Denis Thieffry
- Département de biologie de l'Ecole normale supérieure, PSL Université, 75005, Paris, France
- Bioinformatics and Computational Systems Biology of Cancer, U900 Institut Curie - INSERM - Mines ParisTech, PSL Université, 75005, Paris, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91190, Gif-sur-Yvette, France
| | - Besim Ogretmen
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Sercan Aksoy
- Department of Medical Oncology, Hacettepe University Cancer Institute, 06100, Ankara, Turkey
| | - Aysegul Uner
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, Turkey
| | - Aytekin Akyol
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, Turkey
| | - Ozgur Sahin
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA.
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA.
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Kaller M, Forné I, Imhof A, Hermeking H. LINC01021 Attenuates Expression and Affects Alternative Splicing of a Subset of p53-Regulated Genes. Cancers (Basel) 2024; 16:1639. [PMID: 38730591 PMCID: PMC11083319 DOI: 10.3390/cancers16091639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/18/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Loss of the p53-inducible LINC01021 in p53-proficient CRC cell lines results in increased sensitivity to DNA-damaging chemotherapeutics. Here, we comprehensively analyze how LINC01021 affects the p53-induced transcriptional program. METHODS Using a CRISPR/Cas9-approach, we deleted the p53 binding site in the LINC01021 promoter of SW480 colorectal cancer cells and subjected them to RNA-Seq analysis after the activation of ectopic p53. RNA affinity purification followed by mass spectrometry was used to identify proteins associated with LINC01021. RESULTS Loss of the p53-inducibility of LINC01021 resulted in an ~1.8-fold increase in the number of significantly regulated mRNAs compared to LINC01021 wild-type cells after ectopic activation of p53. A subset of direct p53 target genes, such as NOXA and FAS, displayed significantly stronger induction when the p53-inducibility of LINC01021 was abrogated. Loss of the p53-inducibility of LINC01021 resulted in alternative splicing of a small number of mRNAs, such as ARHGAP12, HSF2, and LYN. Several RNA binding proteins involved in pre-mRNA splicing were identified as interaction partners of LINC01021 by mass spectrometry. CONCLUSIONS Our results suggest that LINC01021 may restrict the extent and strength of p53-mediated transcriptional changes via context-dependent regulation of the expression and splicing of a subset of p53-regulated genes.
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Affiliation(s)
- Markus Kaller
- Experimental and Molecular Pathology, Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Thalkirchner Strasse 36, D-80337 Munich, Germany
| | - Ignasi Forné
- BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, D-82152 Planegg-Martinsried, Germany
| | - Axel Imhof
- BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, D-82152 Planegg-Martinsried, Germany
| | - Heiko Hermeking
- Experimental and Molecular Pathology, Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Thalkirchner Strasse 36, D-80337 Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, D-69120 Heidelberg, Germany
- German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
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3
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Coan M, Haefliger S, Ounzain S, Johnson R. Targeting and engineering long non-coding RNAs for cancer therapy. Nat Rev Genet 2024:10.1038/s41576-024-00693-2. [PMID: 38424237 DOI: 10.1038/s41576-024-00693-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 03/02/2024]
Abstract
RNA therapeutics (RNATx) aim to treat diseases, including cancer, by targeting or employing RNA molecules for therapeutic purposes. Amongst the most promising targets are long non-coding RNAs (lncRNAs), which regulate oncogenic molecular networks in a cell type-restricted manner. lncRNAs are distinct from protein-coding genes in important ways that increase their therapeutic potential yet also present hurdles to conventional clinical development. Advances in genome editing, oligonucleotide chemistry, multi-omics and RNA engineering are paving the way for efficient and cost-effective lncRNA-focused drug discovery pipelines. In this Review, we present the emerging field of lncRNA therapeutics for oncology, with emphasis on the unique strengths and challenges of lncRNAs within the broader RNATx framework. We outline the necessary steps for lncRNA therapeutics to deliver effective, durable, tolerable and personalized treatments for cancer.
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Affiliation(s)
- Michela Coan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Simon Haefliger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland.
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Dublin, Ireland.
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Hazan JM, Amador R, Ali-Nasser T, Lahav T, Shotan SR, Steinberg M, Cohen Z, Aran D, Meiri D, Assaraf YG, Guigó R, Bester AC. Integration of transcription regulation and functional genomic data reveals lncRNA SNHG6's role in hematopoietic differentiation and leukemia. J Biomed Sci 2024; 31:27. [PMID: 38419051 PMCID: PMC10900714 DOI: 10.1186/s12929-024-01015-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/22/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are pivotal players in cellular processes, and their unique cell-type specific expression patterns render them attractive biomarkers and therapeutic targets. Yet, the functional roles of most lncRNAs remain enigmatic. To address the need to identify new druggable lncRNAs, we developed a comprehensive approach integrating transcription factor binding data with other genetic features to generate a machine learning model, which we have called INFLAMeR (Identifying Novel Functional LncRNAs with Advanced Machine Learning Resources). METHODS INFLAMeR was trained on high-throughput CRISPR interference (CRISPRi) screens across seven cell lines, and the algorithm was based on 71 genetic features. To validate the predictions, we selected candidate lncRNAs in the human K562 leukemia cell line and determined the impact of their knockdown (KD) on cell proliferation and chemotherapeutic drug response. We further performed transcriptomic analysis for candidate genes. Based on these findings, we assessed the lncRNA small nucleolar RNA host gene 6 (SNHG6) for its role in myeloid differentiation. Finally, we established a mouse K562 leukemia xenograft model to determine whether SNHG6 KD attenuates tumor growth in vivo. RESULTS The INFLAMeR model successfully reconstituted CRISPRi screening data and predicted functional lncRNAs that were previously overlooked. Intensive cell-based and transcriptomic validation of nearly fifty genes in K562 revealed cell type-specific functionality for 85% of the predicted lncRNAs. In this respect, our cell-based and transcriptomic analyses predicted a role for SNHG6 in hematopoiesis and leukemia. Consistent with its predicted role in hematopoietic differentiation, SNHG6 transcription is regulated by hematopoiesis-associated transcription factors. SNHG6 KD reduced the proliferation of leukemia cells and sensitized them to differentiation. Treatment of K562 leukemic cells with hemin and PMA, respectively, demonstrated that SNHG6 inhibits red blood cell differentiation but strongly promotes megakaryocyte differentiation. Using a xenograft mouse model, we demonstrate that SNHG6 KD attenuated tumor growth in vivo. CONCLUSIONS Our approach not only improved the identification and characterization of functional lncRNAs through genomic approaches in a cell type-specific manner, but also identified new lncRNAs with roles in hematopoiesis and leukemia. Such approaches can be readily applied to identify novel targets for precision medicine.
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Affiliation(s)
- Joshua M Hazan
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Raziel Amador
- Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
- Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
| | - Tahleel Ali-Nasser
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Tamar Lahav
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Stav Roni Shotan
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Miryam Steinberg
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Ziv Cohen
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
- The Taub Faculty of Computer Science, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Dvir Aran
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
- The Taub Faculty of Computer Science, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - David Meiri
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Assaf C Bester
- Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel.
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5
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Zhang MQ, Yang BZ, Wang ZQ, Guo S. Fatty acid metabolism-related lncRNAs are potential biomarkers for survival prediction in clear cell renal cell carcinoma. Medicine (Baltimore) 2024; 103:e37207. [PMID: 38394500 DOI: 10.1097/md.0000000000037207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/25/2024] Open
Abstract
Metabolic reprogramming of energy is a newly recognized characteristic of cancer. In our current investigation, we examined the possible predictive importance of long noncoding RNAs (lncRNAs) associated to fatty acid metabolism in clear cell renal cell carcinoma (ccRCC). We conducted an analysis of the gene expression data obtained from patients diagnosed with ccRCC using the Cancer Genome Atlas (TCGA) database and the ArrayExpress database. We performed a screening to identify lncRNAs that are differentially expressed in fatty acid metabolism. Based on these findings, we developed a prognostic risk score model using these fatty acid metabolism-related lncRNAs. We then validated this model using Cox regression analysis, Kaplan-Meier survival analysis, and principal-component analysis (PCA). Furthermore, the prognostic risk score model was successfully validated using both the TCGA cohort and the E-MTAB-1980 cohort. We utilized gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) to determine the correlation between fatty acid metabolism and the PPAR signaling pathway in patients with ccRCC at various clinical stages and prognoses. We have discovered compelling evidence of the interaction between immune cells in the tumor microenvironment and tumor cells, which leads to immune evasion and resistance to drugs. This was achieved by the utilization of advanced techniques such as the CIBERSORT method, ESTIMATE R package, ssGSEA algorithm, and TIMER database exploration. Ultimately, we have established a network of competing endogenous RNA (ceRNA) that is related to fatty acid metabolism. The findings of our study suggest that medicines focused on fatty acid metabolism could be clinically significant for individuals with ccRCC. The utilization of this risk model, which is centered around the lncRNAs associated with fatty acid metabolism, could potentially provide valuable prognostic information and hold immunotherapeutic implications for patients with ccRCC.
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Affiliation(s)
- Ming-Qing Zhang
- Department of Urology, Weifang Pepole's Hospital, Weifang, Shandong, China
| | - Bai-Zhi Yang
- Department of Urology, Shouguang Hospital of Traditional Chinese Medicine, Shouguang, China
| | - Zhi-Qiang Wang
- Department of Urology, Shouguang Hospital of Traditional Chinese Medicine, Shouguang, China
| | - Shanchun Guo
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA
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6
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Saatci O, Alam R, Huynh-Dam KT, Isik A, Uner M, Belder N, Ersan PG, Cetin M, Tokat UM, Gedik ME, Bal H, Sahin OS, Riazalhosseini Y, Thieffry D, Gautheret D, Ogretmen B, Aksoy S, Uner A, Akyol A, Sahin O. Targeting LINC00152 activates cAMP/Ca 2+/ferroptosis axis and overcomes tamoxifen resistance in ER+ breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.05.565697. [PMID: 38496603 PMCID: PMC10942410 DOI: 10.1101/2023.11.05.565697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Tamoxifen has been the mainstay therapy to treat early, locally advanced, and metastatic estrogen receptor-positive (ER+) breast cancer, constituting around 75% of all cases. However, emergence of resistance is common, necessitating the identification of novel therapeutic targets. Here, we demonstrated that long-noncoding RNA LINC00152 confers tamoxifen resistance via blocking tamoxifen-induced ferroptosis, an iron-mediated cell death. Mechanistically, inhibiting LINC00152 reduces the mRNA stability of phosphodiesterase 4D (PDE4D), leading to activation of cAMP/PKA/CREB axis and increased expression of TRPC1 Ca2+ channel. This causes cytosolic Ca2+ overload and generation of reactive oxygen species (ROS) that is, on one hand, accompanied by downregulation of FTH1, a member of the iron sequestration unit, thus increasing intracellular Fe2+ levels; and on the other hand, inhibition of the peroxidase activity upon reduced GPX4 and xCT levels. These ultimately induce lipid peroxidation and ferroptotic cell death in combination with tamoxifen. Overexpressing PDE4D rescues LINC00152 inhibition-mediated tamoxifen sensitization by de-activating the cAMP/Ca2+/ferroptosis axis. Importantly, high LINC00152 expression is significantly correlated with high PDE4D/low ferroptosis and worse survival in multiple cohorts of tamoxifen- or tamoxifen-containing endocrine therapy-treated ER+ breast cancer patients. Overall, we identified LINC00152 inhibition as a novel mechanism of ferroptosis induction and tamoxifen sensitization, thereby revealing LINC00152 and its effectors as actionable therapeutic targets to improve clinical outcome in refractory ER+ breast cancer.
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Affiliation(s)
- Ozge Saatci
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Rashed Alam
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Kim-Tuyen Huynh-Dam
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Aynur Isik
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, TURKEY
| | - Meral Uner
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, TURKEY
| | - Nevin Belder
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, 06800, TURKEY
| | - Pelin Gulizar Ersan
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, 06800, TURKEY
| | - Metin Cetin
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Unal Metin Tokat
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, 06800, TURKEY
| | - Mustafa Emre Gedik
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Hilal Bal
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, 06800, TURKEY
| | - Ozlem Sener Sahin
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Yasser Riazalhosseini
- Department of Human Genetics, McGill University, Montreal, Quebec, CANADA
- Victor Philip Dahdaleh Institute of Genomic Medicine at McGill University, Montreal, Quebec, CANADA
| | - Denis Thieffry
- Département de biologie de l'Ecole normale supérieure, PSL Université, 75005 Paris, FRANCE
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CNRS, CEA, 91190, Gifsur-Yvette, FRANCE
| | - Besim Ogretmen
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Sercan Aksoy
- Department of Medical Oncology, Hacettepe University Cancer Institute, 06100, Ankara, TURKEY
| | - Aysegul Uner
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, TURKEY
| | - Aytekin Akyol
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, TURKEY
| | - Ozgur Sahin
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
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7
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lncRNA CYTOR Facilitates Osteogenic Differentiation of Human Periodontal Ligament Stem Cells by Modulating SOX11 via Sponging miR-6512-3p. Stem Cells Int 2023; 2023:5671809. [PMID: 36910334 PMCID: PMC10005871 DOI: 10.1155/2023/5671809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/26/2023] [Accepted: 02/15/2023] [Indexed: 03/06/2023] Open
Abstract
Periodontal ligament stem cells (PDLSCs) are considered ideal cell sources for the regeneration of periodontal and alveolar bone tissue. Cytoskeleton Regulator RNA (CYTOR), a newly discovered long noncoding RNA, has been reported to function as competing endogenous RNA (ceRNA) and to be involved in many biological processes. However, its roles in PDLSC osteogenic differentiation remain unclear. Here, we firstly found CYTOR was mainly sublocalized in the cytoplasm of PDLSCs and CYTOR expression was increased during osteogenic differentiation of PDLSCs. By employing gain- and loss-of-function approaches, we then identified CYTOR overexpression promoted osteogenic differentiation of PDLSCs while CYTOR knockdown inhibited this process. Furthermore, bioinformatics analysis was utilized to show that both CYTOR and SOX11 mRNA contained the same seed sites for miR-6512-3p, which was further confirmed by dual luciferase reporter assay and RNA-binding protein immunoprecipitation. Notably, CYTOR conferred its functions by directly binding to miR-6512-3p and an inverse correlation between CYTOR and miR-6512-3p on the level on SOX11 and osteogenic differentiation of PDLSCs was obtained. Additionally, miR-6512-3p could bind to SOX11 mRNA 3' UTR and repressed SOX11 expression. Moreover, level of SOX11 was significantly increased during osteogenic differentiation of PDLSCs. Knockdown of SOX11 attenuated the increasing effect of CYTOR overexpression on osteogenic differentiation of PDLSCs. Collectively, these data supported that CYTOR positively modulated the expression of SOX11 through competitively binding to miR-6512-3p, thus promoting osteogenic differentiation of PDLSCs. The CYTOR/miR-6512-3p/SOX11 axis could be a novel therapeutic target for periodontal regeneration medicine.
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Yu H, Chen C, Han F, Tang J, Deng M, Niu Y, Lai M, Zhang H. Long Noncoding RNA MIR4435-2HG Suppresses Colorectal Cancer Initiation and Progression By Reprogramming Neutrophils. Cancer Immunol Res 2022; 10:1095-1110. [PMID: 35862232 PMCID: PMC9433964 DOI: 10.1158/2326-6066.cir-21-1011] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/31/2022] [Accepted: 07/15/2022] [Indexed: 01/07/2023]
Abstract
MIR4435-2HG, also known as LINC00978, has previously been described as an oncogenic long noncoding RNA (lncRNA). However, we show here that Mir4435-2hg depletion promoted colorectal tumorigenesis and progression in in vivo models of colitis-associated colorectal cancer, spontaneous intestinal adenomatous polyposis, and subcutaneous tumors. Alteration of MIR4435-2HG in colorectal cancer cells did not change the potential for cell proliferation, migration, or invasion in vitro. RNAscope assays showed that most MIR4435-2HG was located in the tumor stroma, which caused high expression of MIR4435-2HG in colorectal cancer tumor tissue. Transcriptome analysis of colorectal cancer tissues from wild-type and Mir4435-2hg-deficient mice revealed Mir4435-2hg as a tumor suppressor gene that regulated the immune microenvironment. Loss of Mir4435-2hg led to a decline in neutrophils and elevation of polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC). In tissue-specific Mir4435-2hg knockout mice, we confirmed that Mir4435-2hg depletion in neutrophils, but not in intestinal epithelial cells, promoted colorectal cancer progression. Mechanistically, Mir4435-2hg depletion enhanced the immunosuppressive ability of PMN-MDSCs by disturbing their fatty acid metabolism. These findings suggest that MIR4435-2HG is a tumor-suppressing lncRNA whose deficiency could increase tumor-infiltrating PMN-MDSCs and enhance the immunosuppressive potential of PMN-MDSCs to promote colorectal cancer development. This provides a theoretical basis for further illustrating the pathogenesis of colorectal cancer and a potential antitumor immunotherapy target.
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Affiliation(s)
- Hongfei Yu
- Department of Pathology and Women's Hospital, Zhejiang University School of Medicine, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Hangzhou, China
| | - Chaoyi Chen
- Department of Pathology and Women's Hospital, Zhejiang University School of Medicine, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Hangzhou, China
| | - Fengyan Han
- Department of Pathology and Women's Hospital, Zhejiang University School of Medicine, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Hangzhou, China
| | - Jinlong Tang
- Department of Pathology and Women's Hospital, Zhejiang University School of Medicine, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Hangzhou, China
| | - Mengli Deng
- Department of Pathology and Women's Hospital, Zhejiang University School of Medicine, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Hangzhou, China
| | - Yumiao Niu
- Department of Pathology and Women's Hospital, Zhejiang University School of Medicine, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Hangzhou, China
| | - Maode Lai
- Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy of Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China.,Department of Pharmacology, China Pharmaceutical University, Nanjing, China.,Corresponding Authors: Honghe Zhang, Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy of Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Yuhangtang Road 866#, Hangzhou, Zhejiang 310058, China. E-mails: ; and Maode Lai,
| | - Honghe Zhang
- Department of Pathology and Women's Hospital, Zhejiang University School of Medicine, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Hangzhou, China.,Key Laboratory of Disease Proteomics of Zhejiang Province, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China.,Corresponding Authors: Honghe Zhang, Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy of Chinese Academy of Medical Sciences (2019RU042), Zhejiang University School of Medicine, Yuhangtang Road 866#, Hangzhou, Zhejiang 310058, China. E-mails: ; and Maode Lai,
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9
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Najafi S, Khatami SH, Khorsand M, Jamali Z, Shabaninejad Z, Moazamfard M, Majidpoor J, Aghaei Zarch SM, Movahedpour A. Long non-coding RNAs (lncRNAs); roles in tumorigenesis and potentials as biomarkers in cancer diagnosis. Exp Cell Res 2022; 418:113294. [PMID: 35870535 DOI: 10.1016/j.yexcr.2022.113294] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/11/2022] [Accepted: 07/16/2022] [Indexed: 12/15/2022]
Abstract
New research has indicated that long non-coding RNAs (lncRNAs) play critical roles in a broad range of biological processes, including the pathogenesis of many complex human diseases, including cancer. The detailed regulation mechanisms of many lncRNAs in cancer initiation and progression have yet to be discovered, even though a few of lncRNAs' functions in cancer have been characterized. In the present study, we summarize recent advances in the mechanisms and functions of lncRNAs in cancer. We focused on the roles of newly-identified lncRNAs as oncogenes and tumor suppressors, as well as the potential pathways these molecules could play. The paper also discusses their potential uses as biomarkers for the diagnosis and prognosis of cancer.
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Affiliation(s)
- Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marjan Khorsand
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zeinab Jamali
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Shabaninejad
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Jamal Majidpoor
- Department of Anatomy, Faculty of Medicine, Infectious Disease Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Seyed Mohsen Aghaei Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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10
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He Z, Liu H, Guan H, Ji J, Jiang Y, Zhang N, Song Z, Wang X, Shen P, Wang H, Cui R. Construction of a Prognostic Model for Hypoxia-Related LncRNAs and Prediction of the Immune Landscape in the Digestive System Pan-Cancer. Front Oncol 2022; 12:812786. [PMID: 35574385 PMCID: PMC9092832 DOI: 10.3389/fonc.2022.812786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/25/2022] [Indexed: 12/24/2022] Open
Abstract
Digestive system pan-cancer is a general term for digestive system tumors including colorectal carcinoma (CRC), esophageal carcinoma (ESCA), stomach adenocarcinoma (STAD), and liver hepatocellular carcinoma (LIHC). Since the anatomical location, function and metabolism are closely related, there may be similarities in development and progression of these tumors. Hypoxia is the consequence of an imbalance between oxygen demand and supply, and intracellular hypoxia is associated with malignant progression, treatment resistance, and poor prognosis in tumors. Therefore, an urgent and challenging task is to investigate the molecular mechanisms associated with hypoxia in digestive system pan-cancer for the prognosis and treatment of digestive tract tumors. In this study, we identified 18 hypoxia-related lncRNAs (HRlncRNAs) by co-expression analysis between hypoxia genes and lncRNAs from digestive system pan-cancer. Six HRlncRNAs were then obtained using lasso regression and multivariate cox analysis to construct a prognostic model. Next, the Akaike information criterion (AIC) values for 3-year receiver operating curve (ROC) were counted to determine the cut-off point and establish an optimal model to distinguish between high- or low-risk groups among patients with digestive system pan-cancer. To evaluate the stability of the prognosis model, we validated it in terms of survival outcomes, clinicopathological stage, tumor-infiltrating immune cells, immune checkpoint inhibitors (ICIs) and anticancer drugs sensitivity. The results suggested that high- risk group had a worse prognosis and a more positive association with tumor-infiltrating immune cells such as B cells, cancer-associated fibroblasts, endothelial cells, monocytes, macrophages and bone marrow dendritic cells in digestive system pan-cancer. Immune checkpoint inhibitors (ICIs) related biomarkers discovered that high-risk group was positively correlated with high expression of HAVCR2 in digestive system pan-cancer. The anticancer drugs sensitivity analysis showed that the high-risk group was associated with the lower half-inhibitory centration (IC50) of Imatinib in digestive system pan-cancer. In conclusion, the prognostic model of HRlncRNAs showed a promising clinical prediction value and may provide a useful reference for the diagnosis and treatment of the digestive system tumors.
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Affiliation(s)
- Zikang He
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Hongfeng Liu
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Huilin Guan
- Department of Scientific Research, Mudanjiang Medical University, Mudanjiang, China
| | - Jinli Ji
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Ying Jiang
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Naiwen Zhang
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Zheyao Song
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Xingyun Wang
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Ping Shen
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Huan Wang
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
| | - Rongjun Cui
- Department of Biochemistry and Molecular Biology, Mudanjiang Medical University, Mudanjiang, China
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11
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Jafari-Oliayi A, Dabiri S, Hossein Asadi M. LncRNA SNHG6 Silencing Could Arrest Progression of High Grade Colorectal Cancers. IRANIAN JOURNAL OF PATHOLOGY 2021; 17:29-36. [PMID: 35096086 PMCID: PMC8794560 DOI: 10.30699/ijp.2021.527781.2610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/30/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND & OBJECTIVE Colorectal cancer (CRC), like other cancers, needs faster and more accurate identifications. A well-timed prognosis of CRC could be an important turning point in the survival of patients. Supplementary signs, such as long non-coding RNAs (lncRNAs), could be helpful for this purpose. A new possible biomarker for CRC identification is introduced by this study. METHODS RNA extraction was performed by the RNX-Plus solution for 64 tumor and non-tumor tissues. Complementary DNAs (cDNAs) were synthesized, and quantitative real-time PCR was performed for relative expression level measurement and the data was analyzed statistically using the Prism 6 software. For Small nucleolar host gene 6 knockdown, siRNA was designed based on Reynolds rules. The cells were cultured in their appropriate media, and the siRNA-lipofectamine complex was formed. The transfection complex was presented for sw48, sw480, and sw1116 as CRC cells with different grades. After transfection, the SNHG6/β actin ratio was determined. Then, the distribution of siRNA-treated cells was determined by the Partec flow cytometer instrument and analyzed by the FloMax software. RESULTS SNHG6 was more expressed in CRC tumors than non-tumor tissues. In tumor tissues, SNHG6 upregulation and tumors' grade progression were concurrent. SNHG6 was upregulated in cases with lymphovascular invasion than in cases with perineural invasion. The knockdown of SNHG6 conduced to G1 arrest in CRC cells, more noticeably in high-grade ones. CONCLUSION SNHG6 could be applied as a consideration to differentiate tumor and non-tumor tissues and grade definition in colorectal malignancies, and it could participate in colorectal tumor formation as a cell cycle progressive factor.
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Affiliation(s)
- Amin Jafari-Oliayi
- Pathology and Stem Cell Research Center, Department of Pathology, Afzalipour Medical School, Kerman University of Medical Sciences, Kerman, Iran
| | - Shahriar Dabiri
- Pathology and Stem Cell Research Center, Department of Pathology, Afzalipour Medical School, Kerman University of Medical Sciences, Kerman, Iran
| | - Malek Hossein Asadi
- Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology Kerman, Iran
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12
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Hazan J, Bester AC. CRISPR-Based Approaches for the High-Throughput Characterization of Long Non-Coding RNAs. Noncoding RNA 2021; 7:79. [PMID: 34940760 PMCID: PMC8704461 DOI: 10.3390/ncrna7040079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/06/2021] [Accepted: 12/11/2021] [Indexed: 12/17/2022] Open
Abstract
Over the last decade, tens of thousands of new long non-coding RNAs (lncRNAs) have been identified in the human genome. Nevertheless, except for a handful of genes, the genetic characteristics and functions of most of these lncRNAs remain elusive; this is partially due to their relatively low expression, high tissue specificity, and low conservation across species. A major limitation for determining the function of lncRNAs was the lack of methodologies suitable for studying these genes. The recent development of CRISPR/Cas9 technology has opened unprecedented opportunities to uncover the genetic and functional characteristics of the non-coding genome via targeted and high-throughput approaches. Specific CRISPR/Cas9-based approaches were developed to target lncRNA loci. Some of these approaches involve modifying the sequence, but others were developed to study lncRNAs by inducing transcriptional and epigenetic changes. The discovery of other programable Cas proteins broaden our possibilities to target RNA molecules with greater precision and accuracy. These approaches allow for the knock-down and characterization of lncRNAs. Here, we review how various CRISPR-based strategies have been used to characterize lncRNAs with important functions in different biological contexts and how these approaches can be further utilized to improve our understanding of the non-coding genome.
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13
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Matis S, Rossi M, Brondolo L, Cardillo M, Reverberi D, Massara R, Colombo M, Ibatici A, Angelucci E, Vaisitti T, Bruno S, Fabris S, Neri A, Gentile M, Morabito F, Cutrona G, Briata P, Gherzi R, Fais F. LINC00152 expression in normal and Chronic Lymphocytic Leukemia B cells. Hematol Oncol 2021; 40:40-47. [PMID: 34679195 PMCID: PMC9297877 DOI: 10.1002/hon.2938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 11/25/2022]
Abstract
Long non‐coding RNAs are emerging as essential regulators of gene expression, but their role in normal and neoplastic B cells is still largely uncharacterized. Here, we report on the expression pattern of the LINC00152 in normal B cells and Chronic Lymphocytic Leukemia B cell clones. Higher LINC00152 levels were consistently observed in memory B cell populations when compared to naïve B cells in the normal tissues analyzed [peripheral blood (PB), tonsils, and spleen]. In addition, independent stimulation via Immunoglobulins (IG), CD40, or Toll‐like Receptor 9 (TLR9) upregulated LINC00152 in PB B cells. The expression of LINC00152 in a cohort of 107 early stage Binet A CLL patients was highly variable and did not correlate with known prognostic markers or clinical evolution. TLR9 stimulation, but not CD40 or IG challenge, was able to upregulate LINC00152 expression in CLL cells. In addition, LINC00152 silencing in CLL cell lines expressing LINC00152 failed to induce significant cell survival or apoptosis changes. These data suggest that, in normal B cells, the expression of LINC00152 is regulated by immunomodulatory signals, which are only partially effective in CLL cells. However, LINC00152 does not appear to contribute to CLL cell expansion and/or survival in a cohort of newly diagnosed CLL patients.
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Affiliation(s)
- Serena Matis
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Martina Rossi
- Gene Expression Regulation Laboratory, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Lorenzo Brondolo
- Gene Expression Regulation Laboratory, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Martina Cardillo
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Daniele Reverberi
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Rosanna Massara
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Monica Colombo
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Adalberto Ibatici
- Hematology Unit and Transplant Center, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Emanuele Angelucci
- Hematology Unit and Transplant Center, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Tiziana Vaisitti
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Silvia Bruno
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Sonia Fabris
- Fondazione Cà Granda IRCCS, Hematology Ospedale Maggiore Policlinico Milano, Milan, Italy
| | - Antonino Neri
- Fondazione Cà Granda IRCCS, Hematology Ospedale Maggiore Policlinico Milano, Milan, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | | | - Fortunato Morabito
- Biotechnology Research Unit, AO, Cosenza, Italy.,Hematology and Bone Marrow Transplant Unit, Hemato-Oncology Department, Augusta Victoria Hospital, East Jerusalem, Israel
| | - Giovanna Cutrona
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Paola Briata
- Gene Expression Regulation Laboratory, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Roberto Gherzi
- Gene Expression Regulation Laboratory, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Franco Fais
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Department of Experimental Medicine, University of Genoa, Genoa, Italy
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14
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Zou X, Hu X, He F, Zhang M, Kong X, Rui S, Liu Y, Wang L, Zheng X, Liu J, Li Z, Luo H. LncRNA LINC00152 promotes oral squamous cell carcinoma growth via enhancing Upstream Transcription Factor 1 mediated Mitochondrial Ribosomal Protein L52 transcription. J Oral Pathol Med 2021; 51:454-463. [PMID: 34664331 DOI: 10.1111/jop.13253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/21/2021] [Accepted: 10/15/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND LINC00152 (long intergenic non-protein coding RNA 152) was identified as an oncogenic lncRNA in multiple cancers. In the current study, we aimed to explore the transcriptional profile of LINC00152 in oral squamous cell carcinoma (OSCC) and its regulations at the transcriptional level. METHODS Bioinformatic analysis was performed by extracting the OSCC subset from The Cancer Genome Atlas (TCGA)-Head and Neck Squamous Cell Carcinoma (HNSC). LINC00152 subcellular localization and its interacting transcriptional factors (TFs) were explored. Dual-luciferase assay and ChIP-qPCR were applied to study transcriptional regulation. In vitro and in-vivo tumor cell growth models were used for functional assays. RESULTS NR_024206.2 was the dominant isoform that accounts for 80% of all transcripts of LINC00152. LINC00152 upregulation was associated with unfavorable survival of patients with OSCC. LINC00152 knockdown significantly impaired OSCC cell growth in vitro and in vivo. RNA FISH assay confirmed nuclear and cytoplasmic distribution of LINC00152. It physically interacted with Upstream Transcription Factor 1 (USF1), a common transcription factor in mammalian cells. USF1 could bind to the promoter region of MRPL52 (Mitochondrial Ribosomal Protein L52) and activate its transcription. LINC00152 could enhance the binding, thereby indirectly elevating MRPL52 expression. USF1 or MRPL52 knockdown slowed the proliferation of OSCC cells and partly canceled LINC00152 mediated growth-promoting effects. CONCLUSION This study revealed a novel LINC00152-USF1/MRPL52 axis promoting OSCC tumor growth.
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Affiliation(s)
- Xiuhe Zou
- Department of Thyroid and Parathyroid Surgery, Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiaokun Hu
- Outpatient department, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Fenghui He
- Department of Thyroid and Parathyroid Surgery, Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Outpatient department, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ming Zhang
- Department of Thyroid and Parathyroid Surgery, Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Thyroid and Breast Surgery, Pingluo People's Hospital, Ningxia, China
| | - Xiangyu Kong
- Department of Thyroid and Parathyroid Surgery, Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,West China medical school, Sichuan University, Chengdu, Sichuan, China
| | - Shu Rui
- Department of Thyroid and Parathyroid Surgery, Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,West China medical school, Sichuan University, Chengdu, Sichuan, China
| | - Yang Liu
- Department of Thyroid and Parathyroid Surgery, Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,West China medical school, Sichuan University, Chengdu, Sichuan, China
| | - Liying Wang
- Department of Thyroid and Parathyroid Surgery, Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,West China medical school, Sichuan University, Chengdu, Sichuan, China
| | - Xun Zheng
- Department of Thyroid and Parathyroid Surgery, Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jiaye Liu
- Department of Thyroid and Parathyroid Surgery, Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhihui Li
- Department of Thyroid and Parathyroid Surgery, Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Han Luo
- Department of Thyroid and Parathyroid Surgery, Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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15
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lncRNA cytoskeleton regulator RNA (CYTOR): Diverse functions in metabolism, inflammation and tumorigenesis, and potential applications in precision oncology. Genes Dis 2021; 10:415-429. [DOI: 10.1016/j.gendis.2021.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 08/20/2021] [Indexed: 12/19/2022] Open
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16
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Khalili-Tanha G, Moghbeli M. Long non-coding RNAs as the critical regulators of doxorubicin resistance in tumor cells. Cell Mol Biol Lett 2021; 26:39. [PMID: 34425750 PMCID: PMC8381522 DOI: 10.1186/s11658-021-00282-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/17/2021] [Indexed: 12/16/2022] Open
Abstract
Resistance against conventional chemotherapeutic agents is one of the main reasons for tumor relapse and poor clinical outcomes in cancer patients. Various mechanisms are associated with drug resistance, including drug efflux, cell cycle, DNA repair and apoptosis. Doxorubicin (DOX) is a widely used first-line anti-cancer drug that functions as a DNA topoisomerase II inhibitor. However, DOX resistance has emerged as a large hurdle in efficient tumor therapy. Furthermore, despite its wide clinical application, DOX is a double-edged sword: it can damage normal tissues and affect the quality of patients’ lives during and after treatment. It is essential to clarify the molecular basis of DOX resistance to support the development of novel therapeutic modalities with fewer and/or lower-impact side effects in cancer patients. Long non-coding RNAs (lncRNAs) have critical roles in the drug resistance of various tumors. In this review, we summarize the state of knowledge on all the lncRNAs associated with DOX resistance. The majority are involved in promoting DOX resistance. This review paves the way to introducing an lncRNA panel marker for the prediction of the DOX response and clinical outcomes for cancer patients.
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Affiliation(s)
- Ghazaleh Khalili-Tanha
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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17
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Guiducci G, Stojic L. Long Noncoding RNAs at the Crossroads of Cell Cycle and Genome Integrity. Trends Genet 2021; 37:528-546. [PMID: 33685661 DOI: 10.1016/j.tig.2021.01.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/28/2020] [Accepted: 01/18/2021] [Indexed: 12/14/2022]
Abstract
The cell cycle is controlled by guardian proteins that coordinate the process of cell growth and cell division. Alterations in these processes lead to genome instability, which has a causal link to many human diseases. Beyond their well-characterized role of influencing protein-coding genes, an increasing body of evidence has revealed that long noncoding RNAs (lncRNAs) actively participate in regulation of the cell cycle and safeguarding of genome integrity. LncRNAs are versatile molecules that act via a wide array of mechanisms. In this review, we discuss how lncRNAs are implicated in control of the cell cycle and maintenance of genome stability and how changes in lncRNA-regulatory networks lead to proliferative diseases such as cancer.
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Affiliation(s)
- Giulia Guiducci
- Barts Cancer Institute, Centre for Cancer Cell and Molecular Biology, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London EC1M 6BQ, UK
| | - Lovorka Stojic
- Barts Cancer Institute, Centre for Cancer Cell and Molecular Biology, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London EC1M 6BQ, UK.
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18
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Abstract
Non-small cell lung cancer (NSCLC) accounts for about 85% of all lung cancer cases. The pathogenesis of NSCLC involves complex gene networks that include different types of non-coding RNAs, such as long non-coding RNAs (lncRNAs). The role of lncRNAs in NSCLC is gaining an increasing interest as their function is being explored in various human cancers. Recently, a new oncogenic lncRNA, LINC00152 (cytoskeleton regulator RNA (CYTOR)), has been identified in different tumor types. In NSCLC, the high expression of LINC00152 in tumor tissue and peripheral blood samples has been shown to be associated with worse prognoses of NSCLC patients. Overexpression of LINC00152 has been confirmed to promote the proliferation, invasion, and migration of NSCLC cells in vitro, as well as increase tumor growth in vivo. This review discusses the role of LINC00152 in NSCLC.
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Affiliation(s)
- Hong Yu
- Cell Biology Laboratory, Jilin Province Institute of Cancer Prevention and Treatment, Jilin Cancer Hospital, Changchun 130012, China
| | - Shu-Bin Li
- Department of Internal Medicine, Southern Branch of Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 102600, China
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19
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Abstract
Recent advances in sequencing technologies have uncovered the existence of thousands of long noncoding RNAs (lncRNAs) with dysregulated expression in cancer. As a result, there is burgeoning interest in understanding their function and biological significance in both homeostasis and disease. RNA interference (RNAi) enables sequence-specific gene silencing and can, in principle, be employed to silence virtually any gene. However, when applied to lncRNAs, it is important to consider current limitations in their annotation and current principles regarding lncRNA regulation and function when assessing their phenotype in cancer cell lines. In this chapter we describe the analysis of lncRNA splicing variant expression, including subcellular localization, transfection of siRNAs in cancer cell lines, and validation of gene silencing by quantitative PCR and single molecule in situ hybridization. All protocols can be performed in a laboratory with essential equipment for cell culture, molecular biology, and imaging.
