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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.
Bcl11b is needed to establish T cell–lineage identity. Rothenberg and colleagues provide a comprehensive analysis of Bcl11b–cofactor interactions and reveal the functional relevance of direct and indirect Bcl11b binding activity in thymocytes.
MicroRNAs regulate gene expression by targeting mRNAs via complementarity with seed sequences. Rudensky and colleagues provide genome-wide profiles of the microRNA miR-155 in multiple immune cell lineages and identify its cell-type effects on gene expression.
Soumelis and colleagues use RNA-based sequencing to define the transcriptional signatures of DC subsets and monocytes-macrophages in human primary breast cancer.
The immune response to pathogens varies substantially among humans. Netea and colleagues show that integration of multi-omics data and deep phenotyping enables prediction of cytokine production in responses to pathogens.
Influenza can occasionally result in life-threatening sequelae. Openshaw and colleagues describe the functional and transcriptional response to natural infection with influenza virus and find that a transition to an ‘anti-bacterial response’ is associated with more-severe symptoms.
Both environmental factors and genetic factors influence human immunity. Albert and colleagues leverage data from the Milieu Intérieur Consortium to comprehensively describe the effects of lifestyle, environment and genetics on human innate and adaptive immunity.
Specialized populations of regulatory T cells inhabit tissues and maintain homeostasis, and assist with repair functions there. Feuerer and colleagues identify a genome-wide DNA-methylation landscape to define this specialized subset of cells.
T cells undergo myriad changes after antigenic activation. Araki and colleagues show that CD8+ T cells exert dynamic control of mRNA translation during differentiation into effector and memory cells.
Immune cells give rise to the most interconnected system in the body. Meissner and colleagues perform comprehensive proteomics and secretomics to describe in detail the ‘social network’ of human immune cells and throw light on previously unknown cell connectivities.
Antigenic drift and reassortment alters the epitopes of influenza virus. Krammer and colleagues reveal the cross-reactivity of antibody responses to viral hemagglutinin and neuraminidase in humans and several animal models, but the most prominent responses reflect ‘original antigenic sin’ to viral exposure.
A goal of vaccination is to elicit and maintain tissue-resident memory T cells. Amsen and colleagues show human lung-resident memory CD8+ T cells express distinct transcriptional programs, including a role for Notch in cellular metabolism and maintenance.
Holländer and colleagues provide a map of genes that are direct targets of the transcription factor Foxn1 in thymic epithelial cells and show that Foxn1 controls genes encoding products involved in thymocyte development, antigen processing and thymocyte selection.
Immunologic memory promotes faster and more-efficient responses after re-exposure to pathogens. Ahmed and colleagues characterize a subset of human B cells that arise after vaccination against or exposure to influenza or Ebola virus and contribute to the memory cell pool.