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Bier K, Senajova Z, Henrion F, Wang Y, Bruno S, Rauld C, Hörmann LC, Barske C, Delucis-Bronn C, Bergling S, Altorfer M, Hägele J, Knehr J, Junt T, Roediger B, Röhn TA, Kolbinger F. IL-26 Potentiates Type 2 Skin Inflammation in the Presence of IL-1β. J Invest Dermatol 2024; 144:1544-1556.e9. [PMID: 38237730 DOI: 10.1016/j.jid.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 12/12/2023] [Accepted: 12/16/2023] [Indexed: 06/24/2024]
Abstract
Atopic dermatitis (AD) is a debilitating inflammatory skin disorder. Biologics targeting the IL-4/IL-13 axis are effective in AD, but there is still a large proportion of patients who do not respond to IL-4R blockade. Further exploration of potentially pathogenic T-cell-derived cytokines in AD may lead to new effective treatments. This study aimed to investigate the downstream effects of IL-26 on skin in the context of type 2 skin inflammation. We found that IL-26 alone exhibited limited inflammatory activity in the skin. However, in the presence of IL-1β, IL-26 potentiated the secretion of TSLP, CXCL1, and CCL20 from human epidermis through Jak/signal transducer and activator of transcription signaling. Moreover, in an in vivo AD-like skin inflammation model, IL-26 exacerbated skin pathology and locally increased type 2 cytokines, most notably of IL13 in skin T helper cells. Neutralization of IL-1β abrogated IL-26-mediated effects, indicating that the presence of IL-1β is required for full IL-26 downstream action in vivo. These findings suggest that the presence of IL-1β enables IL-26 to be a key amplifier of inflammation in the skin. As such, IL-26 may contribute to the development and pathogenesis of inflammatory skin disorders such as AD.
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Affiliation(s)
- Katharina Bier
- Immunology Disease Area, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland.
| | - Zuzana Senajova
- Immunology Disease Area, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Fanny Henrion
- Immunology Disease Area, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Yichen Wang
- Immunology Disease Area, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Sandro Bruno
- Immunology Disease Area, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Celine Rauld
- Immunology Disease Area, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Lisa C Hörmann
- Immunology Disease Area, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Carmen Barske
- Immunology Disease Area, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Corinne Delucis-Bronn
- Immunology Disease Area, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Sebastian Bergling
- Discovery Science, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Marc Altorfer
- Discovery Science, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Jasmin Hägele
- Discovery Science, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Judith Knehr
- Discovery Science, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Tobias Junt
- Immunology Disease Area, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Ben Roediger
- Immunology Disease Area, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Till A Röhn
- Immunology Disease Area, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Frank Kolbinger
- Immunology Disease Area, Novartis Biomedical Research, Novartis Pharma AG, Basel, Switzerland
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2
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Steinhauser S, Estoppey D, Buehler DP, Xiong Y, Pizzato N, Rietsch A, Wu F, Leroy N, Wunderlin T, Claerr I, Tropberger P, Müller M, Davison LM, Sheng Q, Bergling S, Wild S, Moulin P, Liang J, English WJ, Williams B, Knehr J, Altorfer M, Reyes A, Mickanin C, Hoepfner D, Nigsch F, Frederiksen M, Flynn CR, Fodor BD, Brown JD, Kolter C. The transcription factor ZNF469 regulates collagen production in liver fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591188. [PMID: 38712281 PMCID: PMC11071482 DOI: 10.1101/2024.04.25.591188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Non-alcoholic fatty liver disease (NAFLD) - characterized by excess accumulation of fat in the liver - now affects one third of the world's population. As NAFLD progresses, extracellular matrix components including collagen accumulate in the liver causing tissue fibrosis, a major determinant of disease severity and mortality. To identify transcriptional regulators of fibrosis, we computationally inferred the activity of transcription factors (TFs) relevant to fibrosis by profiling the matched transcriptomes and epigenomes of 108 human liver biopsies from a deeply-characterized cohort of patients spanning the full histopathologic spectrum of NAFLD. CRISPR-based genetic knockout of the top 100 TFs identified ZNF469 as a regulator of collagen expression in primary human hepatic stellate cells (HSCs). Gain- and loss-of-function studies established that ZNF469 regulates collagen genes and genes involved in matrix homeostasis through direct binding to gene bodies and regulatory elements. By integrating multiomic large-scale profiling of human biopsies with extensive experimental validation we demonstrate that ZNF469 is a transcriptional regulator of collagen in HSCs. Overall, these data nominate ZNF469 as a previously unrecognized determinant of NAFLD-associated liver fibrosis.
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3
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Richards SM, Gubser Keller C, Kreutzer R, Greiner G, Ley S, Doelemeyer A, Dubost V, Flandre T, Kirkland S, Carbone W, Pandya R, Knehr J, Roma G, Schuierer S, Bouchez L, Seuwen K, Aebi A, Westhead D, Hintzen G, Jurisic G, Hossain I, Neri M, Manevski N, Balavenkatraman KK, Moulin P, Begrich A, Bertschi B, Huber R, Bouwmeester T, Driver VR, von Schwabedissen M, Schaefer D, Wettstein B, Wettstein R, Ruffner H. Molecular characterization of chronic cutaneous wounds reveals subregion- and wound type-specific differential gene expression. Int Wound J 2024; 21:e14447. [PMID: 38149752 PMCID: PMC10958103 DOI: 10.1111/iwj.14447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 12/28/2023] Open
Abstract
A limited understanding of the pathology underlying chronic wounds has hindered the development of effective diagnostic markers and pharmaceutical interventions. This study aimed to elucidate the molecular composition of various common chronic ulcer types to facilitate drug discovery strategies. We conducted a comprehensive analysis of leg ulcers (LUs), encompassing venous and arterial ulcers, foot ulcers (FUs), pressure ulcers (PUs), and compared them with surgical wound healing complications (WHCs). To explore the pathophysiological mechanisms and identify similarities or differences within wounds, we dissected wounds into distinct subregions, including the wound bed, border, and peri-wound areas, and compared them against intact skin. By correlating histopathology, RNA sequencing (RNA-Seq), and immunohistochemistry (IHC), we identified unique genes, pathways, and cell type abundance patterns in each wound type and subregion. These correlations aim to aid clinicians in selecting targeted treatment options and informing the design of future preclinical and clinical studies in wound healing. Notably, specific genes, such as PITX1 and UPP1, exhibited exclusive upregulation in LUs and FUs, potentially offering significant benefits to specialists in limb preservation and clinical treatment decisions. In contrast, comparisons between different wound subregions, regardless of wound type, revealed distinct expression profiles. The pleiotropic chemokine-like ligand GPR15L (C10orf99) and transmembrane serine proteases TMPRSS11A/D were significantly upregulated in wound border subregions. Interestingly, WHCs exhibited a nearly identical transcriptome to PUs, indicating clinical relevance. Histological examination revealed blood vessel occlusions with impaired angiogenesis in chronic wounds, alongside elevated expression of genes and immunoreactive markers related to blood vessel and lymphatic epithelial cells in wound bed subregions. Additionally, inflammatory and epithelial markers indicated heightened inflammatory responses in wound bed and border subregions and reduced wound bed epithelialization. In summary, chronic wounds from diverse anatomical sites share common aspects of wound pathophysiology but also exhibit distinct molecular differences. These unique molecular characteristics present promising opportunities for drug discovery and treatment, particularly for patients suffering from chronic wounds. The identified diagnostic markers hold the potential to enhance preclinical and clinical trials in the field of wound healing.
