Biology subjects

Almeida, V.

Publications and source records attributed to Almeida, V..

3 recordsLinked to original sources

bioRxiv2024

Genetic ablation of the DNA demethylation pathway in retinal progenitor cells impairs photoreceptor development and function, leading to retinal dystrophy

Rod and cone photoreceptors are critical for vision, and their loss leads to blindness. Photoreceptors are epigenetically unique, because the promoters of the genes required for the development and function of these neurons are hypermethylated in retinal progenitor cells (RPCs) and hypomethylated in photoreceptors. However, the mechanism responsible for DNA demethylation during the differentiation of RPCs into photoreceptors and its role in photoreceptor development and function were unknown. We hypothesized that the Ten-Eleven Translocation (TET) family of dioxygenases plays a key role in this mechanism. To this end, we knocked out all TET genes in RPCs and characterized the TET-deficient and control retinas using various approaches including electron microscopy, electroretinogram (ERG) tests, RNA-seq, whole genome bisulfite sequencing (WGBS), and 5hmC-Seal. We found that genetic ablation of the TET family prevents demethylation of the promoters of genes essential for rod specification and for rod and cone maturation during the differentiation of RPCs into photoreceptors. Preservation of methylated cytosines in the promoters of these genes significantly reduced their expression, which was confirmed by western blot analysis. This impaired expression leads to the underdevelopment or complete absence of outer segments and synaptic termini in the photoreceptors of TET-deficient retinas, which results in loss of rod and cone function, as assayed by ERG. These function-deprived, underdeveloped photoreceptors die over time, which leads to blindness.

neuroscience↗

bioRxiv2024

Polygenic risk for schizophrenia converges on alternative polyadenylation as molecular mechanism underlying synaptic impairment

Schizophrenia (SCZ) is a genetically heterogenous psychiatric disorder of highly polygenic nature. Correlative evidence from genetic studies indicate that the aggregated effects of distinct genetic risk factor combinations found in each patient converge onto common molecular mechanisms. To prove this on a functional level, we employed a reductionistic cellular model system for polygenic risk by differentiating induced pluripotent stem cells (iPSCs) from 104 individuals with high polygenic risk load and controls into cortical glutamatergic neurons (iNs). Multi-omics profiling identified widespread differences in alternative polyadenylation (APA) in the 3 untranslated region of many synaptic transcripts between iNs from SCZ patients and healthy donors. On the cellular level, 3APA was associated with a reduction in synaptic density of iNs. Importantly, differential APA was largely conserved between postmortem human prefrontal cortex from SCZ patients and healthy donors, and strongly enriched for transcripts related to synapse biology. 3APA was highly correlated with SCZ polygenic risk and affected genes were significantly enriched for SCZ associated common genetic variation. Integrative functional genomic analysis identified the RNA binding protein and SCZ GWAS risk gene PTBP2 as a critical trans-acting factor mediating 3APA of synaptic genes in SCZ subjects. Functional characterization of PTBP2 in iNs confirmed its key role in 3APA of synaptic transcripts and regulation of synapse density. Jointly, our findings show that the aggregated effects of polygenic risk converge on 3APA as one common molecular mechanism that underlies synaptic impairments in SCZ.

neuroscience↗

bioRxiv2023

Cannabidiol administration reduces the expression of genes involved in mitochondrial electron transport chain and ribosome biogenesis in mice CA1 neurons

BackgroundCannabidiol (CBD), one of the main cannabinoids present in the female flowers of Cannabis sativa, has been a therapeutic alternative for a plurality of disorders. Previous investigation has already provided insights into the CBD molecular mechanism, however, there is no transcriptome data for CBD effects on hippocampal subfields. Here, we explore the transcriptomic changes in dorsal and ventral CA1 of adult mice hippocampus after 100 mg/kg of CBD administration (i.p.) for one or seven consecutive days. MethodsC57BL/6JUnib mice were divided into 4 groups treated with either vehicle or CBD for 1 or 7 days. The collected brains were sectioned and the hippocampal subregions were laser microdissected for RNA-Seq analysis. Data alignment, quantification and analysis were conducted with the STAR Aligner/DESeq2/clusterProfiler R-package pipeline. ResultsWe found changes in gene expression in CA1 neurons after single and multiple CBD administrations. Furthermore, the enrichment analysis of differentially expressed genes following 7 days of CBD administration indicates a widespread decrease in the expression levels of electron transport chain and ribosome biogenesis transcripts, while chromatin modifications and synapse organization transcripts were increased. ConclusionThis dataset provides a significant contribution toward advancing our comprehension of the mechanisms responsible for CBD effects on hippocampal neurons. The findings suggest that CBD prompts a significant reduction in energy metabolism genes and the protein translation machinery in CA1 neurons. SIGNIFICANT OUTCOMESWe identified distinct changes in gene expression of CA1 neurons following both single and multiple administrations of CBD. This highlights the molecular impact of CBD on hippocampal neurons and expands our understanding of its mechanisms of action. We revealed that repeated CBD administration led to a greater number of gene expression alterations compared to a single administration, emphasizing the importance of treatment frequency in modulating gene expression. We found that daily CBD administration for seven days resulted in the downregulation of genes related to energy metabolism and protein synthesis/degradation, while genes involved in chromatin regulation and synapse organization were upregulated. These specific gene expression changes shed light on potential cellular effects and molecular mechanisms underlying CBDs actions in the hippocampus. LIMITATIONSOne limitation of this study is its reliance on animal models, specifically C57BL/6JUnib mice, which may not fully reflect human responses to CBD. Additionally, the study primarily investigated the effects of CBD under healthy conditions and did not directly address its therapeutic effects for specific disorders or conditions. Thus, the clinical relevance and applicability of the findings to therapeutic interventions remain to be determined.

neuroscience↗