Manuscript abstract: "Multiple genetic association studies have correlated a common allelic block linked to the BAG3 gene with a decreased incidence of heart failure, but the molecular mechanism for such protection remains elusive. One of the variants in this allele block is coding, changing cysteine to arginine at position 151 of BAG3 (rs2234962-BAG3C151R). Here, we use induced pluripotent stem cells (iPSC) to test if the BAG3C151R variant alters protein and cellular function in human cardiac myocytes. Quantitative protein interaction network analysis identified specific changes in BAG3C151R protein interaction partners in cardiomyocytes but not in iPSCs or an immortalized cell line. Knockdown of BAG3 interacting factors in cardiomyocytes followed by myofibrillar analysis revealed that BAG3C151R associates more strongly with proteins involved in the maintenance of myofibrillar integrity. Finally, we demonstrate that cardiomyocytes expressing the BAG3C151R variant have improved response to proteotoxic stress in an allele dose-dependent manner. This study suggests that the BAG3C151R variant increases cardiomyocyte protection from stress by enhancing the recruitment of factors critical to the maintenance of myofibril integrity, hinting that this variant could be responsible for the cardioprotective effect of the haplotype block. By revealing specific changes in preferential binding partners of the BAG3C151R protein variant, we also identify potential targets for the development of novel cardioprotective therapies."

Samples from affinity purification in iPS-CM samples were prepared and analyzed on using unbiased proteomics (see Methods Section: "Immunoprecipitation of iPS/iPS-CM samples and unbiased proteomics analysis"; raw data uploaded to PRIDE). Then, a pooled sample was used to get a deep characterization in 15 fractions (see data), as a way to obtain enough peptides for all the proteins that were deemed interesting. Then selected peptides for selected proteins were used for a Parallel Reaction Monitoring analysis (prepared as in Mehods Section: "Targeted proteomics follow-up of iPS-CM APMS high confidence protein-protein interactions").

Samples were obtained from performing affinity purification in induced pluripotent stem (iPS)-derived cardiomyocytes. This dataset contains the results from Parallel Reaction Monitoring analysis of selected peptides. A skyline file with the characterization used to build the sample library for PRM analysis is also included. See manuscript for full details. (NOTE: sample "part1K22_1-OLD.raw" belongs to an older run and should be dismissed for analyses)