Biology subjects

Caporale, N.

Publications and source records attributed to Caporale, N..

10 recordsLinked to original sources

bioRxiv2025

A molecular cell atlas of endocrine signalling in human neural organoids

Hormonal signalling shapes the development of the human brain and its disruption is implicated in various neuropsychiatric conditions. However, a comprehensive and mechanistic understanding of how hormonal pathways orchestrate human neurodevelopment remains elusive. Here we present a multi-scale high resolution atlas of endocrine signalling in human neural organoids through systematic perturbations with agonists and inhibitors of seven key hormonal pathways: androgen (AND), estrogen (EST), glucocorticoid (GC), thyroid (THY), retinoic acid (RA), liver X (LX), and aryl hydrocarbon (AH). By integrating bulk and single-cell transcriptomics, high-throughput imaging and targeted steroidomics, we mapped the molecular and cellular consequences of their physiologically relevant perturbations. Retinoic acid exerted the most profound effect, promoting neuronal differentiation and maturation, consistent with its established role as a patterning factor. Our analysis further benchmarked neural organoids for in vitro endocrinology and neurotoxicology by confirming previously reported in vivo effects, such as induction of mTOR signalling by AND, alteration of disease relevant genes by GC and enhanced differentiation by TH. Furthermore, we observed that LX activation upregulates genes involved in cholesterol metabolism while AH inhibition promotes neuronal differentiation. We next uncovered extensive crosstalks between these endocrine pathways, as in the paradigmatic convergence induced by AND agonist and inhibitors of GC, TH, and LX, affecting genes related to protein folding and metabolic regulation, as also highlighted by weighted gene co-expression network analysis. Single-cell analyses pinpointed cell-type-specific responses to hormonal challenges, such as the caudalization of progenitors and neurons upon RA activation and the depletion of specific neurodevelopmental states upon AH activation. Finally, we dissected the cytoarchitectural and morphometric impact of hormonal perturbations and demonstrated that neural organoids possess active steroidogenic pathways that are functionally modulated by the tested compounds. This atlas provides a systematic quantification of the hormonal impact on human neurodevelopment, enabling the investigation of uncharted aspects in the developmental origins of neuropsychiatric traits. Through the empowering architecture of its knowledge base for iterative adoption by the community, this resource will thus be key to probe how environmental factors and genetic endocrine vulnerabilities contribute to neurodevelopmental outcomes, as well as to train advanced generative models for improving their predictive power on gene environment interactions in human neurodevelopment.

molecular biology↗

bioRxiv2025

A mixture of endocrine disrupting chemicals linked to lower birth weight induces adipogenesis and transcriptional changes related to birth weight alterations and diabetes

There is increasing evidence that endocrine disrupting chemicals (EDCs) are contributing to the rise in metabolic disorders and obesity. Humans are constantly exposed to numerous EDCs, thus human exposure entails complex EDC mixtures. In this study, we examined the effects of an EDC mixture, mixture G, composed of four phthalate esters, triclosan, and three poly- och perfluorinated alkyl substances. Mixture G had previously been defined based on its association with lower birth weight in a pregnancy cohort, where low birth weight is an early risk factor for metabolic morbidities later in life. Here, we studied its effects on adipogenesis and uncovered their underlying transcriptional changes. Human mesenchymal stem cells (hMSCs) were exposed to mixture G in concentrations and mixing ratios that reflect those measured in human serum. Mixture G induced adipogenesis in hMSCs, as evidenced by a dose-dependent increase in lipid droplet accumulation after 14-21 days. Notably, significant adipogenic effects were observed at concentrations comparable to those detected in humans. RNA-sequencing upon exposure for 48 h revealed dose-dependent transcriptional changes in over 1000 genes. Mixture G-induced differentially expressed genes (DEGs) showed significant overlap with genes involved in osteogenesis, with glucocorticoid-regulated genes, and with genes associated with birth weight alterations and diabetes type II. These results indicate that exposure to an environmentally relevant EDC mixture induces adipogenesis and leads to transcriptional alterations that might change the balance between adipogenic and osteogenic differentiation as well as the functionality of MSCs, possibly via interference with glucocorticoid signalling. Thus our findings underscore the role of EDCs as metabolic disruptors and shed light on the molecular mechanisms underlying their potential contribution to the development of metabolic disorders. HighlightsO_LIAn endocrine disruptor mixture linked to lower birth weight increases adipogenesis C_LIO_LIThe mixture induced transcriptomic changes at low doses C_LIO_LIAffected genes are associated with birth weight and diabetes type II C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/638050v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@12428bforg.highwire.dtl.DTLVardef@ef28b3org.highwire.dtl.DTLVardef@159024corg.highwire.dtl.DTLVardef@a605b7_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2025

