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Kunes RZ, Walle T, Land M, Nawy T, Pe'er D. Supervised discovery of interpretable gene programs from single-cell data. Nat Biotechnol 2024; 42:1084-1095. [PMID: 37735262 PMCID: PMC10958532 DOI: 10.1038/s41587-023-01940-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 08/09/2023] [Indexed: 09/23/2023]
Abstract
Factor analysis decomposes single-cell gene expression data into a minimal set of gene programs that correspond to processes executed by cells in a sample. However, matrix factorization methods are prone to technical artifacts and poor factor interpretability. We address these concerns with Spectra, an algorithm that combines user-provided gene programs with the detection of novel programs that together best explain expression covariation. Spectra incorporates existing gene sets and cell-type labels as prior biological information, explicitly models cell type and represents input gene sets as a gene-gene knowledge graph using a penalty function to guide factorization toward the input graph. We show that Spectra outperforms existing approaches in challenging tumor immune contexts, as it finds factors that change under immune checkpoint therapy, disentangles the highly correlated features of CD8+ T cell tumor reactivity and exhaustion, finds a program that explains continuous macrophage state changes under therapy and identifies cell-type-specific immune metabolic programs.
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Affiliation(s)
- Russell Z Kunes
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Statistics, Columbia University, New York, NY, USA
| | - Thomas Walle
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Max Land
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tal Nawy
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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2
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Hateley C, Olona A, Halliday L, Edin ML, Ko JH, Forlano R, Terra X, Lih FB, Beltrán-Debón R, Manousou P, Purkayastha S, Moorthy K, Thursz MR, Zhang G, Goldin RD, Zeldin DC, Petretto E, Behmoaras J. Multi-tissue profiling of oxylipins reveal a conserved up-regulation of epoxide:diol ratio that associates with white adipose tissue inflammation and liver steatosis in obesity. EBioMedicine 2024; 103:105127. [PMID: 38677183 PMCID: PMC11061246 DOI: 10.1016/j.ebiom.2024.105127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Obesity drives maladaptive changes in the white adipose tissue (WAT) which can progressively cause insulin resistance, type 2 diabetes mellitus (T2DM) and metabolic dysfunction-associated liver disease (MASLD). Obesity-mediated loss of WAT homeostasis can trigger liver steatosis through dysregulated lipid pathways such as those related to polyunsaturated fatty acid (PUFA)-derived oxylipins. However, the exact relationship between oxylipins and metabolic syndrome remains elusive and cross-tissue dynamics of oxylipins are ill-defined. METHODS We quantified PUFA-related oxylipin species in the omental WAT, liver biopsies and plasma of 88 patients undergoing bariatric surgery (female N = 79) and 9 patients (female N = 4) undergoing upper gastrointestinal surgery, using UPLC-MS/MS. We integrated oxylipin abundance with WAT phenotypes (adipogenesis, adipocyte hypertrophy, macrophage infiltration, type I and VI collagen remodelling) and the severity of MASLD (steatosis, inflammation, fibrosis) quantified in each biopsy. The integrative analysis was subjected to (i) adjustment for known risk factors and, (ii) control for potential drug-effects through UPLC-MS/MS analysis of metformin-treated fat explants ex vivo. FINDINGS We reveal a generalized down-regulation of cytochrome P450 (CYP)-derived diols during obesity conserved between the WAT and plasma. Notably, epoxide:diol ratio, indicative of soluble epoxide hydrolyse (sEH) activity, increases with WAT inflammation/fibrosis, hepatic steatosis and T2DM. Increased 12,13-EpOME:DiHOME in WAT and liver is a marker of worsening metabolic syndrome in patients with obesity. INTERPRETATION These findings suggest a dampened sEH activity and a possible role of fatty acid diols during metabolic syndrome in major metabolic organs such as WAT and liver. They also have implications in view of the clinical trials based on sEH inhibition for metabolic syndrome. FUNDING Wellcome Trust (PS3431_WMIH); Duke-NUS (Intramural Goh Cardiovascular Research Award (Duke-NUS-GCR/2022/0020); National Medical Research Council (OFLCG22may-0011); National Institute of Environmental Health Sciences (Z01 ES025034); NIHR Imperial Biomedical Research Centre.
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Affiliation(s)
- Charlotte Hateley
- Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK; Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Antoni Olona
- Centre for Computational Biology and Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Laura Halliday
- Department of Surgery and Cancer, Imperial College London, UK
| | - Matthew L Edin
- Division of Intramural Research, NIEHS/NIH, Research Triangle Park, NC, USA
| | - Jeong-Hun Ko
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, UK
| | - Roberta Forlano
- Department of Metabolism, Digestion and Reproduction, Imperial College London, UK; Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Ximena Terra
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, MoBioFood Research Group, Tarragona, Spain
| | - Fred B Lih
- Division of Intramural Research, NIEHS/NIH, Research Triangle Park, NC, USA
| | - Raúl Beltrán-Debón
- Universitat Rovira i Virgili, Departament de Bioquímica i Biotecnologia, MoBioFood Research Group, Tarragona, Spain
| | - Penelopi Manousou
- Department of Metabolism, Digestion and Reproduction, Imperial College London, UK; Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Sanjay Purkayastha
- Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK; University of Brunel, Kingston Lane, Uxbridge, London, UB8 3PH, UK
| | - Krishna Moorthy
- Department of Surgery and Cancer, Imperial College London, UK; Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Mark R Thursz
- Department of Metabolism, Digestion and Reproduction, Imperial College London, UK; Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Guodong Zhang
- Department of Nutrition, College of Agriculture and Environmental Sciences, 3135 Meyer Hall, One Shields Avenue, UC Davis, Davis, CA, 95616, USA
| | - Robert D Goldin
- Department of Metabolism, Digestion and Reproduction, Imperial College London, UK; Imperial College Healthcare NHS Trust, St. Mary's Hospital, Praed Street, London, W2 1NY, UK
| | - Darryl C Zeldin
- Division of Intramural Research, NIEHS/NIH, Research Triangle Park, NC, USA
| | - Enrico Petretto
- Centre for Computational Biology and Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore; Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University (CPU), Nanjing, China
| | - Jacques Behmoaras
- Centre for Inflammatory Disease, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK; Centre for Computational Biology and Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.
