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Flynn J, Ahmadi MM, McFarland CT, Kubal MD, Taylor MA, Cheng Z, Torchia EC, Edwards MG. Crowdsourcing temporal transcriptomic coronavirus host infection data: Resources, guide, and novel insights. Biol Methods Protoc 2023; 8:bpad033. [PMID: 38107402 PMCID: PMC10723038 DOI: 10.1093/biomethods/bpad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/07/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
The emergence of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) reawakened the need to rapidly understand the molecular etiologies, pandemic potential, and prospective treatments of infectious agents. The lack of existing data on SARS-CoV-2 hampered early attempts to treat severe forms of coronavirus disease-2019 (COVID-19) during the pandemic. This study coupled existing transcriptomic data from severe acute respiratory syndrome-related coronavirus 1 (SARS-CoV-1) lung infection animal studies with crowdsourcing statistical approaches to derive temporal meta-signatures of host responses during early viral accumulation and subsequent clearance stages. Unsupervised and supervised machine learning approaches identified top dysregulated genes and potential biomarkers (e.g. CXCL10, BEX2, and ADM). Temporal meta-signatures revealed distinct gene expression programs with biological implications to a series of host responses underlying sustained Cxcl10 expression and Stat signaling. Cell cycle switched from G1/G0 phase genes, early in infection, to a G2/M gene signature during late infection that correlated with the enrichment of DNA damage response and repair genes. The SARS-CoV-1 meta-signatures were shown to closely emulate human SARS-CoV-2 host responses from emerging RNAseq, single cell, and proteomics data with early monocyte-macrophage activation followed by lymphocyte proliferation. The circulatory hormone adrenomedullin was observed as maximally elevated in elderly patients who died from COVID-19. Stage-specific correlations to compounds with potential to treat COVID-19 and future coronavirus infections were in part validated by a subset of twenty-four that are in clinical trials to treat COVID-19. This study represents a roadmap to leverage existing data in the public domain to derive novel molecular and biological insights and potential treatments to emerging human pathogens.
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Affiliation(s)
- James Flynn
- Illumina Corporation, San Diego, CA 92122, United States
| | - Mehdi M Ahmadi
- Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | | | | | - Mark A Taylor
- Bioinfo Solutions LLC, Parker, CO 80134, United States
| | - Zhang Cheng
- Illumina Corporation, San Diego, CA 92122, United States
| | - Enrique C Torchia
- Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
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Olsen MB, Huse C, de Sousa MML, Murphy SL, Sarno A, Obermann TS, Yang K, Holter JC, Jørgensen MJ, Christensen EE, Wang W, Ji P, Heggelund L, Hoel H, Dyrhol-Riise AM, Gregersen I, Aukrust P, Bjørås M, Halvorsen B, Dahl TB. DNA Repair Mechanisms are Activated in Circulating Lymphocytes of Hospitalized Covid-19 Patients. J Inflamm Res 2022; 15:6629-6644. [PMID: 36514358 PMCID: PMC9741826 DOI: 10.2147/jir.s379331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/20/2022] [Indexed: 12/12/2022] Open
Abstract
Purpose Reactive oxygen species (ROS) are an important part of the inflammatory response during infection but can also promote DNA damage. Due to the sustained inflammation in severe Covid-19, we hypothesized that hospitalized Covid-19 patients would be characterized by increased levels of oxidative DNA damage and dysregulation of the DNA repair machinery. Patients and Methods Levels of the oxidative DNA lesion 8-oxoG and levels of base excision repair (BER) proteins were measured in peripheral blood mononuclear cells (PBMC) from patients (8-oxoG, n = 22; BER, n = 17) and healthy controls (n = 10) (Cohort 1). Gene expression related to DNA repair was investigated in two independent cohorts of hospitalized Covid-19 patients (Cohort 1; 15 patents and 5 controls, Cohort 2; 15 patients and 6 controls), and by publicly available datasets. Results Patients and healthy controls showed comparable amounts of oxidative DNA damage as assessed by 8-oxoG while levels of several BER proteins were increased in Covid-19 patients, indicating enhanced DNA repair in acute Covid-19 disease. Furthermore, gene expression analysis demonstrated regulation of genes involved in BER and double strand break repair (DSBR) in PBMC of Covid-19 patients and expression level of several DSBR genes correlated with the degree of respiratory failure. Finally, by re-analyzing publicly available data, we found that the pathway Hallmark DNA repair was significantly more regulated in circulating immune cells during Covid-19 compared to influenza virus infection, bacterial pneumonia or acute respiratory infection due to seasonal coronavirus. Conclusion Although beneficial by protecting against DNA damage, long-term activation of the DNA repair machinery could also contribute to persistent inflammation, potentially through mechanisms such as the induction of cellular senescence. However, further studies that also include measurements of additional markers of DNA damage are required to determine the role and precise molecular mechanisms for DNA repair in SARS-CoV-2 infection.
