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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T9","span":{"begin":51,"end":55},"obj":"Body_part"}],"attributes":[{"id":"A9","pred":"uberon_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"}],"text":"Both ILC2 and γδ T cells are centrally involved in lung homoeostasis and are rapidly activated in response to pathogens including viruses;19, 21 in COVID-19, IL-4 is upregulated at early stages and in milder forms of the disease,10 whereas IL-9 and activated γδ T cells are observed more frequently in mild-to-moderate disease,9, 22 and IFNγ and IL-17 progressively increase with disease severity.6 Vγ9Vδ2+ T cells from patients with COVID-19 have been found to express an effector memory phenotype three times more frequently than do conventional αβ T cells,23 thus suggesting that this T cell subset is selectively stimulated in COVID-19. Because of significantly higher expression of the chemokine receptor CXCR3 compared with their αβ counterparts,24 γδ T cells might be rapidly recruited into inflamed lungs of patients with COVID-19 in response to the observed strong upregulation of the CXCR3 ligands CXCL9 and CXCL10 (figure 1 ).6, 9, 11, 15, 25, 26, 27, 28\nFigure 1 T-cell polarisation in COVID-19\nIL-33 released from virus-damaged cells might induce dysregulated GATA3+Foxp3+ Tregs and promote IL-2 production by dendritic cells, resulting in further expansion of Tregs. IL-33 might also elicit differentiation of ILC2, with TGFβ enhancing ST2 expression on these cells and facilitating production of IL-9. IL-9 in turn stimulates expansion of effector memory Vγ9Vδ2+ T cells with mixed Th1 and Th17 profiles that express CXCR3 and are recruited to the lungs by CXCL9 and CXCL10. IL-9 possibly induces its own transcription factor PU.1 and thus act in an autocrine and paracrine manner (along with TGFβ) to drive proliferation and survival of ILC2 and γδ T cells. Additional positive loops might be fed by IFNγ, which triggers production of CXCL9 and CXCL10 by macrophages. In severe forms of COVID-19, IL-33, along with IL-2 and IL-7 released by dendritic cells, might further stimulate T-cell expansion through STAT5 and induce production of large amounts of GM-CSF by γδ and T helper cells. At advanced stages of disease, aberrant activation of the MyD88-related NF-κB pathway and activation of the NLRP3 inflammasome might induce virus-exposed cells and infiltrating monocytes–macrophages to overproduce IL-1β, IL-23, and IL-6. IL-1β, IL-23, IL-6, and IL-7 act on STAT3 and RORC, thus promoting differentiation of CCR2+ T cells that are recruited to the lungs by CCL2 and CCL8 into γδT17 and Th17 cells producing IL-17 and GM-CSF. In turn, GM-CSF might further recruit and activate proinflammatory monocytes–macrophages. CCR=C-C motif chemokine receptor. CCL=C-C motif chemokine ligand. CXCL=C-X-C motif chemokine ligand. CXCR=C-X-C chemokine receptor. Foxp=forkhead box protein. GATA=GATA-binding factor. GM-CSF=granulocyte-macrophage colony-stimulating factor. IL=interleukin. ILC2=type 2 innate lymphoid cell. MyD88=myeloid differentiation primary response protein. NF-κB=nuclear factor-kappa B. NLRP=NACHT, LRR, and PYD domains-containing protein. PU.1=transcription factor PU.1. RORC=nuclear receptor ROR-gamma. ST2=ST2 receptor. STAT=signal transducer and transcription activator. TGF=transforming growth factor. Th=T-helper. TLR=toll-like receptors. Treg=regulatory T cell."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T57","span":{"begin":148,"end":156},"obj":"Disease"},{"id":"T58","span":{"begin":434,"end":442},"obj":"Disease"},{"id":"T59","span":{"begin":631,"end":639},"obj":"Disease"},{"id":"T60","span":{"begin":830,"end":838},"obj":"Disease"},{"id":"T61","span":{"begin":998,"end":1006},"obj":"Disease"},{"id":"T62","span":{"begin":1803,"end":1811},"obj":"Disease"},{"id":"T63","span":{"begin":2535,"end":2542},"obj":"Disease"}],"attributes":[{"id":"A57","pred":"mondo_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A58","pred":"mondo_id","subj":"T58","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A59","pred":"mondo_id","subj":"T59","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A60","pred":"mondo_id","subj":"T60","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A61","pred":"mondo_id","subj":"T61","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A62","pred":"mondo_id","subj":"T62","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A63","pred":"mondo_id","subj":"T63","obj":"http://purl.obolibrary.org/obo/MONDO_0007763"}],"text":"Both