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Lin Y, Postma DF, Steeneken LS, Melo dos Santos LS, Kirkland JL, Espindola‐Netto JM, Tchkonia T, Borghesan M, Bouma HR, Demaria M. Circulating monocytes expressing senescence-associated features are enriched in COVID-19 patients with severe disease. Aging Cell 2023; 22:e14011. [PMID: 37969056 PMCID: PMC10726854 DOI: 10.1111/acel.14011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 11/17/2023] Open
Abstract
Accurate biomarkers for predicting COVID-19 severity have remained an unmet need due to an incomplete understanding of virus pathogenesis and heterogeneity among patients. Cellular senescence and its pro-inflammatory phenotype are suggested to be a consequence of SARS-CoV-2 infection and potentially drive infection-dependent pathological sequelae. Senescence-associated markers in infected individuals have been identified primarily in the lower respiratory tract, while little is known about their presence in more easily accessible bio-specimens. Here, we measured the abundance of senescence-associated signatures in whole blood, plasma and peripheral blood mononuclear cells (PBMCs) of COVID-19 patients and patients without an infection. Bulk transcriptomic and targeted proteomic assays revealed that the level of senescence-associated markers, including the senescence-associated secretory phenotype (SASP), is predictive of SARS-CoV-2 infection. Single-cell RNA-sequencing data demonstrated that a senescence signature is particularly enriched in monocytes of COVID-19 patients, partially correlating with disease severity. Our findings suggest that monocytes are prematurely induced to senescence by SARS-CoV-2 infection, might contribute to exacerbating a SASP-like inflammatory response and can serve as markers and predictors for COVID-19 and its sequelae.
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Affiliation(s)
- Y. Lin
- European Research Institute for the Biology of Ageing (ERIBA)University Medical Center Groningen (UMCG), University of Groningen (RUG)GroningenNetherlands
| | - D. F. Postma
- Department of Internal Medicine and Infectious DiseasesUniversity Medical Center Groningen (UMCG)GroningenThe Netherlands
| | - L. S. Steeneken
- European Research Institute for the Biology of Ageing (ERIBA)University Medical Center Groningen (UMCG), University of Groningen (RUG)GroningenNetherlands
| | - L. S. Melo dos Santos
- European Research Institute for the Biology of Ageing (ERIBA)University Medical Center Groningen (UMCG), University of Groningen (RUG)GroningenNetherlands
| | - J. L. Kirkland
- Clinical Pharmacy & PharmacologyUniversity Medical Center Groningen (UMCG)GroningenThe Netherlands
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMinnesotaUSA
| | - J. M. Espindola‐Netto
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMinnesotaUSA
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
| | - T. Tchkonia
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMinnesotaUSA
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
| | - M. Borghesan
- European Research Institute for the Biology of Ageing (ERIBA)University Medical Center Groningen (UMCG), University of Groningen (RUG)GroningenNetherlands
| | - H. R. Bouma
- Department of Internal Medicine and Infectious DiseasesUniversity Medical Center Groningen (UMCG)GroningenThe Netherlands
- Clinical Pharmacy & PharmacologyUniversity Medical Center Groningen (UMCG)GroningenThe Netherlands
| | - M. Demaria
- European Research Institute for the Biology of Ageing (ERIBA)University Medical Center Groningen (UMCG), University of Groningen (RUG)GroningenNetherlands
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Salihefendić L, Čeko I, Bešić L, Mulahuseinović N, Durgut S, Pećar D, Prnjavorac L, Kandić E, Meseldžić N, Bego T, Prnjavorac B, Marjanović D, Konjhodžić R, Ašić A. Identification of human genetic variants modulating the course of COVID-19 infection with importance in other viral infections. Front Genet 2023; 14:1240245. [PMID: 37795240 PMCID: PMC10545899 DOI: 10.3389/fgene.2023.1240245] [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: 06/14/2023] [Accepted: 08/11/2023] [Indexed: 10/06/2023] Open
Abstract
Introduction: COVID-19 has been a major focus of scientific research since early 2020. Due to its societal, economic, and clinical impact worldwide, research efforts aimed, among other questions, to address the effect of host genetics in susceptibility and severity of COVID-19. Methods: We, therefore, performed next-generation sequencing of coding and regulatory regions of 16 human genes, involved in maintenance of the immune system or encoding receptors for viral entry into the host cells, in a subset of 60 COVID-19 patients from the General Hospital Tešanj, Bosnia and Herzegovina, classified into three groups of clinical conditions of different severity ("mild," "moderate," and "severe"). Results: We confirmed that the male sex and older age are risk factors for severe clinical picture and identified 13 variants on seven genes (CD55, IL1B, IL4, IRF7, DDX58, TMPRSS2, and ACE2) with potential functional significance, either as genetic markers of modulated susceptibility to SARS-CoV-2 infection or modifiers of the infection severity. Our results include variants reported for the first time as potentially associated with COVID-19, but further research and larger patient cohorts are required to confirm their effect. Discussion: Such studies, focused on candidate genes and/or variants, have a potential to answer the questions regarding the effect of human genetic makeup on the expected infection outcome. In addition, loci we identified here were previously reported to have clinical significance in other diseases and viral infections, thus confirming a general, broader significance of COVID-19-related research results following the end of the pandemic period.
