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Madur L, Ineichen C, Bergamini G, Greter A, Poggi G, Cuomo-Haymour N, Sigrist H, Sych Y, Paterna JC, Bornemann KD, Viollet C, Fernandez-Albert F, Alanis-Lobato G, Hengerer B, Pryce CR. Stress deficits in reward behaviour are associated with and replicated by dysregulated amygdala-nucleus accumbens pathway function in mice. Commun Biol 2023; 6:422. [PMID: 37061616 PMCID: PMC10105726 DOI: 10.1038/s42003-023-04811-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/05/2023] [Indexed: 04/17/2023] Open
Abstract
Reduced reward interest/learning and reward-to-effort valuation are distinct, common symptoms in neuropsychiatric disorders for which chronic stress is a major aetiological factor. Glutamate neurons in basal amygdala (BA) project to various regions including nucleus accumbens (NAc). The BA-NAc neural pathway is activated by reward and aversion, with many neurons being monovalent. In adult male mice, chronic social stress (CSS) leads to reduced discriminative reward learning (DRL) associated with decreased BA-NAc activity, and to reduced reward-to-effort valuation (REV) associated, in contrast, with increased BA-NAc activity. Chronic tetanus toxin BA-NAc inhibition replicates the CSS-DRL effect and causes a mild REV reduction, whilst chronic DREADDs BA-NAc activation replicates the CSS effect on REV without affecting DRL. This study provides evidence that stress disruption of reward processing involves the BA-NAc neural pathway; the bi-directional effects implicate opposite activity changes in reward (learning) neurons and aversion (effort) neurons in the BA-NAc pathway following chronic stress.
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Affiliation(s)
- Lorraine Madur
- Preclinical Laboratory, Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric University Hospital Zürich (PUK) and University of Zurich (UZH), Zurich, Switzerland
- Zurich Neuroscience Center, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Christian Ineichen
- Preclinical Laboratory, Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric University Hospital Zürich (PUK) and University of Zurich (UZH), Zurich, Switzerland
| | - Giorgio Bergamini
- Preclinical Laboratory, Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric University Hospital Zürich (PUK) and University of Zurich (UZH), Zurich, Switzerland
| | - Alexandra Greter
- Preclinical Laboratory, Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric University Hospital Zürich (PUK) and University of Zurich (UZH), Zurich, Switzerland
| | - Giulia Poggi
- Preclinical Laboratory, Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric University Hospital Zürich (PUK) and University of Zurich (UZH), Zurich, Switzerland
| | - Nagiua Cuomo-Haymour
- Preclinical Laboratory, Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric University Hospital Zürich (PUK) and University of Zurich (UZH), Zurich, Switzerland
- Zurich Neuroscience Center, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Hannes Sigrist
- Preclinical Laboratory, Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric University Hospital Zürich (PUK) and University of Zurich (UZH), Zurich, Switzerland
| | - Yaroslav Sych
- Institute of Cellular and Integrative Neuroscience, University of Strasbourg, Strasbourg, France
| | | | - Klaus D Bornemann
- CNS Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Coralie Viollet
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Francesc Fernandez-Albert
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Gregorio Alanis-Lobato
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Bastian Hengerer
- CNS Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Christopher R Pryce
- Preclinical Laboratory, Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric University Hospital Zürich (PUK) and University of Zurich (UZH), Zurich, Switzerland.
- Zurich Neuroscience Center, University of Zurich and ETH Zurich, Zurich, Switzerland.
