Biology subjects

Romagnani, C.

Publications and source records attributed to Romagnani, C..

7 recordsLinked to original sources

bioRxiv2026

Clonal selection of somatic mutations shapes NK cell memory

Adaptive immune memory relies on selective clonal expansion and persistence of lymphocyte populations. Whether and how clonal selection occurs in innate lymphocytes that lack rearranged antigen receptors remains poorly understood. Here, we used somatic genetics to reconstruct the natural history of human natural killer (NK) cell responses to cytomegalovirus infection. Across a large cohort of healthy seropositive individuals, we found strong clonal dominance in memory NK cells consistent with clonal selection. Dominant memory NK cell clones were marked by coherent receptor and chromatin configurations, emerged early in life and diversified into genetically related subclones. Both an excess of coding mutations, and the reconstructed population dynamics of the dominant clones, provided evidence for positive selection acting on somatic genetic variation. We identified somatic loss-of-function mutations in the chromatin modifier KMT2D, and showed in a mouse model that Kmt2d deletion alters NK-cell fitness depending on timing and environmental context. Together, these findings establish clonal selection as an organizing principle of human NK-cell memory and support a model in which heritable cell states and acquired genetic variation contribute to shape clonal competition.

immunology↗

bioRxiv2026

Tissue-adapted NK cells shape pathogenic cDC1 niches in early arthritis

Chronic forms of autoimmune arthritis, including juvenile idiopathic arthritis (JIA), are characterised by persistent synovial inflammation. While adaptive mechanisms are well-studied, the innate networks driving early joint disease remain poorly defined. Here, through unbiased profiling of innate lymphoid cells from the joints of children with JIA at disease onset, we identify activated natural killer (NK) cells as key orchestrators of adaptive immune niches. The selective upregulation of lymphotactin (XCL1) by activated NK cells is accompanied by the synovial enrichment of XCR1+ type 1 conventional dendritic cells (cDC1s), directly correlating with disease severity. In situ, NK cells spatially anchor with recruited cDC1s to assemble discrete, multicellular effector niches alongside T cells. Finally, we demonstrate this NK-cDC1 spatial architecture represents a conserved pathogenic module across adult arthropathies, including rheumatoid arthritis. Our findings establish the XCL1-XCR1 axis as a fundamental innate feature of chronic joint inflammation, defining a targetable mechanism that precedes and promotes downstream adaptive responses.

immunology↗

bioRxiv2025

Coordinated IFN-γ/TNF Axis Drives Selective Loss of Activated Enteric Glia in Inflammatory Bowel Diseases

