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Shi X, Chen Y, Shi M, Gao F, Huang L, Wang W, Wei D, Shi C, Yu Y, Xia X, Song N, Chen X, Distler JHW, Lu C, Chen J, Wang J. The novel molecular mechanism of pulmonary fibrosis: insight into lipid metabolism from reanalysis of single-cell RNA-seq databases. Lipids Health Dis 2024; 23:98. [PMID: 38570797 PMCID: PMC10988923 DOI: 10.1186/s12944-024-02062-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024] Open
Abstract
Pulmonary fibrosis (PF) is a severe pulmonary disease with limited available therapeutic choices. Recent evidence increasingly points to abnormal lipid metabolism as a critical factor in PF pathogenesis. Our latest research identifies the dysregulation of low-density lipoprotein (LDL) is a new risk factor for PF, contributing to alveolar epithelial and endothelial cell damage, and fibroblast activation. In this study, we first integrative summarize the published literature about lipid metabolite changes found in PF, including phospholipids, glycolipids, steroids, fatty acids, triglycerides, and lipoproteins. We then reanalyze two single-cell RNA-sequencing (scRNA-seq) datasets of PF, and the corresponding lipid metabolomic genes responsible for these lipids' biosynthesis, catabolism, transport, and modification processes are uncovered. Intriguingly, we found that macrophage is the most active cell type in lipid metabolism, with almost all lipid metabolic genes being altered in macrophages of PF. In type 2 alveolar epithelial cells, lipid metabolic differentially expressed genes (DEGs) are primarily associated with the cytidine diphosphate diacylglycerol pathway, cholesterol metabolism, and triglyceride synthesis. Endothelial cells are partly responsible for sphingomyelin, phosphatidylcholine, and phosphatidylethanolamines reprogramming as their metabolic genes are dysregulated in PF. Fibroblasts may contribute to abnormal cholesterol, phosphatidylcholine, and phosphatidylethanolamine metabolism in PF. Therefore, the reprogrammed lipid profiles in PF may be attributed to the aberrant expression of lipid metabolic genes in different cell types. Taken together, these insights underscore the potential of targeting lipid metabolism in developing innovative therapeutic strategies, potentially leading to extended overall survival in individuals affected by PF.
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Affiliation(s)
- Xiangguang Shi
- Department of Dermatology, Huashan Hospital, and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yahui Chen
- Human Phenome Institute, and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China Fudan University, Shanghai, China
| | - Mengkun Shi
- Department of Thoracic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Fei Gao
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, China
| | - Lihao Huang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism & Integrative Biology, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Wei Wang
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, China
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Dong Wei
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, China
| | - Chenyi Shi
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yuexin Yu
- Human Phenome Institute, and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China Fudan University, Shanghai, China
| | - Xueyi Xia
- Human Phenome Institute, and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China Fudan University, Shanghai, China
| | - Nana Song
- Department of Nephrology, Zhongshan Hospital, Fudan University, Fudan Zhangjiang Institute, Shanghai, People's Republic of China
| | - Xiaofeng Chen
- Department of Thoracic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Jörg H W Distler
- Department of Internal Medicine 3 and Institute for Clinical Immunology, University of Erlangen, Nuremberg, Germany
| | - Chenqi Lu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.
| | - Jingyu Chen
- Wuxi Lung Transplant Center, Wuxi People's Hospital affiliated to Nanjing Medical University, Wuxi, China.
- Center for Lung Transplantation, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Jiucun Wang
- Department of Dermatology, Huashan Hospital, and State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
- Human Phenome Institute, and Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China Fudan University, Shanghai, China.
- Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Beijing, China.
- Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China.
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Muntean M, Briciu V, Lupse M, Colcear D, Macicasan RV, Csiszer A, Manole A, Radulescu A. Effects of COVID-19 on the Liver and Mortality in Patients with SARS-CoV-2 Pneumonia Caused by Delta and Non-Delta Variants: An Analysis in a Single Centre. Pharmaceuticals (Basel) 2023; 17:3. [PMID: 38275989 PMCID: PMC10820137 DOI: 10.3390/ph17010003] [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: 09/26/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 01/27/2024] Open
Abstract
The aim of this study was to ascertain patient characteristics, outcomes, and liver injuries in patients infected with different SARS-CoV-2 variants. Data from consecutive adult patients with severe/critical COVID-19 admitted to our hospital during the peak month of the Delta wave were compared to the ancestral, Alpha, and Omicron waves. The dataset of 551 hospitalized patients was similar in the Delta/non-Delta waves. At admission and discharge, the median aminotransferase levels were normal or slightly increased. During the Delta wave (172 vs. 379 non-Delta patients), more patients died (OR 1.69, 95%CI 1.09-2.56) or had liver injury at discharge (alanine aminotransferase, ALT ≥ 2 ULN) (OR 1.97, 95%CI 1.08-3.54). In-hospital mortality was associated with age, lung injury, intensive care unit admission, number of and cardiovascular comorbidities, diabetes, chronic kidney disease, and all inflammatory biomarkers. Serious liver injury at admission (ALT ≥ 5 × ULN) was significantly associated with in-hospital mortality (OR = 7.9, 95%CI 2-28.9). At discharge, drug-induced liver injury (DILI) was found in patients treated with remdesivir, ALT ≥ 2 ULN (OR = 2.62, 95%CI 1.22-5.75). Treatment with dexamethasone, remdesivir, and immunomodulators showed improved survival, OR = 0.50 (95%CI 0.33-0.77). Regardless of the variant and treatment options, less than 2% of patients displayed serious liver injury, which was not found to be a death predictor in multivariable analysis.
