Comparative proteomic analysis of different stages of breast cancer tissues using ultra high performance liquid chromatography tandem mass spectrometer

Abstract

BackgroundBreast cancer is the fifth most prevalent cause of death among women worldwide. It is also one of the most common types of cancer among Malaysian women. This study aimed to characterize and differentiate the proteomics profiles of different stages of breast cancer and its matched adjacent normal tissues in Malaysian breast cancer patients. Also, this study aimed to construct a pertinent protein pathway involved in each stage of cancer. MethodsIn total, 80 samples of tumor and matched adjacent normal tissues were collected from breast cancer patients at Seberang Jaya Hospital (SJH) and Kepala Batas Hospital (KBH), both in Penang, Malaysia. The protein expression profiles of breast cancer and normal tissues were mapped by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The Gel-Eluted Liquid Fractionation Entrapment Electrophoresis (GEL-FREE) Technology System was used for the separation and fractionation of extracted proteins, which also were analyzed to maximize protein detection. The protein fractions were then analyzed by tandem mass spectrometry (LC-MS/MS) analysis using LC/MS LTQ-Orbitrap Fusion and Elite. This study identified the proteins contained within the tissue samples using de novo sequencing and database matching via PEAKS software. We performed two different pathway analyses, DAVID and STRING, in the sets of proteins from stage 2 and stage 3 breast cancer samples. The lists of molecules were generated by the REACTOME-FI plugin, part of the CYTOSCAPE tool, and linker nodes were added in order to generate a connected network. Then, pathway enrichment was obtained, and a graphical model was created to depict the participation of the input proteins as well as the linker nodes.

Expression of Annexin A2 Promotes Cancer Progression in Estrogen Receptor Negative Breast Cancers

“…Transcriptomics also fails to take into account protein turnover and degradation as well as activation state through post-translational modification. Proteomic analysis of breast cancers has revealed prognostic markers [11], novel subtype classifications [12] and targetable protein abundance differences as cancer progresses through clinical stages [13]. Analysis of proteins that are newly translated and synthesized by cells allows for an accurate snapshot of cellular activities during a specific process or duration.…”

Proteomics, Personalized Medicine and Cancer

“…MS-based proteomics relies on success in three main areas: sample pretreatment and analysis and data analysis. Two-dimensional gel electrophoresis (2-DE) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) were the original mainstays for sample separation before MS analysis, with the ability to separate over 10,000 proteoforms [ 13 ], and indeed these systems are still in use [ 20 ]. In this example, proteome information of tumor tissues and normal tissues was obtained by SDS-PAGE for a comparative proteomic analysis of different stages of BC.…”

Understanding Cervical Cancer through Proteomics

“…Depending on the proteomic technique selected, the results obtained by each laboratory may vary. Comparative proteomics is a branch of quantitative proteomics that analyzes changes in the proteome in response to different stimuli produced by the environment or a disease [50,51]. It is used in the analysis and search of cancer biomarkers and relies on reproducible techniques of sample selection, purification, and storage [45,51].…”

“…Comparative proteomics is a branch of quantitative proteomics that analyzes changes in the proteome in response to different stimuli produced by the environment or a disease [50,51]. It is used in the analysis and search of cancer biomarkers and relies on reproducible techniques of sample selection, purification, and storage [45,51]. The main techniques used for the large-scale analysis of comparative data are 2-DE and MS [28,51].…”