Quantitative proteomics by SWATH-MS reveals sophisticated metabolic reprogramming in hepatocellular carcinoma tissues

Abstract

Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide, and understanding its molecular pathogenesis is pivotal to managing this disease. Sequential window acquisition of all theoretical mass spectra (SWATH-MS) is an optimal proteomic strategy to seek crucial proteins involved in HCC development and progression. In this study, a quantitative proteomic study of tumour and adjacent non-tumour liver tissues was performed using a SWATH-MS strategy. In total, 4,216 proteins were reliably quantified, and 338 were differentially expressed, with 191 proteins up-regulated and 147 down-regulated in HCC tissues compared with adjacent non-tumourous tissues. Functional analysis revealed distinct pathway enrichment of up- and down-regulated proteins. The most significantly down-regulated proteins were involved in metabolic pathways. Notably, our study revealed sophisticated metabolic reprogramming in HCC, including alteration of the pentose phosphate pathway; serine, glycine and sarcosine biosynthesis/metabolism; glycolysis; gluconeogenesis; fatty acid biosynthesis; and fatty acid β-oxidation. Twenty-seven metabolic enzymes, including PCK2, PDH and G6PD, were significantly changed in this study. To our knowledge, this study presents the most complete view of tissue-specific metabolic reprogramming in HCC, identifying hundreds of differentially expressed proteins, which together form a rich resource for novel drug targets or diagnostic biomarker discovery.

Identification of a co‐target for enhancing efficacy of sorafenib in HCC through a quantitative modeling approach

“…For each enzymatic reaction, we took the fold change in gene expression values for the corresponding gene(s) in HCC with respect to NL, to be proportional to the variation in the corresponding E t (total enzyme) levels (Eqn 2, Materials and methods). Proteomic data of HCC samples are also available for a few of the enzymes in our model [37]. We compared the fold change in protein abundance in HCC with respect to NL (no etiology information is present in the data) with those of the gene expression variations, and find them to be in good agreement, lending additional support to the hypothesis that the gene expression variations used in the model are biologically meaningful (Table S3).…”

Identification of protein abundance changes in biopsy-level hepatocellular carcinoma tissues using PCT-SWATH

“…In contrast, proteins participated in various metabolism pathways were down-regulated, indicating the suppression of metabolic functionality in liver during oncogenesis. Compared to a previous report of HCC tissue proteome using SWATH-MS 16 , our data are acquired in a shorter time frame but identified similar protein alternation. For instance, we also observed malignant tissue displayed increased abundance of glucose-6-phophate dehydrogenase (G6PD) and perilipin 2 (PLIN2), as well as downregulation of formimidoyltransferase cyclodeaminase (FTCD) and phosphoenolpyruvate carboxykinase 2 (PCK2, mitochondrial).…”

“…In a more recent study, Naboulsi W. et al identified and quantified 2,736 proteins from 19 pairs of HCC tumorous and adjacent non-tumorous tissue using the label-free shotgun proteomics over a 98-min LC gradient 15 . Gao et al 16 applied SWATH-MS to study 14 pairs of HCC and non-HCC tissues and quantified 4,216 proteins in at least one biological replicates and 1,903 proteins in at least three out of five biological replicates using a 120-min LC gradient. For each sample, about 200 mg tissue was used.…”

Probing SWATH-MS as a tool for proteome level quantification in a non-model fish

“…Sequential window acquisition of all theoretical spectra (SWATH/DIA-MS) is a newer method that combines the strengths of shotgun and targeted proteomics (Gillet et al, 2012). SWATH/DIA-MS is a label free and relatively cheap mass spectrometry method using data independent acquisition (DIA) combined with proteome wide spectral libraries created from data-dependent acquisition (DDA) methods against which the fragment ion maps of the DIA method are aligned (Gao et al, 2017;Gillet et al, 2012;Huang et al, 2015). Using the sequential isolation window acquisition has achieved high fragment ion specificity and the ability to identify and quantify thousands of proteins in one measurement (Gillet et al, 2012;Tang et al, 2015).…”