Biology subjects

Angelini, C.

Publications and source records attributed to Angelini, C..

15 recordsLinked to original sources

bioRxiv2026

Regulatory mutants of the Tbx1 gene alter transcription programs of lineage determination and patterning in early mesoderm.

The Tbx1 gene is haploinsufficient in mice and in humans, where it causes a DiGeorge syndrome phenotype characterized by developmental deficits of the pharyngeal apparatus. TBX1 plays a critical role in the differentiation and regionalization of the cardiopharyngeal mesoderm lineage and its derivatives. Nevertheless, its regulation is incompletely understood. Here we used a combination of computational and wet-lab approaches to identify regulatory sequences of the Tbx1 gene, and we use single-cell molecular analysis as a read-out and to establish the consequences of their deletion. Results revealed a cluster of regulatory sequences with at least three distinct elements. Elimination of the entire cluster caused a near shut down of the gene, while individual deletions had milder, quantitative effects. Transcriptomic analyses of the deletion mutants revealed the down regulation of genes related to cardiopharyngeal lineage specification and, more surprisingly, up regulation and anteriorization of genes related to embryonic patterning, thereby providing a rationale for the severe dysmorphogenesis of the posterior pharyngeal apparatus observed in Tbx1 mutant mice.

developmental biology↗

bioRxiv2025

Identification of genetic and non-genetic modifiers of genomic imprinting through whole genome screening in humans

Genomic imprinting is required for normal development, and abnormal methylation of differentially methylated regions (iDMRs) controlling the parent of origin-dependent expression of the imprinted genes has been found in constitutional disorders affecting growth, metabolism, neurobehavior, and in cancer. In most of these cases the cause of the imprinting abnormalities is unknown. Also, these studies have generally been performed on a limited number of CpGs, and a systematic investigation of iDMR methylation in the general population is lacking. By analysing the iDMRs in a large number of peripheral blood DNA methylation array datasets of unaffected individuals and patients with rare disorders, we determined the most common iDMR methylation profiles and identified many genetic and non-genetic factors contributing to their variability. We found that methylation variability is not homogeneous within the iDMRs and that the CpGs closer to the ZFP57 binding sites are less susceptible to methylation changes. We demonstrated the methylation polymorphism of three iDMRs and the atypical behaviour of several others, and reported the association of 25 disease- and 47 non-disease-complex traits, including blood cell type composition, as well as 15 mendelian or chromosomal disorders, with iDMR methylation changes in blood DNA. These findings identify several genetic and non-genetic factors associated with genomic imprinting maintenance in humans, which may have a role in the aetiology of the diseases associated with imprinting abnormalities and have clear implications in molecular diagnostics.

genetics↗

bioRxiv2024

Tbx1 stabilizes differentiation of the cardiopharyngeal mesoderm and drives morphogenesis in the pharyngeal apparatus

BackgroundTBX1 is required for the development of the pharyngeal apparatus. In the mouse, fish, and ascidian, Tbx1 is a marker of cardiopharyngeal mesoderm (CPM), a cell population that provides progenitors to the heart and branchiomeric muscles. However, in mammals: a) the molecular cascade that drives the diversification of this multipotent cell population, and b) the role of Tbx1 therein, are not well defined. Material and methodsWe used in vitro differentiation of WT and Tbx1-/- mouse embryonic stem cells into precardiac mesoderm, and performed single cell RNA-seq and ATAC-seq at two differentiation stages. We then used WT and Tbx1-/- mouse embryos for in vivo validation of the key findings. Results and conclusionsWe found that the response to loss of TBX1 is cell sub-population-specific, both in terms of gene expression and chromatin remodeling. We show that Tbx1 regulates chromatin accessibility and gene expression of an ancient transcriptional module that orchestrates the development of the trunk, pharynx and heart across evolution. This module is co-regulated and includes genes encoding the conserved transcription factor families of Tea Shirt (Tshz), Sine Oculis (Six), Eye absent (Eya), and Ebf/Collier. Analysis of putative regulatory regions of these genes, which were selected using a machine-learning computational procedure, predicted a feed-forward regulatory relationship between TBX1 and SIX factors that drives or stabilizes the module. Most surprisingly, we found a drift in the differentiation trajectory of the Tbx1 mutant CPM that led to a relative expansion of cells with epithelial-like transcriptional features in the cell culture model and in mouse embryos. We conclude that TBX1 is a critical factor for maintaining the transcriptional profile of the CPM.

