Proteomic profiling of soft tissue sarcomas with SWATH mass spectrometry.
View/ Open
Date
2021-06-15Author
Milighetti, M
Krasny, L
Lee, ATJ
Morani, G
Szecsei, C
Chen, Y
Guljar, N
McCarthy, F
Wilding, CP
Arthur, A
Fisher, C
Judson, I
Thway, K
Cheang, MCU
Jones, RL
Huang, PH
Type
Journal Article
Metadata
Show full item recordAbstract
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, undifferentiated pleomorphic sarcoma and dedifferentiated liposarcoma). We quantified 2951 proteins across 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 that have a distinct expression profile in a panel of 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.
Collections
Subject
Humans
Leiomyosarcoma
Sarcoma
Gene Expression Profiling
Proteomics
Mass Spectrometry
Research team
Genomic Analysis – Clinical Trials
Sarcoma Clinical Trials (R Jones)
Molecular and Systems Oncology
Genomic Analysis – Clinical Trials
Sarcoma Clinical Trials (R Jones)
Molecular and Systems Oncology
Language
eng
Date accepted
2021-04-14
Citation
Journal of proteomics, 2021, 241 pp. 104236 - ?
Publisher
ELSEVIER