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Wong SY, Coffre M, Ramanan D, Hines MJ, Gomez LE, Peters LA, Schadt EE, Koralov SB, Cadwell K. B Cell Defects Observed in Nod2 Knockout Mice Are a Consequence of a Dock2 Mutation Frequently Found in Inbred Strains. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2018; 201:1442-1451. [PMID: 30012848 PMCID: PMC6103850 DOI: 10.4049/jimmunol.1800014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 06/22/2018] [Indexed: 02/06/2023]
Abstract
Phenotypic differences among substrains of laboratory mice due to spontaneous mutations or pre-existing genetic variation confound the interpretation of targeted mutagenesis experiments and contribute to challenges with reproducibility across institutions. Notably, C57BL/6 Hsd mice and gene-targeted mice that have been backcrossed to this substrain have been reported to harbor a duplication in exons 28 and 29 of Dock2 In this study, we demonstrate the presence of this Dock2 variant in the widely used Nod2-/- mice. Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) is a cytosolic innate immune receptor associated with inflammatory bowel disease susceptibility. Consistent with a role of NOD2 in an immunological disorder, Nod2-/- mice bred at our institution displayed multiple B cell defects including deficiencies in recirculating B cells, marginal zone B cells, and B1a cells in vivo, as well as defects in class switch recombination in vitro. However, we found that these effects are due to the Dock2 variant and are independent of Nod2 deletion. Despite originating from the same gene-targeted founder mice, Nod2-/- mice from another source did not harbor the Dock2 variant or B cell defects. Finally, we show that Dock2-/- mice display the same B cell defects as mice harboring the Dock2 variant, confirming that the variant is a loss-of-function mutation and is sufficient to explain the alterations to the B cell compartment observed in Nod2-/- mice. Our findings highlight the effects of confounding mutations from widely used inbred strains on gene-targeted mice and reveal new functions of DOCK2 in B cells.
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Affiliation(s)
- Serre-Yu Wong
- Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016
- Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Maryaline Coffre
- Department of Pathology, New York University School of Medicine, New York, NY 10016
| | - Deepshika Ramanan
- Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016
| | - Marcus J Hines
- Department of Pathology, New York University School of Medicine, New York, NY 10016
| | - Luis E Gomez
- Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016
| | - Lauren A Peters
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Sema4, a Mount Sinai Venture, Stamford, CT 06902; and
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Sema4, a Mount Sinai Venture, Stamford, CT 06902; and
| | - Sergei B Koralov
- Department of Pathology, New York University School of Medicine, New York, NY 10016
| | - Ken Cadwell
- Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016;
- Department of Microbiology, New York University School of Medicine, New York, NY 10016
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154
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Hitzel J, Lee E, Zhang Y, Bibli SI, Li X, Zukunft S, Pflüger B, Hu J, Schürmann C, Vasconez AE, Oo JA, Kratzer A, Kumar S, Rezende F, Josipovic I, Thomas D, Giral H, Schreiber Y, Geisslinger G, Fork C, Yang X, Sigala F, Romanoski CE, Kroll J, Jo H, Landmesser U, Lusis AJ, Namgaladze D, Fleming I, Leisegang MS, Zhu J, Brandes RP. Oxidized phospholipids regulate amino acid metabolism through MTHFD2 to facilitate nucleotide release in endothelial cells. Nat Commun 2018; 9:2292. [PMID: 29895827 PMCID: PMC5997752 DOI: 10.1038/s41467-018-04602-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 05/11/2018] [Indexed: 12/20/2022] Open
Abstract
Oxidized phospholipids (oxPAPC) induce endothelial dysfunction and atherosclerosis. Here we show that oxPAPC induce a gene network regulating serine-glycine metabolism with the mitochondrial methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2) as a causal regulator using integrative network modeling and Bayesian network analysis in human aortic endothelial cells. The cluster is activated in human plaque material and by atherogenic lipoproteins isolated from plasma of patients with coronary artery disease (CAD). Single nucleotide polymorphisms (SNPs) within the MTHFD2-controlled cluster associate with CAD. The MTHFD2-controlled cluster redirects metabolism to glycine synthesis to replenish purine nucleotides. Since endothelial cells secrete purines in response to oxPAPC, the MTHFD2-controlled response maintains endothelial ATP. Accordingly, MTHFD2-dependent glycine synthesis is a prerequisite for angiogenesis. Thus, we propose that endothelial cells undergo MTHFD2-mediated reprogramming toward serine-glycine and mitochondrial one-carbon metabolism to compensate for the loss of ATP in response to oxPAPC during atherosclerosis.