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Affiliation(s)
- Maria Belland Olsen
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Camilla Huse
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Mirta Mittelstedt Leal de Sousa
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway,Proteomics and Modomics Experimental Core Facility (PROMEC), NTNU, Trondheim, Norway
| | - Sarah Louise Murphy
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Antonio Sarno
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway,Department of Fisheries and New Biomarine Industry, SINTEF Ocean, Trondheim, Norway
| | - Tobias Sebastian Obermann
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kuan Yang
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
| | - Jan Cato Holter
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Marte Jøntvedt Jørgensen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Erik Egeland Christensen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Wei Wang
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ping Ji
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lars Heggelund
- Department of Internal Medicine, Vestre Viken Hospital Trust, Drammen, Norway,Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Hedda Hoel
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway,Department of Medicine, Lovisenberg Diaconal Hospital, Oslo, Norway
| | - Anne Margarita Dyrhol-Riise
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Ida Gregersen
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway,Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Bente Halvorsen
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tuva Børresdatter Dahl
- Division of Critical Care and Emergencies, Oslo University Hospital, Oslo, Norway,Correspondence: Tuva Børresdatter Dahl, Division of Critical Care and Emergencies and Research Institute of Internal Medicine, Oslo University Hospital, Sognsvannsveien 20, Oslo, Norway, Tel +4723072786, Email
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Schilz JR, Dashner-Titus EJ, Simmons KA, Erdei E, Bolt AM, MacKenzie DA, Hudson LG. The immunotoxicity of natural and depleted uranium: From cells to people. Toxicol Appl Pharmacol 2022; 454:116252. [PMID: 36152676 PMCID: PMC10044422 DOI: 10.1016/j.taap.2022.116252] [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: 06/13/2022] [Revised: 08/30/2022] [Accepted: 09/16/2022] [Indexed: 10/31/2022]
Abstract
Uranium is a naturally occurring element found in the environment as a mixture of isotopes with differing radioactive properties. Enrichment of mined material results in depleted uranium waste with substantially reduced radioactivity but retains the capacity for chemical toxicity. Uranium mine and milling waste are dispersed by wind and rain leading to environmental exposures through soil, air, and water contamination. Uranium exposure is associated with numerous adverse health outcomes in humans, yet there is limited understanding of the effects of depleted uranium on the immune system. The purpose of this review is to summarize findings on uranium immunotoxicity obtained from cell, rodent and human population studies. We also highlight how each model contributes to an understanding of mechanisms that lead to immunotoxicity and limitations inherent within each system. Information from population, animal, and laboratory studies will be needed to significantly expand our knowledge of the contributions of depleted uranium to immune dysregulation, which may then inform prevention or intervention measures for exposed communities.
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Affiliation(s)
- Jodi R Schilz
- Division of Physical Therapy, School of Medicine, University of New Mexico, Albuquerque, NM, United States of America.
| | - Erica J Dashner-Titus
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States of America
| | - Karen A Simmons
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States of America
| | - Esther Erdei
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States of America
| | - Alicia M Bolt
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States of America
| | - Debra A MacKenzie
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States of America
| | - Laurie G Hudson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, United States of America
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Manolakou T, Verginis P, Boumpas DT. DNA Damage Response in the Adaptive Arm of the Immune System: Implications for Autoimmunity. Int J Mol Sci 2021; 22:5842. [PMID: 34072535 PMCID: PMC8198144 DOI: 10.3390/ijms22115842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 12/25/2022] Open
Abstract
In complex environments, cells have developed molecular responses to confront threats against the genome and achieve the maintenance of genomic stability assuring the transfer of undamaged DNA to their progeny. DNA damage response (DDR) mechanisms may be activated upon genotoxic or environmental agents, such as cytotoxic drugs or ultraviolet (UV) light, and during physiological processes requiring DNA transactions, to restore DNA alterations that may cause cellular malfunction and affect viability. In addition to the DDR, multicellular organisms have evolved specialized immune cells to respond and defend against infections. Both adaptive and innate immune cells are subjected to DDR processes, either as a prerequisite to the immune response, or as a result of random endogenous and exogenous insults. Aberrant DDR activities have been extensively studied in the immune cells of the innate arm, but not in adaptive immune cells. Here, we discuss how the aberrant DDR may lead to autoimmunity, with emphasis on the adaptive immune cells and the potential of therapeutic targeting.
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Affiliation(s)
- Theodora Manolakou
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece;
- School of Medicine, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Panayotis Verginis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 700 13 Heraklion, Greece;
- Laboratory of Immune Regulation and Tolerance, Division of Basic Sciences, University of Crete Medical School, 700 13 Heraklion, Greece
| | - Dimitrios T. Boumpas
- Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece;
- Joint Rheumatology Program, 4th Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, 124 62 Athens, Greece
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