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Dehghan Z, Mirmotalebisohi SA, Mozafar M, Sameni M, Saberi F, Derakhshanfar A, Moaedi J, Zohrevand H, Zali H. Deciphering the similarities and disparities of molecular mechanisms behind respiratory epithelium response to HCoV-229E and SARS-CoV-2 and drug repurposing, a systems biology approach. Daru 2024; 32:215-235. [PMID: 38652363 PMCID: PMC11087451 DOI: 10.1007/s40199-024-00507-0] [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: 09/17/2022] [Accepted: 02/08/2024] [Indexed: 04/25/2024] Open
Abstract
PURPOSE Identifying the molecular mechanisms behind SARS-CoV-2 disparities and similarities will help find new treatments. The present study determines networks' shared and non-shared (specific) crucial elements in response to HCoV-229E and SARS-CoV-2 viruses to recommend candidate medications. METHODS We retrieved the omics data on respiratory cells infected with HCoV-229E and SARS-CoV-2, constructed PPIN and GRN, and detected clusters and motifs. Using a drug-gene interaction network, we determined the similarities and disparities of mechanisms behind their host response and drug-repurposed. RESULTS CXCL1, KLHL21, SMAD3, HIF1A, and STAT1 were the shared DEGs between both viruses' protein-protein interaction network (PPIN) and gene regulatory network (GRN). The NPM1 was a specific critical node for HCoV-229E and was a Hub-Bottleneck shared between PPI and GRN in HCoV-229E. The HLA-F, ADCY5, TRIM14, RPF1, and FGA were the seed proteins in subnetworks of the SARS-CoV-2 PPI network, and HSPA1A and RPL26 proteins were the seed in subnetworks of the PPI network of HCOV-229E. TRIM14, STAT2, and HLA-F played the same role for SARS-CoV-2. Top enriched KEGG pathways included cell cycle and proteasome in HCoV-229E and RIG-I-like receptor, Chemokine, Cytokine-cytokine, NOD-like receptor, and TNF signaling pathways in SARS-CoV-2. We suggest some candidate medications for COVID-19 patient lungs, including Noscapine, Isoetharine mesylate, Cycloserine, Ethamsylate, Cetylpyridinium, Tretinoin, Ixazomib, Vorinostat, Venetoclax, Vorinostat, Ixazomib, Venetoclax, and epoetin alfa for further in-vitro and in-vivo investigations. CONCLUSION We suggested CXCL1, KLHL21, SMAD3, HIF1A, and STAT1, ADCY5, TRIM14, RPF1, and FGA, STAT2, and HLA-F as critical genes and Cetylpyridinium, Cycloserine, Noscapine, Ethamsylate, Epoetin alfa, Isoetharine mesylate, Ribavirin, and Tretinoin drugs to study further their importance in treating COVID-19 lung complications.
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Affiliation(s)
- Zeinab Dehghan
- Department of Comparative Biomedical Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Amir Mirmotalebisohi
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Mozafar
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Marzieh Sameni
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Saberi
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amin Derakhshanfar
- Department of Comparative Biomedical Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
- Center of Comparative and Experimental Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Javad Moaedi
- Center of Comparative and Experimental Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Zohrevand
- Student Research Committee, Department of Biomedical Engineering and Medical Physics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Biomedical Engineering and Medical Physics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hakimeh Zali
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Taylor BC, Steinthal LH, Dias M, Yalamanchili HK, Ochsner SA, Zapata GE, Mehta NR, McKenna NJ, Young NL, Nuotio-Antar AM. Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress. Epigenetics Chromatin 2024; 17:12. [PMID: 38678237 PMCID: PMC11055387 DOI: 10.1186/s13072-024-00536-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Regulation of the thermogenic response by brown adipose tissue (BAT) is an important component of energy homeostasis with implications for the treatment of obesity and diabetes. Our preliminary analyses of RNA-Seq data uncovered many nodes representing epigenetic modifiers that are altered in BAT in response to chronic thermogenic activation. Thus, we hypothesized that chronic thermogenic activation broadly alters epigenetic modifications of DNA and histones in BAT. RESULTS Motivated to understand how BAT function is regulated epigenetically, we developed a novel method for the first-ever unbiased top-down proteomic quantitation of histone modifications in BAT and validated our results with a multi-omic approach. To test our hypothesis, wildtype male C57BL/6J mice were housed under chronic conditions of thermoneutral temperature (TN, 28°C), mild cold/room temperature (RT, 22°C), or severe cold (SC, 8°C) and BAT was analyzed for DNA methylation and histone modifications. Methylation of promoters and intragenic regions in genomic DNA decrease in response to chronic cold exposure. Integration of DNA methylation and RNA expression datasets suggest a role for epigenetic modification of DNA in regulation of gene expression in response to cold. In response to cold housing, we observe increased bulk acetylation of histones H3.2 and H4, increased histone H3.2 proteoforms with di- and trimethylation of lysine 9 (K9me2 and K9me3), and increased histone H4 proteoforms with acetylation of lysine 16 (K16ac) in BAT. CONCLUSIONS Our results reveal global epigenetically-regulated transcriptional "on" and "off" signals in murine BAT in response to varying degrees of chronic cold stimuli and establish a novel methodology to quantitatively study histones in BAT, allowing for direct comparisons to decipher mechanistic changes during the thermogenic response. Additionally, we make histone PTM and proteoform quantitation, RNA splicing, RRBS, and transcriptional footprint datasets available as a resource for future research.
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Affiliation(s)
- Bethany C Taylor
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Loic H Steinthal
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
| | - Michelle Dias
- Department of Pediatrics, Division of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Hari Krishna Yalamanchili
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Division of Neurology, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Scott A Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Gladys E Zapata
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
| | - Nitesh R Mehta
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA
| | - Neil J McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nicolas L Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA.
| | - Alli M Nuotio-Antar
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA.
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Kole A, Bag AK, Pal AJ, De D. Generic model to unravel the deeper insights of viral infections: an empirical application of evolutionary graph coloring in computational network biology. BMC Bioinformatics 2024; 25:74. [PMID: 38365632 PMCID: PMC10874019 DOI: 10.1186/s12859-024-05690-0] [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: 11/22/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
PURPOSE Graph coloring approach has emerged as a valuable problem-solving tool for both theoretical and practical aspects across various scientific disciplines, including biology. In this study, we demonstrate the graph coloring's effectiveness in computational network biology, more precisely in analyzing protein-protein interaction (PPI) networks to gain insights about the viral infections and its consequences on human health. Accordingly, we propose a generic model that can highlight important hub proteins of virus-associated disease manifestations, changes in disease-associated biological pathways, potential drug targets and respective drugs. We test our model on SARS-CoV-2 infection, a highly transmissible virus responsible for the COVID-19 pandemic. The pandemic took significant human lives, causing severe respiratory illnesses and exhibiting various symptoms ranging from fever and cough to gastrointestinal, cardiac, renal, neurological, and other manifestations. METHODS To investigate the underlying mechanisms of SARS-CoV-2 infection-induced dysregulation of human pathobiology, we construct a two-level PPI network and employed a differential evolution-based graph coloring (DEGCP) algorithm to identify critical hub proteins that might serve as potential targets for resolving the associated issues. Initially, we concentrate on the direct human interactors of SARS-CoV-2 proteins to construct the first-level PPI network and subsequently applied the DEGCP algorithm to identify essential hub proteins within this network. We then build a second-level PPI network by incorporating the next-level human interactors of the first-level hub proteins and use the DEGCP algorithm to predict the second level of hub proteins. RESULTS We first identify the potential crucial hub proteins associated with SARS-CoV-2 infection at different levels. Through comprehensive analysis, we then investigate the cellular localization, interactions with other viral families, involvement in biological pathways and processes, functional attributes, gene regulation capabilities as transcription factors, and their associations with disease-associated symptoms of these identified hub proteins. Our findings highlight the significance of these hub proteins and their intricate connections with disease pathophysiology. Furthermore, we predict potential drug targets among the hub proteins and identify specific drugs that hold promise in preventing or treating SARS-CoV-2 infection and its consequences. CONCLUSION Our generic model demonstrates the effectiveness of DEGCP algorithm in analyzing biological PPI networks, provides valuable insights into disease biology, and offers a basis for developing novel therapeutic strategies for other viral infections that may cause future pandemic.
