Omics in immunology

Abstract

The term “Omics” broadly refers to a set of genomics technologies that are utilized in cellular and molecular biology to investigate molecular (DNA, RNA), protein and epigenetics signatures. Omics are utilized to study both host and pathogens, and across many disciplines such as immunology, oncology and cell biology. With the high-throughput technologies and the development of new bioinformatics tools, these approaches have significantly contributed to our understanding of how molecular mechanisms determine the structure, function and dynamics of organisms. With the large and growing volume of data generated with these approaches, bioinformatics has become an integral part of research in biology and notably immunology and microbiology. Large omics data sets are now also important components in clinical and translational research. For instance, databases of gene expression, somatic mutations and protein networks can be used to predict disease outcome or to develop new molecular diagnostic tools. In this Special Feature, the four reviews describe some of the most prominent applications of omics and bioinformatics in immunology research and clinical translational applications. These articles exemplify the vast research work that has occurred in the last two decades on the application of omics in medical and basic science research, with the objective to provide the reader with an introductory view of the current state of the art. T-cell receptors are formed from a complex set of genes undergoing homologous recombination, and it has been the result of very long evolutionary processes. T-cell receptor drives one of the most sophisticated weapons that the immune system has against pathogens. Understanding the biology of T-cell receptors is an ongoing subject of investigation since their discovery and sequence in the early 1980s.1 The review from Watkins and Miles 2 brings the reader up to speed with sequencing technologies and bioinformatics that have enabled diagnostic applications and predictive analyses in basic and clinical immunology. Autoimmunity: High-throughput sequencing of genomics has significantly impacted research in autoimmune disorders, with the possibility to screen large sample size and identify genetic variants across the full genome. The review from Field 3 reports the bioinformatics challenges that arose with the high-throughput detection of pathogenic variants and discusses the future applications toward personalized medicine. Single-cell multi-omics: In the last decade, single-cell genomics have permitted unprecedented detection of biological complexity and heterogeneity, notably in immunology.4 Advances in microfluidics and other technologies have allowed investigation of individual cells, thus removing the unwanted noise arising from the analysis of heterogenous cell populations. More recently, new technologies and bioinformatics analyses have enabled the simultaneous investigation of multiple modalities within the same cells utilizing more than one omic technology. The review from Louie and Luciani 5 discusses the recent advances in multi-omics to study immune cells, and also how the near future may be shaped by these technologies. Omics technology in the clinic: In the clinical setting, the application of omics technology has shown considerable promise. From patient stratification and therapeutic selection to the realization of personalized medicine, these technologies are beginning to fundamentally alter the way we approach molecular studies in translational research. The review from Giles et al.6 review current applications of omics technologies in immunology and oncology, along with ethical and practical challenges currently constraining adoption. Omics technologies and bioinformatics are increasingly becoming essential components in biology and specifically immunology. The development of high-throughput technologies has permitted the generation of numerous data sets across human and pathogens, introducing the need for large, centralized repositories, such as the Human Cell Atlas for single-cell genomics.7 Bioinformatics analysis and integration of very large omics data are providing the foundation to address unanswered questions including heterogeneity of biological processes and cell types, and how these can be translated into new treatment and interventions. These reviews represent key examples of the questions that are currently being addressed and a view of the future directions that omics and bioinformatics will shape the next decade of research. Samuel Foster: Conceptualization. Fabio Luciani: Conceptualization; Writing-original draft; Writing-review & editing. The authors declare no conflict of interest for this article.