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Kenny G, Saini G, Gaillard CM, Negi R, Alalwan D, Garcia Leon A, McCann K, Tinago W, Kelly C, Cotter AG, de Barra E, Horgan M, Yousif O, Gautier V, Landay A, McAuley D, Feeney ER, O'Kane C, Mallon PWG. Early inflammatory profiles predict maximal disease severity in COVID-19: An unsupervised cluster analysis. Heliyon 2024; 10:e34694. [PMID: 39144942 PMCID: PMC11320140 DOI: 10.1016/j.heliyon.2024.e34694] [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: 03/14/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 08/16/2024] Open
Abstract
Background The inflammatory changes that underlie the heterogeneous presentations of COVID-19 remain incompletely understood. In this study we aimed to identify inflammatory profiles that precede the development of severe COVID-19, that could serve as targets for optimised delivery of immunomodulatory therapies and provide insights for the development of new therapies. Methods We included individuals sampled <10 days from COVID-19 symptom onset, recruited from both inpatient and outpatient settings. We measured 61 biomarkers in plasma, including markers of innate immune and T cell activation, coagulation, tissue repair and lung injury. We used principal component analysis and hierarchical clustering to derive biomarker clusters, and ordinal logistic regression to explore associations between cluster membership and maximal disease severity, adjusting for known risk factors for severe COVID-19. Results In 312 individuals, median (IQR) 7 (4-9) days from symptom onset, we found four clusters. Cluster 1 was characterised by low overall inflammation, cluster 2 was characterised by higher levels of growth factors and markers of endothelial activation (EGF, VEGF, PDGF, TGFα, PAI-1 and p-selectin). Cluster 3 and 4 both had higher overall inflammation. Cluster 4 had the highest levels of most markers including markers of innate immune activation (IL6, procalcitonin, CRP, TNFα), and coagulation (D-dimer, TPO), in contrast cluster 3 had the highest levels of alveolar epithelial injury markers (RAGE, ST2), but relative downregulation of growth factors and endothelial activation markers, suggesting a dysfunctional inflammatory pattern. In unadjusted and adjusted analysis, compared to cluster 1, cluster 3 had the highest odds of progressing to more severe disease (unadjusted OR (95%CI) 9.02 (4.53-17.96), adjusted OR (95%CI) 6.02 (2.70-13.39)). Conclusion Early inflammatory profiles predicted subsequent maximal disease severity independent of risk factors for severe COVID-19. A cluster with downregulation of growth factors and endothelial activation markers, and early evidence of alveolar epithelial injury, had the highest risk of severe COVID-19.
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Affiliation(s)
- Grace Kenny
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
- Department of Infectious Diseases, St Vincent's University Hospital, Dublin, Ireland
| | - Gurvin Saini
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | - Colette Marie Gaillard
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | - Riya Negi
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | - Dana Alalwan
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | - Alejandro Garcia Leon
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | - Kathleen McCann
- Department of Infectious Diseases, St Vincent's University Hospital, Dublin, Ireland
| | - Willard Tinago
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | - Christine Kelly
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
- Department of Infectious Diseases, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Aoife G. Cotter
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
- Department of Infectious Diseases, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Eoghan de Barra
- Department of International Health and Tropical Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Mary Horgan
- Department of Infectious Diseases, Cork University Hospital, Wilton, Cork, Ireland
| | - Obada Yousif
- Department of Endocrinology, Wexford General Hospital, Wexford, Ireland
| | - Virginie Gautier
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | - Alan Landay
- Department of Internal Medicine, Rush University, Chicago, IL, USA
| | | | - Eoin R. Feeney
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
- Department of Infectious Diseases, St Vincent's University Hospital, Dublin, Ireland
| | | | - Patrick WG. Mallon
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
- Department of Infectious Diseases, St Vincent's University Hospital, Dublin, Ireland
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Günter M, Mueller KAL, Salazar MJ, Gekeler S, Prang C, Harm T, Gawaz MP, Autenrieth SE. Immune signature of patients with cardiovascular disease predicts increased risk for a severe course of COVID-19. Eur J Immunol 2024:e2451145. [PMID: 39094122 DOI: 10.1002/eji.202451145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 08/04/2024]
Abstract
Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection can lead to life-threatening clinical manifestations. Patients with cardiovascular disease (CVD) are at higher risk for severe courses of COVID-19. So far, however, there are hardly any strategies for predicting the course of SARS-CoV-2 infection in CVD patients at hospital admission. Thus, we investigated whether this prediction is achievable by prospectively analysing the blood immunophenotype of 94 nonvaccinated participants, including uninfected and acutely SARS-CoV-2-infected CVD patients and healthy donors, using a 36-colour spectral flow cytometry panel. Unsupervised data analysis revealed little differences between healthy donors and CVD patients, whereas the distribution of the cell populations changed dramatically in SARS-CoV-2-infected CVD patients. The latter had more mature NK cells, activated monocyte subsets, central memory CD4+ T cells, and plasmablasts but fewer dendritic cells, CD16+ monocytes, innate lymphoid cells, and CD8+ T-cell subsets. Moreover, we identified an immune signature characterised by CD161+ T cells, intermediate effector CD8+ T cells, and natural killer T (NKT) cells that is predictive for CVD patients with a severe course of COVID-19. Thus, intensified immunophenotype analyses can help identify patients at risk of severe COVID-19 at hospital admission, improving clinical outcomes through specific treatment.
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Affiliation(s)
- Manina Günter
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, Eberhard Karls University Tuebingen, Tuebingen, Germany
- German Cancer Research Centre, Research Group Dendritic Cells in Infection and Cancer, Heidelberg, Germany
| | - Karin Anne Lydia Mueller
- Department of Cardiology and Angiology, University Hospital Tuebingen, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Mathew J Salazar
- German Cancer Research Centre, Research Group Dendritic Cells in Infection and Cancer, Heidelberg, Germany
| | - Sarah Gekeler
- Department of Cardiology and Angiology, University Hospital Tuebingen, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Carolin Prang
- Department of Cardiology and Angiology, University Hospital Tuebingen, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Tobias Harm
- Department of Cardiology and Angiology, University Hospital Tuebingen, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Meinrad Paul Gawaz
- Department of Cardiology and Angiology, University Hospital Tuebingen, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Stella E Autenrieth
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, Eberhard Karls University Tuebingen, Tuebingen, Germany
- German Cancer Research Centre, Research Group Dendritic Cells in Infection and Cancer, Heidelberg, Germany
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Qin Q, Yu H, Zhao J, Xu X, Li Q, Gu W, Guo X. Machine learning-based derivation and validation of three immune phenotypes for risk stratification and prognosis in community-acquired pneumonia: a retrospective cohort study. Front Immunol 2024; 15:1441838. [PMID: 39114653 PMCID: PMC11303239 DOI: 10.3389/fimmu.2024.1441838] [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: 05/31/2024] [Accepted: 07/05/2024] [Indexed: 08/10/2024] Open
Abstract
Background The clinical presentation of Community-acquired pneumonia (CAP) in hospitalized patients exhibits heterogeneity. Inflammation and immune responses play significant roles in CAP development. However, research on immunophenotypes in CAP patients is limited, with few machine learning (ML) models analyzing immune indicators. Methods A retrospective cohort study was conducted at Xinhua Hospital, affiliated with Shanghai Jiaotong University. Patients meeting predefined criteria were included and unsupervised clustering was used to identify phenotypes. Patients with distinct phenotypes were also compared in different outcomes. By machine learning methods, we comprehensively assess the disease severity of CAP patients. Results A total of 1156 CAP patients were included in this research. In the training cohort (n=809), we identified three immune phenotypes among patients: Phenotype A (42.0%), Phenotype B (40.2%), and Phenotype C (17.8%), with Phenotype C corresponding to more severe disease. Similar results can be observed in the validation cohort. The optimal prognostic model, SuperPC, achieved the highest average C-index of 0.859. For predicting CAP severity, the random forest model was highly accurate, with C-index of 0.998 and 0.794 in training and validation cohorts, respectively. Conclusion CAP patients can be categorized into three distinct immune phenotypes, each with prognostic relevance. Machine learning exhibits potential in predicting mortality and disease severity in CAP patients by leveraging clinical immunological data. Further external validation studies are crucial to confirm applicability.
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Affiliation(s)
- Qiangqiang Qin
- Department of Respiratory Medicine, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Haiyang Yu
- Department of Respiratory Medicine, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jie Zhao
- Department of Hematology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xue Xu
- Department of Respiratory Medicine, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qingxuan Li
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Wen Gu
- Department of Respiratory Medicine, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xuejun Guo
- Department of Respiratory Medicine, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Tang J, Shang C, Chang Y, Jiang W, Xu J, Zhang L, Lu L, Chen L, Liu X, Zeng Q, Cao W, Li T. Peripheral PD-1 +NK cells could predict the 28-day mortality in sepsis patients. Front Immunol 2024; 15:1426064. [PMID: 38953031 PMCID: PMC11215063 DOI: 10.3389/fimmu.2024.1426064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 05/31/2024] [Indexed: 07/03/2024] Open
Abstract
Background Unbalanced inflammatory response is a critical feature of sepsis, a life-threatening condition with significant global health burdens. Immune dysfunction, particularly that involving different immune cells in peripheral blood, plays a crucial pathophysiological role and shows early warning signs in sepsis. The objective is to explore the relationship between sepsis and immune subpopulations in peripheral blood, and to identify patients with a higher risk of 28-day mortality based on immunological subtypes with machine-learning (ML) model. Methods Patients were enrolled according to the sepsis-3 criteria in this retrospective observational study, along with age- and sex-matched healthy controls (HCs). Data on clinical characteristics, laboratory tests, and lymphocyte immunophenotyping were collected. XGBoost and k-means clustering as ML approaches, were employed to analyze the immune profiles and stratify septic patients based on their immunological subtypes. Cox regression survival analysis was used to identify potential biomarkers and to assess their association with 28-day mortality. The accuracy of biomarkers for mortality was determined by the area under the receiver operating characteristic (ROC) curve (AUC) analysis. Results The study enrolled 100 septic patients and 89 HCs, revealing distinct lymphocyte profiles between the two groups. The XGBoost model discriminated sepsis from HCs with an area under the receiver operating characteristic curve of 1.0 and 0.99 in the training and testing set, respectively. Within the model, the top three highest important contributions were the percentage of CD38+CD8+T cells, PD-1+NK cells, HLA-DR+CD8+T cells. Two clusters of peripheral immunophenotyping of septic patients by k-means clustering were conducted. Cluster 1 featured higher proportions of PD1+ NK cells, while cluster 2 featured higher proportions of naïve CD4+T cells. Furthermore, the level of PD-1+NK cells was significantly higher in the non-survivors than the survivors (15.1% vs 8.6%, P<0.01). Moreover, the levels of PD1+ NK cells combined with SOFA score showed good performance in predicting the 28-day mortality in sepsis (AUC=0.91,95%CI 0.82-0.99), which is superior to PD1+ NK cells only(AUC=0.69, sensitivity 0.74, specificity 0.64, cut-off value of 11.25%). In the multivariate Cox regression, high expression of PD1+ NK cells proportion was related to 28-day mortality (aHR=1.34, 95%CI 1.19 to 1.50; P<0.001). Conclusion The study provides novel insights into the association between PD1+NK cell profiles and prognosis of sepsis. Peripheral immunophenotyping could potentially stratify the septic patients and identify those with a high risk of 28-day mortality.