developmental biology↗

bioRxiv2024

Differential Anti-Inflammatory Effects of Electrostimulation in a Standardized Setting

The therapeutic usage of physical stimuli is framed in a highly heterogeneous research area, with variable levels of maturity and of translatability into clinical application. In particular, electrostimulation is deeply studied for its application on the autonomous nervous system, but less is known about the anti-inflammatory effects of such stimuli beyond the inflammatory reflex. Further, reproducibility and meta-analyses on existing results are extremely challenging, owing to the limited rationale on dosage and experimental standardization. In this work we propose a series of controlled experiments on the effects of electrical stimuli (in direct and alternate current) delivered on a standardized 3D bioconstruct constituted by fibroblasts and keratinocytes in a collagen matrix. Transcriptomics backed by metabolomics at selected time points allow to obtain a first systematic overview of the biological functions at stake, highlighting the differential anti-inflammatory potential of such approaches, with promising results for 5V direct current stimuli. We hope that our results will trigger an interest and a facilitation in the study of the anti-inflammatory effects of physical stimuli, highlighting not only the potential but also the limitations of such approaches, offering, ultimately, solid evidence for future translation into the clinic.

systems biology↗

bioRxiv2024

Cardiac Outflow tract septation defects in a DiGeorge syndrome model respond to Minoxidil treatment.

BackgroundThe T-BOX transcription factor TBX1 is essential for the development of the pharyngeal apparatus and it is haploinsufficient in DiGeorge syndrome (DGS), a developmental anomaly associated with congenital heart disease and other abnormalities. The murine model recapitulates the heart phenotype and showed collagen accumulation. MethodsWe first used a cellular model to study gene expression during cardiogenic differentiation of WT and Tbx1-/- mouse embryonic stem cells. Then we used a mouse model of DGS to test whether interfering with collagen accumulation using an inhibitor of lysyl hydroxylase would modify the cardiac phenotype of the mutant. Results and conclusionsIn the cell differentiation model, loss of Tbx1 was associated with up regulation of a subset of ECM-related genes, including several collagen genes. In the in vivo model, early prenatal treatment with Minoxidil, a lysyl hydroxylase inhibitor, ameliorated the cardiac outflow tract septation phenotype in Tbx1 mutant fetuses, but it had no effect on septation in WT fetuses. We conclude that TBX1 suppresses a subset of ECM-related genes. The partial rescue of the septation phenotype through Minoxidil treatment suggests that inhibiting collagen cross-linking reduces the impact of the phenotypic consequences of Tbx1 mutation.

developmental biology↗

bioRxiv2024

Tbx1 haploinsufficiency causes brain metabolic and behavioral anomalies in adult mice which are corrected by vitamin B12 treatment

IntroductionThe brain-related phenotypes observed in 22q11.2 deletion syndrome (22q11.2DS) are highly variable and their origin is poorly understood. Changes in brain metabolism may cause or contribute to the phenotypes, given that many of the deleted genes (approx. 10%) are implicated in metabolic processes, but this is currently unknown. It is clearly important to address this knowledge gap, but in humans, the primary material required for studying brain metabolism is inaccessible. For this reason, we sought to address the issue using two mouse models of 22q11.2DS. MethodsWe used three independent approaches to investigate brain metabolism in young adult mice, namely, mass spectrometry, nuclear magnetic resonance spectroscopy and transcriptomics. We selected to study primarily Tbx1 single gene mutants because it is the primary candidate disease gene. We then confirmed key findings in the multi-gene deletion mutant Df1/+. ResultsWe found that Tbx1 mutants have alterations of specific brain metabolites, including methylmalonic acid, which is highly brain-toxic, as well as a more general metabolomic imbalance. We provide transcriptomic evidence of an interaction genotype-vB12 treatment, and behavioural evidence of a response to vB12 treatment, which rescued some of the behavioural anomaly observed in Tbx1 mutants. We conclude that Tbx1 haploinsufficiency causes extensive brain metabolic anomalies, which are partially responsive to vB12 treatment. We suggest that alterations of glutamine-glutamate metabolism and fatty acid metabolism are key components of the metabolic phenotype in these mutants.