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Affiliation(s)
- Arnab Kole
- Department of Computer Application, The Heritage Academy, Kolkata, W.B., 700107, India.
| | - Arup Kumar Bag
- Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | | | - Debashis De
- Department of Computer Science and Engineering, Maulana Abul Kalam Azad University of Technology, Nadia, W.B., 741249, India
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Taylor BC, Steinthal LH, Dias M, Yalamanchili HK, Ochsner SA, Zapata GE, Mehta NR, McKenna NJ, Young NL, Nuotio-Antar AM. Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.30.551059. [PMID: 38328142 PMCID: PMC10849524 DOI: 10.1101/2023.07.30.551059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Regulation of the thermogenic response by brown adipose tissue (BAT) is an important component of energy homeostasis with implications for the treatment of obesity and diabetes. Our preliminary analyses uncovered many nodes representing epigenetic modifiers that are altered in BAT in response to chronic thermogenic activation. Thus, we hypothesized that chronic thermogenic activation broadly alters epigenetic modifications of DNA and histones in BAT. Motivated to understand how BAT function is regulated epigenetically, we developed a novel method for the first-ever unbiased top-down proteomic quantitation of histone modifications in BAT and validated our results with a multi-omic approach. To test our hypothesis, wildtype male C57BL/6J mice were housed under chronic conditions of thermoneutral temperature (TN, 28.8°C), mild cold/room temperature (RT, 22°C), or severe cold (SC, 8°C) and BAT was analyzed for DNA methylation and histone modifications. Methylation of promoters and intragenic regions in genomic DNA decrease in response to chronic cold exposure. Integration of DNA methylation and RNA expression data suggest a role for epigenetic modification of DNA in gene regulation in response to cold. In response to cold housing, we observe increased bulk acetylation of histones H3.2 and H4, increased histone H3.2 proteoforms with di- and trimethylation of lysine 9 (K9me2 and K9me3), and increased histone H4 proteoforms with acetylation of lysine 16 (K16ac) in BAT. Taken together, our results reveal global epigenetically-regulated transcriptional "on" and "off" signals in murine BAT in response to varying degrees of chronic cold stimuli and establish a novel methodology to quantitatively study histones in BAT, allowing for direct comparisons to decipher mechanistic changes during the thermogenic response. Additionally, we make histone PTM and proteoform quantitation, RNA splicing, RRBS, and transcriptional footprint datasets available as a resource for future research.
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Affiliation(s)
- Bethany C. Taylor
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX
| | - Loic H. Steinthal
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
| | - Michelle Dias
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX
| | - Hari K. Yalamanchili
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
- Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX
| | - Scott A. Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Gladys E. Zapata
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
| | - Nitesh R. Mehta
- Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX
| | - Neil J. McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
| | - Nicolas L. Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
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Rojas-Quintero J, Ochsner SA, New F, Divakar P, Yang CX, Wu TD, Robinson J, Chandrashekar DS, Banovich NE, Rosas IO, Sauler M, Kheradmand F, Gaggar A, Margaroli C, San Jose Estepar R, McKenna NJ, Polverino F. Spatial Transcriptomics Resolve an Emphysema-Specific Lymphoid Follicle B Cell Signature in Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2024; 209:48-58. [PMID: 37934672 PMCID: PMC10870877 DOI: 10.1164/rccm.202303-0507le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/15/2023] [Indexed: 11/09/2023] Open
Abstract
Rationale: Within chronic obstructive pulmonary disease (COPD), emphysema is characterized by a significant yet partially understood B cell immune component. Objectives: To characterize the transcriptomic signatures from lymphoid follicles (LFs) in ever-smokers without COPD and patients with COPD with varying degrees of emphysema. Methods: Lung sections from 40 patients with COPD and ever-smokers were used for LF proteomic and transcriptomic spatial profiling. Formalin- and O.C.T.-fixed lung samples obtained from biopsies or lung explants were assessed for LF presence. Emphysema measurements were obtained from clinical chest computed tomographic scans. High-confidence transcriptional target intersection analyses were conducted to resolve emphysema-induced transcriptional networks. Measurements and Main Results: Overall, 115 LFs from ever-smokers and Global Initiative for Chronic Obstructive Lung Disease (GOLD) 1-2 and GOLD 3-4 patients were analyzed. No LFs were found in never-smokers. Differential gene expression analysis revealed significantly increased expression of LF assembly and B cell marker genes in subjects with severe emphysema. High-confidence transcriptional analysis revealed activation of an abnormal B cell activity signature in LFs (q-value = 2.56E-111). LFs from patients with GOLD 1-2 COPD with emphysema showed significantly increased expression of genes associated with antigen presentation, inflammation, and B cell activation and proliferation. LFs from patients with GOLD 1-2 COPD without emphysema showed an antiinflammatory profile. The extent of centrilobular emphysema was significantly associated with genes involved in B cell maturation and antibody production. Protein-RNA network analysis showed that LFs in emphysema have a unique signature skewed toward chronic B cell activation. Conclusions: An off-targeted B cell activation within LFs is associated with autoimmune-mediated emphysema pathogenesis.