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3
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Noh MR, Jang HS, Salem FE, Ferrer FA, Kim J, Padanilam BJ. Epoxyeicosatrienoic acid administration or soluble epoxide hydrolase inhibition attenuates renal fibrogenesis in obstructive nephropathy. Am J Physiol Renal Physiol 2023; 324:F138-F151. [PMID: 36475868 PMCID: PMC9844979 DOI: 10.1152/ajprenal.00052.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 11/11/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
Epoxyeicosatrienoic acids (EETs) are arachidonic acid metabolites with biological effects, including antiapoptotic, anti-inflammatory, and antifibrotic functions. Soluble epoxide hydrolase (sEH)-mediated hydrolysis of EETs to dihydroxyeicosatrienoic acids (DHETs) attenuates these effects. Recent studies have demonstrated that inhibition of sEH prevents renal tubulointerstitial fibrosis and inflammation in the chronic kidney disease model. Given the pathophysiological role of the EET pathway in chronic kidney disease, we investigated if administration of EET regioisomers and/or sEH inhibition will promote antifibrotic and renoprotective effects in renal fibrosis following unilateral ureteral obstruction (UUO). EETs administration abolished tubulointerstitial fibrogenesis, as demonstrated by reduced fibroblast activation and collagen deposition after UUO. The inflammatory response was prevented as demonstrated by decreased neutrophil and macrophage infiltration and expression of cytokines in EET-administered UUO kidneys. EET administration and/or sEH inhibition significantly reduced M1 macrophage markers, whereas M2 macrophage markers were highly upregulated. Furthermore, UUO-induced oxidative stress, tubular injury, and apoptosis were all downregulated following EET administration. Combined EET administration and sEH inhibition, however, had no additive effect in attenuating inflammation and renal interstitial fibrogenesis after UUO. Taken together, our findings provide a mechanistic understanding of how EETs prevent kidney fibrogenesis during obstructive nephropathy and suggest EET treatment as a potential therapeutic strategy to treat fibrotic diseases.NEW & NOTEWORTHY Epoxyeicosatrienoic acids (EETs) are cytochrome P-450-dependent antihypertensive and anti-inflammatory derivatives of arachidonic acid, which are highly abundant in the kidney and considered renoprotective. We found that EET administration and/or soluble epoxide hydrolase inhibition significantly attenuates oxidative stress, renal cell death, inflammation, macrophage differentiation, and fibrogenesis following unilateral ureteral obstruction. Our findings provide a mechanistic understanding of how EETs prevent kidney fibrogenesis during obstructive nephropathy and suggest that EET treatment may be a potential therapeutic strategy to treat fibrotic diseases.
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Affiliation(s)
- Mi Ra Noh
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Hee-Seong Jang
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska
- Division of Pediatric Surgery, Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Fadi E Salem
- Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Fernando A Ferrer
- Department of Urology, Kravis Children's Hospital, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jinu Kim
- Department of Anatomy, Jeju National University School of Medicine, Jeju, South Korea
- Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju, South Korea
| | - Babu J Padanilam
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska
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4
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Zhang Y, Gao L, Yao B, Huang S, Zhang Y, Liu J, Liu Z, Wang X. Role of epoxyeicosatrienoic acids in cardiovascular diseases and cardiotoxicity of drugs. Life Sci 2022; 310:121122. [DOI: 10.1016/j.lfs.2022.121122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/09/2022]
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5
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Single cell transcriptomics in human osteoarthritis synovium and in silico deconvoluted bulk RNA sequencing. Osteoarthritis Cartilage 2022; 30:475-480. [PMID: 34971754 PMCID: PMC10097426 DOI: 10.1016/j.joca.2021.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 02/05/2023]
Abstract
OBJECTIVES To reveal the heterogeneity of different cell types of osteoarthritis (OA) synovial tissues at a single-cell resolution, and determine by novel methodology whether bulk-RNA-seq data could be deconvoluted to create in silico scRNA-seq data for synovial tissue analyses. METHODS OA scRNA-seq data (102,077 synoviocytes) were provided by 17 patients undergoing total knee arthroplasty; 9 tissues with matched scRNA-seq and bulk RNA-seq data were used to evaluate six in silico gene deconvolution tools. Predicted and observed cell types and proportions were compared to identify the best deconvolution tool for synovium. RESULTS We identified seven distinct cell types in OA synovial tissues. Gene deconvolution identified three (of six) platforms as suitable for extrapolating cellular gene expression from bulk RNA-seq data. Using paired scRNA-seq and bulk RNA-seq data, an "arthritis" specific signature matrix was created and validated to have a significantly better predictive performance for synoviocytes than a default signature matrix. Use of the machine learning tool, Cell-type Identification By Estimating Relative Subsets of RNA Transcripts x (CIBERSORTx), to analyze rheumatoid arthritis (RA) and OA bulk RNA-seq data yielded proportions of T cells and fibroblasts that were similar to the gold standard observations from RA and OA scRNA-seq data, respectively. CONCLUSION This novel study revealed heterogeneity of synovial cell types in OA and the feasibility of gene deconvolution for synovial tissue.
