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Pochet, Nathalie

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Pochet

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Nathalie

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Pochet, Nathalie
Author's Publications: search.filters.isAuthorOfPublication.09ce5c35-d46b-4fb6-9fc3-e34643a2102a

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    miR-135a-5p-mediated downregulation of protein tyrosine phosphatase receptor delta is a candidate driver of HCV-associated hepatocarcinogenesis
    (BMJ Publishing Group, 2018) Van Renne, Nicolaas; Roca Suarez, Armando Andres; Duong, Francois H T; Gondeau, Claire; Calabrese, Diego; Fontaine, Nelly; Ababsa, Amina; Bandiera, Simonetta; Croonenborghs, Tom; Pochet, Nathalie; De Blasi, Vito; Pessaux, Patrick; Piardi, Tullio; Sommacale, Daniele; Ono, Atsushi; Chayama, Kazuaki; Fujita, Masashi; Nakagawa, Hidewaki; Hoshida, Yujin; Zeisel, Mirjam B; Heim, Markus H; Baumert, Thomas F; Lupberger, Joachim
    Background and aims HCV infection is a leading risk factor of hepatocellular carcinoma (HCC). However, even after viral clearance, HCC risk remains elevated. HCV perturbs host cell signalling to maintain infection, and derailed signalling circuitry is a key driver of carcinogenesis. Since protein phosphatases are regulators of signalling events, we aimed to identify phosphatases that respond to HCV infection with relevance for hepatocarcinogenesis. Methods: We assessed mRNA and microRNA (miRNA) expression profiles in primary human hepatocytes, liver biopsies and resections of patients with HCC, and analysed microarray and RNA-seq data from paired liver biopsies of patients with HCC. We revealed changes in transcriptional networks through gene set enrichment analysis and correlated phosphatase expression levels to patient survival and tumour recurrence. Results: We demonstrate that tumour suppressor protein tyrosine phosphatase receptor delta (PTPRD) is impaired by HCV infection in vivo and in HCC lesions of paired liver biopsies independent from tissue inflammation or fibrosis. In liver tissue adjacent to tumour, high PTPRD levels are associated with a dampened transcriptional activity of STAT3, an increase of patient survival from HCC and reduced tumour recurrence after surgical resection. We identified miR-135a-5p as a mechanistic regulator of hepatic PTPRD expression in patients with HCV. Conclusions: We previously demonstrated that STAT3 is required for HCV infection. We conclude that HCV promotes a STAT3 transcriptional programme in the liver of patients by suppressing its regulator PTPRD via upregulation of miR-135a-5p. Our results show the existence of a perturbed PTPRD–STAT3 axis potentially driving malignant progression of HCV-associated liver disease.
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    Module Analysis Captures Pancancer Genetically and Epigenetically Deregulated Cancer Driver Genes for Smoking and Antiviral Response
    (Elsevier, 2017) Champion, Magali; Brennan, Kevin; Croonenborghs, Tom; Gentles, Andrew J.; Pochet, Nathalie; Gevaert, Olivier
    The availability of increasing volumes of multi-omics profiles across many cancers promises to improve our understanding of the regulatory mechanisms underlying cancer. The main challenge is to integrate these multiple levels of omics profiles and especially to analyze them across many cancers. Here we present AMARETTO, an algorithm that addresses both challenges in three steps. First, AMARETTO identifies potential cancer driver genes through integration of copy number, DNA methylation and gene expression data. Then AMARETTO connects these driver genes with co-expressed target genes that they control, defined as regulatory modules. Thirdly, we connect AMARETTO modules identified from different cancer sites into a pancancer network to identify cancer driver genes. Here we applied AMARETTO in a pancancer study comprising eleven cancer sites and confirmed that AMARETTO captures hallmarks of cancer. We also demonstrated that AMARETTO enables the identification of novel pancancer driver genes. In particular, our analysis led to the identification of pancancer driver genes of smoking-induced cancers and ‘antiviral’ interferon-modulated innate immune response. Software availability AMARETTO is available as an R package at https://bitbucket.org/gevaertlab/pancanceramaretto
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    Type I interferons and microbial metabolites of tryptophan modulate astrocyte activity and CNS inflammation via the aryl hydrocarbon receptor
    (2016) Rothhammer, Veit; Mascanfroni, Ivan D.; Bunse, Lukas; Takenaka, Maisa C.; Kenison, Jessica E.; Mayo, Lior; Chao, Chun-Cheih; Patel, Bonny; Yan, Raymond; Blain, Manon; Alvarez, Jorge I.; Kébir, Hania; Anandasabapathy, Niroshana; Izquierdo, Guillermo; Jung, Steffen; Obholzer, Nikolaus; Pochet, Nathalie; Clish, Clary B.; Prinz, Marco; Prat, Alexandre; Antel, Jack; Quintana, Francisco
