Maninjay K. Atianand, Daniel R. Caffrey, K. Fitzgerald
{"title":"Immunobiology of Long Noncoding RNAs.","authors":"Maninjay K. Atianand, Daniel R. Caffrey, K. Fitzgerald","doi":"10.1146/annurev-immunol-041015-055459","DOIUrl":"https://doi.org/10.1146/annurev-immunol-041015-055459","url":null,"abstract":"The discovery of long noncoding RNAs (lncRNA) has provided a new perspective on gene regulation in diverse biological contexts. lncRNAs are remarkably versatile molecules that interact with RNA, DNA, or proteins to promote or restrain the expression of protein-coding genes. Activation of immune cells is associated with dynamic changes in expression of genes, the products of which combat infectious microorganisms, initiate repair, and resolve inflammatory responses in cells and tissues. Recent evidence indicates that lncRNAs play important roles in directing the development of diverse immune cells and controlling the dynamic transcriptional programs that are a hallmark of immune cell activation. The importance of these molecules is underscored by their newly recognized roles in inflammatory diseases. In this review, we discuss the contribution of lncRNAs in the development and activation of immune cells and their roles in immune-related diseases. We also discuss challenges faced in identifying biological functions for this large and complex class of genes.","PeriodicalId":8271,"journal":{"name":"Annual review of immunology","volume":"35 1","pages":"177-198"},"PeriodicalIF":29.7,"publicationDate":"2017-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-immunol-041015-055459","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47950352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
G. Randolph, Stoyan Ivanov, B. Zinselmeyer, J. Scallan
{"title":"The Lymphatic System: Integral Roles in Immunity.","authors":"G. Randolph, Stoyan Ivanov, B. Zinselmeyer, J. Scallan","doi":"10.1146/annurev-immunol-041015-055354","DOIUrl":"https://doi.org/10.1146/annurev-immunol-041015-055354","url":null,"abstract":"The lymphatic vasculature is not considered a formal part of the immune system, but it is critical to immunity. One of its major roles is in the coordination of the trafficking of antigen and immune cells. However, other roles in immunity are emerging. Lymphatic endothelial cells, for example, directly present antigen or express factors that greatly influence the local environment. We cover these topics herein and discuss how other properties of the lymphatic vasculature, such as mechanisms of lymphatic contraction (which immunologists traditionally do not take into account), are nonetheless integral in the immune system. Much is yet unknown, and this nascent subject is ripe for exploration. We argue that to consider the impact of lymphatic biology in any given immunological interaction is a key step toward integrating immunology with organ physiology and ultimately many complex pathologies.","PeriodicalId":8271,"journal":{"name":"Annual review of immunology","volume":"35 1","pages":"31-52"},"PeriodicalIF":29.7,"publicationDate":"2017-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-immunol-041015-055354","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49595355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Annual review of immunologyPub Date : 2017-04-26Epub Date: 2017-01-30DOI: 10.1146/annurev-immunol-051116-052225
Romain Banchereau, Alma-Martina Cepika, Jacques Banchereau, Virginia Pascual
{"title":"Understanding Human Autoimmunity and Autoinflammation Through Transcriptomics.","authors":"Romain Banchereau, Alma-Martina Cepika, Jacques Banchereau, Virginia Pascual","doi":"10.1146/annurev-immunol-051116-052225","DOIUrl":"10.1146/annurev-immunol-051116-052225","url":null,"abstract":"<p><p>Transcriptomics, the high-throughput characterization of RNAs, has been instrumental in defining pathogenic signatures in human autoimmunity and autoinflammation. It enabled the identification of new therapeutic targets in IFN-, IL-1- and IL-17-mediated diseases. Applied to immunomonitoring, transcriptomics is starting to unravel diagnostic and prognostic signatures that stratify patients, track molecular changes associated with disease activity, define personalized treatment strategies, and generally inform clinical practice. Herein, we review the use of transcriptomics to define mechanistic, diagnostic, and predictive signatures in human autoimmunity and autoinflammation. We discuss some of the analytical approaches applied to extract biological knowledge from high-dimensional data sets. Finally, we touch upon emerging applications of transcriptomics to study eQTLs, B and T cell repertoire diversity, and isoform usage.