Rôle de la protéine tyrosine phosphatase DEP-1 dans la régulation du programme angiogénique induit par le VEGF

Depuis la découverte de la première protéine possédant une activité tyrosine kinase (protein tyrosine kinase [PTK]) dans les années 1980, l’importance des PTKs et de la phosphorylation sur résidu tyrosine dans la régulation des événements de signalisation intracellulaire est bien établie. Quant aux protéines qui possèdent une activité tyrosine phosphatase (protein tyrosine phosphatase [PTP]), dont l’existence n’a été dévoilée qu’une dixaine d’années plus tard, elles ont longtemps été perçues comme des enzymes dont le rôle ne se résumait qu'à contrecarrer passivement les activités des PTKs. Il est maintenant clair que les activités des PTPs sont spécifiques, hautement régulées, et qu’elles doivent être coordonnées avec celles des PTKs pour une régulation adéquate des événements de signalisation intracellulaire. En dépit de cette évidence, la contribution des PTPs à la régulation des différents processus physiologiques fondamentaux demeure encore peu caractérisée. C’est le cas, notamment, de l’angiogenèse, le processus par lequel de nouveaux vaisseaux sanguins sont formés à partir de ceux préexistants. Le VEGF (Vascular endothelial growth factor), un des facteurs angiogéniques les plus importants, est connu pour induire majoritairement ses effets biologiques via l’activation du récepteur à activité tyrosine kinase VEGFR2 (Vascular endothelial growth factor receptor 2). Puisque l’angiogenèse est impliquée dans le développement d’une multitude de pathologies, dont la progression tumorale, une meilleure caractérisation des PTPs qui assurent la qualité de la réponse angiogénique en agissant de pair avec le VEGFR2 s’avère cruciale et ce, afin de raffiner les outils thérapeutiques actuels. L’expression de la PTP DEP-1 corrèle avec la déphosphorylation du récepteur VEGFR2 localisé au niveau des jonctions cellules-cellules et contribue à l’inhibition de la prolifération des cellules endothéliales en réponse au VEGF lorsque les cellules sont à confluence. Par contre, la contribution spécifique de DEP-1 à la régulation des voies de signalisation et des réponses biologiques induites par le VEGF demeurait toujours inconnue. Les travaux de recherche présentés dans cette thèse démontrent tout d’abord que DEP-1 régule négativement l’activité tyrosine kinase de VEGFR2 en déphosphorylant spécifiquement les résidus tyrosine Y1054/Y1059 de sa boucle d’activation. Cette déphosphorylation mène par conséquent à une diminution générale de la phosphorylation du récepteur et à une atténuation de la plupart des voies de signalisation induites par le VEGF, incluant la voie mitogénique PLCγ-ERK1/2. Par ailleurs, malgré ce rôle négatif global, nos travaux révèlent étonnement, et pour la première fois, que DEP-1 contribue d’une manière positive à la promotion de la survie des cellules endothéliales via l’activation de la voie Src-Gab1-Akt en aval du récepteur VEGFR2. Ce pouvoir pro-survie de DEP-1 dans les cellules endothéliales réside avant tout dans sa capactié à déphosphoryler la tyrosine inhibitrice de Src (Y529). Au cours de notre étude, nous avons pu identifier deux résidus tyrosine au niveau de l’extrémité carboxy-terminale de DEP-1, Y1311 et Y1320, dont la phosphorylation est dépendante de Src. Nos travaux révèlent par ailleurs que ces deux résidus tyrosine phosphorylés lient le domaine SH2 de Src et que la Y1320 est principalement requise pour l’activation de Src et d’Akt en réponse au VEGF dans les cellules endothéliales. Ces résultats constituent donc une avancée majeure dans la compréhension des mécanismes moléculaires par lesquels DEP-1 peut réguler le programme angiogénique dépendant du VEGF. De plus, cette découverte d’un rôle positif pour DEP-1 dans la survie des cellules endothéliales pourrait mener à l’élaboration de nouvelles approches thérapeutiques visant à inhiber cette fonction spécifique de DEP-1 pour bloquer l'angiogenèse pathologique.Since the discovery of the first protein tyrosine kinase [PTK] in 1980, the importance of these proteins and of tyrosine phosphorylation cascades in the regulation of intracellular signaling events has been well-established. The protein tyrosine phosphatases [PTPs], whose existence was only revealed ten years later, have been regarded for a long time as passive PTKs conteracting enzymes. It is now evident that PTPs activities are specific, exquisitely regulated, and that they have to be coordinated with PTKs activities for an appropriate regulation of intracellular signaling events. Despite these findings, the contribution of PTPs to the regulation of many fundamental physiological processes is not well-characterized. This is the case of angiogenesis, the process whereby new vessels are generated from pre-existing ones. Vascular endothelial growth factor (VEGF), one of the most important angiogenic factors, is known to induce its biological effects mainly by activating VEGFR2 (Vascular endothelial growth factor receptor 2). As angiogenesis is involved in the development of a multitude of pathologies, including tumoral progression, a better characterization of PTPs, which ensure the quality of the angiogenic response by acting together with VEGFR2, is crucial to refine current therapeutic tools. Expression of a PTP called DEP-1 correlates with dephosphorylation of VEGFR2, and contributes to the inhibition of VEGF-induced endothelial cell proliferation at high cell confluence. However, the specific contribution of DEP-1 to the regulation of signaling pathways and biological responses induced by VEGF remained unknown. The research presented in this thesis demonstrates that DEP-1 negatively regulates the tyrosine kinase activity of VEGFR2 by dephosphorylating the specific tyrosine residues Y1054/Y1059 in its activation loop. Consequently, this leads to a global decrease in the phosphorylation of the receptor and to a reduced activation of most of the signaling cascades induced by VEGF, including the mitogenic PLCγ- ERK1/2 pathway. Moreover, despite this negative role, our work reveals for the first time that DEP-1 contributes in a positive way to promote the survival of endothelial cells via the activation of the Src-Gab1-Akt pathway downstream of VEGFR2. This survival function of DEP-1 in endothelial cells is accomplished by the dephosphorylation of the Src inhibitory tyrosine (Y529). During our study, we identified two residues in the carboxy-terminal tail of DEP-1, Y1311 and Y1320, whose phosphorylation is dependent on Src. These two phosphorylated tyrosine residues bind to the SH2 domain of Src, and our work also revealed that mostly Y1320 is required for Src and Akt activation upon VEGF stimulation of endothelial cells. These findings represent a major step forward in our understanding of the molecular mechanisms by which DEP-1 may regulate the VEGF-dependent angiogenic program. Moreover, the discovery of a positive role for DEP-1 in the survival of endothelial cells could lead to the development of new therapeutic approaches to inhibit this specific function of DEP-1 in order to block pathological angiogenesis