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2
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Klee S, Picart-Armada S, Wenger K, Birk G, Quast K, Veyel D, Rist W, Violet C, Luippold A, Haslinger C, Thomas M, Fernandez-Albert F, Kästle M. Transcriptomic and proteomic profiling of young and old mice in the bleomycin model reveals high similarity. Am J Physiol Lung Cell Mol Physiol 2023; 324:L245-L258. [PMID: 36625483 DOI: 10.1152/ajplung.00253.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The most common preclinical, in vivo model to study lung fibrosis is the bleomycin-induced lung fibrosis model in 2- to 3-mo-old mice. Although this model resembles key aspects of idiopathic pulmonary fibrosis (IPF), there are limitations in its predictability for the human disease. One of the main differences is the juvenile age of animals that are commonly used in experiments, resembling humans of around 20 yr. Because IPF patients are usually older than 60 yr, aging appears to play an important role in the pathogenesis of lung fibrosis. Therefore, we compared young (3 months) and old mice (21 months) 21 days after intratracheal bleomycin instillation. Analyzing lung transcriptomics (mRNAs and miRNAs) and proteomics, we found most pathways to be similarly regulated in young and old mice. However, old mice show imbalanced protein homeostasis as well as an increased inflammatory state in the fibrotic phase compared to young mice. Comparisons with published human transcriptomic data sets (GSE47460, GSE32537, and GSE24206) revealed that the gene signature of old animals correlates significantly better with IPF patients, and it also turned human healthy individuals better into "IPF patients" using an approach based on predictive disease modeling. Both young and old animals show similar molecular hallmarks of IPF in the bleomycin-induced lung fibrosis model, although old mice more closely resemble several features associated with IPF in comparison to young animals.
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Affiliation(s)
- Stephan Klee
- Department Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Sergio Picart-Armada
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Kathrin Wenger
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Gerald Birk
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Karsten Quast
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Daniel Veyel
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Wolfgang Rist
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Coralie Violet
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Andreas Luippold
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Christian Haslinger
- Department Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Matthew Thomas
- Department Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Francesc Fernandez-Albert
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Marc Kästle
- Department Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
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Becker K, Weigelt CM, Fuchs H, Viollet C, Rust W, Wyatt H, Huber J, Lamla T, Fernandez-Albert F, Simon E, Zippel N, Bakker RA, Klein H, Redemann NH. Transcriptome analysis of AAV-induced retinopathy models expressing human VEGF, TNF-α, and IL-6 in murine eyes. Sci Rep 2022; 12:19395. [PMID: 36371417 PMCID: PMC9653384 DOI: 10.1038/s41598-022-23065-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/25/2022] [Indexed: 11/14/2022] Open
Abstract
Retinopathies are multifactorial diseases with complex pathologies that eventually lead to vision loss. Animal models facilitate the understanding of the pathophysiology and identification of novel treatment options. However, each animal model reflects only specific disease aspects and understanding of the specific molecular changes in most disease models is limited. Here, we conducted transcriptome analysis of murine ocular tissue transduced with recombinant Adeno-associated viruses (AAVs) expressing either human VEGF-A, TNF-α, or IL-6. VEGF expression led to a distinct regulation of extracellular matrix (ECM)-associated genes. In contrast, both TNF-α and IL-6 led to more comparable gene expression changes in interleukin signaling, and the complement cascade, with TNF-α-induced changes being more pronounced. Furthermore, integration of single cell RNA-Sequencing data suggested an increase of endothelial cell-specific marker genes by VEGF, while TNF-α expression increased the expression T-cell markers. Both TNF-α and IL-6 expression led to an increase in macrophage markers. Finally, transcriptomic changes in AAV-VEGF treated mice largely overlapped with gene expression changes observed in the oxygen-induced retinopathy model, especially regarding ECM components and endothelial cell-specific gene expression. Altogether, our study represents a valuable investigation of gene expression changes induced by VEGF, TNF-α, and IL-6 and will aid researchers in selecting appropriate animal models for retinopathies based on their agreement with the human pathophysiology.
