Biology subjects

Belmadani, M.

Publications and source records attributed to Belmadani, M..

7 recordsLinked to original sources

bioRxiv2025

Loss of brain insulin production impairs learning and memory in female mice

Diabetes is characterized by dysfunctional insulin release and action, and it is a risk factor for Alzheimers disease, the most common form of dementia. Alterations in brain insulin signalling and metabolism have been linked with Alzheimers disease. The ancestral insulin gene, Ins2, is transcribed locally within the brain. Here we demonstrate that hippocampal Ins2 mRNA is higher in females than males, and modulated by diet. To specifically determine how locally-produced insulin influences hippocampal function, we used mice with germline Ins2 knockout (Ins2-/-) and the normal complement of wildtype Ins1 alleles. Compensation from the Ins1 gene ensured normal glucose tolerance, normal insulin sensitivity, normal fasting insulin, and normal body weight under these conditions. Using the Morris water maze, we found that visuo-spatial learning and memory performance of female Ins2-/- mice was significantly impaired relative to wild-type mice, whereas the performance of male Ins2-/- and wild-type mice did not differ. We profiled isolated hippocampi from female Ins2-/- and littermate control mice using RNA sequencing to provide an unbiased analysis of gene expression differences that underlie these behavioural changes. Cyclin D1 (Ccnd1) was significantly reduced in Ins2-/- mice, prompting us to examine adult neurogenesis using exogenous mitotic marker EdU and the immature neuronal marker doublecortin (DCX). Our data demonstrate female-specific roles for brain-derived Ins2 on learning and memory function in mice. Research in contextO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIAlzheimers disease and type 2 diabetes share common risk factors and metabolic dysfunction. C_LIO_LIInsulin and insulin signalling are known to have positive effects on neuronal health and cognition. C_LIO_LILocal insulin production has been reported in the brain, including the hippocampus, which plays critical roles in learning and memory, as well as Alzheimers pathophysiology. C_LI What is the key question?O_LIWhat are the consequences of deleting the Ins2 gene, which selectively prevents local brain insulin production, on learning and memory in mice? C_LI What are the new findings?O_LIHippocampal insulin production via the Ins2 gene is sexually dimorphic and modulated by diet. C_LIO_LIKnocking out brain insulin production in Ins2-/- mice does not have significant effects on glucose homeostasis in these diet and housing conditions. C_LIO_LIKnocking out brain insulin production in Ins2-/- mice results in learning and memory impairments in female but not male mice. C_LI How might this impact on clinical practice in the foreseeable future?O_LIThese pre-clinical observations demonstrate a causal role for insulin in learning and memory, but will require additional human studies before they can impact clinical practice. C_LI

physiology↗

bioRxiv2022

Cataloging the potential functional diversity of Cacna1e splice variants using long-read sequencing

Voltage gated calcium channels (VGCCs) regulate the influx of calcium ions in many cell types, but our lack of knowledge about the plethora of VGCC splice variants remains a gap in our understanding of calcium channel function. A recent advance in profiling gene splice variation is to use long-read RNA-sequencing technology. We sequenced Cacna1e transcripts from the rat thalamus using Oxford Nanopore sequencing, yielding the full structure of 2,110 Cacna1e splice variants. However, we observed that only 154 Cacna1e splice variants were likely to encode for a functional VGCC based on predicted amino acid sequences. We then computationally prioritized these 154 splice variants using expression and evolutionary conservation and found that four splice variants are candidate functionally distinct splice isoforms. Our work not only provides long-read sequencing of Cacna1e for the first time, but also the first computational evaluation of which Cacna1e splice variants are the best candidates for future follow-up. SIGNIFICANCE STATEMENTVoltage gated calcium channels (Cacna1x genes) are implicated in many neurological disorders and their encoding genes are predicted to have complex patterns of alternative splicing. Previous approaches relied on short-read RNA-seq to characterize calcium channel splice variants. Here, we use long-read nanopore sequencing to establish a set of Cacna1e transcripts in the rat thalamus and use computational methods to prioritize four transcripts as functionally distinct splice isoforms. Our work to provide the field with prioritized transcripts will not only improve our understanding of Cacna1e function but its role in disease as well.

neuroscience↗

bioRxiv2020

Curation of over 10,000 transcriptomic studies to enable data reuse

Vast amounts of transcriptomic data reside in public repositories, but effective reuse remains challenging. Issues include unstructured dataset metadata, inconsistent data processing and quality control, and inconsistent probe-gene mappings across microarray technologies. Thus, extensive curation and data reprocessing is necessary prior to any reuse. The Gemma bioinformatics system was created to help address these issues. Gemma consists of a database of curated transcriptomic datasets, analytical software, a web interface, and web services. Here we present an update on Gemmas holdings, data processing and analysis pipelines, our curation guidelines, and software features. As of June 2020, Gemma contains 10,811 manually curated datasets (primarily human, mouse, and rat), over 395,000 samples and hundreds of curated transcriptomic platforms (both microarray and RNA-sequencing). Dataset topics were represented with 10,215 distinct terms from 12 ontologies, for a total of 54,316 topic annotations (mean topics/dataset = 5.2). While Gemma has broad coverage of conditions and tissues, it captures a large majority of available brain-related datasets, accounting for 34% of its holdings. Users can access the curated data and differential expression analyses through the Gemma website, RESTful service, and an R package. Database URL: https://gemma.msl.ubc.ca/home.html

bioinformatics↗

bioRxiv2019

Multi-model functionalization of disease-associated PTEN missense mutations identifies multiple molecular mechanisms underlying protein dysfunction