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Affiliation(s)
- Lana Salihefendić
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Ivana Čeko
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Larisa Bešić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | | | - Selma Durgut
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
| | - Dino Pećar
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
| | | | - Enis Kandić
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
| | - Neven Meseldžić
- Department of Pharmaceutical Biochemistry and Laboratory Diagnostics, Faculty of Pharmacy, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Tamer Bego
- Department of Pharmaceutical Biochemistry and Laboratory Diagnostics, Faculty of Pharmacy, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | | | - Damir Marjanović
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
- Institute for Anthropological Research, University of Zagreb, Zagreb, Croatia
| | - Rijad Konjhodžić
- ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Adna Ašić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
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Zhang J, Shu X, Deng R, Yang Z, Shu M, Ou X, Zhang X, Wu Z, Zeng H, Shao L. Transcriptome Changes of Hematopoietic Stem and Progenitor Cells in the Peripheral Blood of COVID-19 Patients by scRNA-seq. Int J Mol Sci 2023; 24:10878. [PMID: 37446049 DOI: 10.3390/ijms241310878] [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: 05/18/2023] [Revised: 06/19/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) threatens public health all over the world. It is well-accepted that the immune cells in peripheral blood are widely involved in the pathological process of COVID-19. However, hematopoietic stem and progenitor cells (HSPCs), as the main source of peripheral immune cells, have not been well studied during COVID-19 infection. We comprehensively revealed the transcriptome changes of peripheral blood HSPCs after COVID-19 infection and vaccination by single-cell RNA-seq. Compared with healthy individuals, the proportion of HSPCs in COVID-19 patients significantly increased. The increase in the proportion of HSPCs might be partly attributed to the enhancement of the HSPCs proliferation upon COVID-19 infection. However, the stemness damage of HSPCs is reflected by the decrease of differentiation signal, which can be used as a potential specific indicator of the severity and duration of COVID-19 infection. Type I interferon (IFN-I) and translation signals in HSPCs were mostly activated and inhibited after COVID-19 infection, respectively. In addition, the response of COVID-19 vaccination to the body is mild, while the secondary vaccination strengthens the immune response of primary vaccination. In conclusion, our study provides new insights into understanding the immune mechanism of COVID-19 infection.
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Affiliation(s)
- Jinfu Zhang
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
| | - Xin Shu
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
| | - Rong Deng
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
| | - Zihao Yang
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
| | - Manling Shu
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
| | - Xiangying Ou
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
| | - Xuan Zhang
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
| | - Zhenyu Wu
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
| | - Huihong Zeng
- Department of Histology and Embryology, School of Basic Medicine, Nanchang University, Nanchang 330006, China
| | - Lijian Shao
- Department of Occupational Health and Toxicology, School of Public Health, Nanchang University, Nanchang 330006, China
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van der Pan K, Khatri I, de Jager AL, Louis A, Kassem S, Naber BA, de Laat IF, Hameetman M, Comans SE, Orfao A, van Dongen JJ, Díez P, Teodosio C. Performance of spectral flow cytometry and mass cytometry for the study of innate myeloid cell populations. Front Immunol 2023; 14:1191992. [PMID: 37275858 PMCID: PMC10235610 DOI: 10.3389/fimmu.2023.1191992] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/05/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Monitoring of innate myeloid cells (IMC) is broadly applied in basic and translational research, as well as in diagnostic patient care. Due to their immunophenotypic heterogeneity and biological plasticity, analysis of IMC populations typically requires large panels of markers. Currently, two cytometry-based techniques allow for the simultaneous detection of ≥40 markers: spectral flow cytometry (SFC) and mass cytometry (MC). However, little is known about the comparability of SFC and MC in studying IMC populations. Methods We evaluated the performance of two SFC and MC panels, which contained 21 common markers, for the identification and subsetting of blood IMC populations. Based on unsupervised clustering analysis, we systematically identified 24 leukocyte populations, including 21 IMC subsets, regardless of the cytometry technique. Results Overall, comparable results were observed between the two technologies regarding the relative distribution of these cell populations and the staining resolution of individual markers (Pearson's ρ=0.99 and 0.55, respectively). However, minor differences were observed between the two techniques regarding intra-measurement variability (median coefficient of variation of 42.5% vs. 68.0% in SFC and MC, respectively; p<0.0001) and reproducibility, which were most likely due to the significantly longer acquisition times (median 16 min vs. 159 min) and lower recovery rates (median 53.1% vs. 26.8%) associated with SFC vs. MC. Discussion Altogether, our results show a good correlation between SFC and MC for the identification, enumeration and characterization of IMC in blood, based on large panels (>20) of antibody reagents.
