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Yagi Y, Abe R, Tani H. Exploring IDI2-AS1, OIP5-AS1, and LITATS1: Changes in Long Non-coding RNAs Induced by the Poly I:C Stimulation. Biol Pharm Bull 2024; 47:1144-1147. [PMID: 38866523 DOI: 10.1248/bpb.b24-00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Long non-coding RNAs (lncRNAs) are sequences longer than 200 nucleotides, but they do not encode proteins. Nevertheless, they have significant roles in diverse biological functions. It remains unclear how viral infections trigger the expression of lncRNAs. In our previous research, we revealed a distinct type of lncRNAs with a lifespan under 4 h in human HeLa cells. These short-lived lncRNAs might be associated with numerous regulatory roles. Given their potential impact on human physiology, these short-lived lncRNAs could be key indicators to measure polyinosinic:polycytidylic acid (poly I:C) stimulation. In our recent work, we discovered three lncRNAs: IDI2-AS1, OIP5-AS1, and LITATS1. After exposure to poly I:C, imitating viral assault in human A549 cells, IDI2-AS1 levels dropped significantly while OIP5-AS1 and LITATS1 levels rose markedly. Our results indicate that short-lived lncRNAs respond to poly I:C stimulation, exhibiting substantial changes in expression. This indicates that the understanding the role of lncRNAs in the host response to viral infection and the potential for these molecules to serve as novel therapeutic targets.
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Affiliation(s)
- Yuka Yagi
- Department of Clinical Pharmacy, Yokohama University of Pharmacy
- Department of Health Pharmacy, Yokohama University of Pharmacy
| | - Rina Abe
- Department of Clinical Pharmacy, Yokohama University of Pharmacy
- Department of Health Pharmacy, Yokohama University of Pharmacy
| | - Hidenori Tani
- Department of Health Pharmacy, Yokohama University of Pharmacy
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2
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Rajendran P, Sekar R, Zahra HA, Jayaraman S, Rajagopal P, Abdallah BM, Ali EM, Abdelsalam SA, Veeraraghavan V. Salivaomics to decode non-coding RNAs in oral cancer. A narrative review. Noncoding RNA Res 2023; 8:376-384. [PMID: 37250455 PMCID: PMC10220469 DOI: 10.1016/j.ncrna.2023.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/01/2023] [Indexed: 05/31/2023] Open
Abstract
Oral cancer is the most debilitating disease which affects the orderly life of a human. With so much advancement in research and technology, the average life expectancy of an individual with oral cancer appears to be about 5 years. The changing trend in incidence of oral cancer among young individuals and women without tobacco habits are ascending. Non habit related oral cancer are taking centre stage and multiple factors which induce complex biology are associated in such scenarios. To decipher the aetiology and to understand the process, these cancerous conditions are to be studied at molecular level. Saliva, the most non-invasively obtained body fluid are assessed for biomarkers exclusively in liquid biopsy. This fluid gives a huge platform to study number of molecules associated with oral cancer. Non coding RNAs are transcripts with no protein coding function. They are gaining more importance in recent times. Long noncoding RNA, microRNA are major types of noncoding transcriptome that influences in progression of oral cancer. They seem to play an important role in health and disease. Apart from these, circulating tumour cells, exosomes, extracellular vesicles, antigens and other proteins can be studied from saliva. This review is aimed to update the knowledge on current biomarkers in saliva associated with oral cancer and their epigenetic role in disease progression as well recent advances in detecting these markers to identify the stage of the disease, which will help in deciding the treatment protocol.
