Abstract
The immune system is a complex biological network composed of hierarchically organized genes, proteins, and cellular components that combat external pathogens and monitor the onset of internal disease. To meet and ultimately defeat these challenges, the immune system orchestrates an exquisitely complex interplay of numerous cells, often with highly specialized functions, in a tissue-specific manner. One of the major methodologies of systems immunology is to measure quantitatively the components and interaction levels in the immunologic networks to construct a computational network and predict the response of the components to perturbations. The recent advances in high-throughput sequencing techniques have provided us with a powerful approach to dissecting the complexity of the immune system. Here we summarize the latest progress in integrating omics data and network approaches to construct networks and to infer the underlying signaling and transcriptional landscape, as well as cell-cell communication, in the immune system, with a focus on hematopoiesis, adaptive immunity, and tumor immunology. Understanding the network regulation of immune cells has provided new insights into immune homeostasis and disease, with important therapeutic implications for inflammation, cancer, and other immune-mediated disorders.
Highlights
The mammalian immune system maintains a balance between inducing an appropriate immune response to exogenous pathogens and avoiding autoimmune reactions to self-antigens
CD4+-naive T cells can differentiate into T helper cells upon antigen stimulation (Saravia et al, 2019), and regulatory T (Treg) cells can gain tissue-specific signatures to become specific types of tissue-resident Treg cells (Shi and Chi, 2019), both of which require antigen presentation and cytokine stimulation provided by innate immune cells like dendritic cells (DCs) (Eisenbarth, 2019)
These innate and adaptive immune cells are produced through a series of developmental steps called hematopoiesis, which is sustained throughout life by a relatively small pool of hematopoietic stem cells (HSCs) that reside in the marrow
Summary
The immune system is a complex biological network composed of hierarchically organized genes, proteins, and cellular components that combat external pathogens and monitor the onset of internal disease. The recent advances in high-throughput sequencing techniques have provided us with a powerful approach to dissecting the complexity of the immune system. We summarize the latest progress in integrating omics data and network approaches to construct networks and to infer the underlying signaling and transcriptional landscape, as well as cell-cell communication, in the immune system, with a focus on hematopoiesis, adaptive immunity, and tumor immunology. Understanding the network regulation of immune cells has provided new insights into immune homeostasis and disease, with important therapeutic implications for inflammation, cancer, and other immunemediated disorders
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