1
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Mostafa SM, Wang L, Tian B, Graber J, Moore C. Transcriptomic analysis reveals regulation of adipogenesis via long non-coding RNA, alternative splicing, and alternative polyadenylation. Sci Rep 2024; 14:16964. [PMID: 39043790 PMCID: PMC11266407 DOI: 10.1038/s41598-024-67648-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 07/15/2024] [Indexed: 07/25/2024] Open
Abstract
Obesity is characterized by dysregulated adipogenesis that leads to increased number and/or size of adipocytes. Understanding the molecular mechanisms governing adipogenesis is therefore key to designing therapeutic interventions against obesity. In our study, we analyzed 3'-end sequencing data that we generated from human preadipocytes and adipocytes, as well as previously published RNA-seq datasets, to elucidate mechanisms of regulation via long non-coding RNA (lncRNA), alternative splicing (AS) and alternative polyadenylation (APA). We discovered lncRNAs that have not been previously characterized but may be key regulators of white adipogenesis. We also detected 100 AS events and, using motif enrichment analysis, identified RNA binding proteins (RBPs) that could mediate exon skipping-the most prevalent AS event. In addition, we show that usage of alternative poly(A) sites in introns or 3'-UTRs of key adipogenesis genes leads to isoform diversity, which can have significant biological consequences on differentiation efficiency. We also identified RBPs that may modulate APA and defined how 3'-UTR APA can regulate gene expression through gain or loss of specific microRNA binding sites. Taken together, our bioinformatics-based analysis reveals potential therapeutic avenues for obesity through manipulation of lncRNA levels and the profile of mRNA isoforms via alternative splicing and polyadenylation.
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Affiliation(s)
- Salwa Mohd Mostafa
- Graduate School of Biomedical Sciences and Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Luyang Wang
- Gene Expression and Regulation Program, and Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Bin Tian
- Gene Expression and Regulation Program, and Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Joel Graber
- Mount Desert Island Biological Laboratory, Salisbury Cove, ME, 04609, USA
| | - Claire Moore
- Graduate School of Biomedical Sciences and Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA, 02111, USA.
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2
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Lu W, Li L, Li L, Guo N, Ma X. Circular RNA circ_0101675 Promotes NSCLC Cell Proliferation, Migration, Invasion, Angiogenesis and Immune Evasion by Sponging miR-607/PDL1 Axis. Biochem Genet 2024; 62:1539-1555. [PMID: 37646893 DOI: 10.1007/s10528-023-10493-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/06/2023] [Indexed: 09/01/2023]
Abstract
Non-small cell lung cancer (NSCLC) is one of the most common and fatal cancers in the world. Circular RNA (circRNA) can broadly participate in the initiation and progression of the NSCLC. However, the regulatory mechanisms of circRNA in NSCLC remain poorly understood. In present study, we aimed to explore the potential role of circ_0101675 in the progression of NSCLC. Quantitative real-time polymerase chain reaction was performed to examine the expression of circ_0101675, microRNA-607 (miR-607) and programmed cell death receptor ligand 1 (PDL1) in NSCLC tissues and cells. Cell count kit 8 assay, colony formation assay, wound healing assay, transwell assay, tube formation assay and flow cytometry were applied to examine NSCLC cell proliferation, migration, invasion, angiogenesis and apoptosis. NSCLC cells were co-cultured with peripheral blood mononuclear cells to assess immune response. The protein levels of PDL1 and proteins related to apoptosis were detected by western blotting. Dual-luciferase reporter assay and RNA immunoprecipitation assay were conducted to verify the direct target site between miR-607 and circ_0101675 or PDL1. The experiments in vivo were employed to explore the effects of circ_0101675 on tumor growth in NSCLC. Circ_0101675 and PDL1 were high-expressed, while miR-607 was low-expressed in NSCLC cells and cancer tissues. The suppression of circ_0101675 suppressed growth, migration, invasion, angiogenesis and immune escape in NSCLC cells. Mechanistically, we found that high level of circ_0101675 could upregulate PDL1 expression via sponging miR-607. Moreover, the down-regulation of circ_0101675 inhibited the growth of NSCLC tumors in vivo by enhancing miR-607 expression to decrease PDL1 expression. Taken together, our results suggested that circ_0101675 might promote the proliferation, migration, invasion, and immune evasion abilities of NSCLC through miR-607/PDL1 axis.
