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230 results on '"Pascal Barbry"'

1. The MIR34B/C genomic region contains multiple potential regulators of multiciliogenesis

Author: Amélie Cavard, Elisa Redman, Olivier Mercey, Sophie Abelanet, Magali Plaisant, Marie‐Jeanne Arguel, Virginie Magnone, Sandra Ruiz García, Géraldine Rios, Marie Deprez, Kévin Lebrigand, Gilles Ponzio, Ignacio Caballero, Pascal Barbry, Laure‐Emmanuelle Zaragosi, and Brice Marcet
Subjects: Structural Biology, Genetics, Biophysics, Cell Biology, Molecular Biology, Biochemistry
Published: 2023

2. BABA-induced pathogen resistance: a multi-omics analysis of the tomato response reveals a hyper-receptive status involving ethylene

Author: Martina Zapletalová, Corinne Rancurel, Benoit Industri, Marc Bardin, Kevin Le Brigand, Philippe Nicot, Virginie Magnone, Aurélie Seassau, Pascal Barbry, David Potěšil, Zbyněk Zdráhal, Michel Ponchet, and Jan Lochman
Subjects: Genetics, Plant Science, Horticulture, Biochemistry, Biotechnology
Abstract: Prior exposure to microbial-associated molecular patterns or specific chemical compounds can promote plants into a primed state with stronger defence responses. β-aminobutyric acid (BABA) is an endogenous stress metabolite that induces resistance protecting various plants towards diverse stresses. In this study, by integrating BABA-induced changes in selected metabolites with transcriptome and proteome data, we generated a global map of the molecular processes operating in BABA-induced resistance (BABA-IR) in tomato. BABA significantly restricts the growth of the pathogens Oidium neolycopersici and Phytophthora parasitica but not Botrytis cinerea. A cluster analysis of the upregulated processes showed that BABA acts mainly as a stress factor in tomato. The main factor distinguishing BABA-IR from other stress conditions was the extensive induction of signaling and perception machinery playing a key role in effective resistance against pathogens. Interestingly, the signalling processes and immune response activated during BABA-IR in tomato differed from those in Arabidopsis with substantial enrichment of genes associated with jasmonic acid (JA) and ethylene (ET) signalling and no change in Asp levels. Our results revealed key differences between the effect of BABA on tomato and other model plants studied until now. Surprisingly, salicylic acid (SA) is not involved in BABA downstream signalization whereas ET and JA play a crucial role.
Published: 2023

3. Data from Gene expression profiling of imatinib and PD166326-resistant CML cell lines identifies Fyn as a gene associated with resistance to BCR-ABL inhibitors

Author: Patrick Auberger, Bernard Mari, Jill Patrice Cassuto, Marcel Deckert, Pascal Barbry, Kevin Lebrigand, Arnaud Jacquel, Pascal Colosetti, Maeva Dufies, Alexandre Puissant, and Sébastien Grosso
Abstract: Imatinib is used to treat chronic myelogenous leukemia (CML), but resistance develops in all phases of this disease. The purpose of the present study was to identify the mode of resistance of newly derived imatinib-resistant (IM-R) and PD166326-resistant (PD-R) CML cells. IM-R and PD-R clones exhibited an increase in viability and a decrease in caspase activation in response to various doses of imatinib and PD166326, respectively, as compared with parental K562 cells. Resistance involved neither mutations in BCR-ABL nor increased BCR-ABL, MDR1 or Lyn expression, all known modes of resistance. To gain insight into the resistance mechanisms, we used pangenomic microarrays and identified 281 genes modulated in parental versus IM-R and PD-R cells. The gene signature was similar for IM-R and PD-R cells, accordingly with the cross-sensitivity observed for both inhibitors. These genes were functionally associated with pathways linked to development, cell adhesion, cell growth, and the JAK-STAT cascade. Especially relevant were the increased expression of the tyrosine kinases AXL and Fyn as well as CD44 and HMGA2. Small interfering RNA experiments and pharmacologic approaches identified FYN as a candidate for resistance to imatinib. Our findings provide a comprehensive picture of the transcriptional events associated with imatinib and PD166326 resistance and identify Fyn as a new potential target for therapeutic intervention in CML. [Mol Cancer Ther 2009;8(7):1924–33]
Published: 2023

4. Supplemental Figure 1 from Gene expression profiling of imatinib and PD166326-resistant CML cell lines identifies Fyn as a gene associated with resistance to BCR-ABL inhibitors

Author: Patrick Auberger, Bernard Mari, Jill Patrice Cassuto, Marcel Deckert, Pascal Barbry, Kevin Lebrigand, Arnaud Jacquel, Pascal Colosetti, Maeva Dufies, Alexandre Puissant, and Sébastien Grosso
Abstract: Legend to supplemental Figure 1: Ingenuity Pathway Analysis identifies a network of genes upregulated in both resistant clones compared to parental cells. The network is displayed graphically as nodes (genes/gene products) and edges (the biological relationships between the nodes). All grey nodes correspond to up-regulated genes in both IM-R and PD-R resistant cells. As described in the legend provided, nodes are displayed using various shapes that represent the functional class of the gene product. Edges are displayed with various labels that describe the nature of the relationship between the nodes (A, activation; B, binding; E, expression; I, inhibition; P, phosphorylation; T, transcription). Edges without a label represent binding only. White nodes were identified by the pathway analysis as part of the network.
Published: 2023

5. Supplemental Table 1 from Gene expression profiling of imatinib and PD166326-resistant CML cell lines identifies Fyn as a gene associated with resistance to BCR-ABL inhibitors

Author: Patrick Auberger, Bernard Mari, Jill Patrice Cassuto, Marcel Deckert, Pascal Barbry, Kevin Lebrigand, Arnaud Jacquel, Pascal Colosetti, Maeva Dufies, Alexandre Puissant, and Sébastien Grosso
Abstract: All significant (p {less than or equal to} 0.05) categories resulting from each list produced the over-represented biological themes shown in supplementary Table 1.
Published: 2023

6. OligoArchive-DSM: Columnar Design for Error-Tolerant Database Archival using Synthetic DNA

Author: Eugenio Marinelli, Yiqing Yan, Virginie Magnone, Marie-Charlotte Dumargne, Pascal Barbry, Thomas Heinis, and Raja Appuswamy
Abstract: The surge in demand for cost-effective, durable long-term archival media, coupled with density limitations of contemporary magnetic media, has resulted in synthetic DNA emerging as a promising new alternative. Today, the limiting factor for DNA-based data archival is the cost of writing (synthesis) and reading (sequencing) DNA. Newer techniques that reduce the cost often do so at the expense of reliability, as they introduce complex, technology-specific error patterns. In order to deal with such errors, it is important to design efficient pipelines that can carefully use redundancy to mask errors without amplifying overall cost. In this paper, we present OligoArchive-DSM (OA-DSM), an end-to-end DNA archival pipeline that can provide error-tolerant data storage at low read/write costs. Central to OA-DSM is a database-inspired columnar encoding technique that makes it possible to improve efficiency by enabling integrated decoding and consensus calling during data restoration.
Published: 2022

7. Coupling live-cell imaging and in situ isolation of the same single cell to profile the transient states of predicted drug-tolerant cells

Author: Benjamin Bian, Agnès Paquet, Marie-Jeanne Arguel, Mickael Meyer, Ludovic Peyre, Asma Chalabi, Marielle Péré, Kevin Lebrigand, Rainer Waldmann, Pascal Barbry, Paul Hofman, Jérémie Roux, Institut de pharmacologie moléculaire et cellulaire (IPMC), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Biological control of artificial ecosystems (BIOCORE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Université Côte d'Azur (UCA), Interdisciplinary Institute for Artificial Intelligence (3iA Côte d’Azur), Centre de Lutte contre le Cancer Antoine Lacassagne [Nice] (UNICANCER/CAL), and UNICANCER-Université Côte d'Azur (UCA)
Subjects: General Immunology and Microbiology, General Neuroscience, [SDV]Life Sciences [q-bio], [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], [SDV.CAN]Life Sciences [q-bio]/Cancer, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, General Biochemistry, Genetics and Molecular Biology, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI], [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], [INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing, [INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV], [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.IB]Life Sciences [q-bio]/Bioengineering, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BT]Computer Science [cs]/Biotechnology
Abstract: International audience; Cell response variability is a starting point in cancer drug resistance that has been difficult to analyze because the tolerant cell states are short lived. Here, we present fate-seq, an approach to isolate single cells in their transient states of drug sensitivity or tolerance before profiling. The drug response is predicted in live cells, which are laser-captured by microdissection before any drug-induced change can alter their states. This framework enables the identification of the cell-state signatures causing differential cell decisions upon treatment.
Published: 2022

8. Coupling live-cell imaging and

Author: Benjamin, Bian, Agnès, Paquet, Marie-Jeanne, Arguel, Mickael, Meyer, Ludovic, Peyre, Asma, Chalabi, Marielle, Péré, Kevin, Lebrigand, Rainer, Waldmann, Pascal, Barbry, Paul, Hofman, and Jérémie, Roux
Subjects: Diagnostic Imaging, Lasers, Microdissection
Abstract: Cell response variability is a starting point in cancer drug resistance that has been difficult to analyze because the tolerant cell states are short lived. Here, we present fate-seq, an approach to isolate single cells in their transient states of drug sensitivity or tolerance before profiling. The drug response is predicted in live cells, which are laser-captured by microdissection before any drug-induced change can alter their states. This framework enables the identification of the cell-state signatures causing differential cell decisions upon treatment. For complete details on the use and execution of this protocol, please refer to Meyer et al. (2020).
Published: 2022

9. An integrated cell atlas of the human lung in health and disease

Author: Malte Luecken, Lisa Sikkema, Daniel Strobl, Luke Zappia, Elo Madissoon, Nikolay Markov, Laure-Emmanuelle Zaragosi, Meshal Ansari, Marie-Jeanne Arguel, Leonie Apperloo, Christophe Becavin, Marijn Berg, Evgeny Chichelnitskiy, Mei-i Chung, Antoine Collin, Aurore Gay, Baharak Hooshiar Kashani, Manu Jain, Theodore Kapellos, Tessa Kole, Christoph Mayr, Michael von Papen, Lance Peter, Ciro Ramírez-Suástegui, Janine Schniering, Chase Taylor, Thomas Walzthoeni, Chuan Xu, Linh Bui, Carlo de Donno, Leander Dony, Minzhe Guo, Austin Gutierrez, Lukas Heumos, Ni Huang, Ignacio Ibarra Del Río, Nathan Jackson, Preetish Kadur Lakshminarasimha Murthy, Mohammad Lotfollahi, Tracy Tabib, Carlos Talavera-Lopez, Kyle Travaglini, Anna Wilbrey-Clark, Kaylee Worlock, Masahiro Yoshida, Tushar Desai, Orit Rozenblatt-Rosen, Christine Falk, Naftali Kaminski, Mark Krasnow, Robert Lafyatis, Marko Nikolic, Joseph Powell, Jay Rajagopal, Max Seibold, Dean Sheppard, Douglas Shepherd, Sarah Teichmann, Alexander Tsankov, Jeffrey Whitsett, Yan Xu, Nicholas Banovich, Pascal Barbry, Thu Duong, Kerstin Meyer, Jonathan Kropski, Dana Pe'er, Herbert Schiller, Purushothama Rao Tata, Joachim Schultze, Maarten van den Berge, Yuexin Chen, James Hagood, Ahmed Hassan, Peter Horvath, Joakim Lundeberg, Sylvie Leroy, Charles Marquette, Gloria Pryhuber, Christos Samakovlis, Xin Sun, Lorraine Ware, Kun Zhang, Alexander Misharin, Martijn Nawijn, and Fabian Theis
Abstract: Organ- and body-scale cell atlases have the potential to transform our understanding of human biology. To capture the variability present in the population, these atlases must include diverse demographics such as age and ethnicity from both healthy and diseased individuals. The growth in both size and number of single-cell datasets, combined with recent advances in computational techniques, for the first time makes it possible to generate such comprehensive large-scale atlases through integration of multiple datasets. Here, we present the integrated Human Lung Cell Atlas (HLCA) combining 46 datasets of the human respiratory system into a single atlas spanning over 2.2 million cells from 444 individuals across health and disease. The HLCA contains a consensus re-annotation of published and newly generated datasets, resolving under- or misannotation of 59% of cells in the original datasets. The HLCA enables recovery of rare cell types, provides consensus marker genes for each cell type, and uncovers gene modules associated with demographic covariates and anatomical location within the respiratory system. To facilitate the use of the HLCA as a reference for single-cell lung research and allow rapid analysis of new data, we provide an interactive web portal to project datasets onto the HLCA. Finally, we demonstrate the value of the HLCA reference for interpreting disease-associated changes. Thus, the HLCA outlines a roadmap for the development and use of organ-scale cell atlases within the Human Cell Atlas.
Published: 2022

10. Regeneration of airway epithelial cells to study rare cell states in cystic fibrosis

Author: Marc Chanson, Aron B. Jaffe, Amélie Cavard, Pascal Barbry, Lindsey W. Plasschaert, Centre National de la Recherche Scientifique (CNRS), Université Côte d'Azur (UCA), Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)
Subjects: 0301 basic medicine, Pulmonary and Respiratory Medicine, Cell type, Airway epithelium, Cystic Fibrosis, [SDV]Life Sciences [q-bio], Cystic Fibrosis Transmembrane Conductance Regulator, Cellular models, Respiratory Mucosa, Models, Biological, Cystic fibrosis, 03 medical and health sciences, 0302 clinical medicine, medicine, Animals, Humans, Regeneration, Cell Self Renewal, Progenitor cell, ddc:612, ddc:618, business.industry, Regeneration (biology), airway epithelium, medicine.disease, Epithelium, Cell biology, 030104 developmental biology, medicine.anatomical_structure, 030228 respiratory system, repair, Pediatrics, Perinatology and Child Health, Airway Remodeling, Respiratory epithelium, RNA-seq, cellular models, Airway, business, Repair, Function (biology)
Abstract: International audience; Pathological remodeling of the airway epithelium is commonly observed in cystic fibrosis (CF). Thus, tissue repair is critical to restore integrity and maintenance of the epithelial barrier function. Epithelial repair is a multi-step process initiated by progenitor cell migration into the injured area, proliferation, and re-differentiation into all of the cell types that contribute to the function of a normal airway epithelium. Recent technological advances applied to relevant animal and cell injury models have helped in understanding the complexity of progenitor cell differentiation. This short review will introduce the current knowledge of the mechanisms regulating airway epithelial cell (AEC) regeneration and repair, with a focus on the specification of two rare cell types/states: ionocytes and deuterosomal cells. Introduction
Published: 2020