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Affiliation(s)
- Kolja Becker
- grid.420061.10000 0001 2171 7500Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Carina M. Weigelt
- grid.420061.10000 0001 2171 7500Cardiometabolic Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Holger Fuchs
- grid.420061.10000 0001 2171 7500Cardiometabolic Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Coralie Viollet
- grid.420061.10000 0001 2171 7500Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Werner Rust
- grid.420061.10000 0001 2171 7500Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Hannah Wyatt
- grid.420061.10000 0001 2171 7500Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Jochen Huber
- grid.420061.10000 0001 2171 7500Clinical Development & Operations Corporate, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Thorsten Lamla
- grid.420061.10000 0001 2171 7500Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Francesc Fernandez-Albert
- grid.420061.10000 0001 2171 7500Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Eric Simon
- grid.420061.10000 0001 2171 7500Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Nina Zippel
- grid.420061.10000 0001 2171 7500Cardiometabolic Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Remko A. Bakker
- grid.420061.10000 0001 2171 7500Cardiometabolic Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Holger Klein
- grid.420061.10000 0001 2171 7500Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Norbert H. Redemann
- grid.420061.10000 0001 2171 7500Cardiometabolic Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
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Gurbuz O, Alanis-Lobato G, Picart-Armada S, Sun M, Haslinger C, Lawless N, Fernandez-Albert F. Knowledge Graphs for Indication Expansion: An Explainable Target-Disease Prediction Method. Front Genet 2022; 13:814093. [PMID: 35360842 PMCID: PMC8963915 DOI: 10.3389/fgene.2022.814093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/28/2022] [Indexed: 11/19/2022] Open
Abstract
Indication expansion aims to find new indications for existing targets in order to accelerate the process of launching a new drug for a disease on the market. The rapid increase in data types and data sources for computational drug discovery has fostered the use of semantic knowledge graphs (KGs) for indication expansion through target centric approaches, or in other words, target repositioning. Previously, we developed a novel method to construct a KG for indication expansion studies, with the aim of finding and justifying alternative indications for a target gene of interest. In contrast to other KGs, ours combines human-curated full-text literature and gene expression data from biomedical databases to encode relationships between genes, diseases, and tissues. Here, we assessed the suitability of our KG for explainable target-disease link prediction using a glass-box approach. To evaluate the predictive power of our KG, we applied shortest path with tissue information- and embedding-based prediction methods to a graph constructed with information published before or during 2010. We also obtained random baselines by applying the shortest path predictive methods to KGs with randomly shuffled node labels. Then, we evaluated the accuracy of the top predictions using gene-disease links reported after 2010. In addition, we investigated the contribution of the KG’s tissue expression entity to the prediction performance. Our experiments showed that shortest path-based methods significantly outperform the random baselines and embedding-based methods outperform the shortest path predictions. Importantly, removing the tissue expression entity from the KG severely impacts the quality of the predictions, especially those produced by the embedding approaches. Finally, since the interpretability of the predictions is crucial in indication expansion, we highlight the advantages of our glass-box model through the examination of example candidate target-disease predictions.
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Affiliation(s)
- Ozge Gurbuz
- Discovery Research Coordination Germany, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
- *Correspondence: Ozge Gurbuz, ; Francesc Fernandez-Albert,
| | - Gregorio Alanis-Lobato
- Global Computational Biology and Data Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Sergio Picart-Armada
- Global Computational Biology and Data Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Miao Sun
- Global Computational Biology and Data Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Christian Haslinger
- Global Computational Biology and Data Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Nathan Lawless
- Global Computational Biology and Data Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Francesc Fernandez-Albert
- Global Computational Biology and Data Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
- *Correspondence: Ozge Gurbuz, ; Francesc Fernandez-Albert,
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5
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Weckerle J, Picart-Armada S, Klee S, Bretschneider T, Luippold AH, Rist W, Haslinger C, Schlüter H, Thomas MJ, Krawczyk B, Fernandez-Albert F, Kästle M, Veyel D. Mapping the metabolomic and lipidomic changes in the Bleomycin model of pulmonary fibrosis in young and aged mice. Dis Model Mech 2021; 15:274099. [PMID: 34845494 PMCID: PMC8807555 DOI: 10.1242/dmm.049105] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 11/17/2021] [Indexed: 11/20/2022] Open
Abstract
Alterations in metabolic pathways were recently recognized as potential underlying drivers of idiopathic pulmonary fibrosis (IPF), translating into novel therapeutic targets. However, knowledge of metabolic and lipid regulation in fibrotic lungs is limited. To comprehensively characterize metabolic perturbations in the bleomycin mouse model of IPF, we analyzed the metabolome and lipidome by mass spectrometry. We identified increased tissue turnover and repair, evident by enhanced breakdown of proteins, nucleic acids and lipids and extracellular matrix turnover. Energy production was upregulated, including glycolysis, the tricarboxylic acid cycle, glutaminolysis, lactate production and fatty acid oxidation. Higher eicosanoid synthesis indicated inflammatory processes. Because the risk of IPF increases with age, we investigated how age influences metabolomic and lipidomic changes in the bleomycin-induced pulmonary fibrosis model. Surprisingly, except for cytidine, we did not detect any significantly differential metabolites or lipids between old and young bleomycin-treated lungs. Together, we identified metabolomic and lipidomic changes in fibrosis that reflect higher energy demand, proliferation, tissue remodeling, collagen deposition and inflammation, which might serve to improve diagnostic and therapeutic options for fibrotic lung diseases in the future. Editor's choice: Using bleomycin-induced lung injury as a mouse model for idiopathic pulmonary fibrosis, this study identifies metabolomic and lipidomic changes in fibrosis reflecting higher energy demand, proliferation, tissue remodeling, collagen deposition and inflammation.
