Deregulation of Rab and Rab Effector Genes in Bladder Cancer

Growing evidence indicates that Rab GTPases, key regulators of intracellular transport in eukaryotic cells, play an important role in cancer. We analysed the deregulation at the transcriptional level of the genes encoding Rab proteins and Rab-interacting proteins in bladder cancer pathogenesis, distinguishing between the two main progression pathways so far identified in bladder cancer: the Ta pathway characterized by a high frequency of FGFR3 mutation and the carcinoma in situ pathway where no or infrequent FGFR3 mutations have been identified. A systematic literature search identified 61 genes encoding Rab proteins and 223 genes encoding Rab-interacting proteins. Transcriptomic data were obtained for normal urothelium samples and for two independent bladder cancer data sets corresponding to 152 and 75 tumors. Gene deregulation was analysed with the SAM (significant analysis of microarray) test or the binomial test. Overall, 30 genes were down-regulated, and 13 were up-regulated in the tumor samples. Five of these deregulated genes (LEPRE1, MICAL2, RAB23, STXBP1, SYTL1) were specifically deregulated in FGFR3-non-mutated muscle-invasive tumors. No gene encoding a Rab or Rab-interacting protein was found to be specifically deregulated in FGFR3-mutated tumors. Cluster analysis showed that the RAB27 gene cluster (comprising the genes encoding RAB27 and its interacting partners) was deregulated and that this deregulation was associated with both pathways of bladder cancer pathogenesis. Finally, we found that the expression of KIF20A and ZWINT was associated with that of proliferation markers and that the expression of MLPH, MYO5B, RAB11A, RAB11FIP1, RAB20 and SYTL2 was associated with that of urothelial cell differentiation markers. This systematic analysis of Rab and Rab effector gene deregulation in bladder cancer, taking relevant tumor subgroups into account, provides insight into the possible roles of Rab proteins and their effectors in bladder cancer pathogenesis. This approach is applicable to other group of genes and types of cancer

Theoretical model of the interfacial reactions between solid iron and liquid zinc-aluminium alloy

International audienceSteel strip is often coated with a layer of zinc in order to protect it against corrosion. One of the most commonly used coating processes is continuous hot dip galvanizing. In this process, the steel strip is immersed in a molten zinc bath containing small amounts of aluminium (less than 1 wt%). A model has been developed describing the kinetics of the galvanizing reactions that occur at the steel/liquid zinc interface (dissolution of iron, heterogeneous nucleation and growth of the intermetallic phase designated Fe2Al5Znx). The model has been validated using experimental data available in the literature for a classical galvanizing treatment that lasts three second

Therapeutic advances in metastatic pancreatic cancer: a focus on targeted therapies

International audienceMortality from pancreatic ductal adenocarcinoma (PDAC) is increasing worldwide and effective new treatments are urgently needed. The current treatment of metastatic PDAC in fit patients is based on two chemotherapy combinations (FOLFIRINOX and gemcitabine plus nab-paclitaxel) which were validated more than 8 years ago. Although almost all treatments targeting specific molecular alterations have failed so far when administered to unselected patients, encouraging results were observed in the small subpopulations of patients with germline BRCA 1/2 mutations, and somatic gene fusions (neurotrophic tyrosine receptor kinase, Neuregulin 1, which are enriched in KRAS wild-type PDAC), KRAS G12C mutations, or microsatellite instability. While targeted tumor metabolism therapies and immunotherapy have been disappointing, they are still under investigation in combination with other drugs. Optimizing pharmacokinetics and adapting available chemotherapies based on molecular signatures are other promising avenues of research. This review evaluates the current expectations and limits of available treatments and analyses the existing trials. A permanent search for actionable vulnerabilities in PDAC tumor cells and microenvironments will probably result in a more personalized therapeutic approach, keeping in mind that supportive care must also play a major role if real clinical efficacy is to be achieved in these patients

Multi-omics data integration and modeling unravels new mechanisms for pancreatic cancer and improves prognostic prediction