genetics↗

bioRxiv2023

ENDOTHELIAL GENE REGULATORY ELEMENTS ASSOCIATED WITH CARDIOPHARYNGEAL LINEAGE DIFFERENTIATION

Endothelial cells (EC) differentiate from multiple sources, including the cardiopharyngeal mesoderm, which gives rise also to cardiac and branchiomeric muscles. Here, we used a cardiogenic mesoderm cell differentiation model that also activates an endothelial transcription program to identify endothelial regulatory elements activated in early cardiogenic mesoderm. Integrating our chromatin remodeling and gene expression data with available single-cell RNA-seq data from mouse embryos, we identified 101 putative regulatory elements of EC genes. We then applied a machine-learning strategy, trained on validated enhancers, to predict the probability of the sequences to function as enhancers. The computational assay determined that 50% of these sequences were likely enhancers, some of which have been previously reported. We also identified a smaller set of regulatory elements of well-known EC genes and validated them using genetic and epigenetic perturbation. Finally, we used the integration of multiple data sources and computational tools to search for transcriptional factor binding motifs. In conclusion, we identified novel EC regulatory sequences with a high likelihood to be enhancers, and we validated a subset of them using computational and cell culture models. Motif analyses revealed that the core EC transcription factors GATA/ETS/FOS is a likely driver of EC differentiation in cardiopharyngeal mesoderm.

molecular biology↗

bioRxiv2022

The rescue of epigenomic abnormalities in ICF1 patient iPSCs following DNMT3B correction is incomplete at a residual fraction of H3K4me3-enriched regions

BackgroundBi-allelic hypomorphic mutations in DNMT3B disrupt DNA methyltransferase activity and lead to Immunodeficiency, Centromeric instability, Facial anomalies syndrome, type 1 (ICF1). While several ICF1 phenotypes have been linked to abnormally hypomethylated repetitive regions, the unique genomic regions responsible for the remaining disease phenotypes remain largely uncharacterized. Here we explored two ICF1 patient-induced pluripotent stem cells (iPSCs) and their CRISPR/Cas9 corrected clones to determine whether gene correction can overcome DNA methylation defects and related/associated changes in the epigenome of non-repetitive regions. ResultsHypomethylated regions throughout the genome are highly comparable between ICF1 iPSCs carrying different DNMT3B variants, and significantly overlap with those in ICF1-peripheral blood and lymphoblastoid cell lines. These regions include large CpG island domains, as well as promoters and enhancers of several lineage-specific genes, in particular immune-related, suggesting that they are pre- marked during early development. The gene corrected ICF1 iPSCs reveal that the majority of phenotype- related hypomethylated regions re-acquire normal DNA methylation levels following editing. However, at the most severely hypomethylated regions in ICF1 iPSCs, which also display the highest increased H3K4me3 levels and enrichment of CTCF-binding motifs, the epigenetic memory persisted, and hypomethylation was uncorrected. ConclusionsRestoring the catalytic activity of DNMT3B rescues the majority of the aberrant ICF1 epigenome. However, a small fraction of the genome is resilient to this reversal, highlighting the challenge of reverting disease states that are due to genome-wide epigenetic perturbations. Uncovering the basis for the persistent epigenetic memory will promote the development of strategies to overcome this obstacle.

genomics↗

bioRxiv2021

A phenotypic rescue approach identifies lineage regionalization defects in a mouse model of DiGeorge syndrome.

