Maria Rita Passos-Bueno

Non-syndromic cleft lip or palate (NS-CL/P) is an oral birth defect with complex aetiology. We compared the microbial diversity and composition of the oral microbiome of mothers of babies with NS-CL/P (CLP group) and mothers of babies without NS-CL/P (control group). Oral microbiome composition was determined by sequencing the V3-V4 regions of the 16S rRNA gene. CLP and control groups had overall similar microbial compositions, but significant differences were observed. The most significant microbial genus related to these differences was Cutibacterium , which was more abundant in the CLP group. Based on the literature, we hypothesize that a member of the Cutibacterium genus present in the oral microbiota may have a role in inflammation processes that could be related to NS-CL/P development. We found additional differences in terms of differential abundance when subsetting the dataset for mothers with a male child; in this case, depletion of Limosilactobacillus and an unknown taxon, in the CLP group, was a significant result. We conclude that the maternal oral microbiome likely plays a role in the development of the NS-CL/P condition.

This study aimed to compare guided dorsal forebrain neural organoids with unguided neural organoids, focusing on differences in structural organization, cellular composition, and functional properties. Using the same human induced pluripotent stem cell line, we applied two established differentiation protocols in parallel to generate guided and unguided neural organoids. Guided neural organoids exhibited reproducible cytoarchitecture, relatively homogeneous morphology, and robust network activity, making them particularly well-suited for modeling specific aspects of cortical neurodevelopment and neurodevelopmental disorders. In contrast, unguided neural organoids displayed greater heterogeneity in morphology and cellular composition, including prominent development of astrocytes, microglia, and choroid plexus-like structures that respond to inflammatory stimuli, positioning them as valuable models for studying neuroinflammation during brain development. These findings emphasize the importance of selecting neural organoids protocols based on specific research questions, and suggest that the guided and unguided approaches can complement each other to provide insights into neurodevelopmental and neuroinflammatory processes.

Phelan-McDermid Syndrome (PMS), primarily linked to SHANK3 haploinsufficiency, presents with complex neurodevelopmental features, including developmental regression, whose underlying mechanisms are poorly understood. This study investigated the impact of SHANK3 disruption across multiple levels, from gene expression in patient-derived iPSC neurons to in vivo brain network activity. RNA-sequencing of iPSC-derived neurons from PMS patients with SHANK3 disruption only (n = 9) and controls (n = 7) revealed dysregulation in differential gene expression and co-expression modules linked to cell cycle, RNA metabolism, and metabolic pathways in SHANK3 -mutated neurons. All modules were correlated with PMS regression and enriched for genes implicated in neurodevelopmental or neurodegenerative disorders, such as autism, ADHD, and Alzheimer’s disease. At the cellular level, SHANK3 -mutated cultures exhibited increased proliferation of neural progenitors and intermediate progenitor markers. Differentiated neurons showed reduced morphological complexity, specific changes in postsynaptic marker density and puncta size, and electrophysiological characteristics suggestive of neuronal hyperexcitability. Electroencephalography (EEG) in a PMS patient cohort (n = 20) compared to controls (n = 30) demonstrated hyperconnectivity and excessive high-frequency oscillations, suggesting altered neural network dynamics. In summary, the use of different analytical approaches suggested that SHANK3 haploinsufficiency disrupts neurodevelopmental trajectories and revealed that regression in PMS may share common genes and pathways with neurodegeneration. We also characterized molecular and neurophysiological markers that can be useful in therapeutic protocols for PMS.

