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Singh and colleagues leverage genome-wide assays to identify functionally active enhancers that are present in naive and lipopolysaccharide-activated B cells by FAIRE–seq, STARR–seq and Hi-C structural interactome analyses and identify additional transcription factors that regulate gene expression modules.
The International Mouse Phenotyping Consortium (IMPC) aims to identify the function of all protein-coding genes in the mouse genome. Hayday and colleagues leverage 530 knockout lines from the IPMC to develop the 3i Project, which immunophenotypes mice and leads to the identification of new and unexpected gene influences on immune function and on the structural organization of the immune system.
Cantrell and colleagues perform a comparative quantitative mass spectrometric analysis of the proteomes of naïve and activated CD4+ and CD8+ T cells. Proteomes are dynamically regulated and mTORC1 inhibition leads to differential consequences depending on cell state.
Malissen and colleagues provide a quantitative systems-level analysis of 15 distinct signalosomes that form within minutes of TCR stimulation of primary CD4+ T cells.
MAIT cells recognize the microbial metabolite 5-OP-RU and are selected on DP thymocytes expressing the MHC class Ib molecule MR1. Lantz and colleagues identify 5-OP-RU-specific thymocytes that are selected on thymic epithelial cells and differentiate into naive T cells.
Much about the kidney-resident immune populations is a black box. Hacohen and colleagues use single cell RNA sequencing of kidney, skin and urine from lupus nephritis patients to describe the transcriptional state of the immune cells present in each compartment.
Nephritis is a major cause of lupus morbidity. Putterman and colleagues use single-cell RNA sequencing on human renal and skin biopsies to describe the expression landscape associated with lupus nephritis.
Defining cell types and their activation status in rheumatoid arthritis (RA) is critical to understanding this disease. Raychaudhuri and colleagues leverage several single-cell -omics approaches to define the cellular processes and pathways in the human RA joint.
Oliver and colleagues use di-glycine remnant profiling in combination with whole-cell proteomics and transcriptomics to identify ubiquitylated proteins and predict degradative or non-degradative outcomes of ubiquitylation in activated primary mouse CD4+ T cells.
Respiratory infections are the principal cause of asthma exacerbations in children. Altman and colleagues use a systems approach to describe the pathways associated with asthma exacerbations in a cohort of inner-city children.
Muscle damage elicits a sterile immune response that facilitates complete regeneration. Nagy and colleagues map the mediator lipidome during the transition from inflammation to resolution in skeletal muscle injury.
Interferon-stimulated genes (ISGs) are a key component of the antiviral response. Pichlmair and colleagues generate a comprehensive ISG interactome that sheds light on their functions in antiviral responses.
The transcription factor Foxp1 regulates the quiescence of naïve T cells. Rudensky and colleagues show that Foxp1 has a role that is cooperative and synergistic with that of Foxp3 in regulatory T cells, distinct from its roles in conventional CD4+ T cells.