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6
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Imig JD. Orally active epoxyeicosatrienoic acid analogs in hypertension and renal injury. ADVANCES IN PHARMACOLOGY 2022; 94:27-55. [PMID: 35659375 PMCID: PMC10105514 DOI: 10.1016/bs.apha.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Epoxyeicosatrienoic acids (EETs) are arachidonic acid metabolites synthesized by cytochrome P450 epoxygenases. Biological activities for EETs include vasodilation, decreasing inflammation, opposing apoptosis, and inhibiting renal sodium reabsorption. These actions are beneficial in lowering blood pressure and slowing kidney disease progression. Furthermore, evidence in human and experimental animal studies have found that decreased EET levels contribute to hypertension and kidney diseases. Consequently, EET mimics/analogs have been developed as a potential therapeutic for hypertension and acute and chronic kidney diseases. Their development has resulted in EET analogs that are orally active with favorable pharmacological profiles. Analogs for 8,9-EET, 11,12-EET, and 14,15-EET have been tested in several hypertension and kidney disease animal models. More recently, kidney targeted EET analogs have been synthesized and tested against drug-induced nephrotoxicity. Experimental evidence has demonstrated compelling therapeutic potential for EET analogs to oppose cardiovascular and kidney diseases. These EET analogs lower blood pressure, decrease kidney inflammation, improve vascular endothelial function, and decrease kidney fibrosis and apoptosis. Overall, these preclinical studies support the likelihood that EET analogs will advance to clinical trials for hypertension and associated comorbidities or acute and chronic kidney diseases.
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Affiliation(s)
- John D Imig
- Drug Discovery Center, Medical College of Wisconsin, Milwaukee, WI, United States.
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7
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Chenouard V, Remy S, Tesson L, Ménoret S, Ouisse LH, Cherifi Y, Anegon I. Advances in Genome Editing and Application to the Generation of Genetically Modified Rat Models. Front Genet 2021; 12:615491. [PMID: 33959146 PMCID: PMC8093876 DOI: 10.3389/fgene.2021.615491] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
The rat has been extensively used as a small animal model. Many genetically engineered rat models have emerged in the last two decades, and the advent of gene-specific nucleases has accelerated their generation in recent years. This review covers the techniques and advances used to generate genetically engineered rat lines and their application to the development of rat models more broadly, such as conditional knockouts and reporter gene strains. In addition, genome-editing techniques that remain to be explored in the rat are discussed. The review also focuses more particularly on two areas in which extensive work has been done: human genetic diseases and immune system analysis. Models are thoroughly described in these two areas and highlight the competitive advantages of rat models over available corresponding mouse versions. The objective of this review is to provide a comprehensive description of the advantages and potential of rat models for addressing specific scientific questions and to characterize the best genome-engineering tools for developing new projects.
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Affiliation(s)
- Vanessa Chenouard
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
- genOway, Lyon, France
| | - Séverine Remy
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
| | - Laurent Tesson
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
| | - Séverine Ménoret
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
- CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, Nantes Université, Nantes, France
| | - Laure-Hélène Ouisse
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
| | | | - Ignacio Anegon
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
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8
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Jiang T, Zhu AS, Yang CQ, Xu CY, Yang DQ, Lou ZH, Zhang GJ. Cytochrome P450 2A6 is associated with macrophage polarization and is a potential biomarker for hepatocellular carcinoma. FEBS Open Bio 2021; 11:670-683. [PMID: 33455085 PMCID: PMC7931228 DOI: 10.1002/2211-5463.13089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/29/2020] [Accepted: 01/14/2021] [Indexed: 01/06/2023] Open
Abstract
Cytochrome P450 2A6 (CYP2A6) is an important metabolic enzyme and is involved in the progression of hepatocellular carcinoma (HCC). However, its specific function and the mechanism of modulation remain to be elucidated. In this study, we found that CYP2A6 is dramatically downregulated in HCC. CYP2A6 expression is closely associated with pathological grading, histologic grade, hepatitis, vascular metastasis, liver inflammation, and worse prognosis. Reduced expression of CYP2A6 contributes to alternative activation of macrophage polarization and impairs macrophage maturation and phagocytosis. Mechanistically, CYP2A6 participates in arachidonic acid metabolism, initiates 20‐hydroxyeicosatetraenoic acid (HETE) generation, and inhibits epoxyeicosatrienoic acid (EET) generation. Disruption of the equilibrium between 20‐HETE and EETs can induce macrophage polarization, thereby modulating antitumor immunity.
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Affiliation(s)
- Tao Jiang
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Ai-Song Zhu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Chu-Qi Yang
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Chu-Yun Xu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Dan-Qian Yang
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhao-Huan Lou
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Guang-Ji Zhang
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
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9
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Arlauckas S, Oh N, Li R, Weissleder R, Miller MA. Macrophage imaging and subset analysis using single-cell RNA sequencing. Nanotheranostics 2021; 5:36-56. [PMID: 33391974 PMCID: PMC7738942 DOI: 10.7150/ntno.50185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022] Open
Abstract
Macrophages have been associated with drug response and resistance in diverse settings, thus raising the possibility of using macrophage imaging as a companion diagnostic to inform personalized patient treatment strategies. Nanoparticle-based contrast agents are especially promising because they efficiently deliver fluorescent, magnetic, and/or radionuclide labels by leveraging the intrinsic capacity of macrophages to accumulate nanomaterials in their role as professional phagocytes. Unfortunately, current clinical imaging modalities are limited in their ability to quantify broad molecular programs that may explain (a) which particular cell subsets a given imaging agent is actually labeling, and (b) what mechanistic role those cells play in promoting drug response or resistance. Highly multiplexed single-cell approaches including single-cell RNA sequencing (scRNAseq) have emerged as resources to help answer these questions. In this review, we query recently published scRNAseq datasets to support companion macrophage imaging, with particular focus on using dextran-based nanoparticles to predict the action of anti-cancer nanotherapies and monoclonal antibodies.
