Biology subjects

Proietti, M.

Publications and source records attributed to Proietti, M..

7 recordsLinked to original sources

bioRxiv2026

Longitudinal Gut Microbiome Dynamics in Human CTLA-4 pathway Deficiencies: A One-Year Interventional Metagenomic Study

BackgroundCTLA-4 haploinsufficiency (CHAI) and LRBA deficiency cause severe immune dysregulation including enteropathy. Abatacept, a CTLA-4-immunoglobulin fusion protein, targets the underlying pathway defect, but its impact on the gut microbiome remains undefined. MethodsWe performed longitudinal shotgun metagenomics (MetaPhlAn4/HUMAnN3) on stool samples from patients enrolled in the ABACHAI clinical trial, collected at pre-treatment baseline and months 3, 6, and 12. Healthy individuals from the same household served as controls. Compositional and functional microbiome changes were analyzed using linear mixed-effects models and MaAsLin3, and correlated with organ-specific CHAI Morbidity Scores. ResultsAt baseline, patients showed significantly reduced alpha diversity (Shannon index, p=0.0029) and distinct community composition (PERMANOVA p=0.0001) compared to healthy controls, characterised by enrichment of oral-associated taxa (Veillonella, Streptococcus, Lacrimispora) and depletion of butyrate-producing commensals (Ruminococcus, Oscillibacter, Dysosmobacter). Functionally, the baseline metagenome exhibited broad reductions in amino acid and SCFA biosynthesis alongside enrichment of purine salvage and folate pathways. During treatment, beta diversity shifted significantly with treatment duration (Aitchison PERMANOVA R2=0.103, p=0.015), with within-patient community turnover peaking at month 6 ({Delta}=0.216, p=0.006). Longitudinal analyses demonstrated progressive decreases in disease-enriched taxa (Veillonella, Lacrimispora) and recovery of commensals (Collinsella, Adlercreutzia). FDR-significant reductions in microbial folate and purine biosynthesis pathways were observed over the treatment course. Gut CHAI domain severity correlated inversely with butyrate-producer abundance and positively with oral taxon enrichment. ConclusionIn CTLA-4 pathway insufficiency patients, abatacept therapy is associated with an improvement of enteropathy and a progressive, measurable gut microbiome restructuring, positioning microbiome dynamics as a candidate biomarker of treatment response in this monogenic immune dysregulation disorder.

immunology↗

bioRxiv2026

Periweaning diet-induced activation of an IFNγ-mediated regulatory circuit promotes the homeostasis of cytotoxic CD8+ T Cells

Balancing pathogen defence with maintaining tolerance to environmental antigens, such as food or commensals, in neonates is essential for survival and the establishment of life-long immune homeostasis. Instructed by environmental signals type 1 conventional dendritic cells (cDC1) drive either T cell tolerance or immunity. Here, we uncover an interferon (IFN)-{gamma}-driven regulatory circuit in early life that relays dietary cues to spleen cDC1. Loss-of-function demonstrates that IFN{gamma}-mediated STAT1-signaling induces an immunogenic maturation program in spleen cDC1 that instructs cDC1 to expand effector memory CD8 T cells. This program emerges during weaning, when IFN{gamma} production from lymphocytes rises, it occurs in germ-free mice and remains responsive to dietary intervention in adult mice. During the transition from breastfeeding to solid food at weaning, this circuit relays dietary information to spleen cDC1 to shape the effector phenotype of food-antigen specific CD8+ T cells in a feed-forward manner, allowing cDC1 to recalibrate the T cell pool at the moment of nutritional independence.

immunology↗

bioRxiv2023

ARPC5 deficiency leads to severe early onset systemic inflammation and early mortality

The seven subunit Arp2/3 complex drives the formation of branched actin networks that are essential for many cellular processes including cell migration. In humans, the ARPC5 subunit of the Arp2/3 complex is encoded by two paralogous genes (ARPC5 and ARPC5L), resulting in proteins with 67% identity. Through whole-exome sequencing, we identified a biallelic ARPC5 frameshift variant in a female child who presented with recurrent infections, multiple congenital anomalies, diarrhea, and thrombocytopenia, and suffered early demise from sepsis. Her consanguineous parents also had a previous child who died with similar clinical features. Using CRISPR/Cas9-mediated approaches, we demonstrate that loss of ARPC5 affects actin cytoskeleton organization and function, as well as chemokine-dependent cell migration in vitro. Homozygous Arpc5-/- mice do not survive past embryonic day 9 due to severe developmental defects, including loss of the second pharyngeal arch which contributes to craniofacial and heart development. Our results indicate that ARPC5 is important for both prenatal development and postnatal immune signaling, in a non-redundant manner with ARPC5L. Moreover, our observations add the ARPC5 locus to the list of genes that should be considered when patients present with syndromic early-onset immunodeficiency, particularly if recessive inheritance is suspected.

immunology↗

bioRxiv2022

Integrated Multi-omics Analyses of NFKB1 patients B cells points towards an up regula-tion of NF-κB network inhibitors