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Affiliation(s)
- Jia Tang
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chenming Shang
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Yue Chang
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wei Jiang
- Department of Medical ICU, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jun Xu
- Department of Emergency Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Leidan Zhang
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lianfeng Lu
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ling Chen
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaosheng Liu
- School of Medicine, Tsinghua University, Beijing, China
| | - Qingjia Zeng
- Institute of Medical Information, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wei Cao
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Taisheng Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
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Kempaiah P, Libertin CR, Chitale RA, Naeyma I, Pleqi V, Sheele JM, Iandiorio MJ, Hoogesteijn AL, Caulfield TR, Rivas AL. Decoding Immuno-Competence: A Novel Analysis of Complete Blood Cell Count Data in COVID-19 Outcomes. Biomedicines 2024; 12:871. [PMID: 38672225 PMCID: PMC11048687 DOI: 10.3390/biomedicines12040871] [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: 02/10/2024] [Revised: 03/14/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND While 'immuno-competence' is a well-known term, it lacks an operational definition. To address this omission, this study explored whether the temporal and structured data of the complete blood cell count (CBC) can rapidly estimate immuno-competence. To this end, one or more ratios that included data on all monocytes, lymphocytes and neutrophils were investigated. MATERIALS AND METHODS Longitudinal CBC data collected from 101 COVID-19 patients (291 observations) were analyzed. Dynamics were estimated with several approaches, which included non-structured (the classic CBC format) and structured data. Structured data were assessed as complex ratios that capture multicellular interactions among leukocytes. In comparing survivors with non-survivors, the hypothesis that immuno-competence may exhibit feedback-like (oscillatory or cyclic) responses was tested. RESULTS While non-structured data did not distinguish survivors from non-survivors, structured data revealed immunological and statistical differences between outcomes: while survivors exhibited oscillatory data patterns, non-survivors did not. In survivors, many variables (including IL-6, hemoglobin and several complex indicators) showed values above or below the levels observed on day 1 of the hospitalization period, displaying L-shaped data distributions (positive kurtosis). In contrast, non-survivors did not exhibit kurtosis. Three immunologically defined data subsets included only survivors. Because information was based on visual patterns generated in real time, this method can, potentially, provide information rapidly. DISCUSSION The hypothesis that immuno-competence expresses feedback-like loops when immunological data are structured was not rejected. This function seemed to be impaired in immuno-suppressed individuals. While this method rapidly informs, it is only a guide that, to be confirmed, requires additional tests. Despite this limitation, the fact that three protective (survival-associated) immunological data subsets were observed since day 1 supports many clinical decisions, including the early and personalized prognosis and identification of targets that immunomodulatory therapies could pursue. Because it extracts more information from the same data, structured data may replace the century-old format of the CBC.
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Affiliation(s)
- Prakasha Kempaiah
- Department of Medicine, Division of Infectious Diseases, Mayo Clinic, Jacksonville, FL 32224, USA; (P.K.); (V.P.)
| | | | - Rohit A. Chitale
- Mayo Clinic Alix School of Medicine, Mayo Clinic, Jacksonville, FL 32224, USA;
| | - Islam Naeyma
- Department of Neuroscience, Division of QHS Computational Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (I.N.); (T.R.C.)
| | - Vasili Pleqi
- Department of Medicine, Division of Infectious Diseases, Mayo Clinic, Jacksonville, FL 32224, USA; (P.K.); (V.P.)
| | | | - Michelle J. Iandiorio
- Department of Internal Medicine, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA;
| | | | - Thomas R. Caulfield
- Department of Neuroscience, Division of QHS Computational Biology, Mayo Clinic, Jacksonville, FL 32224, USA; (I.N.); (T.R.C.)
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ariel L. Rivas
- Center for Global Health, Department of Internal Medicine, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
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He X, Cui X, Zhao Z, Wu R, Zhang Q, Xue L, Zhang H, Ge Q, Leng Y. A generalizable and easy-to-use COVID-19 stratification model for the next pandemic via immune-phenotyping and machine learning. Front Immunol 2024; 15:1372539. [PMID: 38601145 PMCID: PMC11004273 DOI: 10.3389/fimmu.2024.1372539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
Introduction The coronavirus disease 2019 (COVID-19) pandemic has affected billions of people worldwide, and the lessons learned need to be concluded to get better prepared for the next pandemic. Early identification of high-risk patients is important for appropriate treatment and distribution of medical resources. A generalizable and easy-to-use COVID-19 severity stratification model is vital and may provide references for clinicians. Methods Three COVID-19 cohorts (one discovery cohort and two validation cohorts) were included. Longitudinal peripheral blood mononuclear cells were collected from the discovery cohort (n = 39, mild = 15, critical = 24). The immune characteristics of COVID-19 and critical COVID-19 were analyzed by comparison with those of healthy volunteers (n = 16) and patients with mild COVID-19 using mass cytometry by time of flight (CyTOF). Subsequently, machine learning models were developed based on immune signatures and the most valuable laboratory parameters that performed well in distinguishing mild from critical cases. Finally, single-cell RNA sequencing data from a published study (n = 43) and electronic health records from a prospective cohort study (n = 840) were used to verify the role of crucial clinical laboratory and immune signature parameters in the stratification of COVID-19 severity. Results Patients with COVID-19 were determined with disturbed glucose and tryptophan metabolism in two major innate immune clusters. Critical patients were further characterized by significant depletion of classical dendritic cells (cDCs), regulatory T cells (Tregs), and CD4+ central memory T cells (Tcm), along with increased systemic interleukin-6 (IL-6), interleukin-12 (IL-12), and lactate dehydrogenase (LDH). The machine learning models based on the level of cDCs and LDH showed great potential for predicting critical cases. The model performances in severity stratification were validated in two cohorts (AUC = 0.77 and 0.88, respectively) infected with different strains in different periods. The reference limits of cDCs and LDH as biomarkers for predicting critical COVID-19 were 1.2% and 270.5 U/L, respectively. Conclusion Overall, we developed and validated a generalizable and easy-to-use COVID-19 severity stratification model using machine learning algorithms. The level of cDCs and LDH will assist clinicians in making quick decisions during future pandemics.
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Affiliation(s)
- Xinlei He
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Xiao Cui
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Zhiling Zhao
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Rui Wu
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Qiang Zhang
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Lei Xue
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Hua Zhang
- Department of Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, China
| | - Qinggang Ge
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Yuxin Leng
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
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Moon MK, Ham H, Song SM, Lee C, Goo T, Oh B, Lee S, Kim SW, Park T. The clinical course of hospitalized COVID-19 patients and aggravation risk prediction models: a retrospective, multi-center Korean cohort study. Front Med (Lausanne) 2024; 10:1239789. [PMID: 38239614 PMCID: PMC10794356 DOI: 10.3389/fmed.2023.1239789] [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: 06/29/2023] [Accepted: 12/01/2023] [Indexed: 01/22/2024] Open
Abstract
Background Understanding the clinical course and pivotal time points of COVID-19 aggravation is critical for enhancing patient monitoring. This retrospective, multi-center cohort study aims to identify these significant time points and associate them with potential risk factors, leveraging data from a sizable cohort with mild-to-moderate symptoms upon admission. Methods This study included data from 1,696 COVID-19 patients with mild-to-moderate clinical severity upon admission across multiple hospitals in Daegu-Kyungpook Province (Daegu dataset) between February 18 and early March 2020 and 321 COVID-19 patients at Seoul Boramae Hospital (Boramae dataset) collected from February to July 2020. The approach involved: (1) identifying the optimal time point for aggravation using survival analyses with maximally selected rank statistics; (2) investigating the relationship between comorbidities and time to aggravation; and (3) developing prediction models through machine learning techniques. The models were validated internally among patients from the Daegu dataset and externally among patients from the Boramae dataset. Results The Daegu dataset showed a mean age of 51.0 ± 19.6 years, with 8 days for aggravation and day 5 being identified as the pivotal point for survival. Contrary to previous findings, specific comorbidities had no notable impact on aggravation patterns. Prediction models utilizing factors including age and chest X-ray infiltration demonstrated promising performance, with the top model achieving an AUC of 0.827 in external validation for 5 days aggravation prediction. Conclusion Our study highlights the crucial significance of the initial 5 days period post-admission in managing COVID-19 patients. The identification of this pivotal time frame, combined with our robust predictive models, provides valuable insights for early intervention strategies. This research underscores the potential of proactive monitoring and timely interventions in enhancing patient outcomes, particularly for those at risk of rapid aggravation. Our findings offer a meaningful contribution to understanding the COVID-19 clinical course and supporting healthcare providers in optimizing patient care and resource allocation.