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Affiliation(s)
- Peramaiyan Rajendran
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 600 077, Tamil Nadu, India
| | - Ramya Sekar
- Central Research Laboratory, Meenakshi Academy of Higher Education and Research, West K.K. Nagar, Chennai, 600 078, India
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 600 077, Tamil Nadu, India
| | - Hamad Abu Zahra
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Selvaraj Jayaraman
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 600 077, Tamil Nadu, India
| | - Ponnulakshmi Rajagopal
- Central Research Laboratory, Meenakshi Academy of Higher Education and Research, West K.K. Nagar, Chennai, 600 078, India
| | - Basem M. Abdallah
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Enas M. Ali
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Cairo, 12613, Egypt
| | - Salaheldin Abdelraouf Abdelsalam
- Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- Department of Zoology, Faculty of Science, Assiut University, Assiut, 71515, Egypt
| | - Vishnupriya Veeraraghavan
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 600 077, Tamil Nadu, India
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Yao Y, Yang F, Chen A, Hua Q, Gao W. Costimulatory molecule-related lncRNA model as a potential prognostic biomarker in non-small cell lung cancer. Cancer Med 2023; 12:6419-6436. [PMID: 36305249 PMCID: PMC10028169 DOI: 10.1002/cam4.5391] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 09/14/2022] [Accepted: 10/16/2022] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVE Costimulatory molecules have been demonstrated to exert essential roles in multiple cancers. However, their role in lung cancer remains elusive. Here, we sought to identify costimulatory molecule-related lncRNAs in non-small cell lung cancer (NSCLC) and establish a prognostic signature to predict the prognosis of patients with NSCLC. METHODS A total of 535 lung adenocarcinoma (LUAD) and 502 lung squamous cell carcinoma (LUSC) patients from the cancer genome atlas (TCGA) database were recruited. A novel costimulatory molecule-based lncRNA prognostic model was constructed using the least absolute shrinkage and selection operator (LASSO) algorithm to predict the overall survival. The Homo_sapiens.GRCh38 data set was set as a reference file for probe annotation. RESULTS A total of 593 costimulatory molecule-related lncRNAs were extracted. After analysis, six costimulatory molecule-related lncRNAs (AC084859.1, AC079949.2, HSPC324, LINC01150, LINC01150, and AC090617.5) were screened. A prognostic model based on the six lncRNAs was established using systematic bioinformatics analyses. The prognostic model had a prognostic value in NSCLC patients. Furthermore, a prognostic nomogram was established based on clinical parameters and a risk-score model. Patients with different risk scores had considerably different tumor-infiltrating immune cells, somatic mutational loading, clinical outcomes, signaling pathways, and immunotherapy efficacy. In addition, LINC01137 was associated with unfavorable disease outcomes and fueled tumor progression in NSCLC. CONCLUSION Taken together, our study demonstrated that a costimulatory molecule-related lncRNA model could be a potential prognostic biomarker in NSCLC. Moreover, LINC01137 could facilitate the proliferation and invasion of lung cancer.
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Affiliation(s)
- Yuanshan Yao
- Department of Thoracic Surgery, Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
- Department of Thoracic Oncology, Ningbo No. 2 Hospital, Ningbo, China
| | - Fuzhi Yang
- Department of Thoracic Surgery, Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Anna Chen
- Ningbo CRRC Times Transducer Technology Co., Ltd., Ningbo, China
| | - Qingwang Hua
- Department of Thoracic Oncology, Ningbo No. 2 Hospital, Ningbo, China
| | - Wen Gao
- Department of Thoracic Surgery, Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital Affiliated to Fudan University, Shanghai, China
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Shetty SP, Kiledjian NT, Copeland PR. The selenoprotein P 3' untranslated region is an RNA binding protein platform that fine tunes selenocysteine incorporation. PLoS One 2022; 17:e0271453. [PMID: 35905095 PMCID: PMC9337670 DOI: 10.1371/journal.pone.0271453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/01/2022] [Indexed: 11/19/2022] Open
Abstract
Selenoproteins contain the 21st amino acid, selenocysteine (Sec), which is incorporated at select UGA codons when a specialized hairpin sequence, the Sec insertion sequence (SECIS) element, is present in the 3' UTR. Aside from the SECIS, selenoprotein mRNA 3' UTRs are not conserved between different selenoproteins within a species. In contrast, the 3'-UTR of a given selenoprotein is often conserved across species, which supports the hypothesis that cis-acting elements in the 3'-UTR other than the SECIS exert post-transcriptional control on selenoprotein expression. In order to determine the function of one such SECIS context, we chose to focus on the plasma selenoprotein, SELENOP, which is required to maintain selenium homeostasis as a selenium transport protein that contains 10 Sec residues. It is unique in that its mRNA contains two SECIS elements in the context of a highly conserved 843-nucleotide 3' UTR. Here we have used RNA affinity chromatography and identified PTBP1 as the major RNA binding protein that specifically interacts with the sequence between the two SECIS elements. We then used CRISPR/Cas9 genome editing to delete two regions surrounding the first SECIS element. We found that these sequences are involved in regulating SELENOP mRNA and protein levels, which are inversely altered as a function of selenium concentrations.
