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test3

2_test

{"project":"2_test","denotations":[{"id":"22396652-17942531-98461879","span":{"begin":235,"end":237},"obj":"17942531"},{"id":"22396652-20599425-98461880","span":{"begin":886,"end":888},"obj":"20599425"},{"id":"22396652-20304918-98461881","span":{"begin":1153,"end":1155},"obj":"20304918"},{"id":"22396652-21885437-98461882","span":{"begin":1159,"end":1161},"obj":"21885437"},{"id":"22396652-17991829-98461883","span":{"begin":1748,"end":1750},"obj":"17991829"},{"id":"22396652-18467330-98461884","span":{"begin":1759,"end":1761},"obj":"18467330"},{"id":"22396652-18636086-98461885","span":{"begin":1765,"end":1767},"obj":"18636086"},{"id":"22396652-19996094-98461886","span":{"begin":1779,"end":1781},"obj":"19996094"},{"id":"22396652-16765340-98461887","span":{"begin":1793,"end":1795},"obj":"16765340"},{"id":"22396652-15661910-98461888","span":{"begin":1798,"end":1800},"obj":"15661910"}],"text":"We show that A20 deficient BMDM display enhanced NF-κB and IRF3 activation in response to RIG-I stimulation by synthetic LMW double stranded RNA. RIG-I has previously been shown to play a key role in the innate immune response to IAV [13], suggesting that the increased immune response of A20myel-KO mice to IAV lung infection reflects enhanced RIG-I signaling. We propose that A20 inhibits IAV-induced proinflammatory gene expression (as shown in our manuscript for TNF, IL-6, KC, MIP-2, and IFNβ) by negatively regulating NF-κB and IRF3 activation, which are the major pathways controlling these genes. However, this does not exclude an additional effect of A20 on other signaling pathways that may contribute to proinflammatory gene expression. A20 is believed to exert its NF-κB and IRF3 inhibitory functions by modulating the ubiquitination status of different signaling proteins [80]. In this context, it was recently shown that A20 cooperates with the ubiquitin-binding proteins TAX1BP1 and ABIN1 to to disrupt the TRAF3-TBK1-IKKε complex, thereby negatively affecting K63-polyubiquitination of TBK1 and IKKε, and their ability to activity IRF3 [81], [82]. Whether similar mechanisms are involved in the regulation of RIG-I induced NF-κB activation is still unclear. So far we were unable to clearly detect ubiquitination of TBK1 and IKKε in primary macrophages, preventing us from studying the effect of A20 deficiency on their ubiquitination status. It cannot be excluded however that A20 also targets other substrates that mediate NF-κB and IRF3 activation in myeloid cells. The identification of these substrates will be the topic of future investigations in our laboratory. Multiple other deubiquitinating enzymes (DUBs), such as DUBA [28], CYLD [29], [30], OTUB1/2 [31], and A20 [49]–[52] have been shown to negatively regulate RIG-I signaling to NF-κB and IRF-3, implicating possible redundancy. However, evidence so far was limited to in vitro data and was obtained under non-physiological conditions. The clear protective phenotype of A20myel-KO mice that we here describe indicates that A20 expression in myeloid cells is a central gatekeeper of RIG-I induced signaling in response to IAV infection and that other DUBs cannot substitute for A20 deficiency under physiological conditions. If A20 has a similar non-redundant role in other cell types that are implicated in the response to IAV, such as lung epithelial cells, remains to be investigated."}