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Affiliation(s)
- Sean Arlauckas
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA
| | - Nuri Oh
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA
| | - Ran Li
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA.,Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA.,Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Miles A Miller
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, MA 02114, USA.,Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA
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10
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Schulz EC, Henderson SR, Illarionov B, Crosskey T, Southall SM, Krichel B, Uetrecht C, Fischer M, Wilmanns M. The crystal structure of mycobacterial epoxide hydrolase A. Sci Rep 2020; 10:16539. [PMID: 33024154 PMCID: PMC7538969 DOI: 10.1038/s41598-020-73452-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 09/16/2020] [Indexed: 01/08/2023] Open
Abstract
The human pathogen Mycobacterium tuberculosis is the causative agent of tuberculosis resulting in over 1 million fatalities every year, despite decades of research into the development of new anti-TB compounds. Unlike most other organisms M. tuberculosis has six putative genes for epoxide hydrolases (EH) of the α/β-hydrolase family with little known about their individual substrates, suggesting functional significance for these genes to the organism. Due to their role in detoxification, M. tuberculosis EH’s have been identified as potential drug targets. Here, we demonstrate epoxide hydrolase activity of M. thermoresistibile epoxide hydrolase A (Mth-EphA) and report its crystal structure in complex with the inhibitor 1,3-diphenylurea at 2.0 Å resolution. Mth-EphA displays high sequence similarity to its orthologue from M. tuberculosis and generally high structural similarity to α/β-hydrolase EHs. The structure of the inhibitor bound complex reveals the geometry of the catalytic residues and the conformation of the inhibitor. Comparison to other EHs from mycobacteria allows insight into the active site plasticity with respect to substrate specificity. We speculate that mycobacterial EHs may have a narrow substrate specificity providing a potential explanation for the genetic repertoire of epoxide hydrolase genes in M. tuberculosis.
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Affiliation(s)
- Eike C Schulz
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chausee 149, 22761, Hamburg, Germany. .,European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22603, Hamburg, Germany.
| | - Sara R Henderson
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22603, Hamburg, Germany.,Norwich Medical School, Rosalind Franklin Road, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Boris Illarionov
- Hamburg School of Food Science, Institute of Food Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Thomas Crosskey
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22603, Hamburg, Germany
| | - Stacey M Southall
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22603, Hamburg, Germany.,Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistraße 52, 20251, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistraße 52, 20251, Hamburg, Germany.,European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, Universität Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22603, Hamburg, Germany.,University of Hamburg Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
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Lu J, Chen A, Ma X, Shang X, Zhang Y, Guo Y, Liu M, Wang X. Generation and Characterization of Cytochrome P450 2J3/10 CRISPR/Cas9 Knockout Rat Model. Drug Metab Dispos 2020; 48:1129-1136. [DOI: 10.1124/dmd.120.000114] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 08/04/2020] [Indexed: 12/11/2022] Open
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12
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Szpirer C. Rat models of human diseases and related phenotypes: a systematic inventory of the causative genes. J Biomed Sci 2020; 27:84. [PMID: 32741357 PMCID: PMC7395987 DOI: 10.1186/s12929-020-00673-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
The laboratory rat has been used for a long time as the model of choice in several biomedical disciplines. Numerous inbred strains have been isolated, displaying a wide range of phenotypes and providing many models of human traits and diseases. Rat genome mapping and genomics was considerably developed in the last decades. The availability of these resources has stimulated numerous studies aimed at discovering causal disease genes by positional identification. Numerous rat genes have now been identified that underlie monogenic or complex diseases and remarkably, these results have been translated to the human in a significant proportion of cases, leading to the identification of novel human disease susceptibility genes, helping in studying the mechanisms underlying the pathological abnormalities and also suggesting new therapeutic approaches. In addition, reverse genetic tools have been developed. Several genome-editing methods were introduced to generate targeted mutations in genes the function of which could be clarified in this manner [generally these are knockout mutations]. Furthermore, even when the human gene causing a disease had been identified without resorting to a rat model, mutated rat strains (in particular KO strains) were created to analyze the gene function and the disease pathogenesis. Today, over 350 rat genes have been identified as underlying diseases or playing a key role in critical biological processes that are altered in diseases, thereby providing a rich resource of disease models. This article is an update of the progress made in this research and provides the reader with an inventory of these disease genes, a significant number of which have similar effects in rat and humans.
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Affiliation(s)
- Claude Szpirer
- Université Libre de Bruxelles, B-6041, Gosselies, Belgium.
- , Waterloo, Belgium.
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Imig JD, Jankiewicz WK, Khan AH. Epoxy Fatty Acids: From Salt Regulation to Kidney and Cardiovascular Therapeutics: 2019 Lewis K. Dahl Memorial Lecture. Hypertension 2020; 76:3-15. [PMID: 32475311 DOI: 10.1161/hypertensionaha.120.13898] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epoxyeicosatrienoic acids (EETs) are epoxy fatty acids that have biological actions that are essential for maintaining water and electrolyte homeostasis. An inability to increase EETs in response to a high-salt diet results in salt-sensitive hypertension. Vasodilation, inhibition of epithelial sodium channel, and inhibition of inflammation are the major EET actions that are beneficial to the heart, resistance arteries, and kidneys. Genetic and pharmacological means to elevate EETs demonstrated antihypertensive, anti-inflammatory, and organ protective actions. Therapeutic approaches to increase EETs were then developed for cardiovascular diseases. sEH (soluble epoxide hydrolase) inhibitors were developed and progressed to clinical trials for hypertension, diabetes mellitus, and other diseases. EET analogs were another therapeutic approach taken and these drugs are entering the early phases of clinical development. Even with the promise for these therapeutic approaches, there are still several challenges, unexplored areas, and opportunities for epoxy fatty acids.