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Affiliation(s)
| | | | - Robert Kreutzer
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Department of PathologyAnaPath Services GmbHLiestalSwitzerland
| | | | - Svenja Ley
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Arno Doelemeyer
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Valerie Dubost
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Thierry Flandre
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Susan Kirkland
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Harvantis Pharma Consulting LtdLondonUK
| | - Walter Carbone
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Research and Development CoordinatorELI TechGroup Corso SvizzeraTorinoItaly
| | - Rishika Pandya
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Judith Knehr
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Guglielmo Roma
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Discovery Data ScienceGSK VaccinesSienaItaly
| | - Sven Schuierer
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Laure Bouchez
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Therapeutics Department, Executive in ResidenceGeneral InceptionBaselSwitzerland
| | - Klaus Seuwen
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Alexandra Aebi
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - David Westhead
- Leeds Institute of Data AnalyticsUniversity of LeedsLeedsUK
| | - Gabriele Hintzen
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Translational ScienceAffimed GmbHMannheimGermany
| | - Giorgia Jurisic
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Imtiaz Hossain
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Marilisa Neri
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Nenad Manevski
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- Translational PKPD and Clinical Pharmacology, Pharmaceutical Sciences, pREDF. Hoffmann‐La Roche AGBaselSwitzerland
| | | | - Pierre Moulin
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | - Annette Begrich
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | | | - Roland Huber
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
| | | | - Vickie R. Driver
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
- INOVA HealthcareWound Healing and Hyperbaric CentersFalls ChurchVirginiaUSA
| | | | - Dirk Schaefer
- Plastic, Reconstructive, Aesthetic and Hand SurgeryUniversity Hospital BaselBaselSwitzerland
| | - Barbara Wettstein
- Plastic, Reconstructive, Aesthetic and Hand SurgeryUniversity Hospital BaselBaselSwitzerland
| | - Reto Wettstein
- Plastic, Reconstructive, Aesthetic and Hand SurgeryUniversity Hospital BaselBaselSwitzerland
| | - Heinz Ruffner
- Novartis Biomedical ResearchNovartis Pharma AGBaselSwitzerland
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Li J, Bi H. Molecular mechanisms of atrazine toxicity on H19-7 hippocampal neurons revealed by integrated miRNA and mRNA "omics". ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 253:114681. [PMID: 36841081 DOI: 10.1016/j.ecoenv.2023.114681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Atrazine (ATR) is a widely applied herbicide in Asia and South America with slow natural degradation and documented deleterious effects on human and animal health, including hippocampal toxicity. However, relatively little is known about the molecular mechanisms responsible for ATR-induced hippocampal damage. Screening for differentially expressed mRNAs and microRNAs (miRNAs), and construction of potential miRNA-mRNA regulatory networks can reveal such mechanisms, so we analyzed the mRNA and miRNA expression profiles of rat hippocampus-derived H19-7 cells in response to ATR (500 μM) and conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes enrichment (KEGG) analyses. Integration of miRNA sequencing (miRNA-seq) and mRNA sequencing (mRNA-seq) results identified 114 differentially expressed miRNAs (DEMIs, 40 upregulated and 74 downregulated), and 510 differentially expressed mRNAs (DEMs, 177 upregulated and 333 downregulated) targeted by these DEMIs. The top 10 hub mRNAs (Fos, Prkcb, Ncf1, Vcam1, Atf3, Pak3, Pak1, Cacna1s, Junb, and Ccl2) and 19 related miRNAs (rno-miR-194-5p, rno-miR-24-3p, rno-miR-3074, rno-miR-1949, rno-miR-218a-1-3p, rno-miR-1843a-5p, rno-miR-1843b-5p, rno-miR-296-3p, rno-miR-320-3p, rno-miR-219a-1-3p, rno-miR-122-5p, rno-miR-1839-5p, rno-miR-1843a-3p, rno-miR-215, rno-miR-3583-3p, rno-miR-194-3p, rno-miR-128-1-5p, rno-miR-1956-5p, and rno-miR-466b-2-3p) were validated by quantitative real-time PCR. GO analysis indicated that these DEMs were enriched in genes associated with synaptic plasticity and antioxidant capacity, while KEGG analysis suggested that enriched DEMs were involved in calcium signaling, axon guidance, MAPK signaling, and glial carcinogenesis. The miRNA-mRNA regulatory network identified here may provide potential biomarkers and novel strategies for the treatment of hippocampal neurotoxicity induced by ATR.
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Affiliation(s)
- Jianan Li
- Department of Occupational and Environmental Health, College of Public Health, Xuzhou Medical University, 209 Tongshan Road, Yun Long District, Xuzhou 221000, China.
| | - Haoran Bi
- Department of Biostatistics, College of Public Health, Xuzhou Medical University, 209 Tongshan Road, Yun Long District, Xuzhou 221000, China.
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5
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Identification of marker genes to monitor residual iPSCs in iPSC-derived products. Cytotherapy 2023; 25:59-67. [PMID: 36319564 DOI: 10.1016/j.jcyt.2022.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/08/2022] [Accepted: 09/27/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND Engineered tissues and cell therapies based on human induced pluripotent stem cells (iPSCs) represent a promising approach for novel medicines. However, iPSC-derived cells and tissues may contain residual undifferentiated iPSCs that could lead to teratoma formation after implantation into patients. As a consequence, highly sensitive and specific methods for detecting residual undifferentiated iPSCs are indispensable for safety evaluations of iPSC-based therapies. The present study provides an approach for identifying potential marker genes for iPSC impurities in iPSC-derived cells using RNA sequencing data from iPSCs and various differentiated cell types. METHODS Identifying iPSC marker genes for each cell type individually provided a larger and more specific set of potential marker genes than considering all cell types in the analysis. Thus, the authors focused on identifying markers for iPSC impurities in iPSC-derived cardiomyocytes (iCMs) and validated the selected genes by reverse transcription quantitative polymerase chain reaction. The sensitivity of the candidate genes was determined by spiking different amounts of iPSCs into iCMs and their performance was compared with the previously suggested marker lin-28 homolog A (LIN28A). RESULTS Embryonic stem cell-related gene (ESRG), long intergenic non-protein coding RNA 678 (LINC00678), CaM kinase-like vesicle-associated (CAMKV), indoleamine 2,3-dioxygenase 1 (IDO1), chondromodulin (CNMD), LINE1-type transposase domain containing 1 (L1DT1), LIN28A, lymphocyte-specific protein tyrosine kinase (LCK), vertebrae development-associated (VRTN) and zinc finger and SCAN domain containing 10 (ZSCAN10) detected contaminant iPSCs among iCMs with a limit of detection that ranged from 0.001% to 0.1% depending on the gene and iCM batch used. CONCLUSIONS Using the example of iCMs, the authors provide a strategy for identifying a set of highly specific and sensitive markers that can be used for quality assessment of iPSC-derived products.
