Biology subjects

Pellegrini, S.

Publications and source records attributed to Pellegrini, S..

10 recordsLinked to original sources

bioRxiv2026

Mapping active cis-regulatory elements from transcription initiation events

Determining the activity of cis-regulatory elements (CREs) is essential for modeling gene regulation and interpreting genetic variation. Yet, current methods often lack the specificity to distinguish active regulation from permissive chromatin, the sensitivity to detect unstable enhancer RNAs, or the scalability required to profile limited input material and primary cells. Here, we introduce nucCAGE, a transcription start site (TSS) assay for profiling nuclear, capped RNAs, and PRIME, a computational framework for identifying active CREs from TSS data. Together, these methods increase sensitivity to low-abundance RNAs and enable robust detection of active regulatory elements across diverse contexts. Across multiple orthogonal functional and genetic benchmarks, including fine-mapped eQTLs, ClinVar variants, GWAS loci, and CRISPRi-tested elements, nucCAGE-derived PRIME predictions achieve superior recall compared to state-of-the-art methods while maintaining strong enrichment for phenotype-associated variation. Applying PRIME to the FANTOM5 dataset yields a comprehensive, cell-type-resolved atlas of active CREs that recapitulates known tissue-trait relationships. We demonstrate how this atlas can be used to nominate causal noncoding variants, linking immune-cell enhancer regulation of SMAD3 to asthma and NCOR2 to premature separation of placenta. Together, nucCAGE and PRIME provide a framework for high-sensitivity genome-wide discovery of active CREs and a resource for variant-to-function studies.

genomics↗

bioRxiv2026

Co-expression-based models improve eQTL predictions and highlightnovel transcriptome-wide genes associated with schizophrenia

Non-coding genetic variants statistically associated with complex heritability phenotypes are thought to act primarily through transcriptome regulatory mechanisms. Predictions of gene expression in tissue like the human brain traditionally rely primarily on cis-eQTLs. Here, we introduce INGENE and MODULE, trans-eQTLs models designed to enhance the prediction of gene expression by capturing the collective impact of candidate trans-eQTLs acting within co-expression networks. Exploiting RNA-seq data in six post-mortem brain regions (amygdala, caudate nucleus, dorsal/subgenual anterior cingulate cortex, dorsolateral prefrontal cortex, and hippocampus), we validate our models on two testing datasets, demonstrating increased gene predictability compared to both an original cis-based model and to EpiXcan, the leading benchmark in cis-model performance. Integration of cis- and trans-predictions significantly improves gene-level expression imputation (MLE = 0.05) for 18,744 genes across the six brain regions considered. Applying cis and trans models to PGC wave 3 genotypes identifies 766 SCZ-associated genes across brain regions (pFDR < .01), emphasizing the complementary nature of cis and trans predictions in trait association discovery. Of these genes, 641 represent novel transcriptome-wide associations with schizophrenia, highlighting the role of trans-heritability and genetic interactions underlying risk for this disorder, in addition to further supporting 125 previous candidates.

genomics↗

bioRxiv2025

Latent plasticity of the human pancreas across development, health, and disease.

The pancreas plays a central role in major human diseases, yet our understanding of its cellular diversity and plasticity remains incomplete. Here, we present a single-cell multiomics atlas of the human pancreas, profiling over four million cells and nuclei from 57 donors across fetal development, adult homeostasis, and type 2 diabetes (T2D). Integrating sc/snRNA-seq, snATAC-seq, VASA-seq, spatial transcriptomics (Xenium), and multiplexed proteomics (CODEX), we resolve gene expression, chromatin accessibility, and spatial organization at high resolution. We identify transcriptionally plastic centroacinar-like cells (pCACs) in adults with fetal-like features, delineate endocrine and exocrine lineage trajectories during development, and uncover HNF1A-defined beta cell epigenetic states. In T2D, we observe shifts in beta cell subtypes and altered regulatory programs. Glucose perturbation of healthy islets reveals cell-type-specific adaptation and stress responses. This atlas provides a foundational framework to understand pancreas biology and the role of cellular plasticity in regeneration and disease.

genomics↗

bioRxiv2025

Oncodrive3D: Fast and accurate detection of structural clusters of somatic mutations under positive selection