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Affiliation(s)
- Wei Lu
- Department of Thoracic Surgery, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, No.43 Renmin Avenue, Haikou City, 570208, Hainan Province, People's Republic of China
| | - Liang Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Hainan Medical University, Haikou, People's Republic of China
| | - Li Li
- Department of Thoracic Surgery, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, No.43 Renmin Avenue, Haikou City, 570208, Hainan Province, People's Republic of China
| | - Nanbian Guo
- Department of Thoracic Surgery, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, No.43 Renmin Avenue, Haikou City, 570208, Hainan Province, People's Republic of China
| | - Ximiao Ma
- Department of Thoracic Surgery, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, No.43 Renmin Avenue, Haikou City, 570208, Hainan Province, People's Republic of China.
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3
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Xiao X, Liu M, Xie S, Liu C, Huang X, Huang X. Long non-coding HOXA-AS3 contributes to osteosarcoma progression through the miR-1286/TEAD1 axis. J Orthop Surg Res 2023; 18:730. [PMID: 37752588 PMCID: PMC10523635 DOI: 10.1186/s13018-023-04214-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/17/2023] [Indexed: 09/28/2023] Open
Abstract
Long non-coding RNA (lncRNA) HOXA cluster antisense RNA 3 (HOXA-AS3) regulates the progression of several types of human malignancy. However, the role and potential mechanism of HOXA-AS3 in osteosarcoma (OS) remain unknown. In this study, upregulation of HOXA-AS3 was observed in OS tissues and cell lines and associated with poor clinical outcomes. Silencing of HOXA-AS3 significantly inhibited the proliferation, migration and invasion of OS cells in vitro and suppressed the tumorigenesis of OS cells in vivo. Furthermore, knockdown of HOXA-AS3 inhibited the proliferation and migration of human umbilical vein endothelial cells (HUVECs) and epithelial-to-mesenchymal transition (EMT) in OS. Further investigation of this mechanism revealed that HOXA-AS3 could directly upregulate the expression of TEAD1 via its competing endogenous RNA (ceRNA) activity on miR-1286. This study clarified the oncogenic roles of the HOXA-AS3/miR-1286/TEAD1 axis in OS progression, suggesting a novel therapeutic target for OS.
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Affiliation(s)
- Xiangjun Xiao
- Department of Hand and Foot Surgery, Nanhua Hospital Affiliated to Nanhua University, Hengyang, 421002, China
| | - Mingjiang Liu
- Department of Orthopedic Trauma and Hand Surgery, Changsha Central Hospital Affiliated to Nanhua University, NO. 161 Shaoshan Nan Road, Changsha, 410018, China.
| | - Songlin Xie
- Department of Hand and Foot Surgery, Nanhua Hospital Affiliated to Nanhua University, Hengyang, 421002, China
| | - Changxiong Liu
- Department of Hand and Foot Surgery, Nanhua Hospital Affiliated to Nanhua University, Hengyang, 421002, China
| | - Xinfeng Huang
- Department of Hand and Foot Surgery, Nanhua Hospital Affiliated to Nanhua University, Hengyang, 421002, China
| | - Xiongjie Huang
- Department of Hand and Foot Surgery, Nanhua Hospital Affiliated to Nanhua University, Hengyang, 421002, China
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4
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Zhang L, Liu H, Long Y, Zhang Y. Overexpression of LINC00607 inhibits cell growth and aggressiveness by regulating the miR-1289/EFNA5 axis in non-small-cell lung cancer. Open Med (Wars) 2023; 18:20230649. [PMID: 37333453 PMCID: PMC10276612 DOI: 10.1515/med-2023-0649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 12/09/2022] [Accepted: 01/03/2023] [Indexed: 06/20/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play a key role in cancer progression, including non-small-cell lung cancer (NSCLC). LncRNA long intergenic non-protein-coding RNA 00607 (LINC00607) was previously discovered to be downregulated in lung adenocarcinoma tissues. Nevertheless, the potential role of LINC00607 in NSCLC is still unclear. The expression of LINC00607, miR-1289, and ephrin A5 (EFNA5) in NSCLC tissues and cells was tested by reverse transcription quantitative polymerase chain reaction. Cell viability, proliferation, migration, and invasion were measured by 3-(4,5-dimethylthiazole-2-y1)-2,5-diphenyl tetrazolium bromide, colony formation, wound healing, and Transwell assays. The relationship among LINC00607, miR-1289, and EFNA5 in NSCLC cells was verified by the luciferase reporter assay, RNA pull-down assay, and RNA immunoprecipitation assay. In this study, LINC00607 was downregulated in NSCLC, and its low level is associated with poor prognosis of NSCLC patients. Furthermore, LINC00607 overexpression repressed NSCLC cell viability, proliferation, migration, and invasion. LINC00607 bound with miR-1289 in NSCLC. EFNA5 was a downstream target of miR-1289. EFNA5 overexpression also inhibited NSCLC cell viability, proliferation, migration, and invasion. EFNA5 knockdown antagonized the influence of LINC00607 overexpression on NSCLC cell phenotypes. Overall, LINC00607 serves as a tumor suppressor gene in NSCLC through binding with miR-1289 and modulating the level of EFNA5.
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Affiliation(s)
- Li Zhang
- Department of Clinical Laboratory Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi830011, Xinjiang, China
| | - Huimin Liu
- Department of Clinical Laboratory Center, Hospital of Xinjiang Production and Construction Corps, The Second Affiliated Hospital of Medical College of Shihezi University,
Urumqi830092, Xinjiang, China
| | - Yan Long
- Department of First Aid Center, Hospital of Xinjiang Production and Construction Corps, The Second Affiliated Hospital of Medical College of Shihezi University,
Urumqi830092, Xinjiang, China
| | - Yuan Zhang
- Department of Clinical Laboratory Center, Cancer Hospital of Xinjiang Medical University, No. 789, Suzhou East Street, Xinshi District, Urumqi830000, Xinjiang, China
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5
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Dong S, Wang W, Liao Z, Fan Y, Wang Q, Zhang L. MYC-activated LINC00607 promotes hepatocellular carcinoma progression by regulating the miR-584-3p/ROCK1 axis. J Gene Med 2023; 25:e3477. [PMID: 36740760 DOI: 10.1002/jgm.3477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/27/2022] [Accepted: 12/20/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND There have been many reports of long non-coding RNAs (lncRNAs) in tumors, and abnormally expressed lncRNA is closely related to hepatocellular carcinoma (HCC). The mechanism of LINC00607 in HCC has not been reported. METHODS We utilized qPCR to evaluate the RNA expression level. The mechanism of MYC binding to the LINC00607 promoter was revealed through chromatin immunoprecipitation assay and dual luciferase reporter assay. The proliferation and invasive ability were evaluated by CCK-8 and transwell assays. The relation between LINC00607 and miR-584-3p was assessed by RNA immunoprecipitation assay and dual luciferase reporter assay. The level of ROCK1 was evaluated by qPCR and western blot. RESULTS In this research, we found that the expression of LINC00607 was higher in HCC tissues when compared with that in the adjacent non-tumor tissues. Meanwhile, MYC was observed to interact with the LINC00607 promoter, leading to the upregulation of LINC00607 in HCC. We further revealed that LINC00607 functioned as a sponge for miR-584-3p. Cell proliferation and migration assays showed that miR-584-3p may inhibit the HCC progression. Moreover, we found that the miR-584-3p inhibitor could reverse the effects of LINC00607 downregulation in HCC through rescue experiments. Through verification, miR-584-3p bound to the 3' UTR of ROCK1 to downregulate its expression. CONCLUSION LINC00607 regulated by MYC can promote the proliferation, migration and invasion of HCC cells through the miR-584-3p/ROCK1 axis.