TBX1 is a key regulator of pharyngeal apparatus (PhAp) development. Vitamin B12 treatment partially rescues aortic arch patterning defects of Tbx1+/- embryos. Here we show that it also improves cardiac outflow tract septation and branchiomeric muscle anomalies of Tbx1 hypomorphic mutants. At molecular level, the in vivo vB12 treatment let us to identify genes that were dysregulated by Tbx1 haploinsufficiency and rescued by treatment. We found that SLUG, encoded by the rescued gene Snai2, identified a population of mesodermal cells that was partially overlapping with but distinct from ISL1+ and TBX1+ populations. In addition, SLUG+ cells were mislocalized and had a greater tendency to aggregate in Tbx1+/- and Tbx1-/- embryos and vB12 treatment restore cellular distribution. Adjacent neural crest-derived mesenchymal cells, which do not express TBX1, were also affected, showing enhanced segregation from cardiopharyngeal mesodermal cells. We propose that TBX1 regulates cell distribution in core mesoderm and the arrangement of multiple lineages within the PhAp.

developmental biology↗

bioRxiv2021

Wrack enhancement of post-hurricane vegetation and geomorphological recovery in a coastal dune

Coastal ecosystems such as sand dunes, mangrove forests, and salt marshes provide natural storm protection for vulnerable shorelines. At the same time, storms erode and redistribute biological materials among coastal systems via wrack. Yet how such cross-ecosystem subsidies affect post-storm recovery is not well understood. Here, we report an experimental investigation into the effect of storm wrack on eco-geomorphological recovery of a coastal embryo dune in north-eastern Florida, USA, following hurricane Irma. We contrasted replicated 100-m2 wrack-removal and unmanipulated (control) plots, measuring vegetation and geomorphological responses over 21 months. Relative to controls, grass cover was reduced 4-fold where diverse storm wrack, including seagrass rhizomes, seaweed, and wood, was removed. Wrack removal was also associated with a reduction in mean elevation, which persisted until the end of the experiment when removal plots had a 14% lower mean elevation compared to control plots. These results suggest that subsides of wrack re-distributed from other ecosystem types (e.g. seagrasses, macroalgae, uplands): i) enhances the growth of certain dune-building grasses; and ii) boosts the geomorphological recovery of coastal dunes. Our study also indicates that the practice of post-storm beach cleaning to remove wrack - a practice widespread outside of protected areas - may undermine the resilience of coastal dunes and their services.

ecology↗

bioRxiv2020

Single cell multi-omic analysis identifies a Tbx1-dependent multilineage primed population in the murine cardiopharyngeal mesoderm

The poles of the heart and branchiomeric muscles of the face and neck are formed from the cardiopharyngeal mesoderm (CPM) within the pharyngeal apparatus. The formation of the cardiac outflow tract and branchiomeric muscles are disrupted in patients with 22q11.2 deletion syndrome (22q11.2DS), due to haploinsufficiency of TBX1, encoding a T-box transcription factor. Here, using single cell RNA-sequencing, we identified a multilineage primed population (MLP) within the CPM, marked by the Tbx1 lineage, which has bipotent properties to form cardiac and skeletal muscle cells. The MLPs are localized within the nascent mesoderm of the caudal lateral pharyngeal apparatus and provide a continuous source of progenitors that undergo TBX1-dependent progression towards maturation. Tbx1 also regulates the balance between MLP maintenance and maturation while restricting ectopic non-mesodermal gene expression. We further show that TBX1 confers this balance by direct regulation of MLP enriched genes and downstream pathways, partly through altering chromatin accessibility. Our study thus uncovers a new cell population and reveals novel mechanisms by which Tbx1 directs the development of the pharyngeal apparatus, which is profoundly altered in 22q11.2DS.

developmental biology↗

bioRxiv2020

De novo coding variants in the AGO1 gene cause a neurodevelopmental disorder with intellectual disability

High-impact pathogenic variants in more than 1,000 protein-coding genes cause Mendelian forms of neurodevelopmental disorders (NDD), including the newly reported AGO2 gene. This study describes the molecular and clinical characterization of 28 probands with NDD harboring heterozygous AGO1 coding variants. De novo status was always confirmed when parents were available (26/28). A total of 15 unique variants leading to amino acid changes or deletions were identified: 12 missense variants, two in-frame deletions of one codon, and one canonical splice variant leading to a deletion of two amino acid residues. Some variants were recurrently identified in several unrelated individuals: p.(Phe180del), p.(Leu190Pro), p.(Leu190Arg), p.(Gly199Ser), p.(Val254Ile) and p.(Glu376del). AGO1 encodes the Argonaute 1 protein, which functions in gene-silencing pathways mediated by small non-coding RNAs. Three-dimensional protein structure predictions suggest that these variants might alter the flexibility of the AGO1 linkers domains, which likely would impair its function in mRNA processing. Affected individuals present with intellectual disability of varying severity, as well as speech and motor delay, autistic behavior and additional behavioral manifestations. Our study establishes that de novo coding variants in AGO1 are involved in a novel monogenic form of NDD, highly similar to AGO2 phenotype.