Nanotubular structures developed from whey-based α-lactalbumin fractions for food applications

Whey proteins have high nutritional value providing use in dietary purposes and improvement of technological properties in processed foods. Functionality of the whey-based α-lactalbumin (α-La) may be increased when assembled in the form of nanotubes, promising novel potential applications subject to investigation. The purpose of this study was to extract highly pure α-La from whey protein isolate (WPI) and whey powder (WP) and to construct protein nanotubes from them for industrial applications. For protein fractionation, WPI was directly fed to chromatography, however, WP was first subjected to membrane filtration and the retentate fraction, whey protein concentrate (WPC), was obtained and then used for chromatographic separation. α-La and, additionally β-Lg, were purified at the same batches with the purities in the range of 95%-99%. After enzymatic hydrolysis, WPI-based α-La produced chain-like and long nanotubules with ∼20 nm width while WPC-based α-La produced thinner, miscellaneous, and fibril-like nanostructures by self-assembly. Raman and FT-IR spectroscopies revealed that α-La fractions, obtained from both sources and the nanostructures, developed using both fractions have some structural differences due to conformation of secondary structure elements. Nanotube formation induced gelation and nanotubular gel network entrapped a colorant uniformly with a transparent appearance. Dairy-based α-La protein nanotubules could be served as alternative gelling agents and the carriers of natural colorants in various food processes.Scientific and Technological Research Council of Turkey(109O866); Izmir Institute of Technology (IYTE03

Beneficial effects of reconstituted high-density lipoprotein (rHDL) on circulating CD34+ cells in patients after an acute coronary syndrome