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Affiliation(s)
- Shuilin Dong
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
| | - Wei Wang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
| | - Zhibin Liao
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
| | - Yawei Fan
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
| | - Qi Wang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
| | - Lei Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China.,Department of Hepatobiliary Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Shanxi Medical University; Shanxi Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Taiyuan, China
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6
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Boos F, Oo JA, Warwick T, Günther S, Izquierdo Ponce J, Lopez M, Rafii D, Buchmann G, Pham MD, Msheik ZS, Li T, Seredinski S, Haydar S, Kashefiolasl S, Plate KH, Behr R, Mietsch M, Krishnan J, Pullamsetti SS, Bibli SI, Hinkel R, Baker AH, Boon RA, Schulz MH, Wittig I, Miller FJ, Brandes RP, Leisegang MS. The endothelial-enriched lncRNA LINC00607 mediates angiogenic function. Basic Res Cardiol 2023; 118:5. [PMID: 36700983 PMCID: PMC9879848 DOI: 10.1007/s00395-023-00978-3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/27/2023]
Abstract
Long non-coding RNAs (lncRNAs) can act as regulatory RNAs which, by altering the expression of target genes, impact on the cellular phenotype and cardiovascular disease development. Endothelial lncRNAs and their vascular functions are largely undefined. Deep RNA-Seq and FANTOM5 CAGE analysis revealed the lncRNA LINC00607 to be highly enriched in human endothelial cells. LINC00607 was induced in response to hypoxia, arteriosclerosis regression in non-human primates, post-atherosclerotic cultured endothelial cells from patients and also in response to propranolol used to induce regression of human arteriovenous malformations. siRNA knockdown or CRISPR/Cas9 knockout of LINC00607 attenuated VEGF-A-induced angiogenic sprouting. LINC00607 knockout in endothelial cells also integrated less into newly formed vascular networks in an in vivo assay in SCID mice. Overexpression of LINC00607 in CRISPR knockout cells restored normal endothelial function. RNA- and ATAC-Seq after LINC00607 knockout revealed changes in the transcription of endothelial gene sets linked to the endothelial phenotype and in chromatin accessibility around ERG-binding sites. Mechanistically, LINC00607 interacted with the SWI/SNF chromatin remodeling protein BRG1. CRISPR/Cas9-mediated knockout of BRG1 in HUVEC followed by CUT&RUN revealed that BRG1 is required to secure a stable chromatin state, mainly on ERG-binding sites. In conclusion, LINC00607 is an endothelial-enriched lncRNA that maintains ERG target gene transcription by interacting with the chromatin remodeler BRG1 to ultimately mediate angiogenesis.
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Affiliation(s)
- Frederike Boos
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - James A Oo
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Timothy Warwick
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Stefan Günther
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Judit Izquierdo Ponce
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Melina Lopez
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Diba Rafii
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Giulia Buchmann
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Minh Duc Pham
- Genome Biologics, Frankfurt, Germany
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt, Germany
| | - Zahraa S Msheik
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Department of Internal Medicine, Member of the DZL, Member of Cardio-Pulmonary Institute (CPI), Justus Liebig University, Giessen, Germany
| | - Tianfu Li
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Sandra Seredinski
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Shaza Haydar
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Sepide Kashefiolasl
- Department of Neurosurgery, University Hospital Frankfurt, Frankfurt, Germany
| | - Karl H Plate
- Institute of Neurology (Edinger Institute), Neuroscience Center, Goethe University, Frankfurt, Germany
- Frankfurt Cancer Institute, University Hospital, Goethe University, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt, Germany
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Rüdiger Behr
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany
- Platform Degenerative Diseases, German Primate Center-Leibniz Institute for Primate Research, Göttingen, Germany
| | - Matthias Mietsch
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany
- Laboratory Animal Science Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Jaya Krishnan
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt, Germany
- Cardio-Pulmonary Institute, Giessen, Germany
- Department of Medicine III, Cardiology/Angiology/Nephrology, Goethe University Hospital, Frankfurt am Main, Germany
| | - Soni S Pullamsetti
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
- Department of Internal Medicine, Member of the DZL, Member of Cardio-Pulmonary Institute (CPI), Justus Liebig University, Giessen, Germany
- Cardio-Pulmonary Institute, Giessen, Germany
| | - Sofia-Iris Bibli
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
- Institute for Vascular Signalling, Goethe University, Frankfurt, Germany
| | - Rabea Hinkel
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany
- Laboratory Animal Science Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Institute for Animal Hygiene, Animal Welfare and Farm Animal Behavior, University of Veterinary Medicine, Hannover, Germany
| | - Andrew H Baker
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, Scotland
- CARIM Institute, University of Maastricht, Maastricht, The Netherlands
| | - Reinier A Boon
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt, Germany
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU Medical Center, Amsterdam UMC, Amsterdam, The Netherlands
| | - Marcel H Schulz
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt, Germany
| | - Ilka Wittig
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany
| | - Francis J Miller
- Department of Medicine, Vanderbilt University Medical Center, Nashville, USA
- Veterans Affairs Medical Center, Nashville, TN, USA
| | - Ralf P Brandes
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany.
| | - Matthias S Leisegang
- Institut für Kardiovaskuläre Physiologie, Fachbereich Medizin der Goethe-Universität, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
- German Center of Cardiovascular Research (DZHK), Partner Site RheinMain, Frankfurt, Germany.
