Biology subjects

Merla, G.

Publications and source records attributed to Merla, G..

6 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↗

bioRxiv2026

Epigenetic signature at FOXP3 distal enhancer affects regulatory T cell development in Kabuki syndrome

Kabuki syndrome (KS) is a congenital developmental disorder caused by germinal pathogenic variants in the lysine methyltransferase 2D (KMT2D, KS1) or lysine demethylase 6A (KDM6A, KS2) genes. Kabuki patients display mental retardation, multiorgan malformations and immune dysregulation - ranging from immunodeficiency to autoimmunity - which strongly compromises their life expectancy. We explored whether the complex immunological scenario of Kabuki syndrome 1 subjects (Ks) could be ascribed to an altered generation of CD4+FOXP3+ regulatory T cells (Tregs). We report that pediatric Ks carrying KMT2D pathogenic variants show a significant reduction of Tregs. DNA methylation analysis reveals a specific methylation pattern at the FOXP3 distal enhancer that correlates with decreased FOXP3 transcription early during Treg cell induction and promotes T helper (Th)-2 lineage differentiation. Finally, in vitro T cell demethylation rescues FOXP3 expression and Treg induction in Ks, offering a novel potential therapeutic perspective. Our findings connect KMT2D loss-of-function to the inhibition of human FOXP3 gene transcription and provide novel molecular insights to explain the immunological phenotype in Ks, thus pinpointing this syndrome as a novel Tregopathy.

immunology↗

bioRxiv2025

Novel ciliary protein TRIM8 is a multifunctional workhorse during mitosis

TRIM8 is an E3 ubiquitin ligase that functions as both a tumour suppressor and an oncoprotein. Earlier, we reported that TRIM8 interacts with key regulators of mitotic spindle assembly, and that TRIM8 knockdown results in mitotic delay and aneuploidy. In this study, we implemented a multi-omics strategy with differential transcriptomic (single-cell RNA sequencing or scRNA-seq), translatomic (polysome profiling with RNA-seq), and proteomic (LC-MS/MS) approaches to elucidate the involvement of TRIM8 in different levels (transcription, translation, post-translation) and stages (G0/G1, S, G2/M) of mitotic cell cycle regulation and progression. With the aid of differential transcriptomic (scRNA-seq) and proteomic (LC-MS/MS) approaches, we show that depletion of TRIM8 perturbs the canonical "Cell Cycle Control of Chromosomal Replication" pathway and demonstrate that TRIM8 negatively regulates the expression of TOP2A, known to be essential for genomic integrity. We also show that TRIM8 downregulation induces substantial alterations in the translation activity of cells and results in the upregulation of polysome-bound MALAT1 lncRNA by means of significant changes in polysome profiling coupled with RNA-sequencing. Moreover, we unveil endogenous TRIM8 as a novel ciliary protein that co-localizes with CEP170, required for ciliary function, in the centrosomal region throughout all mitotic phases. Our work shows the dynamic role played by a TRIM family protein across various stages of mitosis for the first time, laying the foundation for exploring the therapeutic potential of TRIM8 in addressing cell cycle-related diseases, including cancer. HIGHLIGHTSO_LITRIM8 is involved in transcriptional and post-translational regulation of "Cell Cycle Control of Chromosomal Replication" pathway and oversees the expression of TOP2A, essential for mitotic chromosome structure maintenance. C_LIO_LIThe silencing of TRIM8 induces changes in cellular translation activity and alters the expression pattern of key translational proteins. Additionally, TRIM8-silencing leads to an elevation of long non-coding RNA (lncRNA) MALAT1 in the polysome-bound fraction. C_LIO_LITRIM8 is identified as a novel ciliary protein. C_LIO_LISilencing of TRIM8 results in the upregulation of the centrosomal protein CEP170, and both proteins co-localize in the centrosomal region throughout all stages of mitosis. C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/646005v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1b03f1borg.highwire.dtl.DTLVardef@1ff16e4org.highwire.dtl.DTLVardef@37f07borg.highwire.dtl.DTLVardef@8d28af_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

Non-cell-autonomous control of gastruloid development by the lncRNA T-UCstem1 through DKK1-dependent modulation of WNT signalling

