[{"_id": "5f9253915b5d711d38327689", "title": "Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans.", "url": "https://doi.org/10.1126/science.abc6261", "authors": ["Arunachalam, Prabhu S", "Wimmers, Florian", "Mok, Chris Ka Pun", "Perera, Ranawaka A P M", "Scott, Madeleine", "Hagan, Thomas", "Sigal, Natalia", "Feng, Yupeng", "Bristow, Laurel", "Tak-Yin Tsang, Owen", "Wagh, Dhananjay", "Coller, John", "Pellegrini, Kathryn L", "Kazmin, Dmitri", "Alaaeddine, Ghina", "Leung, Wai Shing", "Chan, Jacky Man Chun", "Chik, Thomas Shiu Hong", "Choi, Chris Yau Chung", "Huerta, Christopher", "Paine McCullough, Michele", "Lv, Huibin", "Anderson, Evan", "Edupuganti, Srilatha", "Upadhyay, Amit A", "Bosinger, Steve E", "Maecker, Holden Terry", "Khatri, Purvesh", "Rouphael, Nadine", "Peiris, Malik", "Pulendran, Bali"], "journal": "Science", "tags": ["human", "gene", "EN-RAGE", "IFN", "IFN-alpha", "TNFSF14", "mTOR", "mammalian target of rapamycin", "oncostatin M"], "license": "cc-by", "userdata": {"global_fields": {"paper": "Arunachalam, P. S., Wimmers, F., Mok, C. K. P., Perera, R. A., Scott, M., Hagan, T., ... & Pulendran B. (2020). Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans. Science, 369(6508), 1210-1220. Chicago", "contributor": "Bali Pulendran", "contributor_organization": "Stanford"}, "local_data": [{"description": "Genes differentially expressed in COVID-19 patients compared to healthy controls", "exact_source": "Fig. 4, Table S4 Tab \"DEG_healthy_vs_covid-19\"", "tissue": "PBMC", "immune_exposure": "SARS-CoV-2 infection", "cohort": "Adults (38 - 90)", "comparison": "COVID-19 vs healthy", "repository_id": "GSE155673", "platform": "CITE-seq", "response_components": "", "response_behavior": "Up or down"}, {"description": "Interferon-stimulated genes in COVID-19 patients", "exact_source": "Fig. 4G and supplementary fig. 15A", "tissue": "PBMC", "immune_exposure": "SARS-CoV-2 infection", "cohort": "Adults (38 - 90)", "comparison": "COVID-19 vs healthy", "repository_id": "GSE152418", "platform": "Bulk RNAseq", "response_components": "", "response_behavior": "Up"}, {"description": "", "exact_source": "", "tissue": "", "immune_exposure": "", "cohort": "", "comparison": "", "repository_id": "", "platform": "", "response_components": "", "response_behavior": ""}, {"description": "", "exact_source": "", "tissue": "", "immune_exposure": "", "cohort": "", "comparison": "", "repository_id": "", "platform": "", "response_components": "", "response_behavior": ""}]}}, {"_id": "5f9253af5b5d711d38327696", "title": "Natural killer cell immunotypes related to COVID-19 disease severity.", "url": "https://doi.org/10.1126/sciimmunol.abd6832", "authors": ["Maucourant, Christopher", "Filipovic, Iva", "Ponzetta, Andrea", "Aleman, Soo", "Cornillet, Martin", "Hertwig, Laura", "Strunz, Benedikt", "Lentini, Antonio", "Reinius, Bj\u00f6rn", "Brownlie, Demi", "Gomez, Angelica Cuapio", "Ask, Eivind Heggernes", "Hull, Ryan M", "Haroun-Izquierdo, Alvaro", "Schaffer, Marie", "Klingstr\u00f6m, Jonas", "Folkesson, Elin", "Buggert, Marcus", "Sandberg, Johan K", "Eriksson, Lars I", "Rooyackers, Olav", "Ljunggren, Hans-Gustaf", "Malmberg, Karl-Johan", "Micha\u00eblsson, Jakob", "Marquardt, Nicole", "Hammer, Quirin", "Str\u00e5lin, Kristoffer", "Bj\u00f6rkstr\u00f6m, Niklas K"], "journal": "Science immunology", "tags": ["virus", "human", "CD56", "Ksp37", "NKG2C"], "license": "cc-by", "userdata": {"global_fields": {"paper": "Maucourant, C., Filipovic, I., Ponzetta, A., Aleman, S., Cornillet, M., Hertwig, L., ... & Bj\u00f6rkstr\u00f6m NK. (2020). Natural killer cell immunotypes related to COVID-19 disease severity. Science immunology, 5(50).", "contributor": "Niklas K. Bj\u00f6rkstr\u00f6m", "contributor_organization": "Karolinska Institutet"}, "local_data": [{"description": "Hallmarks of the NK cell immunotypes were high expression of perforin, NKG2C, and Ksp37, reflecting increased presence of adaptive NK cells in circulation of patients with severe disease.", "exact_source": "Figure 3 and 4", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "Adults (18-70 years)", "comparison": "Moderate vs severe infection within 5 days from hospital admission", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "up"}]}}, {"_id": "5f9253d25b5d711d3832769f", "title": "Laboratory test alterations in patients with COVID-19 and non COVID-19 interstitial pneumonia: a preliminary report.", "url": "https://doi.org/10.3855/jidc.12879", "authors": ["Paliogiannis, Panagiotis", "Zinellu, Angelo", "Scano, Valentina", "Mulas, Giulia", "De Riu, Giacomo", "Pascale, Rosa M", "Arru, Luigi B", "Carru, Ciriaco", "Pirina, Pietro", "Mangoni, Arduino A", "Fois, Alessandro G"], "journal": "Journal of infection in developing countries", "tags": ["human", "protein", "C reactive protein"], "license": "cc-by", "userdata": {"global_fields": {"paper": "Paliogiannis, P., Zinellu, A., Scano, V., Mulas, G., De Riu, G., Pascale, R. M., Arru, L. B., Carru, C., Pirina, P., Mangoni, A. A., & Fois, A. G. (2020). Laboratory test alterations in patients with COVID-19 and non COVID-19 interstitial pneumonia: a preliminary report. Journal of infection in developing countries, 14(7), 685\u2013690. https://doi.org/10.3855/jidc.12879 ", "contributor": "Panagiotis Paliogiannis", "contributor_organization": "Universit\u00e0 degli Studi di Sassari"}, "local_data": [{"description": "Introduction: Coronavirus disease 19 (COVID-19) is the greatest pandemic in modern history. Laboratory test alterations have been described in COVID-19 patients, but differences with other pneumonias have been poorly investigated to date, especially in Caucasian populations. The aim of this study was to investigate differences and prognostic potential of routine blood tests in a series of Italian patients with COVID-19 and non-COVID-19 interstitial pneumonia.\nMethodology: Clinical data and routine laboratory tests of a consecutive series of 30 COVID-19 patients and 30 age and sex matched patients with non COVID-19 interstitial pneumonia have been retrospectively collected. Differences in laboratory tests between patients with COVID-19 and non COVID-19 pneumonias have been investigated, as well as differences between COVID-19 survivors and non survivors.\nResults: COVID-19 patients had lower white blood cells, monocytes, neutrophils, and higher platelet counts. In addition, COVID-19 patients showed higher mean platelet volume, lower C reactive protein concentrations, and higher De Ritis ratio. Combined blood cell indexes of systemic inflammation were significantly lower in COVID-19 patients. In further analysis of the COVID-19 group, the neutrophil count, neutrophil to lymphocyte ratio (NLR), derived NLR, systemic inflammation response index and De Ritis ratio, were significantly higher in non survivors than in survivors, while the number of platelets was significantly lower in non survivors.\nConclusions: Our study showed several alterations in blood cell populations and indexes in patients with COVID-19 pneumonia in comparison with patients with non COVID-19 pneumonia. Some of these indexes showed promising prognostic abilities. Further studies are necessary to confirm these results.", "exact_source": "Article", "tissue": "Blood", "immune_exposure": "COVID-19 infection", "cohort": "Adults with COVID-19 or other interstitial pneumonia", "comparison": "Blood tests in patients with COVID-19 and non-COVID-19 pneumonia  ", "repository_id": "-", "platform": "-", "response_components": "-", "response_behavior": "-"}]}}, {"_id": "5faeb05640d80ef65b8f06ed", "title": "Unique immunological profile in patients with COVID-19.", "url": "https://doi.org/10.1038/s41423-020-00557-9", "authors": ["Varchetta, Stefania", "Mele, Dalila", "Oliviero, Barbara", "Mantovani, Stefania", "Ludovisi, Serena", "Cerino, Antonella", "Bruno, Raffaele", "Castelli, Alberto", "Mosconi, Mario", "Vecchia, Marco", "Roda, Silvia", "Sachs, Michele", "Klersy, Catherine", "Mondelli, Mario U"], "journal": "Cellular & molecular immunology", "tags": ["immune response", "t-cell", "human", "protein", "CD56", "CD57", "CD69", "IL-1beta", "IL-6", "IL-8", "NKG2D", "T-cell immunoglobulin and mucin domain-3", "TIM-3", "natural killer group 2 member D", "programmed cell death protein 1"], "license": "unk", "userdata": {"global_fields": {"paper": "Varchetta, S., Mele, D., Oliviero, B. et al. Unique immunological profile in patients with COVID-19. Cell Mol Immunol (2020). https://doi.org/10.1038/s41423-020-00557-9", "contributor": "Mario U. Mondelli", "contributor_organization": "Universit\u00e0 di Pavia"}, "local_data": [{"description": "Decreased frequency of CD56bright NK cells when comparing Covid-19 infected patients vs. healthy donors or dead vs. survivor patients.", "exact_source": "Fig. 1b", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "adults (32-92)", "comparison": "COVID-19 patients versus healthy donors; dead versus survivor patients", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "down"}, {"description": "Increased frequency of CD57+ NK cells  when comparing Covid-19 infected patients vs. healthy donors or dead vs. survivor patients.", "exact_source": "Fig. 1c", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "adults (32-92)", "comparison": "COVID-19 patients versus healthy donors; dead versus survivors patients", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "up"}, {"description": "Increased frequency of adaptive NK cells  when comparing dead vs. survivor Covid-19 infected patients.", "exact_source": "Fig. 1d", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "adults (32-92)", "comparison": "Dead versus survivor patients", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "up"}, {"description": "Increased frequency of NK cells expressing CD69, TIM-3, PD1 when comparing Covid-19 infected patients vs. healthy donors", "exact_source": "Fig. 2a; Fig.2b; Fig.2c", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "adults (32-92)", "comparison": "COVID-19 patients versus healthy donors", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "up"}, {"description": "Decreased frequencies of NK cells expressing NKG2D, Siglec-7, DNAM-1 and CXCR6 when comparing Covid-19 infected patients vs. healthy donors", "exact_source": "Fig. 2d; Fig.2e; Fig.2f; Fig.2g", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "adults (32-92)", "comparison": "COVID-19 patients versus healthy donors", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "down"}, {"description": "Decreased frequency of NK cells secreting IFN gamma  when comparing Covid-19 infected patients vs. healthy donors", "exact_source": "Fig. 3a; Fig. 3b", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "adults (32-92)", "comparison": "COVID-19 patients versus healthy donors", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "down"}, {"description": "Increased frequencies of CD4 and CD8 T cells expressing CD69 when comparing Covid-19 infected patients vs. healthy donors or dead vs. survivor patients.", "exact_source": "Fig. 4c; Fig. 4d", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "adults (32-92)", "comparison": "COVID-19 patients versus healthy donors; dead versus survivor patients", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "up"}, {"description": "Increased frequencies of CD4 and CD8 T cells expressing TIM-3 when comparing Covid-19 infected patients vs. healthy donors", "exact_source": "Fig. 4e; Fig. 4f", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "adults (32-92)", "comparison": "COVID-19 patients versus healthy donors", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "up"}, {"description": "Decreased frequencies of CD8 T cells expressing CXCR6 when comparing Covid-19 infected patients vs. healthy donors", "exact_source": "Fig. 4g", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "adults (32-92)", "comparison": "COVID-19 patients versus healthy donors", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "down"}, {"description": "Increased serum level of IL-6, IL8, IL10 in Covid-19 infected patients vs. healthy donors", "exact_source": "Fig. 6a; Fig. 6b; Fig. 6c;", "tissue": "Serum", "immune_exposure": "COVID-19 infection", "cohort": "adults (32-92)", "comparison": "COVID-19 patients versus healthy donors", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "up"}, {"description": "Increased serum level of IL-6 and IL10 in dead vs survivor Covid-19 infected patients.", "exact_source": "Fig. 6a; Fig. 6c", "tissue": "Serum", "immune_exposure": "COVID-19 infection", "cohort": "adults (32-92)", "comparison": "dead versus survivor patients", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "up"}, {"description": "Increased frequency of IL-6, IL-8 and IL-1beta secreted by monocytes in  Covid-19 infected patients vs. healthy donors.", "exact_source": "Fig. 7a; Fig. 7b; Fig. 7c", "tissue": "Whole blood", "immune_exposure": "COVID-19 infection", "cohort": "adults (32-92)", "comparison": "COVID-19 patients versus healthy donors", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "up"}]}}, {"_id": "5faeb05640d80ef65b8f06ee", "title": "Longitudinal analyses reveal immunological misfiring in severe COVID-19.", "url": "https://doi.org/10.1038/s41586-020-2588-y", "authors": ["Lucas, Carolina", "Wong, Patrick", "Klein, Jon", "Castro, Tiago B R", "Silva, Julio", "Sundaram, Maria", "Ellingson, Mallory K", "Mao, Tianyang", "Oh, Ji Eun", "Israelow, Benjamin", "Takahashi, Takehiro", "Tokuyama, Maria", "Lu, Peiwen", "Venkataraman, Arvind", "Park, Annsea", "Mohanty, Subhasis", "Wang, Haowei", "Wyllie, Anne L", "Vogels, Chantal B F", "Earnest, Rebecca", "Lapidus, Sarah", "Ott, Isabel M", "Moore, Adam J", "Muenker, M Catherine", "Fournier, John B", "Campbell, Melissa", "Odio, Camila D", "Casanovas-Massana, Arnau", "Herbst, Roy", "Shaw, Albert C", "Medzhitov, Ruslan", "Schulz, Wade L", "Grubaugh, Nathan D", "Dela Cruz, Charles", "Farhadian, Shelli", "Ko, Albert I", "Omer, Saad B", "Iwasaki, Akiko"], "journal": "Nature", "tags": ["immune response", "t-cell", "human", "IL-13", "IL-5", "interleukin-5"], "license": "unk", "userdata": {"global_fields": {"paper": "Lucas, C., Wong, P., Klein, J., Castro, T. B., Silva, J., Sundaram, M., ... & Iwasaki, A. (2020). Longitudinal analyses reveal immunological misfiring in severe COVID-19. Nature, 584(7821), 463-469.", "contributor": "Carolina