PMC:3585731 / 5289-10103 JSON TXT

Annnotations TAB JSON ListView MergeView

testone

2_test

{"project":"2_test","denotations":[{"id":"23469174-19109899-90505413","span":{"begin":189,"end":191},"obj":"19109899"},{"id":"23469174-16408008-90505414","span":{"begin":195,"end":197},"obj":"16408008"},{"id":"23469174-19109899-90505415","span":{"begin":386,"end":388},"obj":"19109899"},{"id":"23469174-15131264-90505416","span":{"begin":392,"end":394},"obj":"15131264"},{"id":"23469174-16408008-90505417","span":{"begin":563,"end":565},"obj":"16408008"},{"id":"23469174-21368762-90505418","span":{"begin":718,"end":720},"obj":"21368762"},{"id":"23469174-21368763-90505419","span":{"begin":724,"end":726},"obj":"21368763"},{"id":"23469174-21368761-90505420","span":{"begin":730,"end":732},"obj":"21368761"},{"id":"23469174-19632174-90505421","span":{"begin":1218,"end":1220},"obj":"19632174"},{"id":"23469174-22037414-90505422","span":{"begin":1224,"end":1226},"obj":"22037414"},{"id":"23469174-19556857-90505423","span":{"begin":1290,"end":1292},"obj":"19556857"},{"id":"23469174-18408713-90505424","span":{"begin":3058,"end":3060},"obj":"18408713"},{"id":"23469174-16153840-90505425","span":{"begin":3064,"end":3066},"obj":"16153840"},{"id":"23469174-22695613-90505426","span":{"begin":3170,"end":3172},"obj":"22695613"},{"id":"23469174-18408713-90505427","span":{"begin":3606,"end":3608},"obj":"18408713"}],"text":"Basic Fibroblast Growth Factor Promotes Necroptosis in L929 Cells\nIt has been established that mouse fibrosarcoma L929 cells undergo necroptotic cell death following stimulation with TNFα [10], [17]. In addition, inhibition of caspase-8 activity alone, either through siRNA knockdown or by using the pan-caspase inhibitor, zVAD.fmk, is sufficient to trigger necroptosis in these cells [10], [14]. Interestingly, while necroptosis was initially identified as a back-up form of cell death triggered by pro-apoptotic stimuli in the presence of apoptosis inhibitors [17], recent analysis of physiological cell death during mouse development has suggested that the loss of apoptotic regulators, such as caspase-8 and FADD [18], [19], [20], leads to robust induction of necroptosis and death of E10.5 embryos even though apoptosis is not normally induced in wild type embryos. These data are reminiscent of the observations in L929 cells where the loss of caspase activity in healthy cells is sufficient to trigger necroptosis and prompted us to explore the extrinsic or intrinsic cellular factors that promote necroptosis once caspase-8 activity, which cleaves and inactivates RIP1 kinase and the RIP1 deubiquitinase CYLD [21], [22], is removed in L929 cells. Consistent with a previous report [16], we found that serum starvation of L929 cells prevented necroptosis in response to zVAD.fmk (Fig. 1A). The addition of growth factors, such as bFGF, restored zVAD.fmk induced death under serum free conditions (Fig. 1B). Interestingly, this does not reflect a generic requirement for growth factor signaling, as only some growth factors (bFGF and IGF-1, but not EGF and PDGF) promoted death (Fig. 1B). Furthermore, growth factor-dependent necroptosis required the inhibition of caspase activity, as bFGF alone did not induce cell death (Fig. 1C). In contrast, TNFα triggered necroptosis equally efficiently in the absence of serum (Fig. 1A), suggesting that either growth factors and zVAD.fmk or TNFα are required for necroptotic death in L929 cells.