The role and the mechanisms of long non-coding RNA (lncRNAs) in early mammalian embryogenesis remain unclear; this is mostly due to the complexity of the regulatory mechanism of lncRNAs and the limited availability of early embryo samples. The emergence of stem cell-based models of early mammalian embryogenesis offers new opportunities to address these challenging questions. Here we use mouse gastruloids to investigate the role of an ultraconserved lncRNA, T-UCstem1, in the formation of the mammalian body plan. Combining morphological and immunofluorescence analysis with bulk and single cells transcriptomics, we provide unprecedented evidence that T-UCstem1 is a key regulator of gastruloid development and is required for the extension of the anteroposterior axis. Specifically, knock down of T-UCstem1 results in aberrant gastruloid development, which is characterized by altered spatiotemporal expression of the differentiation markers and persistence of pluripotency genes. Single-cell analysis reveals higher cellular heterogeneity in T-UCstem1 KD gastruloids. Notably, the presence of cell populations characterized by the co-expression of pluripotency and differentiation markers points to a key role of T-UCstem1 in establishment and maintenance of proper cellular identity. Mechanistically, we show that T-UCstem1 acts non-cell autonomously through Dickkopf-related protein 1 (DKK-1)-dependent modulation of WNT pathway. Our findings highlight a previously unexplored role for ultraconserved lncRNAs in gastruloid development and open the way for using gastruloids to dissect the functions of lncRNAs in early mammalian development.

developmental biology↗

bioRxiv2021

KMT2D haploinsufficiency in Kabuki Syndrome disrupts neuronal function through transcriptional and chromatin rewiring independent of H3K4-monomethylation

Kabuki syndrome (KS) is a rare multisystem disorder, characterized by intellectual disability, growth delay, and distinctive craniofacial features. It is mostly caused by de novo mutations of KMT2D, which is responsible for histone H3lysine 4 mono-methylation (H3K4me1) that marks active and poised enhancers. We assessed the impact of KMT2D mutations on chromatin and transcriptional regulation in a cohort of multiple KS1 tissues, including primary patient samples and disease-relevant lineages, namely cortical neurons (iN), neural crest stem cells (NCSC), and mesenchymal cells (MC). In parallel, we generated an isogenic line derived from human embryonic stem cells (hESC) for the stepwise characterization of neural precursors and mature neurons. We found that transcriptional dysregulation was particularly pronounced in cortical neurons and widely affected synapse activity pathways. This was consistent with highly specific alterations of spontaneous network-bursts patterns evidenced by Micro-electrode-array (MEA)-based neural network. Profiling of H3K4me1 unveiled the almost complete uncoupling between this chromatin mark and the effects on transcription, which is instead reflected by defects in H3K27ac. Finally, we identified the direct targets of KMT2D in mature cortical neurons, uncovering TEAD2 as the main mediator of KMT2D haploinsufficiency. Our results uncover the multi-tissue architecture of KS1 dysregulation and define a unique electrical phenotype and its molecular underpinnings for the cortical neuronal lineage.

genetics↗

bioRxiv2019

7q11.23 Syndromes Reveal BAZ1B as a Master Regulator of the Modern Human Face and Validate the Self-Domestication Hypothesis

Symmetrical 7q11.23 dosage alterations cause craniofacial and cognitive/behavioral phenotypes that provide a privileged entry point into the evolution of the modern human face and (pro-) sociality. We undertook a functional dissection of chromatin remodeler BAZ1B in neural crest stem cells (NCSCs) from a uniquely informative cohort of typical and atypical patients harboring 7q11.23 Copy Number Variants (CNVs). Our results reveal a key contribution of BAZ1B to NCSC in vitro induction and migration, coupled with a crucial involvement in neural crest (NC)-specific transcriptional circuits and distal regulation. By intersecting our experimental data with new paleogenetic analyses comparing modern and archaic humans, we uncover a modern-specific enrichment for regulatory changes both in BAZ1B and its experimentally defined downstream targets, thereby providing the first empirical validation of the self-domestication hypothesis and positioning BAZ1B as a master regulator of the modern human face.\n\nOne Sentence SummaryBAZ1B dosage shapes the modern human face.

evolutionary biology↗