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Day JD, Park S, Ranard BL, Singh H, Chow CC, Vodovotz Y. Divergent COVID-19 Disease Trajectories Predicted by a DAMP-Centered Immune Network Model. Front Immunol 2021; 12:754127. [PMID: 34777366 PMCID: PMC8582279 DOI: 10.3389/fimmu.2021.754127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/04/2021] [Indexed: 01/08/2023] Open
Abstract
COVID-19 presentations range from mild to moderate through severe disease but also manifest with persistent illness or viral recrudescence. We hypothesized that the spectrum of COVID-19 disease manifestations was a consequence of SARS-CoV-2-mediated delay in the pathogen-associated molecular pattern (PAMP) response, including dampened type I interferon signaling, thereby shifting the balance of the immune response to be dominated by damage-associated molecular pattern (DAMP) signaling. To test the hypothesis, we constructed a parsimonious mechanistic mathematical model. After calibration of the model for initial viral load and then by varying a few key parameters, we show that the core model generates four distinct viral load, immune response and associated disease trajectories termed “patient archetypes”, whose temporal dynamics are reflected in clinical data from hospitalized COVID-19 patients. The model also accounts for responses to corticosteroid therapy and predicts that vaccine-induced neutralizing antibodies and cellular memory will be protective, including from severe COVID-19 disease. This generalizable modeling framework could be used to analyze protective and pathogenic immune responses to diverse viral infections.
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Affiliation(s)
- Judy D Day
- Department of Mathematics, University of Tennessee, Knoxville, TN, United States.,Department of Electrical Engineering & Computer Science, University of Tennessee, Knoxville, TN, United States
| | - Soojin Park
- Department of Neurology & Division of Critical Care and Hospital Neurology, Columbia University College of Physicians and Surgeons, New York Presbyterian Hospital - Columbia University Irving Medical Center, New York, NY, United States.,Program for Hospital and Intensive Care Informatics, Department of Neurology, Columbia University College of Physicians and Surgeons, New York, NY, United States
| | - Benjamin L Ranard
- Program for Hospital and Intensive Care Informatics, Department of Neurology, Columbia University College of Physicians and Surgeons, New York, NY, United States.,Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Columbia University College of Physicians and Surgeons, New York Presbyterian Hospital - Columbia University Irving Medical Center, New York, NY, United States
| | - Harinder Singh
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, United States.,Center for Systems Immunology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Carson C Chow
- Mathematical Biology Section, Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States
| | - Yoram Vodovotz
- Center for Systems Immunology, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Surgery, University of Pittsburgh, Pittsburgh, PA, United States.,Center for Inflammation and Regeneration Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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2
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Rendeiro AF, Casano J, Vorkas CK, Singh H, Morales A, DeSimone RA, Ellsworth GB, Soave R, Kapadia SN, Saito K, Brown CD, Hsu J, Kyriakides C, Chiu S, Cappelli LV, Cacciapuoti MT, Tam W, Galluzzi L, Simonson PD, Elemento O, Salvatore M, Inghirami G. Profiling of immune dysfunction in COVID-19 patients allows early prediction of disease progression. Life Sci Alliance 2021; 4:e202000955. [PMID: 33361110 PMCID: PMC7768198 DOI: 10.26508/lsa.202000955] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 01/08/2023] Open
Abstract
With a rising incidence of COVID-19-associated morbidity and mortality worldwide, it is critical to elucidate the innate and adaptive immune responses that drive disease severity. We performed longitudinal immune profiling of peripheral blood mononuclear cells from 45 patients and healthy donors. We observed a dynamic immune landscape of innate and adaptive immune cells in disease progression and absolute changes of lymphocyte and myeloid cells in severe versus mild cases or healthy controls. Intubation and death were coupled with selected natural killer cell KIR receptor usage and IgM+ B cells and associated with profound CD4 and CD8 T-cell exhaustion. Pseudo-temporal reconstruction of the hierarchy of disease progression revealed dynamic time changes in the global population recapitulating individual patients and the development of an eight-marker classifier of disease severity. Estimating the effect of clinical progression on the immune response and early assessment of disease progression risks may allow implementation of tailored therapies.