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Affiliation(s)
- Kyra van der Pan
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Indu Khatri
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Anniek L. de Jager
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Alesha Louis
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Sara Kassem
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Brigitta A.E. Naber
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Inge F. de Laat
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Marjolijn Hameetman
- Flow Cytometry Core Facility, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Suzanne E.T. Comans
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Alberto Orfao
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca - CSIC), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Jacques J.M. van Dongen
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca - CSIC), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Paula Díez
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
- Sarcomas and Experimental Therapeutics Laboratory, Health Research Institute of Asturias (ISPA) and Asturias Central University Hospital (HUCA), Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Asturias, Spain
| | - Cristina Teodosio
- Department of Immunology, Leiden University Medical Center (LUMC), Leiden, Netherlands
- Translational and Clinical Research Program, Cancer Research Center (IBMCC; University of Salamanca - CSIC), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
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5
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Martínez-Diz S, Marín-Benesiu F, López-Torres G, Santiago O, Díaz-Cuéllar JF, Martín-Esteban S, Cortés-Valverde AI, Arenas-Rodríguez V, Cuenca-López S, Porras-Quesada P, Ruiz-Ruiz C, Abadía-Molina AC, Entrala-Bernal C, Martínez-González LJ, Álvarez-Cubero MJ. Relevance of TMPRSS2, CD163/CD206, and CD33 in clinical severity stratification of COVID-19. Front Immunol 2023; 13:1094644. [PMID: 36969980 PMCID: PMC10031647 DOI: 10.3389/fimmu.2022.1094644] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/15/2022] [Indexed: 03/10/2023] Open
Abstract
BackgroundApproximately 13.8% and 6.1% of coronavirus disease 2019 (COVID-19) patients require hospitalization and sometimes intensive care unit (ICU) admission, respectively. There is no biomarker to predict which of these patients will develop an aggressive stage that we could improve their quality of life and healthcare management. Our main goal is to include new markers for the classification of COVID-19 patients.MethodsTwo tubes of peripheral blood were collected from a total of 66 (n = 34 mild and n = 32 severe) samples (mean age 52 years). Cytometry analysis was performed using a 15-parameter panel included in the Maxpar® Human Monocyte/Macrophage Phenotyping Panel Kit. Cytometry by time-of-flight mass spectrometry (CyTOF) panel was performed in combination with genetic analysis using TaqMan® probes for ACE2 (rs2285666), MX1 (rs469390), and TMPRSS2 (rs2070788) variants. GemStone™ and OMIQ software were used for cytometry analysis.ResultsThe frequency of CD163+/CD206- population of transitional monocytes (T-Mo) was decreased in the mild group compared to that of the severe one, while T-Mo CD163-/CD206- were increased in the mild group compared to that of the severe one. In addition, we also found differences in CD11b expression in CD14dim monocytes in the severe group, with decreased levels in the female group (p = 0.0412). When comparing mild and severe disease, we also found that CD45- [p = 0.014; odds ratio (OR) = 0.286, 95% CI 0.104–0.787] and CD14dim/CD33+ (p = 0.014; OR = 0.286, 95% CI 0.104–0.787) monocytes were the best options as biomarkers to discriminate between these patient groups. CD33 was also indicated as a good biomarker for patient stratification by the analysis of GemStone™ software. Among genetic markers, we found that G carriers of TMPRSS2 (rs2070788) have an increased risk (p = 0.02; OR = 3.37, 95% CI 1.18–9.60) of severe COVID-19 compared to those with A/A genotype. This strength is further increased when combined with CD45-, T-Mo CD163+/CD206-, and C14dim/CD33+.ConclusionsHere, we report the interesting role of TMPRSS2, CD45-, CD163/CD206, and CD33 in COVID-19 aggressiveness. This strength is reinforced for aggressiveness biomarkers when TMPRSS2 and CD45-, TMPRSS2 and CD163/CD206, and TMPRSS2 and CD14dim/CD33+ are combined.