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Affiliation(s)
| | - Scott A. Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Felicia New
- Spatial Data Analysis Services, Nanostring Biotechnologies, Seattle, Washington
| | - Prajan Divakar
- Spatial Data Analysis Services, Nanostring Biotechnologies, Seattle, Washington
| | - Chen Xi Yang
- Center for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Jerid Robinson
- Field Application Scientists, Nanostring Biotechnologies, Seattle, Washington
| | | | | | | | - Maor Sauler
- Pulmonary and Critical Care Medicine, Yale University, New Haven, Connecticut
| | - Farrah Kheradmand
- Pulmonary Division, Department of Medicine, and
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas
| | - Amit Gaggar
- Pulmonary and Critical Care Medicine, and
- Birmingham Veterans Affairs Medical Center, Birmingham, Alabama; and
| | - Camilla Margaroli
- Pathology – Division of Cellular and Molecular Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Raul San Jose Estepar
- Applied Chest Imaging Laboratory, Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Neil J. McKenna
- Spatial Data Analysis Services, Nanostring Biotechnologies, Seattle, Washington
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Celada SI, Lim CX, Carisey AF, Ochsner SA, Arce Deza CF, Rexie P, Poli De Frias F, Cardenas-Castillo R, Polverino F, Hengstschläger M, Tsoyi K, McKenna NJ, Kheradmand F, Weichhart T, Rosas IO, Van Kaer L, Celada LJ. SHP2 promotes sarcoidosis severity by inhibiting SKP2-targeted ubiquitination of TBET in CD8 + T cells. Sci Transl Med 2023; 15:eade2581. [PMID: 37703351 PMCID: PMC11126869 DOI: 10.1126/scitranslmed.ade2581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 08/24/2023] [Indexed: 09/15/2023]
Abstract
Sarcoidosis is an interstitial lung disease (ILD) characterized by interferon-γ (IFN-γ) and T-box expressed in T cells (TBET) dysregulation. Although one-third of patients progress from granulomatous inflammation to severe lung damage, the molecular mechanisms underlying this process remain unclear. Here, we found that pharmacological inhibition of phosphorylated SH2-containing protein tyrosine phosphatase-2 (pSHP2), a facilitator of aberrant IFN-γ abundance, decreased large granuloma formation and macrophage infiltration in the lungs of mice with sarcoidosis-like disease. Positive treatment outcomes were dependent on the effective enhancement of TBET ubiquitination within CD8+ T cells. Mechanistically, we identified a posttranslational modification pathway in which the E3 F-box protein S-phase kinase-associated protein 2 (SKP2) targets TBET for ubiquitination in T cells under normal conditions. However, this pathway was disrupted by aberrant pSHP2 signaling in CD8+ T cells from patients with progressive pulmonary sarcoidosis and end-stage disease. Ex vivo inhibition of pSHP2 in CD8+ T cells from patients with end-stage sarcoidosis enhanced TBET ubiquitination and suppressed IFN-γ and collagen synthesis. Therefore, these studies provided new mechanistic insights into the SHP2-dependent posttranslational regulation of TBET and identified SHP2 inhibition as a potential therapeutic intervention against severe sarcoidosis. Furthermore, these studies also suggest that the small-molecule SHP2 inhibitor SHP099 might be used as a therapeutic measure against human diseases linked to TBET or ubiquitination.
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Affiliation(s)
- Sherly I. Celada
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Clarice X. Lim
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Alexandre F. Carisey
- William T. Shearer Center for Human Immunobiology, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Cell and Molecular Biology, St. Jude Children’s Hospital, Memphis, TN 38105, USA
| | - Scott A. Ochsner
- Department of Molecular and Cellular Biology, Houston, TX 77030, USA
| | - Carlos F. Arce Deza
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Praveen Rexie
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Fernando Poli De Frias
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Mout Sinai Medical Center, Miami Beach, FL 33140, USA
| | - Rafael Cardenas-Castillo
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Francesca Polverino
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Markus Hengstschläger
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Konstantin Tsoyi
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neil J. McKenna
- Department of Molecular and Cellular Biology, Houston, TX 77030, USA
| | - Farrah Kheradmand
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey, Houston, TX 77030, USA
| | - Thomas Weichhart
- Center of Pathobiochemistry and Genetics, Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria
| | - Ivan O. Rosas
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Luc Van Kaer
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232 USA
| | - Lindsay J. Celada
- Department of Medicine, Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232 USA
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Ochsner SA, Pedroza M, Pillich RT, Krishnan V, Konicek BW, Dow ER, Park SY, Agarwal SK, McKenna NJ. IL17A Blockade with Ixekizumab Suppresses MuvB Signaling in Clinical Psoriasis. J Invest Dermatol 2023; 143:1689-1699. [PMID: 36967086 DOI: 10.1016/j.jid.2023.03.1658] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
Abstract
Unbiased informatics approaches have the potential to generate insights into uncharacterized signaling pathways in human disease. In this study, we generated longitudinal transcriptomic profiles of plaque psoriasis lesions from patients enrolled in a clinical trial of the anti-IL17A antibody ixekizumab (IXE). This dataset was then computed against a curated matrix of over 700 million data points derived from published psoriasis and signaling node perturbation transcriptomic and chromatin immunoprecipitation-sequencing datasets. We observed substantive enrichment within both psoriasis-induced and IXE-repressed gene sets of transcriptional targets of members of the MuvB complex, a master regulator of the mitotic cell cycle. These gene sets were similarly enriched for pathways involved in the regulation of the G2/M transition of the cell cycle. Moreover, transcriptional targets for MuvB nodes were strongly enriched within IXE-repressed genes whose expression levels correlated strongly with the extent and severity of the psoriatic disease. In models of human keratinocyte proliferation, genes encoding MuvB nodes were transcriptionally repressed by IXE, and depletion of MuvB nodes reduced cell proliferation. Finally, we made the expression and regulatory networks that supported this study available as a freely accessible, cloud-based hypothesis generation platform. Our study positions inhibition of MuvB signaling as an important determinant of the therapeutic impact of IXE in psoriasis.
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Affiliation(s)
- Scott A Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Mesias Pedroza
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Rudolf T Pillich
- Department of Medicine, University of California San Diego, California, USA
| | | | | | - Ernst R Dow
- Eli Lilly and Company, Indianapolis, Indiana, USA
| | | | - Sandeep K Agarwal
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Neil J McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA.
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Ishola AA, Joshi T, Abdulai SI, Tijjani H, Pundir H, Chandra S. Molecular basis for the repurposing of histamine H2-receptor antagonist to treat COVID-19. J Biomol Struct Dyn 2022; 40:5785-5802. [PMID: 33491579 PMCID: PMC7852284 DOI: 10.1080/07391102.2021.1873191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022]
Abstract
With the world threatened by a second surge in the number of Coronavirus cases, there is an urgent need for the development of effective treatment for the novel coronavirus (COVID-19). Recently, global attention has turned to preliminary reports on the promising anti-COVID-19 effect of histamine H2-receptor antagonists (H2RAs), most especially Famotidine. Therefore, this study was designed to exploit a possible molecular basis for the efficacy of H2RAs against coronavirus. Molecular docking was performed between four H2RAs, Cimetidine, Famotidine, Nizatidine, Ranitidine, and three non-structural proteins viz. NSP3, NSP7/8 complex, and NSP9. Thereafter, a 100 ns molecular dynamics simulation was carried out with the most outstanding ligands to determine the stability. Thereafter, Famotidine and Cimetidine were subjected to gene target prediction analysis using HitPickV2 and eXpression2Kinases server to determine the possible network of genes associated with their anti-COVID activities. Results obtained from molecular docking showed the superiority of Famotidine and Cimetidine compared to other H2RAs with a higher binding affinity to all selected targets. Molecular dynamic simulation and MMPBSA results revealed that Famotidine as well as Cimetidine bind to non-structural proteins more efficiently with high stability over 100 ns. Results obtained suggest that Famotidine and Cimetidine could be a viable option to treat COVID-19 with a mechanism of action that involves the inhibition of viral replication through the inhibition of non-structural proteins. Therefore, Famotidineand Cimetidine qualify for further study as a potential treatment for COVID-19.