Lucas", "contributor_organization": "Yale University"}, "local_data": [{"description": "Identification of a maladapted immune response profile, measured longitudinally in PBMCs and plasma soluble mediators among hospitalized COVID-19 patients with severe vs moderate disease.", "exact_source": "Supplementary Table 1 and ImmPort (https://www.immport.org/shared/ home; study ID SDY1655).", "tissue": "PBMCs and plasma analyses", "immune_exposure": "SARS-CoV-2 infection", "cohort": "Adults: age age (62.96 \u00b1 17.0), sex (Male 46.02% / Females 53.98% , Ethnicity (American Indian -Alaskan Native 0%/ Asian (0.88%) / Black -African American (29.2%)/ Native Hawaiian-Pacific Islander(0%)/ White (53.98%)/ Hispanic (12.39%).", "comparison": "Longitudinally analyses of PBMCs and plasma samples from hospitalized (moderate and severe) COVID-19 patients", "repository_id": "SDY1655", "platform": "", "response_components": "", "response_behavior": ""}]}}, {"_id": "5faeb05740d80ef65b8f06f0", "title": "Two distinct immunopathological profiles in autopsy lungs of COVID-19.", "url": "https://doi.org/10.1038/s41467-020-18854-2", "authors": ["Nienhold, Ronny", "Ciani, Yari", "Koelzer, Viktor H", "Tzankov, Alexandar", "Haslbauer, Jasmin D", "Menter, Thomas", "Schwab, Nathalie", "Henkel, Maurice", "Frank, Angela", "Zsikla, Veronika", "Willi, Niels", "Kempf, Werner", "Hoyler, Thomas", "Barbareschi, Mattia", "Moch, Holger", "Tolnay, Markus", "Cathomas, Gieri", "Demichelis, Francesca", "Junt, Tobias", "Mertz, Kirsten D"], "journal": "Nature communications", "tags": ["lung", "t-cell", "virus", "human", "treatment", "macrophage", "gene", "CD8"], "license": "unk", "userdata": {"global_fields": {"paper": "Nienhold, R., Ciani, Y., Koelzer, V. H., Tzankov, A., Haslbauer, J. D., Menter, T., ... & Mertz, K.D. (2020). Two distinct immunopathological profiles in autopsy lungs of COVID-19. Nature communications, 11(1), 1-13.", "contributor": "Kirsten D. Mertz", "contributor_organization": "Cantonal Hospital Baselland"}, "local_data": [{"description": "Genes differentially expressed in autopsy lungs of COVID-19 patients, compared to patients who died from other diseases without lung pathology and to patients who died from bacterial or viral pneumonias other than COVID-19", "exact_source": "Table 2, Supplementary Table 2 and 3", "tissue": "autopsy lung tissues", "immune_exposure": "COVID-19 infection", "cohort": "autopsy cohort, elderly patients", "comparison": "COVID-19 autopsy lungs versus autopsy lungs of patients who died of other diseases and to patients who died from pneumonias other than COVID-19", "repository_id": "GSE151764", "platform": "", "response_components": "", "response_behavior": ""}]}}, {"_id": "5faeb05a40d80ef65b8f06f6", "title": "Extrafollicular B cell responses correlate with neutralizing antibodies and morbidity in COVID-19.", "url": "https://doi.org/10.1038/s41590-020-00814-z", "authors": ["Woodruff, Matthew C", "Ramonell, Richard P", "Nguyen, Doan C", "Cashman, Kevin S", "Saini, Ankur Singh", "Haddad, Natalie S", "Ley, Ariel M", "Kyu, Shuya", "Howell, J Christina", "Ozturk, Tugba", "Lee, Saeyun", "Suryadevara, Naveenchandra", "Case, James Brett", "Bugrovsky, Regina", "Chen, Weirong", "Estrada, Jacob", "Morrison-Porter, Andrea", "Derrico, Andrew", "Anam, Fabliha A", "Sharma, Monika", "Wu, Henry M", "Le, Sang N", "Jenks, Scott A", "Tipton, Christopher M", "Staitieh, Bashar", "Daiss, John L", "Ghosn, Eliver", "Diamond, Michael S", "Carnahan, Robert H", "Crowe, James E", "Hu, William T", "Lee, F Eun-Hyung", "Sanz, Ignacio"], "journal": "Nature immunology", "tags": ["b-cell", "human", "antibody", "B cell activation"], "license": "unk", "userdata": {"global_fields": {"paper": "Woodruff, M. C., Ramonell, R. P., Nguyen, D. C., Cashman, K. S., Saini, A. S., Haddad, N. S., ... & Sanz, I. (2020). Extrafollicular B cell responses correlate with neutralizing antibodies and morbidity in COVID-19. Nature immunology, 21(12), 1506-1516.", "contributor": "Matthew C. Woodruff", "contributor_organization": "Emory University"}, "local_data": [{"description": "Patients with severe/critical COVID-19 show a robust activation of the extrafollicular B cell pathway \u2013 similar to responses seen in active and flaring autoimmune disease.", "exact_source": "Extrafollicular response signatures in COVID-19, and their comparison to patients with active lupus, are best highlighted in figures 3 and 4 (https://www.nature.com/articles/s41590-020-00814-z#Fig3, https://www.nature.com/articles/s41590-020-00814-z#Fig4)", "tissue": "PBMC; B cell, CD19-positive", "immune_exposure": "COVID-19 infection", "cohort": "ICU patients. Ages 34-81. Clinical data presented in Data Table 2 (https://static-content.springer.com/esm/art%3A10.1038%2Fs41590-020-00814-z/MediaObjects/41590_2020_814_MOESM1_ESM.pdf)", "comparison": "ICU patients (severe/critical) versus outpatients (mild/moderate), active lupus patients, and healthy controls", "repository_id": "Flow data \u2013 (http://flowrepository.org/id/FR-FCM-Z2XF)", "platform": "NA", "response_components": "NA", "response_behavior": "Antibody secreting cells up, DN2 B cells up, DN3 B cells up, Activated Naive B cells up"}]}}, {"_id": "5faeb06440d80ef65b8f0714", "title": "A granulocytic signature identifies COVID-19 and its severity", "url": "https://api.semanticscholar.org/CorpusID:221787401.0", "authors": ["Vitte, Joana", "Diallo, A\u00efssatou Bailo", "Boumaza, Asma", "Lopez, Alexandre", "Michel, Mo\u00efse", "Allardet-Servent, J\u00e9r\u00f4me", "Mezouar, Soraya", "Sereme, Youssouf", "Busnel, Jean-Marc", "Miloud, Tewfik", "Malergue, Fabrice", "Morange, Pierre-Emmanuel", "Halfon, Philippe", "Olive, Daniel", "Leone, Marc", "Mege, Jean-Louis"], "journal": "J. infect. dis", "tags": ["human"], "license": "unk", "userdata": {"global_fields": {"paper": "Vitte, J., Diallo, A. B., Boumaza, A., Lopez, A., Michel, M., Allardet-Servent, J., Mezouar, S., Sereme, Y., Busnel, J. M., Miloud, T., Malergue, F., Morange, P. E., Halfon, P., Olive, D., Leone, M., & Mege, J. L. (2020). A Granulocytic Signature Identifies COVID-19 and Its Severity. The Journal of infectious diseases, 222(12), 1985\u20131996. https://doi.org/10.1093/infdis/jiaa591", "contributor": "Marc Leone", "contributor_organization": "Aix-Marseille University"}, "local_data": [{"description": " Increased counts of CD15+CD16+ neutrophils\n", "exact_source": "Figure 1", "tissue": "Whole blood neutrophils", "immune_exposure": "", "cohort": "adults median age 66", "comparison": "severe vs mild infection vs healthy donors at 1-day and 10-day post-infection", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "up"}, {"description": "decreased granulocytic expression of integrin CD11b", "exact_source": "Figure 1", "tissue": "Whole blood granulocytes", "immune_exposure": "", "cohort": "adults median age 66", "comparison": "severe vs mild infection vs healthy donors at 1-day and 10-day post-infection", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "down"}, {"description": "CRTH2 downregulation in eosinophils and basophils ", "exact_source": "Figure 1", "tissue": "Whole blood eosinophils and basophils", "immune_exposure": "", "cohort": "adults median age 66", "comparison": "severe vs mild infection vs healthy donors at 1-day and 10-day post-infection", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "down"}, {"description": "emergence of PD-L1 checkpoint expression in basophils and eosinophils", "exact_source": "Figure 2", "tissue": "Whole blood eosinophils and basophils", "immune_exposure": "", "cohort": "adults median age 66", "comparison": "severe vs mild infection ", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "up"}]}}, {"_id": "5faeb06440d80ef65b8f0717", "title": "Compartmental immunophenotyping in COVID-19 ARDS: a case series", "url": "https://api.semanticscholar.org/CorpusID:221955283.0", "authors": ["Ronit, Andreas", "Berg, Ronan M G", "Bay, Jakob T", "Haugaard, Anna K", "Ahlstr\u00f6m, Magnus G", "Burgdorf, Kristoffer S", "Ullum, Henrik", "R\u00f8rvig, Sara B", "Tjelle, Klaus", "Foss, Nicolai B", "Benfield, Thomas", "Marquart, Hanne Vibeke", "Plovsing, Ronni R"], "journal": "J. allergy clin. immunol", "tags": ["lung", "t-cell", "human", "macrophage"], "license": "unk", "userdata": {"global_fields": {"paper": "Ronit, A., Berg, R. M., Bay, J. T., Haugaard, A. K., Ahlstr\u00f6m, M. G., Burgdorf, K. S., ... & Plovsing, R. R. (2020). Compartmental immunophenotyping in COVID-19 ARDS: A case series. Journal of Allergy and Clinical Immunology. https://doi.org/10.1016/j.jaci.2020.09.009", "contributor": "Ronni R. Plovsing", "contributor_organization": "Hvidovre Hospital, University of Copenhagen, Denmark"}, "local_data": [{"description": "The cellular immune response of COVID-19 acute respiratory distress syndrome (ARDS) is dominated by immature neutrophils in both the blood and the lungs, with concomitant CD4 and CD8 T-cell lymphopenia and elevated inflammatory chemokine and cytokine levels.", "exact_source": "Figure 2; Figure 5; Figure E4; Figure E10", "tissue": "Bronchoalveolar lavage fluid (BALF); Whole blood", "immune_exposure": "COVID-19 infection", "cohort": "Adults (40-75 years)", "comparison": "Observational and cross-sectional study on severe COVID-19 infection", "repository_id": "-", "platform": "-", "response_components": "-", "response_behavior": "-"}, {"description": "The T-cell profile in the lungs of patients with COVID-19 ARDS is substantially different from that in blood, with expression of much higher levels of activation and higher frequency of Treg cells and TH17 cells.", "exact_source": "Figure 4; Figure E3; Figure E7; Figure E8; Figure E9", "tissue": "Bronchoalveolar lavage fluid (BALF); Whole blood", "immune_exposure": "COVID-19 infection", "cohort": "Adults (40-75 years)", "comparison": "Observational and cross-sectional study on severe COVID-19 infection", "repository_id": "-", "platform": "-", "response_components": "-", "response_behavior": "-"}]}}, {"_id": "5faeb06540d80ef65b8f0719", "title": "Immune responses to SARS-CoV-2 infection in hospitalized pediatric and adult patients", "url": "https://api.semanticscholar.org/CorpusID:221842301.0", "authors": ["Pierce, Carl A", "Preston-Hurlburt, Paula", "Dai, Yile", "Aschner, Clare Burn", "Cheshenko, Natalia", "Galen, Benjamin", "Garforth, Scott J", "Herrera, Natalia G", "Jangra, Rohit K", "Morano, Nicholas C", "Orner, Erika", "Sy, Sharlene", "Chandran, Kartik", "Dziura, James", "Almo, Steven C", "Ring, Aaron", "Keller, Marla J", "Herold, Kevan C", "Herold, Betsy C"], "journal": "Sci. transl. med", "tags": ["immune response", "t-cell", "virus", "human", "antibody", "protein"], "license": "unk", "userdata": {"global_fields": {"paper": "Pierce, C.A., Preston-Hurlburt, P., Dai, Y., Aschner, C.B., Cheshenko, N., Galen, B., Garforth, S., Herrera, N.G., Jangra, R., Morano, N.C., Orner, E., Sy, S., Chandran, K., Dziura, J., Almo, S., Ring, A., Keller, M., Herold, K., & Herold, B. (2020). Immune responses to SARS-CoV-2 infection in hospitalized pediatric and adult patients. Science Translational Medicine, 12.", "contributor": "Kevan Herold", "contributor_organization": "Yale University"}, "local_data": [{"description": "We compared cytokine,humoral, and cellular immune responses in pediatric (children and youth, age < 24 years) (n=65) and adult (n=60) patients with COVID-19 at a metropolitan hospital system in New York City.The serum concentration of IL-17A (Spearman r=-0.5, p<0.0001) and IFN-g (r=-0.44, p=0.0003), but not TNF or IL-6, were inversely related to age. Adults mounted a more robust T cellular response to the spike protein\ncompared to pediatric patients as evidenced by increased expression of CD25+ on CD4+ T cells\nand frequency of IFN-g+CD4+ T cells. Moreover, the serum neutralizing antibody titers and antibody-dependent cellular phagocytosis were significantly higher in adults compared to pediatric patients. The neutralizing titer correlated positively with age and negatively with IL-17A and IFN-g (p < 0.01). Together these findings demonstrate that the poor outcome in adults is not attributable to a failure to generate adaptive immune responses. They suggest that a more robust early immune response characterized by IL-17A and IFN-g that occurs in pediatric patients may prevent the excessive adaptive response associated with enhanced immunopathology.", "exact_source": "Table 1", "tissue": "PBMC and serum", "immune_exposure": "SARS-CoV-2", "cohort": "Children and adults", "comparison": "Severe vs mild disease", "repository_id": "N/A", "platform": "N/A", "response_components": "N/A", "response_behavior": "N/A"}]}}, {"_id": "5faeb07240d80ef65b8f073c", "title": "Systematic examination of T cell responses to SARS-CoV-2 versus influenza virus reveals distinct inflammatory profile", "url": "http://medrxiv.org/cgi/content/short/2020.08.27.20183319v1?rss=1", "authors": ["Law, J. C.", "Koh, W.", "Budylowski, P.", "Lin, J.", "Yue, F.", "Abe, K. T.", "Rathod, B.", "Girard, M.", "Li, Z.", "Rini, J. M.", "Mubareka, S.", "McGeer, A.", "Chan, A. K.", "Gingras, A.