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Affiliation(s)
- John D Imig
- From the Department of Pharmacology and Toxicology, Cardiovascular Center, Medical College of Wisconsin, Milwaukee
| | - Wojciech K Jankiewicz
- From the Department of Pharmacology and Toxicology, Cardiovascular Center, Medical College of Wisconsin, Milwaukee
| | - Abdul H Khan
- From the Department of Pharmacology and Toxicology, Cardiovascular Center, Medical College of Wisconsin, Milwaukee
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Sarmiento-Machado LM, Romualdo GR, Zapaterini JR, Tablas MB, Fernandes AAH, Moreno FS, Barbisan LF. Protective Effects of Dietary Capsaicin on the Initiation Step of a Two-Stage Hepatocarcinogenesis Rat Model. Nutr Cancer 2020; 73:817-828. [PMID: 32400193 DOI: 10.1080/01635581.2020.1764067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Capsaicin (CPS), an ingredient of Capsicum plants, has anti-inflammatory, antioxidant and antitumoral properties. The mechanisms of CPS on hepatocarcinogenesis preclinical bioassays are not described. Thus, the protective effects CPS were evaluated in the early stages of chemically-induced hepatocarcinogenesis. Male Wistar rats received diet containing 0.01% or 0.02% CPS for 3 weeks. Afterwards, animals received a dose of hepatocarcinogen diethylnitrosamine (DEN, 100 mg/kg body weight). From weeks 4-12, groups had their diet replaced by a 0.05% phenobarbital supplemented one to promote DEN-induced preneoplastic lesions. Animals were euthanized 24 h after DEN administration (n = 5/group) or at week 12 (n = 9/group). The estimated CPS intake in rats resembled human consumption. At the end of week 3, dietary 0.02% CPS attenuated DEN-induced oxidative damage and, consequently, hepatocyte necrosis by reducing serum alanine aminotransferase levels, liver CD68-positive macrophages, lipid peroxidation, while increasing antioxidant glutathione system. Additionally, 0.02% CPS upregulated vanilloid Trpv1 receptor and anti-inflammatory epoxygenase Cyp2j4 genes in the liver. Ultimately, previous 0.02% CPS intake decreased the number of GST-P-positive preneoplastic lesions at week 12. Thus, CPS attenuated preneoplastic lesion development, primarily by diminishing DEN-induced oxidative liver injury. Findings indicate that CPS is a promising chemopreventive agent when administered after and during the early stages of hepatocarcinogenesis.
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Affiliation(s)
| | | | - Joyce Regina Zapaterini
- Department of Morphology, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Mariana Baptista Tablas
- Department of Morphology, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | | | - Fernando Salvador Moreno
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Luís Fernando Barbisan
- Department of Morphology, Biosciences Institute, São Paulo State University (UNESP), Botucatu, SP, Brazil
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15
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Han KH, Kim B, Ji SC, Kang HG, Cheong HI, Cho JY, Ha IS. Mechanism of Chronic Kidney Disease Progression and Novel Biomarkers: A Metabolomic Analysis of Experimental Glomerulonephritis. Metabolites 2020; 10:E169. [PMID: 32344531 PMCID: PMC7240957 DOI: 10.3390/metabo10040169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/12/2020] [Accepted: 04/21/2020] [Indexed: 12/21/2022] Open
Abstract
While a complex network of cellular and molecular events is known to be involved in the pathophysiological mechanism of chronic kidney disease (CKD), the divergence point between reversal and progression and the event that triggers CKD progression are still unknown. To understand the different mechanisms between reversible and irreversible kidney disease and to search for urinary biomarkers that can predict prognosis, a metabolomic analysis was applied to compare acute and chronic experimental glomerulonephritis (GN) models. Four metabolites, namely, epoxyoctadecenoic acid (EpOME), epoxyeicosatetraenoic acid (EpETE), α-linolenic acid (ALA), and hydroxyretinoic acid, were identified as predictive markers after comparing the chronic nephritis model with acute nephritis and control groups (false discovery rate adjusted p-value (q-value) < 0.05). Renal mRNA expression of cytochrome P450 and epoxide hydrolase was also identified as being involved in the production of epoxide metabolites from these polyunsaturated fatty acids (p < 0.05). These results suggested that the progression of chronic kidney disease is associated with abnormally activated epoxide hydrolase, leading to an increase in EpOME and EpETE as pro-inflammatory eicosanoids.
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Affiliation(s)
- Kyoung Hee Han
- Department of Pediatrics, Jeju National University School of Medicine, Aran 13gil 15, Jeju-si, Jeju 63241, Korea;
| | - Bora Kim
- Kidney Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (B.K.); (S.C.J.); (H.G.K.)
- Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Korea
| | - Sang Chun Ji
- Kidney Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (B.K.); (S.C.J.); (H.G.K.)
- Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Korea
| | - Hee Gyung Kang
- Kidney Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (B.K.); (S.C.J.); (H.G.K.)
- Department of Pediatrics, Seoul National University College of Medicine and Hospital, 103, Daehak-ro, Jongno-gu, Seoul 03080, Korea;
| | - Hae Il Cheong
- Department of Pediatrics, Seoul National University College of Medicine and Hospital, 103, Daehak-ro, Jongno-gu, Seoul 03080, Korea;
| | - Joo-Youn Cho
- Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul 03080, Korea
| | - Il-Soo Ha
- Kidney Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (B.K.); (S.C.J.); (H.G.K.)
- Department of Pediatrics, Seoul National University College of Medicine and Hospital, 103, Daehak-ro, Jongno-gu, Seoul 03080, Korea;
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Tracing tumorigenesis in a solid tumor model at single-cell resolution. Nat Commun 2020; 11:991. [PMID: 32080185 PMCID: PMC7033116 DOI: 10.1038/s41467-020-14777-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 01/29/2020] [Indexed: 12/28/2022] Open
Abstract
Characterizing the complex composition of solid tumors is fundamental for understanding tumor initiation, progression and metastasis. While patient-derived samples provide valuable insight, they are heterogeneous on multiple molecular levels, and often originate from advanced tumor stages. Here, we use single-cell transcriptome and epitope profiling together with pathway and lineage analyses to study tumorigenesis from a developmental perspective in a mouse model of salivary gland squamous cell carcinoma. We provide a comprehensive cell atlas and characterize tumor-specific cells. We find that these cells are connected along a reproducible developmental trajectory: initiated in basal cells exhibiting an epithelial-to-mesenchymal transition signature, tumorigenesis proceeds through Wnt-differential cancer stem cell-like subpopulations before differentiating into luminal-like cells. Our work provides unbiased insights into tumor-specific cellular identities in a whole tissue environment, and emphasizes the power of using defined genetic model systems. Understanding tumour development at a granular level is a challenge in solid tumours. Here, the authors provide a cell atlas across tumour development in a genetic model of salivary gland squamous cell carcinoma using single-cell transcriptome and epitope profiling.