11. Unravelling the sex-specific diversity and functions of adrenal gland macrophages

Author: Bastien Dolfi, Alexandre Gallerand, Maria M. Firulyova, Yingzheng Xu, Johanna Merlin, Adélie Dumont, Alexia Castiglione, Nathalie Vaillant, Sandrine Quemener, Heidi Gerke, Marion I. Stunault, Patricia R. Schrank, Seung-Hyeon Kim, Alisha Zhu, Jie Ding, Jerome Gilleron, Virginie Magnone, Pascal Barbry, David Dombrowicz, Christophe Duranton, Abdelilah Wakkach, Claudine Blin-Wakkach, Burkhard Becher, Sophie Pagnotta, Rafael J. Argüello, Pia Rantakari, Svetoslav Chakarov, Florent Ginhoux, Konstantin Zaitsev, Ki-Wook Kim, Laurent Yvan-Charvet, Rodolphe R. Guinamard, Jesse W. Williams, Stoyan Ivanov, DUMENIL, Anita, Ciblage des voies cardiométaboliques pour rétablir l'horloge biologique des monocytes - - MOTACARD2017 - ANR-17-CE14-0017 - AAPG2017 - VALID, The Role of the Pentose Phosphate Pathway on Myeloid Cells Functions during Atherosclerosis - - MyPenPath2019 - ANR-19-ECVD-0005 - ERA-CVD - VALID, Epic-ZENITH : Un effort intégratif pour identifier les régulateurs du métabolisme et de l'épigénétique dans le cellules myéloïdes associées aux glioblastomes - - Epic-ZeNITH2020 - ANR-20-CE14-0028 - AAPG2020 - VALID, Idex UCA JEDI - - UCA JEDI2015 - ANR-15-IDEX-0001 - IDEX - VALID, Laboratoire de PhysioMédecine Moléculaire (LP2M), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), ITMO University [Russia], University of Minnesota Medical School, University of Minnesota System, Centre méditerranéen de médecine moléculaire (C3M), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP), University of Turku, University of Illinois College of Medicine, University of Illinois System, Institut de pharmacologie moléculaire et cellulaire (IPMC), Universität Zürich [Zürich] = University of Zurich (UZH), Université Côte d'Azur (UCA), Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Commun de Microscopie Appliquée (CCMA), Université de Nice Sophia-Antipolis (UNSA), Shanghai Jiao Tong University School of Medicine, ANR-17-CE14-0017,MOTACARD,Ciblage des voies cardiométaboliques pour rétablir l'horloge biologique des monocytes(2017), ANR-19-ECVD-0005,MyPenPath,The Role of the Pentose Phosphate Pathway on Myeloid Cells Functions during Atherosclerosis(2019), ANR-20-CE14-0028,Epic-ZeNITH,Epic-ZENITH : Un effort intégratif pour identifier les régulateurs du métabolisme et de l'épigénétique dans le cellules myéloïdes associées aux glioblastomes(2020), ANR-15-IDEX-0001,UCA JEDI,Idex UCA JEDI(2015), Récepteurs Nucléaires, Maladies Métaboliques et Cardiovasculaires - U1011 (RNMCD), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Centre National de la Recherche Scientifique (CNRS), and ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019)
Subjects: Male, [SDV] Life Sciences [q-bio], Leukocyte Count, Mice, Sex Characteristics, Macrophages, [SDV]Life Sciences [q-bio], Adrenal Glands, Histocompatibility Antigens Class II, Animals, Female, General Biochemistry, Genetics and Molecular Biology, Monocytes
Abstract: Despite the ubiquitous function of macrophages across the body, the diversity, origin, and function of adrenal gland macrophages remain largely unknown. We define the heterogeneity of adrenal gland immune cells using single-cell RNA sequencing and use genetic models to explore the developmental mechanisms yielding macrophage diversity. We define populations of monocyte-derived and embryonically seeded adrenal gland macrophages and identify a female-specific subset with low major histocompatibility complex (MHC) class II expression. In adulthood, monocyte recruitment dominates adrenal gland macrophage maintenance in female mice. Adrenal gland macrophage sub-tissular distribution follows a sex-dimorphic pattern, with MHC class II
Published: 2022

12. The discovAIR project

Author: Malte D. Luecken, Laure-Emmanuelle Zaragosi, Elo Madissoon, Lisa Sikkema, Alexandra B. Firsova, Elena De Domenico, Louis Kümmerle, Adem Saglam, Marijn Berg, Aurore C.A. Gay, Janine Schniering, Christoph H. Mayr, Xesús M. Abalo, Ludvig Larsson, Alexandros Sountoulidis, Sarah A. Teichmann, Karen van Eunen, Gerard H. Koppelman, Kourosh Saeb-Parsy, Sylvie Leroy, Pippa Powell, Ugis Sarkans, Wim Timens, Joakim Lundeberg, Maarten van den Berge, Mats Nilsson, Peter Horváth, Jessica Denning, Irene Papatheodorou, Joachim L. Schultze, Herbert B. Schiller, Pascal Barbry, Ilya Petoukhov, Alexander V. Misharin, Ian M. Adcock, Michael von Papen, Fabian J. Theis, Christos Samakovlis, Kerstin B. Meyer, and Martijn C. Nawijn
Subjects: Lung Diseases, Proteomics, Pulmonary and Respiratory Medicine, Humans, ddc:610, Thorax, respiratory system, Lung
Abstract: The Human Cell Atlas (HCA) consortium aims to establish an atlas of all organs in the healthy human body at single-cell resolution to increase our understanding of basic biological processes that govern development, physiology and anatomy, and to accelerate diagnosis and treatment of disease. The Lung Biological Network of the HCA aims to generate the Human Lung Cell Atlas as a reference for the cellular repertoire, molecular cell states and phenotypes, and cell–cell interactions that characterise normal lung homeostasis in healthy lung tissue. Such a reference atlas of the healthy human lung will facilitate mapping the changes in the cellular landscape in disease. The discovAIR project is one of six pilot actions for the HCA funded by the European Commission in the context of the H2020 framework programme. discovAIR aims to establish the first draft of an integrated Human Lung Cell Atlas, combining single-cell transcriptional and epigenetic profiling with spatially resolving techniques on matched tissue samples, as well as including a number of chronic and infectious diseases of the lung. The integrated Human Lung Cell Atlas will be available as a resource for the wider respiratory community, including basic and translational scientists, clinical medicine, and the private sector, as well as for patients with lung disease and the interested lay public. We anticipate that the Human Lung Cell Atlas will be the founding stone for a more detailed understanding of the pathogenesis of lung diseases, guiding the design of novel diagnostics and preventive or curative interventions.
Published: 2022

13. Cutaneous Squamous Cell Carcinoma Development Is Associated with a Temporal Infiltration of ILC1 and NK Cells with Immune Dysfunctions

Author: Roger Rezzonico, Veronique M. Braud, Ophelie Vermeulen, Sokchea Khou, Gilles Poissonnet, Bernard Mari, Alexandra Popa, Roxane Elaldi, Aida Meghraoui-Kheddar, Fabienne Anjuère, Carmelo Luci, Pierre Bourdely, Anne Sudaka, Alexandre Bozec, Franck Bihl, Julie Cazareth, Gilles Ponzio, Pascal Barbry, Selma Bekri, Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), and Centre Antoine Lacassagne, Nice, France
Subjects: 0301 basic medicine, Adoptive cell transfer, Skin Neoplasms, [SDV]Life Sciences [q-bio], Population, Dermatology, Biology, Biochemistry, 03 medical and health sciences, Mice, 0302 clinical medicine, Immunophenotyping, Immune system, TIGIT, Animals, Humans, Lymphocytes, education, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Neoplasm Staging, Tumor microenvironment, education.field_of_study, Natural Cytotoxicity Triggering Receptor 1, Innate lymphoid cell, Cell Biology, Adoptive Transfer, Immunity, Innate, 3. Good health, Killer Cells, Natural, 030104 developmental biology, Basic-Leucine Zipper Transcription Factors, Tumor progression, 030220 oncology & carcinogenesis, Cancer research, Carcinoma, Squamous Cell
Abstract: NK cells and tissue-resident innate lymphoid cells (ILCs) are innate effectors found in the skin. To investigate their temporal dynamics and specific functions throughout the development of cutaneous squamous cell carcinoma (cSCC), we combined transcriptomic and immunophenotyping analyses in mouse and human cSCCs. We identified an infiltration of NK cells and ILC1s as well as the presence of a few ILC3s. Adoptive transfer of NK cells in NK cell‒ and ILC-deficient Nfil3−/− mice revealed a role for NK cells in early control of cSCC. During tumor progression, we identified a population skewing with the infiltration of atypical ILC1 secreting inflammatory cytokines but reduced levels of IFN-γ at the papilloma stage. NK cells and ILC1s were functionally impaired, with reduced cytotoxicity and IFN-γ secretion associated with the downregulation of activating receptors. They also showed a high degree of heterogeneity in mouse and human cSCCs with the expression of several markers of exhaustion, including TIGIT on NK cells and PD-1 and TIM-3 on ILC1s. Our data show an enrichment in inflammatory ILC1 at the precancerous stage together with impaired antitumor functions in NK cells and ILC1 that could contribute to the development of cSCC and thus suggest that future immunotherapies should take both ILC populations into account.
Published: 2021

14. Decoding Of Nanopore-Sequenced Synthetic DNA Storing Digital Images

Author: Marc Antonini, Pascal Barbry, Raja Appuswamy, Eva Gil San Antonio, Melpomeni Dimopoulou, Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), and Eurecom [Sophia Antipolis]
Subjects: Computer science, business.industry, 020207 software engineering, 02 engineering and technology, Nanopore, Digital image, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], Synthetic DNA, [INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV], 0202 electrical engineering, electronic engineering, information engineering, 020201 artificial intelligence & image processing, Computer vision, Artificial intelligence, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, ComputingMilieux_MISCELLANEOUS, Decoding methods
Abstract: International audience
Published: 2021

15. COVID-19 patients age, comorbidity profiles and clinical presentation related to the SARS-CoV-2 UK-variant spread in the Southeast of France

Author: Pascal Barbry, Johan Courjon, Jean Dellamonica, Michel Carles, Géraldine Rios, Julie Contenti, Valérie Giordanengo, David Chirio, Caroline Bonnefoy, Jacques Levraut, and Elisa Demonchy
Subjects: Male, medicine.medical_specialty, Wastewater-Based Epidemiological Monitoring, Coronavirus disease 2019 (COVID-19), Respiratory distress syndrome, Epidemiology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Science, Nice, Comorbidity, Article, Hospitals, University, Internal medicine, Pandemic, medicine, Humans, computer.programming_language, Aged, Aged, 80 and over, Multidisciplinary, Sewage, business.industry, SARS-CoV-2, Incidence (epidemiology), Incidence, Age Factors, COVID-19, Emergency department, Middle Aged, medicine.disease, United Kingdom, Hospitalization, Viral infection, COVID-19 Nucleic Acid Testing, Medicine, Female, France, Presentation (obstetrics), business, computer
Abstract: The variant 20I/501Y.V1, associated to a higher risk of transmissibility, emerged in Nice city (Southeast of France, French Riviera) during January 2021. The pandemic has resumed late December 2020 in this area. A high incidence rate together with a fast turn-over of the main circulating variants, provided us the opportunity to analyze modifications in clinical profile and outcome traits. We performed an observational study in the University hospital of Nice from December 2020 to February 2021. We analyzed data of sequencing of SARS-CoV-2 from the sewage collector and PCR screening from all positive samples at the hospital. Then, we described the characteristics of all COVID-19 patients admitted in the emergency department (ED) (n = 1247) and those hospitalized in the infectious diseases ward or ICU (n = 232). The UK-variant was absent in this area in December, then increasingly spread in January representing 59% of the PCR screening performed mid-February. The rate of patients over 65 years admitted to the ED decreased from 63 to 50% (p = 0.001). The mean age of hospitalized patients in the infectious diseases ward decreased from 70.7 to 59.2 (p
Published: 2021

16. Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing

Author: Bernard Mari, Adele Lazuka, Emmanuel Soyeux, Kevin Lebrigand, Rainer Waldmann, Sébastien Lacroix, Caroline Lacoux, Géraldine Rios, Vianney Leclercq, Aurelie Couesnon, Pascal Barbry, Julien Fassy, Anna Diamant, Christian Pradier, Richard Thiéry, Centre National de la Recherche Scientifique (CNRS), Université Côte d'Azur (UCA), Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Fondation Recherche Médicale (DEQ20180339158)., National Infrastructure France Génomique (Commissariat aux Grands Investissements, ANR-10-INBS-09-03, ANR-10-INBS-09-02), Conseil Départemental 06 (2019-390), Plan Cancer 2018 « ARN non-codants en cancérologie: du fondamental au translationnel » (Inserm number 18CN045, to BM) Cancéropole PACA (BM), and ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019)
Subjects: Lineage (evolution), coronaviruses, [SDV]Life Sciences [q-bio], Population, Sewage, 010501 environmental sciences, Biology, 01 natural sciences, alpha variant,beta variant, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Pandemic, Internal Medicine, beta variant, education, 030304 developmental biology, 0105 earth and related environmental sciences, Genetics, [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, 0303 health sciences, education.field_of_study, business.industry, Health Policy, Outbreak, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 6. Clean water, 3. Good health, alpha variant, Oncology, Wastewater, Infectious disease (medical specialty), variants-of-concern, gamma variant, Nanopore sequencing, business, Research Paper
Abstract: International audience; Background: Wastewater surveillance was proposed as an epidemiological tool to define the prevalence and evolution of the SARS-CoV-2 epidemics. However, most implemented SARS-CoV-2 wastewater surveillance projects were based on qPCR measurement of virus titers and did not address the mutational spectrum of SARS-CoV-2 circulating in the population.Methods: We have implemented a nanopore RNA sequencing monitoring system in the city of Nice (France, 550,000 inhabitants). Between October 2020 and March 2021, we monthly analyzed the SARS-CoV-2 variants in 113 wastewater samples collected in the main wastewater treatment plant and 20 neighborhoods.Findings: We initially detected the lineages predominant in Europe at the end of 2020 (B.1.160, B.1.177, B.1.367, B.1.474, and B.1.221). In January, a localized emergence of a variant (Spike:A522S) of the B.1.1.7 lineage occurred in one neighborhood. It rapidly spread and became dominant all over the city. Other variants of concern (B.1.351, P.1) were also detected in some neighborhoods, but at low frequency. Comparison with individual clinical samples collected during the same week showed that wastewater sequencing correctly identified the same lineages as those found in COVID-19 patients.Interpretation: Wastewater sequencing allowed to document the diversity of SARS-CoV-2 sequences within the different neighborhoods of the city of Nice. Our results illustrate how sequencing of sewage samples can be used to track pathogen sequence diversity in the current pandemics and in future infectious disease outbreaks.; Contexte : La surveillance des eaux usées apparait comme un outil épidémiologique prometteur pour définir la prévalence et suivre l'évolution des épidémies de SRAS-CoV-2 sur un territoire. Jusqu’à présent, la plupart des projets de surveillance du SRAS-CoV-2 dans les eaux usées reposaient sur une mesure des titres de virus par PCR quantitative et ne fournissaient pas une vision exhaustive de toutes les mutations du SRAS-CoV-2 pouvant circuler dans la population. Méthodes : Nous avons mis en place un système de surveillance par séquençage de l’ARN viral sur séquenceur Oxford Nanopore à l’échelle de toute la ville de Nice (France, 550 000 habitants). Entre octobre 2020 et mars 2021, nous avons analysé chaque mois les différents variants du SRAS-CoV-2 à partir de 113 échantillonnages d'eaux usées collectés au niveau de la station centrale d'épuration et de 20 quartiers différents de la ville.Résultats : Nous avons initialement détecté les lignées prédominant en Europe à la fin de 2020 (B.1.160, B.1.177, B.1.367, B.1.474 et B.1.221). En janvier, l’émergence d'un variant de la lignée B.1.1.7 s'est produite dans un des quartiers de la ville, caractérisé par une mutation A522S sur la spicule. Ce variant s'est rapidement répandu dans toute la ville où il est devenu dominant à partir du mois de février. D'autres variants préoccupants (B.1.351, P.1) ont également été détectés dans certains quartiers, mais toujours à une faible fréquence. La comparaison avec les échantillons cliniques individuels collectés au cours de la même semaine a montré que le séquençage des eaux usées identifiait correctement les mêmes lignées que celles trouvées chez des patients COVID-19.Interprétation : Le séquençage des eaux usées a permis de documenter de façon très précise la diversité des séquences du SRAS-CoV-2 présentes dans les différents quartiers de la ville de Nice. Nos résultats illustrent comment le séquençage des échantillons d'eaux usées peut être utilisé comme outil « micro-épidémiologique » pour suivre la dissémination d’agents pathogènes lors d’épisodes pandémiques et/ou épidémiques, présents ou futurs.
Published: 2021

17. TLR5 signalling is hyper-responsive in porcine cystic fibrosis airways epithelium

Author: Isabelle, Fleurot, Raquel, López-Gálvez, Pascal, Barbry, Antoine, Guillon, Mustapha, Si-Tahar, Andrea, Bähr, Nikolai, Klymiuk, Jean-Claude, Sirard, Ignacio, Caballero, Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Centre d’Etude des Pathologies Respiratoires (CEPR), UMR 1100 (CEPR), Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Gene Center and Center for Innovative Medical Models (CIMM), Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 (CIIL), Centre National de la Recherche Scientifique (CNRS)-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Université de Lille-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Association Vaincre la Mucoviscidose (grants RF20150501357, RF20160501644 and RF20170502036), ANR-18-CE20-0024,PIGIMMUNITY,PIGIMMUNITY: une approche de biologie des systèmes pour stimuler la réponse innée chez le porc(2018), Infectiologie et Santé Publique [UMR ISP], Institut de pharmacologie moléculaire et cellulaire [IPMC], Centre d’Etude des Pathologies Respiratoires (CEPR), UMR 1100 [CEPR], Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL], Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Ludwig Maximilian University [Munich] (LMU), CHU Lille, Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Centre National de la Recherche Scientifique (CNRS), brea, deborah, APPEL À PROJETS GÉNÉRIQUE 2018 - PIGIMMUNITY: une approche de biologie des systèmes pour stimuler la réponse innée chez le porc - - PIGIMMUNITY2018 - ANR-18-CE20-0024 - AAPG2018 - VALID, Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université de Tours-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Cystic Fibrosis, Swine, education, Cystic Fibrosis Transmembrane Conductance Regulator, respiratory system, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, Epithelium, respiratory tract diseases, Toll-Like Receptor 5, Animals, Humans, [SDV.MHEP.PSR] Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, Lung, [SDV.IMM.II] Life Sciences [q-bio]/Immunology/Innate immunity, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Flagellin
Abstract: International audience; Excessive lung inflammation and airway epithelium damage are hallmarks of cystic fibrosis (CF) disease. It is unclear whether lung inflammation is related to an intrinsic defect in the immune response or to chronic infection. We aimed to determine whether TLR5-mediated response is defective in the CF airway epithelium. We used a newborn CF pig model to study intrinsic alterations in CF airway epithelium innate immune response. Airway epithelial cells (AECs) were stimulated with flagellin or lipopolysaccharide to determine responses specific for TLR5 and TLR4, respectively. We observed a significant increase in cytokine secretion when CF AECs were stimulated with flagellin compared to wild type (WT) AECs. These results were recapitulated when AECs were treated with an inhibitor of CFTR channel activity. We show that TLR5-signalling is altered in CF lung epithelium at birth. Modulation of TLR5 signalling could contribute to better control the excessive inflammatory response observed in CF lungs.
Published: 2021