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7
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[Overexpression of miR-607 inhibits hepatocellular carcinoma cell growth and metastasis by down-regulating TRPC5]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2022; 42:1587-1593. [PMID: 36504050 PMCID: PMC9742782 DOI: 10.12122/j.issn.1673-4254.2022.11.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To investigate the clinical implications of abnormal expression of miR-607 in hepatocellular carcinoma (HCC) and its influence on HCC cell proliferation and migration. METHODS The expression of miR-607 in 45 pairs of HCC and adjacent tissues were detected with real-time PCR, and the correlation between miR-607 expression and clinicopathological features of the patients was analyzed. The effects of transfection with miR-607 mimics on proliferation, apoptosis, migration and invasion of two HCC cell lines (Huh-7 and HCCLM3) were evaluated using CCK-8 assay, flow cytometry, wound-healing assay and Transwell assay. A dual-luciferase reporter system was used to detect the direct binding between miR-607 and 3'-UTR of TRPC5 mRNA. Western blotting was used to measure the expressions of TRPC5, CCND1, MMP2 and phosphorylated Akt in the HCC cells. RESULTS The expression of miR-607 was significantly decreased in HCC tissues (P=0.029) and HCC cell lines (P < 0.05). In HCC patients, a low expression of miR-607 was associated with a larger tumor size (>5 cm, P=0.031), vascular invasion (P=0.027) and advanced TNM stages (Ⅲ + Ⅳ, P=0.015). In the two HCC cell line, overexpression of miR-607 significantly inhibited cell proliferation, migration, and invasion and enhanced cell apoptosis (P < 0.05). The results of dualluciferase reporter assay confirmed that TRPC5 was a direct target of miR- 607 in HCC cells. Overexpression of miR-607 significantly inhibited the expressions of TRPC5, CCND1, and MMP2 and suppressed Akt phosphorylation in HCC cells (P < 0.05). CONCLUSION A low expression of miR-607 in HCC is associated with poor clinicopathological phenotypes of HCC. Overexpression of miR-607 inhibits HCC growth and metastasis possibly by down- regulating TRPC5, which causes Akt signaling inactivation.
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8
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Wang YM, Zhao QW, Sun ZY, Lin HP, Xu X, Cao M, Fu YJ, Zhao XJ, Ma XM, Ye Q. Circular RNA hsa_circ_0003823 promotes the Tumor Progression, Metastasis and Apatinib Resistance of Esophageal Squamous Cell Carcinoma by miR-607/CRISP3 Axis. Int J Biol Sci 2022; 18:5787-5808. [PMID: 36263172 PMCID: PMC9576509 DOI: 10.7150/ijbs.76096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/30/2022] [Indexed: 01/12/2023] Open
Abstract
Background: Circular RNAs (CircRNAs) have attracted a growing interest of research in cancer. The regulatory roles and mechanisms of circRNAs in progression, metastasis and drug resistance of esophageal squamous cell carcinoma (ESCC) needed to be clarified. Our previous study revealed the crucial role of Apatinib in ESCC therapy. However, the correlation between circRNAs and Apatinib resistance remained unclear. Methods: 3 pairs of tumor and paracancerous tissues of ESCC patients were used for RNA sequencing. Western blot analysis, RNA immunoprecipitation (RIP), dual-luciferase reporter assays, apoptosis and animal assays were conducted to confirm the roles and specific mechanisms of hsa_circ_0003823 as well as the effects of it on Apatinib sensitivity in ESCC. Results: Our results revealed that hsa_circ_0003823 was highly expressed in ESCC and associated with poor prognosis. Further results indicated that hsa_circ_0003823 promoted proliferation and metastasis ability of ESCC. In the section of mechanism experiments, hsa_circ_0003823 regulated CRISP3 by targeting microRNA-607 (miR-607) to promote progression of ESCC. Besides, we found that silencing hsa_circ_0003823 improved Apatinib sensitivity. hsa_circ_0003823 resulted in Apatinib resistance by miR-607/CRISP3 axis. Conclusions: In this study, we elucidated the function of hsa_circ_0003823 and its role in promoting tumor progression, metastasis and Apatinib resistance of ESCC through miR-607/CRISP3 axis.
