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Khader SA, Divangahi M, Hanekom W, Hill PC, Maeurer M, Makar KW, Mayer-Barber KD, Mhlanga MM, Nemes E, Schlesinger LS, van Crevel R, Vankayalapati R(K, Xavier RJ, Netea MG. Targeting innate immunity for tuberculosis vaccination. J Clin Invest 2019; 129:3482-3491. [PMID: 31478909 PMCID: PMC6715374 DOI: 10.1172/jci128877] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Vaccine development against tuberculosis (TB) is based on the induction of adaptive immune responses endowed with long-term memory against mycobacterial antigens. Memory B and T cells initiate a rapid and robust immune response upon encounter with Mycobacterium tuberculosis, thus achieving long-lasting protection against infection. Recent studies have shown, however, that innate immune cell populations such as myeloid cells and NK cells also undergo functional adaptation after infection or vaccination, a de facto innate immune memory that is also termed trained immunity. Experimental and epidemiological data have shown that induction of trained immunity contributes to the beneficial heterologous effects of vaccines such as bacille Calmette-Guérin (BCG), the licensed TB vaccine. Moreover, increasing evidence argues that trained immunity also contributes to the anti-TB effects of BCG vaccination. An interaction among immunological signals, metabolic rewiring, and epigenetic reprogramming underlies the molecular mechanisms mediating trained immunity in myeloid cells and their bone marrow progenitors. Future studies are warranted to explore the untapped potential of trained immunity to develop a future generation of TB vaccines that would combine innate and adaptive immune memory induction.
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Affiliation(s)
- Shabaana A. Khader
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Maziar Divangahi
- Meakins-Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, and Department of Pathology, McGill International TB Centre, McGill University Health Centre, Montreal, Quebec, Canada
| | - Willem Hanekom
- Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Philip C. Hill
- Centre for International Health, Department of Preventive and Social Medicine, University of Otago Medical School, Dunedin, New Zealand
| | - Markus Maeurer
- Department of Oncology/Haematology, Krankenhaus Nordwest (KHNW), Frankfurt, Germany
- ImmunoSurgery Unit, Champalimaud Foundation, Lisbon, Portugal
| | - Karen W. Makar
- Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Katrin D. Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Musa M. Mhlanga
- Division of Chemical Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine (IDM), Faculty of Health Sciences, Department of Integrative Biomedical Sciences, and
| | - Elisa Nemes
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | | | - Reinout van Crevel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Raman (Krishna) Vankayalapati
- Department of Pulmonary Immunology, Center for Biomedical Research, University of Texas Health Science Center at Tyler, Tyler, Texas, USA
| | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Computational and Integrative Biology and
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
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152
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Wang WJ, Guo CA, Li R, Xu ZP, Yu JP, Ye Y, Zhao J, Wang J, Wang WA, Zhang A, Li HT, Wang C, Liu HB. Long non-coding RNA CASC19 is associated with the progression and prognosis of advanced gastric cancer. Aging (Albany NY) 2019; 11:5829-5847. [PMID: 31422382 PMCID: PMC6710062 DOI: 10.18632/aging.102190] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/10/2019] [Indexed: 12/24/2022]
Abstract
Evidence indicates that aberrantly expressed long non-coding RNAs (lncRNAs) are involved in the development and progression of advanced gastric cancer (AGC). Using RNA sequencing data and clinical information obtained from The Cancer Gene Atlas, we combined differential lncRNA expression profiling and weighted gene co-expression network analysis to identify key lncRNAs associated with AGC progression and prognosis. Cancer susceptibility 19 (CASC19) was the top hub lncRNA among the lncRNAs included in the gene module most significantly correlated with AGC’s pathological variables. CASC19 was upregulated in AGC clinical samples and was significantly associated with higher pathologic TNM stage, pathologic T stage, lymph node metastasis, and poor overall survival. Multivariable Cox analysis confirmed that CASC19 overexpression is an independent prognostic factor for overall survival. Furthermore, quantitative real-time PCR assay confirmed that CASC19 expression in four human gastric cancer cells (AGS, BGC-823, MGC-803, and HGC-27) was significantly upregulated compared with human normal gastric mucosal epithelial cell line (GES-1). Functionally, CASC19 knockdown inhibited GC cell proliferation and migration in vitro. These findings suggest that CASC19 may be a novel prognostic biomarker and a potential therapeutic target for AGC.