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Affiliation(s)
- Silvia Martínez-Diz
- Preventive Medicine and Public Health Service, Hospital Universitario Clínico San Cecilio, Granada, Spain
| | - Fernando Marín-Benesiu
- GENYO, Center for Genomics and Oncological Research, Granada, Spain
- Department of Biochemistry, Molecular Biology III and Immunology, Faculty of Medicine, University of Granada, Granada, Spain
| | | | - Olivia Santiago
- GENYO, Center for Genomics and Oncological Research, Granada, Spain
| | | | | | | | | | | | | | - Carmen Ruiz-Ruiz
- Department of Biochemistry, Molecular Biology III and Immunology, Faculty of Medicine, University of Granada, Granada, Spain
- Immunology Unit, Institute of Regenerative Biomedicine (IBIMER), Center for Biomedical Research Center (CIBM), University of Granada, Granada, Spain
| | - Ana C. Abadía-Molina
- Department of Biochemistry, Molecular Biology III and Immunology, Faculty of Medicine, University of Granada, Granada, Spain
- Immunology Unit, Institute of Regenerative Biomedicine (IBIMER), Center for Biomedical Research Center (CIBM), University of Granada, Granada, Spain
| | - Carmen Entrala-Bernal
- LORGEN G.P., PT, Ciencias de la Salud - Business Innovation Centre (BIC), Granada, Spain
| | - Luis J. Martínez-González
- GENYO, Center for Genomics and Oncological Research, Granada, Spain
- *Correspondence: Luis J. Martínez-González,
| | - Maria Jesus Álvarez-Cubero
- GENYO, Center for Genomics and Oncological Research, Granada, Spain
- Department of Biochemistry, Molecular Biology III and Immunology, Faculty of Medicine, University of Granada, Granada, Spain
- Biosanitary Research Institute (ibs. GRANADA), University of Granada, Granada, Spain
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6
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Zhu K, Chen Z, Xiao Y, Lai D, Wang X, Fang X, Shu Q. Multi-omics and immune cells' profiling of COVID-19 patients for ICU admission prediction: in silico analysis and an integrated machine learning-based approach in the framework of Predictive, Preventive, and Personalized Medicine. EPMA J 2023; 14:1-17. [PMID: 36845281 PMCID: PMC9942629 DOI: 10.1007/s13167-023-00317-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/01/2023] [Indexed: 02/23/2023]
Abstract
Background Intensive care unit admission (ICUA) triage has been urgent need for solving the shortage of ICU beds, during the coronavirus disease 2019 (COVID-19) surge. In silico analysis and integrated machine learning (ML) approach, based on multi-omics and immune cells (ICs) profiling, might provide solutions for this issue in the framework of predictive, preventive, and personalized medicine (PPPM). Methods Multi-omics was used to screen the synchronous differentially expressed protein-coding genes (SDEpcGs), and an integrated ML approach to develop and validate a nomogram for prediction of ICUA. Finally, the independent risk factor (IRF) with ICs profiling of the ICUA was identified. Results Colony-stimulating factor 1 receptor (CSF1R) and peptidase inhibitor 16 (PI16) were identified as SDEpcGs, and each fold change (FCij) of CSF1R and PI16 was selected to develop and validate a nomogram to predict ICUA. The area under curve (AUC) of the nomogram was 0.872 (95% confidence interval (CI): 0.707 to 0.950) on the training set, and 0.822 (95% CI: 0.659 to 0.917) on the testing set. CSF1R was identified as an IRF of ICUA, expressed in and positively correlated with monocytes which had a lower fraction in COVID-19 ICU patients. Conclusion The nomogram and monocytes could provide added value to ICUA prediction and targeted prevention, which are cost-effective platform for personalized medicine of COVID-19 patients. The log2fold change (log2FC) of the fraction of monocytes could be monitored simply and economically in primary care, and the nomogram offered an accurate prediction for secondary care in the framework of PPPM. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-023-00317-5.