ILC2 and γδ T cells are centrally involved in lung homoeostasis and are rapidly activated in response to pathogens including viruses;19, 21 in COVID-19, IL-4 is upregulated at early stages and in milder forms of the disease,10 whereas IL-9 and activated γδ T cells are observed more frequently in mild-to-moderate disease,9, 22 and IFNγ and IL-17 progressively increase with disease severity.6 Vγ9Vδ2+ T cells from patients with COVID-19 have been found to express an effector memory phenotype three times more frequently than do conventional αβ T cells,23 thus suggesting that this T cell subset is selectively stimulated in COVID-19. Because of significantly higher expression of the chemokine receptor CXCR3 compared with their αβ counterparts,24 γδ T cells might be rapidly recruited into inflamed lungs of patients with COVID-19 in response to the observed strong upregulation of the CXCR3 ligands CXCL9 and CXCL10 (figure 1 ).6, 9, 11, 15, 25, 26, 27, 28\nFigure 1 T-cell polarisation in COVID-19\nIL-33 released from virus-damaged cells might induce dysregulated GATA3+Foxp3+ Tregs and promote IL-2 production by dendritic cells, resulting in further expansion of Tregs. IL-33 might also elicit differentiation of ILC2, with TGFβ enhancing ST2 expression on these cells and facilitating production of IL-9. IL-9 in turn stimulates expansion of effector memory Vγ9Vδ2+ T cells with mixed Th1 and Th17 profiles that express CXCR3 and are recruited to the lungs by CXCL9 and CXCL10. IL-9 possibly induces its own transcription factor PU.1 and thus act in an autocrine and paracrine manner (along with TGFβ) to drive proliferation and survival of ILC2 and γδ T cells. Additional positive loops might be fed by IFNγ, which triggers production of CXCL9 and CXCL10 by macrophages. In severe forms of COVID-19, IL-33, along with IL-2 and IL-7 released by dendritic cells, might further stimulate T-cell expansion through STAT5 and induce production of large amounts of GM-CSF by γδ and T helper cells. At advanced stages of disease, aberrant activation of the MyD88-related NF-κB pathway and activation of the NLRP3 inflammasome might induce virus-exposed cells and infiltrating monocytes–macrophages to overproduce IL-1β, IL-23, and IL-6. IL-1β, IL-23, IL-6, and IL-7 act on STAT3 and RORC, thus promoting differentiation of CCR2+ T cells that are recruited to the lungs by CCL2 and CCL8 into γδT17 and Th17 cells producing IL-17 and GM-CSF. In turn, GM-CSF might further recruit and activate proinflammatory monocytes–macrophages. CCR=C-C motif chemokine receptor. CCL=C-C motif chemokine ligand. CXCL=C-X-C motif chemokine ligand. CXCR=C-X-C chemokine receptor. Foxp=forkhead box protein. GATA=GATA-binding factor. GM-CSF=granulocyte-macrophage colony-stimulating factor. IL=interleukin. ILC2=type 2 innate lymphoid cell. MyD88=myeloid differentiation primary response protein. NF-κB=nuclear factor-kappa B. NLRP=NACHT, LRR, and PYD domains-containing protein. PU.1=transcription factor PU.1. RORC=nuclear receptor ROR-gamma. ST2=ST2 receptor. STAT=signal transducer and transcription activator. TGF=transforming growth factor. Th=T-helper. TLR=toll-like receptors. Treg=regulatory T cell."