-C.", "Watts, T. H.", "Ostrowski, M."], "journal": NaN, "tags": ["t-cell", "protein"], "license": "medrxiv", "userdata": {"global_fields": {"paper": "Law, J. C., Koh, W. H., Budylowski, P., Lin, J., Yue, F., Abe, K. T., ... & Ostrowski, M. A. (2020). Systematic Examination of Antigen-Specific Recall T Cell Responses to SARS-CoV-2 versus Influenza Virus Reveals a Distinct Inflammatory Profile. The Journal of Immunology, 206(1), 37-50.", "contributor": "Tania H. Watts", "contributor_organization": "University of Toronto"}, "local_data": [{"description": "Analysis of T cell responses to SARS-CoV-2 using multiparameter flow cytometry, Multiplex cytokine assays and proliferation assays on 13 leukapheresis samples from subjects in early convalescent phase of COVID19, range of disease severity from asymptomatic to ICU.", "exact_source": "", "tissue": "PBMC ", "immune_exposure": "PCR Confirmed COVID19  27-90d post symptoms", "cohort": "Adults (range 31-72, average 53 y.o.)", "comparison": "13 subjects,range severe to asymptomatic", "repository_id": "", "platform": "", "response_components": "", "response_behavior": ""}]}}, {"_id": "5faeb08b40d80ef65b8f076a", "title": "Reappearance of Effector T Cells Predicts Successful Recovery from COVID-19", "url": "https://doi.org/10.1101/2020.05.11.20096263", "authors": ["Odak, Ivan", "Barros-Martins, Joana", "Bosnjak, Berislav", "Stahl, Klaus", "David, Sascha", "Wiesner, Olaf", "Busch, Markus", "Hoeper, Marius M", "Pink, Isabell", "Welte, Tobias", "Cornberg, Markus", "Stoll, Matthias", "Goudeva, Lilia", "Blasczyk, Rainer", "Ganser, Arnold", "Prinz, Immo", "Foerster, Reinhold", "Koenecke, Christian", "Schultze-Florey, Christian R"], "journal": NaN, "tags": ["immune response", "t-cell", "human"], "license": "cc-by-nc-nd", "userdata": {"global_fields": {"paper": "Odak, I., Barros-Martins, J., Bo\u0161njak, B., Stahl, K., David, S., Wiesner, O., ... & Schultze-Florey, C. R. (2020). Reappearance of effector T cells is associated with recovery from COVID-19. EBioMedicine, 57, 102885.", "contributor": "Christian Schultze-Florey", "contributor_organization": "Hannover Medical School"}, "local_data": [{"description": "Absolute numbers of lymphocyte subsets were differentially decreased in COVID-19 patients according to clinical severity. In severe disease (SD) patients, all lymphocyte subsets were reduced, whilst in mild disease (MD) NK, NKT and GD T cells were at the level of HC. Additionally, we provide evidence of T cell activation in MD but not SD, when compared to HC. Follow up samples revealed a marked increase in effector T cells and memory subsets in convalescing but not in non-convalescing patients. Understanding T cell-responses in the context of clinical severity might serve as foundation to overcome the lack of effective anti-viral immune response in severely affected COVID-19 patients and can offer prognostic value as biomarker for disease outcome and control.", "exact_source": "https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image%20to%20zoom&p=PMC3&id=7341361_gr2.jpg", "tissue": "Whole blood", "immune_exposure": "SARS-CoV-2 infection", "cohort": "Adults and age/sex matched healthy controls", "comparison": "Severe vs Mild COVID-19; reconvalescing vs non-reconvalescing patients", "repository_id": " ", "platform": " ", "response_components": " ", "response_behavior": " "}]}}, {"_id": "5ff770d59be1e47152a5bcfa", "title": "Identifying Pathways and Networks Associated With the SARS-CoV-2 Cell Receptor ACE2 Based on Gene Expression Profiles in Normal and SARS-CoV-2-Infected Human Tissues", "url": "https://www.ncbi.nlm.nih.gov/pubmed/33195414/", "authors": ["Feng, Qiushi", "Li, Lin", "Wang, Xiaosheng"], "journal": "Front Mol Biosci", "tags": ["upregulated", "immune response", "human", "gene", "ACE2", "ESR1", "ESR2", "androgen receptor"], "license": "cc-by", "userdata": {"global_fields": {"paper": "Feng, Q., Li, L., & Wang, X. (2020). Identifying pathways and networks associated with the SARS-CoV-2 cell receptor ACE2 based on gene expression profiles in normal and SARS-CoV-2-infected human tissues. Frontiers in molecular biosciences, 7. https://www.ncbi.nlm.nih.gov/pubmed/33195414/", "contributor": "Xiaosheng Wang", "contributor_organization": "China Pharmaceutical University"}, "local_data": [{"description": "The list of genes showing significant expression correlations with\u00a0ACE2\u00a0in pan-tissue, female pan-tissue, and male pan-tissue; 77 genes showing significant positive expression correlations with\u00a0ACE2\u00a0in females (Pearson correlation coefficient,\u00a0r\u00a0> 0.5) but negative expression correlations with\u00a0ACE2\u00a0in males (r\u00a0< 0).", "exact_source": "Supplementary Tables 1, 2, 3, and 4", "tissue": "30 different human normal tissues; SARS-CoV-2-infected human tissues from nasopharyngeal swabs", "immune_exposure": "", "cohort": "Adults", "comparison": "SARS-CoV-2-infected vs normal tissues; male vs female", "repository_id": "GSE152075; GTEx", "platform": "RNA-Seq", "response_components": "ACE2 and other genes", "response_behavior": "correlation; differentially expressed"}]}}, {"_id": "5ff7719bda45ce27e3f22bbf", "title": "SARS-CoV-2 Innate Effector Associations and Viral Load in Early Nasopharyngeal Infection", "url": "https://www.ncbi.nlm.nih.gov/pubmed/33173878/", "authors": ["Liou, T. G.", "Adler, F. R.", "Cahill, B. C.", "Cox, D. R.", "Cox, J. E.", "Grant, G. J.", "Hanson, K. E.", "Hartsell, S. C.", "Hatton, N. D.", "Helms, M. N.", "Jensen, J. L.", "Kartsonaki, C.", "Li, Y.", "Leung, D. T.", "Marvin, J. E.", "Middleton, E. A.", "Osburn-Staker, S. M.", "Packer, K. A.", "Shakir, S. M.", "Sturrock, A. B.", "Tardiff, K. D.", "Warren, K. J.", "Waddoups, L. J.", "Weaver, L. J.", "Zimmerman, E.", "Paine, R."], "journal": "medRxiv : the preprint server for health sciences", "tags": ["virus", "protein", "gene", "ACE-2", "IP-10"], "license": "medrxiv", "userdata": {"global_fields": {"paper": "Liou, T. G., Adler, F. R., Cahill, B. C., Cox, D. R., Cox, J. E., Grant, G. J., ... & Paine III, R. (2021). SARS\u2010CoV\u20102 innate effector associations and viral load in early nasopharyngeal infection. Physiological reports, 9(4), e14761. https://doi.org/10.14814/phy2.14761", "contributor": "Ted Liou", "contributor_organization": "U Utah"}, "local_data": [{"description": "Upregulation of ACE2 and TMPRSS2 relative to viral N1 mRNA with SARS-CoV-2 infection ", "exact_source": "Figure 2", "tissue": "Nasopharyngeal Swab", "immune_exposure": "COVID-19 Infection", "cohort": "Adults", "comparison": "Drive-through diagnostic for people reporting viral like symptoms", "repository_id": "", "platform": "", "response_components": "ACE2 and TMPRSS2 mRNA vs viral N1 mRNA", "response_behavior": "ACE2 association with viral load; no response of TMPRSS2."}, {"description": "Upregulation of IL8, IP10, TNFalpha mRNA with SARS-CoV-2 viral load. Down regulation of TRAF1 with infection. Association of decreasing IP10 mRNA with increasing age.", "exact_source": "Figure 3", "tissue": "Nasopharyngeal Swab", "immune_exposure": "COVID-19 Infection", "cohort": "Adults", "comparison": "Drive-through diagnostic for people reporting viral like symptoms", "repository_id": "", "platform": "", "response_components": "IL8, IP10, TNFa, TRAF1 mRNA, SARS-CoV-2 N1 RNA", "response_behavior": "Association of IL8, IP10 and TNFa with N1 RNA; decreased TRAF1 with SARS-CoV-2 infection."}, {"description": "Systemic Inflammatory mRNA Responses to SARS-CoV-2 infection by RT-PCR", "exact_source": "Table 4", "tissue": "Nasopharyngeal Swab", "immune_exposure": "COVID-19 Infection", "cohort": "Adults", "comparison": "Drive-through diagnostic for people reporting viral like symptoms", "repository_id": "", "platform": "", "response_components": "GM-CSF, IL-6, IL-8, IL-10, IP-10, NFkb1, NFkb2, TNFa, TRAF1", "response_behavior": "Statistically significant upregulation IL-8, IL-10, IP-10, TNFa; Statistically significant downregulation TRAF1 mRNA"}, {"description": "Protein responses to SARS-CoV-2 infection by multiplex immunoassay for systemic inflammatory signaling agents.", "exact_source": "Table 5", "tissue": "Nasopharyngeal Swab", "immune_exposure": "COVID-19 Infection", "cohort": "Adults", "comparison": "Drive-through diagnostic for people reporting viral like symptoms", "repository_id": "", "platform": "", "response_components": "GM-CSF, IL-1b, IL-6, IL-8, IL-10, IL-12p70, IP-10", "response_behavior": "Significant increase in IP-10. No changes in other proteins."}, {"description": "Interferon mRNA responses to early SARS-CoV-2 infection measured by RT-PCR", "exact_source": "Table 6", "tissue": "Nasopharyngeal Swab", "immune_exposure": "COVID-19 Infection", "cohort": "Adults", "comparison": "Drive-through diagnostic for people reporting viral like symptoms", "repository_id": "", "platform": "", "response_components": "Interferon (IFN) alpha2, beta1, gamma, lambda1, lambda2, lambda3 responses to SARS-CoV-2 Infection", "response_behavior": "Statistically significant increases in IFN lambda1 and IFN lambda2. No responses in other IFNs."}, {"description": "Interferon (IFN) mRNA (RT-PCR) and protein (multiplex immunoassay) responses to infection and IFN association with viral load", "exact_source": "Figure 4", "tissue": "Nasopharyngeal Swab", "immune_exposure": "COVID-19 Infection", "cohort": "Adults", "comparison": "Drive-through diagnostic for people reporting viral like symptoms", "repository_id": "", "platform": "", "response_components": "Interferon (IFN) alpha2, beta1, gamma, lambda1, lambda2, lambda3 responses to SARS-CoV-2 Infection", "response_behavior": "Statisitcally significant upregulation with infection for IFN lambda1, IFN labmda2 mRNA that are significantly associated with viral N1 mRNA; statistically NOT significant responses of IFNlambda1, IFN lambda2 proteins with infection or viral N1 mRNA"}, {"description": "IFN mRNA responses and associations with viral N1 mRNA", "exact_source": "Table7", "tissue": "Nasopharyngeal Swab", "immune_exposure": "COVID-19 Infection", "cohort": "Adults", "comparison": "Drive-through diagnostic for people reporting viral like symptoms", "repository_id": "", "platform": "", "response_components": "IFN alpha2, IFN beta1, IFN gamma, IFN lambda1, IFN lambda2, IFN labmda3 mRNA", "response_behavior": "Statistically significant associations with viral N1 load for IFN lambda1, IFN lambda2 and IFN gamma. Non-significant assocations for IFN beta1, IFN lambda3 and a borderline association for IFN alpha2 with viral N1 RNA.."}, {"description": "IFN protein responses by multiplex immunoassay in response to SARS-CoV-2 infection", "exact_source": "Table 8", "tissue": "Nasopharyngeal Swab", "immune_exposure": "COVID-19 Infection", "cohort": "Adults", "comparison": "Drive-through diagnostic for people reporting viral like symptoms", "repository_id": "", "platform": "", "response_components": "IFN alpha2, IFN beta1, IFN gamma, IFN lambda1, IFN lambda2, IFN labmda3 proteins", "response_behavior": "Statisitcally significant reductions compared to non-infected patients inIFN alpha2, IFN gamma, IFN lambda 2 and 3 (combined) proteins"}, {"description": "Anti-viral Inteferon Stimulated Gene mRNA responses to SARS-CoV-2 Infection by RT-PCR", "exact_source": "Table 9", "tissue": "Nasopharyngeal Swab", "immune_exposure": "COVID-19 Infection", "cohort": "Adults", "comparison": "Drive-through diagnostic for people reporting viral like symptoms", "repository_id": "", "platform": "", "response_components": "BST2, IFIT1, IFIT3, IFTM1, MX1 mRNA by RT-PCR", "response_behavior": "Statistically significant upregulation of BST2, IFIT1 IFIT3, MX1 with SARS-CoV-2 infection."}, {"description": "Anti-viral Inteferon Stimulated Gene protein responses to SARS-CoV-2 Infection by Mass Spectrometry", "exact_source": "Table 10", "tissue": "Nasopharyngeal Swab", "immune_exposure": "COVID-19 Infection", "cohort": "Adults", "comparison": "Drive-through diagnostic for people reporting viral like symptoms", "repository_id": "", "platform": "", "response_components": "BST2, IFIT1, IFIT3, IFTM1, MX1 proteins by Data-Dependent Acquisition by Mass Spectrometry", "response_behavior": "Statistically Significant Upregulation of BST2, IFIT1, IFIT3, MX1 with SARS-CoV-2 infection. Non-significant effect on IFITM1."}, {"description": "Anti-viral Inteferon Stimulated Gene mRNA responses to SARS-CoV-2 Infection by RT-PCR", "exact_source": "Figure 5", "tissue": "Nasopharyngeal Swab", "immune_exposure": "COVID-19 Infection", "cohort": "Adults", "comparison": "Drive-through diagnostic for people reporting viral like symptoms", "repository_id": "", "platform": "", "response_components": "BST2, IFIT1, IFIT3, MX1 mRNA by RT-PCR", "response_behavior": "Statistically significant upregulation of mRNA for BST2, IFIT1, IFIT3, MX1 mRNA with Infection; Statistically significant assocation of IFIT3 mRNA and protein with viral N1 RNA and statistically significant correlation between IFIT3 mRNA and protein."}, {"description": "Correlations between Innate Immune Protein levels with SARS-CoV-2 Infection", "exact_source": "Table 11", "tissue": "Nasopharyngeal Swab", "immune_exposure": "COVID-19 Infection", "cohort": "Adults", "comparison": "Drive-through diagnostic for people reporting viral like symptoms", "repository_id": "", "platform": "", "response_components": "IFN alpha2, IFN beta1, IFN gamma, IFN lambda1, IFN lambda2, IFN labmda3, IL1beta, IL6, IL8, IL10, IL12p70, IP10, TNFalpha determined by multiplex immunoassay and IFIT3 protein determined by DDA Mass Spectrometry", "response_behavior": "Strongly statistically significant but moderate pairwise correlations among multiple components"}, {"description": "Correlations between Innate Immune mRNA and Protein levels with SARS-CoV-2 Infection", "exact_source": "Table 12", "tissue": "Nasopharyngeal Swab", "immune_exposure": "COVID-19 Infection", "cohort": "Adults", "comparison": "Drive-through diagnostic for people reporting viral like symptoms", "repository_id": "", "platform": "", "response_components": "GMCSF, IFN alpha2, IFN beta1, IFN gamma, IFN lambda1, IFN lambda2, IFN labmda3, IL1beta, IL6, IL8, IL10, IL12p70, IP10, TNFalpha determined by multiplex immunoassay and IFIT3 protein determined by DDA Mass Spectrometry", "response_behavior": "Only 1 highly significant strong correlation between IP10 protein and IFIT3 mRNA, several additional moderate to strong statistically significant and stron to moderate correlations among other components."}, {"description": "Correlations between Innate Immune mRNA levels with SARS-CoV-2 Infection", "exact_source": "Table 13", "tissue": "Nasopharyngeal Swab", "immune_exposure": "COVID-19 Infection", "cohort": "Adults", "comparison": "Drive-through diagnostic for people reporting viral like symptoms", "repository_id": "", "platform": "", "response_components": "GMCSF, IFN alpha2, IFN beta1, IFN gamma, IFN lambda1, IFN lambda2, IFN labmda3, IL1beta, IL6, IL8, IL10, IL12p70, IP10, TNFalpha  and IFIT3 mRNA determined by RT-PCR", "response_behavior": "Several strongly significant and highly correlated measurements among various components."