Identifying the genes capable of driving tumorigenesis in different tissues is one of the central goals of cancer genomics. Computational methods that exploit different signals of positive selection in the pattern of mutations observed in genes across tumors have been developed to this end. One such signal of positive selection is clustering of mutations in areas of the three-dimensional (3D) structure of the protein above the expectation under neutrality. Methods that exploit this signal have been hindered by the paucity in proteins with experimentally solved 3D structures covering their entire sequence. Here, we present Oncodrive3D, a computational method that by exploiting AlphaFold 2 structural models extends the identification of proteins with significant mutational 3D clusters to the entire human proteome. Oncodrive3D shows sensitivity and specificity on par with state-of-the-art cancer driver gene identification methods exploiting mutational clustering, and clearly outperforms them in computational efficiency. We demonstrate, through several examples, how significant mutational 3D clusters identified by Oncodrive3D in different known or potential cancer driver genes can reveal details about the mechanism of tumorigenesis in different cancer types and in clonal hematopoiesis.

bioinformatics↗

bioRxiv2024

Liraglutide treatment reverses unconventional cellular defects in induced pluripotent stem cell-derived β cells harboring a partially functional WFS1 variant

Aims/hypothesisWolfram Syndrome 1 (WS1) is a rare genetic disorder characterized by very heterogeneous clinical manifestations caused by variants of the WFS1 gene, which encodes for the Endoplasmic Reticulum (ER) protein Wolframin, involved in cellular stress response, Ca2+ handling and autophagy. Given the central role of Wolframin, elucidating the impact of WFS1 variants on cell functions is crucial to provide an association with clinical phenotypes. Therefore, as the understanding of patient-specific defects may also help to develop targeted therapeutic approaches, here we aimed at elucidating the impact on {beta} cell function of the c.316-1G>A mutation harboring the partially functional Wolframin that we have previously characterized, and the molecular changes following treatment with the glucagon-like peptide 1 receptor (GLP-1R) agonist liraglutide. MethodsWe previously generated patient-derived iPSCs (WFS1) and isogenic line in which the c.316-1G>A mutation was genetically corrected (WFS1wt/757A>T), thus performed molecular analysis, including single cell RNAseq (scRNAseq), and functional studies on iPSC-derived {beta} cell (iBeta). Calcium flux imaging and dynamic perifusion assays were used to test glucose responsiveness of iBeta. Treatment with liraglutide was performed to investigate effects on glucose-stimulated insulin secretion (GSIS), unfolded protein response (UPR), autophagy and apoptosis. ResultsWe found that both WFS1 and WFS1wt/757A>T iBeta efficiently differentiated in vitro into pancreatic lineage, but WFS1 showed less mature endocrine phenotype, reduced glucose responsiveness and impaired insulin secretion compared to WFS1wt/757A>T counterpart. The Ca2+ dynamics were altered in WFS1 iBeta as Ca2+ oscillations after glucose challenge were not synchronized mainly due to the CACNA1D and SNAP25 downmodulation. Reduced insulin secretion was correlated with a decrease in PC1/3 levels and overall increase of RGS4 expression in WFS1 iBeta, whereas secretory defects correlated with accelerated autophagic flux. While the functional residual Wolframin in WFS1 iBeta controlled short-term ER stress, prolonged insults or inflammation highlighted ineffective UPR that make the cells unable to escape apoptosis. Interestingly, treatment with liraglutide restored the Ca2+ fluxes and secretory impairments, increasing glucose responsiveness and insulin release of WFS1 iBeta, while protecting these cells from cellular stress and inflammation-induced apoptosis. Conclusion/interpretationOur data highlighted alterations of key cellular pathways involved in WS1 {beta} cell maturation and GSIS and how the pharmacological targeting of the GLP-1/GLP-1R axis was able to restore the physiologic phenotype. This study points out the need to understand the patient-specific molecular determinants associated with WFS1 variants, to design effective therapies to treat the disease.