</p>","PeriodicalId":8271,"journal":{"name":"Annual review of immunology","volume":"35 1","pages":"337-370"},"PeriodicalIF":26.9,"publicationDate":"2017-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5937945/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42694539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mucosal Ecological Network of Epithelium and Immune Cells for Gut Homeostasis and Tissue Healing.","authors":"Y. Kurashima, H. Kiyono","doi":"10.1146/annurev-immunol-051116-052424","DOIUrl":"https://doi.org/10.1146/annurev-immunol-051116-052424","url":null,"abstract":"The intestinal epithelial barrier includes columnar epithelial, Paneth, goblet, enteroendocrine, and tuft cells as well as other cell populations, all of which contribute properties essential for gastrointestinal homeostasis. The intestinal mucosa is covered by mucin, which contains antimicrobial peptides and secretory IgA and prevents luminal bacteria, fungi, and viruses from stimulating intestinal immune responses. Conversely, the transport of luminal microorganisms-mediated by M, dendritic, and goblet cells-into intestinal tissues facilitates the harmonization of active and quiescent mucosal immune responses. The bacterial population within gut-associated lymphoid tissues creates the intratissue cohabitations for harmonized mucosal immunity. Intermolecular and intercellular communication among epithelial, immune, and mesenchymal cells creates an environment conducive for epithelial regeneration and mucosal healing. This review summarizes the so-called intestinal mucosal ecological network-the complex but vital molecular and cellular interactions of epithelial mesenchymal cells, immune cells, and commensal microbiota that achieve intestinal homeostasis, regeneration, and healing.","PeriodicalId":8271,"journal":{"name":"Annual review of immunology","volume":"35 1","pages":"119-147"},"PeriodicalIF":29.7,"publicationDate":"2017-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-immunol-051116-052424","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47603602","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Annual review of immunologyPub Date : 2017-04-26Epub Date: 2017-02-09DOI: 10.1146/annurev-immunol-051116-052358
Marco Colonna, Oleg Butovsky
{"title":"Microglia Function in the Central Nervous System During Health and Neurodegeneration.","authors":"Marco Colonna, Oleg Butovsky","doi":"10.1146/annurev-immunol-051116-052358","DOIUrl":"https://doi.org/10.1146/annurev-immunol-051116-052358","url":null,"abstract":"<p><p>Microglia are resident cells of the brain that regulate brain development, maintenance of neuronal networks, and injury repair. Microglia serve as brain macrophages but are distinct from other tissue macrophages owing to their unique homeostatic phenotype and tight regulation by the central nervous system (CNS) microenvironment. They are responsible for the elimination of microbes, dead cells, redundant synapses, protein aggregates, and other particulate and soluble antigens that may endanger the CNS. Furthermore, as the primary source of proinflammatory cytokines, microglia are pivotal mediators of neuroinflammation and can induce or modulate a broad spectrum of cellular responses. Alterations in microglia functionality are implicated in brain development and aging, as well as in neurodegeneration. Recent observations about microglia ontogeny combined with extensive gene expression profiling and novel tools to study microglia biology have allowed us to characterize the spectrum of microglial phenotypes during development, homeostasis, and disease. In this article, we review recent advances in our understanding of the biology of microglia, their contribution to homeostasis, and their involvement in neurodegeneration. Moreover, we highlight the complexity of targeting microglia for therapeutic intervention in neurodegenerative diseases.</p>","PeriodicalId":8271,"journal":{"name":"Annual review of immunology","volume":"35 ","pages":"441-468"},"PeriodicalIF":29.7,"publicationDate":"2017-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-immunol-051116-052358","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34756088","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
John T. Crowl, Elizabeth E Gray, K. Pestal, Hannah E. Volkman, Daniel B. Stetson