18. Airway Administration of Flagellin Regulates the Inflammatory Response to Pseudomonas aeruginosa

Author: Raquel López-Gálvez, Isabelle Fleurot, Pablo Chamero, Sascha Trapp, Michel Olivier, Claire Chevaleyre, Céline Barc, Mickael Riou, Christelle Rossignol, Antoine Guillon, Mustapha Si-Tahar, Tobias May, Pascal Barbry, Andrea Bähr, Nikolai Klymiuk, Jean-Claude Sirard, Ignacio Caballero
Abstract: Excessive lung inflammation and airway epithelial damage are hallmarks of human inflammatory lung diseases, such as cystic fibrosis (CF). Enhancement of innate immunity provides protection against pathogens while reducing lung-damaging inflammation. However, the mechanisms underlying innate immunity–mediated protection in the lung remain mysterious, in part because of the lack of appropriate animal models for these human diseases. TLR5 (Toll-like receptor 5) stimulation by its specific ligand, the bacterial protein flagellin, has been proposed to enhance protection against several respiratory infectious diseases, although other cellular events, such as calcium signaling, may also control the intensity of the innate immune response. Here, we investigated the molecular events prompted by stimulation with flagellin and its role in regulating innate immunity in the lung of the pig, which is anatomically and genetically more similar to humans than rodent models. We found that flagellin treatment modulated NF-κB signaling and intracellular calcium homeostasis in airway epithelial cells. Flagellin pretreatment reduced the NF-κB nuclear translocation and the expression of proinflammatory cytokines to a second flagellin stimulus as well as toPseudomonas aeruginosainfection. Moreover,invivoadministration of flagellin decreased the severity ofP. aeruginosa–induced pneumonia. Then we confirmed these beneficial effects of flagellin in a pathological model of CF by usingex vivoprecision-cut lung slices from a CF pigz model. These results provide evidence that flagellin treatment contributes to a better regulation of the inflammatory response in inflammatory lung diseases such as CF.
Published: 2021

19. Where Is the Cystic Fibrosis Transmembrane Conductance Regulator?

Author: Ignacio S. Caballero, Brice Marcet, Pascal Barbry, Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Infectiologie et Santé Publique (UMR ISP), Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Vaincre la Mucoviscidose (RF20180502280), Fondation pour la Recherche Médicale (DEQ20180339158), Chan Zuckerberg Initiative (Silicon Valley Foundation), Inserm (Human Developmental Cell Atlas program), ANR-19-CE14-0027,SAHARRA,Analyse par des approches de profilage à large échelle sur cellule unique de la régénération et du remodelage des voies respiratoires chez les patients asthmatiques(2019), ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019), European Project: 874656,discovAIR, Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), and Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Pulmonary and Respiratory Medicine, congenital, hereditary, and neonatal diseases and abnormalities, Cystic Fibrosis, Cell Culture Techniques, Cystic Fibrosis Transmembrane Conductance Regulator, Respiratory Mucosa, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, 030204 cardiovascular system & hematology, Critical Care and Intensive Care Medicine, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, 03 medical and health sciences, 0302 clinical medicine, Medicine, Humans, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Ion Transport, biology, business.industry, Editorials, Epithelial Cells, Original Articles, respiratory system, Cystic fibrosis transmembrane conductance regulator, digestive system diseases, Cell biology, respiratory tract diseases, Case-Control Studies, biology.protein, business, Signal Transduction
Abstract: Rationale: Identification of the specific cell types expressing CFTR (cystic fibrosis [CF] transmembrane conductance regulator) is required for precision medicine therapies for CF. However, a full characterization of CFTR expression in normal human airway epithelia is missing. Objectives: To identify the cell types that contribute to CFTR expression and function within the proximal–distal axis of the normal human lung. Methods: Single-cell RNA (scRNA) sequencing (scRNA-seq) was performed on freshly isolated human large and small airway epithelial cells. scRNA in situ hybridization (ISH) and single-cell qRT-PCR were performed for validation. In vitro culture systems correlated CFTR function with cell types. Lentiviruses were used for cell type–specific transduction of wild-type CFTR in CF cells. Measurements and Main Results: scRNA-seq identified secretory cells as dominating CFTR expression in normal human large and, particularly, small airway superficial epithelia, followed by basal cells. Ionocytes expressed the highest CFTR levels but were rare, whereas the expression in ciliated cells was infrequent and low. scRNA ISH and single-cell qRT-PCR confirmed the scRNA-seq findings. CF lungs exhibited distributions of CFTR and ionocytes similar to those of normal control subjects. CFTR mediated Cl(−) secretion in cultures tracked secretory cell, but not ionocyte, densities. Furthermore, the nucleotide–purinergic regulatory system that controls CFTR-mediated hydration was associated with secretory cells and not with ionocytes. Lentiviral transduction of wild-type CFTR produced CFTR-mediated Cl(−) secretion in CF airway secretory cells but not in ciliated cells. Conclusions: Secretory cells dominate CFTR expression and function in human airway superficial epithelia. CFTR therapies may need to restore CFTR function to multiple cell types, with a focus on secretory cells.
Published: 2021

20. Spread of the SARS-CoV-2 UK-variant in the South East of France: impact on COVID-19 patients’ age, comorbidity profiles and clinical presentation

Author: Elisa Demonchy, David Chirio, M. Carles, Pascal Barbry, Bonnefoy C, Johan Courjon, Géraldine Rios, Dellamonica J, Julie Contenti, Jacques Levraut, and Giordanengo
Subjects: medicine.medical_specialty, Coronavirus disease 2019 (COVID-19), business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Nice, Emergency department, medicine.disease, Comorbidity, Internal medicine, Pandemic, South east, Medicine, Presentation (obstetrics), business, computer, computer.programming_language
Abstract: ObjectivesThe variant 20I/501Y.V1, associated to a higher risk of transmissibility, emerged in Nice city (South East of France, French Riviera) during January 2021. The pandemic has resumed late December 2020 in this aera. A high incidence rate together with a fast turn-over of the main circulating variants, provided us the opportunity to analyze modifications in clinical profile and outcome traits.MethodsObservational study in the University hospital of Nice from December 2020 to February 2021. We analyzed data of sequencing of SARS-CoV-2 from the sewage collector and PCR screening from all positive samples at the hospital. Then, we described the characteristics of all COVID-19 patients admitted in the emergency department (ED) (n=1247) and those hospitalized in the infectious diseases ward or ICU (n=232). Demographic data, clinical signs and severity were recorded by the NEWS-2, SAPS-2 and SOFA scores were recorded and analyzed.Resultsthe UK-variant was absent in the area in December, then increasingly spread in January representing 59% of the PCR screening performed mid-February. The rate of patients over 65 years admitted to the ED decreased from 63% to 50% (p=0.001). The mean age of hospitalized patients in the infectious diseases ward decreased from 70.7 to 59.2 (pConclusionSpread of the UK-variant in the South East of France affects younger and healthier patients.
Published: 2021

21. Correction: The nuclear hypoxia-regulated NLUCAT1 long non-coding RNA contributes to an aggressive phenotype in lung adenocarcinoma through regulation of oxidative stress

Author: Laura Moreno Leon, Marine Gautier, Richard Allan, Marius Ilié, Nicolas Nottet, Nicolas Pons, Agnes Paquet, Kévin Lebrigand, Marin Truchi, Julien Fassy, Virginie Magnone, Garrett Kinnebrew, Milan Radovich, Meyling Hua-Chen Cheok, Pascal Barbry, Georges Vassaux, Charles-Hugo Marquette, Gilles Ponzio, Mircea Ivan, Nicolas Pottier, Paul Hofman, Bernard Mari, and Roger Rezzonico
Subjects: 0303 health sciences, 03 medical and health sciences, Cancer Research, 0302 clinical medicine, 030220 oncology & carcinogenesis, Genetics, Molecular Biology, 030304 developmental biology, 3. Good health
Abstract: Lung cancer is the leading cause of cancer death worldwide, with poor prognosis and a high rate of recurrence despite early surgical removal. Hypoxic regions within tumors represent sources of aggressiveness and resistance to therapy. Although long non-coding RNAs (lncRNAs) are increasingly recognized as major gene expression regulators, their regulation and function following hypoxic stress are still largely unexplored. Combining profiling studies on early-stage lung adenocarcinoma (LUAD) biopsies and on A549 LUAD cell lines cultured in normoxic or hypoxic conditions, we identified a subset of lncRNAs that are both correlated with the hypoxic status of tumors and regulated by hypoxia in vitro. We focused on a new transcript, Nuclear LUCAT1 (NLUCAT1), which is strongly upregulated by hypoxia in vitro and correlated with hypoxic markers and poor prognosis in LUADs. Full molecular characterization showed that NLUCAT1 is a large nuclear transcript composed of six exons and mainly regulated by NF-κB and NRF2 transcription factors. CRISPR-Cas9-mediated invalidation of NLUCAT1 revealed a decrease in proliferative and invasive properties, an increase in oxidative stress and a higher sensitivity to cisplatin-induced apoptosis. Transcriptome analysis of NLUCAT1-deficient cells showed repressed genes within the antioxidant and/or cisplatin-response networks. We demonstrated that the concomitant knockdown of four of these genes products, GPX2, GLRX, ALDH3A1, and PDK4, significantly increased ROS-dependent caspase activation, thus partially mimicking the consequences of NLUCAT1 inactivation in LUAD cells. Overall, we demonstrate that NLUCAT1 contributes to an aggressive phenotype in early-stage hypoxic tumors, suggesting it may represent a new potential therapeutic target in LUADs.
Published: 2021

22. Brown adipose tissue monocytes support tissue expansion

Author: Alexandre Gallerand, Marion I. Stunault, Johanna Merlin, Hannah P. Luehmann, Deborah H. Sultan, Maria M. Firulyova, Virginie Magnone, Narges Khedher, Antoine Jalil, Bastien Dolfi, Alexia Castiglione, Adelie Dumont, Marion Ayrault, Nathalie Vaillant, Jérôme Gilleron, Pascal Barbry, David Dombrowicz, Matthias Mack, David Masson, Thomas Bertero, Burkhard Becher, Jesse W. Williams, Konstantin Zaitse
Published: 2021
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23. Versatile and flexible microfluidic qPCR test for high-throughput SARS-CoV-2 and cellular response detection in nasopharyngeal swab samples

Author: Martin Rottman, Patrick Touron, Georges Vassaux, Latifa Noussair, Vianney Leclercq, Sylvain Hubac, Aurelien Degoutte, Laure-Emmanuelle Zaragosi, Sylvie Leroy, Charles-Hugo Marquette, Jean-Louis Herrmann, Julien Fassy, Antoinette Lemoine, Caroline Lacoux, Pascal Barbry, Jean-Louis Nahon, Bernard Mari, David Rouquié, Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), FHU OncoAge - Pathologies liées à l’âge [CHU Nice] (OncoAge), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Pharmacologie Moléculaire et Cellulaire [UNIV Côte d'Azur] (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Service de Microbiologie [Garches], Hôpital Raymond Poincaré [AP-HP], Institut de Recherche Criminelle de la Gendarmerie Nationale (Ministère de l'intérieur) (IRCGN), Infection et inflammation (2I), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de la Santé et de la Recherche Médicale (INSERM), 'Centre National de la Recherche Scientifique' (CNRS), 'Université Côte d’Azur', French 'French Defence Innovation Agency – Agence de l’Innovation de Défense ('project 'Safe and direct COV-2 qPCR Test') Département des Alpes Maritimes (COVID-19 Health program). Cancéropole PACA and CL is supported by Plan Cancer 2018 « ARN non-codants en cancérologie: du fondamental au translationnel » (number 18CN045).The Biomark equipment was funded by Canceropole PACA and France Génomique (Commissariat aux Grands Investissements: ANR-10-INBS-6 09–03, ANR-10-INBS-09–02)., and ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019)
Subjects: 0301 basic medicine, Male, RNA viruses, Viral Diseases, Computer science, Coronaviruses, Surfactants, Artificial Gene Amplification and Extension, Biochemistry, Polymerase Chain Reaction, law.invention, COVID-19 Testing, Medical Conditions, law, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Throughput (business), Materials, Polymerase chain reaction, Pathology and laboratory medicine, Virus Testing, 0303 health sciences, Multidisciplinary, Diagnostic test, Microfluidic Analytical Techniques, Medical microbiology, Large sample, Nucleic acids, Infectious Diseases, Ribonucleoproteins, Viruses, Physical Sciences, Medicine, RNA, Viral, [SDV.IB]Life Sciences [q-bio]/Bioengineering, Female, RNA extraction, SARS CoV 2, Pathogens, Research Article, Adult, 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), SARS coronavirus, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Science, 030106 microbiology, Microfluidics, Materials Science, Detergents, Computational biology, Real-Time Polymerase Chain Reaction, Sensitivity and Specificity, Microbiology, Specimen Handling, 03 medical and health sciences, Extraction techniques, Diagnostic Medicine, Genetics, Humans, Non-coding RNA, Molecular Biology Techniques, Molecular Biology, 030304 developmental biology, DNA Primers, Medicine and health sciences, Natural antisense transcripts, Biology and life sciences, 030306 microbiology, Diagnostic Tests, Routine, SARS-CoV-2, Organisms, Viral pathogens, COVID-19, Proteins, Covid 19, DNA extraction, Microbial pathogens, Gene regulation, Research and analysis methods, MicroRNAs, 030104 developmental biology, RNA, Gene expression
Abstract: The emergence and quick spread of SARS-CoV-2 has pointed at a low capacity response for testing large populations in many countries, in line of material, technical and staff limitations. The traditional RT-qPCR diagnostic test remains the reference method and is by far the most widely used test. These assays are limited to a few probe sets, require large sample PCR reaction volumes, along with an expensive and time-consuming RNA extraction step. Here we describe a quantitative nanofluidic assay that overcomes some of these shortcomings, based on the BiomarkTM instrument from Fluidigm. This system offers the possibility of performing 4608 qPCR end-points in a single run, equivalent to 192 clinical samples combined with 12 pairs of primers/probe sets in duplicate, thus allowing the monitoring of SARS-CoV-2 including the detection of specific SARS-CoV-2 variants, as well as the detection other pathogens and/or host cellular responses (virus receptors, response markers, microRNAs). The 10 nL-range volume of BiomarkTM reactions is compatible with sensitive and reproducible reactions that can be easily and cost-effectively adapted to various RT-qPCR configurations and sets of primers/probe. Finally, we also evaluated the use of inactivating lysis buffers composed of various detergents in the presence or absence of proteinase K to assess the compatibility of these buffers with a direct reverse transcription enzymatic step and we propose several protocols, bypassing the need for RNA purification. We advocate that the combined utilization of an optimized processing buffer and a high-throughput real-time PCR device would contribute to improve the turn-around-time to deliver the test results to patients and increase the SARS-CoV-2 testing capacities.
Published: 2020