pmc-enju-pas

bionlp-st-ge-2016-coref

{"project":"bionlp-st-ge-2016-coref","denotations":[{"id":"T11814","span":{"begin":1341,"end":1345},"obj":"Antecedent"},{"id":"T11813","span":{"begin":1332,"end":1336},"obj":"Antecedent"},{"id":"T11812","span":{"begin":1430,"end":1435},"obj":"Anaphor"},{"id":"T11811","span":{"begin":1111,"end":1115},"obj":"Antecedent"},{"id":"T11810","span":{"begin":1102,"end":1106},"obj":"Antecedent"},{"id":"T11809","span":{"begin":1121,"end":1126},"obj":"Anaphor"}],"relations":[{"id":"R8525","pred":"boundBy","subj":"T11809","obj":"T11810"},{"id":"R8526","pred":"boundBy","subj":"T11809","obj":"T11811"},{"id":"R8527","pred":"boundBy","subj":"T11812","obj":"T11813"},{"id":"R8528","pred":"boundBy","subj":"T11812","obj":"T11814"}],"namespaces":[{"prefix":"_base","uri":"http://bionlp.dbcls.jp/ontology/ge.owl#"}],"text":"We show that A20 deficient BMDM display enhanced NF-κB and IRF3 activation in response to RIG-I stimulation by synthetic LMW double stranded RNA. RIG-I has previously been shown to play a key role in the innate immune response to IAV [13], suggesting that the increased immune response of A20myel-KO mice to IAV lung infection reflects enhanced RIG-I signaling. We propose that A20 inhibits IAV-induced proinflammatory gene expression (as shown in our manuscript for TNF, IL-6, KC, MIP-2, and IFNβ) by negatively regulating NF-κB and IRF3 activation, which are the major pathways controlling these genes. However, this does not exclude an additional effect of A20 on other signaling pathways that may contribute to proinflammatory gene expression. A20 is believed to exert its NF-κB and IRF3 inhibitory functions by modulating the ubiquitination status of different signaling proteins [80]. In this context, it was recently shown that A20 cooperates with the ubiquitin-binding proteins TAX1BP1 and ABIN1 to to disrupt the TRAF3-TBK1-IKKε complex, thereby negatively affecting K63-polyubiquitination of TBK1 and IKKε, and their ability to activity IRF3 [81], [82]. Whether similar mechanisms are involved in the regulation of RIG-I induced NF-κB activation is still unclear. So far we were unable to clearly detect ubiquitination of TBK1 and IKKε in primary macrophages, preventing us from studying the effect of A20 deficiency on their ubiquitination status. It cannot be excluded however that A20 also targets other substrates that mediate NF-κB and IRF3 activation in myeloid cells. The identification of these substrates will be the topic of future investigations in our laboratory. Multiple other deubiquitinating enzymes (DUBs), such as DUBA [28], CYLD [29], [30], OTUB1/2 [31], and A20 [49]–[52] have been shown to negatively regulate RIG-I signaling to NF-κB and IRF-3, implicating possible redundancy. However, evidence so far was limited to in vitro data and was obtained under non-physiological conditions. The clear protective phenotype of A20myel-KO mice that we here describe indicates that A20 expression in myeloid cells is a central gatekeeper of RIG-I induced signaling in response to IAV infection and that other DUBs cannot substitute for A20 deficiency under physiological conditions. If A20 has a similar non-redundant role in other cell types that are implicated in the response to IAV, such as lung epithelial cells, remains to be investigated."}

