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bionlp-st-ge-2016-reference

bionlp-st-ge-2016-reference-tees

events-check-again

bionlp-st-ge-2016-coref

{"project":"bionlp-st-ge-2016-coref","denotations":[{"id":"T2237","span":{"begin":960,"end":965},"obj":"Antecedent"},{"id":"T2238","span":{"begin":971,"end":976},"obj":"Antecedent"},{"id":"T2239","span":{"begin":1375,"end":1393},"obj":"Anaphor"},{"id":"T2240","span":{"begin":1420,"end":1425},"obj":"Antecedent"},{"id":"T2241","span":{"begin":1483,"end":1488},"obj":"Antecedent"},{"id":"T2242","span":{"begin":1493,"end":1498},"obj":"Antecedent"},{"id":"T2243","span":{"begin":1394,"end":1398},"obj":"Anaphor"},{"id":"T2244","span":{"begin":1375,"end":1393},"obj":"Antecedent"},{"id":"T2234","span":{"begin":1071,"end":1085},"obj":"Anaphor"},{"id":"T2235","span":{"begin":946,"end":951},"obj":"Antecedent"},{"id":"T2236","span":{"begin":953,"end":958},"obj":"Antecedent"}],"relations":[{"id":"R1832","pred":"boundBy","subj":"T2234","obj":"T2237"},{"id":"R1833","pred":"boundBy","subj":"T2234","obj":"T2238"},{"id":"R1836","pred":"boundBy","subj":"T2239","obj":"T2240"},{"id":"R1837","pred":"boundBy","subj":"T2239","obj":"T2241"},{"id":"R1838","pred":"boundBy","subj":"T2239","obj":"T2242"},{"id":"R1840","pred":"boundBy","subj":"T2243","obj":"T2239"},{"id":"R1830","pred":"boundBy","subj":"T2234","obj":"T2235"},{"id":"R1831","pred":"boundBy","subj":"T2234","obj":"T2236"}],"namespaces":[{"prefix":"_base","uri":"http://bionlp.dbcls.jp/ontology/ge.owl#"}],"text":"Introduction\nCD40 signaling in professional antigen-presenting cells, including B cells, macrophages, and dendritic cells, is critical for the efficient activation of humoral and cell-mediated immune responses [1], [2], [3]. CD40 signaling is activated in a T cell-dependent manner, as the ligand for CD40, CD154, is expressed primarily by activated T cells. CD40 engagement leads to the activation of various signaling molecules, including stress-activated protein kinases and the transcription factor NF-κB, which upregulate the expression of cytokines and other factors that promote immune responses. The mechanism by which CD40 induces these signaling pathways has not been completely defined. The cytoplasmic domain of CD40 does not appear to have intrinsic enzymatic activity, but is able to mediate signaling through the recruitment of several intracellular proteins. Members of the TNF receptor-associated factor (TRAF) family, including TRAF1, TRAF2, TRAF3, and TRAF6, appear to be particularly important for the initiation and regulation of CD40 signaling [4]. These proteins function in part as adaptor molecules, binding to the cytoplasmic tail of CD40 and recruiting other proteins to the receptor-associated complex. Some of the TRAFs also function as E3 ubiquitin ligases, and this enzymatic activity may contribute to signal propagation and regulation. Among the multiple TRAFs that associate with CD40, TRAF3 can function as a negative regulator of signaling, while TRAF2 and TRAF6 promote the activation of downstream signaling pathways [4].\nWe recently demonstrated that HOIL-1L interacting protein (HOIP), a ubiquitin ligase that can catalyze the assembly of linear polyubiquitin chains [5], is recruited to CD40 in a TRAF2-dependent manner following engagement of CD40 by agonistic antibody [6]. These and other findings led us to hypothesize that HOIP functions downstream of TRAF2 in the CD40 signaling pathway and that HOIP is necessary for the activation of NF-κB and possibly other signaling molecules. To test this hypothesis, we employed somatic cell gene targeting to ablate expression of HOIP in a mouse B cell line that has proven to be a useful model for B cell CD40 signaling [7], [8], [9]. We found that the CD40-induced upregulation of CD80 (a costimulatory molecule for T cells) was defective in HOIP-deficient cells. Similarly, the CD40 and IL-4 driven production of germline transcripts from the immunoglobulin epsilon heavy chain locus, an event that precedes immunoglobulin gene rearrangement and isotype switching, was defective in the absence of HOIP. We also found that the CD40-mediated activation of NF-κB and the stress-activated protein kinase c-Jun kinase (JNK) was defective in HOIP-deficient cells. Consistent with impaired NF-κB activation, association of the IκB kinase (IKK) complex with CD40 was undetectable in HOIP-deficient cells. Together, our results indicate that HOIP plays a critical role in the activation of signaling pathways that regulate cellular responses to CD40 engagement."}

