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Ta CN, Zucker JE, Chiu PH, Fang Y, Natarajan K, Weng C. Clinical and temporal characterization of COVID-19 subgroups using patient vector embeddings of electronic health records. J Am Med Inform Assoc 2023; 30:256-272. [PMID: 36255273 PMCID: PMC9620768 DOI: 10.1093/jamia/ocac208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/05/2022] [Accepted: 10/17/2022] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVE To identify and characterize clinical subgroups of hospitalized Coronavirus Disease 2019 (COVID-19) patients. MATERIALS AND METHODS Electronic health records of hospitalized COVID-19 patients at NewYork-Presbyterian/Columbia University Irving Medical Center were temporally sequenced and transformed into patient vector representations using Paragraph Vector models. K-means clustering was performed to identify subgroups. RESULTS A diverse cohort of 11 313 patients with COVID-19 and hospitalizations between March 2, 2020 and December 1, 2021 were identified; median [IQR] age: 61.2 [40.3-74.3]; 51.5% female. Twenty subgroups of hospitalized COVID-19 patients, labeled by increasing severity, were characterized by their demographics, conditions, outcomes, and severity (mild-moderate/severe/critical). Subgroup temporal patterns were characterized by the durations in each subgroup, transitions between subgroups, and the complete paths throughout the course of hospitalization. DISCUSSION Several subgroups had mild-moderate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections but were hospitalized for underlying conditions (pregnancy, cardiovascular disease [CVD], etc.). Subgroup 7 included solid organ transplant recipients who mostly developed mild-moderate or severe disease. Subgroup 9 had a history of type-2 diabetes, kidney and CVD, and suffered the highest rates of heart failure (45.2%) and end-stage renal disease (80.6%). Subgroup 13 was the oldest (median: 82.7 years) and had mixed severity but high mortality (33.3%). Subgroup 17 had critical disease and the highest mortality (64.6%), with age (median: 68.1 years) being the only notable risk factor. Subgroups 18-20 had critical disease with high complication rates and long hospitalizations (median: 40+ days). All subgroups are detailed in the full text. A chord diagram depicts the most common transitions, and paths with the highest prevalence, longest hospitalizations, lowest and highest mortalities are presented. Understanding these subgroups and their pathways may aid clinicians in their decisions for better management and earlier intervention for patients.
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Affiliation(s)
- Casey N Ta
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York, USA
| | - Jason E Zucker
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Po-Hsiang Chiu
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York, USA
| | - Yilu Fang
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York, USA
| | - Karthik Natarajan
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York, USA
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Dong Z, Yan Q, Cao W, Liu Z, Wang X. Identification of key molecules in COVID-19 patients significantly correlated with clinical outcomes by analyzing transcriptomic data. Front Immunol 2022; 13:930866. [PMID: 36072597 PMCID: PMC9441550 DOI: 10.3389/fimmu.2022.930866] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/03/2022] [Indexed: 12/15/2022] Open
Abstract
Background Although several key molecules have been identified to modulate SARS-CoV-2 invasion of human host cells, the molecules correlated with outcomes in COVID-19 caused by SARS-CoV-2 infection remain insufficiently explored. Methods This study analyzed three RNA-Seq gene expression profiling datasets for COVID-19 and identified differentially expressed genes (DEGs) between COVID-19 patients and normal people, commonly in the three datasets. Furthermore, this study explored the correlation between the expression of these genes and clinical features in COVID-19 patients. Results This analysis identified 13 genes significantly upregulated in COVID-19 patients’ leukocyte and SARS-CoV-2-infected nasopharyngeal tissue compared to normal tissue. These genes included OAS1, OAS2, OAS3, OASL, HERC6, SERPING1, IFI6, IFI44, IFI44L, CMPK2, RSAD2, EPSTI1, and CXCL10, all of which are involved in antiviral immune regulation. We found that these genes’ downregulation was associated with worse clinical outcomes in COVID-19 patients, such as intensive care unit (ICU) admission, mechanical ventilatory support (MVS) requirement, elevated D-dimer levels, and increased viral loads. Furthermore, this analysis identified two COVID-19 clusters based on the expression profiles of the 13 genes, termed COV-C1 and COV-C2. Compared with COV-C1, COV-C2 more highly expressed the 13 genes, had stronger antiviral immune responses, were younger, and displayed more favorable clinical outcomes. Conclusions A strong antiviral immune response is essential in reducing severity of COVID-19.