\n10.1371/journal.pone.0056576.g001 Figure 1 bFGF and IGF-1 promote necroptosis in concert with zVAD.fmk.\n(A) L929 cells were treated with TNFα or zVAD.fmk under normal serum (10% FBS) or serum free conditions. Cell viability was determined after 24 hr using the CellTiter-Glo Viability assay. The concentrations of all necroptosis-inducing agents are listed in the Materials and Methods section or indicated in the figures. (B) Cells were treated with zVAD.fmk, the indicated growth factors, and Nec-1 under serum free conditions for 24 hrs followed by measurement of cell viability. (C) Cells under serum free conditions were treated with FGF, zVAD.fmk, or both for 24 hrs followed by viability assay. (D) Cell death was induced by zVAD.fmk or TNFα under full serum condition in the presence of 2 µM PD173074 and 20 µM PD166866. In all graphs, average±SD was plotted. Previously we described the development of 7-Cl-O-Nec-1 (Nec-1) as a potent and selective inhibitor of RIP1 kinase and necroptosis (Fig. S1A) [23], [24]. Recently, its selectivity has been further validated against a panel of more than 400 human kinases [15]. This inhibitor efficiently blocked growth factor/zVAD.fmk-induced necroptosis under serum free conditions in L929 cells and both zVAD.fmk and TNFα-induced necroptosis under full serum conditions (Fig. 1B, S1B). To further validate the role of RIP1, we used an inactive analog, 7-Cl-O-Nec-1i (Nec-1i) (Fig. S1A), which contains an extra N-methyl group that leads to almost complete loss of RIP1 kinase inhibitory activity in vitro [23]. Nec-1i was unable to protect L929 cell death under serum condtions treated with zVAD.fmk or TNFα (Fig. S1B) or serum free conditions treated with bFGF/zVAD.fmk (Fig. S1C). This confirms that RIP1 kinase is responsible for necroptosis in L929 cells under both serum and serum free conditions.\nWe next examined whether bFGF contributes to zVAD.fmk-induced necroptosis under normal serum conditions (10% FBS). We used two bFGF receptor tyrosine kinase inhibitors (PD173074 and PD166866), and determined that inhibition of bFGF signaling strongly inhibited zVAD.fmk-induced necroptosis under normal serum conditions (Fig. 1D). In contrast, neither bFGF receptor inhibitor was able to attenuate TNFα-induced necroptosis (Fig. 1D), consistent with growth factors being dispensable for this pathway (Fig. 1A). Overall, these data suggest that the induction of necroptosis by zVAD.fmk is promoted by bFGF under both serum and serum free conditions. The induction of necroptosis, however, is not a simple consequence of growth factor signaling since not all growth factors allowed death to occur. Instead, specific signaling events mediated by particular growth factors appear to contribute to necroptotic death."}

pmc-enju-pas

bionlp-st-ge-2016-coref

{"project":"bionlp-st-ge-2016-coref","denotations":[{"id":"T3038","span":{"begin":1122,"end":1131},"obj":"Antecedent"},{"id":"T3037","span":{"begin":1142,"end":1147},"obj":"Anaphor"}],"relations":[{"id":"R2012","pred":"boundBy","subj":"T3037","obj":"T3038"}],"namespaces":[{"prefix":"_base","uri":"http://bionlp.dbcls.jp/ontology/ge.owl#"}],"text":"Basic Fibroblast Growth Factor Promotes Necroptosis in L929 Cells\nIt has been established that mouse fibrosarcoma L929 cells undergo necroptotic cell death following stimulation with TNFα [10], [17]. In addition, inhibition of caspase-8 activity alone, either through siRNA knockdown or by using the pan-caspase inhibitor, zVAD.fmk, is sufficient to trigger necroptosis in these cells [10], [14]. Interestingly, while necroptosis was initially identified as a back-up form of cell death triggered by pro-apoptotic stimuli in the presence of apoptosis inhibitors [17], recent analysis of physiological cell death during mouse development has suggested that the loss of apoptotic regulators, such as caspase-8 and FADD [18], [19], [20], leads to robust induction of necroptosis and death of E10.5 embryos even though apoptosis is not normally induced in wild type embryos. These data are reminiscent of the observations in L929 cells where the loss of caspase activity in healthy cells is sufficient to trigger necroptosis and prompted us to explore the extrinsic or intrinsic cellular factors that promote necroptosis once caspase-8 activity, which cleaves and inactivates RIP1 kinase and the RIP1 deubiquitinase CYLD [21], [22], is removed in L929 cells. Consistent with a previous report [16], we found that serum starvation of L929 cells prevented necroptosis in response to zVAD.fmk (Fig. 1A). The addition of growth factors, such as bFGF, restored zVAD.fmk induced death under serum free conditions (Fig. 1B). Interestingly, this does not reflect a generic requirement for growth factor signaling, as only some growth factors (bFGF and IGF-1, but not EGF and PDGF) promoted death (Fig. 1B). Furthermore, growth factor-dependent necroptosis required the inhibition of caspase activity, as bFGF alone did not induce cell death (Fig. 1C). In contrast, TNFα triggered necroptosis equally efficiently in the absence of serum (Fig. 1A), suggesting that either growth factors and zVAD.fmk or TNFα are required for necroptotic death in L929 cells.\n10.1371/journal.pone.0056576.g001 Figure 1 bFGF and IGF-1 promote necroptosis in concert with zVAD.fmk.\n(A) L929 cells were treated with TNFα or zVAD.fmk under normal serum (10% FBS) or serum free conditions. Cell viability was determined after 24 hr using the CellTiter-Glo Viability assay. The concentrations of all necroptosis-inducing agents are listed in the Materials and Methods section or indicated in the figures. (B) Cells were treated with zVAD.fmk, the indicated growth factors, and Nec-1 under serum free conditions for 24 hrs followed by measurement of cell viability. (C) Cells under serum free conditions were treated with FGF, zVAD.fmk, or both for 24 hrs followed by viability assay. (D) Cell death was induced by zVAD.fmk or TNFα under full serum condition in the presence of 2 µM PD173074 and 20 µM PD166866. In all graphs, average±SD was plotted. Previously we described the development of 7-Cl-O-Nec-1 (Nec-1) as a potent and selective inhibitor of RIP1 kinase and necroptosis (Fig. S1A) [23], [24]. Recently, its selectivity has been further validated against a panel of more than 400 human kinases [15]. This inhibitor efficiently blocked growth factor/zVAD.fmk-induced necroptosis under serum free conditions in L929 cells and both zVAD.fmk and TNFα-induced necroptosis under full serum conditions (Fig. 1B, S1B). To further validate the role of RIP1, we used an inactive analog, 7-Cl-O-Nec-1i (Nec-1i) (Fig. S1A), which contains an extra N-methyl group that leads to almost complete loss of RIP1 kinase inhibitory activity in vitro [23]. Nec-1i was unable to protect L929 cell death under serum condtions treated with zVAD.fmk or TNFα (Fig. S1B) or serum free conditions treated with bFGF/zVAD.fmk (Fig. S1C). This confirms that RIP1 kinase is responsible for necroptosis in L929 cells under both serum and serum free conditions.\nWe next examined whether bFGF contributes to zVAD.fmk-induced necroptosis under normal serum conditions (10% FBS). We used two bFGF receptor tyrosine kinase inhibitors (PD173074 and PD166866), and determined that inhibition of bFGF signaling strongly inhibited zVAD.fmk-induced necroptosis under normal serum conditions (Fig. 1D). In contrast, neither bFGF receptor inhibitor was able to attenuate TNFα-induced necroptosis (Fig. 1D), consistent with growth factors being dispensable for this pathway (Fig. 1A). Overall, these data suggest that the induction of necroptosis by zVAD.fmk is promoted by bFGF under both serum and serum free conditions. The induction of necroptosis, however, is not a simple consequence of growth factor signaling since not all growth factors allowed death to occur. Instead, specific signaling events mediated by particular growth factors appear to contribute to necroptotic death."}