}]}}, {"_id": "60206cde9567a1c2efa0c0a4", "title": "Immune Alterations in a Patient with SARS-CoV-2-Related Acute Respiratory Distress Syndrome", "userdata": {"global_fields": {"paper": "Bouadma, L., Wiedemann, A., Patrier, J., Sur\u00e9naud, M., Wicky, P., Foucat, E., Diehl, J., Hejblum, B. P., Sinnah, F., de M. E., Lacabaratz, C., Thi\u00e9baut, R., Timsit, J. F. and L\u00e9vy, Y. (2020). Immune Alterations in a Patient with SARS-CoV-2-Related Acute Respiratory Distress Syndrome. J Clin Immunol https://doi.org/10.1007/s10875-020-00839-x", "contributor": "Yves L\u00e9vy", "contributor_organization": "Universit\u00e9 Paris-Est Cr\u00e9teil"}, "local_data": [{"description": " Longitudinal analysis of the immune response associated with a fatal case of COVID-19 in Europe. ", "exact_source": "Figures 2 & 3", "tissue": "Serum and PBMC", "immune_exposure": "COVID-19 infection", "cohort": "Adult 80 years old", "comparison": "severe COVID-19 infection vs Healthy donor", "repository_id": "NA", "platform": "Luminex Bioplex 200 and LSR Fortessa", "response_components": "IL-1\u03b2, IL-1r\u03b1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-8/CXCL8, IL-9, IL-10, IL-12 (p70), IL-13, IL15, IL-17A/CTLA8, Basic FGF (FGF-2), Eotaxin/CCL11, GCSF, GM-CSF, IFN-\u03b3, IP-10/CXCL10, MCP-1/CCL2, MIP- 1\u03b1/CCL3, MIP-1\u03b2/CCL4, PDGF-BB (PDGF-AB/BB), RANTES/CCL5, TNF-\u03b1, VEFG (VEGF-A), IL-1a, IL-2Ra (IL-2R), IL-3, IL-12 (p40), IL-16, IL-18, CTACK/CCL27, GRO-a/CXCL1 (GRO), HGF, IFN-\u03b12, LIF, MCP-3/CCL7, M-CSF, MIF, MIG/CXCL9,b-NGF,SCF, SCGF-b, SDF- 1\u03b1,TNF-b/LTA, and TRAIL. CD3 T cells, B cells, NK cells, gammadelta T cells", "response_behavior": "up and down"}]}, "url": "https://doi.org/10.1007/s10875-020-00839-x", "authors": ["Bouadma, Lila", "Wiedemann, Aur\u00e9lie", "Patrier, Juliette", "Sur\u00e9naud, Mathieu", "Wicky, Paul-Henri", "Foucat, Emile", "Diehl, Jean-Luc", "Hejblum, Boris P.", "Sinnah, Fabrice", "de Montmollin, Etienne", "Lacabaratz, Christine", "Thi\u00e9baut, Rodolphe", "Timsit, J. F.", "L\u00e9vy, Yves"], "journal": "J Clin Immunol", "tags": ["lung", "immune response", "t-cell", "virus", "human", "treatment", "CD57", "PD-1"], "license": "cc-by"}, {"_id": "60206cdf9567a1c2efa0c0a7", "title": "Different Innate and Adaptive Immune Responses to SARS-CoV-2 Infection of Asymptomatic, Mild, and Severe Cases", "userdata": {"global_fields": {"paper": "Carsetti, R., Zaffina, S., Piano M. E., Terreri, S., Corrente, F., Capponi, C., Palomba, P., Mirabella, M., Cascioli, S., Palange, P., Cuccaro, I., Milito, C., Zumla, A., Maeurer, M., Camisa, V., Vinci, M. R., Santoro, A., Cimini, E., Marchioni, L., Nicastri, E., Palmieri, F., Agrati, C., Ippolito, G., Porzio, O., Concato, C., Onetti M. A., Raponi, M., Quintarelli, C., Quinti, I. and Locatelli, F. (2020). Different Innate and Adaptive Immune Responses to SARS-CoV-2 Infection of Asymptomatic, Mild, and Severe Cases. Front Immunol https://www.ncbi.nlm.nih.gov/pubmed/33391280/", "contributor": "Rita Carsetti", "contributor_organization": "Bambino Ges\u00f9 Children\u2019s Hospital"}, "local_data": [{"description": "NK cells were reduced and monocytes increased in patients with severe COVID-19. We show that the ratio between NK cells and monocytes was <1 in asymptomatic individuals, >1 in patients with mild disease and even higher in severe cases. \n", "exact_source": "Figure 1C D and E", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "20 asymptomatic SARS-CoV-2-infected cases; 8 patients with Mild COVID-19 disease; 8 cases of Severe COVID-19 disease.", "comparison": "asymptomatic vs mild vs severe from the first positive swab", "repository_id": "not applicable", "platform": "not applicable", "response_components": "", "response_behavior": ""}, {"description": "Severe patients have the highest levels of IgG and IgA. Our most interesting observation is the different kinetics of response in asymptomatic and mild disease forms of infection. The early\nand transient IgM, IgA, and IgG responses distinguish asymptomatic individuals from mild-disease patients, who have a slower, but more persistent antibody production.", "exact_source": "Figure 6", "tissue": "Serum", "immune_exposure": "COVID-19 infection", "cohort": "20 asymptomatic SARS-CoV-2-infected cases; 8 patients with Mild COVID-19 disease; 8 cases of Severe COVID-19 disease.", "comparison": "asymptomatic vs mild vs severe from the first positive swab", "repository_id": "not applicable ", "platform": "not applicable", "response_components": "", "response_behavior": ""}]}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/33391280/", "authors": ["Carsetti, Rita", "Zaffina, Salvatore", "Piano Mortari, Eva", "Terreri, Sara", "Corrente, Francesco", "Capponi, Claudia", "Palomba, Patrizia", "Mirabella, Mattia", "Cascioli, Simona", "Palange, Paolo", "Cuccaro, Ilaria", "Milito, Cinzia", "Zumla, Alimuddin", "Maeurer, Markus", "Camisa, Vincenzo", "Vinci, Maria Rosaria", "Santoro, Annapaola", "Cimini, Eleonora", "Marchioni, Luisa", "Nicastri, Emanuele", "Palmieri, Fabrizio", "Agrati, Chiara", "Ippolito, Giuseppe", "Porzio, Ottavia", "Concato, Carlo", "Onetti Muda, Andrea", "Raponi, Massimiliano", "Quintarelli, Concetta", "Quinti, Isabella", "Locatelli, Franco"], "journal": "Front Immunol", "tags": ["immune response", "human", "antibody", "IgA"], "license": "cc-by"}, {"_id": "60206cdf9567a1c2efa0c0a8", "title": "Comprehensive mapping of immune perturbations associated with severe COVID-19", "userdata": {"global_fields": {"paper": "Kuri-Cervantes, L., Pampena, M. B., Meng, W., Rosenfeld, A. M., Ittner, C. A., Weisman, A. R., Agyekum, R. S., Mathew, D., Baxter, A. E., Vella, L. A., Kuthuru, O., Apostolidis, S. A., Bershaw, L., Dougherty, J., Greenplate, A. R., Pattekar, A., Kim, J., Han, N., Gouma, S., Weirick, M. E., Arevalo, C. P., Bolton, M. J., Goodwin, E. C., Anderson, E. M., Hensley, S. E., Jones, T. K., Mangalmurti, N. S., Luning P. E. T., Wherry, E. J., Meyer, N. J. and Betts, M. R. (2020). Comprehensive mapping of immune perturbations associated with severe COVID-19. Sci Immunol https://doi.org/10.1126/sciimmunol.abd7114", "contributor": "Michael Betts", "contributor_organization": "University of Pennsylvania"}, "local_data": [{"description": "Immune profile generated from whole blood in moderate, severe and convalescent COVID-19 compared to uninfected controls. ", "exact_source": "Figures 1-6", "tissue": "PBMC", "immune_exposure": "moderate, severe and convalescent COVID-19 infection", "cohort": "adults", "comparison": "uninfected controls, moderate disease, severe disease, convalescent disease, comparison across groups", "repository_id": "https://hpap.pmacs.upenn.edu/", "platform": "fcs flow cytometry files", "response_components": "", "response_behavior": ""}]}, "url": "https://doi.org/10.1126/sciimmunol.abd7114", "authors": ["Kuri-Cervantes, Leticia", "Pampena, M. Betina", "Meng, Wenzhao", "Rosenfeld, Aaron M.", "Ittner, Caroline A.G.", "Weisman, Ariel R.", "Agyekum, Roseline S.", "Mathew, Divij", "Baxter, Amy E.", "Vella, Laura A.", "Kuthuru, Oliva", "Apostolidis, Sokratis A.", "Bershaw, Luanne", "Dougherty, Jeanette", "Greenplate, Allison R.", "Pattekar, Ajinkya", "Kim, Justin", "Han, Nicholas", "Gouma, Sigrid", "Weirick, Madison E.", "Arevalo, Claudia P.", "Bolton, Marcus J.", "Goodwin, Eileen C.", "Anderson, Elizabeth M.", "Hensley, Scott E.", "Jones, Tiffanie K.", "Mangalmurti, Nilam S.", "Luning Prak, Eline T.", "Wherry, E. John", "Meyer, Nuala J.", "Betts, Michael R."], "journal": "Sci Immunol", "tags": ["t-cell", "human"], "license": "cc-by"}, {"_id": "60206ce19567a1c2efa0c0ae", "title": "Marked T cell activation, senescence, exhaustion and skewing towards TH17 in patients with COVID-19 pneumonia", "userdata": {"global_fields": {"paper": "De Biasi S., Meschiari, M., Gibellini, L., Bellinazzi, C., Borella, R., Fidanza, L., Gozzi, L., Iannone, A., Lo T. D., Mattioli, M., Paolini, A., Menozzi, M., Mili\u0107, J., Franceschi, G., Fantini, R., Tonelli, R., Sita, M., Sarti, M., Trenti, T., Brugioni, L., Cicchetti, L., Facchinetti, F., Pietrangelo, A., Clini, E., Girardis, M., Guaraldi, G., Mussini, C. and Cossarizza, A. (2020). Marked T cell activation, senescence, exhaustion and skewing towards TH17 in patients with COVID-19 pneumonia. Nat Commun https://doi.org/10.1038/s41467-020-17292-4", "contributor": "Andrea Cossarizza", "contributor_organization": "Universit\u00e0 degli studi di Modena e Reggio Emilia"}, "local_data": [{"description": "Detailed investigation of T cells and cytokine production in patients affected by COVID-19 pneumonia.", "exact_source": "", "tissue": "PBMC", "immune_exposure": "COVID-19", "cohort": "ADULTS RANGE 35\u201394 YEARS", "comparison": "patients with COVID-19 pneumonia vs healthy donors", "repository_id": "https://flowrepository.org/id/FR-FCM- Z2N5; https://flowrepository.org/id/FR-FCM-Z2N4.", "platform": "", "response_components": "", "response_behavior": ""}]}, "url": "https://doi.org/10.1038/s41467-020-17292-4", "authors": ["De Biasi, Sara", "Meschiari, Marianna", "Gibellini, Lara", "Bellinazzi, Caterina", "Borella, Rebecca", "Fidanza, Lucia", "Gozzi, Licia", "Iannone, Anna", "Lo Tartaro, Domenico", "Mattioli, Marco", "Paolini, Annamaria", "Menozzi, Marianna", "Mili\u0107, Jovana", "Franceschi, Giacomo", "Fantini, Riccardo", "Tonelli, Roberto", "Sita, Marco", "Sarti, Mario", "Trenti, Tommaso", "Brugioni, Lucio", "Cicchetti, Luca", "Facchinetti, Fabio", "Pietrangelo, Antonello", "Clini, Enrico", "Girardis, Massimo", "Guaraldi, Giovanni", "Mussini, Cristina", "Cossarizza, Andrea"], "journal": "Nat Commun", "tags": ["t-cell", "human", "CD4", "IL-17", "TNF", "interferon-gamma", "interleukin (IL)-2", "tumor necrosis factor"], "license": "cc-by"}, {"_id": "60206ce39567a1c2efa0c0b8", "title": "Sustained Cellular Immune Dysregulation in Individuals Recovering from SARS-CoV-2 Infection", "userdata": {"global_fields": {"paper": "Files, J. K., Boppana, S., Perez, M. D., Sarkar, S., Lowman, K. E., Qin, K., ... & Erdmann, N. (2021). Sustained cellular immune dysregulation in individuals recovering from SARS-CoV-2 infection. The Journal of clinical investigation, 131(1). https://www.jci.org/articles/view/140491/pdf", "contributor": "Jacob Files and Nathan Erdmann", "contributor_organization": "University of Alabama at Birmingham"}, "local_data": [{"description": "Flow cytometry findings showed increased upregulation of T-cell and B-cell activation and exhaustion markers in hospitalized patients in comparison to non-hospitalized. Additionally, non-hospitalized patients appeared to show increased expression of many activation/exhaustion markers between visit 1 (~2 weeks) and visit 2 (~4 weeks).", "exact_source": "Figures 1-7 and supplementary information", "tissue": "PBMC", "immune_exposure": "COVID-19 infection (convalescent)", "cohort": "adults, both hospitalized and non-hospitalized", "comparison": "hospitalized vs non-hospitalized; non-hospitalized visit 1 vs non-hospitalized visit 2", "repository_id": "NA", "platform": "NA", "response_components": "NA", "response_behavior": "NA"}]}, "url": "http://medrxiv.org/cgi/content/short/2020.07.30.20165175v1?rss=1", "authors": ["Files, J. K.", "Boppana, S.", "Perez, M. D.", "Sarkar, S.", "Lowman, K. E.", "Qin, K.", "Sterrett, S.", "Carlin, E.", "Bansal, A.", "Sabbaj, S.", "Long, D. M.", "Kutsch, O.", "Kobie, J.", "Goepfert, P. A.", "Erdmann, N."], "journal": NaN, "tags": ["t-cell", "b-cell", "human"], "license": "medrxiv"}, {"_id": "60206ce49567a1c2efa0c0bb", "title": "Host transcriptomic profiling of COVID-19 patients with mild, moderate, and severe clinical outcomes", "userdata": {"global_fields": {"paper": "Jain, R., Ramaswamy, S., Harilal, D., Uddin, M., Loney, T., Nowotny, N., ... & Abou Tayoun, A. (2021). Host transcriptomic profiling of COVID-19 patients with mild, moderate, and severe clinical outcomes. Computational and structural biotechnology journal, 19, 153-160. https://doi.org/10.1016/j.csbj.2020.12.016", "contributor": "Ahmad Tayoun", "contributor_organization": "Al Jalila Genomics Center, Al Jalila Children\u2019s Hospital, Dubai, United Arab Emirates."}, "local_data": [{"description": "Our study highlights key molecular and functional pathways involved in COVID-19 pathogenesis and characterizes a specific early expression signature associated with severe disease outcomes due to SARS-CoV-2. ", "exact_source": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7773686/figure/f0020/?report=objectonly", "tissue": "nasopharyngeal ", "immune_exposure": "COVID-19 infection", "cohort": "3 \u2013 70 years", "comparison": "severe vs mild and moderate clinical outcomes", "repository_id": "GSE162835", "platform": "GPL24676", "response_components": "CCL2, CCL22, CXCL9, CXCL12, IFIH1, IFI44, IFIT1, IL10, CXCL5, IL11, IL12, IL19, IL34, IL10RA, IL21R, IL11RA, CCL25, CCL2, CCR5, CCR7, TNFSF9, TNFSF15, TNFRSF25, TNFRSF9, C2, C5, C6, F12, F8, STAT4, STAT5A, STAT5B ", "response_behavior": "up"}]}, "url": "https://doi.org/10.1101/2020.09.28.316604", "authors": ["Jain, Ruchi", "Ramaswamy, Sathishkumar", "Harilal, Divinlal", "Uddin, Mohammed", "Loney, Tom", "Nowotny, Norbert", "Alsuwaidi, Hanan", "Varghese, Rupa", "Deesi, Zulfa", "Alkhajeh, Abdulmajeed", "Khansaheb, Hamda", "Alsheikh-Ali, Alawi", "Tayoun, Ahmad Abou"], "journal": "bioRxiv", "tags": ["lung", "human", "gene"], "license": "biorxiv"}, {"_id": "60206ce49567a1c2efa0c0bc", "title": "Distinct inflammatory profiles distinguish COVID-19 from influenza with limited contributions from cytokine storm", "userdata": {"global_fields": {"paper": "Mudd, P. A., Crawford, J. C., ..., Powderly, W. G., Thomas, P. G. and Ellebedy, A. H. (2020). Distinct inflammatory profiles distinguish COVID-19 from influenza with limited contributions from cytokine storm. Sci Adv https://www.ncbi.nlm.nih.gov/pubmed/33187979/", "contributor": "Philip A. Mudd", "contributor_organization": "Washington University School of Medicine"}, "local_data": [{"description": "The dataset in our manuscript includes: 1) 35-plex plasma cytokine concentration measurements from 168 individuals with COVID-19, 26 individuals with seasonal influenza and 16 healthy controls; 2) multiparameter flow cytometry from 22 COVID-19, 23 seasonal influenza and 15 healthy controls; 3) single-cell RNA transcriptional profiles from 3 individuals with severe COVID-19, 3 individuals with severe seasonal influenza and 2 healthy controls.", "exact_source": "Multiple signatures are highlighted in several figures.  The cytokine/FACS data are found in Supplementary Material Table S1.  