Biology subjects

Ferretti, E.

Publications and source records attributed to Ferretti, E..

6 recordsLinked to original sources

bioRxiv2026

Automatic orofacial behaviors remap within cortical substrates for voluntary motor control in freely moving primates

Orofacial behaviors, like yawning and emotional facial expressions, involve phylogenetically conserved subcortical circuits. Yet, their context-dependent modulation in primates suggests overlooked cortical contributions. Here, we wirelessly recorded from 640 ventral motor and premotor sites in two freely moving macaques during spontaneous orofacial actions combining automatic and voluntary components to varying degrees (yawning, threat, bite, drink). We identified coupling between synaptic input (local field potential) and spiking output in 169 spatially distributed sites during yawning, while threat display was sparsely represented. Yawn-related sites exhibited an early beta-band suppression followed by high-gamma power enhancement. Of 401 isolated single neurons, 95 (predominantly putative medium-sized pyramidal cells) encoded yawning, mostly together with voluntary biting and drinking actions. No modulation was found during the observation of yawning by conspecifics. Yawn-related units either switched or maintained their mouth opening/closing tuning across yawning and more voluntary actions, suggesting counteracting and synergistic downstream influences on yawning motor control. In contrast, threat-related units predominantly preserved their opening/closing tuning during biting and drinking. Head-free intracortical microstimulation of sites hosting yawn-related units preferentially evoked localized mouth and face movements, supporting their causal role in orofacial motor control. Finally, projecting neural activity into a low-dimensional manifold showed that voluntarily controlled and largely automatic behaviors engaged distinct population dynamics while preserving the discriminability of individual orofacial displays. These findings reveal that cortical substrates of voluntary motor control can be recruited to shape otherwise automatic orofacial displays.

neuroscience↗

bioRxiv2026

ARHGEF6-dependent cytoskeletal regulation underlies a conserved program of forebrain interneuron development

The molecular programs coordinating inhibitory interneuron migration, maturation, and survival during forebrain development remain incompletely understood. Here we investigate ARHGEF6, a RAC1/CDC42 guanine nucleotide exchange factor linked to X-linked intellectual disability (XLID46) and previously studied only at postsynaptic compartments, and reveal an earlier, conserved role in forebrain interneuron development. ARHGEF6 is selectively enriched in the inhibitory lineage during the peak of interneuron generation and migration. Its loss in mice reduces the number of cortical and hippocampal interneurons, disrupts tangential migration, increases developmental cell death, and impairs morphological and electrophysiological maturation. Strikingly, ARHGEF6-knockout human iPSC-derived organoids and assembloids mirror these deficits exhibiting increased apoptosis, reduced neuronal output, disorganized growth cones, impaired neurite branching, and disrupted migratory dynamics. These cross-species findings reframe ARHGEF6 as an early, essential orchestrator of inhibitory circuit assembly and reveal a conserved cytoskeletal program whose disruption produces the excitatory-inhibitory imbalance linked to cognitive dysfunction.

developmental biology↗

bioRxiv2026

ERK activity as a key player in determining cardiac cell fate choices

Heart development is supported by diverse cell types originating from the lateral plate mesoderm (LPM), including the first heart field (FHF), the second heart field (SHF), which is a part of pharyngeal mesoderm, and the newly described juxta-cardiac field (JCF) that harbors progenitor cells of the epicardium. While FGF-MEK-ERK signalling has been implicated in various developmental mechanisms, its role in cardiac specification remains elusive. This signalling pathway involves autoinhibitory loops, acting at translational and post-translational levels, resulting in pulses of ERK activity. We hypothesized that this alternating ERK activity could direct binary cell fate choices during mesodermal specification. Using an in vitro system, we found that inhibition of ERK activity in the LPM, before cardiac commitment, resulted in enriched gene expression of JCF and pharyngeal mesoderm/SHF markers, with high proepicardial marker levels, at the expense of FHF-like cardiomyocyte markers. Our findings reveal a novel contribution of ERK signalling in cell differentiation within the cardiac lineages.

cell biology↗

bioRxiv2025

Transposable Elements and Homotypic Niches Drive Immune Dynamics and Resistance in Melanoma Epigenetic-based immunotherapy