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Affiliation(s)
- Zehua Dong
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, China
| | - Qiyu Yan
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, China
| | - Wenxiu Cao
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, China
| | - Zhixian Liu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Zhixian Liu, ; Xiaosheng Wang,
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, China
- *Correspondence: Zhixian Liu, ; Xiaosheng Wang,
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Valarezo-Sevilla D, Sarzosa-Terán V. The enemy is the virus, not the vaccine. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.02.56] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
If we remember very superficially a little about the complex human immune system, a part of this immune system is made up of leukocytes (especially phagocytes and lymphocytes) that are responsible for detecting invaders and sending them defensive markers that adhere to them (the antibodies) and also to destroy the invaders identified by the system; In addition to the already mentioned leukocytes, our immune system is made up of various other elements such as cells, proteins, tissues and organs, which defend us against germs and microorganisms. 1, 2
Speaking specifically about the immune system and COVID-19, the events mainly involved in the immunopathogenesis of COVID-19 and the dysregulation of the immune response include lymphopenia and increased neutrophil-to-lymphocyte ratio, cytokines, lymphocyte depletion and dysfunction, antibody-dependent enhancement, and monocyte and granulocyte abnormalities. It must be emphasized that lymphopenia is an essential finding in most patients with COVID-19, particularly in those with a severe phenotype.3 It has been shown that multiple viral proteins induce T cells after infection and that T cells that have antiviral signatures related to safety and protection can be achieved by vaccination.4
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Gönen MS, Alaylıoğlu M, Durcan E, Özdemir Y, Şahin S, Konukoğlu D, Nohut OK, Ürkmez S, Küçükece B, Balkan İİ, Kara HV, Börekçi Ş, Özkaya H, Kutlubay Z, Dikmen Y, Keskindemirci Y, Karras SN, Annweiler C, Gezen-Ak D, Dursun E. Rapid and Effective Vitamin D Supplementation May Present Better Clinical Outcomes in COVID-19 (SARS-CoV-2) Patients by Altering Serum INOS1, IL1B, IFNg, Cathelicidin-LL37, and ICAM1. Nutrients 2021; 13:4047. [PMID: 34836309 PMCID: PMC8618389 DOI: 10.3390/nu13114047] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND We aimed to establish an acute treatment protocol to increase serum vitamin D, evaluate the effectiveness of vitamin D3 supplementation, and reveal the potential mechanisms in COVID-19. METHODS We retrospectively analyzed the data of 867 COVID-19 cases. Then, a prospective study was conducted, including 23 healthy individuals and 210 cases. A total of 163 cases had vitamin D supplementation, and 95 were followed for 14 days. Clinical outcomes, routine blood biomarkers, serum levels of vitamin D metabolism, and action mechanism-related parameters were evaluated. RESULTS Our treatment protocol increased the serum 25OHD levels significantly to above 30 ng/mL within two weeks. COVID-19 cases (no comorbidities, no vitamin D treatment, 25OHD <30 ng/mL) had 1.9-fold increased risk of having hospitalization longer than 8 days compared with the cases with comorbidities and vitamin D treatment. Having vitamin D treatment decreased the mortality rate by 2.14 times. The correlation analysis of specific serum biomarkers with 25OHD indicated that the vitamin D action in COVID-19 might involve regulation of INOS1, IL1B, IFNg, cathelicidin-LL37, and ICAM1. CONCLUSIONS Vitamin D treatment shortened hospital stay and decreased mortality in COVID-19 cases, even in the existence of comorbidities. Vitamin D supplementation is effective on various target parameters; therefore, it is essential for COVID-19 treatment.
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Affiliation(s)
- Mustafa Sait Gönen
- Endocrinology and Metabolism Unit, Department of Internal Medicine, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey; (M.S.G.); (E.D.); (S.Ş.); (H.Ö.)
| | - Merve Alaylıoğlu
- Brain and Neurodegenerative Disorders Research Laboratories, Department of Medical Biology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey;
| | - Emre Durcan
- Endocrinology and Metabolism Unit, Department of Internal Medicine, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey; (M.S.G.); (E.D.); (S.Ş.); (H.Ö.)
| | - Yusuf Özdemir
- Department of Infectious Diseases and Clinical Microbiology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey; (Y.Ö.); (İ.İ.B.)
| | - Serdar Şahin
- Endocrinology and Metabolism Unit, Department of Internal Medicine, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey; (M.S.G.); (E.D.); (S.Ş.); (H.Ö.)
| | - Dildar Konukoğlu
- Department of Medical Biochemistry, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey;
| | - Okan Kadir Nohut
- Fikert Biyal Biochemistry Laboratory, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey;
| | - Seval Ürkmez
- Department of Anesthesiology and Reanimation, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey; (S.Ü.); (Y.D.)
| | - Berna Küçükece
- Cerrahpasa Hospital Pharmacy Unit, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey;
| | - İlker İnanç Balkan
- Department of Infectious Diseases and Clinical Microbiology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey; (Y.Ö.); (İ.İ.B.)
| | - H. Volkan Kara
- Department of Thoracic Surgery, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey;
| | - Şermin Börekçi
- Department of Pulmonary Diseases, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey;
| | - Hande Özkaya
- Endocrinology and Metabolism Unit, Department of Internal Medicine, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey; (M.S.G.); (E.D.); (S.Ş.); (H.Ö.)
| | - Zekayi Kutlubay
- Dermatology and Venerology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey;
| | - Yalım Dikmen
- Department of Anesthesiology and Reanimation, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey; (S.Ü.); (Y.D.)
| | - Yılmaz Keskindemirci
- General Directorate of Hospitals, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey;
- Department of Medical Services and Techniques, Health Services Vocational School, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey
| | | | - Cedric Annweiler
- Division of Geriatric Medicine, Department of Neuroscience, Angers University Hospital, 49035 Angers, France;
- Department of Medical Biophysics, Robarts Research Institute, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Duygu Gezen-Ak
- Brain and Neurodegenerative Disorders Research Laboratories, Department of Medical Biology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey;
| | - Erdinç Dursun
- Brain and Neurodegenerative Disorders Research Laboratories, Department of Medical Biology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey;
- Department of Neuroscience, Institute of Neurological Sciences, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey
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