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6
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Mitchell G, Roma G, Voorberg-van der Wel A, Beibel M, Zeeman AM, Schuierer S, Torres L, Flannery EL, Kocken CHM, Mikolajczak SA, Diagana TT. Transcriptional profiling of hepatocytes infected with the replicative form of the malaria parasite Plasmodium cynomolgi. Malar J 2022; 21:393. [PMID: 36564750 PMCID: PMC9789591 DOI: 10.1186/s12936-022-04411-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The zoonotic simian parasite Plasmodium cynomolgi develops into replicating schizonts and dormant hypnozoites during the infection of hepatocytes and is used as a model organism to study relapsing malaria. The transcriptional profiling of P. cynomolgi liver stages was previously reported and revealed many important biological features of the parasite but left out the host response to malaria infection. METHODS Previously published RNA sequencing data were used to quantify the expression of host genes in rhesus macaque hepatocytes infected with P. cynomolgi in comparison to either cells from uninfected samples or uninfected bystander cells. RESULTS Although the dataset could not be used to resolve the transcriptional profile of hypnozoite-infected hepatocytes, it provided a snapshot of the host response to liver stage schizonts at 9-10 day post-infection and identified specific host pathways that are modulated during the exo-erythrocytic stage of P. cynomolgi. CONCLUSIONS This study constitutes a valuable resource characterizing the hepatocyte response to P. cynomolgi infection and provides a framework to build on future research that aims at understanding hepatocyte-parasite interactions during relapsing malaria infection.
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Affiliation(s)
- Gabriel Mitchell
- Open Innovation at Novartis Institute for Tropical Diseases, Novartis Institutes for BioMedical Research, Emeryville, CA, USA.
| | - Guglielmo Roma
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Martin Beibel
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Anne-Marie Zeeman
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Sven Schuierer
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Laura Torres
- Open Innovation at Novartis Institute for Tropical Diseases, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Erika L Flannery
- Novartis Institute for Tropical Diseases, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Clemens H M Kocken
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Sebastian A Mikolajczak
- Novartis Institute for Tropical Diseases, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Thierry T Diagana
- Novartis Institute for Tropical Diseases, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
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7
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Keller CG, Shin Y, Monteys AM, Renaud N, Beibel M, Teider N, Peters T, Faller T, St-Cyr S, Knehr J, Roma G, Reyes A, Hild M, Lukashev D, Theil D, Dales N, Cha JH, Borowsky B, Dolmetsch R, Davidson BL, Sivasankaran R. An orally available, brain penetrant, small molecule lowers huntingtin levels by enhancing pseudoexon inclusion. Nat Commun 2022; 13:1150. [PMID: 35241644 PMCID: PMC8894458 DOI: 10.1038/s41467-022-28653-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/27/2022] [Indexed: 02/07/2023] Open
Abstract
Huntington's Disease (HD) is a progressive neurodegenerative disorder caused by CAG trinucleotide repeat expansions in exon 1 of the huntingtin (HTT) gene. The mutant HTT (mHTT) protein causes neuronal dysfunction, causing progressive motor, cognitive and behavioral abnormalities. Current treatments for HD only alleviate symptoms, but cerebral spinal fluid (CSF) or central nervous system (CNS) delivery of antisense oligonucleotides (ASOs) or virus vectors expressing RNA-induced silencing (RNAi) moieties designed to induce mHTT mRNA lowering have progressed to clinical trials. Here, we present an alternative disease modifying therapy the orally available, brain penetrant small molecule branaplam. By promoting inclusion of a pseudoexon in the primary transcript, branaplam lowers mHTT protein levels in HD patient cells, in an HD mouse model and in blood samples from Spinal Muscular Atrophy (SMA) Type I patients dosed orally for SMA (NCT02268552). Our work paves the way for evaluating branaplam's utility as an HD therapy, leveraging small molecule splicing modulators to reduce expression of dominant disease genes by driving pseudoexon inclusion.
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Affiliation(s)
| | - Youngah Shin
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Alex Mas Monteys
- The Raymond G Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, The Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA
| | - Nicole Renaud
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Martin Beibel
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Natalia Teider
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Thomas Peters
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Thomas Faller
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sophie St-Cyr
- The Raymond G Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Judith Knehr
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Alejandro Reyes
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Marc Hild
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Diethilde Theil
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Natalie Dales
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jang-Ho Cha
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | | | - Beverly L Davidson
- The Raymond G Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Department of Pathology and Laboratory Medicine, The Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA.
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8
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Morozzi G, Rothen J, Toussaint G, De Lange K, Westritschnig K, Doelemeyer A, Ueberschlag VP, Kahle P, Lambert C, Obrecht M, Beckmann N, Ritter V, Panesar M, Stauffer D, Garnier I, Mueller M, Guerini D, Keller CG, Knehr J, Roma G, Bidinosti M, Brachat S, Morvan F, Fornaro M. STING regulates peripheral nerve regeneration and colony stimulating factor 1 receptor (CSF1R) processing in microglia. iScience 2021; 24:103434. [PMID: 34877494 PMCID: PMC8633968 DOI: 10.1016/j.isci.2021.103434] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/29/2021] [Accepted: 11/10/2021] [Indexed: 11/23/2022] Open
Abstract
Inflammatory responses are crucial for regeneration following peripheral nerve injury (PNI). PNI triggers inflammatory responses at the site of injury. The DNA-sensing receptor cyclic GMP-AMP synthase (cGAS) and its downstream effector stimulator of interferon genes (STING) sense foreign and self-DNA and trigger type I interferon (IFN) immune responses. We demonstrate here that following PNI, the cGAS/STING pathway is upregulated in the sciatic nerve of naive rats and dysregulated in old rats. In a nerve crush mouse model where STING is knocked out, myelin content in sciatic nerve is increased resulting in accelerated functional axon recovery. STING KO mice have lower macrophage number in sciatic nerve and decreased microglia activation in spinal cord 1 week post injury. STING activation regulated processing of colony stimulating factor 1 receptor (CSF1R) and microglia survival in vitro. Taking together, these data highlight a previously unrecognized role of STING in the regulation of nerve regeneration. The cGAS/STING pathway is upregulated in sciatic nerve post nerve injury and in aging STING ablation increases myelin content and accelerates functional axon recovery STING KO mice reduces macrophage number in sciatic nerve and microglia activation post injury
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Affiliation(s)
- Giulio Morozzi
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Julian Rothen
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Gauthier Toussaint
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Katrina De Lange
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Katrin Westritschnig
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Arno Doelemeyer
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | | | - Peter Kahle
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Christian Lambert
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Michael Obrecht
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Nicolau Beckmann
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Veronique Ritter
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Moh Panesar
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Daniela Stauffer
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Isabelle Garnier
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Matthias Mueller
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Danilo Guerini
- Autoimmunity and Inflammation, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Caroline Gubser Keller
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Judith Knehr
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Guglielmo Roma
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Michael Bidinosti
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Sophie Brachat
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Frederic Morvan
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
| | - Mara Fornaro
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland
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9
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Wang ZY, Keogh A, Waldt A, Cuttat R, Neri M, Zhu S, Schuierer S, Ruchti A, Crochemore C, Knehr J, Bastien J, Ksiazek I, Sánchez-Taltavull D, Ge H, Wu J, Roma G, Helliwell SB, Stroka D, Nigsch F. Single-cell and bulk transcriptomics of the liver reveals potential targets of NASH with fibrosis. Sci Rep 2021; 11:19396. [PMID: 34588551 PMCID: PMC8481490 DOI: 10.1038/s41598-021-98806-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/15/2021] [Indexed: 12/11/2022] Open
Abstract
Fibrosis is characterized by the excessive production of collagen and other extracellular matrix (ECM) components and represents a leading cause of morbidity and mortality worldwide. Previous studies of nonalcoholic steatohepatitis (NASH) with fibrosis were largely restricted to bulk transcriptome profiles. Thus, our understanding of this disease is limited by an incomplete characterization of liver cell types in general and hepatic stellate cells (HSCs) in particular, given that activated HSCs are the major hepatic fibrogenic cell population. To help fill this gap, we profiled 17,810 non-parenchymal cells derived from six healthy human livers. In conjunction with public single-cell data of fibrotic/cirrhotic human livers, these profiles enable the identification of potential intercellular signaling axes (e.g., ITGAV-LAMC1, TNFRSF11B-VWF and NOTCH2-DLL4) and master regulators (e.g., RUNX1 and CREB3L1) responsible for the activation of HSCs during fibrogenesis. Bulk RNA-seq data of NASH patient livers and rodent models for liver fibrosis of diverse etiologies allowed us to evaluate the translatability of candidate therapeutic targets for NASH-related fibrosis. We identified 61 liver fibrosis-associated genes (e.g., AEBP1, PRRX1 and LARP6) that may serve as a repertoire of translatable drug target candidates. Consistent with the above regulon results, gene regulatory network analysis allowed the identification of CREB3L1 as a master regulator of many of the 61 genes. Together, this study highlights potential cell-cell interactions and master regulators that underlie HSC activation and reveals genes that may represent prospective hallmark signatures for liver fibrosis.
