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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T15","span":{"begin":612,"end":628},"obj":"Body_part"},{"id":"T16","span":{"begin":2465,"end":2477},"obj":"Body_part"}],"attributes":[{"id":"A15","pred":"uberon_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/UBERON_0010754"},{"id":"A16","pred":"uberon_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/UBERON_0034922"}],"text":"Projecting the flow cytometry data for B cells from HD, RD, and COVID-19 patients in tSNE space revealed a distinct picture of B cell populations in COVID-19 compared to controls, whereas RD and HD were similar (Fig. 4J and fig. S5J). The COVID-19 patient B cell phenotype was dominated by loss of CXCR5 and IgD compared to B cells from HD and RD (Fig. 4J). Moreover, the robust PB response was apparent in the upper right section, highlighted by CD27, CD38, CD138, and KI67 (Fig. 4J). The expression of KI67 and CD95 in these CD27+CD38+CD138+ PB (Fig. 4J) could suggest recent generation and/or emigration from germinal centers. We next asked whether there were different groups of COVID-19 patients (or HD and RD) with global differences in the B cell response. We used Earth Movers Distance (EMD) (45) to calculate similarities between the probability distributions within the tSNE map (Fig. 4J) and clustered so that individuals with the most similar distributions grouped together (Fig. 4K). The majority of COVID-19 patients fell into two distinct groups (EMD Groups 1 and 3, Fig. 4L), suggesting two major “immunotypes” of the B cell response. The remainder of the COVID-19 patients (~25%) clustered with the majority of the HD and all of the RD controls, supporting the observation that some individuals had limited evidence of response to infection in their B cell compartment. To identify the population differences between HD, RD and COVID-19 patients, we performed FlowSOM clustering on the tSNE map, and also overlaid each individual EMD group onto this same tSNE map (Fig. 4, M and N). EMD Group 2 containing mostly HD and RD was enriched for naive B cells (IgD+CD27−, Cluster 10) and CXCR5+IgD−CD27+ switched memory (Cluster 2) and, indeed, Clusters 2 and 10 were statistically reduced in COVID-19 patients (Fig. 4P). EMD Groups 1 and 3 displayed distinct patterns across the FlowSOM clusters. B cells from individuals in EMD Group 1 were enriched for the FlowSOM Clusters 1, 5, and 6, all of which were increased in COVID-19 patients (Fig. 4P). FlowSOM Clusters 1 and 6 captured T-bet+ memory B cells whereas FlowSOM Cluster 5 contained the CD27+CD38+CD138+KI67+ PB, all of which were enriched in COVID-19 patients compared to controls (Fig. 4, O and P, and fig. S5K). In contrast, B cells from COVID-19 patients in EMD Group 3 also showed enrichment for the PB FlowSOM Cluster 5, though less prominent than for EMD Group 1, but the T-bet+ memory B cell Cluster 1 was substantially reduced in EMD Group 3. Thus, B cell responses were evident in many hospitalized COVID-19 patients, most often characterized by elevated PB, decreases in memory B cell subsets, enrichment in a T-bet+ B cell subset, and loss of CXCR5 expression. Whether all of these changes in the B cell compartment were due to direct antiviral responses is unclear. Although there was heterogeneity in the B cell responses, COVID-19 patients fell into two distinct patterns containing activated B cell responses and a third group of patients with little evidence of an active B cell response."}