High resolution multi-scale profiling of embryonic germ cell-like cells derivation reveals pluripotent state transitions in humans

Primordial germ cells (PGCs) are the embryonic precursors of the gametes. In mice and rats, PGCs can readily acquire pluripotency in vitro by forming embryonic germ cells (EGCs). To date, a comparable in vitro system has not been established in humans, despite the fact that human PGCs (hPGCs) readily undergo pluripotent conversion in the context of germ cell tumorigenesis. Here we report that hPGC-like cells (hPGCLCs) undergo conversion to human embryonic germ-like cells (hEGCLCs) upon exposure to the same inductive signals previously used to derive mouse EGCs. This defined, feeder-free culture system allows efficient derivation of human EGCLCs which can be expanded and maintained in standard human pluripotent stem cell medium. hEGCLCs are transcriptionally similar to human pluripotent stem cells (hPSCs) and can differentiate into all three germ layers, as well as giving rise to PGCLCs once more - demonstrating the interconvertibility of pluripotent states. This is also evident at the epigenetic level, as the initial DNA demethylation that occurs in hPGCLCs is largely reversed in hEGCLCs, restoring DNA methylation to the level observed in hPSCs. This new in vitro model captures the transition from the pluripotent stem cell state to a germ cell identity and back again, and therefore represents a highly tractable system to study pluripotent and epigenetic transitions, including those which occur during human germ cell tumorigenesis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/632914v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@14572bcorg.highwire.dtl.DTLVardef@6fa7c1org.highwire.dtl.DTLVardef@6eaa99org.highwire.dtl.DTLVardef@1822307_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefWe report the first fully defined system to efficiently convert hPGCLCs to a pluripotent stem cell (PSC) state. We tracked pluripotent state transitions by multi-omic analysis and provided a high-resolution map of the transcriptional and epigenomic transitions upon entry to and exit from the human germline. HighlightsO_LIEfficient derivation of hEGCLC in fully defined feeder-free conditions C_LIO_LISingle-cell transcriptomic profiling of transitions from the hPSC state to hPGCLCs and back. C_LIO_LILongitudinal DNA methylation profiling highlights the overall reversibility of epigenetic states C_LIO_LIMulti-omic gene regulatory network analysis identifies key regulators of pluripotent transitions C_LI

developmental biology↗

bioRxiv2023

Multiplexing cortical brain organoids for the longitudinal dissection of developmental traits at single cell resolution

The combination of brain organoid and single cell omic technologies holds transformative potential to dissect human neurobiology at high resolution and with mechanistic precision. Delivering this promise in the context of human neurodiversity, physiological and pathological alike, requires however a major leap in scalability, given the need for experimental designs that include multiple individuals and, prospectively, population cohorts. To lay the foundation for this, we implemented and benchmarked complementary strategies to multiplex brain organoids. Following an extended longitudinal design with a uniquely informative set of timepoints, we pooled cells from different induced pluripotent stem cell lines either during organoids generation (upstream multiplexing in mosaic models) or before single cell-RNAseq library preparation (downstream multiplexing). We developed a new method, SCanSNP, and an aggregated call to deconvolve organoids cell identities, overcoming current criticalities in doublets prediction and low quality cells identification and improving accuracy over state of the art algorithms. Integrating single cell transcriptomes and analysing cell types across neurodevelopmental stages and multiplexing modalities, we validated the feasibility of both multiplexing methods in charting neurodevelopmental trajectories at high resolution, linking their specificity to genetic variation between individual lines. Together, this multiplexing suite of experimental and computational methods provides an enabling resource for disease modelling at scale and paves the way towards an in vitro epidemiology paradigm.