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Affiliation(s)
- Zhong-Yi Wang
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland.
| | - Adrian Keogh
- Visceral Surgery and Medicine, Inselspital, Bern University Hospital, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Annick Waldt
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Rachel Cuttat
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Marilisa Neri
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Shanshan Zhu
- China Novartis Institutes for BioMedical Research, Shanghai, 201203, China
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Alexandra Ruchti
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | | | - Judith Knehr
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Julie Bastien
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Iwona Ksiazek
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Daniel Sánchez-Taltavull
- Visceral Surgery and Medicine, Inselspital, Bern University Hospital, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Hui Ge
- China Novartis Institutes for BioMedical Research, Shanghai, 201203, China
| | - Jing Wu
- China Novartis Institutes for BioMedical Research, Shanghai, 201203, China
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
| | - Stephen B Helliwell
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland
- Rejuveron Life Sciences AG, 8952, Schlieren, Switzerland
| | - Deborah Stroka
- Visceral Surgery and Medicine, Inselspital, Bern University Hospital, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Florian Nigsch
- Novartis Institutes for BioMedical Research, 4056, Basel, Switzerland.
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10
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ZNRF3 and RNF43 cooperate to safeguard metabolic liver zonation and hepatocyte proliferation. Cell Stem Cell 2021; 28:1822-1837.e10. [PMID: 34129813 DOI: 10.1016/j.stem.2021.05.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 04/02/2021] [Accepted: 05/24/2021] [Indexed: 12/13/2022]
Abstract
AXIN2 and LGR5 mark intestinal stem cells (ISCs) that require WNT/β-Catenin signaling for constant homeostatic proliferation. In contrast, AXIN2/LGR5+ pericentral hepatocytes show low proliferation rates despite a WNT/β-Catenin activity gradient required for metabolic liver zonation. The mechanisms restricting proliferation in AXIN2+ hepatocytes and metabolic gene expression in AXIN2+ ISCs remained elusive. We now show that restricted chromatin accessibility in ISCs prevents the expression of β-Catenin-regulated metabolic enzymes, whereas fine-tuning of WNT/β-Catenin activity by ZNRF3 and RNF43 restricts proliferation in chromatin-permissive AXIN2+ hepatocytes, while preserving metabolic function. ZNRF3 deletion promotes hepatocyte proliferation, which in turn becomes limited by RNF43 upregulation. Concomitant deletion of RNF43 in ZNRF3 mutant mice results in metabolic reprogramming of periportal hepatocytes and induces clonal expansion in a subset of hepatocytes, ultimately promoting liver tumors. Together, ZNRF3 and RNF43 cooperate to safeguard liver homeostasis by spatially and temporally restricting WNT/β-Catenin activity, balancing metabolic function and hepatocyte proliferation.
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11
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Cho H, Shen Q, Zhang LH, Okumura M, Kawakami A, Ambrose J, Sigoillot F, Miller HR, Gleim S, Cobos-Correa A, Wang Y, Piechon P, Roma G, Eggimann F, Moore C, Aspesi P, Mapa FA, Burks H, Ross NT, Krastel P, Hild M, Maimone TJ, Fisher DE, Nomura DK, Tallarico JA, Canham SM, Jenkins JL, Forrester WC. CYP27A1-dependent anti-melanoma activity of limonoid natural products targets mitochondrial metabolism. Cell Chem Biol 2021; 28:1407-1419.e6. [PMID: 33794192 DOI: 10.1016/j.chembiol.2021.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/24/2021] [Accepted: 03/09/2021] [Indexed: 01/18/2023]
Abstract
Three limonoid natural products with selective anti-proliferative activity against BRAF(V600E) and NRAS(Q61K)-mutation-dependent melanoma cell lines were identified. Differential transcriptome analysis revealed dependency of compound activity on expression of the mitochondrial cytochrome P450 oxidase CYP27A1, a transcriptional target of melanogenesis-associated transcription factor (MITF). We determined that CYP27A1 activity is necessary for the generation of a reactive metabolite that proceeds to inhibit cellular proliferation. A genome-wide small interfering RNA screen in combination with chemical proteomics experiments revealed gene-drug functional epistasis, suggesting that these compounds target mitochondrial biogenesis and inhibit tumor bioenergetics through a covalent mechanism. Our work suggests a strategy for melanoma-specific targeting by exploiting the expression of MITF target gene CYP27A1 and inhibiting mitochondrial oxidative phosphorylation in BRAF mutant melanomas.
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Affiliation(s)
- Hyelim Cho
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Qiong Shen
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Lydia H Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Mikiko Okumura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Akinori Kawakami
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jessi Ambrose
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Frederic Sigoillot
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Howard R Miller
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Scott Gleim
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Amanda Cobos-Correa
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Ying Wang
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Philippe Piechon
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Fabian Eggimann
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Charles Moore
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Peter Aspesi
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Felipa A Mapa
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Heather Burks
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Nathan T Ross
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Philipp Krastel
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Marc Hild
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Thomas J Maimone
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - David E Fisher
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94720, USA
| | - John A Tallarico
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Stephen M Canham
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Jeremy L Jenkins
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - William C Forrester
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
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12
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Sun T, Pikiolek M, Orsini V, Bergling S, Holwerda S, Morelli L, Hoppe PS, Planas-Paz L, Yang Y, Ruffner H, Bouwmeester T, Lohmann F, Terracciano LM, Roma G, Cong F, Tchorz JS. AXIN2 + Pericentral Hepatocytes Have Limited Contributions to Liver Homeostasis and Regeneration. Cell Stem Cell 2019; 26:97-107.e6. [PMID: 31866224 DOI: 10.1016/j.stem.2019.10.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 09/05/2019] [Accepted: 10/28/2019] [Indexed: 12/22/2022]
Abstract
The existence of specialized liver stem cell populations, including AXIN2+ pericentral hepatocytes, that safeguard homeostasis and repair has been controversial. Here, using AXIN2 lineage tracing in BAC-transgenic mice, we confirm the regenerative potential of intestinal stem cells (ISCs) but find limited roles for pericentral hepatocytes in liver parenchyma homeostasis. Liver regrowth following partial hepatectomy is enabled by proliferation of hepatocytes throughout the liver, rather than by a pericentral population. Periportal hepatocyte injury triggers local repair as well as auxiliary proliferation in all liver zones. DTA-mediated ablation of AXIN2+ pericentral hepatocytes transiently disrupts this zone, which is reestablished by conversion of pericentral vein-juxtaposed glutamine synthetase (GS)- hepatocytes into GS+ hepatocytes and by compensatory proliferation of hepatocytes across liver zones. These findings show hepatocytes throughout the liver can upregulate AXIN2 and LGR5 after injury and contribute to liver regeneration on demand, without zonal dominance by a putative pericentral stem cell population.