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Affiliation(s)
- Wen-Jie Wang
- Second Clinical Medical College, Lanzhou University, Lanzhou 730030, Gansu, P.R. China.,Department of General Surgery, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, P.R. China.,Key Laboratory of Stem Cells and Gene Drugs of Gansu Province, Lanzhou 730050, Gansu, China
| | - Chang-An Guo
- Second Clinical Medical College, Lanzhou University, Lanzhou 730030, Gansu, P.R. China.,Key Laboratory of Stem Cells and Gene Drugs of Gansu Province, Lanzhou 730050, Gansu, China.,Department of Emergency, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, P.R. China
| | - Rui Li
- Second Clinical Medical College, Lanzhou University, Lanzhou 730030, Gansu, P.R. China.,Department of General Surgery, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, P.R. China
| | - Zi-Peng Xu
- Second Clinical Medical College, Lanzhou University, Lanzhou 730030, Gansu, P.R. China.,Department of General Surgery, The 940th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Lanzhou 730050, Gansu, P.R. China.,Key Laboratory of Stem Cells and Gene Drugs of Gansu Province, Lanzhou 730050, Gansu, China
| | - Jian-Ping Yu
- Second Clinical Medical College, Lanzhou University, Lanzhou 730030, Gansu, P.R. China.,Department of General Surgery, The 940th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Lanzhou 730050, Gansu, P.R. China
| | - Yan Ye
- Key Laboratory of Stem Cells and Gene Drugs of Gansu Province, Lanzhou 730050, Gansu, China
| | - Jun Zhao
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, P.R. China
| | - Jing Wang
- Department of General Surgery, The 940th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Lanzhou 730050, Gansu, P.R. China.,Key Laboratory of Stem Cells and Gene Drugs of Gansu Province, Lanzhou 730050, Gansu, China.,Clinical Medical College, Gansu University of Chinese Medicine, Lanzhou 730030, Gansu, P.R. China
| | - Wen-An Wang
- Department of General Surgery, The 940th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Lanzhou 730050, Gansu, P.R. China.,Key Laboratory of Stem Cells and Gene Drugs of Gansu Province, Lanzhou 730050, Gansu, China.,Clinical Medical College, Gansu University of Chinese Medicine, Lanzhou 730030, Gansu, P.R. China
| | - An Zhang
- Department of General Surgery, The 940th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Lanzhou 730050, Gansu, P.R. China.,Key Laboratory of Stem Cells and Gene Drugs of Gansu Province, Lanzhou 730050, Gansu, China.,Clinical Medical College, Gansu University of Chinese Medicine, Lanzhou 730030, Gansu, P.R. China
| | - Hong-Tao Li
- Department of General Surgery, The 940th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Lanzhou 730050, Gansu, P.R. China
| | - Chen Wang
- Second Clinical Medical College, Lanzhou University, Lanzhou 730030, Gansu, P.R. China.,Department of General Surgery, Lanzhou University Second Hospital, Lanzhou 730030, Gansu, P.R. China
| | - Hong-Bin Liu
- Second Clinical Medical College, Lanzhou University, Lanzhou 730030, Gansu, P.R. China.,Department of General Surgery, The 940th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Lanzhou 730050, Gansu, P.R. China
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153
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Long noncoding RNA LINC02418 regulates MELK expression by acting as a ceRNA and may serve as a diagnostic marker for colorectal cancer. Cell Death Dis 2019; 10:568. [PMID: 31358735 PMCID: PMC6662768 DOI: 10.1038/s41419-019-1804-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/11/2019] [Accepted: 06/17/2019] [Indexed: 12/22/2022]
Abstract
Some types of long noncoding RNAs (lncRNAs) are aberrantly expressed in human diseases, including cancer. However, the overall biological roles and clinical significances of most lncRNAs in colorectal cancer (CRC) are not fully understood. First, The Cancer Genome Atlas (TCGA) was analyzed to identify differentially expressed lncRNAs between CRC tissues and noncancerous tissues. We identified that LINC02418 was highly expressed in CRC tissues and cell lines. Next, we evaluated the effect of LINC02418 on CRC tumorigenesis and its regulatory functions of absorbing microRNA and indirectly stimulating protein expression by acting as a ceRNA. Mechanistically, LINC02418 acted as a ceRNA to upregulate MELK expression by absorbing miR-1273g-3p. In addition, the diagnostic