neuroscience↗

bioRxiv2022

GTF2I dosage regulates neuronal differentiation and social behavior in 7q11.23 neurodevelopmental disorders

Copy number variations at 7q11.23 cause neurodevelopmental disorders with shared and opposite manifestations. Deletion causes Williams-Beuren syndrome (WBS), while duplication causes 7q11.23 microduplication syndrome (7Dup). Converging evidence indicates GTF2I, from the 7q11.23 locus, is a key mediator of the cognitive-behavioral phenotypes associated with WBS and 7Dup. Here we integrate molecular profiling of patient-derived cortical organoids (COs) and transgenic mouse models to dissect 7q11.23 disease mechanisms. Proteomic and transcriptomic profiling of COs revealed opposite dynamics of neural progenitor proliferation and transcriptional imbalances, leading to precocious excitatory neuron production in 7Dup. The accelerated excitatory neuron production in 7Dup COs could be rescued by GTF2I knockdown. Transgenic mice with Gtf2i duplication recapitulated early neuronal differentiation defects and ASD-like behaviors. Remarkably, inhibition of LSD1, a downstream effector of GTF2I, was sufficient to rescue ASD-like phenotypes. We propose that the GTF2I-LSD1 axis constitutes a molecular pathway amenable to therapeutic intervention.

neuroscience↗

bioRxiv2022

7q11.23 CNV alters protein synthesis and REST-mediated neuronal intrinsic excitability

Copy number variations (CNVs) at 7q11.23 cause Williams-Beuren (WBS) and 7q microduplication syndromes (7Dup), two neurodevelopmental disorders with shared and opposite cognitive-behavioral phenotypes. Using patient-derived and isogenic neurons, we integrated transcriptomics, translatomics and proteomics to elucidate the molecular underpinnings of this dosage effect. We found that 7q11.23 CNVs cause opposite alterations in neuronal differentiation and excitability. Genes related to neuronal transmission chiefly followed 7q11.23 dosage and appeared transcriptionally controlled, while translation and ribosomal protein genes followed the opposite trend and were post-transcriptionally buffered. Mechanistically, we uncovered REST regulon as a key mediator of observed phenotypes and rescued transcriptional and excitability alterations through REST inhibition. We identified downregulation of global protein synthesis, mGLUR5 and ERK-mTOR pathways activity in steady-state in both WBS and 7Dup, whereas BDNF stimulation rescued them specifically in 7Dup. Overall, we show that 7q11.23 CNVs alter protein synthesis and neuronal firing-established molecular and cellular phenotypes of neurodevelopmental disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/511483v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1b0fa99org.highwire.dtl.DTLVardef@146624org.highwire.dtl.DTLVardef@13dc89aorg.highwire.dtl.DTLVardef@13d098f_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2022

RAGE engagement by SARS-CoV-2 enables monocyte infection and underlies COVID-19 severity

The spread of SARS-CoV-2 has fueled the COVID-19 pandemic with its enduring medical and socioeconomic challenges due to subsequent waves and long-term consequences of great concern. Here we charted the molecular basis of COVID-19 pathogenesis, by analysing patients immune response at single-cell resolution across disease course and severity. This approach uncovered cell subpopulation-specific dysregulation in COVID-19 across disease course and severity and identified a severity-associated activation of the receptor for advanced glycation endproduct (RAGE) pathway in monocytes. In vitro experiments confirmed that monocytes bind the SARS-CoV-2 S1-RBD via RAGE and that RAGE-Spike interactions drive monocyte infection. Our results demonstrate that RAGE is a novel functional receptor of SARS-CoV-2 contributing to COVID-19 severity. One-Sentence SummaryMonocyte SARS-CoV-2 infection via the receptor for advanced glycation endproduct triggers severe COVID-19.