{"title":"Intracellular Nucleic Acid Detection in Autoimmunity.","authors":"John T. Crowl, Elizabeth E Gray, K. Pestal, Hannah E. Volkman, Daniel B. Stetson","doi":"10.1146/annurev-immunol-051116-052331","DOIUrl":"https://doi.org/10.1146/annurev-immunol-051116-052331","url":null,"abstract":"Protective immune responses to viral infection are initiated by innate immune sensors that survey extracellular and intracellular space for foreign nucleic acids. The existence of these sensors raises fundamental questions about self/nonself discrimination because of the abundance of self-DNA and self-RNA that occupy these same compartments. Recent advances have revealed that enzymes that metabolize or modify endogenous nucleic acids are essential for preventing inappropriate activation of the innate antiviral response. In this review, we discuss rare human diseases caused by dysregulated nucleic acid sensing, focusing primarily on intracellular sensors of nucleic acids. We summarize lessons learned from these disorders, we rationalize the existence of these diseases in the context of evolution, and we propose that this framework may also apply to a number of more common autoimmune diseases for which the underlying genetics and mechanisms are not yet fully understood.","PeriodicalId":8271,"journal":{"name":"Annual review of immunology","volume":"35 1","pages":"313-336"},"PeriodicalIF":29.7,"publicationDate":"2017-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-immunol-051116-052331","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47670969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Annual review of immunologyPub Date : 2017-04-26Epub Date: 2017-02-06DOI: 10.1146/annurev-immunol-041015-055325
Arup K Chakraborty
{"title":"A Perspective on the Role of Computational Models in Immunology.","authors":"Arup K Chakraborty","doi":"10.1146/annurev-immunol-041015-055325","DOIUrl":"https://doi.org/10.1146/annurev-immunol-041015-055325","url":null,"abstract":"<p><p>This is an exciting time for immunology because the future promises to be replete with exciting new discoveries that can be translated to improve health and treat disease in novel ways. Immunologists are attempting to answer increasingly complex questions concerning phenomena that range from the genetic, molecular, and cellular scales to that of organs, whole animals or humans, and populations of humans and pathogens. An important goal is to understand how the many different components involved interact with each other within and across these scales for immune responses to emerge, and how aberrant regulation of these processes causes disease. To aid this quest, large amounts of data can be collected using high-throughput instrumentation. The nonlinear, cooperative, and stochastic character of the interactions between components of the immune system as well as the overwhelming amounts of data can make it difficult to intuit patterns in the data or a mechanistic understanding of the phenomena being studied. Computational models are increasingly important in confronting and overcoming these challenges. I first describe an iterative paradigm of research that integrates laboratory experiments, clinical data, computational inference, and mechanistic computational models. I then illustrate this paradigm with a few examples from the recent literature that make vivid the power of bringing together diverse types of computational models with experimental and clinical studies to fruitfully interrogate the immune system.</p>","PeriodicalId":8271,"journal":{"name":"Annual review of immunology","volume":"35 ","pages":"403-439"},"PeriodicalIF":29.7,"publicationDate":"2017-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-immunol-041015-055325","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34756089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jian K Tan, Craig McKenzie, Eliana Mariño, Laurence Macia, Charles R Mackay
{"title":"Metabolite-Sensing G Protein-Coupled Receptors-Facilitators of Diet-Related Immune Regulation.","authors":"Jian K Tan, Craig McKenzie, Eliana Mariño, Laurence Macia, Charles R Mackay","doi":"10.1146/annurev-immunol-051116-052235","DOIUrl":"https://doi.org/10.1146/annurev-immunol-051116-052235","url":null,"abstract":"Nutrition and the gut microbiome regulate many systems, including the immune, metabolic, and nervous systems. We propose that the host responds to deficiency (or sufficiency) of dietary and bacterial metabolites in a dynamic way, to optimize responses and survival. A family of G protein-coupled receptors (GPCRs) termed the metabolite-sensing GPCRs bind to various metabolites and transmit signals that are important for proper immune and metabolic functions. Members of this family include GPR43, GPR41, GPR109A, GPR120, GPR40, GPR84, GPR35, and GPR91. In addition, bile acid receptors such as GPR131 (TGR5) and proton-sensing receptors