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Affiliation(s)
- Sumangala P. Shetty
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, United States of America
| | - Nora T. Kiledjian
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, United States of America
| | - Paul R. Copeland
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, United States of America
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Olmedo-Suárez MÁ, Ramírez-Díaz I, Pérez-González A, Molina-Herrera A, Coral-García MÁ, Lobato S, Sarvari P, Barreto G, Rubio K. Epigenetic Regulation in Exposome-Induced Tumorigenesis: Emerging Roles of ncRNAs. Biomolecules 2022; 12:513. [PMID: 35454102 PMCID: PMC9032613 DOI: 10.3390/biom12040513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Environmental factors, including pollutants and lifestyle, constitute a significant role in severe, chronic pathologies with an essential societal, economic burden. The measurement of all environmental exposures and assessing their correlation with effects on individual health is defined as the exposome, which interacts with our unique characteristics such as genetics, physiology, and epigenetics. Epigenetics investigates modifications in the expression of genes that do not depend on the underlying DNA sequence. Some studies have confirmed that environmental factors may promote disease in individuals or subsequent progeny through epigenetic alterations. Variations in the epigenetic machinery cause a spectrum of different disorders since these mechanisms are more sensitive to the environment than the genome, due to the inherent reversible nature of the epigenetic landscape. Several epigenetic mechanisms, including modifications in DNA (e.g., methylation), histones, and noncoding RNAs can change genome expression under the exogenous influence. Notably, the role of long noncoding RNAs in epigenetic processes has not been well explored in the context of exposome-induced tumorigenesis. In the present review, our scope is to provide relevant evidence indicating that epigenetic alterations mediate those detrimental effects caused by exposure to environmental toxicants, focusing mainly on a multi-step regulation by diverse noncoding RNAs subtypes.
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Affiliation(s)
- Miguel Ángel Olmedo-Suárez
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Ivonne Ramírez-Díaz
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Facultad de Biotecnología, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Andrea Pérez-González
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Alejandro Molina-Herrera
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Miguel Ángel Coral-García
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Decanato de Ciencias de la Salud, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Sagrario Lobato
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
| | - Pouya Sarvari
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
| | - Guillermo Barreto
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Laboratoire IMoPA, CNRS, Université de Lorraine, UMR 73635 Nancy, France
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico; (M.Á.O.-S.); (I.R.-D.); (A.P.-G.); (A.M.-H.); (M.Á.C.-G.); (S.L.); (P.S.); (G.B.)
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
- Laboratoire IMoPA, CNRS, Université de Lorraine, UMR 73635 Nancy, France
- Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
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Li R, Li JP, Liu TT, Huo C, Yao J, Ji XL, Qu YQ. Prognostic Value of Genomic Instability of m6A-Related lncRNAs in Lung Adenocarcinoma. Front Cell Dev Biol 2022; 10:707405. [PMID: 35309906 PMCID: PMC8928224 DOI: 10.3389/fcell.2022.707405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 02/09/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Genomic instability of N6-methyladenosine (m6A)–related long noncoding RNAs (lncRNAs) plays a pivotal role in the tumorigenesis of lung adenocarcinoma (LUAD). Our study identified a signature of genomic instability of m6A-associated lncRNA signature and revealed its prognostic role in LUAD. Methods: We downloaded RNA-sequencing data and somatic mutation data for LUAD from The Cancer Genome Atlas (TCGA) and the GSE102287 dataset from the Gene Expression Omnibus (GEO) database. The “Limma” R package was used to identify a network of regulatory m6A-related lncRNAs. We used the Wilcoxon test method to identify genomic-instability–derived m6A-related lncRNAs. A competing endogenous RNA (ceRNA) network was constructed to identify the mechanism of the genomic instability of m6A-related lncRNAs. Univariate and multivariate Cox regression analyses were performed to construct a prognostic model for internal testing and validation of the prognostic m6A-related lncRNAs using the GEO dataset. Performance analysis was conducted to compare our prognostic model with the previously published lncRNA models. The CIBERSORT algorithm was used to explore the