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Affiliation(s)
- Kun Zhu
- Department of Pathology, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Zhonghua Chen
- Department of Anesthesiology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China ,Department of Anesthesiology, Shaoxing People’s Hospital (Shaoxing Hospital, Zhejiang University School of Medicine), Shaoxing, China
| | - Yi Xiao
- Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Dengming Lai
- Department of Neonatal Surgery, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Xiaofeng Wang
- Department of Information Center, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Xiangming Fang
- Department of Anesthesiology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiang Shu
- Department of Thoracic and Cardiovascular Surgery, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
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Abarca-Zabalía J, González-Jiménez A, Calle-Rubio M, López-Pastor AR, Fariña T, Ramos-Acosta C, Anguita E, Urcelay E, Espino-Paisán L. Alterations in the immune system persist after one year of convalescence in severe COVID-19 patients. Front Immunol 2023; 14:1127352. [PMID: 36860856 PMCID: PMC9969554 DOI: 10.3389/fimmu.2023.1127352] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/25/2023] [Indexed: 02/16/2023] Open
Abstract
Introduction Severe COVID-19 originates a myriad of alterations in the immune system during active disease, especially in the T and NK cell compartments, but several studies in the last year have unveiled some alterations that persist in convalescence. Although most of the studies follow the participants for a short recovery time, studies following patients up to three or six months still find alterations. We aimed at evaluating changes in the NK, T and B cell compartments after severe COVID-19 in participants with a median recovery time of eleven months. Methods Eighteen convalescent of severe COVID-19 (CSC), 14 convalescent of mild COVID-19 (CMC) and nine controls were recruited. NKG2A, NKG2C, NKG2D and the activating receptor NKp44 were evaluated in NKbright, NKdim and NKT subpopulations. In addition, CD3 and CD19 were measured and a basic biochemistry with IL-6 levels was obtained. Results CSC participants showed lower NKbright/NKdim ratio, higher NKp44 expression in NKbright subpopulations, higher levels of serum IL-6, lower levels of NKG2A+ T lymphocytes and a trend to a lower expression of CD19 in B lymphocytes compared to controls. CMC participants showed no significant alterations in the immune system compared to controls. Conclusions These results are concordant with previous studies, which find alterations in CSC weeks or months after resolution of the symptoms, and point to the possibility of these alterations lasting one year or more after COVID-19 resolution.
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Affiliation(s)
- Judith Abarca-Zabalía
- Laboratorio de Investigación en Genética de Enfermedades Complejas, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Adela González-Jiménez
- Laboratorio de Investigación en Genética de Enfermedades Complejas, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Myriam Calle-Rubio
- Department of Pneumology, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Andrea R. López-Pastor
- Laboratorio de Investigación en Genética de Enfermedades Complejas, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain,*Correspondence: Andrea R. López-Pastor,
| | - Tomás Fariña
- Intensive Care Unit, Hospital Clínico San Carlos, Madrid, Spain
| | - Carlos Ramos-Acosta
- Department of Medicine, Universidad Complutense de Madrid (UCM), Madrid, Spain,Hematology Department, Instituto de Medicina de Laboratorio, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
| | - Eduardo Anguita
- Department of Medicine, Universidad Complutense de Madrid (UCM), Madrid, Spain,Hematology Department, Instituto de Medicina de Laboratorio, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
| | - Elena Urcelay
- Laboratorio de Investigación en Genética de Enfermedades Complejas, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Laura Espino-Paisán
- Laboratorio de Investigación en Genética de Enfermedades Complejas, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
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Nasrollahi H, Talepoor AG, Saleh Z, Eshkevar Vakili M, Heydarinezhad P, Karami N, Noroozi M, Meri S, Kalantar K. Immune responses in mildly versus critically ill COVID-19 patients. Front Immunol 2023; 14:1077236. [PMID: 36793739 PMCID: PMC9923185 DOI: 10.3389/fimmu.2023.1077236] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/12/2023] [Indexed: 01/31/2023] Open
Abstract
The current coronavirus pandemic (COVID-19), caused by SARS-CoV-2, has had devastating effects on the global health and economic system. The cellular and molecular mediators of both the innate and adaptive immune systems are critical in controlling SARS-CoV-2 infections. However, dysregulated inflammatory responses and imbalanced adaptive immunity may contribute to tissue destruction and pathogenesis of the disease. Important mechanisms in severe forms of COVID-19 include overproduction of inflammatory cytokines, impairment of type I IFN response, overactivation of neutrophils and macrophages, decreased frequencies of DC cells, NK cells and ILCs, complement activation, lymphopenia, Th1 and Treg hypoactivation, Th2 and Th17 hyperactivation, as well as decreased clonal diversity and dysregulated B lymphocyte function. Given the relationship between disease severity and an imbalanced immune system, scientists have been led to manipulate the immune system as a therapeutic approach. For example, anti-cytokine, cell, and IVIG therapies have received attention in the treatment of severe COVID-19. In this review, the role of immunity in the development and progression of COVID-19 is discussed, focusing on molecular and cellular aspects of the immune system in mild vs. severe forms of the disease. Moreover, some immune- based therapeutic approaches to COVID-19 are being investigated. Understanding key processes involved in the disease progression is critical in developing therapeutic agents and optimizing related strategies.