Single-cell RNAseq raw data is found in the repositories listed below.", "tissue": "plasma and PBMC", "immune_exposure": "SARS-CoV-2 infection or seasonal influenza infection of varying clinical severity or uninfected controls", "cohort": "adults age 18-92", "comparison": "influenza vs. COVID-19 vs. healthy control; single-cell RNAseq is severe influenza vs. severe COVID-19", "repository_id": "Single-cell gene expression data have been uploaded to the National Center for Biotechnology Information (NCBI) Short Read Archive under BioProject ID PRJNA630932 and SRA accession SRR11233662.", "platform": "Cytokine measurement - Luminex FLEXMAP 3D; Single-cell RNAseq - 10x Genomics 5' (V2) kit with sequencing on Illumina NovaSeq 6000.", "response_components": "multiple responses delineated in manuscript - largest unifying difference is lower type I and type II interferon signaling in COVID-19 when compared with influenza", "response_behavior": "multiple response behaviors delineated in manuscript"}]}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/33187979/", "authors": ["Mudd, Philip A.", "Crawford, Jeremy Chase", "Turner, Jackson S.", "Souquette, Aisha", "Reynolds, Daniel", "Bender, Diane", "Bosanquet, James P.", "Anand, Nitin J.", "Striker, David A.", "Martin, R. Scott", "Boon, Adrianus C. M.", "House, Stacey L.", "Remy, Kenneth E.", "Hotchkiss, Richard S.", "Presti, Rachel M.", "O\u2019Halloran, Jane A.", "Powderly, William G.", "Thomas, Paul G.", "Ellebedy, Ali H."], "journal": "Sci Adv", "tags": ["human", "GCSF", "IL-1RA", "IL-6", "MCP1"], "license": "cc-by"}, {"_id": "60206ce69567a1c2efa0c0c1", "title": "Transcriptional Differences for COVID-19 Disease Map Genes between Males and Females Indicate a Different Basal Immunophenotype Relevant to the Disease", "userdata": {"global_fields": {"paper": "Liu, T., Balzano-Nogueira, L., Lleo, A. and Conesa, A. (2020). Transcriptional Differences for COVID-19 Disease Map Genes between Males and Females Indicate a Different Basal Immunophenotype Relevant to the Disease. Genes (Basel) https://doi.org/10.3390/genes11121447", "contributor": "Liu, T., Balzano-Nogueira, L., Lleo, A. and Conesa, A.", "contributor_organization": "University of Florida"}, "local_data": [{"description": "The baseline gene expression difference between males and females of COVID-19 Disease Map genes in a healthy population.", "exact_source": "https://www.mdpi.com/2073-4425/11/12/1447 https://www.mdpi.com/2073-4425/11/12/1447 https://www.mdpi.com/2073-4425/11/12/1447 https://www.mdpi.com/2073-4425/11/12/1447 https://www.mdpi.com/2073-4425/11/12/1447 https://www.mdpi.com/2073-4425/11/12/1447 https://www.mdpi.com/2073-4425/11/12/1447", "tissue": "Whole Blood\t Kidney-Cortex Stomach Lung Heart Left-Ventricle\t Brain-Cortex\tSpleen Lymphocytes", "immune_exposure": "healthy people ", "cohort": "adults(20-79)", "comparison": "young people vs old people (age 20-60 vs age 60-79) ", "repository_id": "GSE92743", "platform": "Ensembl_Gene_IDs", "response_components": "Ensembl_Gene_IDs", "response_behavior": "up"}]}, "url": "https://doi.org/10.3390/genes11121447", "authors": ["Liu, Tianyuan", "Balzano-Nogueira, Leandro", "Lleo, Ana", "Conesa, Ana"], "journal": "Genes (Basel)", "tags": ["virus", "human", "gene"], "license": "cc-by"}, {"_id": "60206ce89567a1c2efa0c0c5", "title": "Expansion of myeloid-derived suppressor cells in patients with severe coronavirus disease (COVID-19)", "userdata": {"global_fields": {"paper": "Agrati, C., Sacchi, A., Bordoni, V., Cimini, E., Notari, S., Grassi, G., Casetti, R., Tartaglia, E., Lalle, E., D\u2019Abramo, A., Castilletti, C., Marchioni, L., Shi, Y., Mariano, A., Song, J., Zhang, J., Wang, F., Zhang, C., Fimia, G. M., Capobianchi, M. R., Piacentini, M., Antinori, A., Nicastri, E., Maeurer, M., Zumla, A. and Ippolito, G. (2020). Expansion of myeloid-derived suppressor cells in patients with severe coronavirus disease (COVID-19). Cell Death Differ https://www.ncbi.nlm.nih.gov/pubmed/32514047/", "contributor": "Giuseppe Ippolito", "contributor_organization": "Istituto Nazionale per le Malattie Infettive Lazzaro Spallanzani"}, "local_data": [{"description": "Massive expansion of MDSCs was observed, up to 90% of total circulating mononuclear cells in patients with severe disease, and up to 25% in the patients with mild disease; the frequency decreasing with recovery.", "exact_source": "Figure 4 and Figure 6", "tissue": "PBMC", "immune_exposure": "COVID-19 ", "cohort": "adults", "comparison": "severe vs mild disease", "repository_id": "", "platform": "Flow cytometry", "response_components": "Cell type", "response_behavior": "Up"}]}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/32514047/", "authors": ["Agrati, Chiara", "Sacchi, Alessandra", "Bordoni, Veronica", "Cimini, Eleonora", "Notari, Stefania", "Grassi, Germana", "Casetti, Rita", "Tartaglia, Eleonora", "Lalle, Eleonora", "D\u2019Abramo, Alessandra", "Castilletti, Concetta", "Marchioni, Luisa", "Shi, Yufang", "Mariano, Andrea", "Song, Jin-Wen", "Zhang, Ji-Yuan", "Wang, Fu-Sheng", "Zhang, Chao", "Fimia, Gian Maria", "Capobianchi, Maria R.", "Piacentini, Mauro", "Antinori, Andrea", "Nicastri, Emanuele", "Maeurer, Markus", "Zumla, Alimuddin", "Ippolito, Giuseppe"], "journal": "Cell Death Differ", "tags": ["immune response", "t-cell", "human", "CD95", "IL-6", "TGF-beta"], "license": "cc-by"}, {"_id": "60206cee9567a1c2efa0c0dd", "title": "Longitudinal transcriptome analyses show robust T cell immunity during recovery from COVID-19", "userdata": {"global_fields": {"paper": "Zheng, H., Xu, M., Yang, C., Tian, R., Zhang, M., Li, J., Wang, X., Ding, Z., Li, G., Li, X., He, Y., Dong, X., Yao, Y. and Zheng, Y. (2020). Longitudinal transcriptome analyses show robust T cell immunity during recovery from COVID-19. Signal Transduct Target Ther https://doi.org/10.1038/s41392-020-00457-4", "contributor": "Yong-Tang Zheng", "contributor_organization": "University of Chinese Academy of Sciences"}, "local_data": [{"description": "up-regulated genes in PBMC samples from patients with COVID-19 during the recovery.", "exact_source": "Figure 2", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "Children and adults(3.5-69 years old)", "comparison": "Comparison among treatment, convalescence and rehabilitation stages", "repository_id": "GSE157859", "platform": "Ensembl_gene_ID", "response_components": "ENSG00000006652, ENSG00000050344, ENSG00000076826, ENSG00000089723, ENSG00000090971, ENSG00000099860, ENSG00000099985, ENSG00000100906, ENSG00000104804, ENSG00000106328, ENSG00000107968, ENSG00000108375, ENSG00000109321, ENSG00000110848, ENSG00000111537, ENSG00000112149, ENSG00000113369, ENSG00000118298, ENSG00000119508, ENSG00000119986, ENSG00000121101, ENSG00000121764, ENSG00000121966, ENSG00000123358, ENSG00000123689, ENSG00000124575, ENSG00000125462, ENSG00000126262, ENSG00000132002, ENSG00000133316, ENSG00000139438, ENSG00000141682, ENSG00000143443, ENSG00000143878, ENSG00000144749, ENSG00000145632, ENSG00000145675, ENSG00000149243, ENSG00000149646, ENSG00000153234, ENSG00000154640, ENSG00000154764, ENSG00000154920, ENSG00000155307, ENSG00000155719, ENSG00000156232, ENSG00000156966, ENSG00000158050, ENSG00000161835, ENSG00000162783, ENSG00000163141, ENSG00000163874, ENSG00000164099, ENSG00000166444, ENSG00000168026, ENSG00000168298, ENSG00000171757, ENSG00000172803, ENSG00000177606, ENSG00000179029, ENSG00000183598, ENSG00000184545, ENSG00000184557, ENSG00000184588, ENSG00000185338, ENSG00000187837, ENSG00000188163, ENSG00000188886, ENSG00000197019, ENSG00000197837, ENSG00000204186, ENSG00000205189, ENSG00000205710, ENSG00000213085, ENSG00000213386, ENSG00000218281, ENSG00000224796, ENSG00000225808, ENSG00000231461, ENSG00000232810, ENSG00000234816, ENSG00000235618, ENSG00000249884, ENSG00000251682, ENSG00000255040, ENSG00000255274, ENSG00000256683, ENSG00000257838, ENSG00000259950, ENSG00000270276, ENSG00000270903, ENSG00000273802, ENSG00000274997, ENSG00000275714, ENSG00000275993, ENSG00000276410, ENSG00000277632, ENSG00000278463", "response_behavior": "up"}, {"description": "down-regulated genes in PBMC samples from patients with COVID-19 during the recovery.", "exact_source": "Figure 2", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "Children and adults(3.5-69 years old)", "comparison": "Comparison among treatment, convalescence and rehabilitation stages", "repository_id": "GSE157859", "platform": "Ensembl_gene_ID", "response_components": "ENSG00000004799, ENSG00000047457, ENSG00000047597, ENSG00000048342, ENSG00000065618, ENSG00000079385, ENSG00000096060, ENSG00000100154, ENSG00000102230, ENSG00000114737, ENSG00000116675, ENSG00000116962, ENSG00000117009, ENSG00000118276, ENSG00000122025, 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ENSG00000211964, ENSG00000211965, ENSG00000211966, ENSG00000211976, ENSG00000224373, ENSG00000239264, ENSG00000239951, ENSG00000241294, ENSG00000241351, ENSG00000242076, ENSG00000243290, ENSG00000243414, ENSG00000244116, ENSG00000244437, ENSG00000244575, ENSG00000251546, ENSG00000253998, ENSG00000259581, ENSG00000270550, ENSG00000274576, ENSG00000275111, ENSG00000276566, ENSG00000280411, ENSG00000280852", "response_behavior": "down"}]}, "url": "https://doi.org/10.1038/s41392-020-00457-4", "authors": ["Zheng, Hong-Yi", "Xu, Min", "Yang, Cui-Xian", "Tian, Ren-Rong", "Zhang, Mi", "Li, Jian-Jian", "Wang, Xi-Cheng", "Ding, Zhao-Li", "Li, Gui-Mei", "Li, Xiao-Lu", "He, Yu-Qi", "Dong, Xing-Qi", "Yao, Yong-Gang", "Zheng, Yong-Tang"], "journal": "Signal Transduct Target Ther", "tags": ["downregulated", "immune response", "t-cell", "human", "treatment", "AP-1", "activating protein-1"], "license": "cc-by"}, {"_id": "604f8631ed749b2b986d44eb", "title": "Mucosal-Associated Invariant T (MAIT) Cells Are Highly Activated and Functionally Impaired in COVID-19 Patients", "userdata": {"global_fields": {"paper": "Deschler, S., Kager, J., Erber, J., Fricke, L., Koyumdzhieva, P., Georgieva, A., Lahmer, T., Wiessner, J. R., Voit, F., Schneider, J., Horstmann, J., Iakoubov, R., Treiber, M., Winter, C., Ruland, J., Busch, D. H., Knolle, P. A., Protzer, U., Spinner, C. D., Schmid, R. M., Quante, M. and B\u00f6ttcher, K. (2021). Mucosal-Associated Invariant T (MAIT) Cells Are Highly Activated and Functionally Impaired in COVID-19 Patients. Viruses https://doi.org/10.3390/v13020241", "contributor": "Katrin B\u00f6ttcher", "contributor_organization": "Technical University of Munich"}, "local_data": [{"description": "Alterations in immune cell populations in patients with mild and severe COVID-19 in comparison to healthy controls", "exact_source": "Figure 1 and 2", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "adults", "comparison": "severe and mild infection vs. healthy controls", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "up and down"}, {"description": "expression of activation markers and cytokines by MAIT cell ex vivo", "exact_source": "Figure 3, Supplemental Figure 3", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "adults", "comparison": "severe and mild infection vs. healthy controls, acute infection vs. convalescence", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "up"}, {"description": "cytokine expression of MAIT cells in COVID-19 patients following stimulation", "exact_source": "Figure 4, Supplemental Figure 4", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "adults", "comparison": "severe and mild infection vs. healthy controls, acute infection vs. convalescence", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "down"}]}, "url": "https://doi.org/10.3390/v13020241", "authors": ["Deschler, Sebastian", "Kager, Juliane", "Erber, Johanna", "Fricke, Lisa", "Koyumdzhieva, Plamena", "Georgieva, Alexandra", "Lahmer, Tobias", "Wiessner, Johannes R.", "Voit, Florian", "Schneider, Jochen", "Horstmann, Julia", "Iakoubov, Roman", "Treiber, Matthias", "Winter, Christof", "Ruland, J\u00fcrgen", "Busch, Dirk H.", "Knolle, Percy A.", "Protzer, Ulrike", "Spinner, Christoph D.", "Schmid, Roland M.", "Quante, Michael", "B\u00f6ttcher, Katrin"], "journal": "Viruses", "tags": ["lung", "t-cell", "human", "protein", "IL-17A", "TNFalpha", "granzyme B"], "license": "cc-by"}, {"_id": "604f8645ed749b2b986d4524", "title": "Longitudinal proteomic profiling reveals increased early inflammation and sustained apoptosis proteins in severe COVID-19", "userdata": {"global_fields": {"paper": "Haljasm\u00e4gi, L., Salumets, A., Rumm, A. P., J\u00fcrgenson, M., Krassohhina, E., Remm, A., Sein, H., Kareinen, L., Vapalahti, O., Sironen, T., Peterson, H., Milani, L., Tamm, A., Hayday, A., Kisand, K. and Peterson, P. (2020). Longitudinal proteomic profiling reveals increased early inflammation and sustained apoptosis proteins in severe COVID-19. Sci Rep https://www.ncbi.nlm.nih.gov/pubmed/33239683/", "contributor": "P\u00e4rt Peterson", "contributor_organization": "University of Tartu"}, "local_data": [{"description": "Olink Inflammation panel analysis of ca 90 plasma protein levels in Covid-19 patients (ICU vs severe vs mild)\n", "exact_source": "Supplementary Table 2", "tissue": "Blood plasma", "immune_exposure": "COVID-19 infection", "cohort": "older, mostly over 65 years", "comparison": "ICU vs ordinary Covid-19 ward vs mild", "repository_id": "-", "platform": "Proseek Multiplex Inflammation panel by Olink\u00ae Proteomics", "response_components": "-", "response_behavior": "up"}]}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/33239683/", "authors": ["Haljasm\u00e4gi, Liis", "Salumets, Ahto", "Rumm, Anna Pauliina", "J\u00fcrgenson, Meeri", "Krassohhina, Ekaterina", "Remm, Anu", "Sein, Hanna", "Kareinen, Lauri", "Vapalahti, Olli", "Sironen, Tarja", "Peterson, Hedi", "Milani, Lili", "Tamm, Anu", "Hayday, Adrian", "Kisand, Kai", "Peterson, P\u00e4rt"], "journal": "Sci Rep", "tags": ["human", "antibody", "treatment", "protein", "CASP8", "CCL2", "CCL7", "CCL8", "CXCL10", "CXCL11", "HGF", "IFNgamma", "IL-10", "IL-6", "TGFB1", "TNFSF14"], "license": "cc-by"}, {"_id": "604f8646ed749b2b986d4529", "title": "Excessive Neutrophils and Neutrophil Extracellular Traps in COVID-19", "userdata": {"global_fields": {"paper": "Wang, J., Li, Q., Yin, Y., Zhang, Y., Cao, Y., Lin, X., Huang, L., Hoffmann, D., Lu, M. and Qiu, Y. (2020). Excessive Neutrophils and Neutrophil Extracellular Traps in COVID-19. Front Immunol https://www.ncbi.nlm.nih.gov/pubmed/33013872/", "contributor": "Daniel Hoffmann, Mengji Lu, Yuanwang Qiu", "contributor_organization": "University of Duisburg-Essen and Jiangnan