Pancreatic ductal adenocarcinoma (PDAC), has recently been found to be a heterogeneous disease, although the extension of its diversity remains to be fully understood. Here, we harmonize transcriptomic profiles derived from both PDAC epithelial and microenvironment cells to develop a Master Regulators (MR)-Gradient model that allows important inferences on transcriptional networks, epigenomic states, and metabolomics pathways that underlies this disease heterogeneity. This gradient model was generated by applying a blind source separation based on independent components analysis and robust principal component analyses (RPCA), following regulatory network inference. The result of these analyses reveals that PDAC prognosis strongly associates with the tumor epithelial cell phenotype and the immunological component. These studies were complemented by integration of methylome and metabolome datasets generated from patient-derived xenograft (PDX), together experimental measurements of metabolites, immunofluorescence microscopy, and western blot. At the metabolic level, PDAC favorable phenotype showed a positive correlation with enzymes implicated in complex lipid biosynthesis. In contrast, the unfavorable phenotype displayed an augmented OXPHOS independent metabolism centered on the Warburg effect and glutaminolysis. Epigenetically, we find that a global hypermethylation profile associates with the worst prognosis. Lastly, we report that, two antagonistic histone code writers, SUV39H1/SUV39H2 (H3K9Me3) and KAT2B (H3K9Ac) were identified key deregulated pathways in PDAC. Our analysis suggests that the PDAC phenotype, as it relates to prognosis, is determined by a complex interaction of transcriptomic, epigenomic, and metabolic features. Furthermore, we demonstrated that PDAC prognosis could be modulated through epigenetics

Squamousness gain defines pancreatic ductal adenocarcinoma hepatic metastases phenotype, and gemcitabine response

Background: Pancreatic ductal adenocarcinoma (PDAC) is a dismal disease with a survival rate of less than 7%, mainly due to the hepatic metastatic spread. Despite the importance of understanding PDAC metastases, central questions remain concerning their biology and chemosensitivity. Moreover, the transcriptomic divergence between primary tumor (PT) and hepatic metastases (HM) has been poorly studied and without a clear dissection of the confounding tumoral-surrounding tissue. Methods: Here, to unravel key biological features not biased by the surrounding tissue, we implemented a blind source separation based on independent component analysis, ProDenICA, on a treatment-naïve cohort of PDAC paired samples and a cohort of 305 resectable patients. In addition, a time-lapse experiment was performed to assess the gemcitabine chemosensitivity profile between the PT and HM. Results: We identified HM's specific transcriptomic characteristics related to the upregulation of cell cycle checkpoint, mitochondria activity, and extracellular matrix reorganization, which could be associated with metastatic niche adaptation mechanisms. Furthermore, squamous lineage emerged as a key feature linked with a downregulation in the epithelial-to-mesenchymal program that can stratifies PDAC HM independent of the classical/basal-like spectrum. Remarkably, we also demonstrated that gemcitabine response is influenced by the squamous profile, being the HM more refractory to the treatment than the PT. Conclusions: These results pointed out divergent HM aspects compared to PT and allowed their stratification through the squamous lineage. Moreover, we unravel a clinical actionable squamous signature that predicts the gemcitabine response.Fil: Fraunhoffer Navarro, Nicolas Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Centro de Estudios Farmacológicos y Botánicos. Universidad de Buenos Aires. Facultad de Medicina. Centro de Estudios Farmacológicos y Botánicos; Argentina. Inserm; FranciaFil: Meilerman Abuelafia, Miriam Analia. Inserm; FranciaFil: Teyssedou, Carlos. Inserm; FranciaFil: Chuluyan, Hector Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Centro de Estudios Farmacológicos y Botánicos. Universidad de Buenos Aires. Facultad de Medicina. Centro de Estudios Farmacológicos y Botánicos; ArgentinaFil: Bigonnet, Martin. Inserm; FranciaFil: Palazzo, Laurent. Inserm; FranciaFil: Gayet, Odile. Inserm; FranciaFil: Remy, Nicolle. Inserm; FranciaFil: Cros, Jerome. Inserm; FranciaFil: Iovanna, Juan Lucio. Inserm; FranciaFil: Dusetti, Nelson. Inserm; Franci

Immunophenotypic and molecular characterization of pancreatic neuroendocrine tumors producing serotonin.