24. The spatial landscape of gene expression isoforms in tissue sections

Author: Kevin Lebrigand, Joseph Bergenstråhle, Kim Thrane, Annelie Mollbrink, Konstantinos Meletis, Pascal Barbry, Rainer Waldmann, Joakim Lundeberg, Centre National de la Recherche Scientifique (CNRS), Université Côte d'Azur (UCA), Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Fondation Recherche Médicale DEQ20180339158, National Infrastructure France Génomique (Commissariat aux Grands Investissements, ANR-10-INBS-09-03, ANR-10-INBS-09-02), Inserm Cross-cutting Scientific Program HuDeCA 2018, ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019), European Project: 874656,discovAIR, Université Nice Sophia Antipolis (1965 - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)
Subjects: Gene isoform, In situ, 0303 health sciences, [SDV]Life Sciences [q-bio], Context (language use), Computational biology, Biology, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Tissue sections, Gene expression, RNA splicing, Genetics, 030217 neurology & neurosurgery, 030304 developmental biology, Sequence (medicine)
Abstract: In situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding of complex biological systems. However, splicing variants and fulllength sequence heterogeneity cannot be characterized at spatial resolution with current transcriptome profiling methods. To that end, we introduce Spatial Isoform Transcriptomics (SiT), an explorative method for characterizing spatial isoform variation and sequence heterogeneity. We show in mouse brain how SIT can be used to profile isoform expression and sequence heterogeneity in different areas of the tissue. SiT reveals regional isoform switching of Plp1 gene between different layers of the olfactory bulb, and use of external single cell data allowed to nominate cell types expressing each isoform. Furthermore, SiT identifies differential isoform usage for several major genes implicated in brain function (Snap25, Bin1, Gnas) that we independently validated by in situ sequencing. SiT also provides for the first time an in-depth A-to-I RNA editing map of the adult mouse brain. Data exploration can be performed through an online resource (https://www.isomics.eu), where isoform expression and RNA editing can be visualized in a spatial context.
Published: 2020

25. IPMC SARS-CoV-2 One-Step qPCR Protocol on BIOMARK v1

Author: Julien Fassy, Caroline Lacoux, David Rouquié, Jean Louis Nahon, Pascal Barbry, Laure-Emmanuelle Zaragosi, and Bernard Mari
Published: 2020

26. Identification of oncolytic vaccinia restriction factors in canine high-grade mammary tumor cells using single-cell transcriptomics

Author: Roger Rezzonico, Kevin Lebrigand, Georges Vassaux, Bernard Mari, Nicolas Nottet, Jérôme Henriques, Béatrice Cambien, Alberto Baeri, Sophie Giorgetti-Peraldi, Robert Barthel, Christophe N. Peyrefitte, Frédéric Bost, Laure-Emmanuelle Zaragosi, Catherine Compin, Pascal Barbry, Marine Gautier-Isola, Audrey Lamit, Virginie Magnone, Olivier Ferraris, Université Côte d'Azur (UCA), Institut de Recherche Biomédicale des Armées (IRBA), Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)
Subjects: Genetic enhancement, [SDV]Life Sciences [q-bio], Gene Expression, Pathology and Laboratory Medicine, Virus Replication, Transcriptome, chemistry.chemical_compound, 0302 clinical medicine, Single-cell analysis, RNA interference, Breast Tumors, Medicine and Health Sciences, Vaccinia, Biology (General), Oncolytic Virotherapy, 0303 health sciences, Mammary tumor, 030302 biochemistry & molecular biology, Microbial Genetics, Poxviruses, Genomics, 3. Good health, Oncology, Medical Microbiology, 030220 oncology & carcinogenesis, Viral Pathogens, Viruses, Viral Genetics, Female, Pathogens, Single-Cell Analysis, Transcriptome Analysis, Research Article, QH301-705.5, Immunology, Mammary Neoplasms, Animal, Vaccinia virus, Biology, Microbiology, Virus, 03 medical and health sciences, Dogs, Virology, Breast Cancer, Genetics, Animals, Gene Regulation, Molecular Biology, Microbial Pathogens, 030304 developmental biology, Carcinoma, Organisms, Biology and Life Sciences, Cancers and Neoplasms, Computational Biology, RC581-607, Genome Analysis, Viral Replication, Oncolytic virus, Viral Gene Expression, chemistry, Viral replication, Viral Genes, Cancer research, Parasitology, Immunologic diseases. Allergy, DNA viruses, Transcription Factors
Abstract: Mammary carcinoma, including triple-negative breast carcinomas (TNBC) are tumor-types for which human and canine pathologies are closely related at the molecular level. The efficacy of an oncolytic vaccinia virus (VV) was compared in low-passage primary carcinoma cells from TNBC versus non-TNBC. Non-TNBC cells were 28 fold more sensitive to VV than TNBC cells in which VV replication is impaired. Single-cell RNA-seq performed on two different TNBC cell samples, infected or not with VV, highlighted three distinct populations: naïve cells, bystander cells, defined as cells exposed to the virus but not infected and infected cells. The transcriptomes of these three populations showed striking variations in the modulation of pathways regulated by cytokines and growth factors. We hypothesized that the pool of genes expressed in the bystander populations was enriched in antiviral genes. Bioinformatic analysis suggested that the reduced activity of the virus was associated with a higher mesenchymal status of the cells. In addition, we demonstrated experimentally that high expression of one gene, DDIT4, is detrimental to VV production. Considering that DDIT4 is associated with a poor prognosis in various cancers including TNBC, our data highlight DDIT4 as a candidate resistance marker for oncolytic poxvirus therapy. This information could be used to design new generations of oncolytic poxviruses. Beyond the field of gene therapy, this study demonstrates that single-cell transcriptomics can be used to identify cellular factors influencing viral replication., Author summary The identification of cellular genes influencing viral replication/propagation has been studied using hypothesis-driven approaches and/or high-throughput RNA interference screens. In the present report, we propose a methodology based on single-cell transcriptomics. We have studied, in the context of oncolytic virotherapy, the susceptibility of different grades of primary low-passage mammary carcinoma cells of canine origin to an oncolytic vaccinia virus (VV). We highlight a fault in replication of VV in cells that originated from high-grade triple-negative breast carcinomas (TNBC). Single-cell RNA-seq performed on TNBC cell samples infected with VV suggested that the reduced activity of the virus was associated with a higher mesenchymal status of the cells. We also demonstrate that high expression of one gene, DDIT4, is detrimental to VV production. Considering that DDIT4 is associated with a poor prognosis in various cancers including TNBC, our data highlight DDIT4 as a candidate resistance marker for oncolytic poxvirus therapy. Beyond the field of cancer gene therapy, we demonstrate here that single-cell transcriptomics increases the arsenal of tools available to identify cellular factors influencing viral replication.
Published: 2020

27. Evidence of early increased sialylation of airway mucins and defective mucociliary clearance in CFTR-deficient piglets

Author: Catherine Robbe-Masselot, Mustapha Si-Tahar, Ignacio S. Caballero, Renaud Léonard, Nicolas Pons, Andrea Bähr, Pascal Barbry, Antoine Guillon, Agnès Paquet, Claire Chevaleyre, Nikolai Klymiuk, Isabelle Fleurot, Mustapha Berri, Bélinda Ringot-Destrez, Kevin Lebrigand, Carole Baron, Céline Barc, Reuben Ramphal, Isabelle Lantier, Centre National de la Recherche Scientifique (CNRS), Université Côte d'Azur (UCA), Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Université Côte d'Azur (UCA), Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre d’Etude des Pathologies Respiratoires (CEPR), UMR 1100 (CEPR), Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Service de Médecine Intensive et Réanimation [Tours], Plateforme d'Infectiologie Expérimentale (PFIE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ludwig Maximilian University [Munich] (LMU), Association Vaincre la Mucoviscidose (Grant No. RF20150 501357), Association Grégory Lemarchal (Grant No. RIF20160501690), Fondation pour la Recherche Médicale (DEQ20180339158), ANR-11-LABX-0028,SIGNALIFE,Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Chanteloup, Nathalie Katy, Centres d'excellences - Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie - - SIGNALIFE2011 - ANR-11-LABX-0028 - LABX - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Université de Tours (UT), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Tours (UT), Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Gene Center and Center for Innovation Medical Models (CiMM), Ludwig Maximilians University of Munich, Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Tours-Institut National de la Santé et de la Recherche Médicale (INSERM), and Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS)
Subjects: 0301 basic medicine, Pulmonary and Respiratory Medicine, Male, Glycosylation, Mucociliary clearance, Swine, [SDV]Life Sciences [q-bio], Sus scrofa, Cystic Fibrosis Transmembrane Conductance Regulator, Context (language use), Inflammation, Respiratory Mucosa, Mucociliary transport, medicine.disease_cause, Cystic fibrosis, Microbiology, 03 medical and health sciences, 0302 clinical medicine, Medicine, Animals, CFTR, ComputingMilieux_MISCELLANEOUS, Lung, medicine.diagnostic_test, business.industry, Pseudomonas aeruginosa, Mucin, Mucins, respiratory system, medicine.disease, 3. Good health, respiratory tract diseases, Trachea, [SDV] Life Sciences [q-bio], Mucin glycosylation, 030104 developmental biology, medicine.anatomical_structure, Bronchoalveolar lavage, 030228 respiratory system, Animals, Newborn, Mucociliary Clearance, Pediatrics, Perinatology and Child Health, Female, medicine.symptom, MESH: CFTR, business
Abstract: International audience; Background: Bacterial colonization in cystic fibrosis (CF) lungs has been directly associated to the loss of CFTR function, and/or secondarily linked to repetitive cycles of chronic inflammation/infection. We hypothesized that altered molecular properties of mucins could contribute to this process.Methods: Newborn CFTR+/+ and CFTR-/- were sacrificed before and 6 h after inoculation with luminescent Pseudomonas aeruginosa into the tracheal carina. Tracheal mucosa and the bronchoalveolar lavage (BAL) fluid were collected to determine the level of mucin O-glycosylation, bacteria binding to mucins and the airways transcriptome. Disturbances in mucociliary transport were determined by ex-vivo imaging of luminescent Pseudomonas aeruginosa.Results: We provide evidence of an increased sialylation of CF airway mucins and impaired mucociliary transport that occur before the onset of inflammation. Hypersialylation of mucins was reproduced on tracheal explants from non CF animals treated with GlyH101, an inhibitor of CFTR channel activity, indicating a causal relationship between the absence of CFTR expression and the sialylation of mucins. This increased sialylation was correlated to an increased adherence of P. aeruginosa to mucins. In vivo infection of newborn CF piglets by live luminescent P. aeruginosa demonstrated an impairment of mucociliary transport of this bacterium, with no evidence of pre-existing inflammation.Conclusions: Our results document for the first time in a well-defined CF animal model modifications that affect the O-glycan chains of mucins. These alterations precede infection and inflammation of airway tissues, and provide a favorable context for microbial development in CF lung that hallmarks this disease.
Published: 2020

28. Single-cell RNA sequencing reveals intratumoral heterogeneity in primary uveal melanomas and identifies HES6 as a driver of the metastatic disease

Author: Stéphanie Baillif, Marie Irondelle, Arnaud Martel, Chrystel Husser, Nicolas Nottet, Sacha Nahon-Esteve, Irwin Davidson, Pascal Barbry, Thomas Strub, Kevin Lebrigand, Celia Maschi, Yann Cheli, Sandra Lassalle, Corine Bertolotto, Paul Hofman, Florence Pedeutour, Mélanie Dalmasso, Giovanni Gambi, Virginie Magnone, Guillaume E. Beranger, Robert Ballotti, Karine Bille, Jean-Pierre Caujolle, Charlotte Pandiani, Centre Hospitalier Universitaire de Nice (CHU Nice), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de pharmacologie moléculaire et cellulaire (IPMC), Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Uveal Neoplasms, [SDV]Life Sciences [q-bio], Cell, Biology, Article, Metastasis, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Cell Line, Tumor, medicine, Basic Helix-Loop-Helix Transcription Factors, Humans, Neoplasm Metastasis, Molecular Biology, Gene, Transcription factor, Melanoma, ComputingMilieux_MISCELLANEOUS, Sequence Analysis, RNA, RNA, Cell Biology, medicine.disease, Prognosis, Primary tumor, 3. Good health, Repressor Proteins, 030104 developmental biology, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Cancer research, Single-Cell Analysis
Abstract: Intratumor heterogeneity has been recognized in numerous cancers as a major source of metastatic dissemination. In uveal melanomas, the existence and identity of specific subpopulations, their biological function and their contribution to metastasis remain unknown. Here, in multiscale analyses using single-cell RNA sequencing of six different primary uveal melanomas, we uncover an intratumoral heterogeneity at the genomic and transcriptomic level. We identify distinct transcriptional cell states and diverse tumor-associated populations in a subset of the samples. We also decipher a gene regulatory network underlying an invasive and poor prognosis state driven in part by the transcription factor HES6. HES6 heterogenous expression has been validated by RNAscope assays within primary human uveal melanomas, which further unveils the existence of these cells conveying a dismal prognosis in tumors diagnosed with a favorable outcome using bulk analyses. Depletion of HES6 impairs proliferation, migration and metastatic dissemination in vitro and in vivo using the chick chorioallantoic membrane assay, demonstrating the essential role of HES6 in uveal melanomas. Thus, single-cell analysis offers an unprecedented view of primary uveal melanoma heterogeneity, identifies bona fide biomarkers for metastatic cells in the primary tumor, and reveals targetable modules driving growth and metastasis formation. Significantly, our findings demonstrate that HES6 is a valid target to stop uveal melanoma progression.
Published: 2020

29. Tumor-Associated Neutrophils Dampen Adaptive Immunity and Promote Cutaneous Squamous Cell Carcinoma Development

Author: Veronique M. Braud, Franck Bihl, Roger Rezzonico, Fabienne Anjuère, Estelle Cosson, Sokchea Khou, Alain Rubod, Alexandra Popa, Emie Salavagione, Bernard Mari, Aida Meghraoui-Kheddar, Julie Cazareth, Pascal Barbry, Carmelo Luci, Pierre Bourdely, Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), and ANR-15-IDEX-0001,UCA JEDI,Idex UCA JEDI(2015)
Subjects: 0301 basic medicine, PD-L1, Cancer Research, cutaneous squamous cell carcinoma, [SDV]Life Sciences [q-bio], Biology, medicine.disease_cause, lcsh:RC254-282, Article, 03 medical and health sciences, 0302 clinical medicine, Immune system, neutrophils, Gene expression, PD-1, medicine, chemistry.chemical_classification, Reactive oxygen species, integumentary system, Acquired immune system, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, 3. Good health, Arginase, 030104 developmental biology, Oncology, chemistry, 030220 oncology & carcinogenesis, Cancer research, biology.protein, gene expression profile, Carcinogenesis, CD8
Abstract: Cutaneous squamous cell carcinoma (cSCC) development has been linked to immune dysfunctions but the mechanisms are still unclear. Here, we report a progressive infiltration of tumor-associated neutrophils (TANs) in precancerous and established cSCC lesions from chemically induced skin carcinogenesis. Comparative in-depth gene expression analyses identified a predominant protumor gene expression signature of TANs in lesions compared to their respective surrounding skin. In addition, in vivo depletion of neutrophils delayed tumor growth and significantly increased the frequency of proliferating IFN-&gamma, (interferon-&gamma, )-producing CD8+ T cells. Mechanisms that limited antitumor responses involved high arginase activity, production of reactive oxygen species (ROS) and nitrite (NO), and the expression of programmed death-ligand 1 (PD-L1) on TAN, concomitantly with an induction of PD-1 on CD8+ T cells, which correlated with tumor size. Our data highlight the relevance of targeting neutrophils and PD-L1-PD-1 (programmed death-1) interaction in the treatment of cSCC.
Published: 2020

30. ‘All In’: a pragmatic framework for COVID‐19 testing and action on a global scale