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Affiliation(s)
- Ahmed A. Ishola
- Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Nigeria
| | - Tanuja Joshi
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
- Department of Botany, Kumaun University, S.S.J Campus, Almora, Uttarakhand, India
| | | | - Habibu Tijjani
- Department of Biochemistry, Natural Product Research Laboratory, Bauchi State University, Gadau, Nigeria
| | - Hemlata Pundir
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
- Department of Botany, Kumaun University, S.S.J Campus, Almora, Uttarakhand, India
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Ochsner SA, Pillich RT, Rawool D, Grethe JS, McKenna NJ. Transcriptional regulatory networks of circulating immune cells in type 1 diabetes: A community knowledgebase. iScience 2022; 25:104581. [PMID: 35832893 PMCID: PMC9272393 DOI: 10.1016/j.isci.2022.104581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 12/02/2022] Open
Abstract
Investigator-generated transcriptomic datasets interrogating circulating immune cell (CIC) gene expression in clinical type 1 diabetes (T1D) have underappreciated re-use value. Here, we repurposed these datasets to create an open science environment for the generation of hypotheses around CIC signaling pathways whose gain or loss of function contributes to T1D pathogenesis. We firstly computed sets of genes that were preferentially induced or repressed in T1D CICs and validated these against community benchmarks. We then inferred and validated signaling node networks regulating expression of these gene sets, as well as differentially expressed genes in the original underlying T1D case:control datasets. In a set of three use cases, we demonstrated how informed integration of these networks with complementary digital resources supports substantive, actionable hypotheses around signaling pathway dysfunction in T1D CICs. Finally, we developed a federated, cloud-based web resource that exposes the entire data matrix for unrestricted access and re-use by the research community. Re-use of transcriptomic type 1 diabetes (T1D) circulating immune cells (CICs) datasets We generated transcriptional regulatory networks for T1D CICs Use cases generate substantive hypotheses around signaling pathway dysfunction in T1D CICs Networks are freely accessible on the web for re-use by the research community
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Affiliation(s)
- Scott A. Ochsner
- Department of Molecular, Baylor College of Medicine, Houston, TX 77030, USA
- Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rudolf T. Pillich
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Deepali Rawool
- Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeffrey S. Grethe
- Center for Research in Biological Systems, University of California San Diego, La Jolla, CA 92093, USA
| | - Neil J. McKenna
- Department of Molecular, Baylor College of Medicine, Houston, TX 77030, USA
- Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Corresponding author
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10
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Rodrigues P, Costa RS, Henriques R. Enrichment analysis on regulatory subspaces: A novel direction for the superior description of cellular responses to SARS-CoV-2. Comput Biol Med 2022; 146:105443. [PMID: 35533463 PMCID: PMC9040465 DOI: 10.1016/j.compbiomed.2022.105443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/13/2022] [Accepted: 03/20/2022] [Indexed: 12/16/2022]
Abstract
STATEMENT Enrichment analysis of cell transcriptional responses to SARS-CoV-2 infection from biclustering solutions yields broader coverage and superior enrichment of GO terms and KEGG pathways against alternative state-of-the-art machine learning solutions, thus aiding knowledge extraction. MOTIVATION AND METHODS The comprehensive understanding of the impacts of SARS-CoV-2 virus on infected cells is still incomplete. This work aims at comparing the role of state-of-the-art machine learning approaches in the study of cell regulatory processes affected and induced by the SARS-CoV-2 virus using transcriptomic data from both infectable cell lines available in public databases and in vivo samples. In particular, we assess the relevance of clustering, biclustering and predictive modeling methods for functional enrichment. Statistical principles to handle scarcity of observations, high data dimensionality, and complex gene interactions are further discussed. In particular, and without loos of generalization ability, the proposed methods are applied to study the differential regulatory response of lung cell lines to SARS-CoV-2 (α-variant) against RSV, IAV (H1N1), and HPIV3 viruses. RESULTS Gathered results show that, although clustering and predictive algorithms aid classic stances to functional enrichment analysis, more recent pattern-based biclustering algorithms significantly improve the number and quality of enriched GO terms and KEGG pathways with controlled false positive risks. Additionally, a comparative analysis of these results is performed to identify potential pathophysiological characteristics of COVID-19. These are further compared to those identified by other authors for the same virus as well as related ones such as SARS-CoV-1. The findings are particularly relevant given the lack of other works utilizing more complex machine learning algorithms within this context.
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Affiliation(s)
- Pedro Rodrigues
- IDMEC, Instituto Superior Tecnico, Universidade de Lisboa, Lisbon, Portugal; INESC-ID and Instituto Superior Tecnico, Universidade de Lisboa, Lisbon, Portugal
| | - Rafael S Costa
- IDMEC, Instituto Superior Tecnico, Universidade de Lisboa, Lisbon, Portugal; LAQV-REQUIMTE, DQ, NOVA School of Science and Technology, Caparica, Portugal
| | - Rui Henriques
- INESC-ID and Instituto Superior Tecnico, Universidade de Lisboa, Lisbon, Portugal.
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11
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Al-Lami RA. Explaining the Potential Beneficial Roles of Hormone Replacement Therapy in COVID-19 Infection Among Postmenopausal Women. Menopause 2022; 29:636. [PMID: 35231004 DOI: 10.1097/gme.0000000000001970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Rasha A Al-Lami
- Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School, The University of Texas Health Science, Center at Houston, Houston, TX
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12
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Chen KY, De Angulo A, Guo X, More A, Ochsner SA, Lopez E, Saul D, Pang W, Sun Y, McKenna NJ, Tong Q. Adipocyte-Specific Ablation of PU.1 Promotes Energy Expenditure and Ameliorates Metabolic Syndrome in Aging Mice. FRONTIERS IN AGING 2022; 2:803482. [PMID: 35822007 PMCID: PMC9261351 DOI: 10.3389/fragi.2021.803482] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/13/2021] [Indexed: 12/03/2022]
Abstract
Objective: Although PU.1/Spi1 is known as a master regulator for macrophage development and function, we have reported previously that it is also expressed in adipocytes and is transcriptionally induced in obesity. Here, we investigated the role of adipocyte PU.1 in the development of the age-associated metabolic syndrome. Methods: We generated mice with adipocyte-specific PU.1 knockout, assessed metabolic changes in young and older adult PU.1fl/fl (control) and AdipoqCre PU.1fl/fl (aPU.1KO) mice, including body weight, body composition, energy expenditure, and glucose homeostasis. We also performed transcriptional analyses using RNA-Sequencing of adipocytes from these mice. Results: aPU.1KO mice have elevated energy expenditure at a young age and decreased adiposity and increased insulin sensitivity in later life. Corroborating these observations, transcriptional network analysis indicated the existence of validated, adipocyte PU.1-modulated regulatory hubs that direct inflammatory and thermogenic gene expression programs. Conclusion: Our data provide evidence for a previously uncharacterized role of PU.1 in the development of age-associated obesity and insulin resistance.
