Biology subjects

Grosso, A. R.

Publications and source records attributed to Grosso, A. R..

4 recordsLinked to original sources

bioRxiv2025

Tissue-Specific Regulatory and Expression Patterns of CDG-causative genes account to Phenotypic Variability

Congenital disorders of glycosylation (CDGs) are rare metabolic diseases caused by impaired addition of glycans to proteins and lipids. They display wide clinical variability, but the molecular basis remains unclear. Using healthy transcriptomic data from the GTEx project (bulk: 2,833 samples across 36 tissues; single-nucleus: 209,126 nuclei from 25 samples spanning 8 tissue types and 44 cell types), we investigated the expression and regulatory landscapes of 12 CDG-causative genes. CDG-causative genes were broadly but heterogeneously expressed, with both high and low expression aligning with clinical features. Interindividual variability in expression may contribute to phenotypic diversity in CDG. VPS13B was broadly expressed in fibroblasts, supporting their use in patient-derived models, while other genes showed more tissue-restricted expression, underscoring the importance of cellular context. Several genes exhibited tissue-specific deviations from balanced biallelic expression. Five allelic expression types across individuals - biallelic balanced or biased, tissue-specific or constitutive monoallelic, and autosomal random monoallelic - suggest a role for allelic regulation in phenotypic heterogeneity. Tissue-specific eQTLs highlighted regulatory complexity, with many variants located in intronic enhancers of unrelated genes. Finally, gene expression-immune cell correlations recapitulated known immune phenotypes and suggested context-dependent immune roles. Together, these findings reveal how genetic, regulatory, and immune factors shape CDG heterogeneity and provide a framework for future research.

genomics↗

bioRxiv2024

Erosion of X-Chromosome Inactivation in female hiPSCs is heterogeneous and persists during differentiation

During culture, female human pluripotent stem cells (hPSCs), including human induced PSCs (hiPSCs) exhibit a propensity for erosion of X-chromosome inactivation (XCI). This phenomenon is characterized by the loss of XIST RNA expression and reactivation of a subset of X-linked genes from the inactive X chromosome (Xi). XCI erosion, despite its common occurrence, is often overlooked by the stem cell community, hindering a complete understanding of its impact on both fundamental and translational applications of hiPSCs. Investigating erosion dynamics in female hiPSCs, our study reveals that XCI erosion is a frequent yet heterogeneous phenomenon, resulting in the reactivation of several X-linked genes. The likelihood of a gene to erode increases for those located on the short arm of the X chromosome and within H3K27me3-enriched domains. Paradoxically, genes that typically escape XCI are hypersensitive to loss of XIST RNA and XCI erosion. This implies that XIST RNA normally restrains expression levels of these genes on the Xi. Importantly, increased X-linked gene expression upon erosion does not globally impact (hydroxy)methylation levels in hiPSCs or at imprinted regions. By exploring diverse differentiation paradigms, such as trilineage commitment and cardiac differentiation, our study reveals the persistence of abnormal XCI patterns throughout differentiation. This finding has significant implications for fundamental research, translational applications, and clinical use of stem cells. We underscore the importance of raising awareness within the stem cell community regarding XCI erosion and advocate for its inclusion in comprehensive hiPSC quality control.

molecular biology↗

bioRxiv2024

Targeted CRISPR-Cas9 screening identifies transcription factor network controlling murine haemato-endothelial fate commitment

Haematopoiesis is a tightly coordinated process that forms and maintains all blood cells. During development blood generation begins in the yolk sac with the differentiation of haemato-endothelial mesoderm giving rise to haematopoietic progenitors. Which molecular regulators are crucial for haemato-endothelial mesoderm formation remains unclear and has not been studied in an unbiased way. Here we employ a mouse embryonic stem cell model that recapitulates embryonic blood development and perform targeted CRISPR-Cas9 knock out screens focusing on transcription factors and chromatin regulators. Focusing on the transition of primitive towards haematoendothelial mesoderm we identified the known master regulator Etv2 and novel transcription factors including Smad1, Ldb1, Six4 and Zbtb7b acting as crucial drivers or repressors of mesodermal commitment. Our transcriptome analysis highlights that each factor has a precise impact on the gene expression signature of the developing mesoderm resulting in the formation of mesodermal subsets with a defined lineage differentiation bias. Our study reveals novel molecular pathways governing mesodermal development crucial to allow endothelial and haematopoietic lineage specification.

developmental biology↗

bioRxiv2023

SRRM2 splicing factor modulates cell fate in early development

Embryo development is an orchestrated process that relies on tight regulation of gene expression to guide cell differentiation and fate decisions. Alternative splicing is modulated during development as an additional layer of regulation to reprogram gene expression patterns. The Srrm2 splicing factor has recently been implicated in developmental disorders and diseases, but its role in early mammalian development remains unexplored. Here, we show that Srrm2 dosage is critical for maintaining embryonic stem cell pluripotency and cell identity. Srrm2 heterozygosity promotes loss of stemness, characterized by the coexistence of cells expressing naive and formative pluripotency markers, together with extensive changes in gene expression, including genes regulated by serum- response transcription factor and differentiation-related genes. Depletion of Srrm2 by RNA interference in embryonic stem cells shows that the earliest effects of Srrm2 half-dosage are specific alternative splicing events on a small number of genes, followed by expression changes in metabolism and differentiation-related genes. Our findings unveil molecular and cellular roles of Srrm2 in stemness and lineage commitment, shedding light on the roles of splicing regulators in early embryogenesis, developmental diseases and tumorigenesis. Summary statementThis article emphasizes the importance of splicing regulators in early mammalian development by uncovering roles of SRRM2 splicing factor dosage in pluripotency, providing novel insights for a better understanding of Srrm2-related diseases.

developmental biology↗