Melanoma plasticity drives immune evasion and therapy resistance through dynamic cell-state transitions beyond genetic alterations. Epigenetic remodeling critically influences such processes, yet its role in reshaping the tumor ecosystem under therapeutic pressure remains unresolved. Here, we profiled longitudinal biopsies from melanoma patients treated in the phase Ib NIBIT-M4 epi-immunotherapy clinical trial (NCT02608437), testing the combination of a DNMT1 inhibitor with anti-CTLA4 using single-cell multiome and high-resolution spatial transcriptomics. Integrated analyses resolved seven malignant meta-programs, including a rare Wnt/{beta}-catenin-driven melanocytic state and a de-differentiated neural crest-like state enriched in non-responders. Spatial modeling revealed that homotypic clustering stabilizes resistant programs, with neural crest-like cells forming compact, centrally localized niches, whereas Wnt/{beta}-catenin subpopulations displayed a bimodal architecture, either cohesive clusters sustained by adhesion or dispersed, transcriptionally plastic cells. Responders exhibited progressive enrichment of an antigen presentation/interferon program and coordinated remodeling of the tumor microenvironment with T and B cell expansion, whereas tumors from non-responder patients maintained stable composition of neural crest-like clusters. Epigenetic therapy reactivated transposable elements, providing both regulatory signals that prime innate immunity within microenvironment and generating antigens that drive immunoediting and immunogenicity of Antigen presentation/interferon cell states in responders. Finally, NFATC2 emerged as a master regulator of neural crests-like transcriptional phenotypes and promoter of resistance to therapeutic interventions in melanoma patients. NFATC2 perturbation was able to shift tumor cells towards more differentiated and immunogenic states. These findings reveal how epigenetic-based immunotherapy reshapes melanoma ecosystems, provide mechanistic insights into how multiple transcriptional programs promote tumor plasticity and resistance to both combinatorial therapies and immune checkpoint blockade, identify spatial clustering as a principle stabilizing resistant niches, and highlight {beta}-catenin and NFATC2 as actionable vulnerabilities to overcome resistance.

genomics↗

bioRxiv2023

Open-ST: High-resolution spatial transcriptomics in 3D

Spatial transcriptomics (ST) methods have been developed to unlock molecular mechanisms underlying tissue development, homeostasis, or disease. However, there is a need for easy-to-use, high-resolution, cost-efficient, and 3D-scalable methods. Here, we report Open-ST, a sequencing-based, open-source experimental and computational resource to address these challenges and to study the molecular organization of tissues in 3D. In mouse brain, Open-ST captured transcripts at subcellular resolution and reconstructed cell types. In primary tumor and patient-matched healthy/metastatic lymph nodes, Open-ST captured the diversity of immune, stromal and tumor populations in space. Distinct cell states were organized around cell-cell communication hotspots in the tumor, but not the metastasis. Strikingly, the 3D reconstruction and multimodal analysis of the metastatic lymph node revealed spatially contiguous structures not visible in 2D and potential biomarkers precisely at the 3D tumor/lymph node boundary. We anticipate Open-ST to accelerate the identification of spatial molecular mechanisms in 2D and 3D.

systems biology↗

bioRxiv2021

Reduced miR-184-3p expression occurring in Type 2 diabetic pancreatic islets protects β-cells from lipotoxic and proinflammatory apoptosis via a CRTC1-dependent mechanism

Loss of functional {beta}-cell mass in Type 2 diabetes (T2D) involves molecular mechanisms including {beta}-cell apoptosis, dysfunction, and/or dedifferentiation. MicroRNA miR-184-3p has been demonstrated to be involved in multiple {beta}-cell functions including insulin secretion, proliferation and survival. However, downstream targets and upstream regulators of miR-184-3p have not yet been fully elucidated. Here, we showed that levels of miR-184-3p are reduced in human T2D pancreatic islets and that its reduction protected {beta}-cells from lipotoxic- and inflammatory-induced apoptosis. Interestingly, CREB-Transcriptional Coactivator-1 (CRTC1) is a direct target of miR-184-3p and indeed its expression is upregulated in human T2D pancreatic islets. The downregulation of miR-184-3p in {beta}-cells induced the upregulation of CRTC1 both at mRNA and protein level. Of note, miR-184-3p protection effect was dependent on CRTC1, since its silencing in human {beta}-cells abrogates the protective mechanism exerted by miR-184-3p inhibition. Additionally, we found that the {beta}-cell specific transcription factor NKX6.1, whose DNA binding sites were predicted to be present in human and mouse MIR184 gene promoter sequence, was reduced in T2D human pancreatic islets, in line with miR-184-3p downregulation, and was positively correlated with microRNA expression. Using chromatin immunoprecipitation analysis and mRNA silencing experiments, we demonstrated that NKX6.1 directly controls both human and murine miR-184 expression. In conclusion, we found that miR-184-3p expression is controlled by the {beta}-cell specific transcription factor NKX6.1 and that miR-184-3p reduction protects {beta}-cells from apoptosis through the upregulation of its target gene CRTC1.

cell biology↗