BackgroundEnteric glial cells (EGC) play a crucial role in maintaining gut homeostasis, but their dysregulation in inflammatory bowel diseases (IBD) remains poorly understood. Emerging preclinical data suggests activated EGC have beneficial roles in controlling gut pathophysiology. ObjectiveUnderstanding EGC activation and adaptation during experimental and clinical IBD. DesignWe provide the first highly integrated approach to identify EGC activation signature in IBD. Profiling 390 samples from IBD patients via bulk and single-nucleus (sn) transcriptomics and replicate the findings on publicly available bulk and single-cell (sc) datasets from 1160 patients and 19,000 single EGC. Preclinical modelling of Th1/Th17 inflammation, reporter-assisted EGC sorting, analysis of regulated cell death, and Casp8 ablation in EGC was performed ResultsWe identified novel IBD type and sampling associated EGC activation signature. Specific EGC activation markers were shared in biopsies and resection specimens, and were divergent between Crohns disease and Ulcerative colitis. Preclinical modelling of intestinal inflammation identified combinatorial TNF and IFN-{gamma}-driven activation of EGC, associated with elevated necroptosis, and negatively impacting gut motility. Genetic-reporter-enabled sorting and downstream analyses confirmed TNF and IFN-{gamma}-driven EGC necroptosis, potentiated by Casp8 deficiency. Furthermore, snRNA-Seq from IBD patient samples confirmed elevated cell death signature in activated but not in rare neuroglia progenitor-like cluster. ConclusionOur findings identify IBD type-associated activated EGC markers involved in immune and epithelial homeoastasis. We uncover necroptosis of activated EGCs as a constituent of intestinal inflammation. Advancing our understanding of activated EGC survival is pivotal in elucidating their complex roles in maintaining gut immune-epithelial homeostasis. What is already known on this topicActivated EGC have emerged as important contributors in maintaining epithelial, immune and neuronal homeostasis. Increasing evidence from mouse studies points to the role of activated EGC in epithelial regeneration, tolerogenic T-cell activation, relaying psychological stress to the enteric nervous system, post-injury neurogenesis, and helminth clearance. Nevertheless, no consensus has emerged on what might define activated EGC in the context of IBD and how EGC turnover is affected in gut inflammation, limiting translation of their disease associated roles. What this study addsBy combining bulk with single cell and single nucleus transcriptomes from IBD patients we identified new IBD type- and location-associated EGC activation signatures. Some of these are conserved with mouse EGC in gut inflammation models. We identified osteopontin an immunomodulator and Wnt6 an epithelial morphogen elevated in IBD EGC. We also identified IBD-associated EGC cell clusters, which display higher expression of cell death pathway transcripts. To investigate EGC turnover, we utilized preclinical models and found rapid EGC activation upon Th1/Th17 inflammation. This was associated with elevated EGC activation and caspase-independent necroptotic cell death. Ex vivo experiments showed a combinatorial requirement of IFN-{gamma} and TNF in mediating EGC necroptosis. Our findings were replicated on multiple publicly available sc-RNA sequencing datasets from IBD patients. How this study might affect research, practice or policyExpanding on the available repertoire of EGC activation markers in IBD, both shared and unique to sampling procedure, disease type, and location will provide researchers with tools to identify EGC homeostasis during IBD. Moreover, the nature of the identified markers will stimulate research into specific EGC pathways triggered in inflammation. Adding to this, the rapid induction in pathological death of activated but not naive EGC upon IFN-{gamma} and TNF stimulation will shed light on EGC adaptation and turnover. Our identification of markers of activated EGC with immuno-modulatory and epithelial-regenerative properties, including osteopontin and wingless family of morphogenes will stimulate further research in EGC-immune and EGC-epithelial communication in the context of IBD.

neuroscience↗

bioRxiv2024

Perinatal brain group 3 innate lymphoid cells are involved in the formation of murine dural lymphatics

The central nervous system (CNS) contains a pool of innate lymphoid cells (ILCs) of unclear composition and functionality and unknown origin. Here, we demonstrate that group 1 ILCs (inc. ex-ILC3s) and ILC2s are resident cells with low proliferative capacities and subtype specific CNS compartmentalization. We show for the first time that CNS ILC seeding and niche establishment occurs during early life and is initiated by both, ILC progenitors-like PLFZ+PD- 1+ cells and lineage committed ILCs. While group 1 ILCs and ROR{gamma}t+ ILC3s were found within the embryonic and postnatal brain, ILC2s reached the CNS after birth and were predominantly localized within the dura mater, proving early regional distribution. Interestingly, ROR{gamma}t+ ILC3s were only detected perinatally and vanished from the CNS as an outcome of decreased turnover and in situ ILC3-to-ILC1 conversion. Remarkably, we showed that perinatal ROR{gamma}t+ ILC3s are required for the correct development of the lymphatic vessels within the dura.

immunology↗

bioRxiv2024

Cross-species analyses reveal RORγt-expressing dendritic cells are a lineage of antigen presenting cells conserved across tissues

