Proteomics reveals differentially regulated pathways when comparing grade 2 and 4 astrocytomas.

Astrocytic tumors are known for their high progression capacity and high mortality rates; in this regard, proteins correlated to prognosis can aid medical conduct. Although several genetic changes related to progression from grade 2 to grade 4 astrocytoma are already known, mRNA copies do not necessarily correlate with protein abundance and therefore could shadow further comprehension about this tumor's biology. This motivates us to seek for complementary strategies to study tumor progression at the protein level.

Beyond the identifiable proteome: Delving into the proteomics of polymyxin-resistant and non-resistant Acinetobacter baumannii from Brazilian hospitals.

This work discloses a unique, comprehensive proteomic dataset of Acinetobacter baumannii strains, both resistant and non-resistant to polymyxin B, isolated in Brazil generated using Orbitrap Fusion Lumos. From nearly 4 million tandem mass spectra, the software DiagnoMass produced 240,685 quality-filtered mass spectral clusters, of which PatternLab for proteomics identified 44,553 peptides mapping to 3479 proteins. Crucially, DiagnoMass shortlisted 3550 and 1408 unique mass spectral clusters for the resistant and non-resistant strains, respectively, with only about a third with sequences (and PTMs) identified by PatternLab.

DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters.

Motivation: There are several well-established paradigms for identifying and pinpointing discriminative peptides/proteins using shotgun proteomic data; examples are peptide-spectrum matching, de novo sequencing, open searches, and even hybrid approaches. Such an arsenal of complementary paradigms can provide deep data coverage, albeit some unidentified discriminative peptides remain.

Results: We present DiagnoMass, software tool that groups similar spectra into spectral clusters and then shortlists those clusters that are discriminative for biological conditions.

Proteogenomic Analysis Reveals Proteins Involved in the First Step of Adipogenesis in Human Adipose-Derived Stem Cells.

Background: Obesity is characterized as a disease that directly affects the whole-body metabolism and is associated with excess fat mass and several related comorbidities. Dynamics of adipocyte hypertrophy and hyperplasia play an important role in health and disease, especially in obesity. Human adipose-derived stem cells (hASC) represent an important source for understanding the entire adipogenic differentiation process.

The impact of blood-processing time on the proteome of human peripheral blood mononuclear cells.

Human peripheral blood mononuclear cells (PBMC) are key to several diagnostics assays and basic science research. Blood pre-analytical variations that occur before obtaining the PBMC fraction can significantly impact the assays results, including viability, composition, integrity, and gene expression changes of immune cells. With this as motivation, we performed a quantitative shotgun proteomics analysis using Isobaric Tag for Relative and Absolute Quantitation (iTRAQ 8plex) labeling to compare PBMC obtained from 24 h-stored blood at room temperature versus freshly isolated.

Proteomic changes in Trypanosoma cruzi epimastigotes treated with the proapoptotic compound PAC-1.

Apoptosis is a highly regulated process of cell death in metazoans. Therefore, understanding the biochemical changes associated with apoptosis-like death in Trypanosoma cruzi is key to drug development. PAC-1 was recently shown to induce apoptosis in T.

Proteomics pinpoints alterations in grade I meningiomas of male versus female patients.

Meningiomas are among the most common primary tumors of the central nervous system (CNS) and originate from the arachnoid or meningothelial cells of the meninges. Surgery is the first option of treatment, but depending on the location and invasion patterns, complete removal of the tumor is not always feasible. Reports indicate many differences in meningiomas from male versus female patients; for example, incidence is higher in females, whereas males usually develop the malignant and more aggressive type.

Comparing intestinal versus diffuse gastric cancer using a PEFF-oriented proteomic pipeline.

Unlabelled: Gastric cancer is the fifth most common malignant neoplasia and the third leading cause of cancer death worldwide. Mac-Cormick et al. recently showed the importance of considering the anatomical region of the tumor in proteomic gastric cancer studies; more differences were found between distinct anatomical regions than when comparing healthy versus diseased tissue.