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Affiliation(s)
- Jelena Weckerle
- Boehringer Ingelheim Pharma GmbH & Co. KG, Department Immunology and Respiratory Disease research, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Sergio Picart-Armada
- Boehringer Ingelheim Pharma GmbH & Co. KG, Global Computational Biology and Digital Sciences, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Stephan Klee
- Boehringer Ingelheim Pharma GmbH & Co. KG, Department Immunology and Respiratory Disease research, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Tom Bretschneider
- Boehringer Ingelheim Pharma GmbH & Co. KG, Department Drug Discovery Sciences, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Andreas H Luippold
- Boehringer Ingelheim Pharma GmbH & Co. KG, Department Drug Discovery Sciences, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Wolfgang Rist
- Boehringer Ingelheim Pharma GmbH & Co. KG, Department Drug Discovery Sciences, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Christian Haslinger
- Boehringer Ingelheim Pharma GmbH & Co. KG, Global Computational Biology and Digital Sciences, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Holger Schlüter
- Boehringer Ingelheim Pharma GmbH & Co. KG, Department Immunology and Respiratory Disease research, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Matthew J Thomas
- Boehringer Ingelheim Pharma GmbH & Co. KG, Department Immunology and Respiratory Disease research, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Bartlomiej Krawczyk
- Boehringer Ingelheim Pharma GmbH & Co. KG, Department Drug Discovery Sciences, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Francesc Fernandez-Albert
- Boehringer Ingelheim Pharma GmbH & Co. KG, Global Computational Biology and Digital Sciences, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Marc Kästle
- Boehringer Ingelheim Pharma GmbH & Co. KG, Department Immunology and Respiratory Disease research, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Daniel Veyel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Department Drug Discovery Sciences, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
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6
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Pantano L, Agyapong G, Shen Y, Zhuo Z, Fernandez-Albert F, Rust W, Knebel D, Hill J, Boustany-Kari CM, Doerner JF, Rippmann JF, Chung RT, Ho Sui SJ, Simon E, Corey KE. Molecular characterization and cell type composition deconvolution of fibrosis in NAFLD. Sci Rep 2021; 11:18045. [PMID: 34508113 PMCID: PMC8433177 DOI: 10.1038/s41598-021-96966-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/05/2021] [Indexed: 01/16/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common cause of liver disease worldwide. In adults with NAFLD, fibrosis can develop and progress to liver cirrhosis and liver failure. However, the underlying molecular mechanisms of fibrosis progression are not fully understood. Using total RNA-Seq, we investigated the molecular mechanisms of NAFLD and fibrosis. We sequenced liver tissue from 143 adults across the full spectrum of fibrosis stage including those with stage 4 fibrosis (cirrhosis). We identified gene expression clusters that strongly correlate with fibrosis stage including four genes that have been found consistently across previously published transcriptomic studies on NASH i.e. COL1A2, EFEMP2, FBLN5 and THBS2. Using cell type deconvolution, we estimated the loss of hepatocytes versus gain of hepatic stellate cells, macrophages and cholangiocytes with advancing fibrosis stage. Hepatocyte-specific functional analysis indicated increase of pro-apoptotic pathways and markers of bipotent hepatocyte/cholangiocyte precursors. Regression modelling was used to derive predictors of fibrosis stage. This study elucidated molecular and cell composition changes associated with increasing fibrosis stage in NAFLD and defined informative gene signatures for the disease.