The transcription factor NF-{kappa}B plays a pivotal role in the adaptive immune response. Pathogenic variants in NFKB1 are the most common genetic etiology of common variable immunodeficiency (CVID). Patients frequently present with impaired terminal B cell differentiation, autoimmunity, and hyperinflammatory immune dysregulation. NF-{kappa}B signaling and target gene expression are expected to be dysregulated in NFKB1-mutated patients. Here, we performed a multi-omics characterization of B cells from a cohort of clinically affected and unaffected NFKB1 mutation carriers. Our analysis identified specific epigenetic dysregulation and gene expression differences on B cells from NFKB1-mutated patients. We observed an aberrant expression of negative regulators of NF-{kappa}B signaling in NFKB1 mutation carriers, which may be a key factor for the autoinflammatory phenotype of these patients. Moreover, our analysis points towards a dysregulation of XBP1 and BCL3, key players of B cell activation and proliferation at different stages of B cell differentiation. The reduced expression of negative regulators of the NF-{kappa}B network is likely to be one of several mechanisms responsible for the aberrant NF-{kappa}B signaling, which impairs the maintenance of a normal humoral immune response. In summary, our findings highlight epigenetic and gene expression changes in B cells associated with NFKB1 mutations. Our data give insight into future therapeutic opportunities for patients with NFKB1 (haplo)insufficiency.

immunology↗

bioRxiv2022

RIG-I activation primes and trains innate antiviral immune memory

Adaptive processes of the innate immune system, known as trained immunity (TI), are critical to human health and disease, yet they have not been systematically investigated downstream of antiviral sensing. Here, we elucidate the potential of the antiviral cytosolic RNA receptor retinoic acid-inducible gene I (RIG-I) to train, prime and tolerize the innate immune system. Using a specific RIG-I agonist, we observed that repetitive stimulation enhanced interferon-stimulated gene (ISG) and pro-inflammatory cytokine induction in human primary monocytes, epithelial cells and fibroblasts and afforded non-specific antiviral protection. RNA sequencing revealed broad, cell type-specific transcriptional changes, indicative of priming of ISGs and training of the NF{kappa}B pathway, without measurable tolerization, while ATAC sequencing in monocytes demonstrated chromatin remodeling and enhanced accessibility of key transcription factor-binding motifs such as STAT1. Moreover, while STAT1 signaling was critically required, it was not sufficient to recapitulate RIG-I induced TI. Altogether, our data demonstrate that RIG-I-mediated TI promotes an immunologically alert state with important implications for host defense and the application of RIG-I ligands in anti-infective and anti-tumoral therapies. One Sentence SummaryRIG-I activation trains and primes innate immune response at the cellular level, affording non-specific immune protection by immune and non-immune cells.

immunology↗

bioRxiv2022

LRBA balances antigen presentation and T-cell responses by facilitating autophagy through the binding to PIK3R4 and FYCO1

Reduced autophagy is associated with the aberrant humoral response observed in lipopolysaccharide-responsive beige-like anchor protein (LRBA) deficiency; however, the exact molecular mechanism and its impact on T-cell responses remain unknown. We identified two novel LRBA interactors, phosphoinositide 3-kinase regulatory subunit 4 (PIK3R4) and FYVE And Coiled-Coil Domain Autophagy Adaptor 1 (FYCO1). Both proteins play essential roles in different stages of autophagy. PIK3R4 facilitates the production of phosphatidylinositol-3 phosphate (PI(3)P) required for autophagosome formation and autophagosome-lysosome fusion, whereas FYCO1 allows autophagosome movement. LRBA-KO cells showed an impaired PI(3)P production, a delayed autophagosome-lysosome fusion, an accumulation of enlarged autophagosomes, and an atypical lysosomal positioning. These abnormalities led to decreased cargo material degradation and prolonged antigen presentation to T-cells via autophagy, resulting in increased production of proinflammatory cytokines, as autophagy is a major intracellular degradation system for major histocompatibility class II complex (MHCII) loading. Aberrant autophagosome formation, cargo degradation and antigen presentation were rescued by ectopic expression of WT-LRBA. In summary, we identified a novel function of LRBA that is crucial for T-cell-driven response through the interaction with two proteins of the autophagy machinery. These observations may contribute to the exacerbated T-cell dysregulation observed in LRBA-deficient patients.

immunology↗

bioRxiv2020

ADA2 is a lysosomal DNase regulating the type-I interferon response

Deficiency of adenosine deaminase 2 (DADA2) is a severe, congenital syndrome, which manifests with hematologic, immunologic and inflammatory pathologies. DADA2 is caused by biallelic mutations in ADA2, but the function of ADA2, and the mechanistic link between ADA2 deficiency and the severe inflammatory phenotype remains unclear. Here, we show that monocyte-derived proteomes from DADA2 patients are highly enriched in interferon response proteins. Using immunohistochemistry and detailed glycan analysis we demonstrate that ADA2 is post-translationally modified for sorting to the lysosomes. At acidic, lysosomal pH, ADA2 acts as a novel DNase that degrades cGAS/Sting-activating ligands. Furthermore, we define a clear structure-function relationship for this acidic DNase activity. Deletion of ADA2 increased the production of cGAMP and type I interferons upon exposure to dsDNA, which was reverted by ADA2 overexpression or deletion of STING. Our results identify a new level of control in the nucleic acid sensing machinery and provide a mechanistic explanation for the pathophysiology of autoinflammation in DADA2. One Sentence SummaryADA2 is a lysosomal nuclease controlling nucleic acid sensing and type I interferon production.

immunology↗