Author: Yasunari Kanda, Emily A. Bruce, Leah C. Wehmas, Syril D Pettit, Mineo Matsumoto, Pascal Barbry, David Rouquié, Susan D. Hester, Bernard Mari, Keith R. Jerome, Jason Botten, and Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Medicine (General), medicine.medical_specialty, Computer science, [SDV]Life Sciences [q-bio], Pneumonia, Viral, QH426-470, Global Health, Betacoronavirus, 03 medical and health sciences, COVID-19 Testing, R5-920, 0302 clinical medicine, Resource (project management), Multidisciplinary approach, Correspondence, Genetics, medicine, Global health, Humans, Pandemics, ComputingMilieux_MISCELLANEOUS, Strategic planning, Clinical Laboratory Techniques, Reverse Transcriptase Polymerase Chain Reaction, SARS-CoV-2, Public health, COVID-19, Strategic Planning, S&S: Ethics, Microbiology, Virology & Host Pathogen Interaction, 3. Good health, 030104 developmental biology, Risk analysis (engineering), Software deployment, Scale (social sciences), Scalability, RNA, Viral, Molecular Medicine, Coronavirus Infections, 030217 neurology & neurosurgery
Abstract: Current demand for SARS‐CoV‐2 testing is straining material resource and labor capacity around the globe. As a result, the public health and clinical community are hindered in their ability to monitor and contain the spread of COVID‐19. Despite broad consensus that more testing is needed, pragmatic guidance toward realizing this objective has been limited. This paper addresses this limitation by proposing a novel and geographically agnostic framework (the 4Ps framework) to guide multidisciplinary, scalable, resource‐efficient, and achievable efforts toward enhanced testing capacity. The 4Ps (Prioritize, Propagate, Partition, and Provide) are described in terms of specific opportunities to enhance the volume, diversity, characterization, and implementation of SARS‐CoV‐2 testing to benefit public health. Coordinated deployment of the strategic and tactical recommendations described in this framework has the potential to rapidly expand available testing capacity, improve public health decision‐making in response to the COVID‐19 pandemic, and/or to be applied in future emergent disease outbreaks., This paper proposes a novel 4Ps Framework (Prioritize, Propagate, Partition, and Provide) to guide multidisciplinary, scalable, resource‐efficient, and achievable efforts towards enhanced SARS‐CoV‐2 testing capacity and improved public health decision‐making in response to the COVID‐19 pandemic.
Published: 2020

31. Storing Digital Data Into DNA: A Comparative Study Of Quaternary Code Construction

Author: Pascal Barbry, Marc Antonini, Raja Appuswamy, Melpomeni Dimopoulou, Laboratoire d'Informatique, Signaux, et Systèmes de Sophia-Antipolis (I3S) / Projet MEDIACODING, Signal, Images et Systèmes (Laboratoire I3S - SIS), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia-Antipolis (I3S) / Equipe IMAGES-CREATIVE, Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Eurecom [Sophia Antipolis], and ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019)
Subjects: quaternary code, Computer science, Digital data, 02 engineering and technology, computer.software_genre, Field (computer science), 03 medical and health sciences, 0202 electrical engineering, electronic engineering, information engineering, Code (cryptography), [INFO]Computer Science [cs], 030304 developmental biology, 0303 health sciences, Database, data storage, business.industry, Volume (computing), 020206 networking & telecommunications, Durability, sequencing noise robustness, [INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV], Computer data storage, DNA coding, State (computer science), business, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, computer
Abstract: International audience; The exponential increase of digital data that is being generated every year along with the capacity and durability limits of conventional storage devices are raising one of the greatest challenges for the field of data storage. The use of DNA for digital data archiving is a very promising alternative as the biological properties of the DNA molecule allow the storage of a huge amount of information into a very limited volume while also promising data longevity for centuries or even longer. In this paper we present a comparative study of our work with the state of the art solutions, and show that our solution is competitive.
Published: 2020

32. Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

Author: Kamil Slowikowski, Nathan R. Tucker, William Zhao, Alex Sountoulidis, Ross J. Metzger, Allon Zaneta Andrusivova, Marie Deprez, Lolita Penland, Wendy Luo, Sijia Chen, Gökcen Eraslan, Peng Tan, Jessica Tantivit, Monika Litviňuková, Lisa Sikkema, Kyungtae Lim, Hananeh Aliee, Rachel Queen, Alexi McAdams, Brian M. Lin, Michal Slyper, Astrid Gillich, Christopher Smilie, Karthik A. Jagadeesh, Liam Bolt, Christoph Muus, Hattie Chung, Jian Shu, Yoshihiko Kobayashi, Lira Mamanova, Arun C. Habermann, Pascal Barbry, Eeshit Dhaval Vaishnav, Mark Chaffin, Sergio Poli, Malte D Luecken, Xiaomeng Hou, Alok Jaiswal, Rene Sit, Inbal Benhar, Charles-Hugo Marquette, Maximilian Strunz, Christin S. Kuo, Evgenij Fiskin, Thomas M. Conlon, Meshal Ansari, Cancan Qi, Rahul Sinha, Ji Lu, Austin J. Gutierrez, Daniel Reichart, Michael Leney-Greene, Olivier Poirion, Peng He, Tyler Harvey, David Fischer, Neal Smith, Evgeny Chichelnitskiy, Ilias Angelidis, Carlos Talavera-López, Kasidet Manakongtreecheep, Marc Wadsworth, Christophe Bécavin, Kevin Bassler, Kyle J. Travaglini, Graham Heimberg, Dawei Sun, Adam L. Haber, Joshua Gould, Elena Torlai Triglia, Ayshwarya Subramanian, Jonas C. Schupp, Ivan O. Rosas, Leif S. Ludwig, Ian Mbano, Taylor Adams, J. Samuel, Michael S. Cuoco, Carly Ziegler, Lijuan Hu, Avinash Waghray, Joseph Bergenstråhle, Ludvig Larsson, Elizabeth Thu Duong, Julia Waldman, Ludvig Bergenstråhle, Joshua Chiou, Sarah K. Nyquist, Minzhe Guo, Peiwen Cai, Daniel T. Montoro, Peiyong Jiang, Orr Ashenberg, Elo Madissoon, Emelie Braun, Justin Buchanan, Ahmad N. Nabhan, Katherine A. Vernon, Linh T. Bui, Theodoros Kapellos, Wenjun Yan, Henrike Maatz, Xiuting Wang, Centre National de la Recherche Scientifique (CNRS), Université Côte d'Azur (UCA), Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), and ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019)
Subjects: Cancer Research, 0303 health sciences, Cell type, Proteases, [SDV]Life Sciences [q-bio], Cell, Biology, medicine.disease_cause, TMPRSS2, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, Immune system, medicine.anatomical_structure, Cardiovascular and Metabolic Diseases, Viral entry, Immunology, medicine, Tumor necrosis factor alpha, 030217 neurology & neurosurgery, 030304 developmental biology, Coronavirus
Abstract: The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, creates an urgent need for identifying molecular mechanisms that mediate viral entry, propagation, and tissue pathology. Cell membrane bound angiotensin-converting enzyme 2 (ACE2) and associated proteases, transmembrane protease serine 2 (TMPRSS2) and Cathepsin L (CTSL), were previously identified as mediators of SARS-CoV2 cellular entry. Here, we assess the cell type-specific RNA expression of ACE2, TMPRSS2, and CTSL through an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Joint expression of ACE2 and the accessory proteases identifies specific subsets of respiratory epithelial cells as putative targets of viral infection in the nasal passages, airways, and alveoli. Cells that co-express ACE2 and proteases are also identified in cells from other organs, some of which have been associated with COVID-19 transmission or pathology, including gut enterocytes, corneal epithelial cells, cardiomyocytes, heart pericytes, olfactory sustentacular cells, and renal epithelial cells. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels of ACE2, TMPRSS2, and CTSL in specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. Notably, there was a particularly low expression of ACE2 in the few young pediatric samples in the analysis. Further analysis reveals a gene expression program shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues, including genes that may mediate viral entry, subtend key immune functions, and mediate epithelial-macrophage cross-talk. Amongst these are IL6, its receptor and co-receptor, IL1R, TNF response pathways, and complement genes. Cell type specificity in the lung and airways and smoking effects were conserved in mice. Our analyses suggest that differences in the cell type-specific expression of mediators of SARS-CoV-2 viral entry may be responsible for aspects of COVID-19 epidemiology and clinical course, and point to putative molecular pathways involved in disease susceptibility and pathogenesis.
Published: 2020

33. IPMC SARS-CoV-2 Two-Step qPCR Protocol on BIOMARK v1

Author: Julien Fassy, Caroline Lacoux, David Rouquié, Jean Louis Nahon, Pascal Barbry, Laure-Emmanuelle Zaragosi, and Bernard Mari
Subjects: Computer science, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Virology
Published: 2020

34. Using single-cell RNA sequencing to unravel cell lineage relationships in the respiratory tract

Author: Laure-Emmanuelle Zaragosi, Marie Deprez, Pascal Barbry, Centre National de la Recherche Scientifique (CNRS), Université Côte d'Azur (UCA), Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)
Subjects: Cell type, Lineage (genetic), [SDV]Life Sciences [q-bio], Cell, Biology, Biochemistry, 03 medical and health sciences, Mice, 0302 clinical medicine, medicine, Animals, Homeostasis, Humans, Regeneration, Cell Lineage, RNA-Seq, Progenitor cell, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Regeneration (biology), Cell Differentiation, Epithelial Cells, Epithelium, Cell biology, Brush Cell, Trachea, medicine.anatomical_structure, Single-Cell Analysis, 030217 neurology & neurosurgery, Respiratory tract
Abstract: The respiratory tract is lined by a pseudo-stratified epithelium from the nose to terminal bronchioles. This first line of defense of the lung against external stress includes five main cell types: basal, suprabasal, club, goblet and multiciliated cells, as well as rare cells such as ionocytes, neuroendocrine and tuft/brush cells. At homeostasis, this epithelium self-renews at low rate but is able of fast regeneration upon damage. Airway epithelial cell lineages during regeneration have been investigated in the mouse by genetic labeling, mainly after injuring the epithelium with noxious agents. From these approaches, basal cells have been identified as progenitors of club, goblet and multiciliated cells, but also of ionocytes and neuroendocrine cells. Single-cell RNA sequencing, coupled to lineage inference algorithms, has independently allowed the establishment of comprehensive pictures of cell lineage relationships in both mouse and human. In line with genetic tracing experiments in mouse trachea, studies using single-cell RNA sequencing (RNAseq) have shown that basal cells first differentiate into club cells, which in turn mature into goblet cells or differentiate into multiciliated cells. In the human airway epithelium, single-cell RNAseq has identified novel intermediate populations such as deuterosomal cells, ‘hybrid’ mucous-multiciliated cells and progenitors of rare cells. Novel differentiation dynamics, such as a transition from goblet to multiciliated cells have also been discovered. The future of cell lineage relationships in the respiratory tract now resides in the combination of genetic labeling approaches with single-cell RNAseq to establish, in a definitive manner, the hallmarks of cellular lineages in normal and pathological situations.
Published: 2020

35. A single-cell atlas of the human healthy airways

Author: Sandra Ruiz García, Agnès Paquet, Kevin Lebrigand, Pascal Barbry, Laure-Emmanuelle Zaragosi, Sylvie Leroy, Dana Pe'er, Marin Truchi, Marie Deprez, Marie-Jeanne Arguel, and Charles-Hugo Marquette
Subjects: education.field_of_study, Cell type, Pathology, medicine.medical_specialty, Stromal cell, medicine.diagnostic_test, Population, Biology, Epithelium, medicine.anatomical_structure, Immune system, Bronchoscopy, medicine, Respiratory system, education, Respiratory tract
Abstract: RationaleThe respiratory tract constitutes an elaborated line of defense based on a unique cellular ecosystem. Single-cell profiling methods enable the investigation of cell population distributions and transcriptional changes along the airways.MethodsWe have explored cellular heterogeneity of the human airway epithelium in 10 healthy living volunteers by single-cell RNA profiling. 77,969 cells were collected by bronchoscopy at 35 distinct locations, from the nose to the 12th division of the airway tree.ResultsThe resulting atlas is composed of a high percentage of epithelial cells (89.1%), but also immune (6.2%) and stromal (4.7%) cells with peculiar cellular proportions in different sites of the airways. It reveals differential gene expression between identical cell types (suprabasal, secretory, and multiciliated cells) from the nose (MUC4, PI3, SIX3) and tracheobronchial (SCGB1A1, TFF3) airways. By contrast, cell-type specific gene expression was stable across all tracheobronchial samples. Our atlas improves the description of ionocytes, pulmonary neuro-endocrine (PNEC) and brush cells, which are likely derived from a common population of precursor cells. We also report a population of KRT13 positive cells with a high percentage of dividing cells which are reminiscent of “hillock” cells previously described in mouse.ConclusionsRobust characterization of this unprecedented large single-cell cohort establishes an important resource for future investigations. The precise description of the continuum existing from nasal epithelium to successive divisions of lung airways and the stable gene expression profile of these regions better defines conditions under which relevant tracheobronchial proxies of human respiratory diseases can be developed.
Published: 2019

36. miR-600 Acts as a Bimodal Switch that Regulates Breast Cancer Stem Cell Fate through WNT Signaling

Author: Pascal Finetti, Claire Rioualen, François Bertucci, Bernard Mari, Julien Wicinski, Abigaelle Gros, Ricky Bhajun, Christophe Ginestier, Pascal Barbry, Olivier Cabaud, Guillaume Pinna, Daniel Birnbaum, Laurent Guyon, Ghislain Bidaut, Annick Harel-Bellan, Rita El Helou, Emmanuelle Charafe-Jauffret, Centre de Recherche en Cancérologie de Marseille ( CRCM ), Aix Marseille Université ( AMU ) -Institut Paoli-Calmettes-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Laboratoire de Biologie à Grande Échelle ( BGE - UMR S1038 ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Grenoble Alpes [Saint Martin d'Hères]-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Institut de pharmacologie moléculaire et cellulaire ( IPMC ), Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Epigenetique et Cancer, Centre National de la Recherche Scientifique ( CNRS ), Centre de Recherche en Cancérologie de Marseille (CRCM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Aix Marseille Université (AMU), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), and Bidaut, Ghislain
Subjects: 0301 basic medicine, Carcinogenesis, Cellular differentiation, Breast Neoplasms, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, Bioinformatics, medicine.disease_cause, General Biochemistry, Genetics and Molecular Biology, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, 03 medical and health sciences, [SDV.CAN] Life Sciences [q-bio]/Cancer, Cell Line, Tumor, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], microRNA, medicine, Gene silencing, Humans, Wnt Signaling Pathway, lcsh:QH301-705.5, Wnt signaling pathway, Cell Differentiation, 3. Good health, Gene Expression Regulation, Neoplastic, Wnt Proteins, MicroRNAs, 030104 developmental biology, lcsh:Biology (General), Tumor progression, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Cancer research, Neoplastic Stem Cells, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Female, Stem cell, Signal transduction, Stearoyl-CoA Desaturase, Signal Transduction
Abstract: Summary: Breast cancer stem cells (bCSCs) have been implicated in tumor progression and therapeutic resistance; however, the molecular mechanisms that define this state are unclear. We have performed two microRNA (miRNA) gain- and loss-of-function screens to identify miRNAs that regulate the choice between bCSC self-renewal and differentiation. We find that micro-RNA (miR)-600 silencing results in bCSC expansion, while its overexpression reduces bCSC self-renewal, leading to decreased in vivo tumorigenicity. miR-600 targets stearoyl desaturase 1 (SCD1), an enzyme required to produce active, lipid-modified WNT proteins. In the absence of miR-600, WNT signaling is active and promotes self-renewal, whereas overexpression of miR-600 inhibits the production of active WNT and promotes bCSC differentiation. In a series of 120 breast tumors, we found that a low level of miR-600 is correlated with active WNT signaling and a poor prognosis. These findings highlight a miR-600-centered signaling network that governs bCSC-fate decisions and influences tumor progression. : El Helou et al. identify miRNAs that are able to balance bCSC fate. They find that miR-600 silencing results in bCSC expansion, while its overexpression reduces bCSC self-renewal. miR-600 was further found to regulate WNT signaling through SCD1, and miR-600 expression correlates with clinical outcome.
Published: 2017
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37. High throughput, error corrected Nanopore single cell transcriptome sequencing