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Affiliation(s)
- Min Kyong Moon
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, SMG-SNU Boramae Medical Center, Seoul, Republic of Korea
| | - Hyeonjung Ham
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Soo Min Song
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Chanhee Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Taewan Goo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Bumjo Oh
- Department of Family Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Family Medicine, SMG-SNU Boramae Medical Center, Seoul, Republic of Korea
| | - Seungyeoun Lee
- Department of Mathematics & Statistics, Sejong University, Seoul, Republic of Korea
| | - Shin-Woo Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul, Republic of Korea
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8
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Ford ES, Mayer-Blackwell K, Jing L, Laing KJ, Sholukh AM, St Germain R, Bossard EL, Xie H, Pulliam TH, Jani S, Selke S, Burrow CJ, McClurkan CL, Wald A, Greninger AL, Holbrook MR, Eaton B, Eudy E, Murphy M, Postnikova E, Robins HS, Elyanow R, Gittelman RM, Ecsedi M, Wilcox E, Chapuis AG, Fiore-Gartland A, Koelle DM. Repeated mRNA vaccination sequentially boosts SARS-CoV-2-specific CD8 + T cells in persons with previous COVID-19. Nat Immunol 2024; 25:166-177. [PMID: 38057617 PMCID: PMC10981451 DOI: 10.1038/s41590-023-01692-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 10/27/2023] [Indexed: 12/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hybrid immunity is more protective than vaccination or previous infection alone. To investigate the kinetics of spike-reactive T (TS) cells from SARS-CoV-2 infection through messenger RNA vaccination in persons with hybrid immunity, we identified the T cell receptor (TCR) sequences of thousands of index TS cells and tracked their frequency in bulk TCRβ repertoires sampled longitudinally from the peripheral blood of persons who had recovered from coronavirus disease 2019 (COVID-19). Vaccinations led to large expansions in memory TS cell clonotypes, most of which were CD8+ T cells, while also eliciting diverse TS cell clonotypes not observed before vaccination. TCR sequence similarity clustering identified public CD8+ and CD4+ TCR motifs associated with spike (S) specificity. Synthesis of longitudinal bulk ex vivo single-chain TCRβ repertoires and paired-chain TCRɑβ sequences from droplet sequencing of TS cells provides a roadmap for the rapid assessment of T cell responses to vaccines and emerging pathogens.
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Affiliation(s)
- Emily S Ford
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kerry J Laing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Anton M Sholukh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Russell St Germain
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Emily L Bossard
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Thomas H Pulliam
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Saumya Jani
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | | | - Anna Wald
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Michael R Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Brett Eaton
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Elizabeth Eudy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Michael Murphy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Elena Postnikova
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | | | | | - Rachel M Gittelman
- Adaptive Biotechnologies, Seattle, WA, USA
- Guardant Health, Redwood City, CA, USA
| | - Matyas Ecsedi
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Takeda Oncology, Cambridge, MA, USA
| | - Elise Wilcox
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Aude G Chapuis
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, WA, USA.
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Department of Translational Research, Benaroya Research Institute, Seattle, WA, USA.
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9
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Ho M, Levy TJ, Koulas I, Founta K, Coppa K, Hirsch JS, Davidson KW, Spyropoulos AC, Zanos TP. Longitudinal dynamic clinical phenotypes of in-hospital COVID-19 patients across three dominant virus variants in New York. Int J Med Inform 2024; 181:105286. [PMID: 37956643 PMCID: PMC10843635 DOI: 10.1016/j.ijmedinf.2023.105286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/20/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND COVID-19 is a challenging disease to characterize given its wide-ranging heterogeneous symptomatology. Several studies have attempted to extract clinical phenotypes but often relied on data from small patient cohorts, usually limited to only one viral variant and utilizing a static snapshot of patient data. OBJECTIVE This study aimed to identify clinical phenotypes of hospitalized COVID-19 patients and investigate their longitudinal dynamics throughout the pandemic, with the goal to relate these phenotypes to clinical outcomes and treatment strategies. METHODS We utilized routinely collected demographic and clinical data throughout the hospitalization of 38,077 patients admitted between 3/2020 to 5/2022, in 12 New York hospitals. Uniform Manifold Approximation and Projection and agglomerative hierarchical clustering were used to derive the clusters, followed by exploratory data analysis to compare the prevalence of comorbidities and treatments per cluster. RESULTS 4 distinct clinical phenotypes remained robust in multi-site validation and were associated with different mortality rates. The temporal progression of these phenotypes throughout the COVID-19 pandemic demonstrated increased variability across the waves of the three dominant viral variants (alpha, delta, omicron). Longitudinal analysis evaluating changes in clinical phenotypes of each patient throughout the course of a 4-week hospital stay exemplified the dynamic nature of the disease progression. Factors such as sex, race/ethnicity and specific treatment modalities revealed significant and clinically relevant differences between the observed phenotypes. CONCLUSIONS Our proposed methodology has the potential of enabling clinicians and policy makers to draw evidence-based conclusions for guiding treatment modalities in a dynamic fashion.
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Affiliation(s)
- Matthew Ho
- Institute of Health Systems Science, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY 11030; Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY 11030; Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY 11549
| | - Todd J Levy
- Institute of Health Systems Science, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY 11030; Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY 11030
| | - Ioannis Koulas
- Institute of Health Systems Science, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY 11030
| | - Kyriaki Founta
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY 11549
| | - Kevin Coppa
- Department of Clinical Digital Solutions, Northwell Health, New Hyde Park, NY 11042
| | - Jamie S Hirsch
- Institute of Health Systems Science, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY 11030; Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY 11549; Department of Clinical Digital Solutions, Northwell Health, New Hyde Park, NY 11042
| | - Karina W Davidson
- Institute of Health Systems Science, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY 11030; Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY 11549
| | - Alex C Spyropoulos
- Institute of Health Systems Science, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY 11030; Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY 11549
| | - Theodoros P Zanos
- Institute of Health Systems Science, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY 11030; Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY 11030; Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY 11549.
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10
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Li H, Gong H, Wong TH, Zhou J, Wang Y, Lin L, Dou Y, Jia H, Huang X, Gao Z, Shi R, Huang Y, Chen Z, Park W, Li JY, Chu H, Jia S, Wu H, Wu M, Liu Y, Li D, Li J, Xu G, Chang T, Zhang B, Gao Y, Su J, Bai H, Hu J, Yiu CK, Xu C, Hu W, Huang J, Chang L, Yu X. Wireless, battery-free, multifunctional integrated bioelectronics for respiratory pathogens monitoring and severity evaluation. Nat Commun 2023; 14:7539. [PMID: 37985765 PMCID: PMC10661182 DOI: 10.1038/s41467-023-43189-z] [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: 05/02/2023] [Accepted: 11/02/2023] [Indexed: 11/22/2023] Open
Abstract
The rapid diagnosis of respiratory virus infection through breath and blow remains challenging. Here we develop a wireless, battery-free, multifunctional pathogenic infection diagnosis system (PIDS) for diagnosing SARS-CoV-2 infection and symptom severity by blow and breath within 110 s and 350 s, respectively. The accuracies reach to 100% and 92% for evaluating the infection and symptom severity of 42 participants, respectively. PIDS realizes simultaneous gaseous sample collection, biomarker identification, abnormal physical signs recording and machine learning analysis. We transform PIDS into other miniaturized wearable or portable electronic platforms that may widen the diagnostic modes at home, outdoors and public places. Collectively, we demonstrate a general-purpose technology for rapidly diagnosing respiratory pathogenic infection by breath and blow, alleviating the technical bottleneck of saliva and nasopharyngeal secretions. PIDS may serve as a complementary diagnostic tool for other point-of-care techniques and guide the symptomatic treatment of viral infections.
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Affiliation(s)
- Hu Li
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100083, Beijing, China
| | - Huarui Gong
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, 999077, China
| | - Tsz Hung Wong
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Jingkun Zhou
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong, 999077, China
| | - Yuqiong Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100083, Beijing, China
| | - Long Lin
- College of Engineering, Peking University, 100871, Beijing, China
| | - Ying Dou
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, 999077, China
| | - Huiling Jia
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong, 999077, China
| | - Xingcan Huang
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Zhan Gao
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Rui Shi
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Ya Huang
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong, 999077, China
| | - Zhenlin Chen
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Wooyoung Park
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Ji Yu Li
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong, 999077, China
| | - Hongwei Chu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Shengxin Jia
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Han Wu
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100083, Beijing, China
| | - Mengge Wu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Yiming Liu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Dengfeng Li
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Jian Li
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Guoqiang Xu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Tianrui Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100083, Beijing, China
| | - Binbin Zhang
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong, 999077, China
| | - Yuyu Gao
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Jingyou Su
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Hao Bai
- Department of Laboratory Medicine, Med+X Center for Manufacturing, West China Precision Medicine Industrial Technology Institute, Department of Liver Surgery, Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jie Hu
- Department of Laboratory Medicine, Med+X Center for Manufacturing, West China Precision Medicine Industrial Technology Institute, Department of Liver Surgery, Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Chun Ki Yiu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong, 999077, China
| | - Chenjie Xu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China
| | - Wenchuang Hu
- Department of Laboratory Medicine, Med+X Center for Manufacturing, West China Precision Medicine Industrial Technology Institute, Department of Liver Surgery, Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Jiandong Huang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, 999077, China.
- Clinical Oncology Center, Shenzhen Key Laboratory for cancer metastasis and personalized therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
- Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen University, Guangzhou, 510120, China.
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, 100083, Beijing, China.
- School of Biomedical Engineering, Research and Engineering Center of Biomedical Materials, Anhui Medical University, Hefei, 230032, China.
| | - Xinge Yu
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, 999077, China.
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong, 999077, China.
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11
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Khadzhieva MB, Kolobkov DS, Kashatnikova DA, Gracheva AS, Redkin IV, Kuzovlev AN, Salnikova LE. Rare Variants in Primary Immunodeficiency Genes and Their Functional Partners in Severe COVID-19. Biomolecules 2023; 13:1380. [PMID: 37759780 PMCID: PMC10526997 DOI: 10.3390/biom13091380] [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: 07/25/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
The development of severe COVID-19, which is a complex multisystem disease, is thought to be associated with many genes whose action is modulated by numerous environmental and genetic factors. In this study, we focused on the ideas of the omnigenic model of heritability of complex traits, which assumes that a small number of core genes and a large pool of peripheral genes expressed in disease-relevant tissues contribute to the genetics of complex traits through interconnected networks. We hypothesized that primary immunodeficiency disease (PID) genes may be considered as core genes in severe COVID-19, and their functional partners (FPs) from protein-protein interaction networks may be considered as peripheral near-core genes. We used whole-exome sequencing data from patients aged ≤ 45 years with severe (n = 9) and non-severe COVID-19 (n = 11), and assessed the cumulative contribution of rare high-impact variants to disease severity. In patients with severe COVID-19, an excess of rare high-impact variants was observed at the whole-exome level, but maximal association signals were detected for PID + FP gene subsets among the genes intolerant to LoF variants, haploinsufficient and essential. Our exploratory study may serve as a model for new directions in the research of host genetics in severe COVID-19.
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Affiliation(s)
- Maryam B. Khadzhieva
- The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia; (M.B.K.); (A.S.G.); (A.N.K.)
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (D.S.K.); (D.A.K.)
- The Laboratory of Molecular Immunology, National Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia
| | - Dmitry S. Kolobkov
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (D.S.K.); (D.A.K.)
| | - Darya A. Kashatnikova
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (D.S.K.); (D.A.K.)
| | - Alesya S. Gracheva
- The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia; (M.B.K.); (A.S.G.); (A.N.K.)
- The Department of Population Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ivan V. Redkin
- Competence Center for the Development of AI Technology, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia;
| | - Artem N. Kuzovlev
- The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia; (M.B.K.); (A.S.G.); (A.N.K.)
| | - Lyubov E. Salnikova
- The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 107031 Moscow, Russia; (M.B.K.); (A.S.G.); (A.N.K.)
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (D.S.K.); (D.A.K.)
- The Laboratory of Molecular Immunology, National Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia
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12
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Charkoftaki G, Aalizadeh R, Santos-Neto A, Tan WY, Davidson EA, Nikolopoulou V, Wang Y, Thompson B, Furnary T, Chen Y, Wunder EA, Coppi A, Schulz W, Iwasaki A, Pierce RW, Cruz CSD, Desir GV, Kaminski N, Farhadian S, Veselkov K, Datta R, Campbell M, Thomaidis NS, Ko AI, Thompson DC, Vasiliou V. An AI-powered patient triage platform for future viral outbreaks using COVID-19 as a disease model. Hum Genomics 2023; 17:80. [PMID: 37641126 PMCID: PMC10463861 DOI: 10.1186/s40246-023-00521-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/30/2023] [Indexed: 08/31/2023] Open
Abstract
Over the last century, outbreaks and pandemics have occurred with disturbing regularity, necessitating advance preparation and large-scale, coordinated response. Here, we developed a machine learning predictive model of disease severity and length of hospitalization for COVID-19, which can be utilized as a platform for future unknown viral outbreaks. We combined untargeted metabolomics on plasma data obtained from COVID-19 patients (n = 111) during hospitalization and healthy controls (n = 342), clinical and comorbidity data (n = 508) to build this patient triage platform, which consists of three parts: (i) the clinical decision tree, which amongst other biomarkers showed that patients with increased eosinophils have worse disease prognosis and can serve as a new potential biomarker with high accuracy (AUC = 0.974), (ii) the estimation of patient hospitalization length with ± 5 days error (R2 = 0.9765) and (iii) the prediction of the disease severity and the need of patient transfer to the intensive care unit. We report a significant decrease in serotonin levels in patients who needed positive airway pressure oxygen and/or were intubated. Furthermore, 5-hydroxy tryptophan, allantoin, and glucuronic acid metabolites were increased in COVID-19 patients and collectively they can serve as biomarkers to predict disease progression. The ability to quickly identify which patients will develop life-threatening illness would allow the efficient allocation of medical resources and implementation of the most effective medical interventions. We would advocate that the same approach could be utilized in future viral outbreaks to help hospitals triage patients more effectively and improve patient outcomes while optimizing healthcare resources.
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Affiliation(s)
- Georgia Charkoftaki
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Reza Aalizadeh
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Zografou, 15771, Greece
| | - Alvaro Santos-Neto
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos, SP, 13566-590, Brazil
| | - Wan Ying Tan
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA
- Internal Medicine Residency Program, Department of Internal Medicine, Norwalk Hospital, Norwalk, CT, USA
| | - Emily A Davidson
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, CT, USA
| | - Varvara Nikolopoulou
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Zografou, 15771, Greece
| | - Yewei Wang
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Brian Thompson
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Tristan Furnary
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA
- Harvard Medical School, Harvard University, Boston, MA, USA
| | - Ying Chen
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Elsio A Wunder
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA
- Institute Gonçalo Moniz, Fundação Oswaldo Cruz, Brazilian Ministry of Health, Salvador, Brazil
| | - Andreas Coppi
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT, USA
| | - Wade Schulz
- Center for Outcomes Research and Evaluation, Yale-New Haven Hospital, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, MD, Chevy Chase, USA
| | - Richard W Pierce
- Department of Pediatrics , Yale School of Medicine, New Haven, CT, USA
| | - Charles S Dela Cruz
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Gary V Desir
- Department of Internal Medicine, Section of Nephrology, Yale University School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Shelli Farhadian
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, USA
| | - Kirill Veselkov
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, UK
| | - Rupak Datta
- Veterans Affairs Connecticut Healthcare System, CT, West Haven, USA
- Department of Internal Medicine, Yale School of Medicine, CT, New Haven, USA
| | - Melissa Campbell
- Department of Pediatrics, Division of Pediatric Infectious Diseases, School of Medicine, Duke University, NC, Durham, USA
| | - Nikolaos S Thomaidis
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Zografou, 15771, Greece
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA
- Institute Gonçalo Moniz, Fundação Oswaldo Cruz, Brazilian Ministry of Health, Salvador, Brazil
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, USA
| | - David C Thompson
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA.
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13
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Chambliss AB, Aljehani M, Tran B, Chen X, Elton E, Garri C, Ung N, Matasci N, Gross ME. Immune biomarkers associated with COVID-19 disease severity in an urban, hospitalized population. Pract Lab Med 2023; 36:e00323. [PMID: 37649544 PMCID: PMC10462676 DOI: 10.1016/j.plabm.2023.e00323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/17/2023] [Accepted: 06/30/2023] [Indexed: 09/01/2023] Open
Abstract
Objectives We sought to identify immune biomarkers associated with severe Coronavirus disease 2019 (COVID-19) in patients admitted to a large urban hospital during the early phase of the SARS-CoV-2 pandemic. Design The study population consisted of SARS-CoV-2 positive subjects admitted for COVID-19 (n = 58) or controls (n = 14) at the Los Angeles County University of Southern California Medical Center between April 2020 through December 2020. Immunologic markers including chemokine/cytokines (IL-6, IL-8, IL-10, IP-10, MCP-1, TNF-α) and serologic markers against SARS-CoV-2 antigens (including spike subunits S1 and S2, receptor binding domain, and nucleocapsid) were assessed in serum collected on the day of admission using bead-based multiplex immunoassay panels. Results We observed that body mass index (BMI) and SARS-CoV-2 antibodies were significantly elevated in patients with the highest COVID-19 disease severity. IP-10 was significantly elevated in COVID-19 patients and was associated with increased SARS-CoV-2 antibodies. Interactions among all available variables on COVID-19 disease severity were explored using a linear support vector machine model which supported the importance of BMI and SARS-CoV-2 antibodies. Conclusions Our results confirm the known adverse association of BMI on COVID-19 severity and suggest that IP-10 and SARS-CoV-2 antibodies could be useful to identify patients most likely to experience the most severe forms of the disease.
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Affiliation(s)
- Allison B. Chambliss
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Mayada Aljehani
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA
| | - Brian Tran
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA
| | - Xingyao Chen
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA
| | - Elizabeth Elton
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA
| | - Carolina Garri
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA
| | - Nolan Ung
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA
| | - Naim Matasci
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA
| | - Mitchell E. Gross
- Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, CA, USA
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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14
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Qi T, Wu F, Wu C, He L, Huang Y, Xie X. Differentially private knowledge transfer for federated learning. Nat Commun 2023; 14:3785. [PMID: 37355643 DOI: 10.1038/s41467-023-38794-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/15/2023] [Indexed: 06/26/2023] Open
Abstract
Extracting useful knowledge from big data is important for machine learning. When data is privacy-sensitive and cannot be directly collected, federated learning is a promising option that extracts knowledge from decentralized data by learning and exchanging model parameters, rather than raw data. However, model parameters may encode not only non-private knowledge but also private information of local data, thereby transferring knowledge via model parameters is not privacy-secure. Here, we present a knowledge transfer method named PrivateKT, which uses actively selected small public data to transfer high-quality knowledge in federated learning with privacy guarantees. We verify PrivateKT on three different datasets, and results show that PrivateKT can maximally reduce 84% of the performance gap between centralized learning and existing federated learning methods under strict differential privacy restrictions. PrivateKT provides a potential direction to effective and privacy-preserving knowledge transfer in machine intelligent systems.
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Affiliation(s)
- Tao Qi
- Department of Electronic Engineering, Tsinghua University, 100084, Beijing, China
| | - Fangzhao Wu
- Microsoft Research Asia, 100080, Beijing, China.
| | - Chuhan Wu
- Department of Electronic Engineering, Tsinghua University, 100084, Beijing, China.
| | - Liang He
- Department of Electronic Engineering, Tsinghua University, 100084, Beijing, China
| | - Yongfeng Huang
- Department of Electronic Engineering, Tsinghua University, 100084, Beijing, China.
- Zhongguancun Laboratory, 100094, Beijing, China.
- Institute for Precision Medicine, Tsinghua University, 102218, Beijing, China.
| | - Xing Xie
- Microsoft Research Asia, 100080, Beijing, China
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15
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Satta S, Rockwood SJ, Wang K, Wang S, Mozneb M, Arzt M, Hsiai TK, Sharma A. Microfluidic Organ-Chips and Stem Cell Models in the Fight Against COVID-19. Circ Res 2023; 132:1405-1424. [PMID: 37167356 PMCID: PMC10171291 DOI: 10.1161/circresaha.122.321877] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
SARS-CoV-2, the virus underlying COVID-19, has now been recognized to cause multiorgan disease with a systemic effect on the host. To effectively combat SARS-CoV-2 and the subsequent development of COVID-19, it is critical to detect, monitor, and model viral pathogenesis. In this review, we discuss recent advancements in microfluidics, organ-on-a-chip, and human stem cell-derived models to study SARS-CoV-2 infection in the physiological organ microenvironment, together with their limitations. Microfluidic-based detection methods have greatly enhanced the rapidity, accessibility, and sensitivity of viral detection from patient samples. Engineered organ-on-a-chip models that recapitulate in vivo physiology have been developed for many organ systems to study viral pathology. Human stem cell-derived models have been utilized not only to model viral tropism and pathogenesis in a physiologically relevant context but also to screen for effective therapeutic compounds. The combination of all these platforms, along with future advancements, may aid to identify potential targets and develop novel strategies to counteract COVID-19 pathogenesis.
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Affiliation(s)
- Sandro Satta
- Division of Cardiology and Department of Bioengineering, School of Engineering (S.S., K.W., S.W., T.K.H.), University of California, Los Angeles
- Division of Cardiology, Department of Medicine, School of Medicine (S.S., K.W., S.W., T.K.H.), University of California, Los Angeles
- Department of Medicine, Greater Los Angeles VA Healthcare System, California (S.S., K.W., S.W., T.K.H.)
| | - Sarah J Rockwood
- Stanford University Medical Scientist Training Program, Palo Alto, CA (S.J.R.)
| | - Kaidong Wang
- Division of Cardiology and Department of Bioengineering, School of Engineering (S.S., K.W., S.W., T.K.H.), University of California, Los Angeles
- Division of Cardiology, Department of Medicine, School of Medicine (S.S., K.W., S.W., T.K.H.), University of California, Los Angeles
- Department of Medicine, Greater Los Angeles VA Healthcare System, California (S.S., K.W., S.W., T.K.H.)
| | - Shaolei Wang
- Division of Cardiology and Department of Bioengineering, School of Engineering (S.S., K.W., S.W., T.K.H.), University of California, Los Angeles
- Division of Cardiology, Department of Medicine, School of Medicine (S.S., K.W., S.W., T.K.H.), University of California, Los Angeles
- Department of Medicine, Greater Los Angeles VA Healthcare System, California (S.S., K.W., S.W., T.K.H.)
| | - Maedeh Mozneb
- Board of Governors Regenerative Medicine Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Smidt Heart Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Cancer Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
| | - Madelyn Arzt
- Board of Governors Regenerative Medicine Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Smidt Heart Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Cancer Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
| | - Tzung K Hsiai
- Division of Cardiology and Department of Bioengineering, School of Engineering (S.S., K.W., S.W., T.K.H.), University of California, Los Angeles
- Division of Cardiology, Department of Medicine, School of Medicine (S.S., K.W., S.W., T.K.H.), University of California, Los Angeles
- Department of Medicine, Greater Los Angeles VA Healthcare System, California (S.S., K.W., S.W., T.K.H.)
| | - Arun Sharma
- Board of Governors Regenerative Medicine Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Smidt Heart Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Biomedical Sciences (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
- Cancer Institute (M.M., M.A., A.S.), Cedars-Sinai Medical Center, Los Angeles, CA
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16
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Wahadat MJ, van Tilburg SJ, Mueller YM, de Wit H, Van Helden-Meeuwsen CG, Langerak AW, Gruijters MJ, Mubarak A, Verkaaik M, Katsikis PD, Versnel MA, Kamphuis S. Targeted multiomics in childhood-onset SLE reveal distinct biological phenotypes associated with disease activity: results from an explorative study. Lupus Sci Med 2023; 10:10/1/e000799. [PMID: 37012057 PMCID: PMC10083882 DOI: 10.1136/lupus-2022-000799] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/10/2023] [Indexed: 04/05/2023]
Abstract
OBJECTIVE To combine targeted transcriptomic and proteomic data in an unsupervised hierarchical clustering method to stratify patients with childhood-onset SLE (cSLE) into similar biological phenotypes, and study the immunological cellular landscape that characterises the clusters. METHODS Targeted whole blood gene expression and serum cytokines were determined in patients with cSLE, preselected on disease activity state (at diagnosis, Low Lupus Disease Activity State (LLDAS), flare). Unsupervised hierarchical clustering, agnostic to disease characteristics, was used to identify clusters with distinct biological phenotypes. Disease activity was scored by clinical SELENA-SLEDAI (Safety of Estrogens in Systemic Lupus Erythematosus National Assessment-Systemic Lupus Erythematosus Disease Activity Index). High-dimensional 40-colour flow cytometry was used to identify immune cell subsets. RESULTS Three unique clusters were identified, each characterised by a set of differentially expressed genes and cytokines, and by disease activity state: cluster 1 contained primarily patients in LLDAS, cluster 2 contained mainly treatment-naïve patients at diagnosis and cluster 3 contained a mixed group of patients, namely in LLDAS, at diagnosis and disease flare. The biological phenotypes did not reflect previous organ system involvement and over time, patients could move from one cluster to another. Healthy controls clustered together in cluster 1. Specific immune cell subsets, including CD11c+ B cells, conventional dendritic cells, plasmablasts and early effector CD4+ T cells, differed between the clusters. CONCLUSION Using a targeted multiomic approach, we clustered patients into distinct biological phenotypes that are related to disease activity state but not to organ system involvement. This supports a new concept where choice of treatment and tapering strategies are not solely based on clinical phenotype but includes measuring novel biological parameters.
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Affiliation(s)
- Mohamed Javad Wahadat
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
- Department of Paediatric Rheumatology, Erasmus MC Sophia Children's Hospital, Rotterdam, The Netherlands
| | | | - Yvonne M Mueller
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Harm de Wit
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Anton W Langerak
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Marike J Gruijters
- Department of Paediatric Rheumatology, Erasmus MC Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Amani Mubarak
- Department of Paediatric Rheumatology, Erasmus MC Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Marleen Verkaaik
- Department of Paediatric Rheumatology, Erasmus MC Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Peter D Katsikis
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Marjan A Versnel
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Sylvia Kamphuis
- Department of Paediatric Rheumatology, Erasmus MC Sophia Children's Hospital, Rotterdam, The Netherlands
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17
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Bean J, Kuri-Cervantes L, Pennella M, Betts MR, Meyer NJ, Hassan WM. Multivariate indicators of disease severity in COVID-19. Sci Rep 2023; 13:5145. [PMID: 36991002 PMCID: PMC10054197 DOI: 10.1038/s41598-023-31683-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/15/2023] [Indexed: 03/31/2023] Open
Abstract
The novel coronavirus pandemic continues to cause significant morbidity and mortality around the world. Diverse clinical presentations prompted numerous attempts to predict disease severity to improve care and patient outcomes. Equally important is understanding the mechanisms underlying such divergent disease outcomes. Multivariate modeling was used here to define the most distinctive features that separate COVID-19 from healthy controls and severe from moderate disease. Using discriminant analysis and binary logistic regression models we could distinguish between severe disease, moderate disease, and control with rates of correct classifications ranging from 71 to 100%. The distinction of severe and moderate disease was most reliant on the depletion of natural killer cells and activated class-switched memory B cells, increased frequency of neutrophils, and decreased expression of the activation marker HLA-DR on monocytes in patients with severe disease. An increased frequency of activated class-switched memory B cells and activated neutrophils was seen in moderate compared to severe disease and control. Our results suggest that natural killer cells, activated class-switched memory B cells, and activated neutrophils are important for protection against severe disease. We show that binary logistic regression was superior to discriminant analysis by attaining higher rates of correct classification based on immune profiles. We discuss the utility of these multivariate techniques in biomedical sciences, contrast their mathematical basis and limitations, and propose strategies to overcome such limitations.
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Affiliation(s)
- Joe Bean
- Department of Biomedical Sciences, School of Medicine, University of Missouri - Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA
| | - Leticia Kuri-Cervantes
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael Pennella
- Department of Biomedical Sciences, School of Medicine, University of Missouri - Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nuala J Meyer
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Center for Translational Lung Biology, Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Wail M Hassan
- Department of Biomedical Sciences, School of Medicine, University of Missouri - Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA.
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18
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Nie Y, Liu Z, Cao W, Peng Y, Lu H, Sun R, Li J, Peng L, Zhou J, Fei Y, Li M, Zeng X, Li T, Zhang W. Memory CD4 +T cell profile is associated with unfavorable prognosis in IgG4-related disease: Risk stratification by machine-learning. Clin Immunol 2023; 252:109301. [PMID: 36958412 DOI: 10.1016/j.clim.2023.109301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/01/2022] [Accepted: 03/15/2023] [Indexed: 03/25/2023]
Abstract
IgG4-related disease (IgG4-RD) is a chronic immune-mediated disease with heterogeneity. In this study, we used machine-learning approaches to characterize the immune cell profiles and to identify the heterogeneity of IgG4-RD. The XGBoost model discriminated IgG4-RD from HCs with an area under the receiver operating characteristic curve of 0.963 in the testing set. There were two clusters of IgG4-RD by k-means clustering of immunological profiles. Cluster 1 featured higher proportions of memory CD4+T cell and were at higher risk of unfavorable prognosis in the follow-up, while cluster 2 featured higher proportions of naïve CD4+T cell. In the multivariate logistic regression, cluster 2 was shown to be a protective factor (OR 0.30, 95% CI 0.10-0.91, P = 0.011). Therefore, peripheral immunophenotyping might potentially stratify patients with IgG4-RD and predict those patients with a higher risk of relapse at early time.
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Affiliation(s)
- Yuxue Nie
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China
| | - Zheng Liu
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China; Department of Rheumatology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Wei Cao
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yu Peng
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China
| | - Hui Lu
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China
| | - Ruijie Sun
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China
| | - Jingna Li
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China
| | - Linyi Peng
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China
| | - Jiaxin Zhou
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China
| | - Yunyun Fei
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China
| | - Mengtao Li
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China
| | - Xiaofeng Zeng
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China
| | - Taisheng Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.
| | - Wen Zhang
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China.
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19
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Garcia-Donas J, Martínez-Urbistondo D, Velázquez Kennedy K, Villares P, Barquin A, Dominguez A, Rodriguez-Moreno JF, Caro E, Suarez del Villar R, Nistal-Villan E, Yagüe M, Ortiz M, Barba M, Ruiz-Llorente S, Quiralte M, Zanin M, Rodríguez C, Navarro P, Berraondo P, Madurga R. Randomized phase II clinical trial of ruxolitinib plus simvastatin in COVID19 clinical outcome and cytokine evolution. Front Immunol 2023; 14:1156603. [PMID: 37143685 PMCID: PMC10151807 DOI: 10.3389/fimmu.2023.1156603] [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: 02/01/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
Background Managing the inflammatory response to SARS-Cov-2 could prevent respiratory insufficiency. Cytokine profiles could identify cases at risk of severe disease. Methods We designed a randomized phase II clinical trial to determine whether the combination of ruxolitinib (5 mg twice a day for 7 days followed by 10 mg BID for 7 days) plus simvastatin (40 mg once a day for 14 days), could reduce the incidence of respiratory insufficiency in COVID-19. 48 cytokines were correlated with clinical outcome. Participants Patients admitted due to COVID-19 infection with mild disease. Results Up to 92 were included. Mean age was 64 ± 17, and 28 (30%) were female. 11 (22%) patients in the control arm and 6 (12%) in the experimental arm reached an OSCI grade of 5 or higher (p = 0.29). Unsupervised analysis of cytokines detected two clusters (CL-1 and CL-2). CL-1 presented a higher risk of clinical deterioration vs CL-2 (13 [33%] vs 2 [6%] cases, p = 0.009) and death (5 [11%] vs 0 cases, p = 0.059). Supervised Machine Learning (ML) analysis led to a model that predicted patient deterioration 48h before occurrence with a 85% accuracy. Conclusions Ruxolitinib plus simvastatin did not impact the outcome of COVID-19. Cytokine profiling identified patients at risk of severe COVID-19 and predicted clinical deterioration. Trial registration https://clinicaltrials.gov/, identifier NCT04348695.
