Biology subjects

Leonardi, O.

Publications and source records attributed to Leonardi, O..

4 recordsLinked to original sources

bioRxiv2025

Benchmarking cerebellar organoids to model autism spectrum disorder and human brain evolution

While cortical organoids have been used to model different facets of neurodevelopmental conditions and human brain evolution, cerebellar organoids have not yet featured so prominently in the same context, despite increasing evidence of this brain regions importance for cognition and behavior. Here, we provide a longitudinal characterization of cerebellar organoids benchmarked against human fetal data and identify at very early stages of development a significant number of dynamically expressed genes relevant for neurodevelopmental conditions such as autism and attention deficit hyperactivity disorders. Then, we model an ASD mutation impacting CHD8, showing both granule cell and oligodendrocyte lineages prominently affected, resulting in altered network activity in more mature organoids. Lastly, using CRISPR/Cas9 editing, we also model an evolution-relevant mutation in a regulatory region of the CADPS2 gene. We investigate the effect of the derived allele exclusive to Homo sapiens, identifying a rerouting of the CADPS2-expression in rhombic lip cells, coupled with a different sensitivity to hypoxia which in turn lead to a differential timing of granule cell differentiation. HIGHLIGHTSO_LILongitudinal characterization of cerebellar organoids uncovers disorder related genes especially at early stages of development C_LIO_LIMutation in CHD8 alter rhombic lip and oligodendrocytes differentiation via WNT pathway C_LIO_LIRerouting of CADPS2 expression, delaying differentiation and migration, in recent human evolution C_LI IN BRIEFAprile and colleagues longitudinally profiled cerebellar organoids, benchmarking them against a fetal human atlas and identified a highly dynamic expression of genes related to cognitive and behavioral disorders especially at early stages of differentiation. Organoids were used to model the impact of a high-penetrance mutation associated with autism spectrum disorder and a high-frequency derived allele in Homo sapiens predicted to have played a role in recent brain evolution.

neuroscience↗

bioRxiv2025

Regulatory logic of human cortex evolution by combinatorial perturbations

Comparative genomic studies between contemporary and extinct hominins revealed key evolutionary modifications, but their number has hampered a system level investigation of their combined roles in scaffolding modern traits. Through multi-layered integration we selected 15 genes carrying nearly fixed sapiens-specific protein-coding mutations and developed a scalable design of combinatorial CRISPR-Cas9 bidirectional perturbations to uncover their regulatory hierarchy in cortical brain organoids. Interrogating the effects of overexpression and downregulation for all gene pairs in all possible combinations, we defined their impact on transcription and differentiation and reconstructed their regulatory architecture. We uncovered marked cell type-specific effects, including the promotion of alternative fates and the emergence of interneuron populations, alongside a core subnetwork comprising KIF15, NOVA1, RB1CC1 and SPAG5 acting as central regulator across cortical cell types.

systems biology↗

bioRxiv2025

CHD2 Dosage Ties Autolysosomal Pathway to Cortical Maturation in Disease and Evolution

The mechanisms linking evolutionary changes in gene regulation to brain development and neurodevelopmental disease susceptibility remain poorly understood. Here, we identify a human-specific variant in an enhancer region that reduces expression of the chromatin remodeler CHD2. We investigate the variant's functional consequences using genome editing, cross-primate induced pluripotent stem cell models, cortical organoids, single-cell transcriptomics, patient-derived cells, and neuronal network analyses. We demonstrate that CHD2 dosage bidirectionally regulates lysosomal function and autophagosome flux to set the tempo of neuronal maturation. Higher CHD2 expression, as found in ancestralized and non-human primate models, enhances lysosomal degradative capacity and accelerates dendritic and synaptic maturation. Conversely, CHD2 haploinsufficiency yields reciprocal defects and disrupts broader neurodevelopmental transcriptional programs. Restoring lysosomal function genetically or pharmacologically rescues neuronal maturation in CHD2-haploinsufficient neurons, establishing lysosomal dysfunction as a causal and therapeutically tractable mechanism. These findings reveal that CHD2 and lysosomal homeostasis constitute a critical molecular axis regulating the pace of cortical development across evolution and disease.

neuroscience↗

bioRxiv2023

A multi-layered integrative analysis reveals a cholesterol metabolic program in outer radial glia with implications for human brain evolution

The definition of molecular and cellular mechanisms contributing to evolutionary divergences in brain ontogenetic trajectories is essential to formulate hypotheses about the emergence of our species. Yet the functional dissection of evolutionary modifications derived in the Homo sapiens lineage at an appropriate level of granularity remains particularly challenging. Capitalizing on recent single-cell sequencing efforts that have massively profiled neural stem cells from the developing human cortex, we develop an integrative computational framework in which we perform (i) trajectory inference and gene regulatory network reconstruction, (ii) (pseudo)time-informed non-negative matrix factorization for learning the dynamics of gene expression programs, and (iii) paleogenomic analysis for a higher-resolution mapping of the regulatory landscape where our species acquired derived mutations in comparison to our closest relatives. We provide evidence for cell type-specific activation and regulation of gene expression programs during indirect neurogenesis. In particular, our analysis uncovers a zinc-finger transcription factor, KLF6, as a key regulator of a cholesterol metabolic program specifically in outer radial glia. Our strategy allows us to further probe whether the (semi)discrete gene expression programs identified have been under selective pressures in our species lineage. A cartography of the regulatory landscape impacted by Homo sapiens-derived transcription factor binding site disruptions reveals signals of selection clustering around regulatory regions associated with GLI3, a well-known regulator of the radial glial cell cycle. As a whole, our study contributes to the evidence of significant changes impacting metabolic pathways in recent human brain evolution.

evolutionary biology↗