relationship of m6A-related lncRNAs and the immune microenvironment. Prognostic m6A-related lncRNAs in prognosis, the tumor microenvironment, stemness scores, and anticancer drug sensitivity were analyzed to explore the role of prognostic m6A-related lncRNAs in LUAD. Results: A total of 42 genomic instability–derived m6A-related lncRNAs were differentially expressed between the GS (genomic stable) and GU (genomic unstable) groups of LUAD patients. Four differentially expressed lncRNAs, 17 differentially expressed microRNAs, and 75 differentially expressed mRNAs were involved in the genomic-instability–derived m6A-related lncRNA-mediated ceRNA network. A prediction model based on 17 prognostic m6A-associated lncRNAs was constructed based on three TCGA datasets (all, training, and testing) and validated in the GSE102287 dataset. Performance comparison analysis showed that our prediction model (area under the curve [AUC] = 0.746) could better predict the survival of LUAD patients than the previously published lncRNA models (AUC = 0.577, AUC = 0.681). Prognostic m6A-related-lncRNAs have pivotal roles in the tumor microenvironment, stemness scores, and anticancer drug sensitivity of LUAD. Conclusion: A signature of genomic instability of m6A-associated lncRNAs to predict the survival of LUAD patients was validated. The prognostic, immune microenvironment and anticancer drug sensitivity analysis shed new light on the potential novel therapeutic targets in LUAD.
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Affiliation(s)
- Rui Li
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jian-Ping Li
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ting-Ting Liu
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chen Huo
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jie Yao
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiu-Li Ji
- Department of Pulmonary Disease, Traditional Chinese Medicine Hospital of Jinan, Jinan, China
| | - Yi-Qing Qu
- Shandong Key Laboratory of Infectious Respiratory Diseases, Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- *Correspondence: Yi-Qing Qu,
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Aulicino A, Antanaviciute A, Frost J, Sousa Geros A, Mellado E, Attar M, Jagielowicz M, Hublitz P, Sinz J, Preciado-Llanes L, Napolitani G, Bowden R, Koohy H, Drakesmith H, Simmons A. Dual RNA sequencing reveals dendritic cell reprogramming in response to typhoidal Salmonella invasion. Commun Biol 2022; 5:111. [PMID: 35121793 PMCID: PMC8816929 DOI: 10.1038/s42003-022-03038-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 12/15/2021] [Indexed: 12/19/2022] Open
Abstract
Salmonella enterica represent a major disease burden worldwide. S. enterica serovar Typhi (S. Typhi) is responsible for potentially life-threatening Typhoid fever affecting 10.9 million people annually. While non-typhoidal Salmonella (NTS) serovars usually trigger self-limiting diarrhoea, invasive NTS bacteraemia is a growing public health challenge. Dendritic cells (DCs) are key professional antigen presenting cells of the human immune system. The ability of pathogenic bacteria to subvert DC functions and prevent T cell recognition contributes to their survival and dissemination within the host. Here, we adapted dual RNA-sequencing to define how different Salmonella pathovariants remodel their gene expression in tandem with that of infected DCs. We find DCs harness iron handling pathways to defend against invading Salmonellas, which S. Typhi is able to circumvent by mounting a robust response to nitrosative stress. In parallel, we uncover the alternative strategies invasive NTS employ to impair DC functions.
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Affiliation(s)
- Anna Aulicino
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Agne Antanaviciute
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
- MRC WIMM Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Joe Frost
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ana Sousa Geros
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Esther Mellado
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK
| | - Moustafa Attar
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FY, UK
| | - Marta Jagielowicz
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Philip Hublitz
- MRC Weatherall Institute of Molecular Medicine, Genome Engineering Facility, University of Oxford, Oxford, OX3 9DS, UK
| | - Julia Sinz
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Lorena Preciado-Llanes
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Giorgio Napolitani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK
| | - Hashem Koohy
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- MRC WIMM Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Hal Drakesmith
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Alison Simmons
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
- Translational Gastroenterology Unit, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK.
