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Gao L, Kyubwa EM, Starbird MA, Diaz de Leon J, Nguyen M, Rogers CJ, Menon N. Circulating miRNA profiles in COVID-19 patients and meta-analysis: implications for disease progression and prognosis. Sci Rep 2023; 13:21656. [PMID: 38065980 PMCID: PMC10709343 DOI: 10.1038/s41598-023-48227-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
We compared circulating miRNA profiles of hospitalized COVID-positive patients (n = 104), 27 with acute respiratory distress syndrome (ARDS) and age- and sex-matched healthy controls (n = 18) to identify miRNA signatures associated with COVID and COVID-induced ARDS. Meta-analysis incorporating data from published studies and our data was performed to identify a set of differentially expressed miRNAs in (1) COVID-positive patients versus healthy controls as well as (2) severe (ARDS+) COVID vs moderate COVID. Gene ontology enrichment analysis of the genes these miRNAs interact with identified terms associated with immune response, such as interferon and interleukin signaling, as well as viral genome activities associated with COVID disease and severity. Additionally, we observed downregulation of a cluster of miRNAs located on chromosome 14 (14q32) among all COVID patients. To predict COVID disease and severity, we developed machine learning models that achieved AUC scores between 0.81-0.93 for predicting disease, and between 0.71-0.81 for predicting severity, even across diverse studies with different sample types (plasma versus serum), collection methods, and library preparations. Our findings provide network and top miRNA feature insights into COVID disease progression and contribute to the development of tools for disease prognosis and management.
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Taliaferro LP, Agarwal RK, Coleman CN, DiCarlo AL, Hofmeyer KA, Loelius SG, Molinar-Inglis O, Tedesco DC, Satyamitra MM. Sex differences in radiation research. Int J Radiat Biol 2023; 100:466-485. [PMID: 37991728 PMCID: PMC10922591 DOI: 10.1080/09553002.2023.2283089] [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: 08/23/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023]
Abstract
PURPOSE The Sex Differences in Radiation Research workshop addressed the role of sex as a confounder in radiation research and its implication in real-world radiological and nuclear applications. METHODS In April 2022, HHS-wide partners from the Radiation and Nuclear Countermeasures Program, the Office of Research on Women's Health National Institutes of Health Office of Women's Health, U.S. Food and Drug Administration, and the Radiological and Nuclear Countermeasures Branch at the Biomedical Advanced Research and Development Authority conducted a workshop to address the scientific implication and knowledge gaps in understanding sex in basic and translational research. The goals of this workshop were to examine sex differences in 1. Radiation animal models and understand how these may affect radiation medical countermeasure development; 2. Biodosimetry and/or biomarkers used to assess acute radiation syndrome, delayed effects of acute radiation exposure, and/or predict major organ morbidities; 3. medical research that lacks representation from both sexes. In addition, regulatory policies that influence inclusion of women in research, and the gaps that exist in drug development and device clearance were discussed. Finally, real-world sex differences in human health scenarios were also considered. RESULTS This report provides an overview of the two-day workshop, and open discussion among academic investigators, industry researchers, and U.S. government representatives. CONCLUSIONS This meeting highlighted that current study designs lack the power to determine statistical significance based on sex, and much is unknown about the underlying factors that contribute to these differences. Investigators should accommodate both sexes in all stages of research to ensure that the outcome is robust, reproducible, and accurate, and will benefit public health.
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Affiliation(s)
- Lanyn P. Taliaferro
- Division of Allergy, Immunology, and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Radiation and Nuclear Countermeasures Program (RNCP), Rockville, MD, USA
| | - Rajeev K. Agarwal
- Office of Research on Women’s Health (ORWH), Office of the Director, NIH, Rockville, MD, USA
| | - C. Norman Coleman
- Radiation Research Program Division of Cancer Treatment and Diagnosis, Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute (NCI) and Administration for Strategic Preparedness and Response (ASPR), U.S. Department of Health and Human Services (HHS), Washington, DC, USA
| | - Andrea L. DiCarlo
- Division of Allergy, Immunology, and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Radiation and Nuclear Countermeasures Program (RNCP), Rockville, MD, USA
| | - Kimberly A. Hofmeyer
- Radiological and Nuclear Countermeasures Branch, Biomedical Advanced Research and Development Authority (BARDA), ASPR, HHS, Washington, DC, USA
| | - Shannon G. Loelius
- Radiological and Nuclear Countermeasures Branch, Biomedical Advanced Research and Development Authority (BARDA), ASPR, HHS, Washington, DC, USA
| | - Olivia Molinar-Inglis
- Previously RNCP, DAIT, NIAID, NIH; now Antivirals and Antitoxins Program, Division of CBRN Countermeasures, BARDA, ASPR, HHS, Washington, DC, USA
| | - Dana C. Tedesco
- Radiological and Nuclear Countermeasures Branch, Biomedical Advanced Research and Development Authority (BARDA), ASPR, HHS, Washington, DC, USA
| | - Merriline M. Satyamitra
- Division of Allergy, Immunology, and Transplantation (DAIT), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Radiation and Nuclear Countermeasures Program (RNCP), Rockville, MD, USA
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Shuryak I, Ghandhi SA, Laiakis EC, Garty G, Wu X, Ponnaiya B, Kosowski E, Pannkuk E, Kaur SP, Harken AD, Deoli N, Fornace AJ, Brenner DJ, Amundson SA. Biomarker integration for improved biodosimetry of mixed neutron + photon exposures. Sci Rep 2023; 13:10936. [PMID: 37414809 PMCID: PMC10325958 DOI: 10.1038/s41598-023-37906-3] [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: 03/02/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023] Open
Abstract
There is a persistent risk of a large-scale malicious or accidental exposure to ionizing radiation that may affect a large number of people. Exposure will consist of both a photon and neutron component, which will vary in magnitude between individuals and is likely to have profound impacts on radiation-induced diseases. To mitigate these potential disasters, there exists a need for novel biodosimetry approaches that can estimate the radiation dose absorbed by each person based on biofluid samples, and predict delayed effects. Integration of several radiation-responsive biomarker types (transcripts, metabolites, blood cell counts) by machine learning (ML) can improve biodosimetry. Here we integrated data from mice exposed to various neutron + photon mixtures, total 3 Gy dose, using multiple ML algorithms to select the strongest biomarker combinations and reconstruct radiation exposure magnitude and composition. We obtained promising results, such as receiver operating characteristic curve area of 0.904 (95% CI: 0.821, 0.969) for classifying samples exposed to ≥ 10% neutrons vs. < 10% neutrons, and R2 of 0.964 for reconstructing photon-equivalent dose (weighted by neutron relative biological effectiveness) for neutron + photon mixtures. These findings demonstrate the potential of combining various -omic biomarkers for novel biodosimetry.