University"}, "local_data": [{"description": "Transcriptome analysis of the lung and BALF in COVID-19 patient. Marker genes  were used to identify Neutrophils, T cells, Monocytes, and B cells in both Lung and BALF samples of COVID-19 patients and healthy controls, respectively.", "exact_source": "Figure 4", "tissue": "Lung and BALF", "immune_exposure": "COVID-19 infection", "cohort": "Old Adult (>60 years) for GSE147507, Adult (18-60 years) for CRA002390", "comparison": "COVID-19 patients and healthy controls", "repository_id": "CRA002390, GSE147507", "platform": "Illumina NextSeq 500", "response_components": " LGALS9, HCK, LCP1, CEACAM1, S100A8, LGALS9, CTSC", "response_behavior": "up"}]}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/33013872/", "authors": ["Wang, Jun", "Li, Qian", "Yin, Yongmei", "Zhang, Yingying", "Cao, Yingying", "Lin, Xiaoming", "Huang, Lihua", "Hoffmann, Daniel", "Lu, Mengji", "Qiu, Yuanwang"], "journal": "Front Immunol", "tags": ["lung", "human", "gene"], "license": "cc-by"}, {"_id": "604f8649ed749b2b986d4532", "title": "Monocytopenia, monocyte morphological anomalies and hyperinflammation characterise severe COVID\u201019 in type 2 diabetes", "userdata": {"global_fields": {"paper": "Alzaid, F., Julla, J., Diedisheim, M., Potier, C., Potier, L., Velho, G., Gaborit, B., Manivet, P., Germain, S., Vidal\u2010Trecan, T., Roussel, R., Riveline, J., Dalmas, E., Venteclef, N. and Gautier, J. (2020). Monocytopenia, monocyte morphological anomalies and hyperinflammation characterise severe COVID\u201019 in type 2 diabetes. EMBO Mol Med https://doi.org/10.15252/emmm.202013038", "contributor": "Fawaz Alzaid and Jean-Fran\u00e7ois Gautier", "contributor_organization": "Sorbonne Universit\u00e9, Universit\u00e9 de Paris, INSERM, AP-HP"}, "local_data": [{"description": "Immune cell population frequencies in peripheral blood of hospitalised patients with COVID-19 that have type-2 diabetes or are non-diabetic. Patients were further separated into those requiring critical care and those not requiring critical care. ", "exact_source": "https://doi.org/10.15252/emmm.202013038", "tissue": "PBMC", "immune_exposure": "COVID-19 infection +/- type-2 diabetes +/- critical care", "cohort": "adults: 52 y to 77 y", "comparison": "diabetic versus non-diabetes", "repository_id": "NA", "platform": "NA", "response_components": "lymphocytes, monocytes", "response_behavior": "down, down"}, {"description": "Immune cell population frequencies in peripheral blood of hospitalised patients with COVID-19 that have type-2 diabetes or are non-diabetic. Patients were further separated into those requiring critical care and those not requiring critical care. ", "exact_source": "https://doi.org/10.15252/emmm.202013038", "tissue": "PBMC", "immune_exposure": "COVID-19 infection +/- type-2 diabetes +/- critical care", "cohort": "adults: 52 y to 77 y", "comparison": "Critical care versus non-critical care", "repository_id": "NA", "platform": "NA", "response_components": "lymphocytes, monocytes", "response_behavior": "down, down"}]}, "url": "https://doi.org/10.15252/emmm.202013038", "authors": ["Alzaid, Fawaz", "Julla, Jean\u2010Baptiste", "Diedisheim, Marc", "Potier, Charline", "Potier, Louis", "Velho, Gilberto", "Gaborit, B\u00e9n\u00e9dicte", "Manivet, Philippe", "Germain, St\u00e9phane", "Vidal\u2010Trecan, Tiphaine", "Roussel, Ronan", "Riveline, Jean\u2010Pierre", "Dalmas, Elise", "Venteclef, Nicolas", "Gautier, Jean\u2010Fran\u00e7ois"], "journal": "EMBO Mol Med", "tags": ["human", "CCL2", "CD14", "CD16", "CD8", "IL6", "IL8"], "license": "cc-by"}, {"_id": "60b7f3ed6bd17889a8ced009", "title": "Immune Profile in Patients With COVID-19: Lymphocytes Exhaustion Markers in Relationship to Clinical Outcome", "userdata": {"global_fields": {"paper": "Bobcakova, A., Petriskova, J., Vysehradsky, R., Kocan, I., Kapustova, L., Barnova, M., Diamant, Z. and Jesenak, M. (2021). Immune Profile in Patients With COVID-19: Lymphocytes Exhaustion Markers in Relationship to Clinical Outcome. Front Cell Infect Microbiol https://doi.org/10.3389/fcimb.2021.646688", "contributor": "Anna Bobcakova, Milos Jesenak", "contributor_organization": "Comenius University in Bratislava"}, "local_data": [{"description": "Total lymphocytes count on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 3", "tissue": "total lymphocytes", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "fatal vs. mild/moderate on admission", "repository_id": "not applicable", "platform": "total lymphocytes", "response_components": "", "response_behavior": "down"}, {"description": "Total lymphocytes count on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 3", "tissue": "total lymphocytes", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "fatal vs. severe on admission", "repository_id": "not applicable", "platform": "total lymphocytes", "response_components": "", "response_behavior": "down"}, {"description": "Total lymphocytes count on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 3", "tissue": "total lymphocytes ", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "critical vs. mild/moderate on admission", "repository_id": "not applicable", "platform": "total lymphocytes", "response_components": "", "response_behavior": "down"}, {"description": "Total lymphocytes count on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 3", "tissue": "total lymphocytes ", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "severe vs. mild/moderate on admission", "repository_id": "not applicable", "platform": "total lymphocytes", "response_components": "", "response_behavior": "down"}, {"description": "The lowest lymphocyte count during hospitalization of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 4", "tissue": "total lymphocytes ", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "fatal vs. severe ", "repository_id": "not applicable", "platform": "total lymphocytes", "response_components": "", "response_behavior": "down"}, {"description": "The lowest lymphocyte count during hospitalization of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 4", "tissue": "total lymphocytes", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "fatal vs. mild/moderate", "repository_id": "not applicable", "platform": "total lymphocytes", "response_components": "", "response_behavior": "down"}, {"description": "The lowest lymphocyte count during hospitalization of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 4", "tissue": "total lymphocytes", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "critilal vs. severe", "repository_id": "not applicable ", "platform": "total lymphocytes", "response_components": "", "response_behavior": "down"}, {"description": "The lowest lymphocyte count during hospitalization of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 4", "tissue": "total lymphocytes", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "critical vs. mild/moderate", "repository_id": "not applicable", "platform": "total lymphocytes", "response_components": "", "response_behavior": "down"}, {"description": "Neutrophil-to-lymphocyte ratio on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 5B", "tissue": "neutrophils-to-lymphocytes ratio", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "fatal vs. mild/moderate", "repository_id": "not applicable", "platform": "neutrophils, lymphocytes", "response_components": "", "response_behavior": "up"}, {"description": "Neutrophil-to-lymphocyte ratio on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 5B", "tissue": "neutrophils-to-lymphocytes ratio", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "fatal vs. severe", "repository_id": "", "platform": "neutrophils, lymphocytes", "response_components": "", "response_behavior": "up"}, {"description": "Neutrophil-to-lymphocyte ratio on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 5B", "tissue": "neutrophils-to-lymphocytes ratio", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "critical vs. mild/moderate", "repository_id": "", "platform": "neutrophils, lymphocytes", "response_components": "", "response_behavior": "up"}, {"description": "Neutrophil-to-lymphocyte ratio on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 5B", "tissue": "neutrophils-to-lymphocytes ratio", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "critical vs.severe", "repository_id": "", "platform": "neutrophils, lymphocytes", "response_components": "", "response_behavior": "up"}, {"description": "Neutrophil-to-lymphocyte ratio on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 5B", "tissue": "neutrophils-to-lymphocytes ratio", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "severe vs mild/moderate", "repository_id": "", "platform": "neutrophils, lymphocytes", "response_components": "", "response_behavior": "up"}, {"description": "CD3-positive T cells on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 6A", "tissue": "CD3-positive T cells ", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "fatal vs. severe", "repository_id": "", "platform": "CD3-positive T cells ", "response_components": "", "response_behavior": "down"}, {"description": "CD3-positive T cells on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 6A", "tissue": "CD3-positive T cells ", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "fatal vs mild/moderate", "repository_id": "", "platform": "CD3-positive T cells ", "response_components": "", "response_behavior": "down"}, {"description": "CD3-positive T cells on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 6A", "tissue": "CD3-positive T cells ", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "critical vs. severe", "repository_id": "", "platform": "CD3-positive T cells ", "response_components": "", "response_behavior": "down"}, {"description": "CD3-positive T cells on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 6A", "tissue": "CD3-positive T cells ", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "critical vs mild/moderate", "repository_id": "", "platform": "CD3-positive T cells ", "response_components": "", "response_behavior": "down"}, {"description": "CD3-positive T cells on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 6A", "tissue": "CD3-positive T cells ", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "severe vs mild/moderate", "repository_id": "", "platform": "CD3-positive T cells ", "response_components": "", "response_behavior": "down"}, {"description": "CD4-positive helper T cells on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 6B", "tissue": "CD4-positive helper T cells ", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "fatal vs mild/moderate", "repository_id": "", "platform": "CD4-positive helper T cells ", "response_components": "", "response_behavior": "down"}, {"description": "CD8-positive cytotoxic T cells on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 6C", "tissue": "CD8-positive cytotoxic T cells", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "fatal vs severe", "repository_id": "", "platform": "CD8-positive cytotoxic T cells", "response_components": "", "response_behavior": "down"}, {"description": "CD8-positive cytotoxic T cells on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 6C", "tissue": "CD8-positive cytotoxic T cells", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "fatal vs mild/moderate", "repository_id": "", "platform": "CD8-positive cytotoxic T cells", "response_components": "", "response_behavior": "down"}, {"description": "CD8-positive cytotoxic T cells on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 6C", "tissue": "CD8-positive cytotoxic T cells", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "critical vs severe", "repository_id": "", "platform": "CD8-positive cytotoxic T cells", "response_components": "", "response_behavior": "down"}, {"description": "CD8-positive cytotoxic T cells on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 6C", "tissue": "CD8-positive cytotoxic T cells", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "critical vs mild/moderate", "repository_id": "", "platform": "CD8-positive cytotoxic T cells", "response_components": "", "response_behavior": "down"}, {"description": "CD8-positive cytotoxic T cells on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 6C", "tissue": "CD8-positive cytotoxic T cells", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "severe vs mild/moderate", "repository_id": "", "platform": "CD8-positive cytotoxic T cells", "response_components": "", "response_behavior": "down"}, {"description": "CD19-positive B-cells on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 6D", "tissue": "CD19-positive B-cells", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "fatal vs severe", "repository_id": "", "platform": "CD19-positive B-cells", "response_components": "", "response_behavior": "down"}, {"description": "CD19-positive B-cells on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 6D", "tissue": "CD19-positive B-cells", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "fatal vs mild/moderate", "repository_id": "", "platform": "CD19-positive B-cells", "response_components": "", "response_behavior": "down"}, {"description": "CD19-positive B-cells on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 6D", "tissue": "CD19-positive B-cells", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "critical  vs mild/moderate", "repository_id": "", "platform": "CD19-positive B-cells", "response_components": "", "response_behavior": "down"}, {"description": "CD19-positive B-cells on admission of adult patients hospitalized with Covid-19 when comparing mild/moderate; severe; critical and fatal course of the disease", "exact_source": "Figure 6D", "tissue": "CD19-positive B-cells", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "critical  vs severe", "repository_id": "", "platform": "CD19-positive B-cells", "response_components": "", "response_behavior": "down"}, {"description": "The dynamics of CD3-positive T cells from admission to recovery in symptomatic survivors (critical, severe patients) ", "exact_source": "Figure 7A", "tissue": "CD3-positive T cells ", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "recovery vs admission", "repository_id": "", "platform": "CD3-positive T cells ", "response_components": "", "response_behavior": "up"}, {"description": "The