Proteomics

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Proteomic profiling of soft tissue sarcomas with SWATH mass spectrometry


ABSTRACT: In this work, we utilise sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) for proteomic profiling of formalin fixed paraffin embedded (FFPE) specimens from a cohort of STS patients (n=36) across four histological subtypes (leiomyosarcoma, synovial sarcoma, undifferentiated pleomorphic sarcoma and dedifferentiated liposarcoma). We quantified 2951 proteins in all cases and show that there is a significant enrichment of gene sets associated with smooth muscle contraction in leiomyosarcoma, RNA splicing regulation in synovial sarcoma and leukocyte activation in undifferentiated pleomorphic sarcoma. We further identified a subgroup of STS cases (independent of histological subtype) that have a distinct expression profile in a panel of 133 proteins, with worse survival outcomes when compared to the rest of the cohort. Our study highlights the value of comprehensive proteomic characterisation as a means to identify histotype-specific STS profiles that describe key biological pathways of clinical and therapeutic relevance; as well as for discovering new prognostic biomarkers in this group of rare and difficult-to-treat diseases.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Striated Muscle Cell, Mesenchymal Cell, Connective Tissue, Stromal Cell, Adipose Tissue, Synovial Tissue

DISEASE(S): Sarcoma

SUBMITTER: Lukas Krasny  

LAB HEAD: Paul Huang

PROVIDER: PXD019719 | Pride | 2021-05-11

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
201800607_SS001_R1.wiff Wiff
201800607_SS001_R1.wiff.scan Wiff
201800607_SS001_R2.wiff Wiff
201800607_SS001_R2.wiff.scan Wiff
201800607_SS004_R1.wiff Wiff
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Publications


Soft tissue sarcomas (STS) are a group of rare and heterogeneous cancers. While large-scale genomic and epigenomic profiling of STS have been undertaken, proteomic analysis has thus far been limited. Here we utilise sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) for proteomic profiling of formalin fixed paraffin embedded (FFPE) specimens from a cohort of STS patients (n = 36) across four histological subtypes (leiomyosarcoma, synovial sarcoma,  ...[more]

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