Serotonin producing pancreatic neuroendocrine tumors (SP-PanNET) account for 0.58-1.4% of all pancreatic neuroendocrine tumors (PanNET). They may present with atypical symptoms, such as acute pancreatitis and are often radiologically characterized by main pancreatic duct dilatation. SP-PanNET are well differentiated neuroendocrine tumors (NET) distinct from classical PanNET by atypical serotonin secretion and abundant dense stroma deposition, like serotonin producing ileal NET leading in some cases to difficulties to reliably distinguish SP-PanNET from ileal NET metastases. The biology and molecular profile of SP-PanNET remain poorly characterized and the cell of origin within the pancreas is unclear. To address these questions, we analyzed a large cohort of SP-PanNET by immunohistochemistry (n = 29; ATRX, DAXX, MENIN, Islet1, PAX6, PDX1, ARX, CDX2), whole genome copy number array (Oncoscan™) and a large NGS panel (NovoPM™) (n = 10), FISH (n = 13) and RNA sequencing (n = 24) together with 21 ileal NET and 29 nonfunctioning PanNET (NF-PanNET). These analyses revealed a unique genomic profile with frequent isolated loss of chromosome 1 (14 cases-61%) and few pathogenic mutations (KMT2C in 2 cases, ARID1A in 1 case). Unsupervised RNAseq-based clustering showed that SP-PanNET were closer to NF-PanNET than ileal NET with an exclusive beta cell-like signature. SP-PanNET showed TGF-β pathway activation signatures associated with extracellular matrix remodeling and similar signature were reproduced in vitro when pancreatic stellate cells were exposed to serotonin. SP-PanNET immunohistochemical profile resemble that of ileal NET except for PDX1 and PAX6 expression to a lesser extend suggesting that these two markers may be useful to diagnose SP-PanNET. Taken together, this suggests that SP-PanNET are a very specific PanNET entity with a peculiar biology leading to the characteristic fibrotic aspect

Flow chart of the different analysis steps.

<p>The first step is the identification through public data bases and expert knowledge of the genes of interest to study, here the Rabs and their effectors. The second step consists of selecting subgroups of tumors and analysing the expression of the different genes selected in the first step in these subgroups compared to the normal urothelium. The subgrouping here has been done taking into account the <i>FGFR3</i> mutation status, the stage and the grade, separating the tumors into two pathways. A comparison of the expression observed in bladder cancer cell lines and in cultured normal human urothelial cells allowed discarding of genes for which the expression could be possibly due to the presence of stroma (in comparison to normal cells, upregulation in bladder tumors but not in bladder tumor cell lines). Different types of analysis were then performed on the selected deregulated genes: 1) a comparison of the expression in <i>FGFR3</i>-mutated tumors and <i>FGFR3</i>-non-mutated tumors allowed the identification of genes specifically deregulated in one of the two pathways of bladder cancer pathogenesis; 2) by grouping genes into cluster of genes (here the Rab clusters), we identified clusters with deregulated expression; 3) by analysing the possible correlation between the expression of the deregulated genes and the expression of proliferation or differentiation marker genes, we identified the deregulated genes associated with proliferation or differentiation.</p

Genes specifically deregulated in one of the two pathways of bladder cancer pathogenesis.

<p>SAM analysis of the deregulated genes was performed comparing their expression, for a given stage, <i>FGFR3</i>-mutated tumors and <i>FGFR3</i>-non-mutated tumors. Only the genes found differentially expressed are presented. <i>SYTL1</i>, which is down-regulated in <i>FGFR3</i>-non-mutated T2–4 tumors compared to normal urothelium (first 2 columns and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039469#pone-0039469-t002" target="_blank">Table 2</a>) is also specifically down-regulated in <i>FGFR3</i>-non-mutated T2–4 tumors compared to <i>FGFR3</i>-mutated T2–4 tumors (last 2 columns). <i>LEPRE1</i>, <i>MICAL2</i>, <i>RAB23</i> and <i>STXBP1</i>, which are up-regulated in <i>FGFR3</i>-non-mutated T2–4 tumors compared to normal urothelium (first 2 columns and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039469#pone-0039469-t002" target="_blank">Table 2</a>) are also specifically up-regulated in <i>FGFR3</i>-non-mutated T2–4 tumors compared to <i>FGFR3</i>-mutated T2–4 tumors (last 2 columns). FC: Fold Change.</p