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20
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Functional Screening Techniques to Identify Long Non-Coding RNAs as Therapeutic Targets in Cancer. Cancers (Basel) 2020; 12:cancers12123695. [PMID: 33317042 PMCID: PMC7763270 DOI: 10.3390/cancers12123695] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Long non-coding RNAs (lncRNAs) are a recently discovered class of molecules in the cell, with potential to be utilized as therapeutic targets in cancer. A number of lncRNAs have been described to play important roles in tumor progression and drive molecular processes involved in cell proliferation, apoptosis or invasion. However, the vast majority of lncRNAs have not been studied in the context of cancer thus far. With the advent of CRISPR/Cas genome editing, high-throughput functional screening approaches to identify lncRNAs that impact cancer growth are becoming more accessible. Here, we review currently available methods to study hundreds to thousands of lncRNAs in parallel to elucidate their role in tumorigenesis and cancer progression. Abstract Recent technological advancements such as CRISPR/Cas-based systems enable multiplexed, high-throughput screening for new therapeutic targets in cancer. While numerous functional screens have been performed on protein-coding genes to date, long non-coding RNAs (lncRNAs) represent an emerging class of potential oncogenes and tumor suppressors, with only a handful of large-scale screens performed thus far. Here, we review in detail currently available screening approaches to identify new lncRNA drivers of tumorigenesis and tumor progression. We discuss the various approaches of genomic and transcriptional targeting using CRISPR/Cas9, as well as methods to post-transcriptionally target lncRNAs via RNA interference (RNAi), antisense oligonucleotides (ASOs) and CRISPR/Cas13. We discuss potential advantages, caveats and future applications of each method to provide an overview and guide on investigating lncRNAs as new therapeutic targets in cancer.
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21
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Glaß M, Dorn A, Hüttelmaier S, Haemmerle M, Gutschner T. Comprehensive Analysis of LincRNAs in Classical and Basal-Like Subtypes of Pancreatic Cancer. Cancers (Basel) 2020; 12:cancers12082077. [PMID: 32727085 PMCID: PMC7464731 DOI: 10.3390/cancers12082077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/09/2020] [Accepted: 07/23/2020] [Indexed: 02/07/2023] Open
Abstract
Pancreatic ductal adenocarcinomas (PDAC) belong to the deadliest malignancies in the western world. Mutations in TP53 and KRAS genes along with some other frequent polymorphisms occur almost universally and are major drivers of tumour initiation. However, these mutations cannot explain the heterogeneity in therapeutic responses and differences in overall survival observed in PDAC patients. Thus, recent classifications of PDAC tumour samples have leveraged transcriptome-wide gene expression data to account for epigenetic, transcriptional and post-transcriptional mechanisms that may contribute to this deadly disease. Intriguingly, long intervening RNAs (lincRNAs) are a special class of long non-coding RNAs (lncRNAs) that can control gene expression programs on multiple levels thereby contributing to cancer progression. However, their subtype-specific expression and function as well as molecular interactions in PDAC are not fully understood yet. In this study, we systematically investigated the expression of lincRNAs in pancreatic cancer and its molecular subtypes using publicly available data from large-scale studies. We identified 27 deregulated lincRNAs that showed a significant different expression pattern in PDAC subtypes suggesting context-dependent roles. We further analyzed these lincRNAs regarding their common expression patterns. Moreover, we inferred clues on their functions based on correlation analyses and predicted interactions with RNA-binding proteins, microRNAs, and mRNAs. In summary, we identified several PDAC-associated lincRNAs of prognostic relevance and potential context-dependent functions and molecular interactions. Hence, our study provides a valuable resource for future investigations to decipher the role of lincRNAs in pancreatic cancer.
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Affiliation(s)
- Markus Glaß
- Institute of Molecular Medicine, Section for Cell Biology, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany; (M.G.); (S.H.)
| | - Agnes Dorn
- Institute of Pathology, Section for Experimental Pathology, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany;
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Section for Cell Biology, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany; (M.G.); (S.H.)
| | - Monika Haemmerle
- Institute of Pathology, Section for Experimental Pathology, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany;
- Correspondence: (M.H.); (T.G.)
| | - Tony Gutschner
- Junior Research Group ‘RNA Biology and Pathogenesis’, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany
- Correspondence: (M.H.); (T.G.)
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22
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Rath JA, Bajwa G, Carreres B, Hoyer E, Gruber I, Martínez-Paniagua MA, Yu YR, Nouraee N, Sadeghi F, Wu M, Wang T, Hebeisen M, Rufer N, Varadarajan N, Ho PC, Brenner MK, Gfeller D, Arber C. Single-cell transcriptomics identifies multiple pathways underlying antitumor function of TCR- and CD8αβ-engineered human CD4 + T cells. SCIENCE ADVANCES 2020; 6:eaaz7809. [PMID: 32923584 PMCID: PMC7455496 DOI: 10.1126/sciadv.aaz7809] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
Transgenic coexpression of a class I-restricted tumor antigen-specific T cell receptor (TCR) and CD8αβ (TCR8) redirects antigen specificity of CD4+ T cells. Reinforcement of biophysical properties and early TCR signaling explain how redirected CD4+ T cells recognize target cells, but the transcriptional basis for their acquired antitumor function remains elusive. We, therefore, interrogated redirected human CD4+ and CD8+ T cells by single-cell RNA sequencing and characterized them experimentally in bulk and single-cell assays and a mouse xenograft model. TCR8 expression enhanced CD8+ T cell function and preserved less differentiated CD4+ and CD8+ T cells after tumor challenge. TCR8+CD4+ T cells were most potent by activating multiple transcriptional programs associated with enhanced antitumor function. We found sustained activation of cytotoxicity, costimulation, oxidative phosphorylation- and proliferation-related genes, and simultaneously reduced differentiation and exhaustion. Our study identifies molecular features of TCR8 expression that can guide the development of enhanced immunotherapies.
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Affiliation(s)
- Jan A. Rath
- Department of Oncology UNIL-CHUV, Lausanne University Hospital, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Gagan Bajwa
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children’s Hospital, Houston, TX, USA
| | - Benoit Carreres
- Department of Oncology UNIL-CHUV, Lausanne University Hospital, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Elisabeth Hoyer
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children’s Hospital, Houston, TX, USA
| | - Isabelle Gruber
- Department of Oncology UNIL-CHUV, Lausanne University Hospital, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | | | - Yi-Ru Yu
- Department of Oncology UNIL-CHUV, Lausanne University Hospital, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Nazila Nouraee
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children’s Hospital, Houston, TX, USA
| | - Fatemeh Sadeghi
- Department of Chemical and Biomolecular Engineering, University of Houston, TX, USA
| | - Mengfen Wu
- Biostatistics Shared Resource, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Tao Wang
- Biostatistics Shared Resource, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael Hebeisen
- Department of Oncology UNIL-CHUV, Lausanne University Hospital, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Nathalie Rufer
- Department of Oncology UNIL-CHUV, Lausanne University Hospital, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Navin Varadarajan
- Department of Chemical and Biomolecular Engineering, University of Houston, TX, USA
| | - Ping-Chih Ho
- Department of Oncology UNIL-CHUV, Lausanne University Hospital, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Malcolm K. Brenner
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children’s Hospital, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David Gfeller
- Department of Oncology UNIL-CHUV, Lausanne University Hospital, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Caroline Arber
- Department of Oncology UNIL-CHUV, Lausanne University Hospital, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital and Texas Children’s Hospital, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
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23
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Biasini A, Smith AAT, Abdulkarim B, Ferreira da Silva M, Tan JY, Marques AC. The Contribution of lincRNAs at the Interface between Cell Cycle Regulation and Cell State Maintenance. iScience 2020; 23:101291. [PMID: 32619701 PMCID: PMC7334372 DOI: 10.1016/j.isci.2020.101291] [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: 12/04/2019] [Revised: 04/24/2020] [Accepted: 06/15/2020] [Indexed: 12/27/2022] Open
Abstract
Cell cycle progression is controlled by the interplay of established cell cycle regulators. Changes in these regulators' activity underpin differences in cell cycle kinetics between cell types. We investigated whether long intergenic noncoding RNAs (lincRNAs) contribute to embryonic stem cell cycle adaptations. Using single-cell RNA sequencing data for mouse embryonic stem cells (mESCs) staged as G1, S, or G2/M we found differentially expressed lincRNAs are enriched among cell cycle-regulated genes. These lincRNAs (CC-lincRNAs) are co-expressed with genes involved in cell cycle regulation. We tested the impact of two CC-lincRNA candidates and show using CRISPR activation that increasing their expression is associated with deregulated cell cycle progression. Interestingly, CC-lincRNAs are often differentially expressed between G1 and S, their promoters are enriched in pluripotency transcription factor (TF) binding sites, and their transcripts are frequently co-regulated with genes involved in the maintenance of pluripotency, suggesting a contribution of CC-lincRNAs to mESC cell cycle adaptations. Genes differentially expressed between mESC cell cycle stages are enriched in lincRNAs CC-lincRNAs are co-expressed with cell cycle and pluripotency genes CC-lincRNAs are often mESC specific and their promoters enriched in pluripotency TFs Upregulation of two CC-lincRNAs results in deregulated mESC cell cycle progression
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Affiliation(s)
- Adriano Biasini
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Baroj Abdulkarim
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Jennifer Yihong Tan
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Ana Claudia Marques
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
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24
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Grillone K, Riillo C, Scionti F, Rocca R, Tradigo G, Guzzi PH, Alcaro S, Di Martino MT, Tagliaferri P, Tassone P. Non-coding RNAs in cancer: platforms and strategies for investigating the genomic "dark matter". J Exp Clin Cancer Res 2020; 39:117. [PMID: 32563270 PMCID: PMC7305591 DOI: 10.1186/s13046-020-01622-x] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/11/2020] [Indexed: 12/18/2022] Open
Abstract
The discovery of the role of non-coding RNAs (ncRNAs) in the onset and progression of malignancies is a promising frontier of cancer genetics. It is clear that ncRNAs are candidates for therapeutic intervention, since they may act as biomarkers or key regulators of cancer gene network. Recently, profiling and sequencing of ncRNAs disclosed deep deregulation in human cancers mostly due to aberrant mechanisms of ncRNAs biogenesis, such as amplification, deletion, abnormal epigenetic or transcriptional regulation. Although dysregulated ncRNAs may promote hallmarks of cancer as oncogenes or antagonize them as tumor suppressors, the mechanisms behind these events remain to be clarified. The development of new bioinformatic tools as well as novel molecular technologies is a challenging opportunity to disclose the role of the "dark matter" of the genome. In this review, we focus on currently available platforms, computational analyses and experimental strategies to investigate ncRNAs in cancer. We highlight the differences among experimental approaches aimed to dissect miRNAs and lncRNAs, which are the most studied ncRNAs. These two classes indeed need different investigation taking into account their intrinsic characteristics, such as length, structures and also the interacting molecules. Finally, we discuss the relevance of ncRNAs in clinical practice by considering promises and challenges behind the bench to bedside translation.
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Affiliation(s)
- Katia Grillone
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Caterina Riillo
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Medical and Translational Oncology Units, AOU Mater Domini, 88100 Catanzaro, Italy
| | - Francesca Scionti
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Roberta Rocca
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Net4science srl, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Giuseppe Tradigo
- Laboratory of Bioinformatics, Department of Medical and Surgical Sciences, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Pietro Hiram Guzzi
- Laboratory of Bioinformatics, Department of Medical and Surgical Sciences, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Net4science srl, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Department of Health Sciences, Magna Græcia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Maria Teresa Di Martino
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Medical and Translational Oncology Units, AOU Mater Domini, 88100 Catanzaro, Italy
| | - Pierosandro Tagliaferri
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Medical and Translational Oncology Units, AOU Mater Domini, 88100 Catanzaro, Italy
| | - Pierfrancesco Tassone
- Laboratory of Translational Medical Oncology, Department of Experimental and Clinical Medicine, Magna Graecia University, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
- Medical and Translational Oncology Units, AOU Mater Domini, 88100 Catanzaro, Italy
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25
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Farzaneh F, Salimi S, Razavi M, Rezaei M, Saravani M. Association of H19 rs3741219 polymorphism with the susceptibility to uterine leiomyomas. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Yildirim O, Izgu EC, Damle M, Chalei V, Ji F, Sadreyev RI, Szostak JW, Kingston RE. S-phase Enriched Non-coding RNAs Regulate Gene Expression and Cell Cycle Progression. Cell Rep 2020; 31:107629. [PMID: 32402276 PMCID: PMC7954657 DOI: 10.1016/j.celrep.2020.107629] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/20/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022] Open
Abstract
Many proteins that are needed for progression through S-phase are produced from transcripts that peak in the S-phase, linking temporal expression of those proteins to the time that they are required in cell cycle. Here, we explore the potential roles of long non-coding RNAs in cell cycle progression. We use a sensitive click-chemistry approach to isolate nascent RNAs in a human cell line, and we identify more than 900 long non-coding RNAs (lncRNAs) whose synthesis peaks during the S-phase. More than 200 of these are long intergenic non-coding RNAs (lincRNAs) with S-phase-specific expression. We characterize three of these lincRNAs by knockdown and find that all three lincRNAs are required for appropriate S-phase progression. We infer that non-coding RNAs are key regulatory effectors during the cell cycle, acting on distinct regulatory networks, and herein, we provide a large catalog of candidate cell-cycle regulatory RNAs.
