Aida Kamalian (Baltimore, MD / US), Polina Shichkova (Schlieren / CH), Marco Tognetti (Schlieren / CH), Sara Ho (Baltimore, MD / US), Christopher Below (Schlieren / CH), Roland Bruderer (Schlieren / CH), Yuehan Feng (Schlieren / CH), Lukas Reiter (Schlieren / CH), Michael Lutz (Durham, NC / US), Abhay Moghekar (Baltimore, MD / US)
Aging is the leading risk factor for many neurodegenerative disorders [1]. However, the transition between healthy and diseased state in advanced age is poorly understood. Furthermore, neurodegeneration related changes are present in the brain years before the symptoms' onset [2]. To elucidate potential early signs of degeneration-related changes in healthy aging, we aimed to find differential cleavage, alternative splicing and phosphorylation events in aging CSF and plasma of cognitively normal adults. To this end, we applied data-independent acquisition mass spectrometry (DIA-MS) with Biognosys" TrueDiscovery Ultra Deep offering and analysed raw data using Spectronaut® software.
We quantified 5599 and 3112 protein groups, and 127560 and 94415 peptides in CSF and plasma respectively. We performed differential abundance analysis at both peptide and protein levels. Then we applied a strict filtering for contribution of technical factors and found 27 genes with potential differential cleavage and alternative splicing events in CSF, including well-known APOE, APP and APLP1 among others. Proteins of these genes are not among significantly differentially abundant. About half of these genes are among aging and longevity associated genes and about half (with intersection of 6 genes) are known to have more than one transcript. Plasma data appeared to be noisier with no genes passing the same strict criteria as for CSF.
In the second part of this work, we compared fold changes of peptide abundances in aging for phosphorylated and non-phosphorylated peptides. This way, we found differentially phosphorylated proteins of 32 genes in CSF data. About one third of these genes are known as related to aging and longevity. Protein phosphorylation plays important regulatory role and is known as being affected by aging.
To sum up, in this work we focused on the peptide differential abundance to perform large-scale analysis of protein cleavage, splicing and phosphorylation changes in aging. We found differential cleavage, potential alternative splicing and phosphorylation both known aging and neurodegeneration associated genes as well as novel genes for which association with aging and neurodegeneration has not yet been established.
References:
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