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Affiliation(s)
- Tianliang Sun
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Monika Pikiolek
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Vanessa Orsini
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Sebastian Bergling
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Sjoerd Holwerda
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Lapo Morelli
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Philipp S Hoppe
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Lara Planas-Paz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Yi Yang
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Heinz Ruffner
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Tewis Bouwmeester
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Felix Lohmann
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | | | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Feng Cong
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Jan S Tchorz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland.
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13
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Tang C, Ksiazek I, Siccardi N, Gapp B, Weber D, Wirsching J, Beck V, Reist M, Gaudet L, Stuber N, Surber SS, Mao X, Nicholson TB, Carbone W, Beibel M, Roma G, Gubser Keller C, Bassilana F. UTS2B Defines a Novel Enteroendocrine Cell Population and Regulates GLP-1 Secretion Through SSTR5 in Male Mice. Endocrinology 2019; 160:2849-2860. [PMID: 31556942 DOI: 10.1210/en.2019-00549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/20/2019] [Indexed: 12/25/2022]
Abstract
The gut-pancreas axis plays a key role in the regulation of glucose homeostasis and may be therapeutically exploited to treat not only type 2 diabetes but also hypoglycemia and hyperinsulinemia. We identify a novel enteroendocrine cell type expressing the peptide hormone urotensin 2B (UTS2B). UTS2B inhibits glucagon-like peptide-1 (GLP-1) secretion in mouse intestinal crypts and organoids, not by signaling through its cognate receptor UTS2R but through the activation of the somatostatin receptor (SSTR) 5. Circulating UTS2B concentrations in mice are physiologically regulated during starvation, further linking this peptide hormone to metabolism. Furthermore, administration of UTS2B to starved mice demonstrates that it is capable of regulating blood glucose and plasma concentrations of GLP-1 and insulin in vivo. Altogether, our results identify a novel cellular source of UTS2B in the gut, which acts in a paracrine manner to regulate GLP-1 secretion through SSTR5. These findings uncover a fine-tuning mechanism mediated by a ligand-receptor pair in the regulation of gut hormone secretion, which can potentially be exploited to correct metabolic unbalance caused by overactivation of the gut-pancreas axis.
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Affiliation(s)
- Cong Tang
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Iwona Ksiazek
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Noemie Siccardi
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Berangere Gapp
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Delphine Weber
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Valerie Beck
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Matthias Reist
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Laurent Gaudet
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Nathalie Stuber
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Xiaohong Mao
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | | | - Walter Carbone
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Martin Beibel
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Basel, Switzerland
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14
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Mannick JB, Morris M, Hockey HUP, Roma G, Beibel M, Kulmatycki K, Watkins M, Shavlakadze T, Zhou W, Quinn D, Glass DJ, Klickstein LB. TORC1 inhibition enhances immune function and reduces infections in the elderly. Sci Transl Med 2019; 10:10/449/eaaq1564. [PMID: 29997249 DOI: 10.1126/scitranslmed.aaq1564] [Citation(s) in RCA: 286] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 11/01/2017] [Accepted: 03/23/2018] [Indexed: 12/15/2022]
Abstract
Inhibition of the mechanistic target of rapamycin (mTOR) protein kinase extends life span and ameliorates aging-related pathologies including declining immune function in model organisms. The objective of this phase 2a randomized, placebo-controlled clinical trial was to determine whether low-dose mTOR inhibitor therapy enhanced immune function and decreased infection rates in 264 elderly subjects given the study drugs for 6 weeks. A low-dose combination of a catalytic (BEZ235) plus an allosteric (RAD001) mTOR inhibitor that selectively inhibits target of rapamycin complex 1 (TORC1) downstream of mTOR was safe and was associated with a significant (P = 0.001) decrease in the rate of infections reported by elderly subjects for a year after study drug initiation. In addition, we observed an up-regulation of antiviral gene expression and an improvement in the response to influenza vaccination in this treatment group. Thus, selective TORC1 inhibition has the potential to improve immune function and reduce infections in the elderly.
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Affiliation(s)
- Joan B Mannick
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA.
| | - Melody Morris
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | | | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland
| | - Martin Beibel
- Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland
| | | | - Mollie Watkins
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Tea Shavlakadze
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Weihua Zhou
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Dean Quinn
- P3 Research, Newtown, Wellington 6242, New Zealand
| | - David J Glass
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
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15
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Singh AP, Sosa MX, Fang J, Shanmukhappa SK, Hubaud A, Fawcett CH, Molind GJ, Tsai T, Capodieci P, Wetzel K, Sanchez E, Wang G, Coble M, Tang W, Cadena SM, Fishman MC, Glass DJ. αKlotho Regulates Age-Associated Vascular Calcification and Lifespan in Zebrafish. Cell Rep 2019; 28:2767-2776.e5. [DOI: 10.1016/j.celrep.2019.08.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/02/2019] [Accepted: 07/31/2019] [Indexed: 10/26/2022] Open
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16
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Shavlakadze T, Morris M, Fang J, Wang SX, Zhu J, Zhou W, Tse HW, Mondragon-Gonzalez R, Roma G, Glass DJ. Age-Related Gene Expression Signature in Rats Demonstrate Early, Late, and Linear Transcriptional Changes from Multiple Tissues. Cell Rep 2019; 28:3263-3273.e3. [PMID: 31533046 DOI: 10.1016/j.celrep.2019.08.043] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/06/2019] [Accepted: 08/13/2019] [Indexed: 12/25/2022] Open
Abstract
To understand the changes in gene expression that occur as a result of age, which might create a permissive or causal environment for age-related diseases, we produce a multi-time point age-related gene expression signature (AGES) from liver, kidney, skeletal muscle, and hippocampus of rats, comparing 6-, 9-, 12-, 18-, 21-, 24-, and 27-month-old animals. We focus on genes that changed in one direction throughout the lifespan of the animal, either early in life (early logistic changes), at mid-age (mid-logistic), late in life (late-logistic), or linearly, throughout the lifespan of the animal. The pathways perturbed because of chronological age demonstrate organ-specific and more-global effects of aging and point to mechanisms that could potentially be counter-regulated pharmacologically to treat age-associated diseases. A small number of genes are regulated by aging in the same manner in every tissue, suggesting they may be more-universal markers of aging.
