Biology subjects

Diwan, G.

Publications and source records attributed to Diwan, G..

3 recordsLinked to original sources

bioRxiv2024

PROTEORIZER: A holistic approach to untangle functional consequences of variants of unknown significance.

Most in silico tools only use data closely related to the gene-of-interest or initial research question. This gene-focused research is prone to ignoring low-count and rare variants in the same or similar genes, even if available informational could be sufficient to deduce functional consequences by combining knowledge from many similar genes. Proteorizer is a web tool that aims to bridge the gap between protein-centric knowledge and the functional context this knowledge creates. We use curated and reviewed data from UniProt to collect available residue information for the queried protein as well as orthologs. By defining functional clusters based on intramolecular distances of residues with available functional information it is possible to use these to extrapolate the effect of a VUS solely based on known functions of nearby residues, hence contextualizing the variant with pre-existing knowledge. We show that pathogenic variants are more likely to be a part of functional hotspots and present several case studies (ALPP p.Ser244Gly, CANT1 p.Ile171Phe, ARL3 p.Tyr90Cys, IL6R p.His280Pro and RAF1 p.Ser259Ala) to highlight the applicability and usefulness of this approach. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/603688v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@a1d75forg.highwire.dtl.DTLVardef@142c339org.highwire.dtl.DTLVardef@1f1161org.highwire.dtl.DTLVardef@1adfe85_HPS_FORMAT_FIGEXP M_FIG C_FIG Proteorizer is an explorative tool that takes variants from laboratory or clinical settings and contextualizes the variants based on prior information from the protein of interest and similar proteins according to where these functional positions are located in the 3D structure of the protein of interest.

bioinformatics↗

bioRxiv2024

Eukaryotic Elongation Factor 2 Kinase EFK-1/eEF2K promotes starvation resistance by preventing oxidative damage in C. elegans

Cells and organisms frequently experience starvation. To adapt and survive, they mount an evolutionarily conserved stress response. A vital component in the mammalian starvation response is eukaryotic elongation factor 2 (eEF2) kinase (eEF2K), which responds to starvation by phosphorylating and inactivating the translation elongation driver eEF2, thus shutting down translation and facilitating survival. C. elegans efk-1/eEF2K phosphorylates EEF-2/eEF2 on a conserved residue and is required for starvation survival, but how it promotes survival remains unclear. Surprisingly, we found that eEF2 phosphorylation is unchanged in starved C. elegans, suggesting that efk-1 promotes survival via a noncanonical pathway. We show that efk-1 upregulates transcription of the DNA repair pathways, nucleotide excision repair (NER) and base excision repair (BER), to promote starvation survival. Furthermore, efk-1 suppresses oxygen consumption and ROS production in starvation to prevent oxidative stress. Thus, efk-1 enables starvation survival by protecting animals from starvation-induced oxidative damage through a translation-independent pathway.

genetics↗

bioRxiv2023

De-suppression of mesenchymal cell identities and variable phenotypic outcomes associated with knockout of Bbs1.

Bardet-Biedl syndrome (BBS) is an archetypal ciliopathy caused by dysfunction of primary cilia. BBS affects multiple tissues, including the kidney, eye and hypothalamic satiety response. Understanding pan-tissue mechanisms of pathogenesis versus those which are tissue specific, and gauging their associated inter-individual variation owing to genetic background and stochastic processes, is of paramount importance in syndromology. The BBSome is a membrane trafficking and intraflagellar transport (IFT) adaptor protein complex formed by 8 BBS proteins, including BBS1, which is the most commonly mutated gene in BBS. To investigate disease pathogenesis we generated a series of clonal renal collecting duct IMCD3 cell lines carrying defined biallelic nonsense or frameshift mutations in Bbs1, as well as a panel of matching wild-type CRISPR control clones. Using a phenotypic screen and an unbiased multi-omics approach we note significant clonal variability for all assays, emphasising the importance of analysing panels of genetically-defined clones. Our results suggest that BBS1 is required for suppression of mesenchymal cell identities as IMCD3 cell passage number increases. This was associated with a failure to express epithelial cell markers and tight junction formation, which was variable amongst clones. Transcriptomic analysis of hypothalamic preparations from BBS mutant mice, and BBS patient fibroblasts, suggested that dysregulation of epithelial-to-mesenchymal transition (EMT) genes is a general predisposing feature of BBS across tissues. Collectively this work suggests that the dynamic stability of the BBSome is essential for suppression of mesenchymal cell identities as epithelial cells differentiate.

genetics↗