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Wooten S, Smith KN. Long non-coding RNA OIP5-AS1 (Cyrano): A context-specific regulator of normal and disease processes. Clin Transl Med 2022; 12:e706. [PMID: 35040588 PMCID: PMC8764876 DOI: 10.1002/ctm2.706] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/21/2021] [Accepted: 12/29/2021] [Indexed: 12/17/2022] Open
Abstract
Long non-coding (lnc) RNAs have been implicated in a plethora of normal biological functions, and have also emerged as key molecules in various disease processes. OIP5-AS1, also commonly known by the alias Cyrano, is a lncRNA that displays broad expression across multiple tissues, with significant enrichment in particular contexts including within the nervous system and skeletal muscle. Thus far, this multifaceted lncRNA has been found to have regulatory functions in normal cellular processes including cell proliferation and survival, as well as in the development and progression of a myriad disease states. These widespread effects on normal and disease states have been found to be mediated through context-specific intermolecular interactions with dozens of miRNAs and proteins identified to date. This review explores recent studies to highlight OIP5-AS1's contextual yet pleiotropic roles in normal homeostatic functions as well as disease oetiology and progression, which may influence its utility in the generation of future theranostics.
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Affiliation(s)
- Serena Wooten
- Department of GeneticsUniversity of North Carolina at Chapel HillNorth CarolinaUSA
| | - Keriayn N. Smith
- Department of GeneticsUniversity of North Carolina at Chapel HillNorth CarolinaUSA
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Liu B, Yang S. A Five Autophagy-Related Long Non-Coding RNA Prognostic Model for Patients with Lung Adenocarcinoma. Int J Gen Med 2021; 14:7145-7158. [PMID: 34737609 PMCID: PMC8558832 DOI: 10.2147/ijgm.s334601] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/28/2021] [Indexed: 12/19/2022] Open
Abstract
Purpose Lung adenocarcinoma is the most common pathological type among non-small cell lung cancer. Although huge progress has been made in terms of early diagnosis and precision treatment in recent years, the overall 5-year survival rate of a patient remains low. In our study, we try to construct an autophagy-related lncRNA prognostic signature that may guide clinical practice. Methods The mRNA and lncRNA expression matrix of lung adenocarcinoma patients were retrieved from the TCGA database. Next, we constructed a co-expression network of lncRNAs and autophagy-related genes. Lasso regression and multivariate Cox regression were then applied to establish a prognostic risk model. Subsequently, a risk score was generated to differentiate the high and low risk groups and a ROC curve and nomogram to visualize the predictive ability of the current signature. Finally, gene ontology and pathway enrichment analysis were executed via GSEA. Results A total of 1,703 autophagy-related lncRNAs were screened and five autophagy-related lncRNAs (LINC01137, AL691432.2, LINC01116, AL606489.1, and HLA-DQB1-AS1) were finally included in our signature. Judging from univariate (HR=1.075, 95% CI=1.046–1.104) and multivariate (HR=1.088, 95% CI=1.057−1.120) Cox regression analysis, the risk score is an independent factor for LUAD patients. Further, the AUC value based on the risk score for 1-year, 3-years, and 5-years, was 0.735, 0.672, and 0.662, respectively, indicating a reliable model. Drug sensitivity analysis revealed low risk patients were more sensitive to Gemcitabine and Gefitinib, while high risk patients had a better response to Paclitaxel and Erlotinib. Moreover, the lncRNAs included in our signature were primarily enriched in the autophagy process, metabolism, p53 pathway, and JAK/STAT pathway. Finally, a multi-omics analysis of correlated genes showed CFLAR overexpressed in the tumor sample, while GAPDH and MLST8 had a slightly higher expression in the normal sample. Conclusion Overall, our study indicated that the prognostic model we generated had certain predictability for LUAD patients’ prognosis and the related genes might be potential biomarkers and therapeutic targets.
