A Comparative Quantitative LC-MS/MS Profiling Analysis of Human Pancreatic Adenocarcinoma, Adjacent-Normal Tissue, and Patient-Derived Tumour Xenografts

Abstract

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers worldwide; it develops in a relatively symptom-free manner, leading to rapid disease progression and metastasis, leading to a 5-year survival rate of less than 5%. A lack of dependable diagnostic markers and rapid development of resistance to conventional therapies are among the problems associated with management of the disease. A better understanding of pancreatic tumour biology and discovery of new potential therapeutic targets are important goals in pancreatic cancer research. This study describes the comparative quantitative LC-MS/MS proteomic analysis of the membrane-enriched proteome of 10 human pancreatic ductal adenocarcinomas, 9 matched adjacent-normal pancreas and patient-derived xenografts (PDXs) in mice (10 at F1 generation and 10 F2). Quantitative label-free LC-MS/MS data analysis identified 129 proteins upregulated, and 109 downregulated, in PDAC, compared to adjacent-normal tissue. In this study, analysing peptide MS/MS data from the xenografts, great care was taken to distinguish species-specific peptides definitively derived from human sequences, or from mice, which could not be distinguished. The human-only peptides from the PDXs are of particular value, since only human tumour cells survive, and stromal cells are replaced during engraftment in the mouse; this list is, therefore, enriched in tumour-associated proteins, some of which might be potential therapeutic or diagnostic targets. Using human-specific sequences, 32 proteins were found to be upregulated, and 113 downregulated in PDX F1 tumours, compared to primary PDAC. Differential expression of CD55 between PDAC and normal pancreas, and expression across PDX generations, was confirmed by Western blotting. These data indicate the value of using PDX models in PDAC research. This study is the first comparative proteomic analysis of PDAC which employs PDX models to identify patient tumour cell-associated proteins, in an effort to find robust targets for therapeutic treatment of PDAC.

Establishment and Characterisation by Expression Microarray of Patient-Derived Xenograft Panel of Human Pancreatic Adenocarcinoma Patients

“…In comparison, between F1 and F2 generation of PDX tumour, only eight human-specific proteins were differentially expressed when analysed by quantitative label-free differential analysis. This demonstrates the fidelity of tumour phenotype once engrafted [30]. This is in line with previously published data the shows, once established, xenografts tend to be robust with stable gene expression profile between early and late passage PDX tumours [31].…”

The fidelity of cancer cells in PDX models: Characteristics, mechanism and clinical significance

“…provides a comprehensive view of the proteomic inconsistency between PDX models and parental tumors. In our study, the researchers used liquid chromatography–tandem mass spectrometry (LC–MS/MS) technology to profile the proteome and identified human‐specific and species‐indistinguishable proteins . In contrast to matched PDAC parental tumors, a total of 143 (32 upregulated and 111 downregulated) human‐specific proteins were differentially expressed in Passage 1 xenograft tumors.…”

“…Particular proteins and pathways in PDX models show a poor correlation with the corresponding tumors (Table ), such as erb‐b2 receptor tyrosine kinase 2 (HER2), EGFR and P53 in two pancreatic carcinoma PDX models and mechanistic target of rapamycin kinase (mTOR) pathway activation and elevated ribosomal protein S6 (pS235 or pS240) levels in estrogen receptor‐positive breast cancer PDX models. In addition, the subcellular localization of various proteins is markedly different in xenograft tumors than in parental tumors.…”

“…profiled the proteomes of xenograft tumors over two passages by using an LC–MS/MS approach. A subsequent comparison of 10 Passage 2 xenograft tumors with their corresponding Passage 1 tumors yielded a list of differentially expressed proteins, including 8 human‐specific and 41 species‐indistinguishable proteins …”

“…Serially transplanted PDX tumors are more aggressive than parental tumors at the molecular level and are more similar to metastatic or recurrent tumors. In a proteomics study, the lower average coefficient of variance for differentially expressed proteins suggested the orthogenesis of xenograft tumors . Gene ontology (GO) analysis revealed that cell division and catabolic process gene sets are upregulated in PDX tumors; conversely, ECM organization, immune response and angiogenesis gene sets are downregulated .…”