pmc-enju-pas

2_test

{"project":"2_test","denotations":[{"id":"21829693-19426221-89653748","span":{"begin":211,"end":212},"obj":"19426221"},{"id":"21829693-10647992-89653749","span":{"begin":216,"end":217},"obj":"10647992"},{"id":"21829693-18499506-89653750","span":{"begin":221,"end":222},"obj":"18499506"},{"id":"21829693-17633023-89653751","span":{"begin":1067,"end":1068},"obj":"17633023"},{"id":"21829693-17633023-89653752","span":{"begin":1556,"end":1557},"obj":"17633023"},{"id":"21829693-17006537-89653753","span":{"begin":1708,"end":1709},"obj":"17006537"},{"id":"21829693-20614026-89653754","span":{"begin":1813,"end":1814},"obj":"20614026"},{"id":"21829693-12958312-89653755","span":{"begin":2210,"end":2211},"obj":"12958312"},{"id":"21829693-17878362-89653756","span":{"begin":2215,"end":2216},"obj":"17878362"},{"id":"21829693-14981114-89653757","span":{"begin":2220,"end":2221},"obj":"14981114"},{"id":"T47453","span":{"begin":211,"end":212},"obj":"19426221"},{"id":"T32221","span":{"begin":216,"end":217},"obj":"10647992"},{"id":"T20683","span":{"begin":221,"end":222},"obj":"18499506"},{"id":"T36519","span":{"begin":1067,"end":1068},"obj":"17633023"},{"id":"T85269","span":{"begin":1556,"end":1557},"obj":"17633023"},{"id":"T1216","span":{"begin":1708,"end":1709},"obj":"17006537"},{"id":"T18092","span":{"begin":1813,"end":1814},"obj":"20614026"},{"id":"T40872","span":{"begin":2210,"end":2211},"obj":"12958312"},{"id":"T96147","span":{"begin":2215,"end":2216},"obj":"17878362"},{"id":"T94358","span":{"begin":2220,"end":2221},"obj":"14981114"}],"text":"Introduction\nCD40 signaling in professional antigen-presenting cells, including B cells, macrophages, and dendritic cells, is critical for the efficient activation of humoral and cell-mediated immune responses [1], [2], [3]. CD40 signaling is activated in a T cell-dependent manner, as the ligand for CD40, CD154, is expressed primarily by activated T cells. CD40 engagement leads to the activation of various signaling molecules, including stress-activated protein kinases and the transcription factor NF-κB, which upregulate the expression of cytokines and other factors that promote immune responses. The mechanism by which CD40 induces these signaling pathways has not been completely defined. The cytoplasmic domain of CD40 does not appear to have intrinsic enzymatic activity, but is able to mediate signaling through the recruitment of several intracellular proteins. Members of the TNF receptor-associated factor (TRAF) family, including TRAF1, TRAF2, TRAF3, and TRAF6, appear to be particularly important for the initiation and regulation of CD40 signaling [4]. These proteins function in part as adaptor molecules, binding to the cytoplasmic tail of CD40 and recruiting other proteins to the receptor-associated complex. Some of the TRAFs also function as E3 ubiquitin ligases, and this enzymatic activity may contribute to signal propagation and regulation. Among the multiple TRAFs that associate with CD40, TRAF3 can function as a negative regulator of signaling, while TRAF2 and TRAF6 promote the activation of downstream signaling pathways [4].\nWe recently demonstrated that HOIL-1L interacting protein (HOIP), a ubiquitin ligase that can catalyze the assembly of linear polyubiquitin chains [5], is recruited to CD40 in a TRAF2-dependent manner following engagement of CD40 by agonistic antibody [6]. These and other findings led us to hypothesize that HOIP functions downstream of TRAF2 in the CD40 signaling pathway and that HOIP is necessary for the activation of NF-κB and possibly other signaling molecules. To test this hypothesis, we employed somatic cell gene targeting to ablate expression of HOIP in a mouse B cell line that has proven to be a useful model for B cell CD40 signaling [7], [8], [9]. We found that the CD40-induced upregulation of CD80 (a costimulatory molecule for T cells) was defective in HOIP-deficient cells. Similarly, the CD40 and IL-4 driven production of germline transcripts from the immunoglobulin epsilon heavy chain locus, an event that precedes immunoglobulin gene rearrangement and isotype switching, was defective in the absence of HOIP. We also found that the CD40-mediated activation of NF-κB and the stress-activated protein kinase c-Jun kinase (JNK) was defective in HOIP-deficient cells. Consistent with impaired NF-κB activation, association of the IκB kinase (IKK) complex with CD40 was undetectable in HOIP-deficient cells. Together, our results indicate that HOIP plays a critical role in the activation of signaling pathways that regulate cellular responses to CD40 engagement."}