Author: Rainer Waldmann, Pascal Barbry, Virginie Magnone, Kevin Lebrigand, Institut de pharmacologie moléculaire et cellulaire (IPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), This project was funded by grants from the Institut National contre le Cancer (PLBIO2018-156), the Conseil Départemental des Alpes Maritimes (2016-294DGADSH-CV), FRM (DEQ20180339158), the Inserm Cross-cutting Scientific Program HuDeCA 2018, the National Infrastructure France Génomique (Commissariat aux Grands Investissements, ANR-10-INBS-09-03, ANR-10-INBS-09-02). This publication is part of the Human Cell Atlas - https://www.humancellatlas.org/publications., and ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019)
Subjects: 0301 basic medicine, Computer science, Bioinformatics, [SDV]Life Sciences [q-bio], Science, General Physics and Astronomy, Gene Expression, Genomics, 02 engineering and technology, Computational biology, General Biochemistry, Genetics and Molecular Biology, Deep sequencing, Article, 03 medical and health sciences, Mice, Nanopores, 0302 clinical medicine, Genome-wide analysis of gene expression, Single cell transcriptome, Animals, Protein Isoforms, Cell isolation, Receptors, AMPA, lcsh:Science, Throughput (business), 030304 developmental biology, 0303 health sciences, Multidisciplinary, Sequence Analysis, RNA, Gene Expression Profiling, Brain, High-Throughput Nucleotide Sequencing, General Chemistry, Sequence Analysis, DNA, 021001 nanoscience & nanotechnology, Mice, Inbred C57BL, Nanopore, Nanopore Sequencing, 030104 developmental biology, Single cell sequencing, RNA editing, RNA splicing, lcsh:Q, Nanopore sequencing, 0210 nano-technology, Transcriptome, 030217 neurology & neurosurgery
Abstract: Droplet-based high throughput single cell sequencing techniques tremendously advanced our insight into cell-to-cell heterogeneity. However, those approaches only allow analysis of one extremity of the transcript after short read sequencing. In consequence, information on splicing and sequence heterogeneity is lost. To overcome this limitation, several approaches that use long-read sequencing were introduced recently. Yet, those techniques are limited by low sequencing depth and/or lacking or inaccurate assignment of unique molecular identifiers (UMIs), which are critical for elimination of PCR bias and artifacts. We introduce ScNaUmi-seq, an approach that combines the high throughput of Oxford Nanopore sequencing with an accurate cell barcode and UMI assignment strategy. UMI guided error correction allows to generate high accuracy full length sequence information with the 10x Genomics single cell isolation system at high sequencing depths. We analyzed transcript isoform diversity in embryonic mouse brain and show that ScNaUmi-seq allows defining splicing and SNVs (RNA editing) at a single cell level., Droplet-based high throughput single cell sequencing techniques can often lose information on transcript splicing and heterogenity. Here the authors introduce ScNaUmi-seq, which uses Oxford Nanopore sequencing and barcoding to generate high accuracy full length sequences.
Published: 2019
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38. The nuclear hypoxia-regulated NLUCAT1 long non-coding RNA contributes to an aggressive phenotype in lung adenocarcinoma through regulation of oxidative stress

Author: Roger Rezzonico, Garrett Kinnebrew, Mircea Ivan, Marin Truchi, Marius Ilie, Bernard Mari, Julien Fassy, Nicolas Nottet, Laura Moreno Leon, Nicolas Pottier, Richard Allan, Milan Radovich, Gilles Ponzio, Nicolas Pons, Kevin Lebrigand, Pascal Barbry, Charles-Hugo Marquette, Marine Gautier, Agnès Paquet, Meyling Hua Chen Cheok, Georges Vassaux, Virginie Magnone, Paul Hofman, Infection bactérienne, inflammation, et carcinogenèse digestive, Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-IFR50-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Institut Sophia Agrobiotech (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Institut de pharmacologie moléculaire et cellulaire (IPMC), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Centre National de la Recherche Scientifique (CNRS), FHU OncoAge - Pathologies liées à l’âge [CHU Nice] (OncoAge), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Pharmacologie Moléculaire et Cellulaire [UNIV Côte d'Azur] (UPMC)-Université Côte d'Azur (UCA), Department of Microbiology and Immunology, Division of Infectious Diseases, Walther Oncology Center, Indiana University School of Medicine, Indiana University System-Indiana University System, Targeted Therapy Laboratory, Section of Cell and Molecular Biology, The Institute of Cancer Research, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Biologie et physiopathologie cutanées : expression génique, signalisation et thérapie, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-IFR50-Institut National de la Santé et de la Recherche Médicale (INSERM), Indiana University System, Impact de l'environnement chimique sur la santé humaine - ULR 4483 (IMPECS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Ponzio, Gilles, Centres d'excellences - Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie - - SIGNALIFE2011 - ANR-11-LABX-0028 - LABX - VALID, Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Hôpital Pasteur [Nice] (CHU), Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer - U837 (JPArc), Université Lille Nord de France (COMUE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille, Centre Hospitalier Universitaire de Nice (CHU Nice), Faculté de Médecine Henri Warembourg - Université de Lille, ANR-11-LABX-0028,SIGNALIFE,Réseau d'Innovation sur les Voies de Signalisation en Sciences de la Vie(2011), Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Pharmacologie Moléculaire et Cellulaire [UNIV Côte d'Azur] (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer - U1172 Inserm - U837 (JPArc), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Lille Nord de France (COMUE)-Université de Lille, Université Lille 2 - Faculté de Médecine, Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-IFR50-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Institut de Pharmacologie Moléculaire et Cellulaire [UNIV Côte d'Azur] (UPMC), Université Côte d'Azur (UCA), Impact de l'Environnement Chimique sur la Santé Humain, and PRES Université Lille Nord de France
Subjects: Cancer Research, Lung Neoplasms, [SDV]Life Sciences [q-bio], NF-KAPPA-B, Adenocarcinoma of Lung, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, ANNOTATION, CELL-PROLIFERATION, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Downregulation and upregulation, POOR-PROGNOSIS, Genetics, medicine, Humans, TRANSCRIPTION, Lung cancer, Molecular Biology, Transcription factor, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, GENE-EXPRESSION, DRUG-RESISTANCE, 0303 health sciences, Gene knockdown, EPITHELIAL-CELLS, Hypoxia (medical), medicine.disease, CANCER, Long non-coding RNA, 3. Good health, Gene Expression Regulation, Neoplastic, Oxidative Stress, Phenotype, CIGARETTE-SMOKE, 030220 oncology & carcinogenesis, Cancer research, Adenocarcinoma, RNA, Long Noncoding, medicine.symptom
Abstract: International audience; Lung cancer is the leading cause of cancer death worldwide, with poor prognosis and a high rate of recurrence despite early surgical removal. Hypoxic regions within tumors represent sources of aggressiveness and resistance to therapy. Although long non-coding RNAs (lncRNAs) are increasingly recognized as major gene expression regulators, their regulation and function following hypoxic stress are still largely unexplored. Combining profiling studies on early-stage lung adenocarcinoma (LUAD) biopsies and on A549 LUAD cell lines cultured in normoxic or hypoxic conditions, we identified a subset of lncRNAs that are both correlated with the hypoxic status of tumors and regulated by hypoxia in vitro. We focused on a new transcript, NLUCAT1, which is strongly upregulated by hypoxia in vitro and correlated with hypoxic markers and poor prognosis in LUADs. Full molecular characterization showed that NLUCAT1 is a large nuclear transcript composed of six exons and mainly regulated by NF-κB and NRF2 transcription factors. CRISPR-Cas9-mediated invalidation of NLUCAT1 revealed a decrease in proliferative and invasive properties, an increase in oxidative stress and a higher sensitivity to cisplatin-induced apoptosis. Transcriptome analysis of NLUCAT1-deficient cells showed repressed genes within the antioxidant and/or cisplatin-response networks. We demonstrated that the concomitant knockdown of four of these genes products, GPX2, GLRX, ALDH3A1, and PDK4, significantly increased ROS-dependent caspase activation, thus partially mimicking the consequences of NLUCAT1 inactivation in LUAD cells. Overall, we demonstrate that NLUCAT1 contributes to an aggressive phenotype in early-stage hypoxic tumors, suggesting it may represent a new potential therapeutic target in LUADs.
Published: 2019

39. A biologically constrained encoding solution for long-term storage of images onto synthetic DNA

Author: Melpomeni Dimopoulou, Marc Antonini, Raja Appuswamy, Pascal Barbry, Laboratoire d'Informatique, Signaux, et Systèmes de Sophia-Antipolis (I3S) / Equipe IMAGES-CREATIVE, Signal, Images et Systèmes (Laboratoire I3S - SIS), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut de pharmacologie moléculaire et cellulaire (IPMC), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), and Eurecom [Sophia Antipolis]
Subjects: FOS: Computer and information sciences, robust encoding, Computer science, DNA digital data storage, 02 engineering and technology, Optical storage, chemistry.chemical_compound, Digital image, 0202 electrical engineering, electronic engineering, information engineering, FOS: Electrical engineering, electronic engineering, information engineering, Quantitative Biology - Genomics, [INFO]Computer Science [cs], Genomics (q-bio.GN), Image and Video Processing (eess.IV), 020206 networking & telecommunications, Electrical Engineering and Systems Science - Image and Video Processing, image compression, Multimedia (cs.MM), DNA data storage, chemistry, FOS: Biological sciences, [INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV], 020201 artificial intelligence & image processing, Algorithm, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Decoding methods, DNA, Computer Science - Multimedia, Image compression
Abstract: Living in the age of the digital media explosion, the amount of data that is being stored increases dramatically. However, even if existing storage systems suggest efficiency in capacity, they are lacking in durability. Hard disks, flash, tape or even optical storage have limited lifespan in the range of 5 to 20 years. Interestingly, recent studies have proven that it was possible to use synthetic DNA for the storage of digital data, introducing a strong candidate to achieve data longevity. The DNA's biological properties allows the storage of a great amount of information into an extraordinary small volume while also promising efficient storage for centuries or even longer with no loss of information. However, encoding digital data onto DNA is not obvious, because when decoding, we have to face the problem of sequencing noise robustness. Furthermore, synthesizing DNA is an expensive process and thus, controlling the compression ratio by optimizing the rate-distortion trade-off is an important challenge we have to deal with. This work proposes a coding solution for the storage of digital images onto synthetic DNA. We developed a new encoding algorithm which generates a DNA code robust to biological errors coming from the synthesis and the sequencing processes. Furthermore, thanks to an optimized allocation process the solution is able to control the compression ratio and thus the length of the synthesized DNA strand. Results show an improvement in terms of coding potential compared to previous state-of-the-art works., Comment: Submitted to EUSIPCO 2019 conference
Published: 2019

40. On the reduction of the cost for encoding/decoding digital images stored on synthetic DNA

Author: Melpomeni Dimopoulou, Eva Gil San Antonio, Marc Antonini, Pascal Barbry, Raja Appuswamy, Laboratoire d'Informatique, Signaux, et Systèmes de Sophia-Antipolis (I3S) / Projet MEDIACODING, Signal, Images et Systèmes (Laboratoire I3S - SIS), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Laboratoire d'Informatique, Signaux, et Systèmes de Sophia-Antipolis (I3S) / Equipe IMAGES-CREATIVE, Institut de pharmacologie moléculaire et cellulaire (IPMC), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), and Eurecom [Sophia Antipolis]
Subjects: [INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing, [INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV], [INFO]Computer Science [cs]
Abstract: International audience; Living in the age of data explosion, the research of solutions for efficient long term storage of the infrequently used "cold" data is becoming of great interest. Recent studies have proven that due to its biological properties, the DNA is a strong candidate for the storage of digital information allowing also data longevity. However the biological procedures of DNA synthesis and sequencing are expensive while also introducing important restrictions in the encoding process. In this work we present a new constrained encoding method for the robust encoding /decoding of images to be stored into DNA. Furthermore we study the possibility of fully retrieving the stored information using less sequencing samples and consequently reducing the sequencing cost.; De nos jours, nous assistons à une explosion du volume des données numériques produites dans le monde entier. La question de leur archivage devient donc de plus en plus cruciale, tant pour pérenniser notre héritage scientifique et culturel que pour permettre leur réutilisation. Ainsi, la recherche de solutions pour un stockage efficace à long terme des données "froides", c'est-à-dire des données peu ou plus utilisées, suscite un intérêt de plus en plus grand. Des études récentes ont prouvé qu'en raison de ses propriétés biologiques, l'ADN peut être un excellent candidat pour le stockage d'informations numériques, permettant également une conservation des données sur le long terme. Cependant, les procédures biologiques de synthèse et de séquençage de l'ADN sont coûteuses, tout en introduisant d'importantes contraintes dans le processus de codage. Dans cet article, nous proposons un schéma de codage adapté au stockage d'images sur ADN, qui respecte les contraintes introduites par les procédures biologiques. D'autre part, la solution proposée permet de réduire les coûts introduits par la synthèse et le séquençage.
Published: 2019

41. The Long Noncoding RNA DNM3OS Is a Reservoir of FibromiRs with Major Functions in Lung Fibroblast Response to TGF-β and Pulmonary Fibrosis

Author: Nihal Martis, Virginie Magnone, Franck Broly, Bruno Crestani, Pascal Barbry, Nicolas Nottet, Elisabeth Courcot, Nicolas Pottier, Imène-Sarah Henaoui, Grégoire Savary, Nicolas Pons, Roger Rezzonico, Benoit Wallaert, Bernard Mari, Kevin Lebrigand, Agnès Paquet, Matthieu Buscot, Véronique Hofman, Michael Perrais, François Glowacki, Julien Fassy, Cynthia Van der Hauwaert, Paul Hofman, Charles-Hugo Marquette, Sylvie Leroy, Edmone Dewaeles, Georges Vassaux, Christian L. Lino Cardenas, Andreas Günther, Christelle Cauffiez, Saverio Bellusci, Serena Diazzi, Julie Lemaire, Thierry Brousseau, Laurent Plantier, Impact de l'environnement chimique sur la santé humaine - ULR 4483 (IMPECS), Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), FHU OncoAge - Pathologies liées à l’âge [CHU Nice] (OncoAge), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Pharmacologie Moléculaire et Cellulaire [UNIV Côte d'Azur] (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Faculté de Médecine H. Warembourg, EA 2679, Institut de pharmacologie moléculaire et cellulaire (IPMC), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Université Nice Sophia Antipolis - Faculté de Médecine (UNS UFR Médecine), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Infection bactérienne, inflammation, et carcinogenèse digestive, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-IFR50-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Service de Physiologie-Explorations Fonctionnelles, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Targeted Therapy Laboratory, Section of Cell and Molecular Biology, The Institute of Cancer Research, Immunité muqueuse et vaccination, Institut National de la Santé et de la Recherche Médicale (INSERM), Konrad-Zuse-Zentrum für Informationstechnik Berlin (ZIB), Zuse Institute Berlin (ZIB), AP-HP - Hôpital Bichat - Claude Bernard [Paris], Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Biologie et physiopathologie cutanées : expression génique, signalisation et thérapie, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-IFR50-Institut National de la Santé et de la Recherche Médicale (INSERM), Biochimie Automatisée [Lille] (UF Analyses automatisée de Biochimie), Department of Internal Medicine II [Giessen, Germany] (Cardio-Pulmonary Institute), University of Giessen Lung Center [Giessen, Germany], Laboratoire de Toxicologie, Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Pharmacologie Moléculaire et Cellulaire [UNIV Côte d'Azur] (UPMC)-Université Côte d'Azur (UCA), Faculté de Médecine Henri Warembourg - Université de Lille, Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Impact de l'environnement chimique sur la santé humaine (IMPECS), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Institut de Pharmacologie Moléculaire et Cellulaire [UNIV Côte d'Azur] (UPMC), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA), Institut des Sciences de la Terre de Paris (iSTeP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-IFR50-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Nice Sophia Antipolis (... - 2019) (UNS)
Subjects: Pulmonary and Respiratory Medicine, [SDV]Life Sciences [q-bio], Caveolin 1, Smad Proteins, SMAD, Critical Care and Intensive Care Medicine, Transcriptome, 03 medical and health sciences, Idiopathic pulmonary fibrosis, Mice, 0302 clinical medicine, Transforming Growth Factor beta, microRNA, Pulmonary fibrosis, medicine, Animals, Myofibroblasts, Wnt Signaling Pathway, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, business.industry, Editorials, Fibroblasts, medicine.disease, Long non-coding RNA, Idiopathic Pulmonary Fibrosis, 3. Good health, MicroRNAs, 030220 oncology & carcinogenesis, Cancer research, RNA, Long Noncoding, business, Myofibroblast, Transforming growth factor, Signal Transduction
Abstract: Rationale: Given the paucity of effective treatments for idiopathic pulmonary fibrosis (IPF), new insights into the deleterious mechanisms controlling lung fibroblast activation, the key cell type driving the fibrogenic process, are essential to develop new therapeutic strategies. TGF-β (transforming growth factor-β) is the main profibrotic factor, but its inhibition is associated with severe side effects because of its pleiotropic role. Objectives: To determine if downstream noncoding effectors of TGF-β in fibroblasts may represent new effective therapeutic targets whose modulation may be well tolerated. Methods: We investigated the whole noncoding fraction of TGF-β-stimulated lung fibroblast transcriptome to identify new genomic determinants of lung fibroblast differentiation into myofibroblasts. Differential expression of the long noncoding RNA (lncRNA) DNM3OS (dynamin 3 opposite strand) and its associated microRNAs (miRNAs) was validated in a murine model of pulmonary fibrosis and in IPF tissue samples. Distinct and complementary antisense oligonucleotide-based strategies aiming at interfering with DNM3OS were used to elucidate the role of DNM3OS and its associated miRNAs in IPF pathogenesis. Measurements and Main Results: We identified DNM3OS as a fibroblast-specific critical downstream effector of TGF-β-induced lung myofibroblast activation. Mechanistically, DNM3OS regulates this process in trans by giving rise to three distinct profibrotic mature miRNAs (i.e., miR-199a-5p/3p and miR-214-3p), which influence SMAD and non-SMAD components of TGF-β signaling in a multifaceted way. In vivo, we showed that interfering with DNM3OS function not only prevents lung fibrosis but also improves established pulmonary fibrosis. Conclusions: Pharmacological approaches aiming at interfering with the lncRNA DNM3OS may represent new effective therapeutic strategies in IPF.
Published: 2019