performance of cell-free LINC02418 and exosomal LINC02418 were both evaluated by the receiver operating characteristic curve and the area under the curve (AUC). Exosomal LINC02418 could distinguish the patients with CRC from the healthy controls (AUC = 0.8978, 95% confidence interval = 0.8644–0.9351) better than cell-free LINC02418 (AUC = 0.6784, 95% confidence interval = 0.6116–0.7452). Collectively, we determined that LINC02418 was significantly overexpressed in CRC and that the LINC02418–miR-1273g-3p–MELK axis played a critical role in CRC tumorigenesis. Finally, exosomal LINC02418 is a promising, novel biomarker that can be used for the clinical diagnosis of CRC.
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154
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Adaptive innate immunity or innate adaptive immunity? Clin Sci (Lond) 2019; 133:1549-1565. [DOI: 10.1042/cs20180548] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/05/2019] [Accepted: 07/10/2019] [Indexed: 12/19/2022]
Abstract
Abstract
The innate immunity is frequently accepted as a first line of relatively primitive defense interfering with the pathogen invasion until the mechanisms of ‘privileged’ adaptive immunity with the production of antibodies and activation of cytotoxic lymphocytes ‘steal the show’. Recent advancements on the molecular and cellular levels have shaken the traditional view of adaptive and innate immunity. The innate immune memory or ‘trained immunity’ based on metabolic changes and epigenetic reprogramming is a complementary process insuring adaptation of host defense to previous infections.
Innate immune cells are able to recognize large number of pathogen- or danger- associated molecular patterns (PAMPs and DAMPs) to behave in a highly specific manner and regulate adaptive immune responses. Innate lymphoid cells (ILC1, ILC2, ILC3) and NK cells express transcription factors and cytokines related to subsets of T helper cells (Th1, Th2, Th17). On the other hand, T and B lymphocytes exhibit functional properties traditionally attributed to innate immunity such as phagocytosis or production of tissue remodeling growth factors. They are also able to benefit from the information provided by pattern recognition receptors (PRRs), e.g. γδT lymphocytes use T-cell receptor (TCR) in a manner close to PRR recognition. Innate B cells represent another example of limited combinational diversity usage participating in various innate responses. In the view of current knowledge, the traditional black and white classification of immune mechanisms as either innate or an adaptive needs to be adjusted and many shades of gray need to be included.
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155
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Rotival M. Characterising the genetic basis of immune response variation to identify causal mechanisms underlying disease susceptibility. HLA 2019; 94:275-284. [PMID: 31115186 DOI: 10.1111/tan.13598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 05/15/2019] [Indexed: 12/12/2022]
Abstract
Over the last 10 years, genome-wide association studies (GWAS) have identified hundreds of susceptibility loci for autoimmune diseases. However, despite increasing power for the detection of both common and rare coding variants affecting disease susceptibility, a large fraction of disease heritability has remained unexplained. In addition, a majority of the identified loci are located in noncoding regions, and translation of disease-associated loci into new biological insights on the etiology of immune disorders has been lagging. This highlights the need for a better understanding of noncoding variation and new strategies to identify causal genes at disease loci. In this review, I will first detail the molecular basis of gene expression and review the various mechanisms that contribute to alter gene activity at the transcriptional and post-transcriptional level. I will then review the findings from 10 years of functional genomics studies regarding the genetics on gene expression, in particular in the context of infection. Finally, I will discuss the extent to which genetic variants that modulate gene expression at transcriptional and post-transcriptional level contribute to disease susceptibility and present strategies to leverage this information for the identification of causal mechanisms at disease loci in the era of whole genome sequencing.
