Biology subjects

Gaun, A.

Publications and source records attributed to Gaun, A..

5 recordsLinked to original sources

bioRxiv2026

Site-specific combinatorial ubiquitination drives the targeted degradation of plasma membrane proteins

Cullin-RING E3 ligases (CRLs) ubiquitinate their substrates by recruiting them to complexes containing ubiquitin-conjugating enzymes (UCEs). Ubiquitination proceeds through the transfer of ubiquitin from UCEs to substrate lysines, but the specificity of lysine ubiquitination has not been widely investigated in cells. In this study, we use global ubiquitination profiling to identify sites in the kinase domains of receptor tyrosine kinases (RTKs), EGFR and Her2, that undergo CRL-mediated ubiquitination in cells treated with heterobifunctional degrader molecules. We find that VHL- and Cereblon-dependent degraders trigger the ubiquitination of a common subset of accessible lysines. Using mutagenesis, we show that the number of available ubiquitination sites specifies the extent of RTK degradation. Furthermore, introduction of non-native sites mostly fails to rescue clearance of lysine-deficient RTK mutants. These results highlight the specificity with which UCEs ubiquitinate their substrates and suggest that the ubiquitination of multiple sites governs the efficacy of degraders targeting plasma membrane proteins.

cell biology↗

bioRxiv2026

A multiomic lifespan signature in genetically diverse, diet-restricted mice

Dietary restriction extends lifespan across model organisms, but the plasma molecular changes mediating this effect remain incompletely characterized. We present a longitudinal multiomic analysis of 2,234 plasma samples from 960 Diversity Outbred mice subjected to intermittent fasting or caloric restriction and followed to natural death. Using mass spectrometry, we quantified 1,512 metabolites, lipids, and proteins and mapped their associations with diet, age and longevity. DR-induced molecular changes scale with caloric intake and modulate inflammatory, lipid catabolism, and oxidative stress pathways. Aging showed a biphasic signature with sharp acceleration beyond 85% of lifespan, demarcating terminal decline. Mediation and survival modeling both identified superoxide dismutase (SODE) and vascular cell adhesion molecule (VCAM1) as top lifespan predictors. Genetic analysis revealed 9,599 QTL, nine of which coincided with previously identified lifespan QTLs, and were largely related to immune regulation. These findings provide a rich multiomic and genetic resource for the aging research community.

systems biology↗

bioRxiv2025

Platform-dependent effects of genetic variants on plasma APOL1 and their implications for kidney disease

Mutations in apolipoprotein L1 (APOL1) are strongly associated with protection against parasitic infections and increased risk of kidney disease in individuals of African ancestry. To better understand the mechanisms underlying APOL1-related pathologies, we examined genetic drivers of circulating APOL1 in individuals of African and European ancestry from four independent cohorts (UK Biobank, AASK, deCODE, and Health ABC) using three proteomic technologies (Olink, SomaLogic, and mass spectrometry). We found that disease-associated APOL1 G1 and G2 variants are strong cis-pQTLs for plasma APOL1 measured by Olink and SomaLogic, but not mass spectrometry. Critically, the direction of variant effects differed between proteomic platforms, being positive with Olink and negative with SomaLogic. We identified an additional APOL1 missense variant (rs2239785), common in Europeans, exhibiting the same platform-dependent directional discrepancy. Furthermore, variants in the kallikrein-kinin system (KKS), involving KLKB1, F12, and KNG1, and their genetic interactions showed strong trans-pQTL effects on APOL1 measured by Olink, but not SomaLogic. These platform-dependent discrepancies raise the possibility that both intrinsic APOL1 mutations and extrinsic KKS activity induce conformational changes in the APOL1 protein that are differentially recognized by the proteomic platforms.

genetics↗

bioRxiv2024

Automated preparation of plasma lipids, metabolites, and proteins for LC/MS-based analysis of a high-fat diet in mice

Blood plasma is one of the most commonly analyzed and easily accessible biological samples. Here, we describe an automated liquid-liquid extraction (LLE) platform that generates accurate, precise, and reproducible samples for metabolomic, lipidomic, and proteomic analyses from a single aliquot of plasma while minimizing hands-on time and avoiding contamination from plasticware. We applied mass spectrometry to examine the metabolome, lipidome, and proteome of 90 plasma samples to determine the effects of age, time of day, and a high-fat diet in mice. From 25 L of mouse plasma, we identified 907 lipid species from 16 different lipid classes and subclasses, 233 polar metabolites, and 344 proteins. We found that the high-fat diet induced only mild changes in the polar metabolome, upregulated Apolipoproteins, and induced substantial shifts in the lipidome, including a significant increase in arachidonic acid (AA) and a decrease in eicosapentaenoic acid (EPA) content across all lipid classes.

physiology↗

bioRxiv2020

Precise Estimation of In Vivo Protein Turnover Rates

Isotopic labeling with deuterium oxide (D2O) is a common technique for estimating in vivo protein turnover, but its use has been limited by two long-standing problems: (1) identifying non-monoisotopic peptides; and (2) estimating protein turnover rates in the presence of dynamic amino acid enrichment. In this paper, we present a novel experimental and analytical framework for solving these two problems. Peptides with high probabilities of labeling in many amino acids present fragmentation spectra that frequently do not match the theoretical spectra used in standard identification algorithms. We resolve this difficulty using a modified search algorithm we call Conditional Ion Distribution Search (CIDS). Increased identifications from CIDS along with direct measurement of amino acid enrichment and statistical modeling that accounts for heterogeneous information across peptides, dramatically improves the accuracy and precision of half-life estimates. We benchmark the approach in cells, where near-complete labeling is possible, and conduct an in vivo experiment revealing, for the first time, differences in protein turnover between mice and naked mole-rats commensurate with their disparate longevity.

bioinformatics↗