Proteomes

Special Issue Editor

Prof. Dr. Jun Qu

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Guest Editor

Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
Interests: quantitative proteomics; pharmaceutics; biotherapeutics; targeted protein quantificaiton; cancer; cardiovascular diseases; chromatography; high-resolution MS

Special Issue Information

Dear Colleagues,

With the tremendous advances in chromatographic, mass spectrometric, and informatics techniques, proteomics has become a highly valuable tool in pharmaceutical investigation. The last decade has witnessed rapidly increasing applications of proteomics—both quantitatively and qualitatively—in characterizing drug mechanisms of action, safety, efficacy, off-target effects, pharmacodynamics, etc. Such works have not only greatly extended our understanding of the biology, pharmacology, and pharmaceutics of existing therapeutic agents, but have also provided novel insights into the discovery and development of new candidates.

This Special Issue encompasses a broad range of works employing proteomics methods to answer pharmaceutical or related questions.

Prof. Dr. Jun Qu
Guest Editor

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Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Proteomes is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

pharmaceutical investigation
drug effects
safety
efficacy
mechanisms of action
time courses

Published Papers (1 paper)

Research

20 pages, 3319 KiB

Open AccessArticle

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

by Orla Coleman, Michael Henry, Fiona O'Neill, Sandra Roche, Niall Swan, Lorraine Boyle, Jean Murphy, Justine Meiller, Neil T. Conlon, Justin Geoghegan, Kevin C. Conlon, Vincent Lynch, Ninfa L. Straubinger, Robert M. Straubinger, Gerard McVey, Michael Moriarty, Paula Meleady and Martin Clynes

Proteomes 2018, 6(4), 45; https://doi.org/10.3390/proteomes6040045 - 6 Nov 2018

Cited by 21 | Viewed by 4562

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. Full article

(This article belongs to the Special Issue Pharmaceutical Proteomics)

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