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Affiliation(s)
- Jesus Garcia-Donas
- Gynecological, Genitourinary and Skin Cancer Unit HM CIOCC MADRID (Centro Integral Oncológico Clara Campal), Department of Basic Medical Sciences, Hospital Universitario HM Sanchinarro, HM Hospitales, Institute of Applied Molecular Medicine (IMMA), Facultad de Medicina, Universidad San Pablo CEU, CEU Universities, Madrid, Spain
- *Correspondence: Jesus Garcia-Donas, ;
| | | | | | - Paula Villares
- Internal Medicine Service Hospital HM Sanchinarro, Madrid, Spain
| | - Arántzazu Barquin
- Gynecological, Genitourinary and Skin Cancer Unit HM CIOCC MADRID (Centro Integral Oncológico Clara Campal), Department of Basic Medical Sciences, Hospital Universitario HM Sanchinarro, HM Hospitales, Institute of Applied Molecular Medicine (IMMA), Facultad de Medicina, Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Andrea Dominguez
- Internal Medicine Service Hospital HM Sanchinarro, Madrid, Spain
| | - Juan Francisco Rodriguez-Moreno
- Gynecological, Genitourinary and Skin Cancer Unit HM CIOCC MADRID (Centro Integral Oncológico Clara Campal), Department of Basic Medical Sciences, Hospital Universitario HM Sanchinarro, HM Hospitales, Institute of Applied Molecular Medicine (IMMA), Facultad de Medicina, Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Elena Caro
- Internal Medicine Service Hospital HM Sanchinarro, Madrid, Spain
| | | | - Estanislao Nistal-Villan
- Microbiology Section, Dpto. CC, Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, Madrid, Spain
- Facultad de Medicina, Instituto de Medicina Molecular Aplicada (IMMA), Universidad San Pablo-CEU, Madrid, Spain
| | - Monica Yagüe
- Laboratory of Innovation in Oncology HM CIOCC MADRID (Centro Integral Oncológico Clara Campal), Department of Basic Medical Sciences, Facultad de Medicina, Hospital Universitario HM Sanchinarro, HM Hospitales, Institute of Applied Molecular Medicine (IMMA), Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Maria Ortiz
- Clinical Trials Pharmacy, Clara Campal Comprehensive Cancer Center, Hospital Universitario de Sanchinarro, Madrid, Spain
| | - Maria Barba
- Laboratory of Innovation in Oncology HM CIOCC MADRID (Centro Integral Oncológico Clara Campal), Department of Basic Medical Sciences, Facultad de Medicina, Hospital Universitario HM Sanchinarro, HM Hospitales, Institute of Applied Molecular Medicine (IMMA), Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Sergio Ruiz-Llorente
- Laboratory of Innovation in Oncology HM CIOCC MADRID (Centro Integral Oncológico Clara Campal), Department of Basic Medical Sciences, Facultad de Medicina, Hospital Universitario HM Sanchinarro, HM Hospitales, Institute of Applied Molecular Medicine (IMMA), Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Miguel Quiralte
- Laboratory of Innovation in Oncology HM CIOCC MADRID (Centro Integral Oncológico Clara Campal), Department of Basic Medical Sciences, Facultad de Medicina, Hospital Universitario HM Sanchinarro, HM Hospitales, Institute of Applied Molecular Medicine (IMMA), Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Massimiliano Zanin
- Instituto de Física Interdisciplinar y Sistemas Complejos IFISC (CSIC-UIB), Palma de Mallorca, Spain
| | - Cristina Rodríguez
- Grupo de Cáncer Endocirno, Centro Nacional de Investigaciones Oncológicas, Madrid, Spain
| | - Paloma Navarro
- Laboratory of Innovation in Oncology HM CIOCC MADRID (Centro Integral Oncológico Clara Campal), Department of Basic Medical Sciences, Facultad de Medicina, Hospital Universitario HM Sanchinarro, HM Hospitales, Institute of Applied Molecular Medicine (IMMA), Universidad San Pablo CEU, CEU Universities, Madrid, Spain
| | - Pedro Berraondo
- Program of Immunology and Immunotherapy, Cima Universidad de Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Rodrigo Madurga
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid, Spain
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20
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Alexopoulos H, Trougakos IP, Dimopoulos MA, Terpos E. Clinical usefulness of testing for severe acute respiratory syndrome coronavirus 2 antibodies. Eur J Intern Med 2023; 107:7-16. [PMID: 36379820 PMCID: PMC9647045 DOI: 10.1016/j.ejim.2022.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/11/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022]
Abstract
In the COVID-19 pandemic era, antibody testing against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has proven an invaluable tool and herein we highlight some of the most useful clinical and/or epidemiological applications of humoral immune responses recording. Anti-spike circulating IgGs and SARS-CoV-2 neutralizing antibodies can serve as predictors of disease progression or disease prevention, whereas anti-nucleocapsid antibodies can help distinguishing infection from vaccination. Also, in the era of immunotherapies we address the validity of anti-SARS-CoV-2 antibody monitoring post-infection and/or vaccination following therapies with the popular anti-CD20 monoclonals, as well as in the context of various cancers or autoimmune conditions such as rheumatoid arthritis and multiple sclerosis. Additional crucial applications include population immunosurveillance, either at the general population or at specific communities such as health workers. Finally, we discuss how testing of antibodies in cerebrospinal fluid can inform us on the neurological complications that often accompany COVID-19.
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Affiliation(s)
- Harry Alexopoulos
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Athens, 15784, Greece
| | - Ioannis P Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Athens, 15784, Greece
| | - Meletios-Athanasios Dimopoulos
- Department of Clinical Therapeutics, School of Medicine, Alexandra General Hospital, National and Kapodistrian University of Athens, Athens, 11528, Greece
| | - Evangelos Terpos
- Department of Clinical Therapeutics, School of Medicine, Alexandra General Hospital, National and Kapodistrian University of Athens, Athens, 11528, Greece.
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21
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Yu Z, Li X, Zhao J, Sun S. Identification of hospitalized mortality of patients with COVID-19 by machine learning models based on blood inflammatory cytokines. Front Public Health 2022; 10:1001340. [PMID: 36466533 PMCID: PMC9715399 DOI: 10.3389/fpubh.2022.1001340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) spread worldwide and presented a significant threat to people's health. Inappropriate disease assessment and treatment strategies bring a heavy burden on healthcare systems. Our study aimed to construct predictive models to assess patients with COVID-19 who may have poor prognoses early and accurately. This research performed a retrospective analysis on two cohorts of patients with COVID-19. Data from the Barcelona cohort were used as the training set, and data from the Rotterdam cohort were used as the validation set. Cox regression, logistic regression, and different machine learning methods including random forest (RF), support vector machine (SVM), and decision tree (DT) were performed to construct COVID-19 death prognostic models. Based on multiple clinical characteristics and blood inflammatory cytokines during the first day of hospitalization for the 138 patients with COVID-19, we constructed various models to predict the in-hospital mortality of patients with COVID-19. All the models showed outstanding performance in identifying high-risk patients with COVID-19. The accuracy of the logistic regression, RF, and DT models is 86.96, 80.43, and 85.51%, respectively. Advanced age and the abnormal expression of some inflammatory cytokines including IFN-α, IL-8, and IL-6 have been proven to be closely associated with the prognosis of patients with COVID-19. The models we developed can assist doctors in developing appropriate COVID-19 treatment strategies, including allocating limited medical resources more rationally and early intervention in high-risk groups.
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Affiliation(s)
- Zhixiang Yu
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiayin Li
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jin Zhao
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Shiren Sun
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an, China,First Unit, Third Branch of Fangcang Shelter Hospital of National Exhibition and Convention Center, Shanghai, China,*Correspondence: Shiren Sun
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22
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de León UAP, Resendis-Antonio O. Macrophage Boolean networks in the time of SARS-CoV-2. Front Immunol 2022; 13:997434. [DOI: 10.3389/fimmu.2022.997434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022] Open
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23
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Arriaga-Canon C, Contreras-Espinosa L, Rebollar-Vega R, Montiel-Manríquez R, Cedro-Tanda A, García-Gordillo JA, Álvarez-Gómez RM, Jiménez-Trejo F, Castro-Hernández C, Herrera LA. Transcriptomics and RNA-Based Therapeutics as Potential Approaches to Manage SARS-CoV-2 Infection. Int J Mol Sci 2022; 23:11058. [PMID: 36232363 PMCID: PMC9570475 DOI: 10.3390/ijms231911058] [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: 08/01/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
SARS-CoV-2 is a coronavirus family member that appeared in China in December 2019 and caused the disease called COVID-19, which was declared a pandemic in 2020 by the World Health Organization. In recent months, great efforts have been made in the field of basic and clinical research to understand the biology and infection processes of SARS-CoV-2. In particular, transcriptome analysis has contributed to generating new knowledge of the viral sequences and intracellular signaling pathways that regulate the infection and pathogenesis of SARS-CoV-2, generating new information about its biology. Furthermore, transcriptomics approaches including spatial transcriptomics, single-cell transcriptomics and direct RNA sequencing have been used for clinical applications in monitoring, detection, diagnosis, and treatment to generate new clinical predictive models for SARS-CoV-2. Consequently, RNA-based therapeutics and their relationship with SARS-CoV-2 have emerged as promising strategies to battle the SARS-CoV-2 pandemic with the assistance of novel approaches such as CRISPR-CAS, ASOs, and siRNA systems. Lastly, we discuss the importance of precision public health in the management of patients infected with SARS-CoV-2 and establish that the fusion of transcriptomics, RNA-based therapeutics, and precision public health will allow a linkage for developing health systems that facilitate the acquisition of relevant clinical strategies for rapid decision making to assist in the management and treatment of the SARS-CoV-2-infected population to combat this global public health problem.