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Affiliation(s)
- Ke Yun Chen
- Department of Pediatrics, USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
| | - Alejandra De Angulo
- Department of Pediatrics, USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
| | - Xin Guo
- Department of Pediatrics, USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
- Department of Nutrition and Food Hygiene, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Aditya More
- Department of Pediatrics, USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
| | - Scott A. Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Eduardo Lopez
- Department of Pediatrics, USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
| | - David Saul
- Department of Pediatrics, USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
| | - Weijun Pang
- Department of Pediatrics, USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
- Northwestern University of Agriculture and Forestry, Yangling, China
| | - Yuxiang Sun
- Department of Pediatrics, USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
- Department of Nutrition, Texas A&M University, College Station, TX, United States
| | - Neil J. McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
- *Correspondence: Neil J. McKenna, ; Qiang Tong,
| | - Qiang Tong
- Department of Pediatrics, USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Huffington Center on Aging, Houston, TX, United States
- Department of Medicine, Baylor College of Medicine, Huffington Center on Aging, Houston, TX, United States
- *Correspondence: Neil J. McKenna, ; Qiang Tong,
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13
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Identification of transcriptional regulatory network associated with response of host epithelial cells to SARS-CoV-2. Sci Rep 2021; 11:23928. [PMID: 34907210 PMCID: PMC8671548 DOI: 10.1038/s41598-021-03309-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/01/2021] [Indexed: 12/15/2022] Open
Abstract
Identification of transcriptional regulatory mechanisms and signaling networks involved in the response of host cells to infection by SARS-CoV-2 is a powerful approach that provides a systems biology view of gene expression programs involved in COVID-19 and may enable the identification of novel therapeutic targets and strategies to mitigate the impact of this disease. In this study, our goal was to identify a transcriptional regulatory network that is associated with gene expression changes between samples infected by SARS-CoV-2 and those that are infected by other respiratory viruses to narrow the results on those enriched or specific to SARS-CoV-2. We combined a series of recently developed computational tools to identify transcriptional regulatory mechanisms involved in the response of epithelial cells to infection by SARS-CoV-2, and particularly regulatory mechanisms that are specific to this virus when compared to other viruses. In addition, using network-guided analyses, we identified kinases associated with this network. The results identified pathways associated with regulation of inflammation (MAPK14) and immunity (BTK, MBX) that may contribute to exacerbate organ damage linked with complications of COVID-19. The regulatory network identified herein reflects a combination of known hits and novel candidate pathways supporting the novel computational pipeline presented herein to quickly narrow down promising avenues of investigation when facing an emerging and novel disease such as COVID-19.
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14
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Beyond the canonical role of TFIIB in eukaryotic transcription. Curr Genet 2021; 68:61-67. [PMID: 34797379 PMCID: PMC8602988 DOI: 10.1007/s00294-021-01223-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 02/06/2023]
Abstract
The role of general transcription factor TFIIB in transcription extends well beyond its evolutionarily conserved function in initiation. Chromatin localization studies demonstrating binding of TFIIB to both the 5’ and 3’ ends of genes in a diverse set of eukaryotes strongly suggested a rather unexpected role of the factor in termination. TFIIB indeed plays a role in termination of transcription. TFIIB occupancy of the 3’ end is possibly due to its interaction with the termination factors residing there. Interaction of the promoter-bound TFIIB with factors occupying the 3’ end of a gene may be the basis of transcription-dependent gene looping. The proximity of the terminator-bound factors with the promoter in a gene loop has the potential to terminate promoter-initiated upstream anti-sense transcription thereby conferring promoter directionality. TFIIB, therefore, is emerging as a factor with pleiotropic roles in the transcription cycle. This could be the reason for preferential targeting of TFIIB by viruses. Further studies are needed to understand the critical role of TFIIB in viral pathogenesis in the context of its newly identified roles in termination, gene looping and promoter directionality.
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15
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McDonald JT, Enguita FJ, Taylor D, Griffin RJ, Priebe W, Emmett MR, Sajadi MM, Harris AD, Clement J, Dybas JM, Aykin-Burns N, Guarnieri JW, Singh LN, Grabham P, Baylin SB, Yousey A, Pearson AN, Corry PM, Saravia-Butler A, Aunins TR, Sharma S, Nagpal P, Meydan C, Foox J, Mozsary C, Cerqueira B, Zaksas V, Singh U, Wurtele ES, Costes SV, Davanzo GG, Galeano D, Paccanaro A, Meinig SL, Hagan RS, Bowman NM, Wolfgang MC, Altinok S, Sapoval N, Treangen TJ, Moraes-Vieira PM, Vanderburg C, Wallace DC, Schisler JC, Mason CE, Chatterjee A, Meller R, Beheshti A. Role of miR-2392 in driving SARS-CoV-2 infection. Cell Rep 2021; 37:109839. [PMID: 34624208 PMCID: PMC8481092 DOI: 10.1016/j.celrep.2021.109839] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/13/2021] [Accepted: 09/24/2021] [Indexed: 02/08/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provide an exciting avenue toward antiviral therapeutics. From patient transcriptomic data, we determined that a circulating miRNA, miR-2392, is directly involved with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) machinery during host infection. Specifically, we show that miR-2392 is key in driving downstream suppression of mitochondrial gene expression, increasing inflammation, glycolysis, and hypoxia, as well as promoting many symptoms associated with coronavirus disease 2019 (COVID-19) infection. We demonstrate that miR-2392 is present in the blood and urine of patients positive for COVID-19 but is not present in patients negative for COVID-19. These findings indicate the potential for developing a minimally invasive COVID-19 detection method. Lastly, using in vitro human and in vivo hamster models, we design a miRNA-based antiviral therapeutic that targets miR-2392, significantly reduces SARS-CoV-2 viability in hamsters, and may potentially inhibit a COVID-19 disease state in humans.
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Affiliation(s)
- J Tyson McDonald
- COVID-19 International Research Team; Georgetown University School of Medicine, Washington, DC 20007, USA
| | - Francisco J Enguita
- COVID-19 International Research Team; Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Deanne Taylor
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert J Griffin
- COVID-19 International Research Team; University of Arkansas for Medical Sciences, Little Rock, AK 72211, USA
| | - Waldemar Priebe
- COVID-19 International Research Team; University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark R Emmett
- COVID-19 International Research Team; University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | - Anthony D Harris
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jean Clement
- University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Joseph M Dybas
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Joseph W Guarnieri
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Larry N Singh
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Peter Grabham
- COVID-19 International Research Team; Columbia University, New York, NY 10032, USA
| | - Stephen B Baylin
- COVID-19 International Research Team; Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Aliza Yousey
- COVID-19 International Research Team; Morehouse School of Medicine, Atlanta, GA 30310, USA
| | | | - Peter M Corry
- COVID-19 International Research Team; University of Arkansas for Medical Sciences, Little Rock, AK 72211, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team; Logyx LLC, Mountain View, CA 94043, USA; NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | - Sadhana Sharma
- University of Colorado Boulder, Boulder, CO 80303, USA; Sachi Bioworks Inc., Boulder, CO 80301, USA
| | - Prashant Nagpal
- Sachi Bioworks Inc., Boulder, CO 80301, USA; Antimicrobial Regeneration Consortium, Boulder Labs, Boulder, CO 80301, USA; Quantum Biology Inc., Boulder, CO 80301, USA
| | - Cem Meydan
- Weill Cornell Medicine, New York, NY 10065, USA
| | | | | | - Bianca Cerqueira
- COVID-19 International Research Team; KBR Space & Science, San Antonio, TX 78235, USA; United States Air Force School of Aerospace Medicine, Lackland AFB, San Antonio, TX 78236, USA
| | - Viktorija Zaksas
- COVID-19 International Research Team; University of Chicago, Chicago, IL 60615, USA
| | - Urminder Singh
- COVID-19 International Research Team; Iowa State University, Ames, IA 50011, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team; Iowa State University, Ames, IA 50011, USA
| | | | | | - Diego Galeano
- COVID-19 International Research Team; Fundação Getulio Vargas, Rio de Janeiro, Brazil; National University of Asuncion, San Lorenzo, Central, Paraguay
| | - Alberto Paccanaro
- COVID-19 International Research Team; Fundação Getulio Vargas, Rio de Janeiro, Brazil; University of London, Egham Hill, Egham, UK
| | - Suzanne L Meinig
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert S Hagan
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natalie M Bowman
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Selin Altinok
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | | | | | - Douglas C Wallace
- COVID-19 International Research Team; The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan C Schisler
- COVID-19 International Research Team; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christopher E Mason
- COVID-19 International Research Team; Weill Cornell Medicine, New York, NY 10065, USA; New York Genome Center, New York, NY, USA
| | - Anushree Chatterjee
- COVID-19 International Research Team; University of Colorado Boulder, Boulder, CO 80303, USA; Sachi Bioworks Inc., Boulder, CO 80301, USA; Antimicrobial Regeneration Consortium, Boulder Labs, Boulder, CO 80301, USA
| | - Robert Meller
- COVID-19 International Research Team; Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Afshin Beheshti
- COVID-19 International Research Team; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.