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Affiliation(s)
- Lorena Pantano
- Harvard Chan Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, 401 Park Dr, Boston, MA, 02215, USA
| | - George Agyapong
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit St, Boston, MA, 02114, USA.,Harvard Medical School, Boston, MA, USA
| | - Yang Shen
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88937, Biberach Riss, Germany
| | - Zhu Zhuo
- Harvard Chan Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, 401 Park Dr, Boston, MA, 02215, USA
| | | | - Werner Rust
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88937, Biberach Riss, Germany
| | - Dagmar Knebel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88937, Biberach Riss, Germany
| | - Jon Hill
- Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, USA
| | | | - Julia F Doerner
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88937, Biberach Riss, Germany
| | - Jörg F Rippmann
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88937, Biberach Riss, Germany
| | - Raymond T Chung
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit St, Boston, MA, 02114, USA. .,Harvard Medical School, Boston, MA, USA.
| | - Shannan J Ho Sui
- Harvard Chan Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, 401 Park Dr, Boston, MA, 02215, USA.
| | - Eric Simon
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88937, Biberach Riss, Germany.
| | - Kathleen E Corey
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit St, Boston, MA, 02114, USA. .,Harvard Medical School, Boston, MA, USA.
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7
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Kaymaz Y, Ganglberger F, Tang M, Haslinger C, Fernandez-Albert F, Lawless N, Sackton T. HieRFIT: A hierarchical cell type classification tool for projections from complex single-cell atlas datasets. Bioinformatics 2021; 37:4431-4436. [PMID: 34255817 DOI: 10.1093/bioinformatics/btab499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 05/25/2021] [Accepted: 07/02/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The emergence of single-cell RNA sequencing (scRNA-seq) has led to an explosion in novel methods to study biological variation among individual cells, and to classify cells into functional and biologically meaningful categories. RESULTS Here, we present a new cell type projection tool, HieRFIT (Hierarchical Random Forest for Information Transfer), based on hierarchical random forests. HieRFIT uses a priori information about cell type relationships to improve classification accuracy, taking as input a hierarchical tree structure representing the class relationships, along with the reference data. We use an ensemble approach combining multiple random forest models, organized in a hierarchical decision tree structure. We show that our hierarchical classification approach improves accuracy and reduces incorrect predictions especially for inter-dataset tasks which reflect real life applications. We use a scoring scheme that adjusts probability distributions for candidate class labels and resolves uncertainties while avoiding the assignment of cells to incorrect types by labeling cells at internal nodes of the hierarchy when necessary. AVAILABILITY HieRFIT is implemented as an R package, and it is available at (https://github.com/yasinkaymaz/HieRFIT/releases/tag/v1.0.0). t. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yasin Kaymaz
- Informatics Group, Harvard University, Cambridge, MA, USA
| | | | - Ming Tang
- Informatics Group, Harvard University, Cambridge, MA, USA
| | - Christian Haslinger
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH and Co KG, Biberach an der Riss, DE
| | - Francesc Fernandez-Albert
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH and Co KG, Biberach an der Riss, DE
| | - Nathan Lawless
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH and Co KG, Biberach an der Riss, DE
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8
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Becker K, Klein H, Simon E, Viollet C, Haslinger C, Leparc G, Schultheis C, Chong V, Kuehn MH, Fernandez-Albert F, Bakker RA. In-depth transcriptomic analysis of human retina reveals molecular mechanisms underlying diabetic retinopathy. Sci Rep 2021; 11:10494. [PMID: 34006945 PMCID: PMC8131353 DOI: 10.1038/s41598-021-88698-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/15/2021] [Indexed: 02/03/2023] Open
Abstract
