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Woolf and colleagues use single-cell transcriptomics to determine the gene signature of infiltrating immune cells and potential cell–cell interactions between receptors, ligands, ion channels and metabolites expressed on immune cells and sensory neurons in three models of pain.
In this Resource paper, the authors integrate T cell antigen receptor, B cell antigen receptor and exome sequencing comparing early and metastatic breast cancer in humans, showing how the immune response and tumors coevolve.
Jakubzick and colleagues show that interstitial macrophages across various tissues display similar coordinated chemokine signatures in humans and mice.
In this Resource, the authors integrate multiomics data to show the effect of the transcription factors Blimp-1 and c-Maf on IL-10 and type 1 and 17 responses, which together protect against pathobiont-induced colitis.
Kratchmarov et al. identified a GATA3+ TH2 population that expresses the transcription factors TCF1 and LEF1 and sustains type 2 inflammation in tissues over a human lifetime, despite chronic antigen exposure.
In this Resource article, the authors integrate genomic, bioinformatic and flow cytometric data from human bone marrow to provide an atlas of hematopoietic progenitor cell states in health and disease.
Sagar and colleagues provide a comprehensive single-cell multimodal landscape of γδ T cells in various mouse tissues, unveiling site-specific adaptations and highlighting key tissue residency features of γδ T cells.
Anrather and colleagues provide a longitudinal single-cell transcriptomic atlas of brain and mouse blood following stroke, describing brain-infiltrating leukocytes, circulating leukocytes, microglia and endothelium diversity over the ischemic–reperfusion time
Randolph and colleagues analyze the immune cells in the human and mouse peritoneum and show that the major populations of serous cavity-resident macrophages in humans and mice represent distinct differentiation stages of an overlapping differentiation program.
Koelle and colleagues use an activation marker-dependent approach to determine the recruitment of TCR by three doses of mRNA vaccination in individuals previously infected with SARS-CoV-2.
Using TEA-seq, Thomson et al. detail transcriptional and epigenetic alterations in the T cell compartment between healthy children and older adults, leading to the discovery of a novel pediatric CD8αα+ population poised for rapid effector responses.
Streets, Yosef, Robey and colleagues use multiomics analysis to generate a comprehensive timeline of the CD4+ and CD8+ T cell lineage commitment and identify sequential waves of TCR signaling that first initiate CD4+ T cell lineage differentiation and then CD8+ T cells lineage specification.
Garner et al. analyzed the single-cell transcriptome and TCR repertoire of matched blood and liver, and resting and activated, human MAIT cells. They identify donor-specific TCR repertoires shared across tissues and a transcriptome that is largely homogeneous at rest, but highly adaptive to different tissue and stimulation environments.
Stevens and colleagues show that human stem-cell-differentiated microglia can be used to model the extensive transcriptional diversity of human brain microglia.
Glass and colleagues show that the transcription factor SALL1-associated super-enhancer is exclusively activated in microglia, in part through SMAD4-mediated signaling, and that SALL1 subsequently enforces microglia-specific functions of SMAD4.
Akassoglou and colleagues provide a single-cell RNA sequencing and phosphoprotein analysis of the responses of central nervous system microglia and macrophages to blood proteins including activated complement and fibrin. Their findings point to potential therapeutic targeting of microglia activation by immune and vascular signals.
Smith et al. present a resource detailing drivers of transcriptional heterogeneity of synovial fibroblasts cell states in the inflamed joints of human patients with rheumatoid arthritis.
Benhar and colleagues provide an atlas of non-neuronal cells in the adult mouse retina at steady state and after optic nerve injury and identify key cellular and molecular events along the path of neuronal degeneration after injury.
Ruffieux, Hess and colleagues analyze longitudinal phenotyping of patients with coronavirus disease 2019 to show that covariation of innate immune cell numbers, kynurenine metabolites and lipid metabolites influence the restoration of homeostasis, the risk of death and that of long COVID.
Colonna and colleagues report dysregulated gene expression in microglia harboring homozygous mutations of DAP12 from individuals with Nasu–Hakola disease, a form of early-onset dementia.