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Affiliation(s)
- Juliane Hitzel
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, 60590, Germany
- German Center for Cardiovascular Research (DZHK) (Partner site Rhine-Main), Frankfurt am Main, 60590, Germany
| | - Eunjee Lee
- Icahn Institute of Genomics and Multiscale Biology, Mount Sinai Icahn School of Medicine, New York, 10029, NY, USA
- Sema4 Genomics (a Mount Sinai venture), Stamford, 06902, CT, USA
| | - Yi Zhang
- Icahn Institute of Genomics and Multiscale Biology, Mount Sinai Icahn School of Medicine, New York, 10029, NY, USA
- Department of Mathematics, Hebei University of Science and Technology, Shijiazhuang, 050018, Hebei, China
| | - Sofia Iris Bibli
- German Center for Cardiovascular Research (DZHK) (Partner site Rhine-Main), Frankfurt am Main, 60590, Germany
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt am Main, 60590, Germany
| | - Xiaogang Li
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany
| | - Sven Zukunft
- German Center for Cardiovascular Research (DZHK) (Partner site Rhine-Main), Frankfurt am Main, 60590, Germany
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt am Main, 60590, Germany
| | - Beatrice Pflüger
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, 60590, Germany
- German Center for Cardiovascular Research (DZHK) (Partner site Rhine-Main), Frankfurt am Main, 60590, Germany
| | - Jiong Hu
- German Center for Cardiovascular Research (DZHK) (Partner site Rhine-Main), Frankfurt am Main, 60590, Germany
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt am Main, 60590, Germany
| | - Christoph Schürmann
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, 60590, Germany
- German Center for Cardiovascular Research (DZHK) (Partner site Rhine-Main), Frankfurt am Main, 60590, Germany
| | - Andrea Estefania Vasconez
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, 60590, Germany
- German Center for Cardiovascular Research (DZHK) (Partner site Rhine-Main), Frankfurt am Main, 60590, Germany
| | - James A Oo
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, 60590, Germany
- German Center for Cardiovascular Research (DZHK) (Partner site Rhine-Main), Frankfurt am Main, 60590, Germany
| | - Adelheid Kratzer
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, 12203, Germany
- German Center for Cardiovascular Research (DZHK) (Partner site Berlin), Berlin, 13316, Germany
| | - Sandeep Kumar
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, 30332, GA, USA
| | - Flávia Rezende
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, 60590, Germany
- German Center for Cardiovascular Research (DZHK) (Partner site Rhine-Main), Frankfurt am Main, 60590, Germany
| | - Ivana Josipovic
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, 60590, Germany
- German Center for Cardiovascular Research (DZHK) (Partner site Rhine-Main), Frankfurt am Main, 60590, Germany
| | - Dominique Thomas
- Institute of Clinical Pharmacology, Pharmazentrum Frankfurt/ZAFES, Faculty of Medicine, Goethe University, Frankfurt am Main, 60590, Germany
| | - Hector Giral
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, 12203, Germany
- German Center for Cardiovascular Research (DZHK) (Partner site Berlin), Berlin, 13316, Germany
| | - Yannick Schreiber
- Fraunhofer Institute of Molecular Biology and Applied Ecology-Project Group Translational Medicine and Pharmacology (IME-TMP), Frankfurt am Main, 60596, Germany
| | - Gerd Geisslinger
- Institute of Clinical Pharmacology, Pharmazentrum Frankfurt/ZAFES, Faculty of Medicine, Goethe University, Frankfurt am Main, 60590, Germany
- Fraunhofer Institute of Molecular Biology and Applied Ecology-Project Group Translational Medicine and Pharmacology (IME-TMP), Frankfurt am Main, 60596, Germany
| | - Christian Fork
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, 60590, Germany
- German Center for Cardiovascular Research (DZHK) (Partner site Rhine-Main), Frankfurt am Main, 60590, Germany
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 90095, CA, USA
| | - Fragiska Sigala
- 1st Department of Propaedeutic Surgery, University of Athens Medical School, Hippocration Hospital, Athens, 11364, Greece
| | - Casey E Romanoski
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, 85724, AZ, USA
| | - Jens Kroll
- Department of Vascular Biology and Tumor Angiogenesis, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany
| | - Hanjoong Jo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, 30332, GA, USA
| | - Ulf Landmesser
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, 12203, Germany
- German Center for Cardiovascular Research (DZHK) (Partner site Berlin), Berlin, 13316, Germany
- Berlin Institute of Health (BIH), Berlin, 10178, Germany
| | - Aldons J Lusis
- Departments of Medicine, Microbiology and Human Genetics, University of California, Los Angeles, 90095, CA, USA
| | - Dmitry Namgaladze
- Institute of Biochemistry I, Goethe University, Frankfurt am Main, 60590, Germany
| | - Ingrid Fleming
- German Center for Cardiovascular Research (DZHK) (Partner site Rhine-Main), Frankfurt am Main, 60590, Germany
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt am Main, 60590, Germany
| | - Matthias S Leisegang
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, 60590, Germany
- German Center for Cardiovascular Research (DZHK) (Partner site Rhine-Main), Frankfurt am Main, 60590, Germany
| | - Jun Zhu
- Icahn Institute of Genomics and Multiscale Biology, Mount Sinai Icahn School of Medicine, New York, 10029, NY, USA.