bionlp-st-ge-2016-test-proteins

{"project":"bionlp-st-ge-2016-test-proteins","denotations":[{"id":"T11844","span":{"begin":2163,"end":2168},"obj":"Protein"},{"id":"T11843","span":{"begin":1870,"end":1875},"obj":"Protein"},{"id":"T11842","span":{"begin":1841,"end":1846},"obj":"Protein"},{"id":"T11841","span":{"begin":1753,"end":1757},"obj":"Protein"},{"id":"T11840","span":{"begin":1551,"end":1555},"obj":"Protein"},{"id":"T11839","span":{"begin":1341,"end":1345},"obj":"Protein"},{"id":"T11838","span":{"begin":1332,"end":1336},"obj":"Protein"},{"id":"T11837","span":{"begin":1225,"end":1230},"obj":"Protein"},{"id":"T11836","span":{"begin":1147,"end":1151},"obj":"Protein"},{"id":"T11835","span":{"begin":1111,"end":1115},"obj":"Protein"},{"id":"T11834","span":{"begin":1102,"end":1106},"obj":"Protein"},{"id":"T11833","span":{"begin":998,"end":1003},"obj":"Protein"},{"id":"T11832","span":{"begin":787,"end":791},"obj":"Protein"},{"id":"T11831","span":{"begin":534,"end":538},"obj":"Protein"},{"id":"T11830","span":{"begin":493,"end":497},"obj":"Protein"},{"id":"T11829","span":{"begin":482,"end":487},"obj":"Protein"},{"id":"T11828","span":{"begin":478,"end":480},"obj":"Protein"},{"id":"T11827","span":{"begin":472,"end":476},"obj":"Protein"},{"id":"T11826","span":{"begin":467,"end":470},"obj":"Protein"},{"id":"T11825","span":{"begin":345,"end":350},"obj":"Protein"},{"id":"T11824","span":{"begin":146,"end":151},"obj":"Protein"},{"id":"T11823","span":{"begin":90,"end":95},"obj":"Protein"},{"id":"T11822","span":{"begin":59,"end":63},"obj":"Protein"}],"namespaces":[{"prefix":"_base","uri":"http://bionlp.dbcls.jp/ontology/ge.owl#"}],"text":"We show that A20 deficient BMDM display enhanced NF-κB and IRF3 activation in response to RIG-I stimulation by synthetic LMW double stranded RNA. RIG-I has previously been shown to play a key role in the innate immune response to IAV [13], suggesting that the increased immune response of A20myel-KO mice to IAV lung infection reflects enhanced RIG-I signaling. We propose that A20 inhibits IAV-induced proinflammatory gene expression (as shown in our manuscript for TNF, IL-6, KC, MIP-2, and IFNβ) by negatively regulating NF-κB and IRF3 activation, which are the major pathways controlling these genes. However, this does not exclude an additional effect of A20 on other signaling pathways that may contribute to proinflammatory gene expression. A20 is believed to exert its NF-κB and IRF3 inhibitory functions by modulating the ubiquitination status of different signaling proteins [80]. In this context, it was recently shown that A20 cooperates with the ubiquitin-binding proteins TAX1BP1 and ABIN1 to to disrupt the TRAF3-TBK1-IKKε complex, thereby negatively affecting K63-polyubiquitination of TBK1 and IKKε, and their ability to activity IRF3 [81], [82]. Whether similar mechanisms are involved in the regulation of RIG-I induced NF-κB activation is still unclear. So far we were unable to clearly detect ubiquitination of TBK1 and IKKε in primary macrophages, preventing us from studying the effect of A20 deficiency on their ubiquitination status. It cannot be excluded however that A20 also targets other substrates that mediate NF-κB and IRF3 activation in myeloid cells. The identification of these substrates will be the topic of future investigations in our laboratory. Multiple other deubiquitinating enzymes (DUBs), such as DUBA [28], CYLD [29], [30], OTUB1/2 [31], and A20 [49]–[52] have been shown to negatively regulate RIG-I signaling to NF-κB and IRF-3, implicating possible redundancy. However, evidence so far was limited to in vitro data and was obtained under non-physiological conditions. The clear protective phenotype of A20myel-KO mice that we here describe indicates that A20 expression in myeloid cells is a central gatekeeper of RIG-I induced signaling in response to IAV infection and that other DUBs cannot substitute for A20 deficiency under physiological conditions. If A20 has a similar non-redundant role in other cell types that are implicated in the response to IAV, such as lung epithelial cells, remains to be investigated."}