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Affiliation(s)
- Boxuan Liu
- Department of Critical Care and Respiratory Medicine, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China
| | - Shuanying Yang
- Department of Critical Care and Respiratory Medicine, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, People's Republic of China
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10
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Ren J, Wang A, Liu J, Yuan Q. Identification and validation of a novel redox-related lncRNA prognostic signature in lung adenocarcinoma. Bioengineered 2021; 12:4331-4348. [PMID: 34338158 PMCID: PMC8806475 DOI: 10.1080/21655979.2021.1951522] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is one of the main causes of cancer deaths globally. Redox is emerging as a crucial contributor to the pathophysiology of LUAD, which can be regulated by long non-coding RNAs (lncRNAs). The aim of our research is to identify a novel redox-related lncRNA prognostic signature (redox-LPS) for better prediction of LUAD prognosis. 535 LUAD samples from The Cancer Genome Atlas (TCGA) database and 226 LUAD samples from the Gene Expression Omnibus (GEO) database were included in our study. 67 redox genes and 313 redox-related lncRNAs were identified. After performing LASSO-Cox regression analysis, a redox-LPS consisting of four lncRNAs (i.e., CRNDE, CASC15, LINC01137, and CYP1B1-AS1) was developed and validated. Our redox-LPS was superior to another three established models in predicting survival probability of LUAD patients. Univariate and multivariate Cox regression analysis revealed that risk score and stage were independent prognostic indicators. A nomogram plot including risk score and stage was constructed to predict survival probability of LUAD patients; this was further verified by calibration curves. Functional enrichment analysis and gene set enrichment analysis, were performed to determine the differences in cellular processes and signaling pathways between the high – and low-risk subgroups. A variety of algorithms (such as single-sample gene set enrichment analysis and CIBERSOFT) were conducted to uncover the landscape of tumor immune microenvironment in the high- and low-risk subgroups. In conclusion, a novel independent redox-LPS was constructed and validated for LUAD patients, which might provide new insights for clinical decision-making and precision medicine.
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Affiliation(s)
- Jie Ren
- Department of Oncology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Aman Wang
- Department of Oncology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Jiwei Liu
- Department of Oncology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Qihang Yuan
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
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11
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Du Y, Yang H, Li Y, Guo W, Zhang Y, Shen H, Xing L, Li Y, Wu W, Zhang X. Long non-coding RNA LINC01137 contributes to oral squamous cell carcinoma development and is negatively regulated by miR-22-3p. Cell Oncol (Dordr) 2021; 44:595-609. [PMID: 33797737 DOI: 10.1007/s13402-021-00586-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 01/02/2021] [Accepted: 01/05/2021] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Long noncoding RNAs (lncRNAs) are emerging as key regulators in cancer initiation and progression. LINC01137 is a recently identified lncRNA of which the functional role in the development of oral squamous cell carcinoma (OSCC) has not been determined yet. METHODS We analyzed the expression of LINC01137 using a microarray-based OSCC gene expression dataset (GSE31056), and validated the results obtained using RT-qPCR in 26 pairs of primary OSCC tumor tissues and adjacent non-tumor tissues. The proliferative and invasive effects of LINC01137 on OSCC cells were determined using CCK-8, colony formation and transwell assays, respectively. Targeted binding between miR-22-3p and LINC01137 was verified using a dual luciferase reporter assay. RESULTS We found that LINC01137 was significantly upregulated in primary OSCCs. LINC01137 knockdown inhibited OSCC cell proliferation, migration and invasion, whereas LINC01137 overexpression induced opposite effects. LINC01137 upregulation along with p53 inhibition enhanced the malignant transformation of oral cells. In addition, we found that miR-22-3p can directly target LINC01137 through interaction with a putative miR-22-3p-binding site present within the LINC01137 sequence. A significant negative correlation was observed between LINC01137 and miR-22-3p expression in primary OSCC specimens. Exogenous overexpression of miR-22-3p markedly reduced the endogenous expression level of LINC01137 in OSCC cells. Additional functional assays showed that miR-22-3p overexpression enhanced the inhibitory effect of siRNA-mediated LINC01137 silencing on OSCC cell proliferation, migration and invasion, whereas miR-22-3p inhibition had the opposite effect. CONCLUSIONS Our results indicate that LINC01137 functions as an oncogenic lncRNA in OSCC. miR-22-3p can directly target LINC01137 and negatively regulate its expression and function.