- Sema4 Genomics (a Mount Sinai venture), Stamford, 06902, CT, USA.
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, 60590, Germany.
- German Center for Cardiovascular Research (DZHK) (Partner site Rhine-Main), Frankfurt am Main, 60590, Germany.
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156
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de Souza HSP, Fiocchi C. Network Medicine: A Mandatory Next Step for Inflammatory Bowel Disease. Inflamm Bowel Dis 2018; 24:671-679. [PMID: 29562278 DOI: 10.1093/ibd/izx111] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Indexed: 12/12/2022]
Abstract
Despite unquestionable progress in the management of inflammatory bowel disease (IBD) and the much improved clinical results achievable today in Crohn's disease (CD) and ulcerative colitis (UC) patients, the overall therapeutic outcome remains far from optimal. The main reason of this partial success is that all current medications only block individual components of a highly complex disease process that results from the integration of multiple and incompletely identified pathogenic components. Thus, if further progress is to be achieved in IBD therapeutics and we want to move from the current success rate to nearly 100%, bold new ideas must be entertained and new approaches put into practice. Both are necessary because in IBD we are dealing with a prototypical complex disease superimposed to the background of the extreme biological diversity of humans in response to injury. An unresolved challenge mandates the adoption of new solutions specifically designed to address the unique features of that challenge. Translated to a disease condition, and IBD in particular, the unresolved challenges of CD and UC demand bold new thinking leading to the conception and implementation of totally innovative therapies. In this article, we propose that one such new thinking is the notion of network medicine for IBD, and that the development of brand new treatments should be based on the identification of the molecular structure of the IBD interactome with the purpose of targeting its controlling elements (central nodes or hubs). This specific targeting of the underlying molecular disease modules will lead to the disruption of the IBD interactome and foster the resolution of intestinal inflammatory process.
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Affiliation(s)
- Heitor S P de Souza
- Department of Gastroenterology & Multidisciplinary Research Laboratory, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,The D'Or Institute for Research and Education, Rua Diniz Cordeiro, Rio de Janeiro, Brazil
| | - Claudio Fiocchi
- Department of Pathobiology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Gastroenterology and Hepatology, Digestive Disease Institute, Cleveland Clinic, Cleveland, Ohio, USA
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158
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Zhao J, Cheng F, Jia P, Cox N, Denny JC, Zhao Z. An integrative functional genomics framework for effective identification of novel regulatory variants in genome-phenome studies. Genome Med 2018; 10:7. [PMID: 29378629 PMCID: PMC5789733 DOI: 10.1186/s13073-018-0513-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 01/04/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Genome-phenome studies have identified thousands of variants that are statistically associated with disease or traits; however, their functional roles are largely unclear. A comprehensive investigation of regulatory mechanisms and the gene regulatory networks between phenome-wide association study (PheWAS) and genome-wide association study (GWAS) is needed to identify novel regulatory variants contributing to risk for human diseases. METHODS In this study, we developed an integrative functional genomics framework that maps 215,107 significant single nucleotide polymorphism (SNP) traits generated from the PheWAS Catalog and 28,870 genome-wide significant SNP traits collected from the GWAS Catalog into a global human genome regulatory map via incorporating various functional annotation data, including transcription factor (TF)-based motifs, promoters, enhancers, and expression quantitative trait loci (eQTLs) generated from four major functional genomics databases: FANTOM5, ENCODE, NIH Roadmap, and Genotype-Tissue Expression (GTEx). In addition, we performed a tissue-specific regulatory circuit analysis through the integration of the identified regulatory variants and tissue-specific gene expression profiles in 7051 samples across 32 tissues from GTEx. RESULTS We found that the disease-associated loci in both the PheWAS and GWAS Catalogs were significantly enriched with functional SNPs. The integration of functional annotations significantly improved the power of detecting novel associations in PheWAS, through which we found a number of functional associations with strong regulatory evidence in the PheWAS Catalog. Finally, we constructed tissue-specific regulatory circuits for several complex traits: mental diseases, autoimmune diseases, and cancer, via exploring tissue-specific TF-promoter/enhancer-target gene interaction networks. We uncovered several promising tissue-specific regulatory TFs or genes for Alzheimer's disease (e.g. ZIC1 and STX1B) and asthma (e.g. CSF3 and IL1RL1). CONCLUSIONS This study offers powerful tools for exploring the functional consequences of variants generated from genome-phenome association studies in terms of their mechanisms on affecting multiple complex diseases and traits.
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Affiliation(s)
- Junfei Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA
| | - Feixiong Cheng
- Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
- Center for Complex Networks Research, Northeastern University, Boston, MA, 02215, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA
| | - Nancy Cox
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Joshua C Denny
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 820, Houston, TX, 77030, USA.
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
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