bionlp-st-ge-2016-spacy-parsed

UBERON-AE

{"project":"UBERON-AE","denotations":[{"id":"T1113","span":{"begin":1152,"end":1156},"obj":"http://purl.obolibrary.org/obo/UBERON_0002415"}],"text":"Introduction\nCD40 signaling in professional antigen-presenting cells, including B cells, macrophages, and dendritic cells, is critical for the efficient activation of humoral and cell-mediated immune responses [1], [2], [3]. CD40 signaling is activated in a T cell-dependent manner, as the ligand for CD40, CD154, is expressed primarily by activated T cells. CD40 engagement leads to the activation of various signaling molecules, including stress-activated protein kinases and the transcription factor NF-κB, which upregulate the expression of cytokines and other factors that promote immune responses. The mechanism by which CD40 induces these signaling pathways has not been completely defined. The cytoplasmic domain of CD40 does not appear to have intrinsic enzymatic activity, but is able to mediate signaling through the recruitment of several intracellular proteins. Members of the TNF receptor-associated factor (TRAF) family, including TRAF1, TRAF2, TRAF3, and TRAF6, appear to be particularly important for the initiation and regulation of CD40 signaling [4]. These proteins function in part as adaptor molecules, binding to the cytoplasmic tail of CD40 and recruiting other proteins to the receptor-associated complex. Some of the TRAFs also function as E3 ubiquitin ligases, and this enzymatic activity may contribute to signal propagation and regulation. Among the multiple TRAFs that associate with CD40, TRAF3 can function as a negative regulator of signaling, while TRAF2 and TRAF6 promote the activation of downstream signaling pathways [4].\nWe recently demonstrated that HOIL-1L interacting protein (HOIP), a ubiquitin ligase that can catalyze the assembly of linear polyubiquitin chains [5], is recruited to CD40 in a TRAF2-dependent manner following engagement of CD40 by agonistic antibody [6]. These and other findings led us to hypothesize that HOIP functions downstream of TRAF2 in the CD40 signaling pathway and that HOIP is necessary for the activation of NF-κB and possibly other signaling molecules. To test this hypothesis, we employed somatic cell gene targeting to ablate expression of HOIP in a mouse B cell line that has proven to be a useful model for B cell CD40 signaling [7], [8], [9]. We found that the CD40-induced upregulation of CD80 (a costimulatory molecule for T cells) was defective in HOIP-deficient cells. Similarly, the CD40 and IL-4 driven production of germline transcripts from the immunoglobulin epsilon heavy chain locus, an event that precedes immunoglobulin gene rearrangement and isotype switching, was defective in the absence of HOIP. We also found that the CD40-mediated activation of NF-κB and the stress-activated protein kinase c-Jun kinase (JNK) was defective in HOIP-deficient cells. Consistent with impaired NF-κB activation, association of the IκB kinase (IKK) complex with CD40 was undetectable in HOIP-deficient cells. Together, our results indicate that HOIP plays a critical role in the activation of signaling pathways that regulate cellular responses to CD40 engagement."}