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Affiliation(s)
- Yong Du
- Department of Stomatology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Department of Pathology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Haiyan Yang
- Laboratory of Pathology, Hebei Medical University, Shijiazhuang, China
| | - Yue Li
- Department of Pathology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Department of Pathology, The Fourth Hospital of Shijiazhuang, Shijiazhuang, China
| | - Wenli Guo
- Department of Pathology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yufeng Zhang
- Department of Radiotherapy, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Haitao Shen
- Department of Pathology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lingxiao Xing
- Department of Pathology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yuehong Li
- Laboratory of Pathology, Hebei Medical University, Shijiazhuang, China
| | - Wenxin Wu
- Laboratory of Pathology, Hebei Medical University, Shijiazhuang, China
| | - Xianghong Zhang
- Department of Pathology, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
- Laboratory of Pathology, Hebei Medical University, Shijiazhuang, China.
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12
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Fan F, Huang Z, Chen Y. Integrated analysis of immune-related long noncoding RNAs as diagnostic biomarkers in psoriasis. PeerJ 2021; 9:e11018. [PMID: 33732554 PMCID: PMC7950217 DOI: 10.7717/peerj.11018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 02/06/2021] [Indexed: 12/16/2022] Open
Abstract
Background Psoriasis is a chronic immune-mediated inflammatory dermatosis. Long noncoding RNAs (lncRNAs) play an important role in immune-related diseases. This study aimed to identify potential immune-related lncRNA biomarkers for psoriasis. Methods We screened differentially expressed immune-related lncRNAs biomarkers using GSE13355 (skin biopsy samples of 180 cases) from Gene Expression Omnibus (GEO). Moreover, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and Gene Set Enrichment Analysis (GSEA) were performed to explore biological mechanisms in psoriasis. In addition, we performed LASSO logistic regression to identify potential diagnostic lncRNAs and further verify the diagnostic value and relationship with drug response using two validation sets: GSE30999 (skin biopsy samples of 170 cases) and GSE106992 (skin biopsy samples of 192 cases). Furthermore, we estimated the degree of infiltrated immune cells and investigated the correlation between infiltrated immune cells and diagnostic lncRNA biomarkers. Results A total of 394 differentially expressed genes (DEGs) were extracted from gene expression profile. GO and KEGG analysis of target genes found that immune-related lncRNAs were primarily associated with epidermis development, skin development, collagen-containing extracellular matrix, and glycosaminoglycan binding and mainly enriched in cytokine-cytokine receptor interaction and influenza A and chemokine signaling pathway. We found that LINC01137, LINC01215, MAPKAPK5-AS1, TPT1-AS1, CARMN, CCDC18-AS1, EPB41L4A-AS, and LINC01214 exhibited well diagnostic efficacy. The ROC and ROC CI were 0.944 (0.907–0.982), 0.953 (0.919–0.987), 0.822 (0.758–0.887), 0.854 (0.797–0.911), 0.957(0.929–0.985), 0.894 (0.846–0.942), and 0.964 (0.937–0.991) for LINC01137, LINC01215, MAPKAPK5-AS1, TPT1-AS1,CARMN, CCDC18-AS1, EPB41L4A-AS1, and LINC01214. LINC01137, LINC01215, and LINC01214 were correlated with drug response. LINC01137, CCDC18-AS1, and CARMN were positively correlated with activated memory CD4 T cell, activated myeloid dendritic cell (DC), neutrophils, macrophage M1, and T follicular helper (Tfh) cells, while negatively correlated with T regulatory cell (Treg). LINC01215, MAPKAPK5-AS1, TPT1-AS1, EPB41L4A-AS, and LINC01214 were negatively correlated with activated memory CD4 T cell, activated myeloid DC, neutrophils, macrophage M1, and Tfh, while positively correlated with Treg. Conclusions These findings indicated that these immune-related lncRNAs may be used as potential diagnostic and predictive biomarkers for psoriasis.