Diabetic Retinopathy (DR) is among the major global causes for vision loss. With the rise in diabetes prevalence, an increase in DR incidence is expected. Current understanding of both the molecular etiology and pathways involved in the initiation and progression of DR is limited. Via RNA-Sequencing, we analyzed mRNA and miRNA expression profiles of 80 human post-mortem retinal samples from 43 patients diagnosed with various stages of DR. We found differentially expressed transcripts to be predominantly associated with late stage DR and pathways such as hippo and gap junction signaling. A multivariate regression model identified transcripts with progressive changes throughout disease stages, which in turn displayed significant overlap with sphingolipid and cGMP-PKG signaling. Combined analysis of miRNA and mRNA expression further uncovered disease-relevant miRNA/mRNA associations as potential mechanisms of post-transcriptional regulation. Finally, integrating human retinal single cell RNA-Sequencing data revealed a continuous loss of retinal ganglion cells, and Müller cell mediated changes in histidine and β-alanine signaling. While previously considered primarily a vascular disease, attention in DR has shifted to additional mechanisms and cell-types. Our findings offer an unprecedented and unbiased insight into molecular pathways and cell-specific changes in the development of DR, and provide potential avenues for future therapeutic intervention.
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Affiliation(s)
- Kolja Becker
- Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Holger Klein
- Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Eric Simon
- Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Coralie Viollet
- Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Christian Haslinger
- Global Computational Biology & Digital Sciences, Boehringer Ingelheim RCV GmbH & Co. KG, Vienna, Austria
| | - German Leparc
- Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Christian Schultheis
- Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Victor Chong
- Therapeutic Area CNS Retinopathies Emerging Areas, BI International GmbH, Ingelheim, Germany
| | - Markus H Kuehn
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
- Department of Veterans Affairs, Center for the Prevention and Treatment of Visual Loss, Iowa City, IA, 52246, USA
| | - Francesc Fernandez-Albert
- Global Computational Biology & Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany.
| | - Remko A Bakker
- Global Department Cardio-Metabolic Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany.
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9
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Scott HL, Buckner N, Fernandez-Albert F, Pedone E, Postiglione L, Shi G, Allen N, Wong LF, Magini L, Marucci L, O'Sullivan GA, Cole S, Powell J, Maycox P, Uney JB. Correction: A dual druggable genome-wide siRNA and compound library screening approach identifies modulators of parkin recruitment to mitochondria. J Biol Chem 2020; 295:5835. [PMID: 32332132 PMCID: PMC7186173 DOI: 10.1074/jbc.aac120.013668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024] Open
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10
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Scott HL, Buckner N, Fernandez-Albert F, Pedone E, Postiglione L, Shi G, Allen N, Wong LF, Magini L, Marucci L, O'Sullivan GA, Cole S, Powell J, Maycox P, Uney JB. A dual druggable genome-wide siRNA and compound library screening approach identifies modulators of parkin recruitment to mitochondria. J Biol Chem 2020; 295:3285-3300. [PMID: 31911436 PMCID: PMC7062187 DOI: 10.1074/jbc.ra119.009699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/20/2019] [Indexed: 01/07/2023] Open
Abstract
Genetic and biochemical evidence points to an association between mitochondrial dysfunction and Parkinson's disease (PD). PD-associated mutations in several genes have been identified and include those encoding PTEN-induced putative kinase 1 (PINK1) and parkin. To identify genes, pathways, and pharmacological targets that modulate the clearance of damaged or old mitochondria (mitophagy), here we developed a high-content imaging-based assay of parkin recruitment to mitochondria and screened both a druggable genome-wide siRNA library and a small neuroactive compound library. We used a multiparameter principal component analysis and an unbiased parameter-agnostic machine-learning approach to analyze the siRNA-based screening data. The hits identified in this analysis included specific genes of the ubiquitin proteasome system, and inhibition of ubiquitin-conjugating enzyme 2 N (UBE2N) with a specific antagonist, Bay 11-7082, indicated that UBE2N modulates parkin recruitment and downstream events in the mitophagy pathway. Screening of the compound library identified kenpaullone, an inhibitor of cyclin-dependent kinases and glycogen synthase kinase 3, as a modulator of parkin recruitment. Validation studies revealed that kenpaullone augments the mitochondrial network and protects against the complex I inhibitor MPP+. Finally, we used a microfluidics platform to assess the timing of parkin recruitment to depolarized mitochondria and its modulation by kenpaullone in real time and with single-cell resolution. We demonstrate that the high-content imaging-based assay presented here is suitable for both genetic and pharmacological screening approaches, and we also provide evidence that pharmacological compounds modulate PINK1-dependent parkin recruitment.