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Affiliation(s)
- Ozlem Yildirim
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Enver C Izgu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Manashree Damle
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vladislava Chalei
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jack W Szostak
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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27
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Stojic L, Lun ATL, Mascalchi P, Ernst C, Redmond AM, Mangei J, Barr AR, Bousgouni V, Bakal C, Marioni JC, Odom DT, Gergely F. A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division. Nat Commun 2020; 11:1851. [PMID: 32296040 PMCID: PMC7160116 DOI: 10.1038/s41467-020-14978-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 02/09/2020] [Indexed: 01/21/2023] Open
Abstract
Genome stability relies on proper coordination of mitosis and cytokinesis, where dynamic microtubules capture and faithfully segregate chromosomes into daughter cells. With a high-content RNAi imaging screen targeting more than 2,000 human lncRNAs, we identify numerous lncRNAs involved in key steps of cell division such as chromosome segregation, mitotic duration and cytokinesis. Here, we provide evidence that the chromatin-associated lncRNA, linc00899, leads to robust mitotic delay upon its depletion in multiple cell types. We perform transcriptome analysis of linc00899-depleted cells and identify the neuronal microtubule-binding protein, TPPP/p25, as a target of linc00899. We further show that linc00899 binds TPPP/p25 and suppresses its transcription. In cells depleted of linc00899, upregulation of TPPP/p25 alters microtubule dynamics and delays mitosis. Overall, our comprehensive screen uncovers several lncRNAs involved in genome stability and reveals a lncRNA that controls microtubule behaviour with functional implications beyond cell division.
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Affiliation(s)
- Lovorka Stojic
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK.
| | - Aaron T L Lun
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Genentech, Inc., South San Francisco, CA, USA
| | - Patrice Mascalchi
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- DRVision Technologies, Bordeaux, France
| | - Christina Ernst
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Aisling M Redmond
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Jasmin Mangei
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Molecular Genetics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Alexis R Barr
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
- MRC London Institute of Medical Sciences (LMS), Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Vicky Bousgouni
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Chris Bakal
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- Division of Regulatory Genomics and Cancer Evolution, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
| | - Fanni Gergely
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
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28
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Bárcenas-López DA, Núñez-Enríquez JC, Hidalgo-Miranda A, Beltrán-Anaya FO, May-Hau DI, Jiménez-Hernández E, Bekker-Méndez VC, Flores-Lujano J, Medina-Sansón A, Tamez-Gómez EL, López-García VH, Lara-Ramos JR, Núñez-Villegas NN, Peñaloza-González JG, Flores-Villegas LV, Amador-Sánchez R, Espinosa-Elizondo RM, Martín-Trejo JA, Velázquez-Aviña MM, Merino-Pasaye LE, Pérez-Saldívar ML, Duarte-Rodríguez DA, Torres-Nava JR, Cortés-Herrera B, Solís-Labastida KA, González-Ávila AI, Santillán-Juárez JD, García-Velázquez AJ, Rosas-Vargas H, Mata-Rocha M, Sepúlveda-Robles OA, Mejía-Aranguré JM, Jiménez-Morales S. Transcriptome Analysis Identifies LINC00152 as a Biomarker of Early Relapse and Mortality in Acute Lymphoblastic Leukemia. Genes (Basel) 2020; 11:genes11030302. [PMID: 32183133 PMCID: PMC7140896 DOI: 10.3390/genes11030302] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 12/16/2022] Open
Abstract
Evidence showing the role of long non-coding RNAs (lncRNAs) in leukemogenesis have emerged in the last decade. It has been proposed that these genes can be used as diagnosis and/or prognosis biomarkers in childhood acute lymphoblastic leukemia (ALL). To know if lncRNAs are associated with early relapse and early mortality, a microarray-based gene expression analysis in children with B-lineage ALL (B-ALL) was conducted. Cox regression analyses were performed. Hazard ratios (HR) and 95% confidence intervals (95% CI) were calculated. LINC00152 and LINC01013 were among the most differentially expressed genes in patients with early relapse and early mortality. For LINC00152 high expression, the risks of relapse and death were HR: 4.16 (95% CI: 1.46–11.86) and HR: 1.99 (95% CI: 0.66–6.02), respectively; for LINC01013 low expression, the risks of relapse and death were HR: 3.03 (95% CI: 1.14–8.05) and HR: 6.87 (95% CI: 1.50–31.48), respectively. These results were adjusted by NCI risk criteria and chemotherapy regimen. The lncRNA–mRNA co-expression analysis showed that LINC00152 potentially regulates genes involved in cell substrate adhesion and peptidyl–tyrosine autophosphorylation biological processes. The results of the present study point out that LINC00152 could be a potential biomarker of relapse in children with B-ALL.
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Affiliation(s)
- Diego Alberto Bárcenas-López
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiologia Clínica, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (J.C.N.-E.); (J.F.-L.); (M.L.P.-S.); (D.A.D.-R.)
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico;
| | - Fredy Omar Beltrán-Anaya
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Didier Ismael May-Hau
- Programa de Maestría en Investigación Clínica Experimental en Salud, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Elva Jiménez-Hernández
- Servicio de Hematología Pediátrica, Hospital General “Gaudencio González Garza”, Centro Médico Nacional “La Raza”, IMSS, Mexico City 02990, Mexico; (E.J.-H.); (N.N.N.-V.)
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología “Dr. Daniel Méndez Hernández”, Centro Médico Nacional “La Raza”, IMSS, Mexico City 02990, Mexico;
| | - Janet Flores-Lujano
- Unidad de Investigación Médica en Epidemiologia Clínica, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (J.C.N.-E.); (J.F.-L.); (M.L.P.-S.); (D.A.D.-R.)
| | - Aurora Medina-Sansón
- Servicio de Hemato-Oncologia, Hospital Infantil de México Federico Gómez, Secretaria de Salud (SS), Mexico City 06720, Mexico;
| | - Edna Liliana Tamez-Gómez
- Servicio de Hemato-Oncología Hospital Infantil de Tamaulipas, Secretaría de Salud (SS), Cd. Victoria Tamaulipas 87070, Mexico;
| | - Víctor Hugo López-García
- Servicio de Ortopedia Pediátrica, Hospital Infantil de Tamaulipas, Secretaría de Salud (SS), Cd. Victoria Tamaulipas 87070, Mexico;
| | - José Ramón Lara-Ramos
- Departamento de Genética, Hospital Infantil de Tamaulipas, Secretaría de Salud (SS), Cd. Victoria Tamaulipas 87070, Mexico;
| | - Nora Nancy Núñez-Villegas
- Servicio de Hematología Pediátrica, Hospital General “Gaudencio González Garza”, Centro Médico Nacional “La Raza”, IMSS, Mexico City 02990, Mexico; (E.J.-H.); (N.N.N.-V.)
| | - José Gabriel Peñaloza-González
- Servicio de Onco-Pediatría, Hospital Juárez de México, Secretaría de Salud (SS), Mexico City 07760, Mexico; (J.G.P.-G.); (M.M.V.-A.)
| | - Luz Victoria Flores-Villegas
- Servicio de Hematología Pediátrica, Centro Médico Nacional “20 de Noviembre”, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City 03100, Mexico; (L.V.F.-V.); (L.E.M.-P.)
| | - Raquel Amador-Sánchez
- Hospital General Regional 1 “Dr. Carlos McGregor Sánchez Navarro”, IMSS, Mexico City 03103, Mexico; (R.A.-S.); (A.I.G.-Á.)
| | - Rosa Martha Espinosa-Elizondo
- Servicio de Hematología Pediátrica, Hospital General de México “Dr. Eduardo Liceaga”, Secretaría de Salud (SS), Mexico City 06720, Mexico; (R.M.E.-E.); (B.C.-H.)
| | - Jorge Alfonso Martín-Trejo
- Servicio de Hematología Pediátrica UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, IMSS, Mexico City 06720, Mexico; (J.A.M.-T.); (K.A.S.-L.)
| | - Martha Margarita Velázquez-Aviña
- Servicio de Onco-Pediatría, Hospital Juárez de México, Secretaría de Salud (SS), Mexico City 07760, Mexico; (J.G.P.-G.); (M.M.V.-A.)
| | - Laura Elizabeth Merino-Pasaye
- Servicio de Hematología Pediátrica, Centro Médico Nacional “20 de Noviembre”, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City 03100, Mexico; (L.V.F.-V.); (L.E.M.-P.)
| | - María Luisa Pérez-Saldívar
- Unidad de Investigación Médica en Epidemiologia Clínica, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (J.C.N.-E.); (J.F.-L.); (M.L.P.-S.); (D.A.D.-R.)
| | - David Aldebarán Duarte-Rodríguez
- Unidad de Investigación Médica en Epidemiologia Clínica, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (J.C.N.-E.); (J.F.-L.); (M.L.P.-S.); (D.A.D.-R.)
| | - José Refugio Torres-Nava
- Servicio de Oncología, Hospital Pediátrico de Moctezuma, Secretaria de Salud del D.F., Mexico City 15530, Mexico;
| | - Beatriz Cortés-Herrera
- Servicio de Hematología Pediátrica, Hospital General de México “Dr. Eduardo Liceaga”, Secretaría de Salud (SS), Mexico City 06720, Mexico; (R.M.E.-E.); (B.C.-H.)
| | - Karina Anastacia Solís-Labastida
- Servicio de Hematología Pediátrica UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, IMSS, Mexico City 06720, Mexico; (J.A.M.-T.); (K.A.S.-L.)
| | - Ana Itamar González-Ávila
- Hospital General Regional 1 “Dr. Carlos McGregor Sánchez Navarro”, IMSS, Mexico City 03103, Mexico; (R.A.-S.); (A.I.G.-Á.)
| | - Jessica Denisse Santillán-Juárez
- Servicio de Hemato-Oncología Pediátrica, Hospital Regional No. 1 de Octubre, ISSSTE, Mexico City 07300, Mexico; (J.D.S.-J.); (A.J.G.-V.)
| | - Alejandra Jimena García-Velázquez
- Servicio de Hemato-Oncología Pediátrica, Hospital Regional No. 1 de Octubre, ISSSTE, Mexico City 07300, Mexico; (J.D.S.-J.); (A.J.G.-V.)
| | - Haydee Rosas-Vargas
- Unidad de Investigación en Genética Humana, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, IMSS, Mexico City 06720, Mexico; (H.R.-V.); (M.M.-R.); (O.A.S.-R.)
| | - Minerva Mata-Rocha
- Unidad de Investigación en Genética Humana, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, IMSS, Mexico City 06720, Mexico; (H.R.-V.); (M.M.-R.); (O.A.S.-R.)
| | - Omar Alejandro Sepúlveda-Robles
- Unidad de Investigación en Genética Humana, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, IMSS, Mexico City 06720, Mexico; (H.R.-V.); (M.M.-R.); (O.A.S.-R.)
| | - Juan Manuel Mejía-Aranguré
- Unidad de Investigación Médica en Epidemiologia Clínica, UMAE Hospital de Pediatría “Dr. Silvestre Frenk Freund”, Centro Médico Nacional “Siglo XXI”, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (J.C.N.-E.); (J.F.-L.); (M.L.P.-S.); (D.A.D.-R.)
- Coordinación de Investigación en Salud, IMSS, Mexico City 06720, Mexico
- Correspondence: or (J.M.M.-A.); (S.J.-M.); Tel.: +52–55–5350–1900 (ext. 1155) (S.J.-M.)
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City 14610, Mexico;
- Correspondence: or (J.M.M.-A.); (S.J.-M.); Tel.: +52–55–5350–1900 (ext. 1155) (S.J.-M.)
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Dong X, Yang Z, Yang H, Li D, Qiu X. Long Non-coding RNA MIR4435-2HG Promotes Colorectal Cancer Proliferation and Metastasis Through miR-206/YAP1 Axis. Front Oncol 2020; 10:160. [PMID: 32154166 PMCID: PMC7044350 DOI: 10.3389/fonc.2020.00160] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 01/29/2020] [Indexed: 12/18/2022] Open
Abstract
Objective: Long non-coding RNAs (lncRNAs) are critical to colorectal cancer (CRC) progression. In the current study, the objective was the exploration of the role played by lncRNA MIR4435-2HG in CRC proliferation and metastasis. Methods: lncRNA MIR4435-2HG expression and its association with CRC were analyzed using database and clinical specimens. The influences exerted by MIR4435-2HG on cell proliferating process, invading process, and migrating process of CRC were identified after MIR4435-2HG knockdown. The influences exerted by MIR4435-2HG on tumor growth and metastasis were assessed in vivo. The underlying mechanistic associations between MIR4435-2HG, microRNA miR-206, and the transcription factor Yes-associated protein 1 (YAP1) were assessed using bioinformatics and a luciferase reporter gene assay. Results: MIR4435-2HG was highly expressed in CRC tissue in contrast with that in regular tissues and displayed relations to poor prognosis. MIR4435-2HG knockdown could suppress CRC cell proliferation, invasion, and migration. Moreover, MIR4435-2HG knockdown inhibited CRC growth and liver metastasis in vitro. We found MIR4435-2HG knockdown reduced YAP1, CTGF, AREG, vimentin, Snail, Slug, and Twist expression but enhanced E-cadherin expression. Functionally, MIR4435-2HG acted as a competing endogenous RNA (ceRNA) to upregulate YAP1 by sponging miR-206. Conclusions: MIR4435-2HG promoted CRC growth and metastasis through miR-206/YAP1 axis and is likely to play prognostic marker roles and be therapeutically targeted in CRC.