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Affiliation(s)
- Maxime Rotival
- Unit of Human Evolutionary Genetics, CNRS UMR2000, Institut Pasteur, Paris, France
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156
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Whole Transcriptome Sequencing Reveals How Acupuncture and Moxibustion Increase Pregnancy Rate in Patients Undergoing In Vitro Fertilization-Embryo Transplantation. BIOMED RESEARCH INTERNATIONAL 2019; 2019:4179617. [PMID: 31275970 PMCID: PMC6558619 DOI: 10.1155/2019/4179617] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 05/08/2019] [Indexed: 01/13/2023]
Abstract
Background In vitro fertilization and embryo transfer (IVF-ET) technology has been widely used in the therapy of refractory infertility. Previous studies showed that acupuncture can effectively increase the clinical pregnancy rate of IVF-ET. However, the molecular mechanism is unknown. Materials and Methods In this study, we performed whole transcriptome sequencing for endometrial samples from infertile women who underwent acupuncture and moxibustion therapy or not. Differentially expressed noncoding RNAs (ncRNAs) and mRNAs were identified and their functions were predicted. Besides, a competitive endogenous RNA network was constructed to further interpret the molecular mechanism of acupuncture and moxibustion therapy on infecund patients. In addition, real-time PCR was applied to validate the RNA-seq results. Results We identified 317 differentially expressed mRNAs and 82 ncRNAs in acupuncture and moxibustion therapy group compared with control group. Functional enrichment analysis suggested that these genes were significantly enriched in GO-BP terms associated with cellular transport, such as ATP hydrolysis coupled proton transport, vacuolar acidification, transferrin transport, and proton transport and metabolic process, including small molecule metabolic process and metabolic process. Pathway enrichment analysis enriched 11 terms, including oxidative phosphorylation, synaptic vesicle cycle, mineral absorption, and metabolic pathways. Four of five selected differentially expressed genes were validated by real-time PCR. Conclusion Our results suggested that acupuncture and moxibustion therapy might increase the pregnancy rate of patients undergoing IVF-ET by the regulation of ncRNAs.
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157
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Agliano F, Rathinam VA, Medvedev AE, Vanaja SK, Vella AT. Long Noncoding RNAs in Host-Pathogen Interactions. Trends Immunol 2019; 40:492-510. [PMID: 31053495 DOI: 10.1016/j.it.2019.04.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 02/08/2023]
Abstract
Long noncoding RNAs (lncRNAs) are key molecules that regulate gene expression in a variety of organisms. LncRNAs can drive different transcriptional and post-transcriptional events that impact cellular functions. Recent studies have identified many lncRNAs associated with immune cell development and activation; however, an understanding of their functional role in host immunity to infection is just emerging. Here, we provide a detailed and updated review of the functional roles of lncRNAs in regulating mammalian immune responses during host-pathogen interactions, because these functions may be either beneficial or detrimental to the host. With increased mechanistic insight into the roles of lncRNAs, it may be possible to design and/or improve lncRNA-based therapies to treat a variety of infectious and inflammatory diseases.
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Affiliation(s)
- Federica Agliano
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Vijay A Rathinam
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Andrei E Medvedev
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Sivapriya Kailasan Vanaja
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA.
| | - Anthony T Vella
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA.