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Affiliation(s)
- Helen L Scott
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Nicola Buckner
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom
| | | | - Elisa Pedone
- Department of Engineering and Mathematics, University of Bristol, Bristol BS8 1TD, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Lorena Postiglione
- Department of Engineering and Mathematics, University of Bristol, Bristol BS8 1TD, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Gongyu Shi
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Nicholas Allen
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, United Kingdom
| | - Liang-Fong Wong
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Lorenzo Magini
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Lucia Marucci
- Department of Engineering and Mathematics, University of Bristol, Bristol BS8 1TD, United Kingdom; BrisSynBio, Bristol BS8 1QU, United Kingdom
| | - Gregory A O'Sullivan
- Takeda Cambridge Ltd., Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Sarah Cole
- Takeda Ventures, Inc., 61 Aldwych, London WC2B 4A, United Kingdom
| | - Justin Powell
- Takeda Cambridge Ltd., Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Peter Maycox
- Takeda Ventures, Inc., 61 Aldwych, London WC2B 4A, United Kingdom
| | - James B Uney
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom.
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11
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Wohnhaas CT, Leparc GG, Fernandez-Albert F, Kind D, Gantner F, Viollet C, Hildebrandt T, Baum P. DMSO cryopreservation is the method of choice to preserve cells for droplet-based single-cell RNA sequencing. Sci Rep 2019; 9:10699. [PMID: 31337793 PMCID: PMC6650608 DOI: 10.1038/s41598-019-46932-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/04/2019] [Indexed: 11/15/2022] Open
Abstract
Combining single-cell RNA sequencing (scRNA-seq) with upstream cell preservation procedures such as cryopreservation or methanol fixation has recently become more common. By separating cell handling and preparation, from downstream library generation, scRNA-seq workflows are more flexible and manageable. However, the inherent transcriptomic changes associated with cell preservation and how they may bias further downstream analysis remain unknown. Here, we present a side-by-side droplet-based scRNA-seq analysis, comparing the gold standard - fresh cells - to three different cell preservation workflows: dimethyl sulfoxide based cryopreservation, methanol fixation and CellCover reagent. Cryopreservation proved to be the most robust protocol, maximizing both cell integrity and low background ambient RNA. Importantly, gene expression profiles from fresh cells correlated most with those of cryopreserved cells. Such similarities were consistently observed across the tested cell lines (R ≥ 0.97), monocyte-derived macrophages (R = 0.97) and immune cells (R = 0.99). In contrast, both methanol fixation and CellCover preservation showed an increased ambient RNA background and an overall lower gene expression correlation to fresh cells. Thus, our results demonstrate the superiority of cryopreservation over other cell preservation methods. We expect our comparative study to provide single-cell omics researchers invaluable support when integrating cell preservation into their scRNA-seq studies.
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Affiliation(s)
- Christian T Wohnhaas
- Computational Biology, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397, Biberach, Germany
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Germán G Leparc
- Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397, Biberach, Germany
| | | | - David Kind
- Computational Biology, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397, Biberach, Germany
| | - Florian Gantner
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397, Biberach, Germany
| | - Coralie Viollet
- Computational Biology, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397, Biberach, Germany
| | - Tobias Hildebrandt
- Computational Biology, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397, Biberach, Germany
| | - Patrick Baum
- Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397, Biberach, Germany.
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