Conventional dendritic cells (cDCs) are potent antigen presenting cells (APCs) that exhibit tissue and age-specific diversity allowing them to direct situation-adapted immunity. Thereby they harbor great potential for being targeted in vaccination and cancer. Here, we resolve conflicting data about expression of retinoic acid receptor-related orphan receptor-{gamma}t (ROR{psi}t) in cDCs. We show that ROR{psi}t+ DCs exist in murine lymphoid and non-lymphoid tissues across age. Fate mapping, functional assays and single cell multiomic profiling reveal these cells as ontogenetically and transcriptionally distinct from other well characterized cDC subtypes, as well as from ROR{psi}t+ type 3 innate lymphocytes (ILC3s). We show that ROR{psi}t+ DCs can migrate to lymph nodes and activate naive CD4+ T cells in response to inflammatory triggers. Comparative and cross-species transcriptomics revealed homologous populations in human spleen, lymph nodes and intestines. Further, integrated meta-analyses aligned ROR{psi}t+ DCs identified here with other emerging populations of ROR{psi}t+APCs, including R-DC-like cells, Janus cells/extrathymic Aire expressing cells (eTACs) and subtypes of Thetis cells. While ROR{psi}t+APCs have primarily been linked to T cell tolerance, our work establishes ROR{psi}t+ DCs as unique lineage of immune sentinel cells conserved across tissues and species that expands the functional repertoire of ROR{psi}t+ APCs beyond promoting tolerance. One sentence summaryROR{gamma}t+ DC exhibit versatile APC functions and are a distinct immune lineage conserved across age, tissues and species that entails Thetis cells, Janus cells/ROR{gamma}t+ eTACs and R-DC-like cells.

immunology↗

bioRxiv2022

An unbiased characterization of the HLA-E and CD94/NKG2x peptide repertoire reveals peptide ligands that skew NK cell activation

HLA-E is a non-classical class I MHC protein involved in innate and adaptive immune recognition. While recent studies have shown HLA-E can present diverse peptides to NK cells and T cells, the HLA-E and NK receptor peptide repertoire has remained poorly defined, with only a limited number of peptide ligands identified. Here we screen a yeast-displayed peptide library in the context of HLA-E to identify 500 high-confidence unique peptides that bind both HLA-E and CD94/NKG2A or CD94/NKG2C. Utilizing the sequences identified via yeast display selections, we train prediction algorithms and identify human and cytomegalovirus (CMV) proteome-derived, HLA-E-presented peptides capable of binding and signaling through both CD94/NKG2A and CD94/NKG2C. In addition, we identify peptides which selectively activate NKG2C+ NK cells. Taken together, characterization of the HLA-E-binding peptide repertoire and identification of NK activity-modulating peptides present opportunities for studies of NK cell regulation in health and disease, in addition to vaccine and therapeutic design.

immunology↗

bioRxiv2020

Mobilization of tissue-resident memory CD4+ T lymphocytes and their contribution to a systemic secondary immune reaction

While it is generally accepted that tissue-resident memory T lymphocytes protect host tissues from secondary immune challenges, it is unclear whether, and if so, how they contribute to systemic secondary immune responses. Here we show that in human individuals with an established immune memory to measles, mumps and rubella viruses, when challenged with the measles-mumps-rubella (MMR) vaccine again, tissue-resident memory CD4+ T cells are mobilized into the blood within 16 to 48 hours after vaccination. These cells then leave the blood again, and apparently contribute to the systemic secondary immune reaction, as is evident from the representation of mobilized T cell receptor V{beta} clonotypes among newly generated circulating memory T lymphocytes, from day 7 onwards. Mobilization of the tissue-resident memory T cells is cognate, in that memory T lymphocytes recognizing other antigens, e.g. tetanus toxin, are not mobilized, unless they cross-react with the vaccine. These data originally demonstrate the essential contribution of tissue-resident memory T cells to secondary systemic immune responses, confirming that immunological memories to systemic pathogens are maintained (also) by tissue-resident memory T cells. In practical terms, the present work defines day 1 to 2 after antigenic challenge as a time window to assess the entire immunological T cell memory for a certain pathogen, including mobilized tissue-resident memory T cells, and its correlates of effectivity. Capsule summaryThe study demonstrates the rapid and cognate mobilization of tissue-resident memory CD4+ T cells into the blood upon antigenic rechallenge, and their contribution to secondary systemic immune responses.

immunology↗