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Affiliation(s)
- Hamid Nasrollahi
- Radio-Oncology Department, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Atefe Ghamar Talepoor
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Saleh
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahsa Eshkevar Vakili
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Paria Heydarinezhad
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Narges Karami
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Noroozi
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seppo Meri
- Department of Bacteriology and Immunology, University of Helsinki and Diagnostic Center of the Helsinki University Hospital, Helsinki, Finland
| | - Kurosh Kalantar
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Autoimmune Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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Ilieva M, Tschaikowski M, Vandin A, Uchida S. The current status of gene expression profilings in COVID‐19 patients. CLINICAL AND TRANSLATIONAL DISCOVERY 2022; 2:e104. [PMID: 35942159 PMCID: PMC9350144 DOI: 10.1002/ctd2.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 11/26/2022]
Abstract
Background The global pandemic of coronavirus disease 2019 (COVID‐19) caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has swept through every part of the world. Because of its impact, international efforts have been underway to identify the variants of SARS‐CoV‐2 by genome sequencing and to understand the gene expression changes in COVID‐19 patients compared to healthy donors using RNA sequencing (RNA‐seq) assay. Within the last two and half years since the emergence of SARS‐CoV‐2, a large number of OMICS data of COVID‐19 patients have accumulated. Yet, we are still far from understanding the disease mechanism. Further, many people suffer from long‐term effects of COVID‐19; calling for a more systematic way to data mine the generated OMICS data, especially RNA‐seq data. Methods By searching gene expression omnibus (GEO) using the key terms, COVID‐19 and RNA‐seq, 108 GEO entries were identified. Each of these studies was manually examined to categorize the studies into bulk or single‐cell RNA‐seq (scRNA‐seq) followed by an inspection of their original articles. Results The currently available RNA‐seq data were generated from various types of patients’ samples, and COVID‐19 related sample materials have been sequenced at the level of RNA, including whole blood, different components of blood [e.g., plasma, peripheral blood mononuclear cells (PBMCs), leukocytes, lymphocytes, monocytes, T cells], nasal swabs, and autopsy samples (e.g., lung, heart, liver, kidney). Of these, RNA‐seq studies using whole blood, PBMCs, nasal swabs and autopsy/biopsy samples were reviewed to highlight the major findings from RNA‐seq data analysis. Conclusions Based on the bulk and scRNA‐seq data analysis, severe COVID‐19 patients display shifts in cell populations, especially those of leukocytes and monocytes, possibly leading to cytokine storms and immune silence. These RNA‐seq data form the foundation for further gene expression analysis using samples from individuals suffering from long COVID.
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Affiliation(s)
- Mirolyuba Ilieva
- Center for RNA Medicine, Department of Clinical Medicine Aalborg University Copenhagen Denmark
| | - Max Tschaikowski
- Department of Computer Science Aalborg University Aalborg Denmark
| | - Andrea Vandin
- Institute of Economics and EMbeDS Sant'Anna School of Advanced Studies Pisa Italy
- Department of Applied Mathematics and Computer Science Technical University of Denmark Kongens Lyngby Denmark
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine Aalborg University Copenhagen Denmark
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