LitCovid-PubTator

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T68","span":{"begin":1724,"end":1730},"obj":"http://purl.obolibrary.org/obo/GO_0007613"},{"id":"T69","span":{"begin":2102,"end":2108},"obj":"http://purl.obolibrary.org/obo/GO_0007613"},{"id":"T70","span":{"begin":2456,"end":2462},"obj":"http://purl.obolibrary.org/obo/GO_0007613"},{"id":"T71","span":{"begin":2652,"end":2658},"obj":"http://purl.obolibrary.org/obo/GO_0007613"},{"id":"T72","span":{"begin":2817,"end":2836},"obj":"http://purl.obolibrary.org/obo/GO_0051607"}],"text":"Projecting the flow cytometry data for B cells from HD, RD, and COVID-19 patients in tSNE space revealed a distinct picture of B cell populations in COVID-19 compared to controls, whereas RD and HD were similar (Fig. 4J and fig. S5J). The COVID-19 patient B cell phenotype was dominated by loss of CXCR5 and IgD compared to B cells from HD and RD (Fig. 4J). Moreover, the robust PB response was apparent in the upper right section, highlighted by CD27, CD38, CD138, and KI67 (Fig. 4J). The expression of KI67 and CD95 in these CD27+CD38+CD138+ PB (Fig. 4J) could suggest recent generation and/or emigration from germinal centers. We next asked whether there were different groups of COVID-19 patients (or HD and RD) with global differences in the B cell response. We used Earth Movers Distance (EMD) (45) to calculate similarities between the probability distributions within the tSNE map (Fig. 4J) and clustered so that individuals with the most similar distributions grouped together (Fig. 4K). The majority of COVID-19 patients fell into two distinct groups (EMD Groups 1 and 3, Fig. 4L), suggesting two major “immunotypes” of the B cell response. The remainder of the COVID-19 patients (~25%) clustered with the majority of the HD and all of the RD controls, supporting the observation that some individuals had limited evidence of response to infection in their B cell compartment. To identify the population differences between HD, RD and COVID-19 patients, we performed FlowSOM clustering on the tSNE map, and also overlaid each individual EMD group onto this same tSNE map (Fig. 4, M and N). EMD Group 2 containing mostly HD and RD was enriched for naive B cells (IgD+CD27−, Cluster 10) and CXCR5+IgD−CD27+ switched memory (Cluster 2) and, indeed, Clusters 2 and 10 were statistically reduced in COVID-19 patients (Fig. 4P). EMD Groups 1 and 3 displayed distinct patterns across the FlowSOM clusters. B cells from individuals in EMD Group 1 were enriched for the FlowSOM Clusters 1, 5, and 6, all of which were increased in COVID-19 patients (Fig. 4P). FlowSOM Clusters 1 and 6 captured T-bet+ memory B cells whereas FlowSOM Cluster 5 contained the CD27+CD38+CD138+KI67+ PB, all of which were enriched in COVID-19 patients compared to controls (Fig. 4, O and P, and fig. S5K). In contrast, B cells from COVID-19 patients in EMD Group 3 also showed enrichment for the PB FlowSOM Cluster 5, though less prominent than for EMD Group 1, but the T-bet+ memory B cell Cluster 1 was substantially reduced in EMD Group 3. Thus, B cell responses were evident in many hospitalized COVID-19 patients, most often characterized by elevated PB, decreases in memory B cell subsets, enrichment in a T-bet+ B cell subset, and loss of CXCR5 expression. Whether all of these changes in the B cell compartment were due to direct antiviral responses is unclear. Although there was heterogeneity in the B cell responses, COVID-19 patients fell into two distinct patterns containing activated B cell responses and a third group of patients with little evidence of an active B cell response."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T183","span":{"begin":0,"end":234},"obj":"Sentence"},{"id":"T184","span":{"begin":235,"end":357},"obj":"Sentence"},{"id":"T185","span":{"begin":358,"end":485},"obj":"Sentence"},{"id":"T186","span":{"begin":486,"end":629},"obj":"Sentence"},{"id":"T187","span":{"begin":630,"end":763},"obj":"Sentence"},{"id":"T188","span":{"begin":764,"end":996},"obj":"Sentence"},{"id":"T189","span":{"begin":997,"end":1150},"obj":"Sentence"},{"id":"T190","span":{"begin":1151,"end":1386},"obj":"Sentence"},{"id":"T191","span":{"begin":1387,"end":1599},"obj":"Sentence"},{"id":"T192","span":{"begin":1600,"end":1832},"obj":"Sentence"},{"id":"T193","span":{"begin":1833,"end":1908},"obj":"Sentence"},{"id":"T194","span":{"begin":1909,"end":2060},"obj":"Sentence"},{"id":"T195","span":{"begin":2061,"end":2284},"obj":"Sentence"},{"id":"T196","span":{"begin":2285,"end":2521},"obj":"Sentence"},{"id":"T197","span":{"begin":2522,"end":2742},"obj":"Sentence"},{"id":"T198","span":{"begin":2743,"end":2848},"obj":"Sentence"},{"id":"T199","span":{"begin":2849,"end":3075},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Projecting the flow cytometry data for B cells from HD, RD, and COVID-19 patients in tSNE space revealed a distinct picture of B cell populations in COVID-19 compared to controls, whereas RD and HD were similar (Fig. 4J and fig. S5J). The COVID-19 patient B cell phenotype was dominated by loss of CXCR5 and IgD compared to B cells from HD and RD (Fig. 4J). Moreover, the robust PB response was apparent in the upper right section, highlighted by CD27, CD38, CD138, and KI67 (Fig. 4J). The expression of KI67 and CD95 in these CD27+CD38+CD138+ PB (Fig. 4J) could suggest recent generation and/or emigration from germinal centers. We next asked whether there were different groups of COVID-19 patients (or HD and RD) with global differences in the B cell response. We used Earth Movers Distance (EMD) (45) to calculate similarities between the probability distributions within the tSNE map (Fig. 4J) and clustered so that individuals with the most similar distributions grouped together (Fig. 4K). The majority of COVID-19 patients fell into two distinct groups (EMD Groups 1 and 3, Fig. 4L), suggesting two major “immunotypes” of the B cell response. The remainder of the COVID-19 patients (~25%) clustered with the majority of the HD and all of the RD controls, supporting the observation that some individuals had limited evidence of response to infection in their B cell compartment. To identify the population differences between HD, RD and COVID-19 patients, we performed FlowSOM clustering on the tSNE map, and also overlaid each individual EMD group onto this same tSNE map (Fig. 4, M and N). EMD Group 2 containing mostly HD and RD was enriched for naive B cells (IgD+CD27−, Cluster 10) and CXCR5+IgD−CD27+ switched memory (Cluster 2) and, indeed, Clusters 2 and 10 were statistically reduced in COVID-19 patients (Fig. 4P). EMD Groups 1 and 3 displayed distinct patterns across the FlowSOM clusters. B cells from individuals in EMD Group 1 were enriched for the FlowSOM Clusters 1, 5, and 6, all of which were increased in COVID-19 patients (Fig. 4P). FlowSOM Clusters 1 and 6 captured T-bet+ memory B cells whereas FlowSOM Cluster 5 contained the CD27+CD38+CD138+KI67+ PB, all of which were enriched in COVID-19 patients compared to controls (Fig. 4, O and P, and fig. S5K). In contrast, B cells from COVID-19 patients in EMD Group 3 also showed enrichment for the PB FlowSOM Cluster 5, though less prominent than for EMD Group 1, but the T-bet+ memory B cell Cluster 1 was substantially reduced in EMD Group 3. Thus, B cell responses were evident in many hospitalized COVID-19 patients, most often characterized by elevated PB, decreases in memory B cell subsets, enrichment in a T-bet+ B cell subset, and loss of CXCR5 expression. Whether all of these changes in the B cell compartment were due to direct antiviral responses is unclear. Although there was heterogeneity in the B cell responses, COVID-19 patients fell into two distinct patterns containing activated B cell responses and a third group of patients with little evidence of an active B cell response."}