such as GPR65 show similar features. A consistent feature of this family of GPCRs is that they provide anti-inflammatory signals; many also regulate metabolism and gut homeostasis. These receptors represent one of the main mechanisms whereby the gut microbiome affects vertebrate physiology, and they also provide a link between the immune and metabolic systems. Insufficient signaling through one or more of these metabolite-sensing GPCRs likely contributes to human diseases such as asthma, food allergies, type 1 and type 2 diabetes, hepatic steatosis, cardiovascular disease, and inflammatory bowel diseases.","PeriodicalId":8271,"journal":{"name":"Annual review of immunology","volume":"35 ","pages":"371-402"},"PeriodicalIF":29.7,"publicationDate":"2017-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-immunol-051116-052235","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34945303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genetics of Infectious and Inflammatory Diseases: Overlapping Discoveries from Association and Exome-Sequencing Studies.","authors":"D. Langlais, N. Fodil, P. Gros","doi":"10.1146/annurev-immunol-051116-052442","DOIUrl":"https://doi.org/10.1146/annurev-immunol-051116-052442","url":null,"abstract":"Genome technologies have defined a complex genetic architecture in major infectious, inflammatory, and autoimmune disorders. High density marker arrays and Immunochips have powered genome-wide association studies (GWAS) that have mapped nearly 450 genetic risk loci in 22 major inflammatory diseases, including a core of common genes that play a central role in pathological inflammation. Whole-exome and whole-genome sequencing have identified more than 265 genes in which mutations cause primary immunodeficiencies and rare forms of severe inflammatory bowel disease. Combined analysis of inflammatory disease GWAS and primary immunodeficiencies point to shared proteins and pathways that are required for immune cell development and protection against infections and are also associated with pathological inflammation. Finally, sequencing of chromatin immunoprecipitates containing specific transcription factors, with parallel RNA sequencing, has charted epigenetic regulation of gene expression by proinflammatory transcription factors in immune cells, providing complementary information to characterize morbid genes at infectious and inflammatory disease loci.","PeriodicalId":8271,"journal":{"name":"Annual review of immunology","volume":"35 1","pages":"1-30"},"PeriodicalIF":29.7,"publicationDate":"2017-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-immunol-051116-052442","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44953888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Annual review of immunologyPub Date : 2017-04-26Epub Date: 2017-02-06DOI: 10.1146/annurev-immunol-051116-052206
Peter J M Openshaw, Chris Chiu, Fiona J Culley, Cecilia Johansson
{"title":"Protective and Harmful Immunity to RSV Infection.","authors":"Peter J M Openshaw, Chris Chiu, Fiona J Culley, Cecilia Johansson","doi":"10.1146/annurev-immunol-051116-052206","DOIUrl":"https://doi.org/10.1146/annurev-immunol-051116-052206","url":null,"abstract":"<p><p>Respiratory syncytial virus (RSV) is an exceptional mucosal pathogen. It specializes in infection of the ciliated respiratory epithelium, causing disease of variable severity with little or no direct systemic effects. It infects virtually all children by the age of three years and then repeatedly infects throughout life; this it does despite relatively slight variations in antigenicity, apparently by inducing selective immunological amnesia. Inappropriate or dysregulated responses to RSV can be pathogenic, causing disease-enhancing inflammation that contributes to short- and long-term effects. In addition, RSV's importance as a largely unrecognized pathogen of debilitated older people is increasingly evident. Vaccines that induce nonpathogenic protective immunity may soon be available, and it is possible that different vaccines will be optimal for infants; older children; young to middle-age adults (including pregnant women); and elderly persons. At the dawn of RSV vaccination, it is timely to review what is known (and unknown) about immune responses to this fascinating virus.</p>","PeriodicalId":8271,"journal":{"name":"Annual review of immunology","volume":"35 ","pages":"501-532"},"PeriodicalIF":29.7,"publicationDate":"2017-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-immunol-051116-052206","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34756159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}