Functional variomics provides the foundation for personalized medicine by linking genetic variation to disease expression, outcome and treatment, yet its utility is dependent on appropriate assays to evaluate mutation impact on protein function. To fully assess the effects of 106 missense and nonsense variants of PTEN associated with autism spectrum disorder, somatic cancer and PHTS, we take a deep phenotypic profiling approach using 18 assays in 5 model systems spanning diverse cellular environments ranging from molecular function to neuronal morphogenesis and behavior. Variants inducing instability occurred across the protein, resulting in partial to complete loss of function (LoF), which was well correlated across models. However, assays were selectively sensitive to variants located in substrate binding and catalytic domains, which exhibited complete LoF or dominant negativity independent of effects on stability. Our results indicate that full characterization of variant impact requires assays sensitive to instability and a range of protein functions.

genetics↗

bioRxiv2019

Systematic phenomics analysis of ASD-associated genes reveals shared functions and parallel networks underlying reversible impairments in habituation learning

A major challenge facing the genetics of Autism Spectrum Disorders (ASD) is the large and growing number of candidate risk genes and gene variants of unknown functional significance. Here, we used Caenorhabditis elegans to systematically functionally characterize ASD-associated genes in vivo. Using our custom machine vision system we quantified 26 phenotypes spanning morphology, locomotion, tactile sensitivity, and habituation learning in 87 strains each carrying a mutation in an ortholog of an ASD-associated gene. We identified hundreds of novel genotype-phenotype relationships ranging from severe developmental delays and uncoordinated movement to subtle deficits in sensory and learning behaviors. We clustered genes by similarity in phenomic profiles and used epistasis analysis to discover parallel networks centered on CHD8*chd-7 and NLGN3*nlg-1 that underlie mechanosensory hyper-responsivity and impaired habituation learning. We then leveraged our data for in vivo functional assays to gauge missense variant effect. Expression of wild-type NLG-1 in nlg-1 mutant C. elegans rescued their sensory and learning impairments. Testing the rescuing ability of all conserved ASD-associated neuroligin variants revealed varied partial loss-of-function despite proper subcellular localization. Finally, we used CRISPR-Cas9 auxin inducible degradation to determine that phenotypic abnormalities caused by developmental loss of NLG-1 can be reversed by adult expression. This work charts the phenotypic landscape of ASD-associated genes, offers novel in vivo variant functional assays, and potential therapeutic targets for ASD.

neuroscience↗

bioRxiv2019

VariCarta: a comprehensive database of harmonized genomic variants found in ASD sequencing studies

BackgroundRecent years has seen a boom in the application of the next-generation sequencing technology to the study of human diseases, including Autism Spectrum Disorder (ASD), where the focus has been on identifying rare, possibly causative genomic variants in ASD individuals. Because of the high genetic heterogeneity of ASD, a large number of subjects is needed to establish evidence for a variant or gene ASD-association, thus aggregating data across cohorts and studies is necessary. However, methodological inconsistencies and subject overlap across studies complicate data aggregation.\n\nDescriptionHere we present VariCarta, a web-based database developed to address these challenges by collecting, reconciling and consistently cataloguing literature-derived genomic variants found in ASD subjects using ongoing semi-manual curation. The careful manual curation combined with a robust data import pipeline rectifies errors, converts variants into a standardized format, identifies and harmonizes cohort overlaps and documents data provenance. The harmonization aspect is especially important since it prevents the potential double-counting of variants which can lead to inflation of gene-based evidence for ASD-association.\n\nConclusionVariCarta is the largest collection of systematically curated, harmonized and comprehensively annotated literature-derived ASD-associated variants. The database currently contains 35,615 variant events from 8,044 subjects, collected across 50 publications, and reconciles 6,057 variants that have been reported in literature multiple times. VariCarta is freely accessible at http://varicarta.msl.ubc.ca.

genomics↗

bioRxiv2018

Data-driven approaches for improving the interpretability of patch-seq data

Patch-seq, enabling simultaneous measurement of a transcriptomic, electrophysiological, and morphological features, has recently emerged as a powerful tool for neuronal characterization. However, we show the method is susceptible to technical artifacts, including the presence of mRNA contaminants from multiple cells, that limit the interpretability of the data. We present a straightforward marker gene-based approach for controlling for these artifacts and show that our method improves the correspondence between gene expression and electrophysiological features.

neuroscience↗