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Affiliation(s)
- Xinhua Dong
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhen Yang
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongwei Yang
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dongyan Li
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinguang Qiu
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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30
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Billing AM, Dib SS, Bhagwat AM, da Silva IT, Drummond RD, Hayat S, Al-Mismar R, Ben-Hamidane H, Goswami N, Engholm-Keller K, Larsen MR, Suhre K, Rafii A, Graumann J. A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells. Mol Cell Proteomics 2019; 18:1950-1966. [PMID: 31332097 PMCID: PMC6773553 DOI: 10.1074/mcp.ra119.001356] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
Mesenchymal stem/stromal cells (MSCs) are self-renewing multipotent cells with regenerative, secretory and immunomodulatory capabilities that are beneficial for the treatment of various diseases. To avoid the issues that come with using tissue-derived MSCs in therapy, MSCs may be generated by the differentiation of human embryonic stems cells (hESCs) in culture. However, the changes that occur during the differentiation process have not been comprehensively characterized. Here, we combined transcriptome, proteome and phosphoproteome profiling to perform an in-depth, multi-omics study of the hESCs-to-MSCs differentiation process. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation. Among the earliest and strongest induced proteins with extensive differential phosphorylation was AHNAK, which we hypothesized to be a defining factor in MSC biology. We observed two distinct expression waves of developmental HOX genes and an AGO2-to-AGO3 switch in gene silencing. Exploring the kinetic of noncoding ORFs during differentiation, we mapped new functions to well annotated long noncoding RNAs (CARMN, MALAT, NEAT1, LINC00152) as well as new candidates which we identified to be important to the differentiation process. Phosphoproteome analysis revealed ESC and MSC-specific phosphorylation motifs with PAK2 and RAF1 as top predicted upstream kinases in MSCs. Our data represent a rich systems-level resource on ESC-to-MSC differentiation that will be useful for the study of stem cell biology.
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Affiliation(s)
- Anja M Billing
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar.
| | - Shaima S Dib
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Aditya M Bhagwat
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Israel T da Silva
- Laboratory of Bioinformatics and Computational Biology, A. C., Camargo Cancer Center, São Paulo 01508-010, Brazil; Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065
| | - Rodrigo D Drummond
- Laboratory of Bioinformatics and Computational Biology, A. C., Camargo Cancer Center, São Paulo 01508-010, Brazil
| | - Shahina Hayat
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Rasha Al-Mismar
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Hisham Ben-Hamidane
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Neha Goswami
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Kasper Engholm-Keller
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark; Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Karsten Suhre
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar
| | - Arash Rafii
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar; Department of Gynecology and Obstetrics, Hôpital Foch, 92100 Suresnes, France
| | - Johannes Graumann
- Research Division, Weill Cornell Medicine Qatar, Weill Cornell University, P.O. Box 24144, Doha, Qatar.
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31
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Vakkilainen S, Skoog T, Einarsdottir E, Middleton A, Pekkinen M, Öhman T, Katayama S, Krjutškov K, Kovanen PE, Varjosalo M, Lindqvist A, Kere J, Mäkitie O. The human long non-coding RNA gene RMRP has pleiotropic effects and regulates cell-cycle progression at G2. Sci Rep 2019; 9:13758. [PMID: 31551465 PMCID: PMC6760211 DOI: 10.1038/s41598-019-50334-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/03/2019] [Indexed: 12/14/2022] Open
Abstract
RMRP was the first non-coding nuclear RNA gene implicated in a disease. Its mutations cause cartilage-hair hypoplasia (CHH), an autosomal recessive skeletal dysplasia with growth failure, immunodeficiency, and a high risk for malignancies. This study aimed to gain further insight into the role of RNA Component of Mitochondrial RNA Processing Endoribonuclease (RMRP) in cellular physiology and disease pathogenesis. We combined transcriptome analysis with single-cell analysis using fibroblasts from CHH patients and healthy controls. To directly assess cell cycle progression, we followed CHH fibroblasts by pulse-labeling and time-lapse microscopy. Transcriptome analysis identified 35 significantly upregulated and 130 downregulated genes in CHH fibroblasts. The downregulated genes were significantly connected to the cell cycle. Multiple other pathways, involving regulation of apoptosis, bone and cartilage formation, and lymphocyte function, were also affected, as well as PI3K-Akt signaling. Cell-cycle studies indicated that the CHH cells were delayed specifically in the passage from G2 phase to mitosis. Our findings expand the mechanistic understanding of CHH, indicate possible pathways for therapeutic intervention and add to the limited understanding of the functions of RMRP.
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Affiliation(s)
- Svetlana Vakkilainen
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland. .,Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.
| | - Tiina Skoog
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Elisabet Einarsdottir
- Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Anna Middleton
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Minna Pekkinen
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland
| | - Tiina Öhman
- Institute of Biotechnology, and Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Competence Centre on Health Technologies, Tartu, Estonia
| | - Panu E Kovanen
- Department of Pathology, University of Helsinki, and HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, and Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Arne Lindqvist
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Department of Medical and Molecular Genetics, King's College, London, UK
| | - Outi Mäkitie
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.,Department of Molecular Medicine and Surgery, Karolinska Institutet and Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Mahmoud AD, Ballantyne MD, Miscianinov V, Pinel K, Hung J, Scanlon JP, Iyinikkel J, Kaczynski J, Tavares AS, Bradshaw AC, Mills NL, Newby DE, Caporali A, Gould GW, George SJ, Ulitsky I, Sluimer JC, Rodor J, Baker AH. The Human-Specific and Smooth Muscle Cell-Enriched LncRNA SMILR Promotes Proliferation by Regulating Mitotic CENPF mRNA and Drives Cell-Cycle Progression Which Can Be Targeted to Limit Vascular Remodeling. Circ Res 2019; 125:535-551. [PMID: 31339449 PMCID: PMC6693924 DOI: 10.1161/circresaha.119.314876] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 07/05/2019] [Accepted: 07/19/2019] [Indexed: 12/20/2022]
Abstract
RATIONALE In response to blood vessel wall injury, aberrant proliferation of vascular smooth muscle cells (SMCs) causes pathological remodeling. However, the controlling mechanisms are not completely understood. OBJECTIVE We recently showed that the human long noncoding RNA, SMILR, promotes vascular SMCs proliferation by a hitherto unknown mechanism. Here, we assess the therapeutic potential of SMILR inhibition and detail the molecular mechanism of action. METHODS AND RESULTS We used deep RNA-sequencing of human saphenous vein SMCs stimulated with IL (interleukin)-1α and PDGF (platelet-derived growth factor)-BB with SMILR knockdown (siRNA) or overexpression (lentivirus), to identify SMILR-regulated genes. This revealed a SMILR-dependent network essential for cell cycle progression. In particular, we found using the fluorescent ubiquitination-based cell cycle indicator viral system that SMILR regulates the late mitotic phase of the cell cycle and cytokinesis with SMILR knockdown resulting in ≈10% increase in binucleated cells. SMILR pulldowns further revealed its potential molecular mechanism, which involves an interaction with the mRNA of the late mitotic protein CENPF (centromere protein F) and the regulatory Staufen1 RNA-binding protein. SMILR and this downstream axis were also found to be activated in the human ex vivo vein graft pathological model and in primary human coronary artery SMCs and atherosclerotic plaques obtained at carotid endarterectomy. Finally, to assess the therapeutic potential of SMILR, we used a novel siRNA approach in the ex vivo vein graft model (within the 30 minutes clinical time frame that would occur between harvest and implant) to assess the reduction of proliferation by EdU incorporation. SMILR knockdown led to a marked decrease in proliferation from ≈29% in controls to ≈5% with SMILR depletion. CONCLUSIONS Collectively, we demonstrate that SMILR is a critical mediator of vascular SMC proliferation via direct regulation of mitotic progression. Our data further reveal a potential SMILR-targeting intervention to limit atherogenesis and adverse vascular remodeling.
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MESH Headings
- Cell Cycle/physiology
- Cell Proliferation/physiology
- Cells, Cultured
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Humans
- Microfilament Proteins/genetics
- Microfilament Proteins/metabolism
- Mitosis/physiology
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/metabolism
- Myocytes, Smooth Muscle/metabolism
- Organ Culture Techniques
- RNA, Long Noncoding/biosynthesis
- RNA, Long Noncoding/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Saphenous Vein/cytology
- Saphenous Vein/metabolism
- Vascular Remodeling/physiology
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Affiliation(s)
- Amira D. Mahmoud
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Margaret D. Ballantyne
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Vladislav Miscianinov
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Karine Pinel
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - John Hung
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Jessica P. Scanlon
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Jean Iyinikkel
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Jakub Kaczynski
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Adriana S. Tavares
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Angela C. Bradshaw
- Institute of Cardiovascular and Medical Sciences, BHF Cardiovascular Research Centre, University of Glasgow, United Kingdom (A.C.B.)
| | - Nicholas L. Mills
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - David E. Newby
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Andrea Caporali
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Gwyn W. Gould
- Institute of Molecular Cell and Systems Biology, College of Medicine, Veterinary and Life Sciences, University of Glasgow, United Kingdom (G.W.G.)
| | - Sarah J. George
- School of Clinical Sciences, University of Bristol, Research Floor Level Seven, Bristol Royal Infirmary, United Kingdom (S.J.G.)
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel (I.U.)
| | - Judith C. Sluimer
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
- Department of Pathology, Maastricht University Medical Center, the Netherlands (J.C.S., A.H.B.)
| | - Julie Rodor
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
| | - Andrew H. Baker
- From the Queens Medical Research Institute, BHF Centre for Cardiovascular Sciences, University of Edinburgh, United Kingdom (A.D.M., M.D.B., V.M., K.P., J.H., J.P.S., J.I., J.K., A.S.T., N.L.M., D.E.N., A.C., J.C.S., J.R., A.H.B.)
- Department of Pathology, Maastricht University Medical Center, the Netherlands (J.C.S., A.H.B.)
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Xu J, Guo J, Jiang Y, Liu Y, Liao K, Fu Z, Xiong Z. Improved characterization of the relationship between long intergenic non-coding RNA Linc00152 and the occurrence and development of malignancies. Cancer Med 2019; 8:4722-4731. [PMID: 31270960 PMCID: PMC6712457 DOI: 10.1002/cam4.2245] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/28/2019] [Accepted: 04/30/2019] [Indexed: 12/15/2022] Open
Abstract
Linc00152, located on chromosome 2p11.2, is a long intergenic non-coding RNA molecule with 828 nucleotides that is highly expressed in many types of human tumor tissues, especially in malignant tumors of the digestive system. Linc00152 promotes the occurrence and development of tumors by increasing tumor cell proliferation, invasion, metastasis, and apoptosis. Additionally, linc00152 contributes to the carcinogenesis of several cancers, including gastric cancer, liver cancer, hepatocellular carcinoma, gallbladder cancer, clear cell renal cell carcinoma, and colorectal cancer, by disturbing various signaling pathways (eg PI3K/AKT, mTOR, IL-1, and NOTCH 1 signaling pathways). High linc00152 expression levels are associated with chemoresistance as well as poor prognosis and shorter survival. Continual advances made in the relevant research have indicated that linc00152 may be useful as a new tumor molecular biomarker, applicable for tumor diagnosis, targeted therapy, and prognosis assessment. This review summarizes the progress in the research into the relationship between linc00152 and the occurrence and development of malignancies based on molecular functions, regulatory mechanisms, and clinical applications.