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Affiliation(s)
- André F Rendeiro
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Joseph Casano
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Charles Kyriakos Vorkas
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Harjot Singh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ayana Morales
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Robert A DeSimone
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Grant B Ellsworth
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Rosemary Soave
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shashi N Kapadia
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Kohta Saito
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher D Brown
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - JingMei Hsu
- Division of Hematology/Oncology, Department of Medicine Weill Cornell Medicine, New York, NY, USA
| | - Christopher Kyriakides
- Department of Rehabilitation Medicine at New York University Grossman School of Medicine New York, NY, USA
| | - Steven Chiu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Luca Vincenzo Cappelli
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Wayne Tam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lorenzo Galluzzi
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, New York, NY, USA
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - Paul D Simonson
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mirella Salvatore
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
- Division of Public Health Programs, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
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3
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Abstract
The encoded biosynthesis of proteins provides the ultimate paradigm for high-fidelity synthesis of long polymers of defined sequence and composition, but it is limited to polymerizing the canonical amino acids. Recent advances have built on genetic code expansion - which commonly permits the cellular incorporation of one type of non-canonical amino acid into a protein - to enable the encoded incorporation of several distinct non-canonical amino acids. Developments include strategies to read quadruplet codons, use non-natural DNA base pairs, synthesize completely recoded genomes and create orthogonal translational components with reprogrammed specificities. These advances may enable the genetically encoded synthesis of non-canonical biopolymers and provide a platform for transforming the discovery and evolution of new materials and therapeutics.
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Affiliation(s)
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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4
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Rendeiro AF, Casano J, Kyriakos Vorkas C, Singh H, Morales A, DeSimone RA, Ellsworth GB, Soave R, Kapadia SN, Saito K, Brown CD, Hsu J, Kyriakides C, Chiu S, Cappelli L, Teresa Cacciapuoti M, Tam W, Galluzzi L, Simonson PD, Elemento O, Salvatore M, Inghirami G. Longitudinal immune profiling of mild and severe COVID-19 reveals innate and adaptive immune dysfunction and provides an early prediction tool for clinical progression. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.09.08.20189092. [PMID: 32935114 PMCID: PMC7491529 DOI: 10.1101/2020.09.08.20189092] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
With a rising incidence of COVID-19-associated morbidity and mortality worldwide, it is critical to elucidate the innate and adaptive immune responses that drive disease severity. We performed longitudinal immune profiling of peripheral blood mononuclear cells from 45 patients and healthy donors. We observed a dynamic immune landscape of innate and adaptive immune cells in disease progression and absolute changes of lymphocyte and myeloid cells in severe versus mild cases or healthy controls. Intubation and death were coupled with selected natural killer cell KIR receptor usage and IgM+ B cells and associated with profound CD4 and CD8 T cell exhaustion. Pseudo-temporal reconstruction of the hierarchy of disease progression revealed dynamic time changes in the global population recapitulating individual patients and the development of an eight-marker classifier of disease severity. Estimating the effect of clinical progression on the immune response and early assessment of disease progression risks may allow implementation of tailored therapies.
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Affiliation(s)
- André F Rendeiro
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Joseph Casano
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Charles Kyriakos Vorkas
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Harjot Singh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ayana Morales
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Robert A DeSimone
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Grant B Ellsworth
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Rosemary Soave
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shashi N Kapadia
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Kohta Saito
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher D Brown
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - JingMei Hsu
- Division of Hematology/Oncology, Department of Medicine Weill Cornell Medicine, New York, NY, 10065, USA
| | - Christopher Kyriakides
- Department of Rehabilitation Medicine at NYU Grossman School of Medicine New York, NY, USA
| | - Steven Chiu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Luca Cappelli
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Wayne Tam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lorenzo Galluzzi
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, New York, NY, USA
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - Paul D Simonson
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mirella Salvatore
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
- Division of Public Health Programs, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
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5
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Moya P, Molins A, Chiva S, Bastida J, Barreno E. Symbiotic microalgal diversity within lichenicolous lichens and crustose hosts on Iberian Peninsula gypsum biocrusts. Sci Rep 2020; 10:14060. [PMID: 32820199 PMCID: PMC7441164 DOI: 10.1038/s41598-020-71046-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/05/2020] [Indexed: 11/16/2022] Open
Abstract
This study analyses the interactions among crustose and lichenicolous lichens growing on gypsum biocrusts. The selected community was composed of Acarospora nodulosa, Acarospora placodiiformis, Diploschistes diacapsis, Rhizocarpon malenconianum and Diplotomma rivas-martinezii. These species represent an optimal system for investigating the strategies used to share phycobionts because Acarospora spp. are parasites of D. diacapsis during their first growth stages, while in mature stages, they can develop independently. R. malenconianum is an obligate lichenicolous lichen on D. diacapsis, and D. rivas-martinezii occurs physically close to D. diacapsis. Microalgal diversity was studied by Sanger sequencing and 454-pyrosequencing of the nrITS region, and the microalgae were characterized ultrastructurally. Mycobionts were studied by performing phylogenetic analyses. Mineralogical and macro- and micro-element patterns were analysed to evaluate their influence on the microalgal pool available in the substrate. The intrathalline coexistence of various microalgal lineages was confirmed in all mycobionts. D. diacapsis was confirmed as an algal donor, and the associated lichenicolous lichens acquired their phycobionts in two ways: maintenance of the hosts' microalgae and algal switching. Fe and Sr were the most abundant microelements in the substrates but no significant relationship was found with the microalgal diversity. The range of associated phycobionts are influenced by thallus morphology.