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Fleming I. New Lipid Mediators in Retinal Angiogenesis and Retinopathy. Front Pharmacol 2019; 10:739. [PMID: 31333461 PMCID: PMC6624440 DOI: 10.3389/fphar.2019.00739] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 06/07/2019] [Indexed: 12/31/2022] Open
Abstract
Retinal diseases associated with vascular destabilization and the inappropriate proliferation of retinal endothelial cells have major consequences on the retinal vascular network. In extreme cases, the development of hypoxia, the upregulation of growth factors, and the hyper-proliferation of unstable capillaries can result in bleeding and vision loss. While anti-vascular endothelial growth factor therapy and laser retinal photocoagulation can be used to treat the symptoms of late stage disease, there is currently no treatment available that can prevent disease progression. Cytochrome P450 enzymes metabolize endogenous substrates (polyunsaturated fatty acids) to bioactive fatty acid epoxides that demonstrate biological activity with generally protective/anti-inflammatory and insulin-sensitizing effects. These epoxides are further metabolized by the soluble epoxide hydrolase (sEH) to fatty acid diols, high concentrations of which have vascular destabilizing effects. Recent studies have identified increased sEH expression and activity and the subsequent generation of the docosahexaenoic acid-derived diol; 19,20-dihydroxydocosapentaenoic acid, as playing a major role in the development of diabetic retinopathy. This review summarizes current understanding of the roles of cytochrome P450 enzyme and sEH–derived PUFA mediators in retinal disease.
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Affiliation(s)
- Ingrid Fleming
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe-University, Frankfurt, Germany.,German Centre for Cardiovascular Research (DZHK) partner site RheinMain, Frankfurt, Germany
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Ziemann M, Kaspi A, El-Osta A. Digital expression explorer 2: a repository of uniformly processed RNA sequencing data. Gigascience 2019; 8:giz022. [PMID: 30942868 PMCID: PMC6446219 DOI: 10.1093/gigascience/giz022] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/17/2019] [Accepted: 02/14/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND RNA sequencing (RNA-seq) is an indispensable tool in the study of gene regulation. While the technology has brought with it better transcript coverage and quantification, there remain considerable barriers to entry for the computational biologist to analyse large data sets. There is a real need for a repository of uniformly processed RNA-seq data that is easy to use. FINDINGS To address these obstacles, we developed Digital Expression Explorer 2 (DEE2), a web-based repository of RNA-seq data in the form of gene-level and transcript-level expression counts. DEE2 contains >5.3 trillion assigned reads from 580,000 RNA-seq data sets including species Escherichia coli, yeast, Arabidopsis, worm, fruit fly, zebrafish, rat, mouse, and human. Base-space sequence data downloaded from the National Center for Biotechnology Information Sequence Read Archive underwent quality control prior to transcriptome and genome mapping using open-source tools. Uniform data processing methods ensure consistency across experiments, facilitating fast and reproducible meta-analyses. CONCLUSIONS The web interface allows users to quickly identify data sets of interest using accession number and keyword searches. The data can also be accessed programmatically using a specifically designed R package. We demonstrate that DEE2 data are compatible with statistical packages such as edgeR or DESeq. Bulk data are also available for download. DEE2 can be found at http://dee2.io.
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Affiliation(s)
- Mark Ziemann
- Deakin University, Geelong, Australia, School of Life and Environmental Sciences, 75 Pigdons Road, Waurn Ponds, VIC 3216, Australia
- Epigenetics in Human Health and Disease, Central Clinical School, Faculty of Medicine, Monash University, 99 Commercial Road, Melbourne, VIC 3004, Australia
| | - Antony Kaspi
- Epigenetics in Human Health and Disease, Central Clinical School, Faculty of Medicine, Monash University, 99 Commercial Road, Melbourne, VIC 3004, Australia
| | - Assam El-Osta
- Epigenetics in Human Health and Disease, Central Clinical School, Faculty of Medicine, Monash University, 99 Commercial Road, Melbourne, VIC 3004, Australia
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, 3/F Lui Che Woo Clinical Sciences Building, 30-32 Ngan Shing Street, Sha Tin, Hong Kong SAR
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Olona A, Terra X, Ko JH, Grau-Bové C, Pinent M, Ardevol A, Diaz AG, Moreno-Moral A, Edin M, Bishop-Bailey D, Zeldin DC, Aitman TJ, Petretto E, Blay M, Behmoaras J. Epoxygenase inactivation exacerbates diet and aging-associated metabolic dysfunction resulting from impaired adipogenesis. Mol Metab 2018; 11:18-32. [PMID: 29656108 PMCID: PMC6001407 DOI: 10.1016/j.molmet.2018.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 02/23/2018] [Accepted: 03/05/2018] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE When molecular drivers of healthy adipogenesis are perturbed, this can cause hepatic steatosis. The role of arachidonic acid (AA) and its downstream enzymatic cascades, such as cyclooxygenase, in adipogenesis is well established. The exact contribution of the P450 epoxygenase pathway, however, remains to be established. Enzymes belonging to this pathway are mainly encoded by the CYP2J locus which shows extensive allelic expansion in mice. Here we aimed to establish the role of endogenous epoxygenase during adipogenesis under homeostatic and metabolic stress conditions. METHODS We took advantage of the simpler genetic architecture of the Cyp2j locus in the rat and used a Cyp2j4 (orthologue of human CYP2J2) knockout rat in two models of metabolic dysfunction: physiological aging and cafeteria diet (CAF). The phenotyping of Cyp2j4-/- rats under CAF was integrated with proteomics (LC-MS/MS) and lipidomics (LC-MS) analyses in the liver and the adipose tissue. RESULTS We report that Cyp2j4 deletion causes adipocyte dysfunction under metabolic challenges. This is characterized by (i) down-regulation of white adipose tissue (WAT) PPARγ and C/EBPα, (ii) adipocyte hypertrophy, (iii) extracellular matrix remodeling, and (iv) alternative usage of AA pathway. Specifically, in Cyp2j4-/- rats treated with a cafeteria diet, the dysfunctional adipogenesis is accompanied by exacerbated weight gain, hepatic lipid accumulation, and dysregulated gluconeogenesis. CONCLUSION These results suggest that AA epoxygenases are essential regulators of healthy adipogenesis. Our results uncover their synergistic role in fine-tuning AA pathway in obesity-mediated hepatic steatosis.