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Affiliation(s)
- Igor Shuryak
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA.
| | - Shanaz A Ghandhi
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
| | - Evagelia C Laiakis
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - Guy Garty
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
| | - Xuefeng Wu
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
| | - Brian Ponnaiya
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
| | - Emma Kosowski
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Evan Pannkuk
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - Salan P Kaur
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
| | - Andrew D Harken
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
| | - Naresh Deoli
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
| | - Albert J Fornace
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - David J Brenner
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
| | - Sally A Amundson
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168Th Street, VC-11-234/5, New York, NY, 10032, USA
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Pannkuk EL, Laiakis EC, Garty G, Ponnaiya B, Wu X, Shuryak I, Ghandhi SA, Amundson SA, Brenner DJ, Fornace AJ. Variable Dose Rates in Realistic Radiation Exposures: Effects on Small Molecule Markers of Ionizing Radiation in the Murine Model. Radiat Res 2023; 200:1-12. [PMID: 37212727 PMCID: PMC10410530 DOI: 10.1667/rade-22-00211.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/27/2023] [Indexed: 05/23/2023]
Abstract
Novel biodosimetry assays for use in preparedness and response to potential malicious attacks or nuclear accidents would ideally provide accurate dose reconstruction independent of the idiosyncrasies of a complex exposure to ionizing radiation. Complex exposures will consist of dose rates spanning the low dose rates (LDR) to very high-dose rates (VHDR) that need to be tested for assay validation. Here, we investigate how a range of relevant dose rates affect metabolomic dose reconstruction at potentially lethal radiation exposures (8 Gy in mice) from an initial blast or subsequent fallout exposures compared to zero or sublethal exposures (0 or 3 Gy in mice) in the first 2 days, which corresponds to an integral time individuals will reach medical facilities after a radiological emergency. Biofluids (urine and serum) were collected from both male and female 9-10-week-old C57BL/6 mice at 1 and 2 days postirradiation (total doses of 0, 3 or 8 Gy) after a VHDR of 7 Gy/s. Additionally, samples were collected after a 2-day exposure consisting of a declining dose rate (1 to 0.004 Gy/min) recapitulating the 7:10 rule-of-thumb time dependency of nuclear fallout. Overall similar perturbations were observed in both urine and serum metabolite concentrations irrespective of sex or dose rate, with the exception of xanthurenic acid in urine (female specific) and taurine in serum (VHDR specific). In urine, we developed identical multiplex metabolite panels (N6, N6,N6-trimethyllysine, carnitine, propionylcarnitine, hexosamine-valine-isoleucine, and taurine) that could identify individuals receiving potentially lethal levels of radiation from the zero or sublethal cohorts with excellent sensitivity and specificity, with creatine increasing model performance at day 1. In serum, individuals receiving a 3 or 8 Gy exposure could be identified from their pre-irradiation samples with excellent sensitivity and specificity, however, due to a lower dose response the 3 vs. 8 Gy groups could not be distinguished from each other. Together with previous results, these data indicate that dose-rate-independent small molecule fingerprints have potential in novel biodosimetry assays.
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Affiliation(s)
- Evan L. Pannkuk
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC
- Center for Metabolomic Studies, Georgetown University, Washington, DC
| | - Evagelia C. Laiakis
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC
- Center for Metabolomic Studies, Georgetown University, Washington, DC
| | - Guy Garty
- Radiological Research Accelerator Facility, Columbia University, Irvington, New York
- Center for Radiological Research, Columbia University Irving Medical Center, New York, New York
| | - Brian Ponnaiya
- Center for Radiological Research, Columbia University Irving Medical Center, New York, New York
| | - Xuefeng Wu
- Center for Radiological Research, Columbia University Irving Medical Center, New York, New York
| | - Igor Shuryak
- Center for Radiological Research, Columbia University Irving Medical Center, New York, New York
| | - Shanaz A. Ghandhi
- Center for Radiological Research, Columbia University Irving Medical Center, New York, New York
| | - Sally A. Amundson
- Center for Radiological Research, Columbia University Irving Medical Center, New York, New York
| | - David J. Brenner
- Center for Radiological Research, Columbia University Irving Medical Center, New York, New York
| | - Albert J. Fornace
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC
- Center for Metabolomic Studies, Georgetown University, Washington, DC
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