SWATH‐based proteomics reveals processes associated with immune evasion and metastasis in poor prognosis colorectal tumours

Abstract

Newly emerged proteomic methodologies, particularly data‐independent acquisition (DIA) analysis–related approaches, would improve current gene expression–based classifications of colorectal cancer (CRC). Therefore, this study was aimed to identify protein expression signatures using SWATH‐MS DIA and targeted data extraction, to aid in the classification of molecular subtypes of CRC and advance in the diagnosis and development of new drugs. For this purpose, 40 human CRC samples and 7 samples of healthy tissue were subjected to proteomic and bioinformatic analysis. The proteomic analysis identified three different molecular CRC subtypes: P1, P2 and P3. Significantly, P3 subtype showed high agreement with the mesenchymal/stem‐like subtype defined by gene expression signatures and characterized by poor prognosis and survival. The P3 subtype was characterized by decreased expression of ribosomal proteins, the spliceosome, and histone deacetylase 2, as well as increased expression of osteopontin, SERPINA 1 and SERPINA 3, and proteins involved in wound healing, acute inflammation and complement pathway. This was also confirmed by immunodetection and gene expression analyses. Our results show that these tumours are characterized by altered expression of proteins involved in biological processes associated with immune evasion and metastasis, suggesting new therapeutic options in the treatment of this aggressive type of CRC.

Alternative splicing of mRNA in colorectal cancer: new strategies for tumor diagnosis and treatment

“…In CRC, alternative splicing can be regulated by trans-regulatory factors in form of mutations, dysregulated expressions or protein-modifications of RNA-binding proteins (RBPs) that occur in spliceosome components and splicing regulators [ 49 , 50 ]. Alterations that occur in trans-regulatory factors are shown in Table 2 .…”

“…It is an oncogenic factor that promotes tumorigenesis by regulating various AS events, such as splicing of Rac Family Small GTPase 1 (RAC1), Tyrosine-protein kinase (SYK), Marker of proliferation Ki-67(MKI67) and heterogeneous nuclear ribonucleoprotein L like (HNRPLL) [ 51 , 54 , 55 ]. In CRC, SRSF1 has been found to be upregulated and is associated with DNA damage and cell cycle progression [ 50 ]. Elevated SRSF1 binds 3’SS of DBF4B exon 6 in colon cancer cells to activate it [ 54 , 55 ].…”

Discovery and Evaluation of Protein Biomarkers as a Signature of Wellness in Late-Stage Cancer Patients in Early Phase Clinical Trials

“…SWATH-MS uses the reproducibility and relatively swift sample preparation and run time plus standardised informatics capabilities to generate digitised proteomic maps. SWATH-MS has been used to identify proteomics signatures in a wide range of diseases and conditions with recent cancer based studies finding signatures of interest in breast and colorectal cancer [ 29 , 30 ], endometrial cancer [ 31 ], ovarian [ 32 ] lung cancer [ 33 ] and other health conditions such as weight loss [ 34 ].…”

Non‐targeted screening of pyranosides in Rhodiola crenulata using an all ion fragmentation‐exact neutral loss strategy combined with liquid chromatography‐quadrupole time‐of‐flight mass spectrometry

“…This acquisition window is then sequentially moved from the lowest to the highest mass selection range, resulting in MS/MS acquisition over a wide specific mass range. SWATH has been widely used for the high‐throughput analysis of biological macromolecules, such as in proteomics and peptide analysis, 35–37 and has been shown to be applicable to the detection of small molecules, such as pesticides 38,39 . There are fewer reports on the applications of AIF than of SWATH, and most AIF applications have focused on reactive metabolites rather than natural products in plants 40–42 .…”