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Affiliation(s)
- Jiasheng Xu
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jingjing Guo
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yangkai Jiang
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yujun Liu
- Queen Mary College of Nanchang University, Nanchang, China
| | - Kaili Liao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhonghua Fu
- Department of Burns, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhenfang Xiong
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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Li M, Wang Q, Xue F, Wu Y. lncRNA- CYTOR Works as an Oncogene Through the CYTOR/miR-3679-5p/ MACC1 Axis in Colorectal Cancer. DNA Cell Biol 2019; 38:572-582. [PMID: 31144988 DOI: 10.1089/dna.2018.4548] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Pieces of evidence have shown that cytoskeleton regulator RNA (CYTOR), a long noncoding RNA (lncRNA), played a pivotal role in development and progression of a variety of cancers. In contrast, further research is needed to study the clinical significance and the detailed mechanism of action of lncRNA-CYTOR in colorectal cancer (CRC). This study aimed to investigate the clinical significance of CYTOR in CRC prognosis and identify the relevant potential signaling pathways and underlying mechanism of competing endogenous RNA. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) indicated that the expression of CYTOR was significantly elevated in CRC tumor tissues and cell lines. Aberrant expression of CYTOR was significantly related to TNM stage, T stage, N stage, and perineural and venous invasions. Survival analysis indicated that high-CYTOR expression was associated with poor overall survival in CRC patients (p = 0.0057), and multivariate analysis showed that high-CYTOR expression was an independent prognostic factor, which led to poor OS. In addition, bioinformatics analysis revealed that there were 18 microRNAs (miRNAs) interacted with CYTOR, and one of them, miR-3679-5p might collaborate with metastasis-associated in colon cancer-1 (MACC1), which was selected for further analysis. Pearson correlation analysis showed a significant positive correlation between the expression levels of CYTOR and MACC1. In conclusion, this study suggested that lncRNA-CYTOR played an important role in tumorigenesis and development through the CYTOR/miR-3679-5p/MACC1 axis.
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Affiliation(s)
- Mingjie Li
- 1 Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Qianyun Wang
- 2 Fuzhou Center for Disease Control and Prevention, Fuzhou, China
| | - Fangqin Xue
- 3 Department of Gastrointestinal Surgery, Fujian Provincial Hospital, Fuzhou, China
| | - Yan'an Wu
- 1 Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China.,4 Department of Clinical Laboratory, Fujian Provincial Hospital, Fuzhou, China
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Ouyang W, Ren L, Liu G, Chi X, Wei H. LncRNA MIR4435-2HG predicts poor prognosis in patients with colorectal cancer. PeerJ 2019; 7:e6683. [PMID: 30972258 PMCID: PMC6450379 DOI: 10.7717/peerj.6683] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/21/2019] [Indexed: 12/30/2022] Open
Abstract
Background LncRNA MIR4435-2HG is observed in a variety of cancers, while its role in colorectal cancer is unknown. We aimed to demonstrate the relationship between MIR4435-2HG and colorectal cancer based on The Cancer Genome Atlas (TCGA) database. Materials and Methods Patients with colorectal cancer were collected from TCGA. We compared the expression of MIR4435-2HG in colorectal cancer and normal tissues with Wilcoxon rank sum test, and logistic regression was used to evaluate the relationship between MIR4435-2HG and clinicopathological characters. Moreover, Kaplan–Meier and Cox regression was performed to evaluate the correlation between MIR4435-2HG and survival rate. Gene set enrichment analysis (GSEA) was also conducted to annotate biological function of MIR4435-2HG. Results MIR4435-2HG level was elevated in colorectal cancer tissues. Increased level of MIR4435-2HG was significantly correlated with TNM stage (OR = 1.66 for T1/T2 vs. T3/T4; OR = 1.68 for N0 vs. N1/N2), stage (OR = 1.66 for stage 1/2 vs. stage 3/4), and carcinoembryonic antigen level before treatment (OR = 1.70 for <5 vs. ≥5) (all P-value <0.05). High MIR4435-2HG expression had a poorer progression-free survival (p = 0.048), and overall survival (OS) (P = 0.028), which were validated in the GSE92921 and GSE29621 datasets. MIR4435-2HG expression (P = 0.040, HR = 1.955 (95% CI [1.031–3.710])) was independently correlated with OS. GSEA demonstrated that the P38/MAPK pathway, the VEGF pathway, the cell adhesion molecules cams, the NOD-like receptor signaling pathway, the cell surface interactions at the vascular wall, and integrin cell surface interactions were differentially enriched in MIR4435-2HG high expression phenotype. Conclusions Increased MIR4435-2HG might be a potential biomarker for the diagnosis and prognosis of colorectal cancer. Moreover, MIR4435-2HG might participate in the development of colorectal cancer via the P38/MAPK and VEGF pathway.
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Affiliation(s)
- Wen Ouyang
- The Second Clinical Medical College, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Linlin Ren
- Department of Gastroenterology, Affiliated hospital of Qingdao University, Qingdao, Shandong, China
| | - Guohong Liu
- Department of Gastroenterology, Affiliated hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiaosa Chi
- Department of Gastroenterology, Affiliated hospital of Qingdao University, Qingdao, Shandong, China
| | - Hongyun Wei
- Department of Gastroenterology, Affiliated hospital of Qingdao University, Qingdao, Shandong, China
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Abstract
Biomarker-driven personalized cancer therapy is a field of growing interest, and several molecular tests have been developed to detect biomarkers that predict, e.g., response of cancers to particular therapies. Identification of these molecules and understanding their molecular mechanisms is important for cancer prognosis and the development of therapeutics for late stage diseases. In the past, significant efforts have been placed on the discovery of protein or DNA-based biomarkers while only recently the class of long non-coding RNA (lncRNA) has emerged as a new category of biomarker. The mammalian genome is pervasively transcribed yielding a vast amount of non-protein-coding RNAs including lncRNAs. Hence, these transcripts represent a rich source of information that has the potential to significantly contribute to precision medicine in the future. Importantly, many lncRNAs are differentially expressed in carcinomas and they are emerging as potent regulators of tumor progression and metastasis. Here, we will highlight prime examples of lncRNAs that serve as marker for cancer progression or therapy response and which might represent promising therapeutic targets. Furthermore, we will introduce lncRNA targeting tools and strategies, and we will discuss potential pitfalls in translating these into clinical trials.
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Tiessen I, Abildgaard MH, Lubas M, Gylling HM, Steinhauer C, Pietras EJ, Diederichs S, Frankel LB, Lund AH. A high-throughput screen identifies the long non-coding RNA DRAIC as a regulator of autophagy. Oncogene 2019; 38:5127-5141. [DOI: 10.1038/s41388-019-0783-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 02/15/2019] [Accepted: 03/02/2019] [Indexed: 12/11/2022]
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38
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Guo YZ, Sun HH, Wang XT, Wang MT. Transcriptomic analysis reveals key lncRNAs associated with ribosomal biogenesis and epidermis differentiation in head and neck squamous cell carcinoma. J Zhejiang Univ Sci B 2019; 19:674-688. [PMID: 30178634 DOI: 10.1631/jzus.b1700319] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
OBJECTIVE In this study, we aimed to expand current knowledge of head and neck squamous cell carcinoma (HNSCC)-associated long noncoding RNAs (lncRNAs), and to discover potential lncRNA prognostic biomarkers for HNSCC based on next-generation RNA-seq. METHODS RNA-seq data of 546 samples from patients with HNSCC were downloaded from The Cancer Genome Atlas (TCGA), including 43 paired samples of tumor tissue and adjacent normal tissue. An integrated analysis incorporating differential expression, weighted gene co-expression networks, functional enrichment, clinical parameters, and survival analysis was conducted to discover HNSCC-associated lncRNAs. The function of CYTOR was verified by cell-based experiments. To further identify lncRNAs with prognostic significance, a multivariate Cox proportional hazard regression analysis was performed. The identified lncRNAs were validated with an independent cohort using clinical feature relevance analysis and multivariate Cox regression analysis. RESULTS We identified nine HNSCC-relevant lncRNAs likely to play pivotal roles in HNSCC onset and development. By functional enrichment analysis, we revealed that CYTOR might participate in the multistep pathological processes of cancer, such as ribosome biogenesis and maintenance of genomic stability. CYTOR was identified to be positively correlated with lymph node metastasis, and significantly negatively correlated with overall survival (OS) and disease free survival (DFS) of HNSCC patients. Moreover, CYTOR inhibited cell apoptosis following treatment with the chemotherapeutic drug diamminedichloroplatinum (DDP). HCG22, the most dramatically down-regulated lncRNA in tumor tissue, may function in epidermis differentiation. It was also significantly associated with several clinical features of patients with HNSCC, and positively correlated with patient survival. CYTOR and HCG22 maintained their prognostic values independent of several clinical features in multivariate Cox hazards analysis. Notably, validation either based on an independent HNSCC cohort or by laboratory experiments confirmed these findings. CONCLUSIONS Our transcriptomic analysis suggested that dysregulation of these HNSCC-associated lncRNAs might be involved in HNSCC oncogenesis and progression. Moreover, CYTOR and HCG22 were confirmed as two independent prognostic factors for HNSCC patient survival, providing new insights into the roles of these lncRNAs in HNSCC as well as clinical applications.
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Affiliation(s)
- Yu-Zhu Guo
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Hui-Hui Sun
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Xiang-Ting Wang
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Mei-Ting Wang
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China.,College of Liren, Yanshan University, Qinhuangdao 066004, China
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39
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Klingenberg M, Groß M, Goyal A, Polycarpou-Schwarz M, Miersch T, Ernst AS, Leupold J, Patil N, Warnken U, Allgayer H, Longerich T, Schirmacher P, Boutros M, Diederichs S. The Long Noncoding RNA Cancer Susceptibility 9 and RNA Binding Protein Heterogeneous Nuclear Ribonucleoprotein L Form a Complex and Coregulate Genes Linked to AKT Signaling. Hepatology 2018; 68:1817-1832. [PMID: 29790588 DOI: 10.1002/hep.30102] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/08/2018] [Accepted: 05/12/2018] [Indexed: 12/31/2022]
Abstract
The identification of viability-associated long noncoding RNAs (lncRNAs) might be a promising rationale for new therapeutic approaches in liver cancer. Here, we applied an RNA interference screening approach in hepatocellular carcinoma (HCC) cell lines to find viability-associated lncRNAs. Among the multiple identified lncRNAs with a significant impact on HCC cell viability, we selected cancer susceptibility 9 (CASC9) due to the strength of its phenotype, expression, and up-regulation in HCC versus normal liver. CASC9 regulated viability across multiple HCC cell lines as shown by clustered regularly interspaced short palindromic repeats interference and single small interfering RNA (siRNA)-mediated and siRNA pool-mediated depletion of CASC9. Further, CASC9 depletion caused an increase in apoptosis and a decrease of proliferation. We identified the RNA binding protein heterogeneous nuclear ribonucleoprotein L (HNRNPL) as a CASC9 interacting protein by RNA affinity purification and validated it by native RNA immunoprecipitation. Knockdown of HNRNPL mimicked the loss-of-viability phenotype observed upon CASC9 depletion. Analysis of the proteome (stable isotope labeling with amino acids in cell culture) of CASC9-depleted and HNRNPL-depleted cells revealed a set of coregulated genes which implied a role of the CASC9:HNRNPL complex in AKT signaling and DNA damage sensing. CASC9 expression levels were elevated in patient-derived tumor samples compared to normal control tissue and had a significant association with overall survival of HCC patients. In a xenograft chicken chorioallantoic membrane model, we measured decreased tumor size after knockdown of CASC9. Conclusion: Taken together, we provide a comprehensive list of viability-associated lncRNAs in HCC; we identified the CASC9:HNRNPL complex as a clinically relevant viability-associated lncRNA/protein complex which affects AKT signaling and DNA damage sensing in HCC.
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Affiliation(s)
- Marcel Klingenberg
- Division of RNA Biology & Cancer, German Cancer Research Center.,Faculty of Biosciences, Heidelberg University.,Institute of Pathology, University Hospital Heidelberg.,Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology, University of Heidelberg
| | - Matthias Groß
- Division of RNA Biology & Cancer, German Cancer Research Center.,Institute of Pathology, University Hospital Heidelberg
| | - Ashish Goyal
- Division of RNA Biology & Cancer, German Cancer Research Center
| | | | - Thilo Miersch
- Division of Signaling and Functional Genomics, German Cancer Research Center
| | - Anne-Sophie Ernst
- Faculty of Biosciences, Heidelberg University.,Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology, University of Heidelberg.,Institute of Physiology and Pathophysiology, University of Heidelberg
| | - Jörg Leupold
- Department of Experimental Surgery-Cancer Metastasis, Medical Faculty Mannheim, and Centre for Biomedicine and Medical Technology Mannheim, University of Heidelberg
| | - Nitin Patil
- Department of Experimental Surgery-Cancer Metastasis, Medical Faculty Mannheim, and Centre for Biomedicine and Medical Technology Mannheim, University of Heidelberg
| | - Uwe Warnken
- Genomics and Proteomics Core Facility, German Cancer Research Center, Heidelberg, Germany
| | - Heike Allgayer
- Department of Experimental Surgery-Cancer Metastasis, Medical Faculty Mannheim, and Centre for Biomedicine and Medical Technology Mannheim, University of Heidelberg
| | | | | | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center
| | - Sven Diederichs
- Division of RNA Biology & Cancer, German Cancer Research Center.,Division of Cancer Research, Department of Thoracic Surgery, Medical Center, University of Freiburg.,Faculty of Medicine, University of Freiburg.,German Cancer Consortium, Freiburg, Germany
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40
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Pyatnitskiy MA, Karpov DS, Moshkovskii SA. [Searching for essential genes in cancer genomes]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2018; 64:303-314. [PMID: 30135277 DOI: 10.18097/pbmc20186404303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The concept of essential genes, whose loss of functionality leads to cell death, is one of the fundamental concepts of genetics and is important for fundamental and applied research. This field is particularly promising in relation to oncology, since the search for genetic vulnerabilities of cancer cells allows us to identify new potential targets for antitumor therapy. The modern biotechnology capacities allow carrying out large-scale projects for sequencing somatic mutations in tumors, as well as directly interfering the genetic apparatus of cancer cells. They provided accumulation of a considerable body of knowledge about genetic variants and corresponding phenotypic manifestations in tumors. In the near future this knowledge will find application in clinical practice. This review describes the main experimental and computational approaches to the search for essential genes, concentrating on the application of these methods in the field of molecular oncology.