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Affiliation(s)
- Tea Shavlakadze
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Melody Morris
- Respiratory Diseases, Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jian Fang
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Sharon X Wang
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jiang Zhu
- Informatics Systems and Data Analysis, Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Weihua Zhou
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Herman W Tse
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Ricardo Mondragon-Gonzalez
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Guglielmo Roma
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - David J Glass
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
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17
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Wegmann R, Neri M, Schuierer S, Bilican B, Hartkopf H, Nigsch F, Mapa F, Waldt A, Cuttat R, Salick MR, Raymond J, Kaykas A, Roma G, Keller CG. CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data. Genome Biol 2019; 20:142. [PMID: 31315641 PMCID: PMC6637521 DOI: 10.1186/s13059-019-1739-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/13/2019] [Indexed: 01/08/2023] Open
Abstract
We develop CellSIUS (Cell Subtype Identification from Upregulated gene Sets) to fill a methodology gap for rare cell population identification for scRNA-seq data. CellSIUS outperforms existing algorithms for specificity and selectivity for rare cell types and their transcriptomic signature identification in synthetic and complex biological data. Characterization of a human pluripotent cell differentiation protocol recapitulating deep-layer corticogenesis using CellSIUS reveals unrecognized complexity in human stem cell-derived cellular populations. CellSIUS enables identification of novel rare cell populations and their signature genes providing the means to study those populations in vitro in light of their role in health and disease.
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Affiliation(s)
- Rebekka Wegmann
- Novartis Institutes for Biomedical Research, Basel, Switzerland
- Present Address: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Marilisa Neri
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sven Schuierer
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Bilada Bilican
- Novartis Institutes for Biomedical Research, Cambridge, USA
- Present Address: Flagship Pioneering, Cambridge, USA
| | - Huyen Hartkopf
- Novartis Institutes for Biomedical Research, Cambridge, USA
| | - Florian Nigsch
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Felipa Mapa
- Novartis Institutes for Biomedical Research, Cambridge, USA
| | - Annick Waldt
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Rachel Cuttat
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Max R. Salick
- Novartis Institutes for Biomedical Research, Cambridge, USA
- Present Address: Insitro, San Francisco, USA
| | - Joe Raymond
- Novartis Institutes for Biomedical Research, Cambridge, USA
| | - Ajamete Kaykas
- Novartis Institutes for Biomedical Research, Cambridge, USA
- Present Address: Insitro, San Francisco, USA
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, Basel, Switzerland
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18
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Planas-Paz L, Sun T, Pikiolek M, Cochran NR, Bergling S, Orsini V, Yang Z, Sigoillot F, Jetzer J, Syed M, Neri M, Schuierer S, Morelli L, Hoppe PS, Schwarzer W, Cobos CM, Alford JL, Zhang L, Cuttat R, Waldt A, Carballido-Perrig N, Nigsch F, Kinzel B, Nicholson TB, Yang Y, Mao X, Terracciano LM, Russ C, Reece-Hoyes JS, Gubser Keller C, Sailer AW, Bouwmeester T, Greenbaum LE, Lugus JJ, Cong F, McAllister G, Hoffman GR, Roma G, Tchorz JS. YAP, but Not RSPO-LGR4/5, Signaling in Biliary Epithelial Cells Promotes a Ductular Reaction in Response to Liver Injury. Cell Stem Cell 2019; 25:39-53.e10. [PMID: 31080135 DOI: 10.1016/j.stem.2019.04.005] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 01/29/2019] [Accepted: 04/04/2019] [Indexed: 12/13/2022]
Abstract
Biliary epithelial cells (BECs) form bile ducts in the liver and are facultative liver stem cells that establish a ductular reaction (DR) to support liver regeneration following injury. Liver damage induces periportal LGR5+ putative liver stem cells that can form BEC-like organoids, suggesting that RSPO-LGR4/5-mediated WNT/β-catenin activity is important for a DR. We addressed the roles of this and other signaling pathways in a DR by performing a focused CRISPR-based loss-of-function screen in BEC-like organoids, followed by in vivo validation and single-cell RNA sequencing. We found that BECs lack and do not require LGR4/5-mediated WNT/β-catenin signaling during a DR, whereas YAP and mTORC1 signaling are required for this process. Upregulation of AXIN2 and LGR5 is required in hepatocytes to enable their regenerative capacity in response to injury. Together, these data highlight heterogeneity within the BEC pool, delineate signaling pathways involved in a DR, and clarify the identity and roles of injury-induced periportal LGR5+ cells.
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Affiliation(s)
- Lara Planas-Paz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Tianliang Sun
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Monika Pikiolek
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Nadire R Cochran
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Sebastian Bergling
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Vanessa Orsini
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Zinger Yang
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Frederic Sigoillot
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Jasna Jetzer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Maryam Syed
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Marilisa Neri
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Lapo Morelli
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Philipp S Hoppe
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Wibke Schwarzer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Carlos M Cobos
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland; Hospital Aleman, Buenos Aires, Argentina
| | - John L Alford
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Le Zhang
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Rachel Cuttat
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Annick Waldt
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | | | - Florian Nigsch
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Bernd Kinzel
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Thomas B Nicholson
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Yi Yang
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Xiaohong Mao
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | | | - Carsten Russ
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - John S Reece-Hoyes
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | | | - Andreas W Sailer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Tewis Bouwmeester
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Linda E Greenbaum
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, East Hanover, NJ, USA
| | - Jesse J Lugus
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Feng Cong
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Gregory McAllister
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Gregory R Hoffman
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Jan S Tchorz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland.
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19
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Bertschi NL, Voorberg-van der Wel A, Zeeman AM, Schuierer S, Nigsch F, Carbone W, Knehr J, Gupta DK, Hofman SO, van der Werff N, Nieuwenhuis I, Klooster E, Faber BW, Flannery EL, Mikolajczak SA, Chuenchob V, Shrestha B, Beibel M, Bouwmeester T, Kangwanrangsan N, Sattabongkot J, Diagana TT, Kocken CH, Roma G. Transcriptomic analysis reveals reduced transcriptional activity in the malaria parasite Plasmodium cynomolgi during progression into dormancy. eLife 2018; 7:41081. [PMID: 30589413 PMCID: PMC6344078 DOI: 10.7554/elife.41081] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/23/2018] [Indexed: 02/06/2023] Open
Abstract
Relapses of Plasmodium dormant liver hypnozoites compromise malaria eradication efforts. New radical cure drugs are urgently needed, yet the vast gap in knowledge of hypnozoite biology impedes drug discovery. We previously unraveled the transcriptome of 6 to 7 day-old P. cynomolgi liver stages, highlighting pathways associated with hypnozoite dormancy (Voorberg-van der Wel et al., 2017). We now extend these findings by transcriptome profiling of 9 to 10 day-old liver stage parasites, thus revealing for the first time the maturation of the dormant stage over time. Although progression of dormancy leads to a 10-fold decrease in transcription and expression of only 840 genes, including genes associated with housekeeping functions, we show that pathways involved in quiescence, energy metabolism and maintenance of genome integrity remain the prevalent pathways active in mature hypnozoites.