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Affiliation(s)
- Feixiang Fan
- Department of Dermatology, Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Department of Dermatology, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Zhen Huang
- Department of Dermatology, Shenzhen Longhua District Central Hospital, Shenzhen, Guangdong, China
| | - Yongfeng Chen
- Department of Dermatology, Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
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13
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Mohapatra S, Pioppini C, Ozpolat B, Calin GA. Non-coding RNAs regulation of macrophage polarization in cancer. Mol Cancer 2021; 20:24. [PMID: 33522932 PMCID: PMC7849140 DOI: 10.1186/s12943-021-01313-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/12/2021] [Indexed: 12/19/2022] Open
Abstract
Noncoding RNA (ncRNA) transcripts that did not code proteins but regulate their functions were extensively studied for the last two decades and the plethora of discoveries have instigated scientists to investigate their dynamic roles in several diseases especially in cancer. However, there is much more to learn about the role of ncRNAs as drivers of malignant cell evolution in relation to macrophage polarization in the tumor microenvironment. At the initial stage of tumor development, macrophages have an important role in directing Go/No-go decisions to the promotion of tumor growth, immunosuppression, and angiogenesis. Tumor-associated macrophages behave differently as they are predominantly induced to be polarized into M2, a pro-tumorigenic type when recruited with the tumor tissue and thereby favoring the tumorigenesis. Polarization of macrophages into M1 or M2 subtypes plays a vital role in regulating tumor progression, metastasis, and clinical outcome, highlighting the importance of studying the factors driving this process. A substantial number of studies have demonstrated that ncRNAs are involved in the macrophage polarization based on their ability to drive M1 or M2 polarization and in this review we have described their functions and categorized them into oncogenes, tumor suppressors, Juggling tumor suppressors, and Juggling oncogenes.
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Affiliation(s)
- Swati Mohapatra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences (GSBS), Houston, TX, USA
| | - Carlotta Pioppini
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bulent Ozpolat
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Life Science Plaza, Suite: LSP9.3012, 2130 W, Holcombe Blvd, Ste. 910, Houston, TX, 77030, USA.
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14
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Mullani N, Porozhan Y, Mangelinck A, Rachez C, Costallat M, Batsché E, Goodhardt M, Cenci G, Mann C, Muchardt C. Reduced RNA turnover as a driver of cellular senescence. Life Sci Alliance 2021; 4:4/3/e202000809. [PMID: 33446491 PMCID: PMC7812316 DOI: 10.26508/lsa.202000809] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/27/2022] Open
Abstract
RNAs originating from transcription upstream and downstream of genes accumulate in the cytoplasm of a subset of senescent cells, suggesting an RNA alternative to cytoplasmic DNA in the triggering of senescence. Accumulation of senescent cells is an important contributor to chronic inflammation upon aging. The inflammatory phenotype of senescent cells was previously shown to be driven by cytoplasmic DNA. Here, we propose that cytoplasmic double-stranded RNA has a similar effect. We find that several cell types driven into senescence by different routes share an accumulation of long promoter RNAs and 3′ gene extensions rich in retrotransposon sequences. Accordingly, these cells display increased expression of genes involved in response to double stranded RNA of viral origin downstream of the interferon pathway. The RNA accumulation is associated with evidence of reduced RNA turnover, including in some cases, reduced expression of RNA exosome subunits. Reciprocally, depletion of RNA exosome subunit EXOSC3 accelerated expression of multiple senescence markers. A senescence-like RNA accumulation was also observed in cells exposed to oxidative stress, an important trigger of cellular senescence. Altogether, we propose that in a subset of senescent cells, repeat-containing transcripts stabilized by oxidative stress or reduced RNA exosome activity participate in driving and maintaining the permanent inflammatory state characterizing cellular senescence.
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Affiliation(s)
- Nowsheen Mullani
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France.,Sorbonne Université, Ecole Doctorale "Complexité du Vivant" (ED515), Paris, France
| | - Yevheniia Porozhan
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France
| | - Adèle Mangelinck
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Christophe Rachez
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France
| | - Mickael Costallat
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France
| | - Eric Batsché
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France
| | - Michele Goodhardt
- Institut National de la Santé et de la Recherche Médicale (INSERM) U976, Institut de Recherche Saint Louis, Université de Paris, Paris, France
| | - Giovanni Cenci
- Dipartimento Biologia e Biotecnologie "C. Darwin," SAPIENZA Università di Roma, Rome, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Carl Mann
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Christian Muchardt
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) UMR3738, Dpt Biologie du Développement et Cellules Souches, Unité de Régulation Epigénétique, Paris, France
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15
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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: 123] [Impact Index Per Article: 30.8] [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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