Background: High-density lipoproteins (HDL) favorably affect endothelial progenitor cells (EPC). Circulating progenitor cell level and function are impaired in patients with acute coronary syndrome (ACS). This study investigates the short-term effects of reconstituted HDL (rHDL) on circulating progenitor cells in patients with ACS. Methods and Findings: The study population consisted of 33 patients with recent ACS: 20 patients from the ERASE trial (randomized to receive 4 weekly intravenous infusions of CSL-111 40 mg/kg or placebo) and 13 additional patients recruited as controls using the same enrolment criteria. Blood was collected from 16 rHDL (CSL-111)-treated patients and 17 controls at baseline and at 6–7 weeks (i.e. 2–3 weeks after the fourth infusion of CSL-111 in ERASE). CD34+ and CD34+/kinase insert domain receptor (KDR+) progenitor cell counts were analyzed by flow cytometry. We found preserved CD34+ cell counts in CSL-111-treated subjects at follow-up (change of 1.6%), while the number of CD34+ cells was reduced (-32.9%) in controls (p = 0.017 between groups). The level of circulating SDF-1 (stromal cell-derived factor-1), a chemokine involved in progenitor cell recruitment, increased significantly (change of 21.5%) in controls, while it remained unchanged in CSL-111-treated patients (p = 0.031 between groups). In vitro exposure to CSL-111 of early EPC isolated from healthy volunteers significantly increased CD34+ cells, reduced early EPC apoptosis and enhanced their migration capacity towards SDF-1. Conclusions: The relative increase in circulating CD34+ cells and the low SDF-1 levels observed following rHDL infusions in ACS patients point towards a role of rHDL in cardiovascular repair mechanisms

predictors of flares in infliximab treated children with inflammatory bowel disease

Abstract One third of pediatric IBD patients who initially respond to infliximab (IFX) lose that response over time. This retrospective study, including 62 children treated with IFX from 2004 to 2017, aimed to identify factors associated with clinical flare. Ulcerative colitis, extreme body mass index, and lowest IFX trough levels were associated with clinical flare in the whole population. In Crohn disease patients, perianal disease was pejorative, while location proximal to ligament of Treitz was protective. Underweight patients probably correspond to the most severe cases who are more likely to relapse, with hypoalbuminemia responsible for lower systemic IFX availability. Obesity probably induces higher IFX clearance

Comparison of the diagnostic accuracy of three current guidelines for the evaluation of asymptomatic pancreatic cystic neoplasms.

Asymptomatic pancreatic cysts are a common clinical problem but only a minority of these cases progress to cancer. Our aim was to compare the accuracy to detect malignancy of the 2015 American Gastroenterological Association (AGA), the 2012 International Consensus/Fukuoka (Fukuoka guidelines [FG]), and the 2010 American College of Radiology (ACR) guidelines.We conducted a retrospective study at 3 referral centers for all patients who underwent resection for an asymptomatic pancreatic cyst between January 2008 and December 2013. We compared the accuracy of 3 guidelines in predicting high-grade dysplasia (HGD) or cancer in resected cysts. We performed logistic regression analyses to examine the association between cyst features and risk of HGD or cancer.A total of 269 patients met inclusion criteria. A total of 228 (84.8%) had a benign diagnosis or low-grade dysplasia on surgical pathology, and 41 patients (15.2%) had either HGD (n = 14) or invasive cancer (n = 27). Of the 41 patients with HGD or cancer on resection, only 3 patients would have met the AGA guideline\u27s indications for resection based on the preoperative cyst characteristics, whereas 30/41 patients would have met the FG criteria for resection and 22/41 patients met the ACR criteria. The sensitivity, specificity, positive predictive value, negative predictive value of HGD, and/or cancer of the AGA guidelines were 7.3%, 88.2%, 10%, and 84.1%, compared to 73.2%, 45.6%, 19.5%, and 90.4% for the FG and 53.7%, 61%, 19.8%, and 88% for the ACR guidelines. In multivariable analysis, cyst size \u3e3 cm, compared to ≤3 cm, (odds ratio [OR] = 2.08, 95% confidence interval [CI] = 1.11, 4.2) and each year increase in age (OR = 1.07, 95% CI = 1.03, 1.11) were positively associated with risk of HGD or cancer on resection.In patients with asymptomatic branch duct-intraductal papillary mucinous neoplasms or mucinous cystic neoplasms who underwent resection, the prevalence rate of HGD or cancer was 15.2%. Using the 2015 AGA criteria for resection would have missed 92.6% of patients with HGD or cancer. The more inclusive FG and ACR had a higher sensitivity for HGD or cancer but lower specificity. Given the current deficiencies of these guidelines, it will be important to determine the acceptable rate of false-positives in order to prevent a single true-positive

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin