Proteomic-based stratification of intermediate-risk prostate cancer patients

Gleason grading is an important prognostic indicator for prostate adenocarcinoma and is crucial for patient treatment decisions. However, intermediate-risk patients diagnosed in the Gleason grade group (GG) 2 and GG3 can harbour either aggressive or non-aggressive disease, resulting in under- or overtreatment of a significant number of patients. Here, we performed proteomic, differential expression, machine learning, and survival analyses for 1,348 matched tumour and benign sample runs from 278 patients. Three proteins (F5, TMEM126B, and EARS2) were identified as candidate biomarkers in patients with biochemical recurrence. Multivariate Cox regression yielded 18 proteins, from which a risk score was constructed to dichotomize prostate cancer patients into low- and high-risk groups. This 18-protein signature is prognostic for the risk of biochemical recurrence and completely independent of the intermediate GG. Our results suggest that markers generated by computational proteomic profiling have the potential for clinical applications including integration into prostate cancer management

Simultaneous Analysis of Proteome, Phospho- and Glycoproteome of Rat Kidney Tissue with Electrostatic Repulsion Hydrophilic Interaction Chromatography

Protein post-translational modifications (PTMs) are regulated separately from protein expression levels. Thus, simultaneous characterization of the proteome and its PTMs is pivotal to an understanding of protein regulation, function and activity. However, concurrent analysis of the proteome and its PTMs by mass spectrometry is a challenging task because the peptides bearing PTMs are present in sub-stoichiometric amounts and their ionization is often suppressed by unmodified peptides of high abundance. We describe here a method for concurrent analysis of phosphopeptides, glycopeptides and unmodified peptides in a tryptic digest of rat kidney tissue with a sequence of ERLIC and RP-LC-MS/MS in a single experimental run, thereby avoiding inter-experimental variation. Optimization of loading solvents and elution gradients permitted ERLIC to be performed with totally volatile solvents. Two SCX and four ERLIC gradients were compared in details, and one ERLIC gradient was found to perform the best, which identified 2929 proteins, 583 phosphorylation sites in 338 phosphoproteins and 722 N-glycosylation sites in 387 glycoproteins from rat kidney tissue. Two hundred low-abundance proteins with important functions were identified only from the glyco- or phospho-subproteomes, reflecting the importance of the enrichment and separation of modified peptides by ERLIC. In addition, this strategy enables identification of unmodified and corresponding modified peptides (partial phosphorylation and N-glycosylation) from the same protein. Interestingly, partially modified proteins tend to occur on proteins involved in transport. Moreover, some membrane or extracellular proteins, such as versican core protein and fibronectin, were found to have both phosphorylation and N-glycosylation, which may permit an assessment of the potential for cross talk between these two vital PTMs and their roles in regulation

DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000

Proteomic studies on gastric cancer to understand the underlying molecular mechanisms of oncogenesis

Gastric cancer ranks as the fourth most common cancer and the second leading cause of cancer mortality globally. One of the main reasons for gastric cancers’ poor outlook is the limited knowledge of the underlying molecular mechanisms of gastric oncogenesis. Proteomics has evolved rapidly in recent years and is now recognised as a powerful suite of tools to systematically dissect molecular abnormalities in cancer cells. However, proteomics has yet to be intensively applied to gastric cancer; consequently few global insights into gastric oncogenesis to date have emerged from this approach. In this thesis, we employed advanced proteomic techniques to study phosphorylated proteins, methylated proteins, and cell surface proteins of multiple gastric cancer cells on a large scale. Proteomic data were correlated with transcriptome data sets to gain deeper insights into aberrantly expressed proteins in gastric cancer cells. We found MET, a receptor tyrosine kinase, to be a dominant aberrant protein that was overexpressed in some gastric cancers. A quantitative proteomic approach was utilized to investigate molecular events associated with MET-directed therapy in gastric cancer cells. Remarkably MET was found to be present in the mitochondria of gastric cancer cells, as it was on the plasma membrane. Moreover, mitochondrial MET was identified as a direct target of the MET kinase inhibitor, PHA-665752. Taken together, data presented in this thesis offer a systematic and unbiased profile of multiple molecular abnormalities in gastric cancer cells, and has uncovered a novel mechanism of action of molecularly-directed cancer therapy.DOCTOR OF PHILOSOPHY (SBS

Étude exploratoire de la personnalité et du profil psychologique chez les individus ayant l’ataxie récessive spastique de Charlevoix-Saguenay (ARSCS)

L'ataxie récessive-spastique de Charlevoix-Saguenay (ARSCS) est une maladie neurodégénérative rare et héréditaire qui se retrouve principalement dans les régions de Charlevoix et du Saguenay–Lac-Saint-Jean (SLSJ). Cette maladie se caractérise, entre autres, par une atrophie cérébelleuse évolutive qui entraine de graves troubles de la coordination. Les récentes avancées scientifiques portant sur les fonctions du cervelet démontrent que les personnes avec des dommages cérébelleux sont susceptibles de présenter le syndrome cognitivo-affectif cérébelleux (SCAC) composé de divers troubles cognitifs et affectifs. D’ailleurs, il est intéressant de faire un parallèle entre certains symptômes du SCAC et les caractéristiques psychologiques depuis longtemps observées en clinique chez la clientèle atteinte d’ARSCS. Cette étude descriptive exploratoire vise à documenter, pour la première fois, le profil psychologique de huit adultes atteints d’ARSCS âgés entre 20 et 59 ans, en décrivant les traits de personnalité et les symptômes psychologiques à l’aide du NEO-FFI et du SCL-90-R. L’analyse des résultats met en évidence des tendances intéressantes dans l’expression de la personnalité, malgré l’impossibilité d’établir un profil typique des individus atteints d’ARCSC. Cette analyse permet de constater qu’une majorité des participants présentent une faible ouverture à l’expérience, une agréabilité élevée ainsi qu’un névrosisme, une extraversion et un caractère consciencieux dans la moyenne. Une tendance vers l’obtention de scores plus faibles peut être constatée pour l’ouverture et pour le caractère consciencieux. En effet, aucun participant ne présente une ouverture élevée, et un seul participant présente un caractère consciencieux élevé. Des traits de rigidité mentale apparaissent également chez tous les individus. L’évaluation des symptômes psychologiques démontre, quant à elle, que les individus atteints d’ARSCS étudiés souffrent d’une détresse psychologique significativement importante et présentent des symptômes psychologiques tels des obsessions-compulsions, de l’anxiété phobique, du psychotisme ainsi que de l’anxiété et des idéations paranoïdes. Les profils de personnalité ici observés concordent avec ceux préalablement décrits chez des personnes atteintes d’autres types d’ataxies (D’Agata et al., 2011; Fancellu et al., 2013; Mantovan et al., 2006; Schmahmann et al., 2007). Plusieurs participants de notre échantillon présentent également des traits qui rappellent les manifestations du SCAC (p.ex. émoussement affectif, indifférence, instabilité, traits obsessifs-compulsifs, détresse psychologique). Enfin, les pistes de réflexion offertes lors de l’interprétation des résultats ouvrent la voie à de nouvelles hypothèses, comme celles de la contribution des stratégies défensives et de la contribution de la théorie de l’esprit. Une surutilisation de défenses psychologiques, comme le déni, ainsi qu’une difficulté liée à la capacité à se représenter les états mentaux de soi et des autres pourraient expliquer les difficultés émotives et les difficultés d’adaptation vécues par plusieurs individus atteints d’ARSCS. De nouvelles études visant l’exploration des réactions psychologiques et des stratégies de coping chez des individus atteints d’ARSCS s’avèrent nécessaires

Convergent network effects along the axis of gene expression during prostate cancer progression

Background Tumor-specific genomic aberrations are routinely determined by high-throughput genomic measurements. It remains unclear how complex genome alterations affect molecular networks through changing protein levels and consequently biochemical states of tumor tissues. Results Here, we investigate the propagation of genomic effects along the axis of gene expression during prostate cancer progression. We quantify genomic, transcriptomic, and proteomic alterations based on 105 prostate samples, consisting of benign prostatic hyperplasia regions and malignant tumors, from 39 prostate cancer patients. Our analysis reveals the convergent effects of distinct copy number alterations impacting on common downstream proteins, which are important for establishing the tumor phenotype. We devise a network-based approach that integrates perturbations across different molecular layers, which identifies a sub-network consisting of nine genes whose joint activity positively correlates with increasingly aggressive tumor phenotypes and is predictive of recurrence-free survival. Further, our data reveal a wide spectrum of intra-patient network effects, ranging from similar to very distinct alterations on different molecular layers. Conclusions This study uncovers molecular networks with considerable convergent alterations across tumor sites and patients. It also exposes a diversity of network effects: we could not identify a single sub-network that is perturbed in all high-grade tumor regions

Additional file 3: of Quantitative proteomics signature profiling based on network contextualization

Renal cancer dataset (RC). (TXT 485 kb