Splicify – a proteogenomic pipeline to detect differentially expressed protein isoforms based on integrating RNA-Seq and Mass Spec data

Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, we focus on this rich source of cancer specific biomarkers.

To this end, researchers at the Netherlands Cancer Institute developed a proteogenomic pipeline, Splicify, which is able to detect differentially expressed protein isoforms. Splicify is based on integrating RNA massive parallel sequencing data and tandem mass spectrometry proteomics data to identify protein isoforms resulting from differential splicing between two conditions. Proof of concept was obtained by applying Splicify to RNA sequencing and mass spectrometry data obtained from colorectal cancer cell line SW480, before and after siRNA-mediated down-modulation of the splicing factors SF3B1 and SRSF1. These analyses revealed 2172 and 149 differentially expressed isoforms, respectively, with peptide confirmation upon knock-down of SF3B1 and SRSF1 compared to their controls. Splice variants identified included RAC1, OSBPL3, MKI67 and SYK. One additional sample was analyzed by PacBio Iso-Seq full-length transcript sequencing after SF3B1 down-modulation. This analysis verified the alternative splicing identified by Splicify and in addition identified novel splicing events that were not represented in the human reference genome annotation. Therefore, Splicify offers a validated proteogenomic data analysis pipeline for identification of disease specific protein biomarkers resulting from mRNA alternative splicing.

Splicify, the proteogenomic pipeline for identification of differential splice variants

rna-seq
A The schematic overview of the Splicify data analysis. Within Splicify RNA-seq data analysis is performed by combining exemplar open-source RNA-seq analysis software, including quality and adapter trimming with Trimmomatic (36), readsmapping with STAR (38), differential splicing analysis with rMATS (37), where differential splice variants on RNA level are identified. These splice variants undergo 3-frame translation into potential protein isoform sequence database (FASTA). This database together with the human protein database from Uniprot (39) can be further used with MaxQuant (40), a search engine to identify MS/MS spectra originating from the same samples as RNA-seq reads. Downstream analysis of MaxQuant output is performed with the use of the results from RNA-seq analysis. Isoform-specific peptides are extracted and quantified and based on these peptides differential protein isoforms are identified. Splicify produces a final table with both RNA and protein isoform information. B Example of peptides supporting translation of splicing events for skipped exon and retained intron. Split peptides map to both sides of an exon-exon junction, spanning peptides span exon-intron junctions (specific for inclusion variants for retained intron, alternative 3’ and 5’ splice sites) and peptides on target map to a spliced fragment.

Splicify is suitable to address basic research questions using pre-clinical model systems as well as translational research questions using patient-derived samples, e.g. allowing to identify clinically relevant biomarkers.

Availability – Splicify is publicly available on GitHub: https://github.com/NKI-TGO/SPLICIFY

Komor MA, Pham T, Hiemstra AC, Piersma SR, Bolijn AS, Schelfhorst T, Delis-van Diemen PM, Tijssen M, Sebra RP, Ashby M, Meijer GA, Jimenez CR, Fijneman RJA. (2017) Identification of differentially expressed splice variants by the proteogenomic pipeline Splicify. Mol Cell Proteomics [Epub ahead of print]. [article]

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