bionlp-st-ge-2016-uniprot

UBERON-AE

{"project":"UBERON-AE","denotations":[{"id":"T11701","span":{"begin":2141,"end":2148},"obj":"http://purl.obolibrary.org/obo/UBERON_0012131"},{"id":"T11698","span":{"begin":2417,"end":2421},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T11697","span":{"begin":312,"end":316},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"}],"text":"We show that A20 deficient BMDM display enhanced NF-κB and IRF3 activation in response to RIG-I stimulation by synthetic LMW double stranded RNA. RIG-I has previously been shown to play a key role in the innate immune response to IAV [13], suggesting that the increased immune response of A20myel-KO mice to IAV lung infection reflects enhanced RIG-I signaling. We propose that A20 inhibits IAV-induced proinflammatory gene expression (as shown in our manuscript for TNF, IL-6, KC, MIP-2, and IFNβ) by negatively regulating NF-κB and IRF3 activation, which are the major pathways controlling these genes. However, this does not exclude an additional effect of A20 on other signaling pathways that may contribute to proinflammatory gene expression. A20 is believed to exert its NF-κB and IRF3 inhibitory functions by modulating the ubiquitination status of different signaling proteins [80]. In this context, it was recently shown that A20 cooperates with the ubiquitin-binding proteins TAX1BP1 and ABIN1 to to disrupt the TRAF3-TBK1-IKKε complex, thereby negatively affecting K63-polyubiquitination of TBK1 and IKKε, and their ability to activity IRF3 [81], [82]. Whether similar mechanisms are involved in the regulation of RIG-I induced NF-κB activation is still unclear. So far we were unable to clearly detect ubiquitination of TBK1 and IKKε in primary macrophages, preventing us from studying the effect of A20 deficiency on their ubiquitination status. It cannot be excluded however that A20 also targets other substrates that mediate NF-κB and IRF3 activation in myeloid cells. The identification of these substrates will be the topic of future investigations in our laboratory. Multiple other deubiquitinating enzymes (DUBs), such as DUBA [28], CYLD [29], [30], OTUB1/2 [31], and A20 [49]–[52] have been shown to negatively regulate RIG-I signaling to NF-κB and IRF-3, implicating possible redundancy. However, evidence so far was limited to in vitro data and was obtained under non-physiological conditions. The clear protective phenotype of A20myel-KO mice that we here describe indicates that A20 expression in myeloid cells is a central gatekeeper of RIG-I induced signaling in response to IAV infection and that other DUBs cannot substitute for A20 deficiency under physiological conditions. If A20 has a similar non-redundant role in other cell types that are implicated in the response to IAV, such as lung epithelial cells, remains to be investigated."}

GO-BP

GO-MF

{"project":"GO-MF","denotations":[{"id":"T11924","span":{"begin":1701,"end":1725},"obj":"http://purl.obolibrary.org/obo/GO_0004843"},{"id":"T11923","span":{"begin":1332,"end":1336},"obj":"http://purl.obolibrary.org/obo/GO_0008384"},{"id":"T11922","span":{"begin":1102,"end":1106},"obj":"http://purl.obolibrary.org/obo/GO_0008384"},{"id":"T11921","span":{"begin":1028,"end":1032},"obj":"http://purl.obolibrary.org/obo/GO_0008384"},{"id":"T11920","span":{"begin":969,"end":985},"obj":"http://purl.obolibrary.org/obo/GO_0005515"},{"id":"T11919","span":{"begin":969,"end":976},"obj":"http://purl.obolibrary.org/obo/GO_0005488"},{"id":"T11918","span":{"begin":959,"end":985},"obj":"http://purl.obolibrary.org/obo/GO_0032182"},{"id":"T11917","span":{"begin":959,"end":985},"obj":"http://purl.obolibrary.org/obo/GO_0031625"},{"id":"T11916","span":{"begin":959,"end":976},"obj":"http://purl.obolibrary.org/obo/GO_0043130"},{"id":"T11915","span":{"begin":959,"end":968},"obj":"http://purl.obolibrary.org/obo/GO_0031386"},{"id":"T11911","span":{"begin":472,"end":476},"obj":"http://purl.obolibrary.org/obo/GO_0005138"}],"text":"We show that A20 deficient BMDM display enhanced NF-κB and IRF3 activation in response to RIG-I stimulation by synthetic LMW double stranded RNA. RIG-I has previously been shown to play a key role in the innate immune response to IAV [13], suggesting that the increased immune response of A20myel-KO mice to IAV lung infection reflects enhanced RIG-I signaling. We propose that A20 inhibits IAV-induced proinflammatory gene expression (as shown in our manuscript for TNF, IL-6, KC, MIP-2, and IFNβ) by negatively regulating NF-κB and IRF3 activation, which are the major pathways controlling these genes. However, this does not exclude an additional effect of A20 on other signaling pathways that may contribute to proinflammatory gene expression. A20 is believed to exert its NF-κB and IRF3 inhibitory functions by modulating the ubiquitination status of different signaling proteins [80]. In this context, it was recently shown that A20 cooperates with the ubiquitin-binding proteins TAX1BP1 and ABIN1 to to disrupt the TRAF3-TBK1-IKKε complex, thereby negatively affecting K63-polyubiquitination of TBK1 and IKKε, and their ability to activity IRF3 [81], [82]. Whether similar mechanisms are involved in the regulation of RIG-I induced NF-κB activation is still unclear. So far we were unable to clearly detect ubiquitination of TBK1 and IKKε in primary macrophages, preventing us from studying the effect of A20 deficiency on their ubiquitination status. It cannot be excluded however that A20 also targets other substrates that mediate NF-κB and IRF3 activation in myeloid cells. The identification of these substrates will be the topic of future investigations in our laboratory. Multiple other deubiquitinating enzymes (DUBs), such as DUBA [28], CYLD [29], [30], OTUB1/2 [31], and A20 [49]–[52] have been shown to negatively regulate RIG-I signaling to NF-κB and IRF-3, implicating possible redundancy. However, evidence so far was limited to in vitro data and was obtained under non-physiological conditions. The clear protective phenotype of A20myel-KO mice that we here describe indicates that A20 expression in myeloid cells is a central gatekeeper of RIG-I induced signaling in response to IAV infection and that other DUBs cannot substitute for A20 deficiency under physiological conditions. If A20 has a similar non-redundant role in other cell types that are implicated in the response to IAV, such as lung epithelial cells, remains to be investigated."}