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Affiliation(s)
- M A Pyatnitskiy
- Institute of Biomedical Chemistry, Moscow, Russia; Higher School of Economics, Moscow, Russia
| | - D S Karpov
- Institute of Biomedical Chemistry, Moscow, Russia; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - S A Moshkovskii
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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41
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Reon BJ, Takao Real Karia B, Kiran M, Dutta A. LINC00152 Promotes Invasion through a 3'-Hairpin Structure and Associates with Prognosis in Glioblastoma. Mol Cancer Res 2018; 16:1470-1482. [PMID: 29991527 DOI: 10.1158/1541-7786.mcr-18-0322] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/07/2018] [Accepted: 06/29/2018] [Indexed: 01/24/2023]
Abstract
Long noncoding RNAs (lncRNA) are increasingly implicated in oncogenesis. Here, it is determined that LINC00152/CYTOR is upregulated in glioblastoma multiforme (GBM) and aggressive wild-type IDH1/2 grade 2/3 gliomas and upregulation associates with poor patient outcomes. LINC00152 is similarly upregulated in over 10 other cancer types and associates with a poor prognosis in 7 other cancer types. Inhibition of the mostly cytoplasmic LINC00152 decreases, and overexpression increases cellular invasion. LINC00152 knockdown alters the transcription of genes important to epithelial-to-mesenchymal transition (EMT). PARIS and Ribo-seq data, together with secondary structure prediction, identified a protein-bound 121-bp stem-loop structure at the 3' end of LINC00152 whose overexpression is sufficient to increase invasion of GBM cells. Point mutations in the stem-loop suggest that stem formation in the hairpin is essential for LINC00152 function. LINC00152 has a nearly identical homolog, MIR4435-2HG, which encodes a near identical hairpin, is equally expressed in low-grade glioma (LGG) and GBM, predicts poor patient survival in these tumors, and is also reduced by LINC00152 knockdown. Together, these data reveal that LINC00152 and its homolog MIR4435-2HG associate with aggressive tumors and promote cellular invasion through a mechanism that requires the structural integrity of a hairpin structure.Implications: Frequent upregulation of the lncRNA, LINC00152, in glioblastoma and other tumor types combined with its prognostic potential and ability to promote invasion suggests LINC00152 as a potential biomarker and therapeutic target. Mol Cancer Res; 16(10); 1470-82. ©2018 AACR.
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Affiliation(s)
- Brian J Reon
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | - Bruno Takao Real Karia
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | - Manjari Kiran
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia.
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Huang Y, Luo H, Li F, Yang Y, Ou G, Ye X, Li N. LINC00152 down-regulated miR-193a-3p to enhance MCL1 expression and promote gastric cancer cells proliferation. Biosci Rep 2018; 38:BSR20171607. [PMID: 29339419 PMCID: PMC5938421 DOI: 10.1042/bsr20171607] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/09/2017] [Accepted: 01/16/2018] [Indexed: 12/13/2022] Open
Abstract
The present work aimed to probe into the effect of long non-coding RNA (lncRNA) LINC00152 on gastric cancer (GC) cells proliferation by regulating miR-193a-3p and its target gene MCL1 Transfected si-LINC00152 was used to down-regulate LINC00152, and cells proliferation was measured by the cell counting kit-8 (CCK-8) assay. Cell apoptosis and cell cycle were analyzed by flow cytometry (FCM). Besides, we also detected the potential functional effects of differential expression of LINC00152 in vivo using nude mouse xenograft model. We overexpressed and downexpressed miR-193a-3p to study the in vitro effect of miR-193a-3p on GC cells proliferation and vitality. And MCL1 was silenced by shRNA to investigate the effect of MCL1 on proliferation of GC cells. In this research, LINC00152 was proven to have a higher expression level in GC tissues than in the adjacent normal tissues. GC cells proliferation was inhibited after LINC00152 was down-regulated. LINC00152 inhibited the expression of miR-193a-3p, which negatively regulated MCL1 In addition, GC cells proliferation was inhibited by cell transfection with shRNA-MCL1, and enhanced by transfection with miR-193a-3p mimics. Our study suggested that LINC00152 was overexpressed in GC tissues, and it down-regulated miR-193a-3p to enhance MCL1 expression thereby promoting GC cells proliferation.
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Affiliation(s)
- Yong Huang
- Department of Gastrointestinal Surgery, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, Guangdong, China
| | - Hui Luo
- Anesthesia Surgery Center, Lingnan Hospital, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 51000, Guangdong, China
| | - Fang Li
- Supply Room, Lingnan Hospital, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 51000, Guangdong, China
| | - Yun'e Yang
- Department of Gastrointestinal Surgery, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, Guangdong, China
| | - Guangsheng Ou
- Department of Gastrointestinal Surgery, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, Guangdong, China
| | - Xiaolong Ye
- Department of Gastrointestinal Surgery, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, Guangdong, China
| | - Nianchu Li
- Department of Hepatobiliary Surgery, Nanning Second People's Hospital, Nanning 530031, Guangxi, China
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Ma P, Wang H, Sun J, Liu H, Zheng C, Zhou X, Lu Z. LINC00152 promotes cell cycle progression in hepatocellular carcinoma via miR-193a/b-3p/CCND1 axis. Cell Cycle 2018; 17:974-984. [PMID: 29895195 PMCID: PMC6103663 DOI: 10.1080/15384101.2018.1464834] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 04/08/2018] [Indexed: 01/08/2023] Open
Abstract
Long intergenic non-coding RNA 00152 (LINC00152) is aberrantly expressed in various human malignancies and plays an important role in the pathogenesis. Here, we found that LINC00152 is upregulated in hepatocellular carcinoma (HCC) tissues as compared to adjacent non-neoplastic tissues; gain-and-loss-of-function analyses in vitro showed that LINC00152 facilitates HCC cell cycle progression through regulating the expression of CCND1. LINC00152 knockdown inhibits tumorigenesis in vivo. MS2-RIP analysis indicated that LINC00152 binds directly to miR-193a/b-3p, as confirmed by luciferase reporter assays. Furthermore, ectopic expression of LINC00152 partially halted the decrease in CCND1 expression and cell proliferation capacity induced by miR-193a/b-3p overexpression. Thus, LINC00152 acts as a competing endogenous RNA (ceRNA) by sponging miR-193a/b-3p to modulate its target gene, CCND1. Our findings establish a ceRNA mechanism regulating cell proliferation in HCC via the LINC00152/miR-193a/b-3p/CCND1 signalling axis, and identify LINC00152 as a potential therapeutic target for HCC.
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Affiliation(s)
- Pei Ma
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Haitao Wang
- Department of General Surgery, Research Center of Digestive Diseases, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jiangyang Sun
- Department of Hepatobiliary and Pancreas, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hongzhou Liu
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chao Zheng
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xin Zhou
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zhongxin Lu
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Sun K, Hu P, Xu F. LINC00152/miR-139-5p regulates gastric cancer cell aerobic glycolysis by targeting PRKAA1. Biomed Pharmacother 2017; 97:1296-1302. [PMID: 29156518 DOI: 10.1016/j.biopha.2017.11.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 12/30/2022] Open
Abstract
Gastric cancer is one of the most common cancers in the world and glycolysis is a major feature of gastric cancer. MicroRNAs (miRNAs) involve in gastric cancer cell proliferation, glycolysis and other cellular processes. MiR-139-5p is reported as a tumor suppressor in cancers, however, the role of miR-139-5p including glycolytic metabolism is unclear in gastric cancer. So, the purpose of the present study is to elucidate the underlying mechanism in gastric cancer metabolism mediated by miR-139-5p. Our results revealed that miR-139-5p inhibited glycolysis by regulating AMP-activated, alpha 1 catalytic subunit (PRKAA1) expression in gastric cancer cells. We also found that miR-139-5p was down-regulated by long intergenic non-coding RNA 152 (LINC00152) in gastric cancer cells. Our results indicate that LINC00152/miR-139-5p facilitates gastric cancer cell glycolysis by regulating PRKAA1 expression.
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Affiliation(s)
- Keke Sun
- Department of Gastroenterology, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo, Zhejiang, China.
| | - Pingping Hu
- Department of Gastroenterology, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Feng Xu
- Department of Gastroenterology, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo, Zhejiang, China
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Acharya S, Hartmann M, Erhardt S. Chromatin-associated noncoding RNAs in development and inheritance. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28840663 DOI: 10.1002/wrna.1435] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 12/13/2022]
Abstract
Noncoding RNAs (ncRNAs) have emerged as crucial players in chromatin regulation. Their diversity allows them to partake in the regulation of numerous cellular processes across species. During development, long and short ncRNAs act in conjunction with each other where long ncRNAs (lncRNAs) are best understood in establishing appropriate gene expression patterns, while short ncRNAs (sRNAs) are known to establish constitutive heterochromatin and suppress mobile elements. Additionally, increasing evidence demonstrates roles of sRNAs in several typically lncRNA-mediated processes such as dosage compensation, indicating a complex regulatory network of noncoding RNAs. Together, various ncRNAs establish many mitotically heritable epigenetic marks during development. Additionally, they participate in mechanisms that regulate maintenance of these epigenetic marks during the lifespan of the organism. Interestingly, some epigenetic traits are transmitted to the next generation(s) via paramutations or transgenerational inheritance mediated by sRNAs. In this review, we give an overview of the various functions and regulations of ncRNAs and the mechanisms they employ in the establishment and maintenance of epigenetic marks and multi-generational transmission of epigenetic traits. WIREs RNA 2017, 8:e1435. doi: 10.1002/wrna.1435 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Sreemukta Acharya
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, and CellNetworks, Im Neuenheimer Feld 282, Heidelberg, Germany
| | - Mark Hartmann
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sylvia Erhardt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, and CellNetworks, Im Neuenheimer Feld 282, Heidelberg, Germany
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Quan FY, Jiang J, Zhai YF, Li B, Wu XH, Nie W. The prognostic effect of LINC00152 for cancer: a meta-analysis. Oncotarget 2017; 8:75427-75433. [PMID: 29088878 PMCID: PMC5650433 DOI: 10.18632/oncotarget.20130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 07/30/2017] [Indexed: 12/26/2022] Open
Abstract
No meta-analysis has been performed to evaluate the association between LINC00152 and the survival of patients with cancers. We thus carried out this study. The online databases, such as PubMed, EMBASE, and the Cochrane controlled trials register, were searched to identify relevant articles. Dichotomous data were analyzed using the odds ratio (OR) as the summary statistic. The association between LINC00152 and survival of cancer was analyzed by pooling the hazard ratio (HR) with its corresponding 95% confidence interval (CI). Nine studies with 862 patients with cancer were included in this meta-analysis. The expression of LINC00152 was not associated with the age of patients (OR = 0.79, 95% CI = 0.55–1.14) and gender (OR = 1.08, 95% CI = 0.74–1.58). However, we found significant positive associations between LINC00152 and lymph node metastasis (OR = 2.54, 95% CI = 1.54–4.18) and TNM stage (OR = 2.32, 95% CI = 1.36–3.93). Furthermore, the expression of LINC00152 was significantly associated with tumor recurrence (OR = 3.32, 95% CI = 1.98–5.57) and shorter OS (HR = 1.94, 95% CI = 1.25–3.02). In conclusion, the results of this meta-analysis suggest that LINC00152 might be a biomarker for shorter OS and tumor recurrence in cancers.
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Affiliation(s)
- Fei-Yu Quan
- The 425th Hospital of PLA, Sanya, Hainan, China
| | - Jun Jiang
- Department of Respiratory Medicine, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Yi-Fan Zhai
- Department of Respiratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Bing Li
- Department of Respiratory Medicine, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Xin-Hua Wu
- Department of Internal Medicine, The 425th Hospital of PLA, Hainan, China
| | - Wei Nie
- Department of Internal Medicine, The 425th Hospital of PLA, Hainan, China
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