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Affiliation(s)
- Yu-Ming Wang
- Department of Thoracic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Qi-Wu Zhao
- Department of General Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200000, P.R. China
| | - Zhi-Yong Sun
- Department of Thoracic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Hai-Ping Lin
- Department of Thoracic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Xin Xu
- Department of Radiation Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Min Cao
- Department of Thoracic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Yu-Jie Fu
- Department of Thoracic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Xiao-Jing Zhao
- Department of Thoracic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Xiu-Mei Ma
- Department of Radiation Oncology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China.,✉ Corresponding authors: Qing Ye, Pujian road 160#, Shanghai, China (Tel: +8602168383707, ); Xiu-Mei Ma, Pujian road 160#, Shanghai, China ()
| | - Qing Ye
- Department of Thoracic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China.,✉ Corresponding authors: Qing Ye, Pujian road 160#, Shanghai, China (Tel: +8602168383707, ); Xiu-Mei Ma, Pujian road 160#, Shanghai, China ()
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9
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Sriram K, Luo Y, Yuan D, Malhi NK, Tapia A, Samara VA, Natarajan R, Bouman Chen Z. Vascular Regulation by Super Enhancer-Derived LINC00607. Front Cardiovasc Med 2022; 9:881916. [PMID: 35837599 PMCID: PMC9274098 DOI: 10.3389/fcvm.2022.881916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/23/2022] [Indexed: 01/28/2023] Open
Abstract
Vascular endothelial cells (ECs) play a pivotal role in whole body homeostasis. Recent advances have revealed enhancer-associated long non-coding RNAs (lncRNAs) as essential regulators in EC function. We investigated LINC00607, a super enhancer-derived lncRNA (SE-lncRNA) in human arteries with an emphasis on ECs. Based on public databases and our single cell RNA-sequencing (scRNA-seq) data from human arteries collected from healthy and diabetic donors, we found that LINC00607 is abundantly expressed in the arteries and its level is increased in diabetic humans. Using RNA-sequencing, we characterized the transcriptomes regulated by LINC00607 in ECs and vascular smooth muscle cells (VSMCs) and in basal and diabetic conditions in ECs. Furthermore, through transcriptomic and promoter analysis, we identified c-Myc as an upstream transcription factor of LINC00607. Finally, using scRNA-seq, we demonstrated that modified antisense oligonucleotide inhibitor of LINC00607 can reverse dysfunctional changes induced by high glucose and TNFα in ECs. Collectively, our study demonstrates a multi-pronged approach to characterize LINC00607 in vascular cells and its gene regulatory networks in ECs and VSMCs. Our findings provide new insights into the regulation and function of SE-derived lncRNAs in both vascular homeostasis and dysfunction in a cell-type and context-dependent manner, which could have a significant impact on our understanding of epigenetic regulation implicated in cardiovascular health and diseases like diabetes.
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Affiliation(s)
- Kiran Sriram
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Duarte, CA, United States
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Yingjun Luo
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Duarte, CA, United States
- Yingjun Luo
| | - Dongqiang Yuan
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Duarte, CA, United States
| | - Naseeb Kaur Malhi
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Duarte, CA, United States
| | - Alonso Tapia
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Duarte, CA, United States
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Vishnu Amaram Samara
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Duarte, CA, United States
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Duarte, CA, United States
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, United States
- Rama Natarajan
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Duarte, CA, United States
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, United States
- *Correspondence: Zhen Bouman Chen
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10
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Qi F, Du X, Zhao Z, Zhang D, Huang M, Bai Y, Yang B, Qin W, Xia J. Tumor Mutation Burden-Associated LINC00638/miR-4732-3p/ULBP1 Axis Promotes Immune Escape via PD-L1 in Hepatocellular Carcinoma. Front Oncol 2021; 11:729340. [PMID: 34568062 PMCID: PMC8456090 DOI: 10.3389/fonc.2021.729340] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/24/2021] [Indexed: 12/11/2022] Open
Abstract
Tumor mutation burden (TMB) is associated with immune infiltration, while its underlying mechanism in hepatocellular carcinoma (HCC) remains unclear. A long noncoding RNA (lncRNA)-related competitive endogenous RNA (ceRNA) network can regulate various tumor behaviors, and research about its correlation with TMB and immune infiltration is warranted. Data were downloaded from TCGA and ArrayExpress databases. Cox analysis and machine learning algorithms were employed to establish a lncRNA-based prognostic model for HCC. We then developed a nomogram model to predict overall survival and odds of death for HCC patients. The association of this prognostic model with TMB and immune infiltration was also analyzed. In addition, a ceRNA network was constructed by using DIANA-LncBasev2 and the starBase database and verified by luciferase reporter and colocalization analysis. Multiplex immunofluorescence was applied to determine the correlation between ULBP1 and PD-L1. An eight-lncRNA (SLC25A30-AS1, HPN-AS1, LINC00607, USP2-AS1, HCG20, LINC00638, MKLN1-AS and LINC00652) prognostic score model was constructed for HCC, which was highly associated with TMB and immune infiltration. Next, we constructed a ceRNA network, LINC00638/miR-4732-3p/ULBP1, that may be responsible for NK cell infiltration in HCC with high TMB. However, patients with high ULBP1 possessed a poorer prognosis. Using multiplex immunofluorescence, we found a significant correlation between ULBP1 and PD-L1 in HCC, and patients with high ULBP1 and PD-L1 had the worst prognosis. In brief, the eight-lncRNA model is a reliable tool to predict the prognosis of HCC patients. The LINC00638/miR-4732-3p/ULBP1 axis may regulate immune escape via PD-L1 in HCC with high TMB.