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Affiliation(s)
- Nicole L Bertschi
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | | | - Anne-Marie Zeeman
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Florian Nigsch
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Walter Carbone
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Judith Knehr
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Devendra K Gupta
- Novartis Institute for Tropical Diseases, Novartis Pharma AG, Emeryville, United States
| | - Sam O Hofman
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Nicole van der Werff
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Ivonne Nieuwenhuis
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Els Klooster
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Bart W Faber
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Erika L Flannery
- Novartis Institute for Tropical Diseases, Novartis Pharma AG, Emeryville, United States
| | | | - Vorada Chuenchob
- Novartis Institute for Tropical Diseases, Novartis Pharma AG, Emeryville, United States
| | - Binesh Shrestha
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Martin Beibel
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Tewis Bouwmeester
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
| | - Niwat Kangwanrangsan
- Department of Pathobiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Thierry T Diagana
- Novartis Institute for Tropical Diseases, Novartis Pharma AG, Emeryville, United States
| | - Clemens Hm Kocken
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Europe
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20
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Wang Z, Plasschaert LW, Aryal S, Renaud NA, Yang Z, Choo-Wing R, Pessotti AD, Kirkpatrick ND, Cochran NR, Carbone W, Maher R, Lindeman A, Russ C, Reece-Hoyes J, McAllister G, Hoffman GR, Roma G, Jaffe AB. TRRAP is a central regulator of human multiciliated cell formation. J Cell Biol 2018; 217:1941-1955. [PMID: 29588376 PMCID: PMC5987713 DOI: 10.1083/jcb.201706106] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 02/07/2018] [Accepted: 03/08/2018] [Indexed: 12/24/2022] Open
Abstract
Multiciliated cells (MCCs) function to promote directional fluid flow across epithelial tissues. Wang et al. show that TRRAP, a component of multiple histone acetyltransferase complexes, is required for airway MCC formation and regulates a network of genes involved in MCC differentiation and function. The multiciliated cell (MCC) is an evolutionarily conserved cell type, which in vertebrates functions to promote directional fluid flow across epithelial tissues. In the conducting airway, MCCs are generated by basal stem/progenitor cells and act in concert with secretory cells to perform mucociliary clearance to expel pathogens from the lung. Studies in multiple systems, including Xenopus laevis epidermis, murine trachea, and zebrafish kidney, have uncovered a transcriptional network that regulates multiple steps of multiciliogenesis, ultimately leading to an MCC with hundreds of motile cilia extended from their apical surface, which beat in a coordinated fashion. Here, we used a pool-based short hairpin RNA screening approach and identified TRRAP, an essential component of multiple histone acetyltransferase complexes, as a central regulator of MCC formation. Using a combination of immunofluorescence, signaling pathway modulation, and genomic approaches, we show that (a) TRRAP acts downstream of the Notch2-mediated basal progenitor cell fate decision and upstream of Multicilin to control MCC differentiation; and (b) TRRAP binds to the promoters and regulates the expression of a network of genes involved in MCC differentiation and function, including several genes associated with human ciliopathies.
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Affiliation(s)
- Zhao Wang
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Lindsey W Plasschaert
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Shivani Aryal
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Nicole A Renaud
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Zinger Yang
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Rayman Choo-Wing
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Angelica D Pessotti
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | - Nadire R Cochran
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Walter Carbone
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Rob Maher
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Alicia Lindeman
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Carsten Russ
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - John Reece-Hoyes
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Gregory McAllister
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Gregory R Hoffman
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Aron B Jaffe
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA
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21
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Genome-wide CRISPR screen for PARKIN regulators reveals transcriptional repression as a determinant of mitophagy. Proc Natl Acad Sci U S A 2017; 115:E180-E189. [PMID: 29269392 PMCID: PMC5777035 DOI: 10.1073/pnas.1711023115] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In mitophagy, damaged mitochondria are targeted for disposal by the autophagy machinery. PARKIN promotes signaling of mitochondrial damage to the autophagy machinery for engagement, and PARKIN mutations cause Parkinson’s disease, possibly because damaged mitochondria accumulate in neurons. Because regulation of PARKIN abundance and the impact on signaling are poorly understood, we performed a genetic screen to identify PARKIN abundance regulators. Both positive and negative regulators were identified and will help us to further understand mitophagy and Parkinson’s disease. We show that some of the identified genes negatively regulate PARKIN gene expression, which impacts signaling of mitochondrial damage in mitophagy. This link between transcriptional repression and mitophagy is also apparent in neurons in culture, bearing implications for disease. PARKIN, an E3 ligase mutated in familial Parkinson’s disease, promotes mitophagy by ubiquitinating mitochondrial proteins for efficient engagement of the autophagy machinery. Specifically, PARKIN-synthesized ubiquitin chains represent targets for the PINK1 kinase generating phosphoS65-ubiquitin (pUb), which constitutes the mitophagy signal. Physiological regulation of PARKIN abundance, however, and the impact on pUb accumulation are poorly understood. Using cells designed to discover physiological regulators of PARKIN abundance, we performed a pooled genome-wide CRISPR/Cas9 knockout screen. Testing identified genes individually resulted in a list of 53 positive and negative regulators. A transcriptional repressor network including THAP11 was identified and negatively regulates endogenous PARKIN abundance. RNAseq analysis revealed the PARKIN-encoding locus as a prime THAP11 target, and THAP11 CRISPR knockout in multiple cell types enhanced pUb accumulation. Thus, our work demonstrates the critical role of PARKIN abundance, identifies regulating genes, and reveals a link between transcriptional repression and mitophagy, which is also apparent in human induced pluripotent stem cell-derived neurons, a disease-relevant cell type.
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22
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Voorberg-van der Wel A, Roma G, Gupta DK, Schuierer S, Nigsch F, Carbone W, Zeeman AM, Lee BH, Hofman SO, Faber BW, Knehr J, Pasini E, Kinzel B, Bifani P, Bonamy GMC, Bouwmeester T, Kocken CHM, Diagana TT. A comparative transcriptomic analysis of replicating and dormant liver stages of the relapsing malaria parasite Plasmodium cynomolgi. eLife 2017; 6:29605. [PMID: 29215331 PMCID: PMC5758109 DOI: 10.7554/elife.29605] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 12/05/2017] [Indexed: 01/23/2023] Open
Abstract
Plasmodium liver hypnozoites, which cause disease relapse, are widely considered to be the last barrier towards malaria eradication. The biology of this quiescent form of the parasite is poorly understood which hinders drug discovery. We report a comparative transcriptomic dataset of replicating liver schizonts and dormant hypnozoites of the relapsing parasite Plasmodium cynomolgi. Hypnozoites express only 34% of Plasmodium physiological pathways, while 91% are expressed in replicating schizonts. Few known malaria drug targets are expressed in quiescent parasites, but pathways involved in microbial dormancy, maintenance of genome integrity and ATP homeostasis were robustly expressed. Several transcripts encoding heavy metal transporters were expressed in hypnozoites and the copper chelator neocuproine was cidal to all liver stage parasites. This transcriptomic dataset is a valuable resource for the discovery of vaccines and effective treatments to combat vivax malaria.