dynamics of CD4-positive helper T cells from admission to recovery in symptomatic survivors (critical, severe patients) ", "exact_source": "Figure 7B", "tissue": "CD4-positive helper T cells", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "recovery vs. admission", "repository_id": "", "platform": "CD4-positive helper T cells", "response_components": "", "response_behavior": "up"}, {"description": "PD1 positive helper T-cells in hospitalized patients with Covid-19, when comparing survivors and non-survivors", "exact_source": "Figure 8A", "tissue": "PD1 positive helper T-cells ", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "survivors vs non-survivors", "repository_id": "", "platform": "PD1 positive helper T-cells ", "response_components": "", "response_behavior": "down"}, {"description": "PD1 positive cytotoxic T-cells in hospitalized patients with Covid-19, when comparing survivors and non-survivors", "exact_source": "Figure 8B", "tissue": "PD1 positive cytotoxic T-cells ", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "survivors vs non-survivors", "repository_id": "", "platform": "PD1 positive cytotoxic T-cells ", "response_components": "", "response_behavior": "down"}, {"description": "The dynamics of Tim-3 positive cytotoxic T-cells in hospitalized patients with Covid-19, from admission to recovery in symptomatic survivors (critical, severe patients) ", "exact_source": "Figure 9B", "tissue": "Tim-3 positive cytotoxic T-cells", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "recovery vs admission", "repository_id": "", "platform": "Tim-3 positive cytotoxic T-cells", "response_components": "", "response_behavior": "down"}, {"description": "The dynamics of Tim-3 positive helper T-cells in hospitalized patients with Covid-19, from admission to recovery in symptomatic survivors (critical, severe patients) ", "exact_source": "Figure 9A", "tissue": "Tim-3 positive helper T-cells", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "recovery vs admission", "repository_id": "", "platform": "Tim-3 positive helper T-cells", "response_components": "", "response_behavior": "down"}, {"description": "CD38 positive cytotoxic T-cells in hospitalized patients with Covid-19, when comparing survivors and non-survivors", "exact_source": "Figure 10A", "tissue": "CD38 positive cytotoxic T-cells", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "survivors vs non-survivors", "repository_id": "", "platform": "CD38 positive cytotoxic T-cells", "response_components": "", "response_behavior": "down"}, {"description": "CD38 positive HLA-DR positive cytotoxic T-cells in hospitalized patients with Covid-19, when comparing survivors and non-survivors", "exact_source": "Figure 10B", "tissue": "CD38 positive HLA-DR positive cytotoxic T-cells", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "survivors vs non-survivors", "repository_id": "", "platform": "CD38 positive HLA-DR positive cytotoxic T-cells", "response_components": "", "response_behavior": "up"}, {"description": "The dynamics of CD38 positive cytotoxic T-cells in hospitalized patients with Covid-19,  from admission to recovery in symptomatic survivors (critical, severe patients) ", "exact_source": "Figure 10C", "tissue": "CD38 positive cytotoxic T-cells ", "immune_exposure": "Covid-19 infection", "cohort": "hospitalized adult patients", "comparison": "recovery vs admission ", "repository_id": "", "platform": "CD38 positive cytotoxic T-cells ", "response_components": "", "response_behavior": "down"}]}, "url": "https://doi.org/10.3389/fcimb.2021.646688", "authors": ["Bobcakova, Anna", "Petriskova, Jela", "Vysehradsky, Robert", "Kocan, Ivan", "Kapustova, Lenka", "Barnova, Martina", "Diamant, Zuzana", "Jesenak, Milos"], "journal": "Front Cell Infect Microbiol", "tags": ["t-cell", "human", "CD19", "CD3", "CD38", "CD4", "CD8", "Tim-3"], "license": "cc-by"}, {"_id": "60b7f3ee6bd17889a8ced00c", "title": "Severely ill COVID-19 patients display impaired exhaustion features in SARS-CoV-2-reactive CD8(+) T cells", "userdata": {"global_fields": {"paper": "Kusnadi, A., Ram\u00edrez-Su\u00e1stegui, C., Fajardo, V., Chee, S. J., Meckiff, B. J., Simon, H., Pelosi, E., Seumois, G., Ay, F., Vijayanand, P. and Ottensmeier, C. H. (2021). Severely ill COVID-19 patients display impaired exhaustion features in SARS-CoV-2-reactive CD8(+) T cells. Sci Immunol https://doi.org/10.1126/sciimmunol.abe4782", "contributor": "Pandurangan Vijayanand; Christian H. Ottensmeier", "contributor_organization": "La Jolla Institute for Immunology"}, "local_data": [{"description": "Differentially expressed genes (adj. p value < 0.05 and LFC > 0.25) in SARS-CoV-2-reactive CD8+ T cells (from cluster 0 representing non-exhausted cells) when comparing severe vs. mild disease in acute COVID-19 infection. ", "exact_source": "Table S8, tab \"A - Cluster 0\". Link: https://immunology.sciencemag.org/highwire/filestream/644191/field_highwire_adjunct_files/10/abe4782_Table_S8.xlsx", "tissue": "PBMC", "immune_exposure": "SARS-CoV-2 infection", "cohort": "The cohort consisted of 17 non-hospitalized patients with mild COVID-19 disease and 22 hospitalized patients with severe COVID-19 disease. The median age of the hospitalized patients was 60 (33-82) and 77% were male. The median age of the non-hospitalized participants was 39 (22-50) and 47% were male.", "comparison": "SARS-CoV-2-reactive CD8+ T cells from COVID-19 patients with severe vs. mild disease", "repository_id": "GSE153931", "platform": "HGNC symbol", "response_components": "RPS4Y1,ITM2A,DUSP4,CRTAM,CLDND1,MT2A,HLA-DRB1,LMNA,MYO1G,BCL2L1,SAMSN1,IL2RA,FGFBP2,CD96,LINC00944,WAS,BIRC3,CXCR4,EWSR1,SNHG15,AMICA1,ZFP36L1,AD000671.6,TNFRSF9,MIR4435-1HG,LPXN,DNAJC15,PIM2,MCL1,ACTA2,CD70,PHLDA1,CD6,SLA,GADD45B,SH2D2A,HMGA1,MIR155HG,REL,BHLHE40,MAP2K3,RNF114,GABARAPL1,PIM3,EIF1AY,HLA-DQA1,SF3B4,CNBP,MTHFD2,NONO,NFKB1,SUPT4H1,CMTM6,BCL2L11,SATB1,LYST,TNIP3,LITAF,EGR2,EIF4G2,CD83,WBP2,RBPJ,RHOG,TUBA1B,SRSF2,RP11-291B21.2,HLA-DPB1,PSMD5-AS1,ANP32E,ITM2C,DARS,FOXP1,SELT,DUSP10,CXorf40B,TNFAIP8,HNRNPK,PRDM1,DDB2,RPS27L,UBE2A,MAPK1IP1L,RABGGTB,ZFR,RGCC,ITGA1,DDX3Y,RELA,CHMP5,PRR14,EIF5,SF3A1,SERPINB9,UBE2B,PABPC1,TNFAIP3,BTG3,APBB1IP,CTLA4,MFSD10,NUP62,GPX4,HLA-DMA,YWHAE,PPP1R15A,LDHA,KPNA2,MCOLN2,DNAJA1,KXD1,YWHAQ,IRF4,LIMA1,PRR13,CD97,TOB1,KPNB1,FKBP1A,FAS,CLEC2D,FNDC9,SRGN,PSMD7,CTD-2020K17.1,CAPZA1,LAIR2,SDHD,ZNF267,UBC,UBASH3A,CACYBP,ISCU,MSMO1,CIRBP,KIF5B,RARG,TRAF1,HIST1H1C,DGUOK,MT1X,STAT5A,GORASP2,SNX6,STARD7,TANK,FDFT1,ATF4,JAKMIP1,SAP30BP,YARS,DUSP2,TRIM69,ARPC4,ABI1,CREM,IL21R,ATP1B3,SQRDL,MAT2B,CMC1,TUBA1C,NAB2,TXN,FDPS,CCNDBP1,SREBF2,POLR2K,SPPL2A,DHCR24,NR4A2,GNG4,HLA-DPA1,TSC22D3,ARL16,CASP1,AC017002.1,RAD21,PYHIN1,SERPINB6,PCNP,PSMB2,PSMB5,DDIT4,PRDX3,AKIRIN2,MRPL20,BLOC1S2,RANGAP1,HMGN2,SUB1,DTHD1,PSMF1,SAP18,NOP14,ZNRD1,CPSF7,EMD,CNOT7,PSMA6,ACAT2,SF3B2,LMNB1,PLK3,HMGCS1,BCL2A1,ADRM1,CCR7,ITGAL,VIM,NRBP1,SHISA5,HIF1A,WARS,CBLL1,SMAP2,C16orf13,LRMP,LSM14A,MT1E,TAGAP,DDX5,MVP,DHRS3,BAG6,SYTL3,CD44,ZEB2,SRP9,MRPL4,HMGB2,SDC4,RNF10,SMARCE1,FMNL1,RNF181,CCAR1,U2AF1L4,CASC3,NGRN,MOB1A,GLO1,ATP6V0C,TBC1D17,NFKBIA,CYCS,GATA3,PSMC2,PPP1R18,RSRC2,CCDC90B,HIST1H2AC,CYB5R3,SRM,NPTN,ZBTB38,CBR1,CBLB,SF3A2,PPDPF,HNRNPLL,KDELR2,TMEM123,C14orf1,QRICH1,ZFY,VAPA,SRSF3,TRIM22,SLMO2,PIGT,C7orf73,HIST1H1E,PSMD11,C11orf58,NDUFS2,TMBIM1,NDUFB5,RAB11A,DENND4A,PDCD10,KIF3A,MYADM,GRSF1,NAMPT,RP11-81H14.2,DPF2,ARHGEF2,CCNK,ZNF281,EXOSC3,H2AFZ,NFE2L2,MRPL37,NDUFA3,NR4A1,INPP5F,MRPL50,C7orf55-LUC7L2,KLRG1,SERTAD1,MT1F,JUN,EIF4A2,YPEL5,FAM96A,CPSF6,PLP2,PCNA,ARHGAP25,DUSP11,TNFSF4,ATF7IP,EPS15,RNF115,ZBED2,TROVE2,SFI1,ZNF410,MECP2,PRCC,SH3BGRL,STX5,CEP57,MRPS18C,SH3BP2,CARS,PQLC3,WBP11,PRKAR1A,COX17,KMT2A,NUP98,NUMA1,GGA2,NDUFS8,TECR,DIMT1,PQBP1,SNRPB2,ANXA11,EOMES,SLC1A5,UBLCP1,PSMD8,TMEM30A,NCL,GTF2H5,PTBP1,DESI1,C10orf128,TIMM17A,EBI3,LRRC41,SHFM1,MRFAP1,LEPROT,DAZAP2,MED15,MARCH7,CCDC115,NINJ1,BSG,KDM6B,INSIG1,RALGDS,CERS5,DDX24,IER2,KIAA1671,KLF10,KANSL1,UBE2I,PSMC6,KCNN4,CGGBP1,ILKAP,VCP,C7orf50,LCP2,TNIP1,BIRC2,SNHG12,SDCBP,CSRP1,PPP6C,EIF6,ATP5B,ALOX5AP,POLR2A,MAST3,ZNFX1,FASLG,SNRPN,SYNGR2,BRD2,CDCA4,MRPS18B,AKT2,IFNG,EED,ZNF580,C21orf91,TGIF1,AKIRIN1,PTP4A1,RNF149,TNFSF9,CLK3,SLC3A2,CHMP1B,ZBTB1,SNX11,YIPF4,RHBDD2,PPT1,MDH2,PRDX6", "response_behavior": "up"}, {"description": "Differentially expressed genes (adj. p value < 0.05 and LFC > 0.25) in SARS-CoV-2-reactive CD8+ T cells (from cluster 1 representing exhausted cells) when comparing severe vs. mild disease in acute COVID-19 infection.", "exact_source": "Table S8, tab \"B - Cluster 1\". Link: https://immunology.sciencemag.org/highwire/filestream/644191/field_highwire_adjunct_files/10/abe4782_Table_S8.xlsx", "tissue": "PBMC", "immune_exposure": "SARS-CoV-2 infection", "cohort": "The cohort consisted of 17 non-hospitalized patients with mild COVID-19 disease and 22 hospitalized patients with severe COVID-19 disease. The median age of the hospitalized patients was 60 (33-82) and 77% were male. The median age of the non-hospitalized participants was 39 (22-50) and 47% were male.", "comparison": "SARS-CoV-2-reactive CD8+ T cells from COVID-19 patients with severe vs. mild disease", "repository_id": "GSE153931", "platform": "HGNC symbol", "response_components": "RPS4Y1,WAS,TUBA1C,GNLY,PHLDA1,TUBA1B,LTB,LTA,LAG3,ALOX5AP,GZMB,CCL3,EWSR1,EIF1AY,GZMH,SF3B4,LCP2,STIP1,FASLG,SH2D2A,BCL7C,CCL4,WARS,CD6,CD97,CD8A,NONO,ZYX,NUP62,PPP1R18,RELA,ZFP36L1,CSF2,PIM1,MAPK1IP1L,VASP,SELT,HMGA1,MCL1,C10orf128,MAP2K3,IER3,SRM,ITGA4,PTMS,CISH,SLC1A5,SF1,BCL2L1,CYB5R3,NFKBIA,SHISA5,ITM2A,ATP1B3,DDX3Y,TNF,IL2RB,GATA3,GNB2,NDFIP2,CHCHD10,PDE4A,WBP2,KXD1,BHLHE40,MYADM,SDF4,DOK2,SH3BP1,TNFRSF18,DUSP1,ARF6,SFPQ,MT-ATP8,SLC9A3R1,PPP1R15A,IL2RA,ARRB2,LIM2,NFAT5,SF3A2,BAG6,FOS,ZFP36,ARHGEF1,ODC1,TUBA4A,PTBP1,EIF4G2,YWHAH,ITGB7,TNFRSF1B,RBMX,YARS,CITED2,ABI3,CPSF6,MAP7D1,SF3A1,CYBA,KLRG1,LAMP1,SOCS1,CAMTA2,PIM3,GYPC,MAPKAPK3,NUTF2,TNFRSF9,PTPN7,MRPL4,PRR14,JUNB,JAKMIP1,UPP1,RNF187,LPXN,APBB1IP,RASAL3,SF3B2,ACTN4,FXYD5,CS,GMIP,NOLC1,FMNL1,RNPS1,ZFP36L2,CPSF7,HNRNPH1,PBX4,HNRNPAB,HNRNPK,UBAP2L,TCERG1,CD69,CISD3,AKT2,IFI6,CD68,H2AFY,RP11-345J4.5,FKBP4,SATB1,RAD23B,NFKB2,CD7,SNRNP70,ACAA2,AK2,GORASP2,TBX21,MED15,STX3,YBX1,CLPTM1,EAF1,QRICH1,FAM3C,FLOT1,ELAVL1,EGR2,WDR1,LRP10,HSF1,RRAS2,SYNGR2,DAZAP1,KHDRBS1,H2AFX,SRSF2,MRPS6,PNP,CBLL1,SNX10,SURF4,ANXA11,MIR155HG,CCND3,ZFR,PSMD3,FEZ1,SASH3,ADRM1,HIST1H1E,PDLIM2,PRR13,FLT3LG,CXCR3,SCAF4,TNFRSF1A,RALGDS,ARL2,EOMES,DCTPP1,CBFB,RGS16,S1PR5,RASSF5,SAMSN1,SLC43A3,MYBL1,IVNS1ABP,NOP16,RGS3,NDUFA6,P4HB,NAA20,FERMT3,RPIA,CDC37,SMARCA4,SYNGR1,DEF6,LYST,DHCR24,TSPAN17,KLRD1,CYC1,BTG1,NDUFS8,HNRNPUL1,TAF9,IFI44L,PSMC4,FARSA,RAB8A,TAGLN2,ACTN1,DIMT1,PRCC,R3HDM4,RBM42,ETS1,EIF5,SRRT,TMEM189,E2F4,SS18,TBC1D10C,TPM4,TGFB1,APOBEC3G,SNHG7,MYO1G,TIMM10,SRPK2,UTY,ARHGAP9,RELB,HIGD1A,ZFY,NFATC3,RNF10,DAD1,PLK3,ARHGEF2,TUFM,CST3,ATAD3B,FKBP11,IDH2,SNX9,PPDPF,PCSK1N,ABI1,FHOD1,ATP2A3,MRPL12,RABGGTB,CYFIP2,QSOX1,AHCY,TOMM40,HNRNPA0,CHPF,CEBPB,SAP30BP,SELPLG,TERF2IP,C19orf24,TMEM248,MVD,BSG,FKBP1A,SLC39A8,WIPF1,ATP6V0C,PNPLA2,ELK1,PCNP,DUSP10,GGA2,SLC3A2,PIGT,TESPA1,HDGFRP3,CNOT3,MARS,IMPDH2,CCDC86,SEMA4D,FAM195A,TPGS1,SYVN1,UBE2I,GOT2,BOP1,ATXN2L,RBMS1,TNFRSF4,RNF44,PABPC4,ATF5,SERPINB9,RNF40,ICAM1,CXCR6,JUND,GRINA,CCDC97,TICAM1,POLD2,SREBF2,RBPJ,SRRM2,SAP18,SNRPD1,PUF60,RP11-81H14.2,PPM1M,FASN,FBRS,TTTY15,PRDM1,KPNA2,RALY,PTP4A1,RTN4,PML,APEX1,MRPL20,FAM50A,RNF11,PCBP2,ATIC,STRA13,SOCS2,MYC,IFRD2,PDCD2,KPNB1,C20orf24,CLPP,IARS,TMC6,SHMT2,NIFK,RAVER1,ZFAND5,GRWD1,LSM4,GLIPR2,POLDIP2,EML2,PABPC1,CCNK,CARD11,CD8B,TMEM43,COMT,RIN3,TRABD,ETFA,SCAMP4,MAP3K11,AGFG2,ACSL5,CLTB,MSN,CD55,ARSA,RAP1A,MATK,TRAP1,ILKAP,TUBA1A,PFN1,ARMC10,ACLY,AIMP2,MLF2,GGA3,GPR141,VCP,MT-CO1,GART,YWHAQ,TAF6,LAGE3,PRDX2,S1PR4,PRRC2A,RAB7A,WBP11,HGS,MZT2A,CRTC2,AHSA1,MT-ATP6,EXOSC4,RANGRF,CIRH1A,FPGS,CD63,SLC39A6,TEX30,FLNA,SP2,TSC22D3,TMEM256-PLSCR3,HLA-DQB1,DUSP5,CYCS,EVL,STARD7,TMBIM1,MRTO4,APOL3,XBP1,COMMD7,CD300A,CSRNP1,CCT4,DTX2,ATP5G3,SCAF1,ALKBH6,TYMP,STRAP,DESI1,RHOF,COA4,TXN,YIF1A,DCXR,NFKB1,TOMM70A,CCR5,LRRC47,CBLB,GFI1,UBE2V1,C9orf16,UFC1,NPTN,SMG9,STT3A,DIAPH1,ZNF593,GSPT1,SLC10A3,ARL4A,SF3B3,ATP13A1,DNTTIP2,CRYZ,ILF3,RRP9,VARS,NOP10,CADM1,CMTM3,GDI1,PFDN2,HAVCR2,KEAP1,C6orf136,PRF1,PRELID1,ARHGAP17,UBE2L3,ACTG1,MON1B,TNIP2,GTF3A,GPATCH4,CHERP,SPN,APOA1BP,EEF1E1,NUP98,OGFR,SLC7A5,LSM14A,SIT1,KCNAB2,PRSS21,BRPF1,ATG4D,ASXL1,PTGER2,SRSF3,SLC25A33,NABP2,DHRS3,UBR4,CD72,PKM,U2AF2,ARPC5L,ATAD3A,PTDSS1,NDUFAF4,SSBP4,MED25,LAIR1,UBQLN1,ETF1,SRP9,HSPA9,SMPD4,HMHA1,CHMP5,PDIA6,CRLS1,DDB1,NSUN2,RUVBL2,ZFAND3,SRSF10,AURKAIP1,ACADM,PRMT1,ALAS1,TMC8,DHCR7,GCH1,GET4,SPINT1,PARVG,GRSF1,LETM1,LILRB1,CCND2,IER2,NT5C,EMD,NSG1,DAZAP2,TMEM147,CHD1L,WDR77,DUSP23,PTOV1,ADAP1,SSU72,EIF5A,USP39,CD58,GLUD1,NOC4L,STOML2,PPP5C,RANBP1,MPHOSPH6,OGDH,CCDC124,GSTP1,CES2,BCL2A1,SEC24B,NELFA,GTF2E2,GRK6,HRASLS2,C8orf88,EIF2S1,RHOB,C10orf54,ISG20L2,KDELR2,LATS1,ZDHHC3,DUSP2,SARS,DNAJC1,GUCD1,PHB,KDM5D,PPP4C,FAM49A,MKNK1,MT-CO2,CMPK1,ADSL,HSPD1,SUPT4H1,IKBKG,PGP,ANXA6,TBC1D17,RARA,SUN2,RCE1,DDX27,PPP6R2,HNRNPL,FAM46C,AP2A1,ITGA1,GTF3C1,CASP1,PA2G4,POU2F2,HLA-F,SGK1,PSMB5,SLC25A22,SNHG12,NME1,TPRA1,THEMIS2,TMEM204,EIF4A2,DNM2,STUB1,PDCD5,PSTPIP1,SHC1,CD320,PPP1R11,PXN,SNX3,SLC52A2,BCL7B,DUSP4,LRRC41,ARF4,CCT2,CSNK1D,EMC10,DNPEP,CNN2,EDC4,TMUB1,VPS37B,MAP2K2,PSME3,NOP14,S100A11,PSMC2,BUD31,UBE2F,MTA2,PNPLA6,TCIRG1,RQCD1,GUSB,EHD1,PREX1,EBNA1BP2,TOMM34,NCLN,DBNL,PES1,YTHDF3,NOL11,CNIH1,ANKRD28,PSMC1,CANT1,SACM1L,IL15RA,TFDP1,CENPV,AKAP17A,GARS,PANK2,B3GAT3,PRKD2,SNF8,BAZ1B,DHPS,MED16,PRKAR1A,NFKBIB,OSBPL3,PHC3,PSMF1,IRF7,MAP1S,NENF,PCK2,IMP4,YWHAE,CAPRIN1,SZRD1,PREB,EIF4G1,DAP,UBE2A,NOP2,SERPINB1,UNC13D,GNPTAB,CD2BP2,FAM207A,RPS6KA1,NAA10,PPP1R10,ATPAF1,HSPB1,DCAF13,TESC,PUS1", "response_behavior": "up"}, {"description": "Differentially expressed genes (adj. p value < 0.05 and LFC > 0.25) in SARS-CoV-2-reactive CD8+ T cells (from cluster 2 representing non-exhausted cells) when comparing severe vs. mild disease in acute COVID-19 infection. ", "exact_source": "Table S8, tab \"C - Cluster 2\". Link: https://immunology.sciencemag.org/highwire/filestream/644191/field_highwire_adjunct_files/10/abe4782_Table_S8.xlsx", "tissue": "PBMC", "immune_exposure": "SARS-CoV-2 infection", "cohort": "The cohort consisted of 17 non-hospitalized patients with mild COVID-19 disease and 22 hospitalized patients with severe COVID-19 disease. The median age of