cell biology↗

bioRxiv2024

Implications of noncoding regulatory functions in the development of insulinomas

Insulinomas are rare neuroendocrine tumours arising from the pancreatic {beta}-cells. While retaining the ability to produce insulin, insulinomas feature aberrant proliferation and altered hormone secretion resulting in failure to maintain glucose homeostasis. With the aim of uncovering the role of noncoding regulatory regions and their aberrations to the development of these tumors, we coupled epigenetic and gene expression profiling with whole-genome sequencing. As a result, we mapped H3K27ac sites in the tumoral tissue and unraveled overlapping somatic mutations associated with changes in regulatory functions. Critically, these regions impact insulin secretion, tumor development and epigenetic modifying genes, including key components of the polycomb complex. Chromatin remodeling is apparent as insulinoma-selective regions are mostly clustered in regulatory domains, shared across patients and containing a specific set of regulatory sequences dominated by the binding motif of the transcription factor SOX17. Moreover, a large fraction of these regions are H3K27me3-repressed in unaffected {beta}-cells, suggesting that tumoral transition is coupled with derepression of {beta}-cell polycomb-targeted domains. Our work provides a compendium of aberrant cis-regulatory elements and transcription factors that alter {beta}-cell function and fate in their progression to pancreatic neuroendocrine tumors and a framework to identify coding and noncoding driver mutations.

genomics↗

bioRxiv2023

Tick-borne flavivirus NS5 antagonizes interferon signaling by inhibiting the catalytic activity of TYK2

The mechanisms utilized by different flaviviruses to evade antiviral functions of interferons are varied and incompletely understood. Using virological approaches, biochemical assays and mass spectrometry analysis, we report here that the NS5 protein of tick-borne encephalitis virus (TBEV) and Louping Ill virus (LIV), two related tick-borne flaviviruses, antagonize JAK-STAT signaling through interactions with tyrosine kinase 2 (TYK2). Co-immunoprecipitation (co-IP) experiments, yeast gap-repair assays, computational protein-protein docking and functional studies identified a stretch of 10 residues of the RNA dependent RNA polymerase domain of tick-borne flavivirus NS5, but not mosquito-borne NS5, that is critical for interaction with the TYK2 kinase domain. Additional co-IP assays performed with several TYK2 orthologs revealed that the interaction was conserved across mammal species. In vitro kinase assays showed that TBEV and LIV NS5 reduced the catalytic activity of TYK2. Our results thus illustrate a novel mechanism by which viruses suppress the interferon response. TeaserInhibition of the catalytic activity of a key kinase of the JAK/STAT pathway by a viral protein

microbiology↗

bioRxiv2023

Brain structure reflects empathy and psychopathy in incarcerated males

BackgroundReduced empathy is a hallmark of individuals with high (i.e., clinical) levels of psychopathy, who are overrepresented among incarcerated men. Yet, a comprehensive, well-powered mapping of cortical structure in relation to empathy and psychopathy is still lacking. MethodsIn 804 incarcerated adult men, we administered the Perspective Taking (IRI-PT) and Empathic Concern (IRI-EC) subscales of the Interpersonal Reactivity Index, the Psychopathy Checklist-Revised (PCL-R; with Interpersonal/Affective [F1] and Lifestyle/Antisocial [F2] factors), and T1-weighted MRI to quantify cortical thickness (CT), surface area (SA), and structural-covariance gradients. ResultsPCL-R F1 was uniquely negatively related to IRI-EC, while PCL-R F2 was uniquely negatively related to IRI-PT. Cortical structure was not related to the IRI subscales. In contrast, CT was related to PCL-R F1 (mostly positively), SA was related to both PCL-R factors (only positively), and both cortical indices demonstrated out-of-sample predictive utility for PCL-R F1. Compared to low-psychopathy men, high-psychopathy men had uniquely lower IRI-EC scores and increased SA (but not CT); across the cortex, effect sizes were largest in the paralimbic class and somatomotor network, while meta-analytic task-based activations further highlighted spatial overlap with (social-)affective/sensory regions. Finally, the total sample revealed canonical anterior-posterior structural-covariance gradients. In high-psychopathy men, the gradient of CT (but not SA) was globally compressed. ConclusionsHigh-psychopathy men had reduced empathic concern, increased SA, and a compressed macroscale organization of CT, suggesting specific co-occurring alterations in empathy and cortical structure. Future work should build upon these novel insights in both the general and incarcerated populations to inform the treatment of psychopathy.

