Proteomic profiling of soft tissue sarcomas with SWATH mass spectrometry

Abstract

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.

Proteomic Profiling Identifies Co-Regulated Expression of Splicing Factors as a Characteristic Feature of Intravenous Leiomyomatosis

“…The samples were processed as previously described [ 18 ]. Briefly, tissue sections from each sample were deparaffinized in multiple washes in xylene.…”

“…Proteins are the critical drivers of cellular communication in normal cells and dysregulation of protein function is causative of many diseases including cancer [ 16 , 17 ]. We hypothesized that, unlike genomic and transcriptomic analysis, proteomic profiling will provide a more direct readout of the biological pathways and protein complexes that may play a role in the pathogenesis of IVLM [ 18 , 19 ]. Here we undertake a comparative mass spectrometry-based proteomic analysis of IVLM and other smooth muscle tumours (uLM, soft tissue leiomyoma (stLM) and BML), and demonstrate that at the protein level, IVLM is characterised by the unique co-regulated expression of splicing factors that comprise the spliceosome.…”

Proteomic profiling identifies co-regulated expression of splicing factors as a characteristic feature of intravenous leiomyomatosis

“…The samples were processed as previously described [18]. Briefly, 20µm tissue sections from each sample were deparaffinised in xylene, rehydrated by washes with decreasing ethanol gradient and then dried.…”

Mass spectrometry analysis of human tear fluid biomarkers specific for ocular and systemic diseases in the context of 3P medicine

“…Moreover, "top-down" MS and two-dimensional gel electrophoresis coupled with MS (2DE-MS) can provide super-high resolution power in identification of large-scale proteoforms. Recent years, four-dimensional MS (4D-MS; including retention time, m/z value, intensity, and ion mobility) [224] and data-independent acquisition (DIA) technologies such as sequential window acquisition of all theoretical spectra (SWATH) [225] are rapidly developing to significantly improve the capability to detect, identify, and quantify lowabundance and extremely low-abundance metabolites and proteoforms.…”