the hospitalized patients was 60 (33-82) and 77% were male. The median age of the non-hospitalized participants was 39 (22-50) and 47% were male.", "comparison": "SARS-CoV-2-reactive CD8+ T cells from COVID-19 patients with severe vs. mild disease", "repository_id": "GSE153931", "platform": "HGNC symbol", "response_components": "RPS4Y1,CRTAM,CLDND1,LMNA,ITM2A,MT2A,CD70,DUSP4,C10orf128,HLA-DRB1,AMICA1,STMN1,DNAJC15,PCNA,CBR1,IRF4,MT1X,TNFAIP8,PIM2,LITAF,CMC1,LINC00944,LGALS3,ZBTB38,FGFBP2,SERPINB6,MCM7,CD96,TNIP3,MYO1G,ANP32E,MT-ATP8,ALOX5AP,ZNRD1,LMNB1,HLA-DQA1,KLRG1,PSMD5-AS1,RP11-1407O15.2,MCM5,BIRC3,TAGAP,SAMSN1,WAS,TYMS,CXCR4,REL,MTHFD2,EIF1AY,MIR4435-1HG,ZBED2,CD83,HLA-DQB1,HMGB2,CNBP,CMTM6,C7orf73,TRAT1,NFKB1,BCL2L1,LYST,C14orf1,ACTA2,LIMA1,FAS,PPP1R15A,KIF3A,EIF4A2,LPXN,NUP62,RABGGTB,RPA3,HLA-DPB1,MRPL15,STAT1,MCM2,DUSP2,MCL1,MIR155HG,TNFAIP3,YWHAQ,CD44,HMGCS1,SF3B4,HLA-DMA,RNF114,MCM6,BCL2L11,MRPL37,SLC38A5,CLEC2D,INPP4B,FOXP1,GABARAPL1,ARID5B,KPNA2,PRDM1,NUDT21,EIF4G2,GADD45B,CENPM,XCL2,NSMCE4A,SLC1A5,CACYBP,ATF7IP,PPDPF,AD000671.6,TRIM69,GINS2,SNHG15,RAD21,DDB2,TNFRSF14,BHLHE40,DPM2,STAT5A,CASP1,PSMB5,SNRNP25,EED,EWSR1,DHCR24,EXOC2,SRSF2,NEAT1,RAD50,DNAJA1,NAMPT,H2AFV,SHMT2,EMC6,HADH,NONO,DUT,LBH,SRGN,FOXN3,MCM3,WDR18,MCM4,C19orf48,HINT2,PPT1,INSIG1,SLC43A3,CEP57,ARL16,CHID1,H2AFZ,SUPT4H1,COPG2,C19orf24,PQLC3,MOB1A,MRPL50,SF3A1,UBL7,EGR2,EXOSC3,TNFRSF9,SH3BGRL,POLD2,RPS27L,C12orf75,TMEM167A,ITGA1,FEN1,SELT,MAPK1IP1L,MAT2B,SPAG7,IL2RA,UBE2T,MRPL16,ZDHHC12,CDCA4,EOMES,SDHD,MCOLN2,MT1F,SMC2,CASP3,NAA38,DESI1,GPX4,POLR3K,ZNF267,THOC3,DARS,CTD-2020K17.1,SIGMAR1,TIMMDC1,HBS1L,CTSA,SERPINB9,TMEM106C,HMGA1,NDUFB5,NUP37,PSMG2,NAP1L1,ACAT2,MRPL51,MAP2K3,PRPF38A,NDUFS8,PHGDH,DLD,SDC4,MT1E,FAM96A,MATR3,NFKBIA,CSRP1,SATB1,RPS10,TMEM97,KIF22,JUNB,DHRS4L2,SUB1,CENPK,SRSF3,SEPT2,KDELR1,SLC25A3,NSG1,SLBP,GLO1,NDUFS2,ERCC1,UNG,NIP7,EXOSC8,ATF4,CCR7,PTRHD1,BCL2L12,EIF4E,HMGCR,MDP1,AOAH,CKS1B,PELP1,PEX2,NOB1,EIF4EBP1,IL21R,HMBS,CXorf40B,WBP2,SF3A2,TMEM14A,TIAL1,PABPC1,IRF1,TANK,CLSPN,CENPU,TMPO,QRICH1,TRAF4,UROS,ESD,TMEM219,CSDE1,SH2D1A,EBI3,CRTAP,IL12RB2,RPS26,PAFAH1B3,IFI27L1,JAKMIP1,SQRDL,DSN1,SNRPD3,CPSF7,RQCD1,C6orf48,KCNN4,PRDX6,RBBP4,EPS15,ZNF622,RFC2,FNDC9,MAD2L1,RPP25L,MED28,GIMAP4,CCDC109B,ZNF410,COQ4,RDX,GMNN,VRK1,PCK2,CCNDBP1,DDX41,BTG3,HIF1A,DGUOK,LIM2,PDCD4,NDUFS4,TIFA,MSMO1,APEX1,CAPZA1,MRPL34,TCF19,C16orf80,DTHD1,COPS8,PIM3,CCDC167,SPPL2A,ZFP36L1,GSDMD,GSKIP,HNRNPA0,CHEK1,PIN4,AKIP1,LRPPRC,NRBP1,CD2BP2,NAP1L4,CCNK,LIG1,NSMCE1,PTCD3,SKA2,SNRPC,LAMTOR2,NDUFA5,CUEDC2,TMEM69,SREBF2,ALKBH7,MPHOSPH6,CTBS,ATP6V0E2,STARD7,EXOSC7,VPS29,DNAJA2,RNF115,NGRN,POLD1,TUBA1B,IFI16,TRIM26,HNRNPLL,HIF1AN,PRIM1,SMAD2,PCBD1,MYCBP,SPSB3,SNRPN,ZC3H7A,CDCA7,VRK3,SRM,CXorf40A,SUPT7L,TMEM230,IPO7,SS18,RELA,DERA,PHF5A,POLR2H,FANCL,KDELR2,ZNF706,FIS1,TTC38,TBP,MED16,ERH,YWHAE,GATA3,ETS2,PTTG1,CCNG1,TSN,FAM129A,PIGS,KXD1,NBN,CDKN2A,SSRP1,RPS29,CASC3,TRAFD1,NINJ1,ZFR,CD8B,ZFY,RP11-277P12.20,RAB7A,TRIM22,ACTR6,UBLCP1,TNFSF4,IDI1,GAMT,SCYL1,CAND1,KMT2A,PSIP1,ZWINT,SLC30A5,IMPDH2,POLR2G,AKIRIN1,MRPL10,NUDT8,FXR1,CALCOCO2,SNAP29,YEATS4,CNOT7,CTLA4,UBE2B,DHFR,ABHD5,FRG1,AZIN1,KIF5B,IL13,POLR2K,BCAP29,WDR75,NOL8,ADI1,GTF2H5,RBMX,MED6,C11orf58,CCDC28A,KIAA0101,ASF1B,LSM5,GTF2H2C", "response_behavior": "up"}]}, "url": "https://doi.org/10.1126/sciimmunol.abe4782", "authors": ["Kusnadi, Anthony", "Ram\u00edrez-Su\u00e1stegui, Ciro", "Fajardo, Vicente", "Chee, Serena J", "Meckiff, Benjamin J", "Simon, Hayley", "Pelosi, Emanuela", "Seumois, Gr\u00e9gory", "Ay, Ferhat", "Vijayanand, Pandurangan", "Ottensmeier, Christian H"], "journal": "Sci Immunol", "tags": ["t-cell", "virus", "human", "CD8"], "license": "cc-by"}, {"_id": "60b7f3f26bd17889a8ced00e", "title": "Distinct cellular immune profiles in the airways and blood of critically ill patients with COVID-19", "userdata": {"global_fields": {"paper": "Saris, A., Reijnders, T. D., Nossent, E. J., Schuurman, A. R., Verhoeff, J., van A. S., Bontkes, H., Blok, S., Duitman, J., Bogaard, H., Heunks, L., Lutter, R., van d. P. T. and Garcia V. J. J. (2021). Distinct cellular immune profiles in the airways and blood of critically ill patients with COVID-19. Thorax https://www.ncbi.nlm.nih.gov/pubmed/33846275/", "contributor": "Anno Saris", "contributor_organization": "Center for Experimental and Molecular Medicine"}, "local_data": [{"description": "Immunophenotyping of bronchoalveolar lavage and blood mononuclear cells of COVID-19 patients admitted to the ICU using a 32-color spectral flow cytometry panel. In addition, 45-panel Luminex (R&D) and 10-panel coagulation CBA (biolegend) was performed on BALF and plasma. In parralel PBMCs from healthy controls were measured. ", "exact_source": "Figure 1-3 & S2-S4 and table 1", "tissue": "Mononuclear cells from bronchoalveolar lavage and paired blood", "immune_exposure": "COVID-19 and possibly subsequent superinfection", "cohort": "33-79yr ICU admitted COVID-19 patients", "comparison": "Bronchoalveolar lavage vs blood in COVID-19. ", "repository_id": "data avaialble upon request, not (yet) publically", "platform": "", "response_components": "", "response_behavior": "variable"}]}, "url": "https://www.ncbi.nlm.nih.gov/pubmed/33846275/", "authors": ["Saris, Anno", "Reijnders, Tom DY", "Nossent, Esther J", "Schuurman, Alex R", "Verhoeff, Jan", "van Asten, Saskia", "Bontkes, Hetty", "Blok, Siebe", "Duitman, Janwillem", "Bogaard, Harm-Jan", "Heunks, Leo", "Lutter, Rene", "van der Poll, Tom", "Garcia Vallejo, Juan J"], "journal": "Thorax", "tags": ["lung", "immune response", "t-cell", "human", "macrophage", "CD4", "CD8"], "license": "cc-by-nc"}, {"_id": "613f9f9b84f9575d93a3ba6e", "title": "Cutting Edge: Distinct B Cell Repertoires Characterize Patients with Mild and Severe COVID-19.", "userdata": {"global_fields": {"paper": "Hoehn, K. B., Ramanathan, P., Unterman, A., Sumida, T. S., Asashima, H., Hafler, D. A., Kaminski, N., Dela C. C. S., Sealfon, S. C., Bukreyev, A. and Kleinstein, S. H. (2021). Cutting Edge: Distinct B Cell Repertoires Characterize Patients with Mild and Severe COVID-19. Journal of immunology https://doi.org/10.4049/jimmunol.2100135", "contributor": "Steven Kleinstein", "contributor_organization": "Yale University"}, "local_data": [{"description": "Increased frequency of memory B cells among total B cells in mildly symptomatic vs hospitalized COVID-19 patients approximately one month after onset of symptoms.", "exact_source": "Figure 2", "tissue": "PBMC", "immune_exposure": "COVID-19 infection", "cohort": "Mildly symptomatic and hospitalized COVID-19 patients", "comparison": "Mild vs severe infection approximately one month after the onset of symptoms", "repository_id": "GSE164381", "platform": "10X Genomics scRNA-seq + BCR", "response_components": "Memory B cells", "response_behavior": "up"}]}, "url": "https://doi.org/10.4049/jimmunol.2100135", "authors": ["Hoehn, Kenneth B", "Ramanathan, Palaniappan", "Unterman, Avraham", "Sumida, Tomokazu S", "Asashima, Hiromitsu", "Hafler, David A", "Kaminski, Naftali", "Dela Cruz, Charles S", "Sealfon, Stuart C", "Bukreyev, Alexander", "Kleinstein, Steven H"], "journal": "Journal of immunology", "tags": ["b-cell", "human"], "license": "unk"}, {"_id": "613f9fa884f9575d93a3ba8f", "title": "Uncontrolled Innate and Impaired Adaptive Immune Responses in Patients with COVID-19 ARDS", "userdata": {"global_fields": {"paper": "Hue, S., Beldi-Ferchiou, A., Bendib, I., Surenaud, M., Fourati, S., Frapard, T., Rivoal, S., Razazi, K., Carteaux, G., Delfau-Larue, M., Mekontso D. A., Audureau, E. and de Prost. N. (2020). Uncontrolled Innate and Impaired Adaptive Immune Responses in Patients with COVID-19 ARDS. Am. j. respir. crit. care med https://doi.org/10.1164/rccm.202005-1885OC", "contributor": "Nicolas de Prost", "contributor_organization": "Universit\u00e9 Paris Est-Cr\u00e9teil"}, "local_data": [{"description": " Prospective observational monocenter study. Immunocompetent patients diagnosed with RT-PCR-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and ARDS admitted between March 8 and March 30, 2020, were included and compared with patients with non-COVID-19 ARDS.  As compared with patients with non-COVID-19 ARDS (n = 36), those with COVID-19 (n = 38) were not significantly different regarding age, sex, and Sequential Organ Failure Assessment and Simplified Acute Physiology Score II scores but exhibited a higher Day-28 mortality (34% vs. 11%, P = 0.030). ", "exact_source": "Figure 1 ", "tissue": "Blood and serum", "immune_exposure": "patients with severe COVID-19 ", "cohort": "adults admitted in the intensive care unit", "comparison": "severe COVID-19 patients vs non-COVID-19 patients with acute respiratory distress syndrome", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "Down: Patients with COVID-19 showed profound and sustained T CD4+ (P = 0.002), CD8+ (P < 0.0001), and B (P < 0.0001) lymphopenia; "}, {"description": "", "exact_source": "Figures 1 and 2, Table 3", "tissue": "Blood and serum", "immune_exposure": "patients with severe COVID-19 ", "cohort": "adults admitted in the intensive care unit", "comparison": "severe COVID-19 patients vs non-COVID-19 patients with acute respiratory distress syndrome", "repository_id": "", "platform": "", "response_components": "", "response_behavior": "Up: Patients with COVID-19 showed higher HLA-DR expression on monocytes (P < 0.001) and higher serum concentrations of EGF (epithelial growth factor), GM-CSF, IL-10, CCL2/MCP-1, CCL3/MIP-1a, CXCL10/IP-10, CCL5/RANTES, and CCL20/MIP-3a. After adjusting on age and Sequential Organ Failure Assessment, serum CXCL10/IP-10 (P = 0.047) and GM-CSF (P = 0.050) were higher in patients with COVID-19 who were dead at Day 28.         "}]}, "url": "https://api.semanticscholar.org/CorpusID:221405365", "authors": ["Hue, Sophie", "Beldi-Ferchiou, Asma", "Bendib, In\u00e8s", "Surenaud, Mathieu", "Fourati, Slim", "Frapard, Thomas", "Rivoal, Simon", "Razazi, Keyvan", "Carteaux, Guillaume", "Delfau-Larue, Marie-H\u00e9l\u00e8ne", "Mekontso Dessap, Armand", "Audureau, Etienne", "de Prost, Nicolas"], "journal": "Am. j. respir. crit. care med", "tags": ["immune response", "virus", "human"], "license": "unk"}, {"_id": "613f9fcc84f9575d93a3bad9", "title": "Distinct immunological signatures discriminate severe COVID-19 from non-SARS-CoV-2-driven critical pneumonia", "userdata": {"global_fields": {"paper": "Kreutmair, S., Unger, S., N\u00fa\u00f1ez, N. G., Ingelfinger, F., Alberti, C., De F. D., Krishnarajah, S., Kauffmann, M., Friebel, E., Babaei, S., Gaborit, B., Lutz, M., Jurado, N. P., Malek, N. P., Goepel, S., Rosenberger, P., H\u00e4berle, H. A., Ayoub, I., Al-Hajj, S., Nilsson, J., Classen, M., Liblau, R., Martin-Blondel, G., Bitzer, M., Roquilly, A. and Becher, B. (2021). Distinct immunological signatures discriminate severe COVID-19 from non-SARS-CoV-2-driven critical pneumonia. Immunity https://api.elsevier.com/content/article/pii/S1074761321002089", "contributor": "Burkhard Becher", "contributor_organization": "Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland."}, "local_data": [{"description": "FlowSOM-generated CD56+ T cell subset among T cells of adult COVID-19 patients in the first week of hospital admission, measured by single-cell cytometry. 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G. J., Acharjee, A., Bankar, R., Palanivel, V., Salkar, A., Verma, A., Mukherjee, A., Choudhury, M., Ghantasala, S., Ghosh, S., Singh, A., Banerjee, A., Badaya, A., Bihani, S., Loya, G., Mantri, K., Burli, A., Roy, J., Srivastava, A., Agrawal, S., Shrivastav, O., Shastri, J. and Srivastava, S. (2021). Proteomics and Machine Learning Approaches Reveal a Set of Prognostic Markers for COVID-19 Severity With Drug Repurposing Potential. Front Physiol https://doi.org/10.3389/fphys.2021.652799", "contributor": "Sanjeeva Srivastava", "contributor_organization": "Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India"}, "local_data": [{"description": "Deep plasma proteome analysis to identify proteins differentially expressed between non-severe and severe groups of COVID-19 infected patients.  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E., Song, K., Hwang, W., Ham, S. Y., Jeong, H., Kim, J., Oh, H. S., Kang, Y. M., Lee, E. B., Kim, N. J., Chin, B. S. and Park, J. K. (2021). Pattern of inflammatory immune response determines the clinical course and outcome of COVID-19: unbiased clustering analysis. Sci Rep https://doi.org/10.1038/s41598-021-87668-z", "contributor": "Bum Sik Chin", "contributor_organization": "Division of Infectious Diseases, Department of Internal Medicine, National Medical Center, Euljiro 245, Jung-gu, Seoul, 04564, Korea."}, "local_data": [{"description": "Different inflammatory markers of patients after hospital admission when comparing severe vs. mild disease in COVID-19", "exact_source": "Figure 2", "tissue": "Serum", "immune_exposure": "", "cohort": "COVID-19 patients, mainly adults", "comparison": "severe vs. mild disease since admission to day 25", "repository_id": "NA", "platform": "NA", "response_components": "NA", "response_behavior": "NA"}]}, "url": "https://doi.org/10.1038/s41598-021-87668-z", "authors": ["Lee, Eunyoung Emily", "Song, Kyoung-Ho", "Hwang, Woochang", "Ham, Sin Young", "Jeong, Hyeonju", "Kim, Jeong-Han", "Oh, Hong Sang", "Kang, Yu Min", "Lee, Eun Bong", "Kim, Nam Joong", "Chin, Bum Sik", "Park, Jin Kyun"], "journal": "Sci Rep", "tags": ["immune response", "human", "protein", "C-reactive protein", "CRP"], "license": "cc-by"}, {"_id": "613f9fde84f9575d93a3bb00", "title": "Myeloid phenotypes in severe COVID-19 predict secondary infection and mortality: a pilot study", "userdata": {"global_fields": {"paper": "Marais, C., Claude, C., Semaan, N., Charbel, R., Barreault, S., Travert, B., Piloquet, J., Demailly, Z., Morin, L., Merchaoui, Z., Teboul, J., Durand, P., Miatello, J. and Tissi\u00e8res, P. 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A., Shaw, T. N., Knight, S. B., Wemyss, K., McClure, F. A., Pearmain, L., Prise, I., Jagger, C., Morgan, D., Khan, S., Brand, O., Mann, E. R., Ustianowski, A., Bakerly, N. D., Dark, P., Brightling, C. E., Brij, S., Felton, T., Simpson, A., Grainger, J. R., Hussell, T., Konkel, J. E. and Menon, M. (2021). Alterations in T and B cell function persist in convalescent COVID-19 patients. 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