Genomic studies of autism spectrum disorder (ASD) have largely excluded admixed populations. To address this gap, we characterized the genomic landscape of ASD in Brazil by combining a systematic literature review with whole-exome sequencing analysis of 441 Brazilian individuals and their families. Our analysis revealed a conclusive molecular diagnosis in 13.1% of probands. The diagnostic yield was higher among individuals with clinical features, particularly comorbid signs of intellectual disability, hypotonia, and seizures, providing a basis for prioritizing genetic testing. The sample presented a diverse ancestry, with major European, African, and Native American contributions. Notably, more than half of the identified rare risk variants were located on non-European haplotypes. Both de novo and inherited variants contributed to ASD risk, and we reinforce NPAS3 as a candidate ASD risk gene. This study provides the first comprehensive genomic overview of ASD in a large Brazilian cohort, reinforcing the critical need to include diversely admixed populations in genomic research to expand the understanding of ASD architecture and improve diagnostic strategies in resource-limited settings.

Deleterious variants in the BRSK2 gene, which encodes a serine/threonine kinase crucial for neuronal polarisation and brain development, have recently been linked to the pathogenesis of autism spectrum disorder (ASD). However, comprehensive clinical descriptions of individuals with pathogenic BRSK2 variants remain limited, and the molecular and cellular consequences of these mutations are poorly understood. This case report provides a detailed clinical, cognitive and molecular characterisation of a male patient with ASD harbouring a de novo BRSK2 frameshift variant, who developed catatonia, developmental regression and cognitive decline during early adolescence. To assess the functional impact of the variant, induced pluripotent stem cells (iPSCs) and iPSC-derived neural organoids were generated from the patient. Molecular analyses revealed a significant reduction in BRSK2 transcript and protein levels. Sequencing of BRSK2 mRNA showed exclusive expression from the wild-type allele, consistent with degradation of the mutant transcript via nonsense-mediated decay. These findings broaden the mutational and phenotypic spectrum associated with BRSK2 -related neurodevelopmental disorders and provide functional evidence supporting the pathogenicity of the identified variant. Furthermore, this report demonstrates the role of BRSK2 in complex neuropsychiatric features—such as catatonia and cognitive deterioration, which remain underreported in the existing literature—and emphasises the importance of longitudinal cognitive and behavioural monitoring in individuals with BRSK2 mutations.

Cleft lip with or without palate (CLP) is a multifactorial trait associated with environmental exposures such as smoking, alcohol consumption, and pro-inflammatory conditions during early pregnancy, as well as with both common and rare genetic variants. Our group identified CDH1 loss-of-function variants segregating in families with CLP, with incomplete penetrance linked to promoter hypermethylation. Previously, we demonstrated that gene-environment interactions driven by pro-inflammatory factors can induce this methylation, downregulate E-cadherin expression, and impair neural crest migration, thereby contributing to the etiology of CLP. However, the embryonic consequences of the two-hit CLP model ( CDH1 haploinsufficiency combined with pro-inflammatory insult) have not yet been explored in mammals. Here, under single dose of floxed- Cdh1 , we investigated the pro-inflammatory response at the maternal-fetal interface, its impact on cytokine and Cdh1 expression along the anteroposterior axis, the associated epigenetic landscape in the embryonic head, and the effect on cranial structures. We found that pro-inflammatory activation differentially signals to the embryo between anterior and posterior regions, impairing Cdh1 /E-cadherin expression in NC cells of the head, accompanied by Cdh1 promoter hypermethylation and other differentially methylated genes involved in cell-junction maintenance. Our findings support a model in which maternal pro-inflammatory responses act as environmental factors that repress NC CDH1 expression through epigenetic mechanisms, contributing to CLP development by downregulating E-cadherin and potentially compromising overall epithelial integrity. Animal Ethics Committee (CEUA IB/USP) number approval: 394/2022