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16
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McDonald JT, Enguita FJ, Taylor D, Griffin RJ, Priebe W, Emmett MR, Sajadi MM, Harris AD, Clement J, Dybas JM, Aykin-Burns N, Guarnieri JW, Singh LN, Grabham P, Baylin SB, Yousey A, Pearson AN, Corry PM, Saravia-Butler A, Aunins TR, Sharma S, Nagpal P, Meydan C, Foox J, Mozsary C, Cerqueira B, Zaksas V, Singh U, Wurtele ES, Costes SV, Davanzo GG, Galeano D, Paccanaro A, Meinig SL, Hagan RS, Bowman NM, Wolfgang MC, Altinok S, Sapoval N, Treangen TJ, Moraes-Vieira PM, Vanderburg C, Wallace DC, Schisler J, Mason CE, Chatterjee A, Meller R, Beheshti A. The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33948587 DOI: 10.1101/2021.04.23.441024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provides an exciting avenue towards antiviral therapeutics. From patient transcriptomic data, we have discovered a circulating miRNA, miR-2392, that is directly involved with SARS-CoV-2 machinery during host infection. Specifically, we show that miR-2392 is key in driving downstream suppression of mitochondrial gene expression, increasing inflammation, glycolysis, and hypoxia as well as promoting many symptoms associated with COVID-19 infection. We demonstrate miR-2392 is present in the blood and urine of COVID-19 positive patients, but not detected in COVID-19 negative patients. These findings indicate the potential for developing a novel, minimally invasive, COVID-19 detection method. Lastly, using in vitro human and in vivo hamster models, we have developed a novel miRNA-based antiviral therapeutic that targets miR-2392, significantly reduces SARS-CoV-2 viability in hamsters and may potentially inhibit a COVID-19 disease state in humans.
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17
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Park A, Harris LK. Gene Expression Meta-Analysis Reveals Interferon-Induced Genes Associated With SARS Infection in Lungs. Front Immunol 2021; 12:694355. [PMID: 34367154 PMCID: PMC8342995 DOI: 10.3389/fimmu.2021.694355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/05/2021] [Indexed: 01/01/2023] Open
Abstract
Background Severe Acute Respiratory Syndrome (SARS) corona virus (CoV) infections are a serious public health threat because of their pandemic-causing potential. This work is the first to analyze mRNA expression data from SARS infections through meta-analysis of gene signatures, possibly identifying therapeutic targets associated with major SARS infections. Methods This work defines 37 gene signatures representing SARS-CoV, Middle East Respiratory Syndrome (MERS)-CoV, and SARS-CoV2 infections in human lung cultures and/or mouse lung cultures or samples and compares them through Gene Set Enrichment Analysis (GSEA). To do this, positive and negative infectious clone SARS (icSARS) gene panels are defined from GSEA-identified leading-edge genes between two icSARS-CoV derived signatures, both from human cultures. GSEA then is used to assess enrichment and identify leading-edge icSARS panel genes between icSARS gene panels and 27 other SARS-CoV gene signatures. The meta-analysis is expanded to include five MERS-CoV and three SARS-CoV2 gene signatures. Genes associated with SARS infection are predicted by examining the intersecting membership of GSEA-identified leading-edges across gene signatures. Results Significant enrichment (GSEA p<0.001) is observed between two icSARS-CoV derived signatures, and those leading-edge genes defined the positive (233 genes) and negative (114 genes) icSARS panels. Non-random significant enrichment (null distribution p<0.001) is observed between icSARS panels and all verification icSARSvsmock signatures derived from human cultures, from which 51 over- and 22 under-expressed genes are shared across leading-edges with 10 over-expressed genes already associated with icSARS infection. For the icSARSvsmock mouse signature, significant, non-random significant enrichment held for only the positive icSARS panel, from which nine genes are shared with icSARS infection in human cultures. Considering other SARS strains, significant, non-random enrichment (p<0.05) is observed across signatures derived from other SARS strains for the positive icSARS panel. Five positive icSARS panel genes, CXCL10, OAS3, OASL, IFIT3, and XAF1, are found across mice and human signatures regardless of SARS strains. Conclusion The GSEA-based meta-analysis approach used here identifies genes with and without reported associations with SARS-CoV infections, highlighting this approach’s predictability and usefulness in identifying genes that have potential as therapeutic targets to preclude or overcome SARS infections.
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Affiliation(s)
- Amber Park
- Harris Interdisciplinary Research, Davenport University, Grand Rapids, MI, United States
| | - Laura K Harris
- Harris Interdisciplinary Research, Davenport University, Grand Rapids, MI, United States.,Institute for Cyber-Enabled Research, Michigan State University, East Lansing, MI, United States
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18
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Zapata RC, Chaudry BS, Valencia ML, Zhang D, Ochsner SA, McKenna NJ, Osborn O. Conserved immunomodulatory transcriptional networks underlie antipsychotic-induced weight gain. Transl Psychiatry 2021; 11:405. [PMID: 34294678 PMCID: PMC8296828 DOI: 10.1038/s41398-021-01528-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/05/2021] [Accepted: 07/07/2021] [Indexed: 12/20/2022] Open
Abstract
Although antipsychotics, such as olanzapine, are effective in the management of psychiatric conditions, some patients experience excessive antipsychotic-induced weight gain (AIWG). To illuminate pathways underlying AIWG, we compared baseline blood gene expression profiles in two cohorts of mice that were either prone (AIWG-P) or resistant (AIWG-R) to weight gain in response to olanzapine treatment for two weeks. We found that transcripts elevated in AIWG-P mice relative to AIWG-R are enriched for high-confidence transcriptional targets of numerous inflammatory and immunomodulatory signaling nodes. Moreover, these nodes are themselves enriched for genes whose disruption in mice is associated with reduced body fat mass and slow postnatal weight gain. In addition, we identified gene expression profiles in common between our mouse AIWG-P gene set and an existing human AIWG-P gene set whose regulation by immunomodulatory transcription factors is highly conserved between species. Finally, we identified striking convergence between mouse AIWG-P transcriptional regulatory networks and those associated with body weight and body mass index in humans. We propose that immunomodulatory transcriptional networks drive AIWG, and that these networks have broader conserved roles in whole body-metabolism.