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Affiliation(s)
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Sven Schuierer
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Florian Nigsch
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Walter Carbone
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Anne-Marie Zeeman
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Boon Heng Lee
- Novartis Institute for Tropical Diseases, Singapore, Singapore
| | - Sam O Hofman
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Bart W Faber
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Judith Knehr
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Erica Pasini
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Bernd Kinzel
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Pablo Bifani
- Novartis Institute for Tropical Diseases, Singapore, Singapore
| | | | | | - Clemens H M Kocken
- Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, Netherlands
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23
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Odhams CA, Cunninghame Graham DS, Vyse TJ. Profiling RNA-Seq at multiple resolutions markedly increases the number of causal eQTLs in autoimmune disease. PLoS Genet 2017; 13:e1007071. [PMID: 29059182 PMCID: PMC5695635 DOI: 10.1371/journal.pgen.1007071] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 11/02/2017] [Accepted: 10/11/2017] [Indexed: 01/12/2023] Open
Abstract
Genome-wide association studies have identified hundreds of risk loci for autoimmune disease, yet only a minority (~25%) share genetic effects with changes to gene expression (eQTLs) in immune cells. RNA-Seq based quantification at whole-gene resolution, where abundance is estimated by culminating expression of all transcripts or exons of the same gene, is likely to account for this observed lack of colocalisation as subtle isoform switches and expression variation in independent exons can be concealed. We performed integrative cis-eQTL analysis using association statistics from twenty autoimmune diseases (560 independent loci) and RNA-Seq data from 373 individuals of the Geuvadis cohort profiled at gene-, isoform-, exon-, junction-, and intron-level resolution in lymphoblastoid cell lines. After stringently testing for a shared causal variant using both the Joint Likelihood Mapping and Regulatory Trait Concordance frameworks, we found that gene-level quantification significantly underestimated the number of causal cis-eQTLs. Only 5.0-5.3% of loci were found to share a causal cis-eQTL at gene-level compared to 12.9-18.4% at exon-level and 9.6-10.5% at junction-level. More than a fifth of autoimmune loci shared an underlying causal variant in a single cell type by combining all five quantification types; a marked increase over current estimates of steady-state causal cis-eQTLs. Causal cis-eQTLs detected at different quantification types localised to discrete epigenetic annotations. We applied a linear mixed-effects model to distinguish cis-eQTLs modulating all expression elements of a gene from those where the signal is only evident in a subset of elements. Exon-level analysis detected disease-associated cis-eQTLs that subtly altered transcription globally across the target gene. We dissected in detail the genetic associations of systemic lupus erythematosus and functionally annotated the candidate genes. Many of the known and novel genes were concealed at gene-level (e.g. IKZF2, TYK2, LYST). Our findings are provided as a web resource.
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Affiliation(s)
- Christopher A. Odhams
- Department of Medical & Molecular Genetics, King’s College London, London, United Kingdom
| | - Deborah S. Cunninghame Graham
- Department of Medical & Molecular Genetics, King’s College London, London, United Kingdom
- Academic Department of Rheumatology, Division of Immunology, Infection and Inflammatory Disease, King’s College London, London, United Kingdom
| | - Timothy J. Vyse
- Department of Medical & Molecular Genetics, King’s College London, London, United Kingdom
- Academic Department of Rheumatology, Division of Immunology, Infection and Inflammatory Disease, King’s College London, London, United Kingdom
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24
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Schuierer S, Carbone W, Knehr J, Petitjean V, Fernandez A, Sultan M, Roma G. A comprehensive assessment of RNA-seq protocols for degraded and low-quantity samples. BMC Genomics 2017; 18:442. [PMID: 28583074 PMCID: PMC5460543 DOI: 10.1186/s12864-017-3827-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/29/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND RNA-sequencing (RNA-seq) has emerged as one of the most sensitive tool for gene expression analysis. Among the library preparation methods available, the standard poly(A) + enrichment provides a comprehensive, detailed, and accurate view of polyadenylated RNAs. However, on samples of suboptimal quality ribosomal RNA depletion and exon capture methods have recently been reported as better alternatives. METHODS We compared for the first time three commercial Illumina library preparation kits (TruSeq Stranded mRNA, TruSeq Ribo-Zero rRNA Removal, and TruSeq RNA Access) as representatives of these three different approaches using well-established human reference RNA samples from the MAQC/SEQC consortium on a wide range of input amounts (from 100 ng down to 1 ng) and degradation levels (intact, degraded, and highly degraded). RESULTS We assessed the accuracy of the generated expression values by comparison to gold standard TaqMan qPCR measurements and gained unprecedented insight into the limits of applicability in terms of input quantity and sample quality of each protocol. We found that each protocol generates highly reproducible results (R 2 > 0.92) on intact RNA samples down to input amounts of 10 ng. For degraded RNA samples, Ribo-Zero showed clear performance advantages over the other two protocols as it generated more accurate and better reproducible gene expression results even at very low input amounts such as 1 ng and 2 ng. For highly degraded RNA samples, RNA Access performed best generating reliable data down to 5 ng input. CONCLUSIONS We found that the ribosomal RNA depletion protocol from Illumina works very well at amounts far below recommendation and over a good range of intact and degraded material. We also infer that the exome-capture protocol (RNA Access, Illumina) performs better than other methods on highly degraded and low amount samples.
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Affiliation(s)
- Sven Schuierer
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland.
| | - Walter Carbone
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Judith Knehr
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Virginie Petitjean
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Anita Fernandez
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Marc Sultan
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland.
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland.
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25
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Kiessling MK, Schuierer S, Stertz S, Beibel M, Bergling S, Knehr J, Carbone W, de Vallière C, Tchinda J, Bouwmeester T, Seuwen K, Rogler G, Roma G. Identification of oncogenic driver mutations by genome-wide CRISPR-Cas9 dropout screening. BMC Genomics 2016; 17:723. [PMID: 27613601 PMCID: PMC5016932 DOI: 10.1186/s12864-016-3042-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 08/24/2016] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Genome-wide CRISPR-Cas9 dropout screens can identify genes whose knockout affects cell viability. Recent CRISPR screens detected thousands of essential genes required for cellular survival and key cellular processes; however discovering novel lineage-specific genetic dependencies from the many hits still remains a challenge. RESULTS To assess whether CRISPR-Cas9 dropout screens can help identify cancer dependencies, we screened two human cancer cell lines carrying known and distinct oncogenic mutations using a genome-wide sgRNA library. We found that the gRNA targeting the driver mutation EGFR was one of the highest-ranking candidates in the EGFR-mutant HCC-827 lung adenocarcinoma cell line. Likewise, sgRNAs for NRAS and MAP2K1 (MEK1), a downstream kinase of mutant NRAS, were identified among the top hits in the NRAS-mutant neuroblastoma cell line CHP-212. Depletion of these genes targeted by the sgRNAs strongly correlated with the sensitivity to specific kinase inhibitors of the EGFR or RAS pathway in cell viability assays. In addition, we describe other dependencies such as TBK1 in HCC-827 cells and TRIB2 in CHP-212 cells which merit further investigation. CONCLUSIONS We show that genome-wide CRISPR dropout screens are suitable for the identification of oncogenic drivers and other essential genes.
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Affiliation(s)
- Michael K. Kiessling
- Department of Gastroenterology and Hepatology, University Hospital Zürich, Zürich, Switzerland
| | - Sven Schuierer
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Silke Stertz
- Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| | - Martin Beibel
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Sebastian Bergling
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Judith Knehr
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Walter Carbone
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Cheryl de Vallière
- Department of Gastroenterology and Hepatology, University Hospital Zürich, Zürich, Switzerland
| | - Joelle Tchinda
- Department of Oncology, Children University Hospital Zürich, Zürich, Switzerland
| | - Tewis Bouwmeester
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Klaus Seuwen
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zürich, Zürich, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
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