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Affiliation(s)
- Feng Qi
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Department of Oncology, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Xiaojing Du
- Minhang Branch, Zhongshan Hospital, Fudan University, Shanghai, China.,The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhiying Zhao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ding Zhang
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Mengli Huang
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Yuezong Bai
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Biwei Yang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wenxing Qin
- Department of Oncology, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Jinglin Xia
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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11
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He Y, Chen Y, Tong Y, Long W, Liu Q. Identification of a circRNA-miRNA-mRNA regulatory network for exploring novel therapeutic options for glioma. PeerJ 2021; 9:e11894. [PMID: 34434651 PMCID: PMC8351580 DOI: 10.7717/peerj.11894] [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: 05/21/2021] [Accepted: 07/12/2021] [Indexed: 12/19/2022] Open
Abstract
Background Glioma is the most common brain neoplasm with a poor prognosis. Circular RNA (circRNA) and their associated competing endogenous RNA (ceRNA) network play critical roles in the pathogenesis of glioma. However, the alteration of the circRNA-miRNA-mRNA regulatory network and its correlation with glioma therapy haven't been systematically analyzed. Methods With GEO, GEPIA2, circBank, CSCD, CircInteractome, mirWalk 2.0, and mirDIP 4.1, we constructed a circRNA-miRNA-mRNA network in glioma. LASSO regression and multivariate Cox regression analysis established a hub mRNA signature to assess the prognosis. GSVA was used to estimate the immune infiltration level. Potential anti-glioma drugs were forecasted using the cMap database and evaluated with GSEA using GEO data. Results A ceRNA network of seven circRNAs (hsa_circ_0030788/0034182/0000227/ 0018086/0000229/0036592/0002765), 15 miRNAs(hsa-miR-1200/1205/1248/ 1303/3925-5p/5693/581/586/599/607/640/647/6867-5p/767-3p/935), and 46 mRNAs (including 11 hub genes of ARHGAP11A, DRP2, HNRNPA3, IGFBP5, IP6K2, KLF10, KPNA4, NRP2, PAIP1, RCN1, and SEMA5A) was constructed. Functional enrichment showed they influenced majority of the hallmarks of tumors. Eleven hub genes were proven to be decent prognostic signatures for glioma in both TCGA and CGGA datasets. Forty-six LASSO regression significant genes were closely related to immune infiltration. Finally, five compounds (fulvestrant, tanespimycin, mifepristone, tretinoin, and harman) were predicted as potential treatments for glioma. Among them, mifepristone and tretinoin were proven to inhibit the cell cycle and DNA repair in glioma. Conclusion This study highlights the potential pathogenesis of the circRNA-miRNA-mRNA regulatory network and identifies novel therapeutic options for glioma.
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Affiliation(s)
- Yi He
- Neurosurgery Department, Xiangya Hospital Central South University, Changsha, Hunan, China
| | - Yihong Chen
- Neurosurgery Department, Xiangya Hospital Central South University, Changsha, Hunan, China
| | - Yuxin Tong
- Department of Ophthalmology, Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, China
| | - Wenyong Long
- Neurosurgery Department, Xiangya Hospital Central South University, Changsha, Hunan, China
| | - Qing Liu
- Neurosurgery Department, Xiangya Hospital Central South University, Changsha, Hunan, China
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