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Affiliation(s)
- Rizaldy C. Zapata
- grid.266100.30000 0001 2107 4242Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Besma S. Chaudry
- grid.266100.30000 0001 2107 4242Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Mariela Lopez Valencia
- grid.266100.30000 0001 2107 4242Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Dinghong Zhang
- grid.266100.30000 0001 2107 4242Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Scott A. Ochsner
- grid.39382.330000 0001 2160 926XSignaling Pathways Project and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Neil J. McKenna
- grid.39382.330000 0001 2160 926XSignaling Pathways Project and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Olivia Osborn
- Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
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19
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Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. Cell Rep 2021; 36:109364. [PMID: 34214467 PMCID: PMC8220945 DOI: 10.1016/j.celrep.2021.109364] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/25/2021] [Accepted: 06/17/2021] [Indexed: 12/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) variants govern transmissibility, responsiveness to vaccination, and disease severity. In a screen for new models of SARS-CoV-2 infection, we identify human H522 lung adenocarcinoma cells as naturally permissive to SARS-CoV-2 infection despite complete absence of angiotensin-converting enzyme 2 (ACE2) expression. Remarkably, H522 infection requires the E484D S variant; viruses expressing wild-type S are not infectious. Anti-S monoclonal antibodies differentially neutralize SARS-CoV-2 E484D S in H522 cells as compared to ACE2-expressing cells. Sera from vaccinated individuals block this alternative entry mechanism, whereas convalescent sera are less effective. Although the H522 receptor remains unknown, depletion of surface heparan sulfates block H522 infection. Temporally resolved transcriptomic and proteomic profiling reveal alterations in cell cycle and the antiviral host cell response, including MDA5-dependent activation of type I interferon signaling. These findings establish an alternative SARS-CoV-2 host cell receptor for the E484D SARS-CoV-2 variant, which may impact tropism of SARS-CoV-2 and consequently human disease pathogenesis.
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20
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Salgado-Albarrán M, Navarro-Delgado EI, Del Moral-Morales A, Alcaraz N, Baumbach J, González-Barrios R, Soto-Reyes E. Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection. NPJ Syst Biol Appl 2021; 7:21. [PMID: 34031419 PMCID: PMC8144203 DOI: 10.1038/s41540-021-00181-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/08/2021] [Indexed: 02/04/2023] Open
Abstract
COVID-19 is an infection caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome coronavirus 2), which has caused a global outbreak. Current research efforts are focused on the understanding of the molecular mechanisms involved in SARS-CoV-2 infection in order to propose drug-based therapeutic options. Transcriptional changes due to epigenetic regulation are key host cell responses to viral infection and have been studied in SARS-CoV and MERS-CoV; however, such changes are not fully described for SARS-CoV-2. In this study, we analyzed multiple transcriptomes obtained from cell lines infected with MERS-CoV, SARS-CoV, and SARS-CoV-2, and from COVID-19 patient-derived samples. Using integrative analyses of gene co-expression networks and de-novo pathway enrichment, we characterize different gene modules and protein pathways enriched with Transcription Factors or Epifactors relevant for SARS-CoV-2 infection. We identified EP300, MOV10, RELA, and TRIM25 as top candidates, and more than 60 additional proteins involved in the epigenetic response during viral infection that has therapeutic potential. Our results show that targeting the epigenetic machinery could be a feasible alternative to treat COVID-19.
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Affiliation(s)
- Marisol Salgado-Albarrán
- grid.7220.70000 0001 2157 0393Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico ,grid.6936.a0000000123222966Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Erick I. Navarro-Delgado
- grid.419167.c0000 0004 1777 1207Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Aylin Del Moral-Morales
- grid.7220.70000 0001 2157 0393Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
| | - Nicolas Alcaraz
- grid.5254.60000 0001 0674 042XThe Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jan Baumbach
- grid.9026.d0000 0001 2287 2617Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany ,grid.10825.3e0000 0001 0728 0170Computational BioMedicine Lab, Institute of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Rodrigo González-Barrios
- grid.419167.c0000 0004 1777 1207Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Ernesto Soto-Reyes
- grid.7220.70000 0001 2157 0393Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
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21
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O'Brien MJ, Ansari A. Critical Involvement of TFIIB in Viral Pathogenesis. Front Mol Biosci 2021; 8:669044. [PMID: 33996913 PMCID: PMC8119876 DOI: 10.3389/fmolb.2021.669044] [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: 02/17/2021] [Accepted: 04/08/2021] [Indexed: 11/23/2022] Open
Abstract
Viral infections and the harm they cause to their host are a perpetual threat to living organisms. Pathogenesis and subsequent spread of infection requires replication of the viral genome and expression of structural and non-structural proteins of the virus. Generally, viruses use transcription and translation machinery of the host cell to achieve this objective. The viral genome encodes transcriptional regulators that alter the expression of viral and host genes by manipulating initiation and termination steps of transcription. The regulation of the initiation step is often through interactions of viral factors with gene specific factors as well as general transcription factors (GTFs). Among the GTFs, TFIIB (Transcription Factor IIB) is a frequent target during viral pathogenesis. TFIIB is utilized by a plethora of viruses including human immunodeficiency virus, herpes simplex virus, vaccinia virus, Thogoto virus, hepatitis virus, Epstein-Barr virus and gammaherpesviruses to alter gene expression. A number of viral transcriptional regulators exhibit a direct interaction with host TFIIB in order to accomplish expression of their genes and to repress host transcription. Some viruses have evolved proteins with a three-dimensional structure very similar to TFIIB, demonstrating the importance of TFIIB for viral persistence. Upon viral infection, host transcription is selectively altered with viral transcription benefitting. The nature of viral utilization of TFIIB for expression of its own genes, along with selective repression of host antiviral genes and downregulation of general host transcription, makes TFIIB a potential candidate for antiviral therapies.
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Affiliation(s)
- Michael J O'Brien
- Department of Biological Science, Wayne State University, Detroit, MI, United States
| | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI, United States
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22
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Bissig-Choisat B, Alves-Bezerra M, Zorman B, Ochsner SA, Barzi M, Legras X, Yang D, Borowiak M, Dean AM, York RB, Galvan NTN, Goss J, Lagor WR, Moore DD, Cohen DE, McKenna NJ, Sumazin P, Bissig KD. A human liver chimeric mouse model for non-alcoholic fatty liver disease. JHEP Rep 2021; 3:100281. [PMID: 34036256 PMCID: PMC8138774 DOI: 10.1016/j.jhepr.2021.100281] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 12/11/2022] Open
Abstract
Background & Aims The accumulation of neutral lipids within hepatocytes underlies non-alcoholic fatty liver disease (NAFLD), which affects a quarter of the world's population and is associated with hepatitis, cirrhosis, and hepatocellular carcinoma. Despite insights gained from both human and animal studies, our understanding of NAFLD pathogenesis remains limited. To better study the molecular changes driving the condition we aimed to generate a humanised NAFLD mouse model. Methods We generated TIRF (transgene-free Il2rg -/-/Rag2 -/-/Fah -/-) mice, populated their livers with human hepatocytes, and fed them a Western-type diet for 12 weeks. Results Within the same chimeric liver, human hepatocytes developed pronounced steatosis whereas murine hepatocytes remained normal. Unbiased metabolomics and lipidomics revealed signatures of clinical NAFLD. Transcriptomic analyses showed that molecular responses diverged sharply between murine and human hepatocytes, demonstrating stark species differences in liver function. Regulatory network analysis indicated close agreement between our model and clinical NAFLD with respect to transcriptional control of cholesterol biosynthesis. Conclusions These NAFLD xenograft mice reveal an unexpected degree of evolutionary divergence in food metabolism and offer a physiologically relevant, experimentally tractable model for studying the pathogenic changes invoked by steatosis. Lay summary Fatty liver disease is an emerging health problem, and as there are no good experimental animal models, our understanding of the condition is poor. We here describe a novel humanised mouse system and compare it with clinical data. The results reveal that the human cells in the mouse liver develop fatty liver disease upon a Western-style fatty diet, whereas the mouse cells appear normal. The molecular signature (expression profiles) of the human cells are distinct from the mouse cells and metabolic analysis of the humanised livers mimic the ones observed in humans with fatty liver. This novel humanised mouse system can be used to study human fatty liver disease.