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Affiliation(s)
- Monica Muntean
- Department of Infectious Diseases and Epidemiology, The “Iuliu Hatieganu” University of Medicine and Pharmacy, 400348 Cluj-Napoca, Romania; (M.M.); (M.L.); (R.V.M.); (A.C.); (A.M.); (A.R.)
- The Teaching Hospital of Infectious Diseases, 400348 Cluj-Napoca, Romania;
| | - Violeta Briciu
- Department of Infectious Diseases and Epidemiology, The “Iuliu Hatieganu” University of Medicine and Pharmacy, 400348 Cluj-Napoca, Romania; (M.M.); (M.L.); (R.V.M.); (A.C.); (A.M.); (A.R.)
- The Teaching Hospital of Infectious Diseases, 400348 Cluj-Napoca, Romania;
| | - Mihaela Lupse
- Department of Infectious Diseases and Epidemiology, The “Iuliu Hatieganu” University of Medicine and Pharmacy, 400348 Cluj-Napoca, Romania; (M.M.); (M.L.); (R.V.M.); (A.C.); (A.M.); (A.R.)
- The Teaching Hospital of Infectious Diseases, 400348 Cluj-Napoca, Romania;
| | - Doina Colcear
- The Teaching Hospital of Infectious Diseases, 400348 Cluj-Napoca, Romania;
| | - Raul Vlad Macicasan
- Department of Infectious Diseases and Epidemiology, The “Iuliu Hatieganu” University of Medicine and Pharmacy, 400348 Cluj-Napoca, Romania; (M.M.); (M.L.); (R.V.M.); (A.C.); (A.M.); (A.R.)
| | - Agnes Csiszer
- Department of Infectious Diseases and Epidemiology, The “Iuliu Hatieganu” University of Medicine and Pharmacy, 400348 Cluj-Napoca, Romania; (M.M.); (M.L.); (R.V.M.); (A.C.); (A.M.); (A.R.)
| | - Alexandra Manole
- Department of Infectious Diseases and Epidemiology, The “Iuliu Hatieganu” University of Medicine and Pharmacy, 400348 Cluj-Napoca, Romania; (M.M.); (M.L.); (R.V.M.); (A.C.); (A.M.); (A.R.)
| | - Amanda Radulescu
- Department of Infectious Diseases and Epidemiology, The “Iuliu Hatieganu” University of Medicine and Pharmacy, 400348 Cluj-Napoca, Romania; (M.M.); (M.L.); (R.V.M.); (A.C.); (A.M.); (A.R.)
- The Teaching Hospital of Infectious Diseases, 400348 Cluj-Napoca, Romania;
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Cousins HC, Kline AS, Wang C, Qu Y, Zengel J, Carette J, Wang M, Altman RB, Luo Y, Cong L. Integrative analysis of functional genomic screening and clinical data identifies a protective role for spironolactone in severe COVID-19. CELL REPORTS METHODS 2023; 3:100503. [PMID: 37529368 PMCID: PMC10243122 DOI: 10.1016/j.crmeth.2023.100503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 04/01/2023] [Accepted: 05/23/2023] [Indexed: 08/03/2023]
Abstract
We demonstrate that integrative analysis of CRISPR screening datasets enables network-based prioritization of prescription drugs modulating viral entry in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by developing a network-based approach called Rapid proXimity Guidance for Repurposing Investigational Drugs (RxGRID). We use our results to guide a propensity-score-matched, retrospective cohort study of 64,349 COVID-19 patients, showing that a top candidate drug, spironolactone, is associated with improved clinical prognosis, measured by intensive care unit (ICU) admission and mechanical ventilation rates. Finally, we show that spironolactone exerts a dose-dependent inhibitory effect on viral entry in human lung epithelial cells. Our RxGRID method presents a computational framework, implemented as an open-source software package, enabling genomics researchers to identify drugs likely to modulate a molecular phenotype of interest based on high-throughput screening data. Our results, derived from this method and supported by experimental and clinical analysis, add additional supporting evidence for a potential protective role of the potassium-sparing diuretic spironolactone in severe COVID-19.
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Affiliation(s)
- Henry C. Cousins
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
- Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Adrienne Sarah Kline
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Chengkun Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yuanhao Qu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James Zengel
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jan Carette
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mengdi Wang
- Department of Electronic Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Russ B. Altman
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yuan Luo
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Le Cong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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