GO-BP

GO-MF

GO-CC

{"project":"GO-CC","denotations":[{"id":"T2413","span":{"begin":63,"end":68},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T2414","span":{"begin":82,"end":87},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T2415","span":{"begin":116,"end":121},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T2416","span":{"begin":352,"end":357},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T2417","span":{"begin":2308,"end":2313},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T2418","span":{"begin":2347,"end":2352},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T2419","span":{"begin":2742,"end":2747},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T2420","span":{"begin":2881,"end":2886},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T2421","span":{"begin":851,"end":864},"obj":"http://purl.obolibrary.org/obo/GO_0005622"},{"id":"T2422","span":{"begin":1803,"end":1811},"obj":"http://purl.obolibrary.org/obo/GO_0019815"},{"id":"T2423","span":{"begin":1803,"end":1811},"obj":"http://purl.obolibrary.org/obo/GO_0042571"},{"id":"T2424","span":{"begin":2823,"end":2835},"obj":"http://purl.obolibrary.org/obo/GO_0008385"}],"text":"Introduction\nCD40 signaling in professional antigen-presenting cells, including B cells, macrophages, and dendritic cells, is critical for the efficient activation of humoral and cell-mediated immune responses [1], [2], [3]. CD40 signaling is activated in a T cell-dependent manner, as the ligand for CD40, CD154, is expressed primarily by activated T cells. CD40 engagement leads to the activation of various signaling molecules, including stress-activated protein kinases and the transcription factor NF-κB, which upregulate the expression of cytokines and other factors that promote immune responses. The mechanism by which CD40 induces these signaling pathways has not been completely defined. The cytoplasmic domain of CD40 does not appear to have intrinsic enzymatic activity, but is able to mediate signaling through the recruitment of several intracellular proteins. Members of the TNF receptor-associated factor (TRAF) family, including TRAF1, TRAF2, TRAF3, and TRAF6, appear to be particularly important for the initiation and regulation of CD40 signaling [4]. These proteins function in part as adaptor molecules, binding to the cytoplasmic tail of CD40 and recruiting other proteins to the receptor-associated complex. Some of the TRAFs also function as E3 ubiquitin ligases, and this enzymatic activity may contribute to signal propagation and regulation. Among the multiple TRAFs that associate with CD40, TRAF3 can function as a negative regulator of signaling, while TRAF2 and TRAF6 promote the activation of downstream signaling pathways [4].\nWe recently demonstrated that HOIL-1L interacting protein (HOIP), a ubiquitin ligase that can catalyze the assembly of linear polyubiquitin chains [5], is recruited to CD40 in a TRAF2-dependent manner following engagement of CD40 by agonistic antibody [6]. These and other findings led us to hypothesize that HOIP functions downstream of TRAF2 in the CD40 signaling pathway and that HOIP is necessary for the activation of NF-κB and possibly other signaling molecules. To test this hypothesis, we employed somatic cell gene targeting to ablate expression of HOIP in a mouse B cell line that has proven to be a useful model for B cell CD40 signaling [7], [8], [9]. We found that the CD40-induced upregulation of CD80 (a costimulatory molecule for T cells) was defective in HOIP-deficient cells. Similarly, the CD40 and IL-4 driven production of germline transcripts from the immunoglobulin epsilon heavy chain locus, an event that precedes immunoglobulin gene rearrangement and isotype switching, was defective in the absence of HOIP. We also found that the CD40-mediated activation of NF-κB and the stress-activated protein kinase c-Jun kinase (JNK) was defective in HOIP-deficient cells. Consistent with impaired NF-κB activation, association of the IκB kinase (IKK) complex with CD40 was undetectable in HOIP-deficient cells. Together, our results indicate that HOIP plays a critical role in the activation of signaling pathways that regulate cellular responses to CD40 engagement."}

sentences

bionlp-st-ge-2016-uniprot

test2

PMC:3148254 / 1857-4900 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:3148254 / 1857-4900 JSON TXT