2_test

{"project":"2_test","denotations":[{"id":"32669297-27008164-135105211","span":{"begin":801,"end":803},"obj":"27008164"}],"text":"Projecting the flow cytometry data for B cells from HD, RD, and COVID-19 patients in tSNE space revealed a distinct picture of B cell populations in COVID-19 compared to controls, whereas RD and HD were similar (Fig. 4J and fig. S5J). The COVID-19 patient B cell phenotype was dominated by loss of CXCR5 and IgD compared to B cells from HD and RD (Fig. 4J). Moreover, the robust PB response was apparent in the upper right section, highlighted by CD27, CD38, CD138, and KI67 (Fig. 4J). The expression of KI67 and CD95 in these CD27+CD38+CD138+ PB (Fig. 4J) could suggest recent generation and/or emigration from germinal centers. We next asked whether there were different groups of COVID-19 patients (or HD and RD) with global differences in the B cell response. We used Earth Movers Distance (EMD) (45) to calculate similarities between the probability distributions within the tSNE map (Fig. 4J) and clustered so that individuals with the most similar distributions grouped together (Fig. 4K). The majority of COVID-19 patients fell into two distinct groups (EMD Groups 1 and 3, Fig. 4L), suggesting two major “immunotypes” of the B cell response. The remainder of the COVID-19 patients (~25%) clustered with the majority of the HD and all of the RD controls, supporting the observation that some individuals had limited evidence of response to infection in their B cell compartment. To identify the population differences between HD, RD and COVID-19 patients, we performed FlowSOM clustering on the tSNE map, and also overlaid each individual EMD group onto this same tSNE map (Fig. 4, M and N). EMD Group 2 containing mostly HD and RD was enriched for naive B cells (IgD+CD27−, Cluster 10) and CXCR5+IgD−CD27+ switched memory (Cluster 2) and, indeed, Clusters 2 and 10 were statistically reduced in COVID-19 patients (Fig. 4P). EMD Groups 1 and 3 displayed distinct patterns across the FlowSOM clusters. B cells from individuals in EMD Group 1 were enriched for the FlowSOM Clusters 1, 5, and 6, all of which were increased in COVID-19 patients (Fig. 4P). FlowSOM Clusters 1 and 6 captured T-bet+ memory B cells whereas FlowSOM Cluster 5 contained the CD27+CD38+CD138+KI67+ PB, all of which were enriched in COVID-19 patients compared to controls (Fig. 4, O and P, and fig. S5K). In contrast, B cells from COVID-19 patients in EMD Group 3 also showed enrichment for the PB FlowSOM Cluster 5, though less prominent than for EMD Group 1, but the T-bet+ memory B cell Cluster 1 was substantially reduced in EMD Group 3. Thus, B cell responses were evident in many hospitalized COVID-19 patients, most often characterized by elevated PB, decreases in memory B cell subsets, enrichment in a T-bet+ B cell subset, and loss of CXCR5 expression. Whether all of these changes in the B cell compartment were due to direct antiviral responses is unclear. Although there was heterogeneity in the B cell responses, COVID-19 patients fell into two distinct patterns containing activated B cell responses and a third group of patients with little evidence of an active B cell response."}

PMC:7402624 / 31626-34701 JSONTXT

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PMC:7402624 / 31626-34701 JSON TXT