42. Cell dissociation from airway biopsies with cold-active protease for single-cell RNA-seq v1

Author: Laure-emmanuelle Zaragosi and Pascal Barbry
Subjects: medicine.anatomical_structure, Protease, Chemistry, medicine.medical_treatment, Cell, medicine, RNA-Seq, Airway, Molecular biology, Cell dissociation
Abstract: This protocol provides details on the cell dissociation that should be performed to obtain single-cell suspensions from airway biopsies. Biopsies may come from tracheal, bronchial or nasal epithelium. Cell dissociation is performed at 4°C to avoid gene expression alterations and maximize viability. The typical cell number recovery is 40 000 cells for one biopsy. Cell suspensions are suitable for single-cell RNA-sequencing protocols.
Published: 2019

43. Novel dynamics of human mucociliary differentiation revealed by single-cell RNA sequencing of nasal epithelial cultures

Author: Marin Truchi, Sylvie Leroy, Marie-Jeanne Arguel, Agnès Paquet, Marie Deprez, Ignacio S. Caballero, Brice Marcet, Kevin Lebrigand, Amélie Cavard, Pascal Barbry, Charles-Hugo Marquette, Virginie Magnone, Laure-Emmanuelle Zaragosi, Sandra Ruiz García, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours, Service de Pneumologie, Centre Hospitalier Universitaire de Nice (CHU Nice)-Hôpital de l'Archet, Fondation pour la Recherche Medicale (DEQ20180339158), Labex Signalife (ANR-11-LABX-0028-01), Association Vaincre la Mucoviscidose (RF20180502280), Commissariat aux Grands Investissements (ANR-10-INBS-09-03, ANR-10-INBS-09-02), Chan Zuckerberg Initiative [(Silicon Valley Community Foundation) 2017-175159-5022], Canceropole PACA, Institut de pharmacologie moléculaire et cellulaire (IPMC), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Centre National de la Recherche Scientifique (CNRS), Université Côte d'Azur (UCA), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Physiological Genomics of the Eukaryotes, Hôpital Pasteur [Nice] (CHU), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), UR Infectiologie animale et Santé publique (UR IASP), Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Barbry, Pascal, and Zaragosi, Laure-Emmanuelle
Subjects: épithélium, Swine, Cell, Pneumologie et système respiratoire, Basal cells, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, Transcriptome, Mice, 0302 clinical medicine, Keratin, mucociliary differentiation, RNA-Seq, tractus respiratoire, [SDV.BDD]Life Sciences [q-bio]/Development Biology, immunohistologie, Cells, Cultured, cell trajectory, Goblet cells, chemistry.chemical_classification, 0303 health sciences, Biologie du développement, Wnt signaling pathway, Cell Differentiation, scRNAseq, Development Biology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, Cell biology, Trachea, medicine.anatomical_structure, Deuterosome, Differentiation, cellule isolée, Keratins, single cell RNA seq, Airway epithelium, Club cells, Multiciliated cells, Pathways, Single-cell RNA-seq, Respiratory Mucosa, Biology, 03 medical and health sciences, Techniques and Resources, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, Animals, Humans, Pulmonology and respiratory tract, Molecular Biology, 030304 developmental biology, différenciation cellulaire, Regeneration (biology), Epithelial Cells, voie de signalisation, chemistry, Respiratory epithelium, 030217 neurology & neurosurgery, Function (biology), Developmental Biology
Abstract: The upper airway epithelium, which is mainly composed of multiciliated, goblet, club and basal cells, ensures proper mucociliary function and can regenerate in response to assaults. In chronic airway diseases, defective repair leads to tissue remodeling. Delineating key drivers of differentiation dynamics can help understand how normal or pathological regeneration occurs. Using single-cell transcriptomics and lineage inference, we have unraveled trajectories from basal to luminal cells, providing novel markers for specific populations. We report that: (1) a precursor subgroup of multiciliated cells, which we have entitled deuterosomal cells, is defined by specific markers, such as DEUP1, FOXN4, YPEL1, HES6 and CDC20B; (2) goblet cells can be precursors of multiciliated cells, thus explaining the presence of hybrid cells that co-express markers of goblet and multiciliated cells; and (3) a repertoire of molecules involved in the regeneration process, such as keratins or components of the Notch, Wnt or BMP/TGFβ pathways, can be identified. Confirmation of our results on fresh human and pig airway samples, and on mouse tracheal cells, extend and confirm our conclusions regarding the molecular and cellular choreography at work during mucociliary epithelial differentiation., Highlighted Article: Single-cell RNAseq data in fresh human airway epithelial tissues and air liquid cultures identifies novel cell populations and offers new insights into the molecular mechanisms occurring during mucociliary epithelium regeneration.
Published: 2019

44. GAPDH Expression Predicts the Response to R-CHOP, the Tumor Metabolic Status, and the Response of DLBCL Patients to Metabolic Inhibitors

Author: Vincent Delwail, Jean-Ehrland Ricci, Isabelle Peyrottes, Celine Delpech-Debiais, Sandrine Marchetti, Julie Reverso-Meinietti, Jacqueline Lehmann-Che, Gabriel Brisou, Jozef P. Bossowski, Manuel Grima-Reyes, Christiane Copie-Bergman, Camila Rubio-Patiño, Konstantina Fragaki, Eric de Kerviler, Véronique Paquis-Flucklinger, Thierry Jo Molina, Frederic Peyrade, Annabelle Mouchotte, Tony Petrella, Emma Proïcs, Bertrand Nadel, Els Verhoeyen, Bruno Taillan, Richard Delarue, Catherine Thieblemont, Laetitia Shintu, Agnès Paquet, Rana Mhaidly, Johanna Chiche, Elodie Villa, Georges Garnier, Pascal Barbry, Josette Brière, Damien Ambrosetti, Nicolas Mounier, André Bosly, Jean-François Michiels, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Université Nice Sophia Antipolis - Faculté de Médecine (UNS UFR Médecine), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Centre méditerranéen de médecine moléculaire (C3M), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Institut de pharmacologie moléculaire et cellulaire (IPMC), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Service d'anatomo-pathologie [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Hôpital Pasteur [Nice] (CHU), Hôpital Hôtel Dieu, INSERM U955, équipe 9, Département de pathologie [Mondor], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Pathologie cellulaire : aspects moléculaires et viraux / Pathologie et Virologie Moléculaire, Institut Universitaire d'Hématologie (IUH), Université Paris Diderot - Paris 7 (UPD7)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), Department of Pathology, Centre de Lutte contre le Cancer Antoine Lacassagne [Nice] (UNICANCER/CAL), UNICANCER-Université Côte d'Azur (UCA)-UNICANCER-Université Côte d'Azur (UCA), UNICANCER-Université Côte d'Azur (UCA), Hôpital Princesse Grace [Monaco], Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des Sciences Moléculaires de Marseille (ISM2), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), CIC - Poitiers, Université de Poitiers-Centre hospitalier universitaire de Poitiers (CHU Poitiers)-Direction Générale de l'Organisation des Soins (DGOS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre hospitalier universitaire de Poitiers (CHU Poitiers), Service d'immuno-hématologie pédiatrique [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Cliniques universitaires UCL de Mont-Godinne 5530 Yvoir, Centre de pathologie [Dijon], Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Service hématologie Nice, Centre Hospitalier Universitaire de Nice (CHU Nice), Service d'onco-hématologie [AP-HP Hôpital Saint-Louis], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Physiopathologie de la survie et de la mort cellulaire et infection virale, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-IFR50-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Université Paris Diderot - Paris 7 (UPD7)-Université Paris Diderot - Paris 7 (UPD7)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de pathologie, Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Université Côte d'Azur (UCA), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Nice Sophia Antipolis (... - 2019) (UNS), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris Diderot - Paris 7 (UPD7)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut Mondor de Recherche Biomédicale (IMRB), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), CRLCC Antoine Lacassagne, Centre Antoine Lacassagne, Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR50-Université Nice Sophia Antipolis (... - 2019) (UNS), UCL - (MGD) Service d'hématologie, UCL - SSS/IREC/MIRO - Pôle d'imagerie moléculaire, radiothérapie et oncologie, and UCL - SSS/IREC/MONT - Pôle Mont Godinne
Subjects: 0301 basic medicine, Male, Physiology, Phenformin, Cohort Studies, chemistry.chemical_compound, Mice, 0302 clinical medicine, immune system diseases, hemic and lymphatic diseases, Antineoplastic Combined Chemotherapy Protocols, Glyceraldehyde 3-phosphate dehydrogenase, Cells, Cultured, Aged, 80 and over, Predictive marker, biology, GAPDH, Glyceraldehyde-3-Phosphate Dehydrogenases, OxPhos, Middle Aged, glycolysis, Prognosis, 3. Good health, Metformin, Gene Expression Regulation, Neoplastic, medicine.anatomical_structure, Treatment Outcome, Vincristine, R-CHOP, mTOR, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, Lymphoma, Large B-Cell, Diffuse, Rituximab, predictive marker, medicine.drug, Adult, Antimetabolites, Antineoplastic, Mice, Transgenic, Gene Expression Regulation, Enzymologic, 03 medical and health sciences, Young Adult, stomatognathic system, medicine, Animals, Humans, Molecular Biology, Cyclophosphamide, PI3K/AKT/mTOR pathway, B cell, Aged, Retrospective Studies, Glutaminolysis, business.industry, Cell Biology, medicine.disease, L-asparaginase, Mice, Inbred C57BL, 030104 developmental biology, HEK293 Cells, chemistry, Doxorubicin, DLBCL, biology.protein, Cancer research, Prednisone, business, Diffuse large B-cell lymphoma, 030217 neurology & neurosurgery
Abstract: International audience; Diffuse large B cell lymphoma (DLBCL) is a heterogeneous disease treated with anti-CD20-based immuno-chemotherapy (R-CHOP). We identified that low levels of GAPDH predict a poor response to R-CHOP treatment. Importantly, we demonstrated that GAPDH(low) lymphomas use OxPhos metabolism and rely on mTORC1 signaling and glutaminolysis. Consistently, disruptors of OxPhos metabolism(phenformin) or glutaminolysis (L-asparaginase) induce cytotoxic responses in GAPDH(low) B cells and improve GAPDH(low) B cell-lymphoma-bearing mice survival, while they are low or not efficient on GAPDH(high) B cell lymphomas. Ultimately, we selected four GAPDH(low) DLBCL patients, who were refractory to all anti-CD20-based therapies, and targeted DLBCL metabolism-using L-asparaginase (K), mTOR inhibitor (T), and metformin (M) (called KTM therapy). Three out of the four patients presented a complete response upon one cycle of KTM. These findings establish that the GAPDH expression level predicts DLBCL patients' response to R-CHOP treatment and their sensitivity to specific metabolic inhibitors.
Published: 2019

45. Copy-number analysis identified new prognostic marker in acute myeloid leukemia

Author: Agnès Paquet, Olivier Nibourel, Soizic Guihard, C Demay, Claude Preudhomme, Karine Celli-Lebras, Pauline Peyrouze, Jean Soulier, Christophe Roumier, Aline Renneville, Raouf Ben Abdelali, Pascal Barbry, Antonio José Alberdi, Sylvie Castaigne, Christine Terré, Nicolas Pottier, Hervé Dombret, Sandrine Geffroy, Samuel Quentin, Meyling Cheok, and Bruno Quesnel
Subjects: Adult, Male, 0301 basic medicine, Cancer Research, medicine.medical_specialty, Myeloid, DNA Copy Number Variations, Gene Dosage, Copy number analysis, Genome-wide association study, Bioinformatics, Malignancy, Polymorphism, Single Nucleotide, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, hemic and lymphatic diseases, Internal medicine, Antineoplastic Combined Chemotherapy Protocols, Biomarkers, Tumor, medicine, Humans, Genetic Predisposition to Disease, Genetic Association Studies, Aged, Proportional Hazards Models, Hematology, business.industry, Myeloid leukemia, Genomics, Middle Aged, Genes, p53, Prognosis, medicine.disease, Leukemia, Myeloid, Acute, Leukemia, Treatment Outcome, 030104 developmental biology, medicine.anatomical_structure, Oncology, Drug Resistance, Neoplasm, 030220 oncology & carcinogenesis, Mutation, Cytarabine, Female, business, Genome-Wide Association Study, medicine.drug
Abstract: Recent advances in genomic technologies have revolutionized acute myeloid leukemia (AML) understanding by identifying potential novel actionable genomic alterations. Consequently, current risk stratification at diagnosis not only relies on cytogenetics, but also on the inclusion of several of these abnormalities. Despite this progress, AML remains a heterogeneous and complex malignancy with variable response to current therapy. Although copy-number alterations (CNAs) are accepted prognostic markers in cancers, large-scale genomic studies aiming at identifying specific prognostic CNA-based markers in AML are still lacking. Using 367 AML, we identified four recurrent CNA on chromosomes 11 and 21 that predicted outcome even after adjusting for standard prognostic risk factors and potentially delineated two new subclasses of AML with poor prognosis. ERG amplification, the most frequent CNA, was related to cytarabine resistance, a cornerstone drug of AML therapy. These findings were further validated in The Cancer Genome Atlas data. Our results demonstrate that specific CNA are of independent prognostic relevance, and provide new molecular information into the genomic basis of AML and cytarabine response. Finally, these CNA identified two potential novel risk groups of AML, which when confirmed prospectively, may improve the clinical risk stratification and potentially the AML outcome.
Published: 2016