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Affiliation(s)
- Patricia Moya
- Botánica, ICBIBE, Fac. CC. Biológicas, Universitat de València, C/ Dr. Moliner, 50, 46100, Burjassot, Valencia, Spain.
| | - Arantzazu Molins
- Botánica, ICBIBE, Fac. CC. Biológicas, Universitat de València, C/ Dr. Moliner, 50, 46100, Burjassot, Valencia, Spain
| | - Salvador Chiva
- Botánica, ICBIBE, Fac. CC. Biológicas, Universitat de València, C/ Dr. Moliner, 50, 46100, Burjassot, Valencia, Spain
| | - Joaquín Bastida
- Geología, Fac. CC. Biológicas, Universitat de València, C/ Dr. Moliner, 50, 46100, Burjassot, Valencia, Spain
| | - Eva Barreno
- Botánica, ICBIBE, Fac. CC. Biológicas, Universitat de València, C/ Dr. Moliner, 50, 46100, Burjassot, Valencia, Spain
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6
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Albini A, Di Guardo G, Noonan DM, Lombardo M. The SARS-CoV-2 receptor, ACE-2, is expressed on many different cell types: implications for ACE-inhibitor- and angiotensin II receptor blocker-based cardiovascular therapies. Intern Emerg Med 2020; 15:759-766. [PMID: 32430651 PMCID: PMC7236433 DOI: 10.1007/s11739-020-02364-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/02/2020] [Indexed: 01/08/2023]
Abstract
SARS-CoV-2 is characterized by a spike protein allowing viral binding to the angiotensin-converting enzyme (ACE)-2, which acts as a viral receptor and is expressed on the surface of several pulmonary and extra-pulmonary cell types, including cardiac, renal, intestinal and endothelial cells. There is evidence that also endothelial cells are infected by SARS-COV-2, with subsequent occurrence of systemic vasculitis, thromboembolism and disseminated intravascular coagulation. Those effects, together with the "cytokine storm" are involved in a worse prognosis. In clinical practice, angiotensin-converting enzyme inhibitors (ACE-Is) and angiotensin II receptor blockers (ARBs) are extensively used for the treatment of hypertension and other cardiovascular diseases. In in vivo studies, ACE-Is and ARBs seem to paradoxically increase ACE-2 expression, which could favour SARS-CoV-2 infection of host's cells and tissues. By contrast, in patients treated with ACE-Is and ARBs, ACE-2 shows a downregulation at the mRNA and protein levels in kidney and cardiac tissues. Yet, it has been claimed that both ARBs and ACE-Is could result potentially useful in the clinical course of SARS-CoV-2-infected patients. As detected in China and as the Italian epidemiological situation confirms, the most prevalent comorbidities in deceased patients with COVID-19 are hypertension, diabetes and cardiovascular diseases. Older COVID-19-affected patients with cardiovascular comorbidities exhibit a more severe clinical course and a worse prognosis, with many of them being also treated with ARBs or ACE-Is. Another confounding factor is cigarette smoking, which has been reported to increase ACE-2 expression in both experimental models and humans. Sex also plays a role, with chromosome X harbouring the gene coding for ACE-2, which is one of the possible explanations of why mortality in female patients is lower. Viral entry also depends on TMPRSS2 protease activity, an androgen dependent enzyme. Despite the relevance of experimental animal studies, to comprehensively address the question of the potential hazards or benefits of ACE-Is and ARBs on the clinical course of COVID-19-affected patients treated by these anti-hypertensive drugs, we will need randomized human studies. We claim the need of adequately powered, prospective studies aimed at answering the following questions of paramount importance for cardiovascular, internal and emergency medicine: Do ACE-Is and ARBs exert similar or different effects on infection or disease course? Are such effects dangerous, neutral or even useful in older, COVID-19-affected patients? Do they act on multiple cell types? Since ACE-Is and ARBs have different molecular targets, the clinical course of SARS-CoV-2 infection could be also different in patients treated by one or the other of these two drug classes. At present, insufficient detailed data from trials have been made available.
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Affiliation(s)
- Adriana Albini
- Scientific and Technology Pole, IRCCS MultiMedica, Milan, Italy.
| | - Giovanni Di Guardo
- Faculty of Veterinary Medicine, University of Teramo, 64100, Teramo, Italy
| | - Douglas McClain Noonan
- Scientific and Technology Pole, IRCCS MultiMedica, Milan, Italy
- Department of Biotechnology and Life Sciences, University of Insubria, Varèse, Italy
| | - Michele Lombardo
- Cardiology Unit, San Giuseppe Hospital-MultiMedica, Milan, Italy
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