Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify

摘要: Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This especially the case for proteins that differ structurally between disease control conditions. As tumor development associated with aberrant splicing, we focus on this rich source cancer specific To end, developed proteogenomic pipeline, Splicify, which can detect differentially expressed isoforms. Splicify based integrating RNA massive parallel sequencing data tandem mass spectrometry to identify isoforms resulting from differential splicing two Proof concept was obtained by applying colorectal cell line SW480, before after siRNA-mediated downmodulation factors SF3B1 SRSF1. These analyses revealed 2172 149 isoforms, respectively, peptide confirmation upon knock-down SRSF1 compared their controls. Splice variants identified included RAC1, OSBPL3, MKI67, SYK. One additional sample analyzed PacBio Iso-Seq full-length transcript downmodulation. analysis verified alternative in addition events were not represented human reference genome annotation. Therefore, offers validated pipeline identification biomarkers mRNA splicing. publicly available GitHub (https://github.com/NKI-TGO/SPLICIFY) suitable address basic research questions using pre-clinical model systems as well translational patient-derived samples, e.g. allowing clinically relevant