46. MicroRNA-375/SEC23A as biomarkers of the in vitro efficacy of vandetanib

Author: Patrick Brest, Pascal Barbry, Marius Ilie, Paul Hofman, Sandra Lassalle, Elodie Long, Frédérique Tissier, Joséphine Zangari, Philippe Vielh, Géraldine Lemaire, Imène Sarah Henaoui, Catherine Butori, Alexandra Popa, Olivier Blanck, Christelle Bonnetaud, Hélène Trouette, Nicolas Guevara, Olivier Bordone, Alexandre Bozec, Bernard Mari, Geneviève Belléannée, J.-L. Sadoul, José Santini, Isabelle Peyrottes, Bogdan Catargi, Véronique Hofman, Martine Patey, Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), An algorithmic view on genomes, cells, and environments (BAMBOO), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut de la physique de la matière condensée (IPMC), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Universitaire de Nice (CHU Nice), Laboratory of Clinical and Experimental Pathology, Laboratoire d’anatomie et cytologie pathologique, Hôpital Robert Debré, CHU de Reims, CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), CHU Bordeaux [Bordeaux], Department of Pathology, Centre de Lutte contre le Cancer Antoine Lacassagne [Nice] (UNICANCER/CAL), UNICANCER-Université Côte d'Azur (UCA)-UNICANCER-Université Côte d'Azur (UCA), UNICANCER-Université Côte d'Azur (UCA), Service d'Endocrinologie (NICE - Endocrino), Hôpital Pasteur [Nice] (CHU), Institut de pharmacologie moléculaire et cellulaire (IPMC), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Bayer Cropscience, Pathologie morphologique, Département de biologie et pathologie médicales [Gustave Roussy], Institut Gustave Roussy (IGR)-Institut Gustave Roussy (IGR), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Infection bactérienne, inflammation, et carcinogenèse digestive, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-IFR50-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), FHU OncoAge - Pathologies liées à l’âge [CHU Nice] (OncoAge), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Pharmacologie Moléculaire et Cellulaire [UNIV Côte d'Azur] (UPMC)-Université Côte d'Azur (UCA), Université Nice Sophia Antipolis (... - 2019) (UNS), Service de pathologie [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Institut de Pharmacologie Moléculaire et Cellulaire [UNIV Côte d'Azur] (UPMC), Service d'Anatomie et cytologie pathologiques = Service de Pathologie [CHU Pitié-Salpêtrière] (ACP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and Brest, Patrick
Subjects: Male, 0301 basic medicine, [SDV]Life Sciences [q-bio], Vesicular Transport Proteins, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Vandetanib, 0302 clinical medicine, Piperidines, RNA interference, medullary thyroid carcinoma, ComputingMilieux_MISCELLANEOUS, Aged, 80 and over, microRNA, treatment, Thyroid, Middle Aged, 3. Good health, [SDV] Life Sciences [q-bio], Gene Expression Regulation, Neoplastic, medicine.anatomical_structure, Oncology, 030220 oncology & carcinogenesis, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Immunohistochemistry, Female, RNA Interference, Research Paper, medicine.drug, Adult, vandetanib, microRNA-375, [SDV.CAN]Life Sciences [q-bio]/Cancer, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Cell Line, 03 medical and health sciences, [SDV.CAN] Life Sciences [q-bio]/Cancer, Cell Line, Tumor, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Biomarkers, Tumor, medicine, Humans, Gene silencing, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Thyroid Neoplasms, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Aged, Cell Proliferation, business.industry, Cell growth, Gene Expression Profiling, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Carcinoma, Neuroendocrine, Gene expression profiling, MicroRNAs, 030104 developmental biology, Quinazolines, Cancer research, business
Abstract: In this study, we performed microRNA (miRNA) expression profiling on a large series of sporadic and hereditary forms of medullary thyroid carcinomas (MTC). More than 60 miRNAs were significantly deregulated in tumor vs adjacent non-tumor tissues, partially overlapping with results of previous studies. We focused our attention on the strongest up-regulated miRNA in MTC samples, miR-375, the deregulation of which has been previously observed in a variety of human malignancies including MTC. We identified miR-375 targets by combining gene expression signatures from human MTC (TT) and normal follicular (Nthy-ori 3-1) cell lines transfected with an antagomiR-375 inhibitor or a miR-375 mimic, respectively, and from an in silico analysis of thyroid cell lines of Cancer Cell Line Encyclopedia datasets. This approach identified SEC23A as a bona fide miR-375 target, which we validated by immunoblotting and immunohistochemistry of non-tumor and pathological thyroid tissue. Furthermore, we observed that miR-375 overexpression was associated with decreased cell proliferation and synergistically increased sensitivity to vandetanib, the clinically relevant treatment of metastatic MTC. We found that miR-375 increased PARP cleavage and decreased AKT phosphorylation, affecting both cell proliferation and viability. We confirmed these results through SEC23A direct silencing in combination with vandetanib, highlighting the importance of SEC23A in the miR-375-associated increased sensitivity to vandetanib. Since the combination of increased expression of miR-375 and decreased expression of SEC23A point to sensitivity to vandetanib, we question if the expression levels of miR-375 and SEC23A should be evaluated as an indicator of eligibility for treatment of MTC patients with vandetanib.
Published: 2016

47. SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues

Author: Alex K. Shalek, Kun Zhang, Christopher W. Peterson, Orit Rosen, Alison Yu, Robert Lafyatis, Samuel W. Kazer, Oliver Eickelberg, Sarah A. Teichmann, Mauricio Rojas, Martijn C. Nawijn, Colin D. Bingle, Thu Elizabeth Duong, Manuel Garber, Magali Plaisant, Philana Ling Lin, Christine S. Falk, Jennifer P. Wang, Xin Sun, Hengqi Betty Zheng, G. James Gatter, Sarah K. Nyquist, Malte Kühnemund, Joachim L. Schultze, Mark A. Krasnow, Maarten van den Berge, Yan Xu, Samuel J. Allon, Daniel F. Dwyer, Peter Horvath, Benjamin Doran, Brian M. Lin, Herbert B. Schiller, Blake M. Hauser, Fabian J. Theis, Avrum Spira, Paul A. Reyfman, Hans-Peter Kiem, Shaina L. Carroll, Zhiru Guo, Douglas P. Shepherd, Michael von Papen, Ian M. Mbano, Michael Farzan, Daniel Lingwood, JoAnne L. Flynn, Christoph Muus, Dana Pe'er, Stephen R. Quake, Travis K. Hughes, Sarah M. Fortune, Sten Linnarson, Chase J. Taylor, Tanya M. Laidlaw, Emma L. Rawlins, Bonnie Berger, Ashraf S. Yousif, Joakim Lundeberg, Jeffrey A. Whitsett, Ian A. Glass, Delphine Gras, Max A. Seibold, Jay Rajagopal, Jared Feldman, Victor Tkachev, Benjamin E. Mead, Joseph E. Powell, Aviv Regev, Alasdair Leslie, Robert W. Finberg, Yuming Cao, Jennifer M.S. Sucre, Marko Vukovic, Scott B. Snapper, Vincent N. Miao, Naftali Kaminski, Laure-Emmanuelle Zaragosi, Caylin G. Winchell, Faith Taliaferro, Marko Nikolic, Ilias Angelidis, Leslie S. Kean, Lucrezia Colonna, Kathleen M. Buchheit, Aaron G. Schmidt, Ramnik J. Xavier, Tushar J. Desai, Marc H. Wadsworth, Joshua A. Boyce, Alexander M. Tsankov, Nora A. Barrett, Pascal Barbry, Muzlifah Haniffa, Heiko Adler, Alvis Brazma, Hannah P. Gideon, Meshal Ansari, Jason R. Spence, Avinash Waghray, Constantine N. Tzouanas, Jose Ordovas-Montanes, Jonathan A. Kropski, Nicholas E. Banovich, Purushothama Rao Tata, Kerstin B. Meyer, Christos Samakovlis, Haeock Lee, Carly G. K. Ziegler, Alexander V. Misharin, Deborah T. Hung, Sylvie Leroy, Julia Bals, Vanessa Mitsialis, Kourosh Saeb-Parsy, Centre recherche en CardioVasculaire et Nutrition = Center for CardioVascular and Nutrition research (C2VN), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), FRM (DEQ20180339158), National Infrastructure France Génomique (Commissariat aux Grands Investissements, ANR-10-INBS-09-03, ANR-10-INBS-09-02), ANR-19-P3IA-0002,3IA@cote d'azur,3IA Côte d'Azur(2019), European Project: 874656,discovAIR, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Koch Institute for Integrative Cancer Research at MIT, and Groningen Research Institute for Asthma and COPD (GRIAC)
Subjects: Interferon Type I/immunology, Pneumonia, Viral/virology, Viral/virology, [SDV]Life Sciences [q-bio], ACE2, HIV Infections, non-human primate, HIV Infections/immunology, Mice, 0302 clinical medicine, Single-cell analysis, Alveolar Epithelial Cells/immunology, Interferon, Influenza, Human/immunology, Receptors, Child, Lung, Cells, Cultured, Virus/genetics, 0303 health sciences, Cultured, Serine Endopeptidases, Human/immunology, interferon, Nasal Mucosa/cytology, respiratory system, 3. Good health, Cell biology, Up-Regulation, Interferon Type I, Receptors, Virus, Angiotensin-Converting Enzyme 2, Goblet Cells, Enterocytes/immunology, Single-Cell Analysis, Coronavirus Infections, hormones, hormone substitutes, and hormone antagonists, medicine.drug, Proteases, Coronavirus Infections/virology, Adolescent, Cells, Pneumonia, Viral, Receptors, Virus/genetics, Peptidyl-Dipeptidase A/genetics, Lung injury, Biology, Peptidyl-Dipeptidase A, TMPRSS2, General Biochemistry, Genetics and Molecular Biology, Article, Cell Line, ISG, 03 medical and health sciences, Betacoronavirus, Serine Endopeptidases/metabolism, Downregulation and upregulation, Lung/cytology, Influenza, Human, scRNA-seq, medicine, Ace2, Covid-19, Isg, Sars-cov-2, Human, Influenza, Mouse, Non-human Primate, Scrna-seq, Tuberculosis, Animals, Humans, human, Pandemics, Tuberculosis/immunology, mouse, 030304 developmental biology, Innate immune system, SARS-CoV-2, Betacoronavirus/physiology, Interferon-stimulated gene, COVID-19, Mycobacterium tuberculosis, Pneumonia, Macaca mulatta, respiratory tract diseases, Nasal Mucosa, Enterocytes, Goblet Cells/immunology, Alveolar Epithelial Cells, 030217 neurology & neurosurgery
Abstract: Summary There is pressing urgency to understand the pathogenesis of the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2), which causes the disease COVID-19. SARS-CoV-2 spike (S) protein binds angiotensin-converting enzyme 2 (ACE2), and in concert with host proteases, principally transmembrane serine protease 2 (TMPRSS2), promotes cellular entry. The cell subsets targeted by SARS-CoV-2 in host tissues and the factors that regulate ACE2 expression remain unknown. Here, we leverage human, non-human primate, and mouse single-cell RNA-sequencing (scRNA-seq) datasets across health and disease to uncover putative targets of SARS-CoV-2 among tissue-resident cell subsets. We identify ACE2 and TMPRSS2 co-expressing cells within lung type II pneumocytes, ileal absorptive enterocytes, and nasal goblet secretory cells. Strikingly, we discovered that ACE2 is a human interferon-stimulated gene (ISG) in vitro using airway epithelial cells and extend our findings to in vivo viral infections. Our data suggest that SARS-CoV-2 could exploit species-specific interferon-driven upregulation of ACE2, a tissue-protective mediator during lung injury, to enhance infection., Graphical Abstract, Highlights • Meta-analysis of human, non-human primate, and mouse single-cell RNA-seq datasets for putative SARS-CoV-2 targets • Type II pneumocytes, nasal secretory cells, and absorptive enterocytes are ACE2 + TMPRSS2 + • Interferon and influenza increase ACE2 in human nasal epithelia and lung tissue • Mouse Ace2 is not upregulated by interferon, raising implications for disease modeling, Analysis of single-cell RNA-seq datasets from human, non-human primate, and mouse barrier tissues identifies putative cellular targets of SARS-CoV-2 on the basis of ACE2 and TMPRSS2 expression. ACE2 represents a previously unappreciated interferon-stimulated gene in human, but not mouse, epithelial tissues, identifying anti-viral induction of a host tissue-protective mechanism, but also a potential means for viral exploitation of the host response.
Published: 2020

48. Single-cell RNA sequencing reveals novel cell differentiation dynamics during human airway epithelium regeneration

Author: Virginie Magnone, Ignacio S. Caballero, Agnès Paquet, Laure-Emmanuelle Zaragosi, Marie Deprez, Sylvie Leroy, Brice Marcet, Kevin Lebrigand, Sandra Ruiz García, Pascal Barbry, Amélie Cavard, Marie-Jeanne Arguel, and Charles-Hugo Marquette
Subjects: medicine.anatomical_structure, Cellular differentiation, Regeneration (biology), Cell, medicine, Wnt signaling pathway, Respiratory epithelium, respiratory system, Epithelium regeneration, Biology, Cell fate determination, Epithelium, Cell biology
Abstract: BackgroundIt is usually considered that the upper airway epithelium is composed of multiciliated, goblet, secretory and basal cells, which collectively constitute an efficient first line of defense against inhalation of noxious substances. Upon injury, regeneration of this epithelium through proliferation and differentiation can restore a proper mucociliary function. However, in chronic airway diseases, the injured epithelium frequently displays defective repair leading to tissue remodeling, characterized by a loss of multiciliated cells and mucus hyper-secretion. Delineating drivers of differentiation dynamics and cell fate in the human airway epithelium is important to preserve homeostasis.ResultsWe have used single cell transcriptomics to characterize the sequence of cellular and molecular processes taking place during human airway epithelium regeneration. We have characterized airway subpopulations with high resolution and lineage inference algorithms have unraveled cell trajectories from basal to luminal cells, providing markers for specific cell populations, such as deuterosomal cells, i.e. precursors of multiciliated cells. We report that goblet cells, like secretory cells, can act as precursors of multiciliated cells. Our study provides a repertoire of molecules involved in key steps of the regeneration process, either keratins or components of the Notch, Wnt or BMP/TGFβ signaling pathways. Our findings were confirmed in independent experiments performed on fresh human and pig airway samples, and on mouse tracheal epithelial cells.ConclusionsOur single-cell RNA-seq study provides novel insights about airway epithelium differentiation dynamics, clarifies cell trajectories between secretory, goblet and multiciliated cells, identifies novel cell subpopulations, and maps the activation and repression of key signaling pathways.
Published: 2018

49. Clinical Aspects of STAT3 Gain-of-Function Germline Mutations: A Systematic Review

Author: Sarah Marchal, Pascal Barbry, Bernard Mari, Pierre-Simon Rohrlich, Alexandre Fabre, Lisa R. Forbes, Tiphanie P. Vogel, Vincent Barlogis, Lisa Giovannini-Chami, Institut de Recherche juridique sur l'Entreprise et les Relations Professionnelles (IRERP), Université Paris Nanterre (UPN), Pédiatrie et oncologie pédiatrique [Hôpital de la Timone - APHM], Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), Institut de pharmacologie moléculaire et cellulaire (IPMC), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Interactions hôte-greffon-tumeur, ingénierie cellulaire et génique - UFC (UMR INSERM 1098) (RIGHT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS [Bourgogne-Franche-Comté])-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Service de Pneumologie, Centre Hospitalier Universitaire de Nice (CHU Nice)-Hôpital de l'Archet, Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Interactions hôte-greffon-tumeur, ingénierie cellulaire et génique - UFC (UMR INSERM 1098) (HOTE GREFFON), Université de Franche-Comté (UFC)-Etablissement français du sang [Bourgogne-France-Comté] (EFS [Bourgogne-France-Comté])-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Nice Sophia Antipolis (1965 - 2019) (UNS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang [Bourgogne-Franche-Comté] (EFS BFC)-Université de Franche-Comté (UFC)
Subjects: Lung Diseases, STAT3 Transcription Factor, Evans syndrome, Gastrointestinal Diseases, [SDV]Life Sciences [q-bio], medicine.medical_treatment, Hematopoietic stem cell transplantation, Disease, Bioinformatics, Endocrine System Diseases, Thyroiditis, 03 medical and health sciences, STAT3 GOF, 0302 clinical medicine, Germline mutation, medicine, Immunology and Allergy, Humans, 030212 general & internal medicine, ComputingMilieux_MISCELLANEOUS, Immunodeficiency, Germ-Line Mutation, business.industry, Interstitial lung disease, medicine.disease, Hematologic Diseases, 3. Good health, 030228 respiratory system, Immune System Diseases, Gain of Function Mutation, business
Abstract: Background Signal transducer and activator of transcription 3 (STAT3) gain-of-function (GOF) germline mutations have been recently described. A comprehensive overview of this early-onset multiorgan autoimmune and lymphoproliferative disease has not yet been compiled. Objective We have conducted a systematic review of published STAT3 GOF cases to describe clinical, diagnostic, and therapeutic aspects of the disease. Methods A systematic review including articles published before October 10, 2018, in PubMed, Web of Science, and Cochrane Central Register of Controlled Trials databases was performed. We described cases of patients with STAT3 GOF germline mutations with genetic analysis and a concordant phenotype if functional analyses were not performed for the mutation. Results The search identified 18 publications describing 42 unique patients. Twenty-eight different mutations were described. Onset of disease was very early with an average age of 3 (0.5-5) years. The most frequent manifestations were autoimmune cytopenias (28 of 42), lymphoproliferation (27 of 42), enteropathy (24 of 42), interstitial lung disease (15 of 42), thyroiditis (13 of 42), diabetes (10 of 42), and postnatal growth failure (15 of 21). Immunodeficiency was not always a predominant feature. Most patients required significant immunosuppressive therapy. Five patients received hematopoietic stem cell transplantation, and 4 died from complications. Improvement of symptoms was observed for 8 of 9 patients who received targeted biotherapies. Conclusions STAT3 GOF syndrome is a new clinical entity to consider when confronted with a patient with early-onset polyautoimmunity, lymphoproliferation, and growth failure. At this time, precise therapeutic guidelines are lacking, but use of anti-IL-6 receptor and JAK inhibitor biologics is an attractive possibility.
Published: 2018

50. Cell dissociation from nasal and bronchial brushings withcold-active protease for single-cell RNA-seq v2

Author: Laure-Emmanuelle Zaragosi and Pascal Barbry
Subjects: medicine.anatomical_structure, Protease, Chemistry, medicine.medical_treatment, Cell, medicine, RNA-Seq, Nasal epithelium, Molecular biology, Cell dissociation, Dissociation (chemistry)
Abstract: This protocol provides details on the cell dissociation that should be performed to obtain single-cell suspensions from nasal epithelium brushings. Cell dissociation is performed at 4°C to avoid gene expression alterations and maximize viability. The typical cell number recovery is 200 000 - 300 000 for one brushing. Cell suspensions are suitable for single-cell RNA-sequencing protocols.
Published: 2018

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