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Key Words
- ALP, alkaline phosphatase
- ALT, alanine aminotransferase
- AST, aspartate aminotransferase
- CBPEGs, cholesterol biosynthesis pathway enzyme genes
- CE, cholesteryl ester
- CER, ceramide
- CHHs, chimeric human hepatocytes
- CMHs, chimeric mouse hepatocytes
- CT, confidence transcript
- DAG, diacylglycerol
- DCER, dihydroceramide
- DEG, differentially expressed gene
- FA, fatty acid
- FAH, fumarylacetoacetate hydrolase
- FFA, free fatty acid
- GGT, gamma-glutamyl transpeptidase
- HCC, hepatocellular carcinoma
- HCER, hexosylceramide
- HCT, high confidence transcriptional target
- Human disease modelling
- Humanised mice
- LCER, lactosylceramide
- LPC, lysophosphatidylcholine
- LPE, lysophosphatidylethanolamine
- Lipid metabolism
- MAG, monoacylglycerol
- MUFA, monounsaturated fatty acid
- NAFLD, non-alcoholic fatty liver disease
- NASH, non-alcoholic steatohepatitis
- NC, normal chow
- NTBC, nitisinone
- Non-alcoholic fatty liver disease
- PC, phosphatidylcholine
- PE, phosphatidylethanolamine
- PI, phosphatidylinositol
- PNPLA3, patatin-like-phospholipase domain-containing protein 3
- PUFA, polyunsaturated free FA
- SM, sphingomyelin
- SREBP, sterol regulatory element-binding protein
- Steatosis
- TAG, triacylglycerol
- TIRF, transgene-free Il2rg-/-/Rag2-/-/Fah-/-
- WD, Western-type diet
- hALB, human albumin
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Affiliation(s)
| | - Michele Alves-Bezerra
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Barry Zorman
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Scott A. Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Mercedes Barzi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC, USA
| | - Xavier Legras
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC, USA
| | - Diane Yang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Malgorzata Borowiak
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Institute for Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz Universtiy, Poznan, Poland
| | - Adam M. Dean
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Robert B. York
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | | | - John Goss
- Department of Surgery, Texas Children’s Hospital, Houston, TX, USA
| | - William R. Lagor
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - David D. Moore
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - David E. Cohen
- Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Neil J. McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Pavel Sumazin
- Texas Children’s Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Karl-Dimiter Bissig
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC, USA
- Y.T. and Alice Chen Pediatric Genetics and Genomics Research Center, Duke University, Durham, NC, USA
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
- Duke Cancer Institute, Duke University, Durham, NC, USA
- Corresponding author. Address: Duke University, Division of Medical Genetics, 905 South LaSalle street, Durham, NC-27708, USA. Tel.: +1 919 660 0761; fax: +1 919 660 0762.
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23
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Puray-Chavez M, LaPak KM, Schrank TP, Elliott JL, Bhatt DP, Agajanian MJ, Jasuja R, Lawson DQ, Davis K, Rothlauf PW, Jo H, Lee N, Tenneti K, Eschbach JE, Mugisha CS, Vuong HR, Bailey AL, Hayes DN, Whelan SP, Horani A, Brody SL, Goldfarb D, Major MB, Kutluay SB. Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.01.433431. [PMID: 33688646 PMCID: PMC7941617 DOI: 10.1101/2021.03.01.433431] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Established in vitro models for SARS-CoV-2 infection are limited and include cell lines of non-human origin and those engineered to overexpress ACE2, the cognate host cell receptor. We identified human H522 lung adenocarcinoma cells as naturally permissive to SARS-CoV-2 infection despite complete absence of ACE2. Infection of H522 cells required the SARS-CoV-2 spike protein, though in contrast to ACE2-dependent models, spike alone was not sufficient for H522 infection. Temporally resolved transcriptomic and proteomic profiling revealed alterations in cell cycle and the antiviral host cell response, including MDA5-dependent activation of type-I interferon signaling. Focused chemical screens point to important roles for clathrin-mediated endocytosis and endosomal cathepsins in SARS-CoV-2 infection of H522 cells. These findings imply the utilization of an alternative SARS-CoV-2 host cell receptor which may impact tropism of SARS-CoV-2 and consequently human disease pathogenesis.
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Affiliation(s)
- Maritza Puray-Chavez
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Kyle M. LaPak
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Travis P. Schrank
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Jennifer L. Elliott
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Dhaval P. Bhatt
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Megan J. Agajanian
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ria Jasuja
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Dana Q. Lawson
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Keanu Davis
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Paul W. Rothlauf
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
- Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Heejoon Jo
- University of Tennessee Health Science Center for Cancer Research, Department of Medicine, Division of Hematology and Oncology, University of Tennessee, Memphis, TN, USA
| | - Nakyung Lee
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Kasyap Tenneti
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Jenna E. Eschbach
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Christian Shema Mugisha
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Hung R. Vuong
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Adam L. Bailey
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - D. Neil Hayes
- University of Tennessee Health Science Center for Cancer Research, Department of Medicine, Division of Hematology and Oncology, University of Tennessee, Memphis, TN, USA
| | - Sean P.J. Whelan
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Amjad Horani
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
- Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA
| | - Steven L. Brody
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University in St Louis, St Louis, Mo
| | - Dennis Goldfarb
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
- Institute for Informatics, Washington University in St. Louis, St. Louis, MO, USA
| | - M. Ben Major
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, USA
- Department of Otolaryngology, Washington University in St. Louis, St. Louis, MO, USA
| | - Sebla B. Kutluay
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
- Lead Contact
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24
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STAT2 signaling restricts viral dissemination but drives severe pneumonia in SARS-CoV-2 infected hamsters. Nat Commun 2020; 11:5838. [PMID: 33203860 PMCID: PMC7672082 DOI: 10.1038/s41467-020-19684-y] [Citation(s) in RCA: 174] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/27/2020] [Indexed: 12/15/2022] Open
Abstract
Emergence of SARS-CoV-2 causing COVID-19 has resulted in hundreds of thousands of deaths. In search for key targets of effective therapeutics, robust animal models mimicking COVID-19 in humans are urgently needed. Here, we show that Syrian hamsters, in contrast to mice, are highly permissive to SARS-CoV-2 and develop bronchopneumonia and strong inflammatory responses in the lungs with neutrophil infiltration and edema, further confirmed as consolidations visualized by micro-CT alike in clinical practice. Moreover, we identify an exuberant innate immune response as key player in pathogenesis, in which STAT2 signaling plays a dual role, driving severe lung injury on the one hand, yet restricting systemic virus dissemination on the other. Our results reveal the importance of STAT2-dependent interferon responses in the pathogenesis and virus control during SARS-CoV-2 infection and may help rationalizing new strategies for the treatment of COVID-19 patients.
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