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Affiliation(s)
- Antoni Olona
- Centre for Complement and Inflammation Research, Imperial College London, London, W12 0NN, UK
| | - Ximena Terra
- Centre for Complement and Inflammation Research, Imperial College London, London, W12 0NN, UK; Mobiofood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43007, Tarragona, Spain
| | - Jeong-Hun Ko
- Centre for Complement and Inflammation Research, Imperial College London, London, W12 0NN, UK
| | - Carme Grau-Bové
- Centre for Complement and Inflammation Research, Imperial College London, London, W12 0NN, UK; Mobiofood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43007, Tarragona, Spain
| | - Montserrat Pinent
- Mobiofood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43007, Tarragona, Spain
| | - Anna Ardevol
- Mobiofood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43007, Tarragona, Spain
| | - Ana Garcia Diaz
- Renal and Vascular Inflammation Section, Department of Medicine, Imperial College London, London, W12 0NN, UK
| | - Aida Moreno-Moral
- Duke-NUS Medical School, National University of Singapore, 169857, Singapore
| | - Matthew Edin
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - David Bishop-Bailey
- Comparative Biomedical Sciences, Royal Veterinary College, London, NW1 0TU, UK
| | - Darryl C Zeldin
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Timothy J Aitman
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Enrico Petretto
- Duke-NUS Medical School, National University of Singapore, 169857, Singapore
| | - Mayte Blay
- Mobiofood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43007, Tarragona, Spain
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research, Imperial College London, London, W12 0NN, UK.
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20
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Identification of Ceruloplasmin as a Gene that Affects Susceptibility to Glomerulonephritis Through Macrophage Function. Genetics 2017; 206:1139-1151. [PMID: 28450461 PMCID: PMC5499168 DOI: 10.1534/genetics.116.197376] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/05/2017] [Indexed: 12/31/2022] Open
Abstract
Crescentic glomerulonephritis (Crgn) is a complex disorder where macrophage activity and infiltration are significant effector causes. In previous linkage studies using the uniquely susceptible Wistar Kyoto (WKY) rat strain, we have identified multiple crescentic glomerulonephritis QTL (Crgn) and positionally cloned genes underlying Crgn1 and Crgn2, which accounted for 40% of total variance in glomerular inflammation. Here, we have generated a backcross (BC) population (n = 166) where Crgn1 and Crgn2 were genetically fixed and found significant linkage to glomerular crescents on chromosome 2 (Crgn8, LOD = 3.8). Fine mapping analysis by integration with genome-wide expression QTLs (eQTLs) from the same BC population identified ceruloplasmin (Cp) as a positional eQTL in macrophages but not in serum. Liquid chromatography-tandem mass spectrometry confirmed Cp as a protein QTL in rat macrophages. WKY macrophages overexpress Cp and its downregulation by RNA interference decreases markers of glomerular proinflammatory macrophage activation. Similarly, short incubation with Cp results in a strain-dependent macrophage polarization in the rat. These results suggest that genetically determined Cp levels can alter susceptibility to Crgn through macrophage function and propose a new role for Cp in early macrophage activation.
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21
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Fleming I. The factor in EDHF: Cytochrome P450 derived lipid mediators and vascular signaling. Vascul Pharmacol 2016; 86:31-40. [DOI: 10.1016/j.vph.2016.03.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 01/20/2016] [Accepted: 03/06/2016] [Indexed: 12/31/2022]
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Martínez-Micaelo N, González-Abuín N, Terra X, Ardévol A, Pinent M, Petretto E, Behmoaras J, Blay M. Identification of a nutrient-sensing transcriptional network in monocytes by using inbred rat models on a cafeteria diet. Dis Model Mech 2016; 9:1231-1239. [PMID: 27483348 PMCID: PMC5087837 DOI: 10.1242/dmm.025528] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/04/2016] [Indexed: 01/21/2023] Open
Abstract
Obesity has reached pandemic levels worldwide. The current models of diet-induced obesity in rodents use predominantly high-fat based diets that do not take into account the consumption of variety of highly palatable, energy-dense foods that are prevalent in Western society. We and others have shown that the cafeteria (CAF) diet is a robust and reproducible model of human metabolic syndrome with tissue inflammation in the rat. We have previously shown that inbred rat strains such as Wistar Kyoto (WKY) and Lewis (LEW) show different susceptibilities to CAF diets with distinct metabolic and morphometric profiles. Here, we show a difference in plasma MCP-1 levels and investigate the effect of the CAF diet on peripheral blood monocyte transcriptome, as powerful stress-sensing immune cells, in WKY and LEW rats. We found that 75.5% of the differentially expressed transcripts under the CAF diet were upregulated in WKY rats and were functionally related to the activation of the immune response. Using a gene co-expression network constructed from the genes differentially expressed between CAF diet-fed LEW and WKY rats, we identified acyl-CoA synthetase short-chain family member 2 (Acss2) as a hub gene for a nutrient-sensing cluster of transcripts in monocytes. The Acss2 genomic region is significantly enriched for previously established metabolism quantitative trait loci in the rat. Notably, monocyte expression levels of Acss2 significantly correlated with plasma glucose, triglyceride, leptin and non-esterified fatty acid (NEFA) levels as well as morphometric measurements such as body weight and the total fat following feeding with the CAF diet in the rat. These results show the importance of the genetic background in nutritional genomics and identify inbred rat strains as potential models for CAF-diet-induced obesity. Summary: Feeding with a cafeteria diet (CAF) is a reproducible model of human metabolic syndrome in the rat. By using inbred rat models of nutrigenomics, we have studied the effect of CAF on monocyte transcriptome.