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Affiliation(s)
- Cristian Arriaga-Canon
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 ColC. Sección XVI, Tlalpan. C.P., Mexico City 14080, Mexico
| | - Laura Contreras-Espinosa
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 ColC. Sección XVI, Tlalpan. C.P., Mexico City 14080, Mexico
| | - Rosa Rebollar-Vega
- Genomics Laboratory, Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México, Vasco de Quiroga 15, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico
| | - Rogelio Montiel-Manríquez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 ColC. Sección XVI, Tlalpan. C.P., Mexico City 14080, Mexico
| | - Alberto Cedro-Tanda
- Instituto Nacional de Medicina Genómica, Periférico Sur 4809, Arenal Tepepan, Tlalpan. C.P., Mexico City 14610, Mexico
| | - José Antonio García-Gordillo
- Oncología Médica, Instituto Nacional de Cancerología, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan. C.P., Mexico City 14080, Mexico
| | - Rosa María Álvarez-Gómez
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan. C.P., Mexico City 14080, Mexico
| | - Francisco Jiménez-Trejo
- Instituto Nacional de Pediatría, Insurgentes Sur No. 3700-C, Coyoacán. C.P., Mexico City 04530, Mexico
| | - Clementina Castro-Hernández
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 ColC. Sección XVI, Tlalpan. C.P., Mexico City 14080, Mexico
| | - Luis A. Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 ColC. Sección XVI, Tlalpan. C.P., Mexico City 14080, Mexico
- Instituto Nacional de Medicina Genómica, Periférico Sur 4809, Arenal Tepepan, Tlalpan. C.P., Mexico City 14610, Mexico
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24
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Mavragani CP, Skarlis C, Kostopoulos IV, Maratou E, Moutsatsou P, Terpos E, Tsitsilonis OE, Dimopoulos MA, Sfikakis PP. Distinct type I interferon responses between younger women and older men contribute to the variability of COVID-19 outcomes: Hypothesis generating insights from COVID-19 convalescent individuals. Cytokine 2022; 157:155964. [PMID: 35868117 PMCID: PMC9289092 DOI: 10.1016/j.cyto.2022.155964] [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: 04/19/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/30/2022]
Abstract
Background/Objective Older age and male sex have been consistently found to be associated with dismal outcomes among COVID-19 infected patients. In contrast, premenopausal females present the lowest mortality among adults infected by SARS-CoV-2. The goal of the present study was to investigate whether peripheral blood type I interferon (IFN) signature and interleukin (IL)-6 serum levels -previously shown to contribute to COVID-19-related outcomes in hospitalized patients- is shaped by demographic contributors among COVID-19 convalescent individuals. Patients and Methods Type I IFN-inducible genes in peripheral blood, as well as serum IL-6 levels were quantified in 61 COVID-19 convalescent healthy individuals (34 females, 27 males; age range 18–70 years, mean 35.7 ± 15.9 years) who recovered from COVID-19 without requiring hospitalization within a median of 3 months prior to inclusion in the present study. Among those, 17 were older than 50 years (11 males, 6 females) and 44 equal to or less than 50 years (16 males, 28 females). Expression analysis of type I IFN-inducible genes (MX-1, IFIT-1, IFI44) was performed by real time PCR and a type I IFN score, reflecting type I IFN peripheral activity, was calculated. IL-6 and C-reactive protein levels were determined by a commercially available ELISA. Results COVID-19 convalescent individuals older than 50 years exhibited significantly decreased peripheral blood type I IFN scores along with significantly increased IL-6 serum levels compared to their younger counterparts less than 50 years old (5.4 ± 4.3 vs 16.8 ± 24.7, p = 0.02 and 10.6 ± 16.9 vs 2.9 ± 8.0 ng/L, p = 0.03, respectively). Following sex stratification, peripheral blood type I IFN score was found to be significantly higher in younger females compared to both younger and older males (22.9 ± 29.2 vs 6.3 ± 4.6 vs 4.5 ± 3.7, p = 0.01 and p = 0.002, respectively). Regarding IL-6, an opposite pattern was observed, with the highest levels being detected among older males and the lowest levels among younger females (11.6 ± 18.9 vs 2.5 ± 7.8 ng/L, p = 0.03). Conclusion Constitutive higher type I IFN responses and dampened IL-6 production observed in younger women of premenopausal age, along with lower type I IFN responses and increased IL-6 levels in older males, could account for the discrete clinical outcomes seen in the two population groups, as consistently revealed in COVID-19 epidemiological studies.
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Affiliation(s)
- Clio P Mavragani
- Department of Physiology, School of Medicine, National and Kapodistrian University of Athens (NKUA), M. Asias 75, 11527 Athens, Greece; Fourth Department of Internal Medicine, School of Medicine, University Hospital Attikon, NKUA, 12462 Haidari, Greece; Joint Academic Rheumatology Program, NKUA, Greece.
| | - Charalampos Skarlis
- Department of Physiology, School of Medicine, National and Kapodistrian University of Athens (NKUA), M. Asias 75, 11527 Athens, Greece
| | | | - Eirini Maratou
- Department of Clinical Biochemistry, School of Medicine, University General Hospital Attikon, NKUA, 12462 Haidari, Greece
| | - Paraskevi Moutsatsou
- Department of Clinical Biochemistry, School of Medicine, University General Hospital Attikon, NKUA, 12462 Haidari, Greece
| | - Evangelos Terpos
- Department of Clinical Therapeutics, School of Medicine, Alexandra General Hospital, NKUA, 11528 Athens, Greece
| | | | | | - Petros P Sfikakis
- Joint Academic Rheumatology Program, NKUA, Greece; First Department of Propaedeutic Internal Medicine, School of Medicine, Laiko General Hospital, NKUA, 15772 Athens, Greece
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25
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Sánchez-Montalvá A, Álvarez-Sierra D, Martínez-Gallo M, Perurena-Prieto J, Arrese-Muñoz I, Ruiz-Rodríguez JC, Espinosa-Pereiro J, Bosch-Nicolau P, Martínez-Gómez X, Antón A, Martínez-Valle F, Riveiro-Barciela M, Blanco-Grau A, Rodríguez-Frias F, Castellano-Escuder P, Poyatos-Canton E, Bas-Minguet J, Martínez-Cáceres E, Sánchez-Pla A, Zurera-Egea C, Teniente-Serra A, Hernández-González M, Pujol-Borrell R. Exposing and Overcoming Limitations of Clinical Laboratory Tests in COVID-19 by Adding Immunological Parameters; A Retrospective Cohort Analysis and Pilot Study. Front Immunol 2022; 13:902837. [PMID: 35844497 PMCID: PMC9276968 DOI: 10.3389/fimmu.2022.902837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Background Two years since the onset of the COVID-19 pandemic no predictive algorithm has been generally adopted for clinical management and in most algorithms the contribution of laboratory variables is limited. Objectives To measure the predictive performance of currently used clinical laboratory tests alone or combined with clinical variables and explore the predictive power of immunological tests adequate for clinical laboratories. Methods: Data from 2,600 COVID-19 patients of the first wave of the pandemic in the Barcelona area (exploratory cohort of 1,579, validation cohorts of 598 and 423 patients) including clinical parameters and laboratory tests were retrospectively collected. 28-day survival and maximal severity were the main outcomes considered in the multiparametric classical and machine learning statistical analysis. A pilot study was conducted in two subgroups (n=74 and n=41) measuring 17 cytokines and 27 lymphocyte phenotypes respectively. Findings 1) Despite a strong association of clinical and laboratory variables with the outcomes in classical pairwise analysis, the contribution of laboratory tests to the combined prediction power was limited by redundancy. Laboratory variables reflected only two types of processes: inflammation and organ damage but none reflected the immune response, one major determinant of prognosis. 2) Eight of the thirty variables: age, comorbidity index, oxygen saturation to fraction of inspired oxygen ratio, neutrophil-lymphocyte ratio, C-reactive protein, aspartate aminotransferase/alanine aminotransferase ratio, fibrinogen, and glomerular filtration rate captured most of the combined statistical predictive power. 3) The interpretation of clinical and laboratory variables was moderately improved by grouping them in two categories i.e., inflammation related biomarkers and organ damage related biomarkers; Age and organ damage-related biomarker tests were the best predictors of survival, and inflammatory-related ones were the best predictors of severity. 4) The pilot study identified immunological tests (CXCL10, IL-6, IL-1RA and CCL2), that performed better than most currently used laboratory tests. Conclusions Laboratory tests for clinical management of COVID 19 patients are valuable but limited predictors due to redundancy; this limitation could be overcome by adding immunological tests with independent predictive power. Understanding the limitations of tests in use would improve their interpretation and simplify clinical management but a systematic search for better immunological biomarkers is urgent and feasible.