Exclusive breastfeeding (EBF) plays a crucial role in infant gut microbiome assembly and development. However, few studies have investigated the effects of EBF in restoring a perturbed microbiome. In this study, we applied whole metagenomic sequencing to assess the gut microbiome assembly in 525 Brazilian infants from 3 to 9 months of age of the Germina Cohort, demonstrating the early determinants of microbial taxonomy and function modulation. Our analysis shows that EBF alters the relative abundance of genes related to the microbiome taxonomy and function, with effects varying by delivery mode. EBF alters the pattern of carbohydrates, lipid metabolism, and cell structure pathways depending on the delivery mode. The microbiome age is closer to chronological infant age in EBF than in non-EBF infants, meaning a lower microbiome maturation index (MMI). Using a complementary machine learning approach, we show that Escherichia coli, Ruminococcus gnavus, and Clostridium neonatale, as well as vitamin K and o-antigen pathways contribute strongly to EBF prediction. Moreover, EBF influences the microbiome maturation in early life, toward a microbiome age more similar to the chronological infant's age.

Psychiatric disorders are highly heritable and polygenic, influenced by environmental factors and often comorbid. Large-scale genome-wide association studies (GWASs) through consortium efforts have identified genetic risk loci and revealed the underlying biology of psychiatric disorders and traits. However, over 85% of psychiatric GWAS participants are of European ancestry, limiting the applicability of these findings to non-European populations. Latin America and the Caribbean, regions marked by diverse genetic admixture, distinct environments and healthcare disparities, remain critically understudied in psychiatric genomics. This threatens access to precision psychiatry, where diversity is crucial for innovation and equity. This Review evaluates the current state and advancements in psychiatric genomics within Latin America and the Caribbean, discusses the prevalence and burden of psychiatric disorders, explores contributions to psychiatric GWASs from these regions and highlights methods that account for genetic diversity. We also identify existing gaps and challenges and propose recommendations to promote equity in psychiatric genomics.

Duchenne and Becker Muscular Dystrophy are dystrophinopathies with a prevalence of 1:5000–6000 males, caused by pathogenic variants in DMD. These conditions are often accompanied by neurodevelopmental disorders (NDDs) like autism (ASD; ~20%) and intellectual disability (ID; ~30%). However, their low penetrance in dystrophinopathies suggests additional contributing factors. In our study, 83 individuals with dystrophinopathies were clinically evaluated and categorized based on ASD (36 individuals), ID risk (12 individuals), or controls (35 individuals). Exome sequencing analysis revealed an enrichment of risk de novo variants (DNVs) in ASD-DMD individuals (adjusted p value = 0.0356), with the number of DNVs correlating with paternal age (p value = 0.0133). Additionally, DMD-ASD individuals showed a higher average of rare risk variants (RRVs) compared to DMD-Controls (adjusted p value = 0.0285). Gene ontology analysis revealed an enrichment of extracellular matrix-related genes, especially collagens, and Ehlers-Danlos syndrome genes in ASD-DMD and DMD-ID groups. These findings support an oligogenic model for ASD in dystrophinopathies, highlighting the importance of investigating homogenized samples to elucidate ASD’s genetic architecture.

Baker–Gordon syndrome (BAGOS) is an autosomal dominant neurodevelopmental disorder caused by de novo heterozygous missense mutations in SYT1 . The precise pathogenic mechanism of BAGOS is still unclear, with preliminary data favoring a dominant‐negative effect, although a previous case presenting a reciprocal translocation disrupting SYT1 supports haploinsufficiency as a possible mechanism. We report a child with a syndromic neurodevelopmental disorder compatible with BAGOS and carrying a t(5; 12)(q31; q21) by G‐banded karyotype. Optical genome mapping (OGM) is based on ultrahigh molecular weight DNA molecules allowing the combined analyses of numerical and structural chromosome variants. The rearrangement was investigated using OGM, which revealed an additional structural variant, a paracentric inversion in the segment of Chromosome 12 translocated to der(5). The breakpoint of the paracentric inversion is mapped to Intron 9 of the SYT1 gene, interrupting the C2B domain. This is the second BAGOS case reported in the literature caused by SYT1 disruption, supporting that reduced amounts of functional SYT1, either by haploinsufficiency or dominant‐negative effect, is responsible for SYT1 ‐associated neurodevelopmental syndrome.