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Affiliation(s)
- Neus Martínez-Micaelo
- Mobiofood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43003 Tarragona, Spain
| | - Noemi González-Abuín
- Mobiofood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43003 Tarragona, Spain
| | - Ximena Terra
- Mobiofood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43003 Tarragona, Spain
| | - Ana Ardévol
- Mobiofood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43003 Tarragona, Spain
| | - Montserrat Pinent
- Mobiofood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43003 Tarragona, Spain
| | - Enrico Petretto
- MRC Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK Duke-NUS Graduate Medical School Singapore, 8 College Road, Singapore 169857, Republic of Singapore
| | - Jacques Behmoaras
- Centre of Complement and Inflammation Research, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Mayte Blay
- Mobiofood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, 43003 Tarragona, Spain
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Abstract
Resolution of inflammation has emerged as an active process in immunobiology, with cells of the mononuclear phagocyte system being critical in mediating efferocytosis and wound debridement and bridging the gap between innate and adaptive immunity. Here we investigated the roles of cytochrome P450 (CYP)-derived epoxy-oxylipins in a well-characterized model of sterile resolving peritonitis in the mouse. Epoxy-oxylipins were produced in a biphasic manner during the peaks of acute (4 h) and resolution phases (24-48 h) of the response. The epoxygenase inhibitor SKF525A (epoxI) given at 24 h selectively inhibited arachidonic acid- and linoleic acid-derived CYP450-epoxy-oxlipins and resulted in a dramatic influx in monocytes. The epoxI-recruited monocytes were strongly GR1(+), Ly6c(hi), CCR2(hi), CCL2(hi), and CX3CR1(lo) In addition, expression of F4/80 and the recruitment of T cells, B cells, and dendritic cells were suppressed. sEH (Ephx2)(-/-) mice, which have elevated epoxy-oxylipins, demonstrated opposing effects to epoxI-treated mice: reduced Ly6c(hi) monocytes and elevated F4/80(hi) macrophages and B, T, and dendritic cells. Ly6c(hi) and Ly6c(lo) monocytes, resident macrophages, and recruited dendritic cells all showed a dramatic change in their resolution signature following in vivo epoxI treatment. Markers of macrophage differentiation CD11b, MerTK, and CD103 were reduced, and monocyte-derived macrophages and resident macrophages ex vivo showed greatly impaired phagocytosis of zymosan and efferocytosis of apoptotic thymocytes following epoxI treatment. These findings demonstrate that epoxy-oxylipins have a critical role in monocyte lineage recruitment and activity to promote inflammatory resolution and represent a previously unidentified internal regulatory system governing the establishment of adaptive immunity.
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Garcia Diaz AI, Moyon B, Coan PM, Alfazema N, Venda L, Woollard K, Aitman T. New Wistar Kyoto and spontaneously hypertensive rat transgenic models with ubiquitous expression of green fluorescent protein. Dis Model Mech 2016; 9:463-71. [PMID: 26769799 PMCID: PMC4852507 DOI: 10.1242/dmm.024208] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 01/13/2016] [Indexed: 11/20/2022] Open
Abstract
The Wistar Kyoto (WKY) rat and the spontaneously hypertensive (SHR) rat inbred strains are well-established models for human crescentic glomerulonephritis (CRGN) and metabolic syndrome, respectively. Novel transgenic (Tg) strains add research opportunities and increase scientific value to well-established rat models. We have created two novel Tg strains using Sleeping Beauty transposon germline transgenesis, ubiquitously expressing green fluorescent protein (GFP) under the rat elongation factor 1 alpha (EF1a) promoter on the WKY and SHR genetic backgrounds. The Sleeping Beauty system functioned with high transgenesis efficiency; 75% of new rats born after embryo microinjections were transgene positive. By ligation-mediated PCR, we located the genome integration sites, confirming no exonic disruption and defining a single or low copy number of the transgenes in the new WKY-GFP and SHR-GFP Tg lines. We report GFP-bright expression in embryos, tissues and organs in both lines and show preliminaryin vitroandin vivoimaging data that demonstrate the utility of the new GFP-expressing lines for adoptive transfer, transplantation and fate mapping studies of CRGN, metabolic syndrome and other traits for which these strains have been extensively studied over the past four decades.
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Affiliation(s)
- Ana Isabel Garcia Diaz
- Division of Immunology and Inflammation, Imperial College London, London W2 1PG, UK MRC Clinical Sciences Centre and Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Ben Moyon
- Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
| | - Philip M Coan
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Neza Alfazema
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Lara Venda
- MRC Clinical Sciences Centre and Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Kevin Woollard
- Division of Immunology and Inflammation, Imperial College London, London W2 1PG, UK
| | - Tim Aitman
- MRC Clinical Sciences Centre and Department of Medicine, Imperial College London, London W12 0NN, UK Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
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