neuroscience↗

bioRxiv2020

Human USP18 is regulated by miRNAs via the 3'UTR, a sequence duplicated in lincRNA genes residing in chr22q11.21

Ubiquitin-specific peptidase 18 (USP18) acts as gatekeeper of type I interferon (IFN) responses by binding to the IFN receptor subunit IFNAR2 and preventing activation of the downstream JAK/STAT pathway. In any given cell type, the level of USP18 is a key determinant of the output of interferon-stimulated transcripts. How the baseline level of USP18 is finely tuned in different cell types remains ill defined. Here we explored post-transcriptional regulation of USP18 by microRNAs (miRNAs) and identified four miRNAs (miR-24-3p, miR-191-5p, miR-423-5p and miR-532-3p) that efficiently target USP18 through binding to the 3UTR. Among these, three miRNAs are particularly enriched in circulating monocytes which exhibit low baseline USP18. Intriguingly, the USP18 3UTR sequence is duplicated in human and chimpanzee genomes. In human, we found several copies of the 3UTR that are embedded in long intergenic non-coding (linc) RNA genes residing in chr22q11.21 and exhibiting a tissue-specific expression pattern. Interestingly, one of these lincRNAs (here named linc-UR-B1) is uniquely and highly expressed in testis. RNA-seq data analyses from testicular cell subsets revealed a positive correlation between linc-UR-B1 and USP18 expression in spermatocytes and spermatids. Overall, our findings uncover a set of miRNAs and lincRNAs, which may be part of a network evolved to fine-tune baseline USP18, particularly in cell types where IFN responsiveness needs to be tightly controlled. SIGNIFICANT STATEMENTUSP18 is a non-redundant negative feedback regulator of type I IFN signaling and a key determinant of cell responsiveness to IFN. How baseline USP18 is set in different human cell types is ill defined. We identified three microRNAs that restrain USP18 level notably in primary monocytes through binding the 3UTR. We found several copies of the USP18 3UTR embedded in long intergenic non-coding (linc) RNAs which reside in a complex region of human chromosome 22. These lincRNAs are expressed in a tissue-specific manner. We describe one lincRNA expressed only in testis, and most notably in germ cells. Correlative analyses suggest that microRNAs and lincRNAs may form a network controlling baseline USP18 and IFN responsiveness.

immunology↗

bioRxiv2019

Two common disease-associated TYK2 variants impact exon splicing and TYK2 dosage

TYK2 belongs to the JAK protein tyrosine kinase family and mediates signaling of numerous antiviral and immunoregulatory cytokines (type I and type III IFNs, IL-10, IL-12, IL-22, IL-23) in immune and non-immune cells. After many years of genetic association studies, TYK2 is recognized as a susceptibility gene for some inflammatory and autoimmune diseases (AID). Seven TYK2 variants have been associated with AIDs in Europeans, and establishing their causality remains challenging. Previous work showed that a protective variant (P1104A) is hypomorphic and also a risk allele for mycobacterial infection. Here, we have studied two AID-associated common TYK2 variants: rs12720270 located in intron 7 and rs2304256, a non-synonymous variant in exon 8 that causes a valine to phenylalanine substitution (c.1084 G > T, Val362Phe). We found that this amino acid substitution does not alter TYK2 expression, catalytic activity or ability to relay signaling in EBV-B cell lines or in reconstituted TYK2-null cells. Based on in silico predictions that these variants may impact splicing of exon 8, we: i) analyzed TYK2 transcripts in genotyped EBV-B cells and in CRISPR/Cas9-edited cells, ii) measured splicing using minigene assays, and iii) performed eQTL (expression quantitative trait locus) analysis of TYK2 transcripts in primary monocytes and whole blood cells. Our results reveal that the two variants promote the inclusion of exon 8, which, we demonstrate, is essential for TYK2 binding to cognate receptors. In addition and in line with GTEx (Genetic Tissue Expression) data, our eQTL results show that rs2304256 mildly enhances TYK2 expression in whole blood. In all, these findings suggest that these TYK2 variants are not neutral but instead have a potential impact in AID.

immunology↗