Proteomic assessment of colorectal cancers and respective resection margins from patients of the Amazon state of Brazil.

Unlabelled: Colorectal cancer (CRC) is the third most common type of cancer in the world with a low survival rate and therapeutic efficiency. Tumor surgery implies the removal of an apparently non-tumorous tissue around the tumor in an attempt to reduce recurrence chances; this tissue is referred to as the resection margin. Our analysis employed an 8-plex iTRAQ to label four adenocarcinoma biopsies and their corresponding resection margins at 5cm; our results disclose fifty-six proteins as being differentially abundant.

A Time-Based and Intratumoral Proteomic Assessment of a Recurrent Glioblastoma Multiforme.

Tumors consist of cells in different stages of transformation with molecular and cellular heterogeneity. By far, heterogeneity is the hallmark of glioblastoma multiforme (GBM), the most malignant and aggressive type of glioma. Most proteomic studies aim in comparing tumors from different patients, but here we dive into exploring the intratumoral proteome diversity of a single GBM.

A scoring model for phosphopeptide site localization and its impact on the question of whether to use MSA.

The production of structurally significant product ions during the dissociation of phosphopeptides is a key to the successful determination of phosphorylation sites. These diagnostic ions can be generated using the widely adopted MS/MS approach, MS3 (Data Dependent Neutral Loss - DDNL), or by multistage activation (MSA). The main purpose of this work is to introduce a false-localization rate (FLR) probabilistic model to enable unbiased phosphoproteomics studies.

Proteome analysis of formalin-fixed paraffin-embedded tissues from a primary gastric melanoma and its meningeal metastasis: a case report.

Melanoma is the third most common brain metastasis cause in the United States as it has a relatively high susceptibility to metastasize to the central nervous system. Among the different origins for brain metastasis, those originating from primary gastric melanomas are extremely rare. Here, we compare protein profiles obtained from formalin-fixed paraffin- embedded (FFPE) tissues of a primary gastric melanoma with its meningeal metastasis.

Proteomic profiling of the influence of iron availability on Cryptococcus gattii.

Iron is essential and ubiquitous in living organisms. The competition for this micronutrient between the host and its pathogens has been related to disease establishment. Cryptococcus gattii is an encapsulated yeast that causes cryptococcosis mainly in immunocompetent individuals.

Dynamic proteomic overview of glioblastoma cells (A172) exposed to perillyl alcohol.

Perillyl alcohol (POH) is a naturally occurring terpene and a promising chemotherapeutic agent for glioblastoma multiform; yet, little is known about its molecular effects. Here we present results of a semi-quantitative proteomic analysis of A172 cells exposed to POH for different time-periods (1', 10', 30', 60', 4h, and 24h). The analysis identified more than 4000 proteins; which were clustered using PatternLab for proteomics and then linked to Ras signaling, tissue homeostasis, induction of apoptosis, metallopeptidase activity, and ubiquitin-protein ligase activity.

Anti-thrombin as a prognostic biomarker candidate for patients with recurrent glioblastoma multiform under treatment with perillyl alcohol.

Perillyl alcohol (POH) is a naturally occurring monoterpene with antiangiogenic and anti-tumoral properties. This chemotherapeutic agent has proven effectiveness in several clinical trials, including an ongoing phase I, comprising patients with recurrent glioblastoma multiform (GBM) under treatment with POH by intranasal administration. Proteomics offers tools to distinguish states of biological systems according to protein expression differences and therefore, can be used to gain pathological insights and to search for disease follow-up biomarkers.

Effects of perillyl alcohol and heat shock treatment in gene expression of human lung adenocarcinoma cell line A549.

The K-Ras protein is found mutated in 42.4% of lung adenocarcinoma cases, evidencing its importance as a chemotherapeutic target. The Ras protein becomes functional after farnesylation, a post-transduction modification, allowing its attachment to the cellular membrane permitting signal transduction.