In-depth proteomic profiling captures subtype-specific features of craniopharyngiomas

Abstract

Craniopharyngiomas are rare epithelial tumors derived from pituitary gland embryonic tissue. This epithelial tumor can be categorized as an adamantinomatous craniopharyngioma (ACP) or papillary craniopharyngioma (PCP) subtype with histopathological and genetic differences. Genomic and transcriptomic profiles of craniopharyngiomas have been investigated; however, the proteomic profile has yet to be elucidated and added to these profiles. Recent improvements in high-throughput quantitative proteomic approaches have introduced new opportunities for a better understanding of these diseases and the efficient discovery of biomarkers. We aimed to confirm subtype-associated proteomic changes between ACP and PCP specimens. We performed a system-level proteomic study using an integrated approach that combines mass spectrometry-based quantitative proteomic, statistical, and bioinformatics analyses. The bioinformatics analysis showed that differentially expressed proteins between ACP and PCP were significantly involved in mitochondrial organization, fatty acid metabolic processes, exocytosis, the inflammatory response, the cell cycle, RNA splicing, cell migration, and neuron development. Furthermore, using network analysis, we identified hub proteins that were positively correlated with ACP and PCP phenotypes. Our findings improve our understanding of the pathogenesis of craniopharyngiomas and provide novel insights that may ultimately translate to the development of craniopharyngioma subtype-specific therapeutics.

Protective effect of Cyclo(His‐Pro) on peritoneal fibrosis through regulation of HDAC3 expression

“…All LC–MS/MS analyses were conducted using an Ultimate 3000 UHPLC system (Dionex, Sunnyvale, CA, USA) coupled with a Q‐Exactive HF‐X mass spectrometer (Thermo Scientific, Hamburg, Germany) as previously described with some modifications 26 . The peptides prepared as described above were resuspended in 2% ACN and 0.1% formic acid and spiked with the HRM kit (Biognosys AG, Schlieren‐Zurich, Switzerland) according to the manufacturer's instructions.…”

“…All LC-MS/MS analyses were conducted using an Ultimate 3000 UHPLC system (Dionex, Sunnyvale, CA, USA) coupled with a Q-Exactive HF-X mass spectrometer (Thermo Scientific, Hamburg, Germany) as previously described with some modifications. 26 The peptides prepared as described above were resuspended in 2% ACN and 0.1% formic acid and spiked with the HRM kit (Biognosys AG, Schlieren-Zurich, Switzerland) according to the manufacturer's instructions. Peptide samples were separated on a two-column system with a trap column (300 μm I.D × 5 mm length) and an analytical column (EASY-Spray C18, 75 μm I.D × 50 cm length) with a 90-min gradient from 8% to 30% acetonitrile at 300 nL/min.…”

Discovery of Proteins Responsible for Resistance to Three Chemotherapy Drugs in Breast Cancer Cells Using Proteomics and Bioinformatics Analysis

“…The TMT-labeled tryptic peptides were fractionated offline using the reversed-phase high-pH strategy as described previously [ 83 ]. Before high-pH fractionation, the pooled peptides were desalted using Oasis solid-phase extraction (SPE) columns (Waters, Milford, MA, USA), and the resulting peptides were subjected to Agilent 1290 bioinert HPLC (Agilent, Santa Clara, CA, USA) equipped with an Agilent Zorbax Extend-C18 5 μm 4.6 × 250 mm column.…”

One-Week Dynamic Changes in Cardiac Proteomes After Cardiac Radioablation in Experimental Rat Model

“…Tandem mass tag (TMT) labeling was performed according to the manufacturer's protocol with some modifications ( 10 ). The TMT-labeled peptides were pooled at a 1:1:1:1:1:1:1:1:1:1 ratio, and the mixtures were dried in a speed vacuum.…”