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T15","span":{"begin":482,"end":488},"obj":"http://purl.obolibrary.org/obo/GO_0007613"},{"id":"T16","span":{"begin":1104,"end":1119},"obj":"http://purl.obolibrary.org/obo/GO_0032623"},{"id":"T17","span":{"begin":1363,"end":1369},"obj":"http://purl.obolibrary.org/obo/GO_0007613"},{"id":"T18","span":{"begin":1520,"end":1540},"obj":"http://purl.obolibrary.org/obo/GO_0000981"},{"id":"T19","span":{"begin":1520,"end":1533},"obj":"http://purl.obolibrary.org/obo/GO_0006351"},{"id":"T20","span":{"begin":1900,"end":1914},"obj":"http://purl.obolibrary.org/obo/GO_0016049"},{"id":"T21","span":{"begin":2971,"end":2991},"obj":"http://purl.obolibrary.org/obo/GO_0000981"},{"id":"T22","span":{"begin":2971,"end":2984},"obj":"http://purl.obolibrary.org/obo/GO_0006351"},{"id":"T23","span":{"begin":3076,"end":3089},"obj":"http://purl.obolibrary.org/obo/GO_0006351"},{"id":"T24","span":{"begin":3118,"end":3124},"obj":"http://purl.obolibrary.org/obo/GO_0040007"}],"text":"Both ILC2 and γδ T cells are centrally involved in lung homoeostasis and are rapidly activated in response to pathogens including viruses;19, 21 in COVID-19, IL-4 is upregulated at early stages and in milder forms of the disease,10 whereas IL-9 and activated γδ T cells are observed more frequently in mild-to-moderate disease,9, 22 and IFNγ and IL-17 progressively increase with disease severity.6 Vγ9Vδ2+ T cells from patients with COVID-19 have been found to express an effector memory phenotype three times more frequently than do conventional αβ T cells,23 thus suggesting that this T cell subset is selectively stimulated in COVID-19. Because of significantly higher expression of the chemokine receptor CXCR3 compared with their αβ counterparts,24 γδ T cells might be rapidly recruited into inflamed lungs of patients with COVID-19 in response to the observed strong upregulation of the CXCR3 ligands CXCL9 and CXCL10 (figure 1 ).6, 9, 11, 15, 25, 26, 27, 28\nFigure 1 T-cell polarisation in COVID-19\nIL-33 released from virus-damaged cells might induce dysregulated GATA3+Foxp3+ Tregs and promote IL-2 production by dendritic cells, resulting in further expansion of Tregs. IL-33 might also elicit differentiation of ILC2, with TGFβ enhancing ST2 expression on these cells and facilitating production of IL-9. IL-9 in turn stimulates expansion of effector memory Vγ9Vδ2+ T cells with mixed Th1 and Th17 profiles that express CXCR3 and are recruited to the lungs by CXCL9 and CXCL10. IL-9 possibly induces its own transcription factor PU.1 and thus act in an autocrine and paracrine manner (along with TGFβ) to drive proliferation and survival of ILC2 and γδ T cells. Additional positive loops might be fed by IFNγ, which triggers production of CXCL9 and CXCL10 by macrophages. In severe forms of COVID-19, IL-33, along with IL-2 and IL-7 released by dendritic cells, might further stimulate T-cell expansion through STAT5 and induce production of large amounts of GM-CSF by γδ and T helper cells. At advanced stages of disease, aberrant activation of the MyD88-related NF-κB pathway and activation of the NLRP3 inflammasome might induce virus-exposed cells and infiltrating monocytes–macrophages to overproduce IL-1β, IL-23, and IL-6. IL-1β, IL-23, IL-6, and IL-7 act on STAT3 and RORC, thus promoting differentiation of CCR2+ T cells that are recruited to the lungs by CCL2 and CCL8 into γδT17 and Th17 cells producing IL-17 and GM-CSF. In turn, GM-CSF might further recruit and activate proinflammatory monocytes–macrophages. CCR=C-C motif chemokine receptor. CCL=C-C motif chemokine ligand. CXCL=C-X-C motif chemokine ligand. CXCR=C-X-C chemokine receptor. Foxp=forkhead box protein. GATA=GATA-binding factor. GM-CSF=granulocyte-macrophage colony-stimulating factor. IL=interleukin. ILC2=type 2 innate lymphoid cell. MyD88=myeloid differentiation primary response protein. NF-κB=nuclear factor-kappa B. NLRP=NACHT, LRR, and PYD domains-containing protein. PU.1=transcription factor PU.1. RORC=nuclear receptor ROR-gamma. ST2=ST2 receptor. STAT=signal transducer and transcription activator. TGF=transforming growth factor. Th=T-helper. TLR=toll-like receptors. Treg=regulatory T cell."}

LitCovid-sentences

LitCovid-PubTator

2_test