genetics↗

bioRxiv2020

Easyreporting simplifies the implementation of Reproducible Research Layers in R software

During last years "irreproducibility" became a general problem in omics data analysis due to the use of sophisticated and poorly described computational procedures. For avoiding misleading results, it is necessary to inspect and reproduce the entire data analysis as a unified product. Reproducible Research (RR) provides general guidelines for public access to the analytic data and related analysis code combined with natural language documentation, allowing third-parties to reproduce the findings. We developed easyreporting, a novel R/Bioconductor package, to facilitate the implementation of an RR layer inside reports/tools without requiring any knowledge of the R Markdown language. We describe the main functionalities and illustrate how to create an analysis report using a typical case study concerning the analysis of RNA-seq data. Then, we also show how to trace R functions automatically. Thanks to this latter feature, easyreporting results beneficial for developers to implement procedures that automatically keep track of the analysis steps within Graphical User Interfaces (GUIs). Easyreporting can be useful in supporting the reproducibility of any data analysis project and the implementation of GUIs. It turns out to be very helpful in bioinformatics, where the complexity of the analyses makes it extremely difficult to trace all the steps and parameters used in the study.

bioinformatics↗

bioRxiv2020

Chromatin and transcriptional response to loss of TBX1 in differentiating mouse P19Cl6 and embryonic stem cells.

The T-box transcription factor TBX1 has critical roles in the cardiopharyngeal lineage and the gene is haploinsufficient in DiGeorge syndrome, a typical developmental anomaly of the pharyngeal apparatus. Despite almost two decades of research, if and how TBX1 function triggers chromatin remodeling is not known. Here, we explored genome-wide gene expression and chromatin remodeling in two independent cellular models of Tbx1 loss of function, mouse embryonic carcinoma cells P19Cl6, and mouse embryonic stem cells (mESCs). The results of our study revealed that the loss or knockdown of TBX1 caused extensive transcriptional changes, some of which were cell type-specific, some were in common between the two models. However, unexpectedly we observed only limited chromatin changes in both systems. In P19Cl6 cells, differentially accessible regions (DARs) were not enriched in T-BOX binding motifs; in contrast, in mESCs, 34% (n=47) of all DARs included a T-BOX binding motif and almost all of them gained accessibility in Tbx1-/- cells. In conclusion, despite a clear transcriptional response of our cell models to loss of TBX1 in early cell differentiation, chromatin changes were relatively modest.

genomics↗

bioRxiv2019

Slow life-history strategies are associated with negligible actuarial senescence in western Palearctic salamanders

Actuarial senescence (hereafter \"senescence\") has been viewed for a long time as an inevitable and uniform process. However, the work on senescence has mainly focused on endotherms (especially mammals) with deterministic growth and low regeneration capacity at adult stages, leading to a strong taxonomic bias in the study of aging. Recent studies have highlighted that senescence could indeed display highly variable trajectory shape that correlates with species life history traits. Slow life histories and indeterminate growth seem to be associated with weak and late senescence. Furthermore, a few studies have suggested that high regenerative abilities could make senescence negligible in several ectotherms (e.g., hydra and salamanders). However, demographic data for species that would allow testing of these hypotheses are scarce and fragmented. Here, we investigated senescence patterns in a group of salamanders (i.e. \"true salamanders\") from the Western Palearctic using capture-recapture data and Bayesian modeling. Our results showed that salamanders have slow life histories and that they experience negligible senescence. This pattern was consistent at both intra- and interspecific levels, suggesting that the absence of senescence may be a phylogenetically conserved trait. The regenerative capacities of true salamanders, and urodeles in general, likely explains why these small ectotherms have lifespans similar to that of large endotherms (e.g., ungulates, large birds) and undergo negligible senescence contrary to most amniotes including humans. Our study seriously challenges the idea that senescence is a ubiquitous phenomenon in the living world.

ecology↗