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Here, the authors use genome-scale in vivo CRISPR screens to look at immune evasion mechanisms across cancer models, showing that IFN-mediated upregulation of classical and non-classical MHC class I inhibitory checkpoints facilitate immune escape.
Recent studies suggest that neutrophils can exhibit substantial function diversity. Here, Ostuni and colleagues perform immunophenotyping and transcriptome analysis to characterize the heterogeneity of human neutrophils, both under steady state and upon stress-induced conditions.
Zhang and colleagues use single-cell RNA sequencing on the nasal mucosa to identify cell subsets and molecules that specifically contribute to the pathogenesis of chronic rhinosinusitis subtypes.
Shi and colleagues describe a subset of erythroid precursors with immune characteristics that can be isolated from the yolk sac to the adult bone marrow stages during human ontogenesis.
Goldrath and colleagues define the diversity of gene expression and genome accessibility in mouse CD8+ TRM cells in distinct tissues and identify molecules critical forgeneration of CD8+ TRM cells in response to acute viral infection.
Single-cell RNAseq during initiation and progression of mouse glioblastoma reveals a dynamic immune microenvironment transitioning from pro-inflammatory microglia in early tumors towards an infiltrating macrophage and suppressor cell-centric immune landscape in late-stage tumors.
Malek and colleagues describe the longitudinal transcriptional and epigenetic changes occurring in regulatory T cells following in vivo stimulation with IL-2 or the biologic IL-2–CD25.
Colonna and colleagues present a genome-wide characterization of DNA methylation and hydroxymethylation in innate lymphocytes and identify differentially methylated and hydroxymethylated regions between NK cells, ILC2s and ILC3s.
Sumida et al. resolve the human T cell transcriptional response to type I interferon stimulation at high temporal resolution and reveal a genetic network controlling coinhibitory receptor expression.
MIBI-TOF is a mass spectrometry-based multiplexed imaging platform that has been used to map tumors. In this Resource article, MIBI-TOF is used to provide a spatial atlas of immune responses within human tuberculosis granulomas.
Weisel and colleagues provide a resource that phenotypically profiles naive and memory B cells and provides a comparative analysis of memory B cells found in humans versus mice.
Zhong et al. utilize B6/Cast F1 hybrid mice to examine transcriptional regulation of T cell gene expression upon activation induced by viral challenge. They describe gene accessibility changes that lead to differential gene expression and report a hierarchy of transcription factor families that mediate the chromatin dynamics.
Haas, Velten and colleagues use single-cell multiomics of human blood and bone marrow to generate a reference map allowing the quantitative linking of cytometry and proteo-genomic information.
Pediatric COVID-19 can be associated with subsequent multisystem inflammatory syndrome in children (MIS-C), but how these pathologies are related or differ is unclear. Here the authors compare and contrast pediatric COVID-19 and MIS-C immunophenotypes using SARS-CoV-2 antibody fingerprinting proteomics.
Brown and colleagues generated an atlas of miRNA expression profiles from primary mouse immune cell populations and connected these signatures with ATAC–seq, ChIP–seq and nascent RNA profiles to establish a map of miRNA promoter and enhancer usage in immune cells.
Raychaudhuri and colleagues use high-dimensional single-cell analysis of T cells from a human tuberculosis progression cohort. They identify a TH17–like cluster reactive to Mycobacterium tuberculosis peptides that is reduced in people who previously progressed to active disease.
Multiple myeloma disease progression and therapy response are influenced by the bone marrow niche in which the tumor cells reside. To characterize this supportive niche, Cupedo and colleagues use single-cell transcriptomic analysis of bone marrow stromal cell populations from individuals with multiple myeloma. They identify a myeloma-specific inflammatory mesenchymal stromal cell (iMSC) population that spatially colocalizes with tumor cells. Anti-myeloma induction therapy does not influence iMSC presence, suggesting a role for bone marrow inflammation in myeloma persistence or relapse.
Immune cells exert important effects on white adipose tissue (WAT) in metabolic diseases. O’Sullivan and colleagues generate a comprehensive single-cell atlas of WAT cells in both health and disease to identify new cellular networks and differentiation trajectories.
Malaria immunity can be acquired through natural infection, but the correlates of protection are still being determined. Yazdanbakhsh and colleagues combine experimental infection of volunteers with Plasmodium falciparum with systems analysis to throw light on the nature of protective immune responses.
Sun and colleagues provide a new resource, multi-omics analysis of NK cell Jak–STAT signaling in response to the cytokines IL-2, IL-15, IL-12, IL-18 and IFN-α, showing synergistic and antagonistic interactions that govern NK cell activity.