Detection of candidate biomarkers of prostate cancer progression in serum: a depletion-free 3D LC/MS quantitative proteomics pilot study

Abstract

Background:Prostate cancer (PCa) is the most common male cancer in the United Kingdom and we aimed to identify clinically relevant biomarkers corresponding to stage progression of the disease.Methods:We used enhanced proteomic profiling of PCa progression using iTRAQ 3D LC mass spectrometry on high-quality serum samples to identify biomarkers of PCa.Results:We identified >1000 proteins. Following specific inclusion/exclusion criteria we targeted seven proteins of which two were validated by ELISA and six potentially interacted forming an ‘interactome' with only a single protein linking each marker. This network also includes accepted cancer markers, such as TNF, STAT3, NF-κB and IL6.Conclusions:Our linked and interrelated biomarker network highlights the potential utility of six of our seven markers as a panel for diagnosing PCa and, critically, in determining the stage of the disease. Our validation analysis of the MS-identified proteins found that SAA alongside KLK3 may improve categorisation of PCa than by KLK3 alone, and that TSR1, although not significant in this model, might also be a clinically relevant biomarker.

Indentification of Novel Biomarkers for Paroxysmal Non- Kinesigenic Dyskinesia Diagnosis Via Cerebrospinal Fluid and Plasma Proteomic Analysis

“…The GO is a structured and controlled vocabulary of terms, and widely recognized as the premier tool for the organization and functional annotation of molecular characteristics [18,20,21]. By interpreting the GO of differentially expressed proteins and then analyzing them statistically, we have obtained 42 significant CSF proteins and 57 significant plasma proteins.…”

“…Proteomic technologies have been largely used to search for differentially expressed proteins, in order to clarify the diagnosis and prognosis of diseases such as tumor and neurodegenerative disorders [14][15][16]. Isobaric tags for relative and absolute quantitation (iTRAQ) technique is one of the most widely used approaches because it can simultaneously analyze 8 different specimens, thus increasing throughput while reducing experimental error [17][18][19]. In this study, we used iTRAQ labeling followed by 2D-LC-MS/ MS for the quantitative proteomic analysis of the CSF and plasma samples from PNKD patients and their healthy family members to discover potential effective biomarkers for PNKD diagnosis.…”

Analysis of the plasma proteome using iTRAQ and TMT‐based Isobaric labeling

“…While their data indicated that the two MS platforms gave complementary information, they combined the data from both fractionation methods and did not provide any comparison. Larkin et al implemented HILIC in a variation of the three dimensional depletion‐free strategy initially described by Al‐Daghri, notably identifying in the order of a thousand proteins . Another alternative using anion exchange columns for fractionation is Electrostatic Repulsion‐Hydrophilic Interaction Chromatography (ERLIC), which was used by Datta et al in a study where they enriched plasma mircovesicles in a study of lacunar infarction …”

“…Larkin et al implemented HILIC in a variation of the three dimensional depletion-free strategy initially described by Al-Daghri, 39 notably identifying in the order of a thousand proteins. 57 As a non-chromatographic option, peptide isoelectric focusing has been used with both immobilized pH gradients (IPG) [59][60][61][62] and off-gel approaches. 22,34,36,63,64 Using IPG strips, Pernemalm et al have demonstrated the potential of narrow-range peptide IEF for plasma analysis.…”

“…Human: Boylan et al, 202 Karabudak et al, 218 Li et al, 219 Shetty et al, 102 Wu et al, 68 Russell et al, 220 Wu et al, 97 Rat: Huang et al, 185 Pancreatic Nie et al, 67 Nie et al, 69 Sinclair and Timms, 24 Tan et al, 103 Tonack et al, 12 Tonack et al, 203 Zhou et al, 77 An et al, 98 Prostrate Rehman et al, 221 Larkin et al, 57 Zhang et al, 222 Kidney Zhang et al, 223 Other: Chinese medicine, Endometrial hyperplasia vs. cancer, Glycosylation, Carbonylation…”