GO-CC

{"project":"GO-CC","denotations":[{"id":"T11936","span":{"begin":2433,"end":2438},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T11935","span":{"begin":2130,"end":2135},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T11934","span":{"begin":1578,"end":1583},"obj":"http://purl.obolibrary.org/obo/GO_0005623"}],"text":"We show that A20 deficient BMDM display enhanced NF-κB and IRF3 activation in response to RIG-I stimulation by synthetic LMW double stranded RNA. RIG-I has previously been shown to play a key role in the innate immune response to IAV [13], suggesting that the increased immune response of A20myel-KO mice to IAV lung infection reflects enhanced RIG-I signaling. We propose that A20 inhibits IAV-induced proinflammatory gene expression (as shown in our manuscript for TNF, IL-6, KC, MIP-2, and IFNβ) by negatively regulating NF-κB and IRF3 activation, which are the major pathways controlling these genes. However, this does not exclude an additional effect of A20 on other signaling pathways that may contribute to proinflammatory gene expression. A20 is believed to exert its NF-κB and IRF3 inhibitory functions by modulating the ubiquitination status of different signaling proteins [80]. In this context, it was recently shown that A20 cooperates with the ubiquitin-binding proteins TAX1BP1 and ABIN1 to to disrupt the TRAF3-TBK1-IKKε complex, thereby negatively affecting K63-polyubiquitination of TBK1 and IKKε, and their ability to activity IRF3 [81], [82]. Whether similar mechanisms are involved in the regulation of RIG-I induced NF-κB activation is still unclear. So far we were unable to clearly detect ubiquitination of TBK1 and IKKε in primary macrophages, preventing us from studying the effect of A20 deficiency on their ubiquitination status. It cannot be excluded however that A20 also targets other substrates that mediate NF-κB and IRF3 activation in myeloid cells. The identification of these substrates will be the topic of future investigations in our laboratory. Multiple other deubiquitinating enzymes (DUBs), such as DUBA [28], CYLD [29], [30], OTUB1/2 [31], and A20 [49]–[52] have been shown to negatively regulate RIG-I signaling to NF-κB and IRF-3, implicating possible redundancy. However, evidence so far was limited to in vitro data and was obtained under non-physiological conditions. The clear protective phenotype of A20myel-KO mice that we here describe indicates that A20 expression in myeloid cells is a central gatekeeper of RIG-I induced signaling in response to IAV infection and that other DUBs cannot substitute for A20 deficiency under physiological conditions. If A20 has a similar non-redundant role in other cell types that are implicated in the response to IAV, such as lung epithelial cells, remains to be investigated."}