{"project":"2_test","denotations":[{"id":"33073244-27543964-66244526","span":{"begin":138,"end":140},"obj":"27543964"},{"id":"33073244-28555812-66244527","span":{"begin":142,"end":144},"obj":"28555812"},{"id":"33073244-32460357-66244528","span":{"begin":229,"end":231},"obj":"32460357"},{"id":"33073244-31986264-66244529","span":{"begin":327,"end":328},"obj":"31986264"},{"id":"33073244-32467616-66244530","span":{"begin":559,"end":561},"obj":"32467616"},{"id":"33073244-11994442-66244531","span":{"begin":752,"end":754},"obj":"11994442"},{"id":"33073244-31986264-66244532","span":{"begin":940,"end":941},"obj":"31986264"},{"id":"33073244-32228226-66244533","span":{"begin":943,"end":945},"obj":"32228226"},{"id":"33073244-32398875-66244534","span":{"begin":947,"end":949},"obj":"32398875"},{"id":"33073244-32360286-66244535","span":{"begin":951,"end":953},"obj":"32360286"},{"id":"33073244-32407669-66244536","span":{"begin":955,"end":957},"obj":"32407669"},{"id":"33073244-32416070-66244537","span":{"begin":959,"end":961},"obj":"32416070"}],"text":"Both ILC2 and γδ T cells are centrally involved in lung homoeostasis and are rapidly activated in response to pathogens including viruses;19, 21 in COVID-19, IL-4 is upregulated at early stages and in milder forms of the disease,10 whereas IL-9 and activated γδ T cells are observed more frequently in mild-to-moderate disease,9, 22 and IFNγ and IL-17 progressively increase with disease severity.6 Vγ9Vδ2+ T cells from patients with COVID-19 have been found to express an effector memory phenotype three times more frequently than do conventional αβ T cells,23 thus suggesting that this T cell subset is selectively stimulated in COVID-19. Because of significantly higher expression of the chemokine receptor CXCR3 compared with their αβ counterparts,24 γδ T cells might be rapidly recruited into inflamed lungs of patients with COVID-19 in response to the observed strong upregulation of the CXCR3 ligands CXCL9 and CXCL10 (figure 1 ).6, 9, 11, 15, 25, 26, 27, 28\nFigure 1 T-cell polarisation in COVID-19\nIL-33 released from virus-damaged cells might induce dysregulated GATA3+Foxp3+ Tregs and promote IL-2 production by dendritic cells, resulting in further expansion of Tregs. IL-33 might also elicit differentiation of ILC2, with TGFβ enhancing ST2 expression on these cells and facilitating production of IL-9. IL-9 in turn stimulates expansion of effector memory Vγ9Vδ2+ T cells with mixed Th1 and Th17 profiles that express CXCR3 and are recruited to the lungs by CXCL9 and CXCL10. IL-9 possibly induces its own transcription factor PU.1 and thus act in an autocrine and paracrine manner (along with TGFβ) to drive proliferation and survival of ILC2 and γδ T cells. Additional positive loops might be fed by IFNγ, which triggers production of CXCL9 and CXCL10 by macrophages. In severe forms of COVID-19, IL-33, along with IL-2 and IL-7 released by dendritic cells, might further stimulate T-cell expansion through STAT5 and induce production of large amounts of GM-CSF by γδ and T helper cells. At advanced stages of disease, aberrant activation of the MyD88-related NF-κB pathway and activation of the NLRP3 inflammasome might induce virus-exposed cells and infiltrating monocytes–macrophages to overproduce IL-1β, IL-23, and IL-6. IL-1β, IL-23, IL-6, and IL-7 act on STAT3 and RORC, thus promoting differentiation of CCR2+ T cells that are recruited to the lungs by CCL2 and CCL8 into γδT17 and Th17 cells producing IL-17 and GM-CSF. In turn, GM-CSF might further recruit and activate proinflammatory monocytes–macrophages. CCR=C-C motif chemokine receptor. CCL=C-C motif chemokine ligand. CXCL=C-X-C motif chemokine ligand. CXCR=C-X-C chemokine receptor. Foxp=forkhead box protein. GATA=GATA-binding factor. GM-CSF=granulocyte-macrophage colony-stimulating factor. IL=interleukin. ILC2=type 2 innate lymphoid cell. MyD88=myeloid differentiation primary response protein. NF-κB=nuclear factor-kappa B. NLRP=NACHT, LRR, and PYD domains-containing protein. PU.1=transcription factor PU.1. RORC=nuclear receptor ROR-gamma. ST2=ST2 receptor. STAT=signal transducer and transcription activator. TGF=transforming growth factor. Th=T-helper. TLR=toll-like receptors. Treg=regulatory T cell."}

PMC:7546716 / 6467-9661 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7546716 / 6467-9661 JSON TXT