immunology↗

bioRxiv2022

Benchmarking brain organoid recapitulation of fetal corticogenesis

Brain organoids are becoming increasingly relevant to dissect the molecular mechanisms underlying psychiatric and neurological conditions. The in vitro recapitulation of key features of human brain development affords the unique opportunity of investigating the developmental antecedents of neuropsychiatric conditions in the context of the actual patients genetic backgrounds. Specifically, multiple strategies of brain organoid (BO) differentiation have enabled the investigation of human cerebral corticogenesis in vitro with increasing accuracy. However, the field lacks a systematic investigation of how closely the gene co-expression patterns seen in cultured BO from different protocols match those observed in fetal cortex, a paramount information for ensuring the sensitivity and accuracy of modeling disease trajectories. Here we benchmark BO against fetal corticogenesis by integrating transcriptomes from in-house differentiated cortical BO (CBO), other BO systems, human fetal brain samples processed in-house, and prenatal cortices from the BrainSpan Atlas. We identified co-expression patterns and prioritized hubs of human corticogenesis and CBO differentiation, highlighting both well-preserved and discordant trends across BO protocols, including different degrees of heterochronicity in differentiation across BO models compared to fetal cortex. Our approach provides a framework to directly compare the extent of in vivo/in vitro alignment of neurodevelopmentally relevant processes and their attending temporalities, structured as an accessible resource to query for modelling human corticogenesis and the neuropsychiatric outcomes of its alterations.

developmental biology↗

bioRxiv2018

Longitudinal dissection in brain organoids at single cell resolution uncovers the developmental role of GSK3 in human corticogenesis

The regulation of proliferation and polarity of neural progenitors is crucial for the development of the brain cortex, with modes and timings of cell division intimately related to the stereotypical acquisition of layer-specific neuronal identities. Animal studies have implicated glycogen synthase kinase 3 (GSK3) as a pivotal regulator of both proliferation and polarity, yet the functional relevance of its signaling for the unique features of human corticogenesis remain to be elucidated. Here we harness human cortical brain organoids to probe, at single cell resolution, the longitudinal impact of GSK3 inhibition through multiple developmental stages. Our results indicate that chronic GSK3 inhibition increases the proliferation of neural progenitors and causes massive derangement of cortical tissue architecture. Surprisingly, single cell transcriptome profiling revealed only a discrete impact on early neurogenesis and uncovered the outer radial glia and the astrogenic lineage as the main GSK3-dependent developmental domains. Through this first single cell-level dissection of the GSK3 regulatory network in human corticogenesis, our work uncovers a remarkably specific conduit between the architecture of progenitor niches and lineage specification.

developmental biology↗

bioRxiv2017

From Cohorts to Molecules: Adverse Impacts of Endocrine Disrupting Mixtures

Convergent evidence associates endocrine disrupting chemicals (EDCs) with major, increasingly-prevalent human disorders. Regulation requires elucidation of EDC-triggered molecular events causally linked to adverse health outcomes, but two factors limit their identification. First, experiments frequently use individual chemicals, whereas real life entails simultaneous exposure to multiple EDCs. Second, population-based and experimental studies are seldom integrated. This drawback was exacerbated until recently by lack of physiopathologically meaningful human experimental systems that link epidemiological data with results from model organisms.\n\nWe developed a novel approach, integrating epidemiological with experimental evidence. Starting from 1,874 mother-child pairs we identified mixtures of chemicals, measured during early pregnancy, associated with language delay or low-birth weight in offspring. These mixtures were then tested on multiple complementary in vitro and in vivo models. We demonstrate that each EDC mixture, at levels found in pregnant women, disrupts hormone-regulated and disease-relevant gene regulatory networks at both the cellular and organismal scale.

molecular biology↗