sentences

simple1

{"project":"simple1","denotations":[{"id":"T11998","span":{"begin":2163,"end":2168},"obj":"Protein"},{"id":"T11997","span":{"begin":1870,"end":1875},"obj":"Protein"},{"id":"T11996","span":{"begin":1841,"end":1846},"obj":"Protein"},{"id":"T11995","span":{"begin":1753,"end":1757},"obj":"Protein"},{"id":"T11994","span":{"begin":1551,"end":1555},"obj":"Protein"},{"id":"T11993","span":{"begin":1341,"end":1345},"obj":"Protein"},{"id":"T11992","span":{"begin":1332,"end":1336},"obj":"Protein"},{"id":"T11991","span":{"begin":1225,"end":1230},"obj":"Protein"},{"id":"T11990","span":{"begin":1147,"end":1151},"obj":"Protein"},{"id":"T11989","span":{"begin":1111,"end":1115},"obj":"Protein"},{"id":"T11988","span":{"begin":1102,"end":1106},"obj":"Protein"},{"id":"T11987","span":{"begin":998,"end":1003},"obj":"Protein"},{"id":"T11986","span":{"begin":787,"end":791},"obj":"Protein"},{"id":"T11985","span":{"begin":534,"end":538},"obj":"Protein"},{"id":"T11984","span":{"begin":493,"end":497},"obj":"Protein"},{"id":"T11983","span":{"begin":482,"end":487},"obj":"Protein"},{"id":"T11982","span":{"begin":478,"end":480},"obj":"Protein"},{"id":"T11981","span":{"begin":472,"end":476},"obj":"Protein"},{"id":"T11980","span":{"begin":467,"end":470},"obj":"Protein"},{"id":"T11979","span":{"begin":345,"end":350},"obj":"Protein"},{"id":"T11978","span":{"begin":146,"end":151},"obj":"Protein"},{"id":"T11977","span":{"begin":90,"end":95},"obj":"Protein"},{"id":"T11976","span":{"begin":59,"end":63},"obj":"Protein"}],"text":"We show that A20 deficient BMDM display enhanced NF-κB and IRF3 activation in response to RIG-I stimulation by synthetic LMW double stranded RNA. RIG-I has previously been shown to play a key role in the innate immune response to IAV [13], suggesting that the increased immune response of A20myel-KO mice to IAV lung infection reflects enhanced RIG-I signaling. We propose that A20 inhibits IAV-induced proinflammatory gene expression (as shown in our manuscript for TNF, IL-6, KC, MIP-2, and IFNβ) by negatively regulating NF-κB and IRF3 activation, which are the major pathways controlling these genes. However, this does not exclude an additional effect of A20 on other signaling pathways that may contribute to proinflammatory gene expression. A20 is believed to exert its NF-κB and IRF3 inhibitory functions by modulating the ubiquitination status of different signaling proteins [80]. In this context, it was recently shown that A20 cooperates with the ubiquitin-binding proteins TAX1BP1 and ABIN1 to to disrupt the TRAF3-TBK1-IKKε complex, thereby negatively affecting K63-polyubiquitination of TBK1 and IKKε, and their ability to activity IRF3 [81], [82]. Whether similar mechanisms are involved in the regulation of RIG-I induced NF-κB activation is still unclear. So far we were unable to clearly detect ubiquitination of TBK1 and IKKε in primary macrophages, preventing us from studying the effect of A20 deficiency on their ubiquitination status. It cannot be excluded however that A20 also targets other substrates that mediate NF-κB and IRF3 activation in myeloid cells. The identification of these substrates will be the topic of future investigations in our laboratory. Multiple other deubiquitinating enzymes (DUBs), such as DUBA [28], CYLD [29], [30], OTUB1/2 [31], and A20 [49]–[52] have been shown to negatively regulate RIG-I signaling to NF-κB and IRF-3, implicating possible redundancy. However, evidence so far was limited to in vitro data and was obtained under non-physiological conditions. The clear protective phenotype of A20myel-KO mice that we here describe indicates that A20 expression in myeloid cells is a central gatekeeper of RIG-I induced signaling in response to IAV infection and that other DUBs cannot substitute for A20 deficiency under physiological conditions. If A20 has a similar non-redundant role in other cell types that are implicated in the response to IAV, such as lung epithelial cells, remains to be investigated."}

BioNLP16_DUT

BioNLP16_Messiy

DLUT931

bionlp-st-ge-2016-test-ihmc

bionlp-st-ge-2016-spacy-parsed

bionlp-st-ge-2016-test-tees

testone

PMC:3291650 / 28302-30769 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:3291650 / 28302-30769 JSON TXT