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Will, A.

Publications and source records attributed to Will, A..

4 recordsLinked to original sources

Mapping the endothelial O-GlcNAcome uncovers CCAR1 as a regulator of senescence

O-GlcNAcylation, the reversible addition of O-linked N-acetylglucosamine (O-GlcNAc) to serine and threonine residues, is a dynamic posttranslational modification that integrates nutrient and stress signals to fine-tune protein function and maintain cellular homeostasis. Although dysregulation of O-GlcNAc signaling is associated with age-related pathologies, its role in physiological aging remains unclear. Here we show that chronologically aged human vascular endothelial cells exhibit reduced O-GlcNAcylation due to altered abundance of enzymes in the hexosamine biosynthesis pathway and O-GlcNAc cycling. Conversely, the attenuation of O-GlcNAcylation achieved by genetic or pharmacological means, induced senescence via canonical p53/p21CIP1 and p16INK4a/Rb pathways and impaired key endothelial functions, such as proliferation and angiogenic capacity. Importantly, O-GlcNAcylated substrates identified across the entire proteome in endothelial cells closely aligned with these mechanistic and phenotypic findings. These substrates were enriched in regulators of processes central to senescence and vascular aging, such as genome stability, transcription, cell cycle, and methylation. Among these, we confirmed cell division cycle and apoptosis regulator 1 (CCAR1) as a bona fide O-GlcNAc substrate and demonstrate that its expression and O-GlcNAcylation decline during senescence in endothelial cells. CCAR1 depletion suppressed apoptosis and sensitized cells to oxidative stress-induced DNA damage, whereas restoration of CCAR1 levels mitigated premature and replicative senescence. Together, our findings establish O-GlcNAc signaling as a key regulatory system that integrates metabolic and stress cues to coordinate protein networks controlling genome stability, transcription and cellular stress adaptation, thereby preserving endothelial integrity and restraining senescence onset.

biochemistry↗

μPhos: a scalable and sensitive platform for functional phosphoproteomics

Mass spectrometry has revolutionized cell signaling research by vastly simplifying the identification and quantification of many thousands of phosphorylation sites in the human proteome. Defining the cellular response to internal or external perturbations in space and time is crucial for further illuminating functionality of the phosphoproteome. Here we describe {micro}Phos, an accessible phosphoproteomics platform that permits phosphopeptide enrichment from 96-well cell culture experiments in < 8 hours total processing time. By minimizing transfer steps and reducing liquid volumes to < 200 {micro}L, we demonstrate increased sensitivity, over 90% selectivity, and excellent quantitative reproducibility. Employing highly sensitive trapped ion mobility mass spectrometry, we quantify more than 20,000 unique phosphopeptides in a human cancer cell line using 20 {micro}g starting material, and confidently localize > 5,000 phosphorylation sites from 5 {micro}g. This depth covers key intracellular signaling pathways, rendering sample-limited applications and extensive perturbation experiments with hundreds of samples viable. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/535617v1_ufig1.gif" ALT="Figure 1"> View larger version (87K): org.highwire.dtl.DTLVardef@43d3e9org.highwire.dtl.DTLVardef@10d975forg.highwire.dtl.DTLVardef@14ce090org.highwire.dtl.DTLVardef@2b2e67_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

Peptide collision cross sections of 22 post-translational modifications

Recent advances have rekindled the interest in ion mobility spectrometry as an additional dimension of separation in mass spectrometry (MS)-based proteomics. It separates ions according to their size and shape in the gas phase. Here, we set out to investigate the effect of 22 different post-translational modifications (PTMs) on the collision cross section (CCS) of peptides. In total, we analyzed [~]4700 pairs of matching modified and unmodified peptide ions by trapped ion mobility spectrometry (TIMS). Linear alignment based on spike-in reference peptides resulted in highly reproducible CCS values with a median coefficient of variation of 0.3%. On a global level, we observed a redistribution in the m/z vs. ion mobility space for modified peptides upon changes in their charge state. Pairwise comparison between modified and unmodified peptides of the same charge state revealed median shifts in CCS between - 1.1% (lysine formylation) and +4.5% (O-GlcNAcylation). In general, increasing modified peptide masses were correlated with higher CCS values, in particular within homologous PTM series. However, investigating the ion populations in more detail, we found that the change in CCS can vary substantially for a given PTM depending on the gas phase structure of its unmodified counterpart. In conclusion, our study shows PTM- and sequence-specific effects on the cross section of peptides, which could be further leveraged for proteome-wide PTM analysis.

systems biology↗

A network of DZF proteins controls alternative splicing regulation and fidelity

Proteins containing DZF (domain associated with zinc fingers) modules play important roles throughout gene expression, from transcription to translation. Derived from nucleotidyltransferases but lacking catalytic residues, DZF domains serve as heterodimerization surfaces between DZF protein pairs. Three DZF proteins are widely expressed in mammalian tissues, ILF2, ILF3, and ZFR, which form mutually exclusive ILF2-ILF3 and ILF2-ZFR heterodimers. Using eCLIP-Seq, we find that ZFR binds across broad intronic regions to regulate the alternative splicing of cassette and mutually exclusive exons. ZFR preferentially binds dsRNA in vitro and is enriched on introns containing conserved dsRNA elements in cells. Many splicing events are similarly altered upon depletion of any of the three DZF proteins; however, we also identify independent and opposing roles for ZFR and ILF3 in alternative splicing regulation. Along with widespread involvement in cassette exon splicing, the DZF proteins control the fidelity and regulation of over a dozen highly validated mutually exclusive splicing events. Our findings indicate that the DZF proteins form a complex regulatory network that leverages dsRNA binding by ILF3 and ZFR to modulate splicing regulation and fidelity.

molecular biology↗