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158
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Sharpe HR, Bowyer G, Brackenridge S, Lambe T. HLA-E: exploiting pathogen-host interactions for vaccine development. Clin Exp Immunol 2019; 196:167-177. [PMID: 30968409 PMCID: PMC6468186 DOI: 10.1111/cei.13292] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2019] [Indexed: 12/11/2022] Open
Abstract
Viruses, when used as vectors for vaccine antigen delivery, can induce strong cellular and humoral responses against target epitopes. Recent work by Hansen et al. describes the use of a cytomegalovirus‐vectored vaccine, which is able to generate a stable effector‐memory T cell population at the sites of vaccination in rhesus macaques. This vaccine, targeted towards multiple epitopes in simian immunodeficiency virus (SIV), did not induce classical CD8+ T cells. However, non‐canonical CD8+ T cell induction occurred via major histocompatibility complex (MHC) class II and MHC‐E. The MHC‐E‐restricted T cells could recognize broad epitopes across the SIV peptides, and conferred protection against viral challenge to 55% of vaccinated macaques. The human homologue, human leucocyte antigen (HLA)‐E, is now being targeted as a new avenue for vaccine development. In humans, HLA‐E is an unusually oligomorphic class Ib MHC molecule, in comparison to highly polymorphic MHC class Ia. Whereas MHC class Ia presents peptides derived from pathogens to T cells, HLA‐E classically binds defined leader peptides from class Ia MHC peptides and down‐regulates NK cell cytolytic activity when presented on the cell surface. HLA‐E can also restrict non‐canonical CD8+ T cells during natural infection with various pathogens, although the extent to which they are involved in pathogen control is mostly unknown. In this review, an overview is provided of HLA‐E and its ability to interact with NK cells and non‐canonical T cells. Also discussed are the unforeseen beneficial effects of vaccination, including trained immunity of NK cells from bacille Calmette–Guérin (BCG) vaccination, and the broad restriction of non‐canonical CD8+ T cells by cytomegalovirus (CMV)‐vectored vaccines in pre‐clinical trials.
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Affiliation(s)
- H R Sharpe
- Nuffield Department of Medicine, Jenner Institute, University of Oxford, Oxford, UK
| | - G Bowyer
- Nuffield Department of Medicine, Jenner Institute, University of Oxford, Oxford, UK
| | - S Brackenridge
- Nuffield Department of Medicine, NDM Research Building, University of Oxford, Oxford, UK
| | - T Lambe
- Nuffield Department of Medicine, Jenner Institute, University of Oxford, Oxford, UK
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159
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Being in a loop: how long non-coding RNAs organise genome architecture. Essays Biochem 2019; 63:177-186. [DOI: 10.1042/ebc20180057] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022]
Abstract
Abstract
Chromatin architecture has a significant impact on gene expression. Evidence in the last two decades support RNA as an important component of chromatin structure [Genes Dev. (2005) 19, 1635–1655; PLoS ONE (2007) 2, e1182; Nat. Genet. (2002) 30, 329–334]. Long non-coding RNAs (lncRNAs) are able to control chromatin structure through nucleosome positioning, interaction with chromatin re-modellers and chromosome looping. These functions are carried out in cis at the site of lncRNAs transcription or in trans at distant loci. While the evidence for a role in lncRNAs in regulating gene expression through chromatin interactions is increasing, there is still very little conclusive evidence for a potential role in looping organisation. Here, we review models for the involvement of lncRNAs in genome architecture and the experimental evidence to support them.