    Astrocytes play important roles in the central nervous system (CNS) during health and disease. Through genome-wide analyses we detected a transcriptional response to type I interferons (IFN-I) in astrocytes during experimental CNS autoimmunity and also in CNS lesions from multiple sclerosis (MS) patients. IFN-I signaling in astrocytes reduces inflammation and experimental autoimmune encephalomyelitis (EAE) disease scores via the ligand-activated transcription factor aryl hydrocarbon receptor (AhR) and suppressor of cytokine signaling 2 (SOCS2). The anti-inflammatory effects of nasally administered IFN-β are partly mediated by AhR. Dietary tryptophan is metabolized by the gut microbiota into AhR agonists that act on astrocytes to limit CNS inflammation. EAE scores were increased following ampicillin treatment during the recovery phase, and CNS inflammation was reduced in antibiotic-treated mice by supplementation with the tryptophan metabolites indole, indoxyl-3-sulfate (I3S), indole-3-propionic acid (IPA) and indole-3-aldehyde (IAld), or the bacterial enzyme tryptophanase. In individuals with MS, the circulating levels of AhR agonists were decreased. These findings suggest that IFN-I produced in the CNS act in combination with metabolites derived from dietary tryptophan by the gut flora to activate AhR signaling in astrocytes and suppress CNS inflammation.
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    Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace
    (2015) Qu, Kun; Garamszegi, Sara; Wu, Felix; Thorvaldsdottir, Helga; Liefeld, Ted; Ocana, Marco; Borges-Rivera, Diego; Pochet, Nathalie; Robinson, James T.; Demchak, Barry; Hull, Tim; Ben-Artzi, Gil; Blankenberg, Daniel; Barber, Galt P.; Lee, Brian T.; Kuhn, Robert M.; Nekrutenko, Anton; Segal, Eran; Ideker, Trey; Reich, Michael; Regev, Aviv; Chang, Howard Y.; Mesirov, Jill P.
    Integrative analysis of multiple data types to address complex biomedical questions requires the use of multiple software tools in concert and remains an enormous challenge for most of the biomedical research community. Here we introduce GenomeSpace (http://www.genomespace.org), a cloud-based, cooperative community resource. Seeded as a collaboration of six of the most popular genomics analysis tools, GenomeSpace now supports the streamlined interaction of 20 bioinformatics tools and data resources. To facilitate the ability of non-programming users’ to leverage GenomeSpace in integrative analysis, it offers a growing set of ‘recipes’, short workflows involving a few tools and steps to guide investigators through high utility analysis tasks.
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    Transcriptional signature of human pro-inflammatory TH17 cells identifies reduced IL10 gene expression in multiple sclerosis
    (Nature Publishing Group UK, 2017) Hu, Dan; Notarbartolo, Samuele; Croonenborghs, Tom; Patel, Bonny; Cialic, Ron; Yang, Tun-Hsiang; Aschenbrenner, Dominik; Andersson, Karin M.; Gattorno, Marco; Pham, Minh; Kivisakk, Pia; Pierre, Isabelle V.; Lee, Youjin; Kiani, Karun; Bokarewa, Maria; Tjon, Emily; Pochet, Nathalie; Sallusto, Federica; Kuchroo, Vijay; Weiner, Howard
    We have previously reported the molecular signature of murine pathogenic TH17 cells that induce experimental autoimmune encephalomyelitis (EAE) in animals. Here we show that human peripheral blood IFN-γ+IL-17+ (TH1/17) and IFN-γ−IL-17+ (TH17) CD4+ T cells display distinct transcriptional profiles in high-throughput transcription analyses. Compared to TH17 cells, TH1/17 cells have gene signatures with marked similarity to mouse pathogenic TH17 cells. Assessing 15 representative signature genes in patients with multiple sclerosis, we find that TH1/17 cells have elevated expression of CXCR3 and reduced expression of IFNG, CCL3, CLL4, GZMB, and IL10 compared to healthy controls. Moreover, higher expression of IL10 in TH17 cells is found in clinically stable vs. active patients. Our results define the molecular signature of human pro-inflammatory TH17 cells, which can be used to both identify pathogenic TH17 cells and to measure the effect of treatment on TH17 cells in human autoimmune diseases.
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    Nanowire-Mediated Delivery Enables Functional Interrogation of Primary Immune Cells: Application to the Analysis of Chronic Lymphocytic Leukemia
    (American ChemicalSociety, 2012) Shalek, Alexander; Gaublomme, Jellert; Wang, Lili; Yosef, Nir; Chevrier, Nicolas; Andersen, Mette S.; Robinson, Jacob T.; Pochet, Nathalie; Neuberg, Donna; Gertner, Rona; Amit, Ido; Brown, Jennifer; Hacohen, Nir; Regev, Aviv; Wu, Catherine; Park, Hongkun
    A circuit level understanding of immune cells and hematological cancers has been severely impeded by a lack of techniques that enable intracellular perturbation without significantly altering cell viability and function. Here, we demonstrate that vertical silicon nanowires (NWs) enable gene-specific manipulation of diverse murine and human immune cells with negligible toxicity. To illustrate the power of the technique, we then apply NW-mediated gene silencing to investigate the role of the Wnt signaling pathway in chronic lymphocytic leukemia (CLL). Remarkably, CLL-B cells from different patients exhibit tremendous heterogeneity in their response to the knockdown of a single gene, LEF1. This functional heterogeneity defines three distinct patient groups not discernible by conventional CLL cytogenetic markers and provides a prognostic indicator for patients’ time to first therapy. Analyses of gene expression signatures associated with these functional patient subgroups reveal unique insights into the underlying molecular basis for disease heterogeneity. Overall, our findings suggest a functional classification that can potentially guide the selection of patient-specific therapies in CLL and highlight the opportunities for nanotechnology to drive biological inquiry.