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Affiliation(s)
- Adrián Sánchez-Montalvá
- Infectious Disease Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- International Health Program Institut Català de la Salut, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Department of Medicine, Universitat Autònoma Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Barcelona, Spain
| | - Daniel Álvarez-Sierra
- Translational Immunology Research Group, Vall Hebron Research Institute (VHIR), Barcelona, Spain
| | - Mónica Martínez-Gallo
- Translational Immunology Research Group, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Immunology Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma Barcelona, Barcelona, Spain
| | - Janire Perurena-Prieto
- Translational Immunology Research Group, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma Barcelona, Barcelona, Spain
| | - Iria Arrese-Muñoz
- Immunology Department, Hospital Universitari Vall Hebron, Barcelona, Spain
| | - Juan Carlos Ruiz-Rodríguez
- Intensive Medicine Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- Organ Dysfunction and Resuscitation Research Group, Vall Hebron Research Institute (VHIR), Barcelona, Spain
| | - Juan Espinosa-Pereiro
- Infectious Disease Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- International Health Program Institut Català de la Salut, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Barcelona, Spain
| | - Pau Bosch-Nicolau
- Infectious Disease Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- International Health Program Institut Català de la Salut, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Barcelona, Spain
| | - Xavier Martínez-Gómez
- Epidemiology and Public Health Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- Epidemiology and Public Health Research Group, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Epidemiology and Public Health, Universitat Autònoma Barcelona, Barcelona, Spain
| | - Andrés Antón
- Microbiology Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- Microbiology Research Group, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Department of Genetics and Microbiology, Autonomous University of Barcelona, Barcelona, Spain
| | - Ferran Martínez-Valle
- Department of Medicine, Universitat Autònoma Barcelona, Barcelona, Spain
- Internal Medicine Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- Systemic Disease Research Group, Valle Hebron Research Institute (VHIR), Barcelona, Spain
| | - Mar Riveiro-Barciela
- Department of Medicine, Universitat Autònoma Barcelona, Barcelona, Spain
- Liver Disease Research Group, Valle Hebron Research Institute (VHIR), Barcelona, Spain
- CIBERehd - Instituto de Salud Carlos III, Barcelona, Spain
| | - Albert Blanco-Grau
- Clinical Biochemistry Department, Hospital Universitari Vall d'Hebron and Clinical Biochemistry Research Group, Valle Hebron Research Institute (VHIR), Barcelona, Spain
| | - Francisco Rodríguez-Frias
- Clinical Biochemistry Department, Hospital Universitari Vall d'Hebron and Clinical Biochemistry Research Group, Valle Hebron Research Institute (VHIR), Barcelona, Spain
| | | | - Elisabet Poyatos-Canton
- Immunology Division, Bellvitge University Hospital, Hospitalet de Llobregat, Barcelona, Spain
| | - Jordi Bas-Minguet
- Immunology Division, Bellvitge University Hospital, Hospitalet de Llobregat, Barcelona, Spain
| | - Eva Martínez-Cáceres
- Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma Barcelona, Barcelona, Spain
- Immunology Group, Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona (Barcelona), Spain
- Immunology Department, Hospital Universitari Germans Trias Pujol, Badalona (Barcelona), Spain
| | - Alex Sánchez-Pla
- Bioinformatics and Statistics Group, University of Barcelona, Barcelona, Spain
- Statistics and Bioinformatics Unit, Vall Hebron Research Institute (VHIR), Barcelona, Spain
| | - Coral Zurera-Egea
- Immunology Department, Hospital Universitari Germans Trias Pujol, Badalona (Barcelona), Spain
| | - Aina Teniente-Serra
- Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma Barcelona, Barcelona, Spain
- Immunology Group, Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona (Barcelona), Spain
- Immunology Department, Hospital Universitari Germans Trias Pujol, Badalona (Barcelona), Spain
| | - Manuel Hernández-González
- Translational Immunology Research Group, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Immunology Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma Barcelona, Barcelona, Spain
| | - Ricardo Pujol-Borrell
- Translational Immunology Research Group, Vall Hebron Research Institute (VHIR), Barcelona, Spain
- Immunology Department, Hospital Universitari Vall Hebron, Barcelona, Spain
- Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma Barcelona, Barcelona, Spain
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Network-Based Methods for Approaching Human Pathologies from a Phenotypic Point of View. Genes (Basel) 2022; 13:genes13061081. [PMID: 35741843 PMCID: PMC9222217 DOI: 10.3390/genes13061081] [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: 05/13/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
Network and systemic approaches to studying human pathologies are helping us to gain insight into the molecular mechanisms of and potential therapeutic interventions for human diseases, especially for complex diseases where large numbers of genes are involved. The complex human pathological landscape is traditionally partitioned into discrete “diseases”; however, that partition is sometimes problematic, as diseases are highly heterogeneous and can differ greatly from one patient to another. Moreover, for many pathological states, the set of symptoms (phenotypes) manifested by the patient is not enough to diagnose a particular disease. On the contrary, phenotypes, by definition, are directly observable and can be closer to the molecular basis of the pathology. These clinical phenotypes are also important for personalised medicine, as they can help stratify patients and design personalised interventions. For these reasons, network and systemic approaches to pathologies are gradually incorporating phenotypic information. This review covers the current landscape of phenotype-centred network approaches to study different aspects of human diseases.
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27
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Tajuelo A, Carretero O, García-Ríos E, López-Siles M, Cano O, Vázquez M, Más V, Rodríguez-Goncer I, Lalueza A, López-Medrano F, Juan RS, Fernández-Ruiz M, Aguado JM, McConnell MJ, Pérez-Romero P. Brief Research Report: Virus-Specific Humoral Immunity at Admission Predicts the Development of Respiratory Failure in Unvaccinated SARS-CoV-2 Patients. Front Immunol 2022; 13:878812. [PMID: 35547738 PMCID: PMC9082065 DOI: 10.3389/fimmu.2022.878812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/29/2022] [Indexed: 01/09/2023] Open
Abstract
Introduction There is robust evidence indicating that the SARS-CoV-2-specific humoral response is associated with protection against severe disease. However, relatively little data exist regarding how the humoral immune response at the time of hospital admission correlates with disease severity in unimmunized patients. Our goal was toidentify variables of the humoral response that could potentially serve as prognostic markers for COVID-19 progressionin unvaccinated SARS-CoV-2 patients. Methods A prospective cross-sectional study was carried out in a cohort of 160 unimmunized, adult COVID-19 patients from the Hospital Universitario 12Octubre. Participants were classified into four clinical groups based on disease severity: non-survivors with respiratory failure (RF), RF survivors, patients requiring oxygen therapy and those not receiving oxygen therapy. Serum samples were taken on admission and IgM, IgG, IgG subclass antibody titers were determined by ELISA, and neutralizing antibody titersusing a surrogate neutralization assay. The differences in the antibody titers between groups and the association between the clinical and analytical characteristics of the patients and the antibody titers were analyzed. Results Patients that developed RF and survived had IgM titers that were 2-fold higher than non-survivors (p = 0.001), higher levels of total IgG than those who developed RF and succumbed to infection (p< 0.001), and than patients who required oxygen therapy (p< 0.05), and had 5-fold higher IgG1 titers than RF non-survivors (p< 0.001) and those who needed oxygen therapy (p< 0.001), and 2-fold higher than patients that did not require oxygen therapy during admission (p< 0.05). In contrast, RF non-survivorshad the lowest neutralizing antibodylevels, which were significantly lower compared those with RF that survived (p = 0.03). A positive correlation was found between IgM, total IgG, IgG1 and IgG3 titers and neutralizing antibody titers in the total cohort (p ≤ 0.0036). Conclusions We demonstrate that patients with RF that survived infection had significantly higher IgM, IgG, IgG1 and neutralizing titers compared to patients with RF that succumb to infection, suggesting that using humoral response variables could be used as a prognostic marker for guiding the clinical management of unimmunized patients admitted to the hospital for SARS-CoV-2 infection.
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Affiliation(s)
- Ana Tajuelo
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Octavio Carretero
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain
| | - Estéfani García-Ríos
- Infecciones Víricas e Inmunidad en Enfermos Inmunodeprimidos, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Universidad Internacional de Valencia - VIU, Valencia, Spain
| | - Mireia López-Siles
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Olga Cano
- Biología Viral, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Mónica Vázquez
- Biología Viral, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Vicente Más
- Biología Viral, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Isabel Rodríguez-Goncer
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain
| | - Antonio Lalueza
- Department of Internal Medicine, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Francisco López-Medrano
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain.,Department of Medicine, Universidad Complutense, Madrid, Spain
| | - Rafael San Juan
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain.,Department of Medicine, Universidad Complutense, Madrid, Spain
| | - Mario Fernández-Ruiz
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain.,Department of Medicine, Universidad Complutense, Madrid, Spain
| | - José Mᵃ Aguado
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre", Instituto de Investigación Sanitaria Hospital "12 de Octubre" (imas12), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain.,Department of Medicine, Universidad Complutense, Madrid, Spain
| | - Michael J McConnell
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Pilar Pérez-Romero
- Infecciones Víricas e Inmunidad en Enfermos Inmunodeprimidos, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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Wang H, Jia S, Li Z, Duan Y, Tao G, Zhao Z. A Comprehensive Review of Artificial Intelligence in Prevention and Treatment of COVID-19 Pandemic. Front Genet 2022; 13:845305. [PMID: 35559010 PMCID: PMC9086537 DOI: 10.3389/fgene.2022.845305] [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: 12/29/2021] [Accepted: 03/30/2022] [Indexed: 11/13/2022] Open
Abstract
The unprecedented outbreak of the Corona Virus Disease 2019 (COVID-19) pandemic has seriously affected numerous countries in the world from various aspects such as education, economy, social security, public health, etc. Most governments have made great efforts to control the spread of COVID-19, e.g., locking down hard-hit cities and advocating masks for the population. However, some countries and regions have relatively poor medical conditions in terms of insufficient medical equipment, hospital capacity overload, personnel shortage, and other problems, resulting in the large-scale spread of the epidemic. With the unique advantages of Artificial Intelligence (AI), it plays an extremely important role in medical imaging, clinical data, drug development, epidemic prediction, and telemedicine. Therefore, AI is a powerful tool that can help humans solve complex problems, especially in the fight against COVID-19. This study aims to analyze past research results and interpret the role of Artificial Intelligence in the prevention and treatment of COVID-19 from five aspects. In this paper, we also discuss the future development directions in different fields and prove the validity of the models through experiments, which will help researchers develop more efficient models to control the spread of COVID-19.
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Affiliation(s)
- Haishuai Wang
- College of Computer Science, Zhejiang University, Hangzhou, China
| | - Shangru Jia
- Department of Computer and Information Engineering, Tianjin Normal University, Tianjin, China
| | - Zhao Li
- Alibaba-ZJU Joint Research Institute of Frontier Technologies, Zhejiang University, Hangzhou, China
| | - Yucong Duan
- College of Computer Science and Technology, Hainan University, Haikou, China
| | - Guangyu Tao
- Department of Radiology, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Ziping Zhao
- Department of Computer and Information Engineering, Tianjin Normal University, Tianjin, China
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29
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Severe COVID-19 is characterised by inflammation and immature myeloid cells early in disease progression. Heliyon 2022; 8:e09230. [PMID: 35386227 PMCID: PMC8973020 DOI: 10.1016/j.heliyon.2022.e09230] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/20/2021] [Accepted: 03/28/2022] [Indexed: 12/21/2022] Open
Abstract
SARS-CoV-2 infection causes a wide spectrum of disease severity. Identifying the immunological characteristics of severe disease and the risk factors for their development are important in the management of COVID-19. This study aimed to identify and rank clinical and immunological features associated with progression to severe COVID-19 in order to investigate an immunological signature of severe disease. One hundred and eight patients with positive SARS-CoV-2 PCR were recruited. Routine clinical and laboratory markers were measured, as well as myeloid and lymphoid whole-blood immunophenotyping and measurement of the pro-inflammatory cytokines IL-6 and soluble CD25. All analysis was carried out in a routine hospital diagnostic laboratory. Univariate analysis demonstrated that severe disease was most strongly associated with elevated CRP and IL-6, loss of DLA-DR expression on monocytes and CD10 expression on neutrophils. Unbiased machine learning demonstrated that these four features were strongly associated with severe disease, with an average prediction score for severe disease of 0.925. These results demonstrate that these four markers could be used to identify patients developing severe COVID-19 and allow timely delivery of therapeutics. Severe COVID-19 is characterised by a combination of emergency myelopoiesis and inflammation. These changes can be rapidly identified in a diagnostic laboratory, facilitating intervention. This disease signature was derived from a cohort of patients with a wide range of ages, frailty and COVID-19 severity.
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