Search bioRxiv⌕ Search

Biology subjects

Tremblay, A.

Publications and source records attributed to Tremblay, A..

3 recordsLinked to original sources

Compromised striatal structure and function in mouse models of RARB-related disorder

Dominant variants in the retinoic acid receptor beta (RARB) gene cause a complex disorder known as RARB-related disorder (RARB-RD), characterized by multiple congenital anomalies, global developmental delay, and dystonia. RARB-RD variants have been classified as either gain-of-function (GOF) or dominant-negative (DN) based on their cell-based transcriptional responses to retinoids. To investigate the mechanisms underlying this disorder, we generated mouse models carrying either the p.R387C or p.L402P RARB-RD variant, previously categorized as GOF and DN, respectively. Homozygous mice for either RARB-RD variant died perinatally with colonic aganglionosis, while heterozygous mice survived and recapitulated several features of RARB-RD. In addition to microphthalmia, both RarbR387C/+and RarbL402P/+ mice exhibited progressive coordination deficits, increased active-phase locomotor activity, and cognitive impairment in the novel object recognition test. In contrast, mice heterozygous for a null allele of Rarb (Rarb+/-) did not display these abnormalities. In the brain, Rarb is predominantly expressed in the two major populations of projection neurons of the striatum recognizable by the expression of dopamine receptors D1R/Drd1 and D2R/Drd2. Marker analysis revealed a reduction in Drd2-expressing neurons without changes in Drd1-expressing neurons in both RARB-RD models. Furthermore, RARB-RD mice showed partial resistance to the cataleptic effects of haloperidol, a D2R-specific antagonist. These behavioral, cellular, and dopaminergic deficits--though not the cognitive impairments--have previously been observed in Rarb-/- mice. To determine whether the in vitro effects of RARB-RD variants correlate with distinct transcriptional signatures in vivo, we compared the striatal transcriptome of RarbR387C/+, RarbL402P/+, Rarb-/- and Rarb+/-mice with their littermate controls. We found that the heterozygous RARB-RD variants and the homozygous null allele affected a large subset of common genes, with putative direct RARB targets predominantly downregulated. Notably, the transcriptional impact of the RARB-RD variants was more profound than that of the null allele, regardless of zygosity. Additionally, transcriptional changes in RARB-RD mice extensively overlapped with those observed in mouse models of Huntingtons disease, suggesting shared mechanisms affecting neuronal survival in the striatum. We conclude that the p.R387C and p.L402P variants similarly compromise striatal integrity and function, likely through a DN mechanism. Progressive emergence of most neurologic deficits highlights a potential therapeutic window. Our results support the development of strategies aimed at silencing RARB-RD alleles.

neuroscience↗

Understanding systems level metabolic adaptation resulting from osmotic stress

An organisms survival hinges on maintaining the right thermodynamic conditions. Osmotic constraints limit the concentration range of metabolites, affecting essential cellular pathways. Despite extensive research on osmotic stress and growth, understanding remains limited, especially in hypo-osmotic environments. To delve into this, we developed a novel modeling approach that considers metabolic fluxes and metabolite concentrations along with thermodynamics. Our analysis of E. coli adaptation reveals insights into growth rates, metabolic pathways, and thermodynamic bottlenecks during transitions between hypo- and hyper-osmotic conditions. Both experimental and computational findings show that cells prioritize pathways that have higher thermodynamic driving force, like the pentose phosphate or the Entner-Doudoroff pathway, under low osmolarity. This work offers a systematic and mechanistic explanation for reduced growth rates in hypo- and hyper-osmotic conditions. The developed framework is the first of its kind to incorporate genome wide constraints that consider both natural logarithm and actual metabolite concentrations. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/585265v2_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@193001dorg.highwire.dtl.DTLVardef@1ec76e1org.highwire.dtl.DTLVardef@170c554org.highwire.dtl.DTLVardef@ab4f29_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

Newfound coding potential of transcripts unveils missing members of human protein communities

Recent proteogenomic approaches have led to the discovery that regions of the transcriptome previously annotated as non-coding regions (i.e. UTRs, open reading frames overlapping annotated coding sequences in a different reading frame, and non-coding RNAs) frequently encode proteins (termed alternative proteins). This suggests that previously identified protein-protein interaction networks are partially incomplete since alternative proteins are not present in conventional protein databases. Here we used the proteogenomic resource OpenProt and a combined spectrum- and peptide-centric analysis for the re-analysis of a high throughput human network proteomics dataset thereby revealing the presence of 280 alternative proteins in the network. We found 19 genes encoding both an annotated (reference) and an alternative protein interacting with each other. Of the 136 alternative proteins encoded by pseudogenes, 38 are direct interactors of reference proteins encoded by their respective parental gene. Finally, we experimentally validate several interactions involving alternative proteins. These data improve the blueprints of the human protein-protein interaction network and suggest functional roles for hundreds of alternative proteins.

systems biology↗