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160
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Long Non-Coding RNAs in the Regulation of Gene Expression: Physiology and Disease. Noncoding RNA 2019; 5:ncrna5010017. [PMID: 30781588 PMCID: PMC6468922 DOI: 10.3390/ncrna5010017] [Citation(s) in RCA: 373] [Impact Index Per Article: 74.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 02/07/2023] Open
Abstract
The identification of RNAs that are not translated into proteins was an important breakthrough, defining the diversity of molecules involved in eukaryotic regulation of gene expression. These non-coding RNAs can be divided into two main classes according to their length: short non-coding RNAs, such as microRNAs (miRNAs), and long non-coding RNAs (lncRNAs). The lncRNAs in association with other molecules can coordinate several physiological processes and their dysfunction may impact in several pathologies, including cancer and infectious diseases. They can control the flux of genetic information, such as chromosome structure modulation, transcription, splicing, messenger RNA (mRNA) stability, mRNA availability, and post-translational modifications. Long non-coding RNAs present interaction domains for DNA, mRNAs, miRNAs, and proteins, depending on both sequence and secondary structure. The advent of new generation sequencing has provided evidences of putative lncRNAs existence; however, the analysis of transcriptomes for their functional characterization remains a challenge. Here, we review some important aspects of lncRNA biology, focusing on their role as regulatory elements in gene expression modulation during physiological and disease processes, with implications in host and pathogens physiology, and their role in immune response modulation.
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161
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Fok ET, Davignon L, Fanucchi S, Mhlanga MM. The lncRNA Connection Between Cellular Metabolism and Epigenetics in Trained Immunity. Front Immunol 2019; 9:3184. [PMID: 30761161 PMCID: PMC6361822 DOI: 10.3389/fimmu.2018.03184] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/28/2018] [Indexed: 11/13/2022] Open
Abstract
Trained immunity describes the ability of innate immune cells to form immunological memories of prior encounters with pathogens. Recollection of these memories during a secondary encounter manifests a broadly enhanced inflammatory response characterized by the increased transcription of innate immune genes. Despite this phenomenon having been described over a decade ago, our understanding of the molecular mechanisms responsible for this phenotype is still incomplete. Here we present an overview of the molecular events that lead to training. For the first time, we highlight the mechanistic role of a novel class of long non-coding RNAs (lncRNAs) in the establishment and maintenance of discrete, long lasting epigenetic modifications that are causal to the trained immune response. This recent insight fills in significant gaps in our understanding of trained immunity and reveals novel ways to exploit trained immunity for therapeutic purposes.
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Affiliation(s)
- Ezio T Fok
- Division of Chemical, Systems & Synthetic Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Gene Expression and Biophysics Group, ERA, CSIR Biosciences, Pretoria, South Africa
| | - Laurianne Davignon
- Division of Chemical, Systems & Synthetic Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Stephanie Fanucchi
- Division of Chemical, Systems & Synthetic Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Gene Expression and Biophysics Group, ERA, CSIR Biosciences, Pretoria, South Africa
| | - Musa M Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal
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162
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Fanucchi S, Mhlanga MM. Lnc-ing Trained Immunity to Chromatin Architecture. Front Cell Dev Biol 2019; 7:2. [PMID: 30733945 PMCID: PMC6353842 DOI: 10.3389/fcell.2019.00002] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/10/2019] [Indexed: 11/13/2022] Open
Abstract
Human innate immune cells exposed to certain infections or stimuli develop enhanced immune responses upon re-infection with a different second stimulus, a process termed trained immunity. Recent studies have revealed that hematopoietic stem cells (HSCs) are integral to trained immune responses as they are able to "remember" transcriptional responses and transmit this state to their progeny to educate them how to respond to future infections. The macrophages that arise from trained HSCs are epigenetically reprogrammed and as a result robustly express immune genes, enhancing their capability to resolve infection. Accumulation of H3K4me3 epigenetic marks on multiple immune gene promoters underlie robust transcriptional responses during trained immune responses. However, the mechanism underpinning how these epigenetic marks accumulate at discrete immune gene loci has been poorly understood. In this review, we discuss the previously unexplored contributions of nuclear architecture and long non-coding RNAs on H3K4me3 promoter priming in trained immunity. Altering the activity of these lncRNAs presents a promising therapeutic approach to achieve immunomodulation in inflammatory disease states.
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Affiliation(s)
- Stephanie Fanucchi
- Division of Chemical, Systems & Synthetic Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Gene Expression and Biophysics Group, CSIR Biosciences, Pretoria, South Africa
| | - Musa M Mhlanga
- Division of Chemical, Systems & Synthetic Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
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163
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