bionlp-st-ge-2016-test-proteins

bionlp-st-ge-2016-uniprot

UBERON-AE

GO-BP

GO-MF

{"project":"GO-MF","denotations":[{"id":"T3161","span":{"begin":4035,"end":4059},"obj":"http://purl.obolibrary.org/obo/GO_0030971"},{"id":"T3160","span":{"begin":1663,"end":1667},"obj":"http://purl.obolibrary.org/obo/GO_0005161"},{"id":"T3159","span":{"begin":1655,"end":1658},"obj":"http://purl.obolibrary.org/obo/GO_0005154"},{"id":"T3158","span":{"begin":1197,"end":1211},"obj":"http://purl.obolibrary.org/obo/GO_0004843"},{"id":"T3157","span":{"begin":1771,"end":1787},"obj":"http://purl.obolibrary.org/obo/GO_0097153"},{"id":"T3156","span":{"begin":950,"end":966},"obj":"http://purl.obolibrary.org/obo/GO_0097153"},{"id":"T3155","span":{"begin":1771,"end":1787},"obj":"http://purl.obolibrary.org/obo/GO_0004197"},{"id":"T3154","span":{"begin":950,"end":966},"obj":"http://purl.obolibrary.org/obo/GO_0004197"}],"text":"Basic Fibroblast Growth Factor Promotes Necroptosis in L929 Cells\nIt has been established that mouse fibrosarcoma L929 cells undergo necroptotic cell death following stimulation with TNFα [10], [17]. In addition, inhibition of caspase-8 activity alone, either through siRNA knockdown or by using the pan-caspase inhibitor, zVAD.fmk, is sufficient to trigger necroptosis in these cells [10], [14]. Interestingly, while necroptosis was initially identified as a back-up form of cell death triggered by pro-apoptotic stimuli in the presence of apoptosis inhibitors [17], recent analysis of physiological cell death during mouse development has suggested that the loss of apoptotic regulators, such as caspase-8 and FADD [18], [19], [20], leads to robust induction of necroptosis and death of E10.5 embryos even though apoptosis is not normally induced in wild type embryos. These data are reminiscent of the observations in L929 cells where the loss of caspase activity in healthy cells is sufficient to trigger necroptosis and prompted us to explore the extrinsic or intrinsic cellular factors that promote necroptosis once caspase-8 activity, which cleaves and inactivates RIP1 kinase and the RIP1 deubiquitinase CYLD [21], [22], is removed in L929 cells. Consistent with a previous report [16], we found that serum starvation of L929 cells prevented necroptosis in response to zVAD.fmk (Fig. 1A). The addition of growth factors, such as bFGF, restored zVAD.fmk induced death under serum free conditions (Fig. 1B). Interestingly, this does not reflect a generic requirement for growth factor signaling, as only some growth factors (bFGF and IGF-1, but not EGF and PDGF) promoted death (Fig. 1B). Furthermore, growth factor-dependent necroptosis required the inhibition of caspase activity, as bFGF alone did not induce cell death (Fig. 1C). In contrast, TNFα triggered necroptosis equally efficiently in the absence of serum (Fig. 1A), suggesting that either growth factors and zVAD.fmk or TNFα are required for necroptotic death in L929 cells.\n10.1371/journal.pone.0056576.g001 Figure 1 bFGF and IGF-1 promote necroptosis in concert with zVAD.fmk.\n(A) L929 cells were treated with TNFα or zVAD.fmk under normal serum (10% FBS) or serum free conditions. Cell viability was determined after 24 hr using the CellTiter-Glo Viability assay. The concentrations of all necroptosis-inducing agents are listed in the Materials and Methods section or indicated in the figures. (B) Cells were treated with zVAD.fmk, the indicated growth factors, and Nec-1 under serum free conditions for 24 hrs followed by measurement of cell viability. (C) Cells under serum free conditions were treated with FGF, zVAD.fmk, or both for 24 hrs followed by viability assay. (D) Cell death was induced by zVAD.fmk or TNFα under full serum condition in the presence of 2 µM PD173074 and 20 µM PD166866. In all graphs, average±SD was plotted. Previously we described the development of 7-Cl-O-Nec-1 (Nec-1) as a potent and selective inhibitor of RIP1 kinase and necroptosis (Fig. S1A) [23], [24]. Recently, its selectivity has been further validated against a panel of more than 400 human kinases [15]. This inhibitor efficiently blocked growth factor/zVAD.fmk-induced necroptosis under serum free conditions in L929 cells and both zVAD.fmk and TNFα-induced necroptosis under full serum conditions (Fig. 1B, S1B). To further validate the role of RIP1, we used an inactive analog, 7-Cl-O-Nec-1i (Nec-1i) (Fig. S1A), which contains an extra N-methyl group that leads to almost complete loss of RIP1 kinase inhibitory activity in vitro [23]. Nec-1i was unable to protect L929 cell death under serum condtions treated with zVAD.fmk or TNFα (Fig. S1B) or serum free conditions treated with bFGF/zVAD.fmk (Fig. S1C). This confirms that RIP1 kinase is responsible for necroptosis in L929 cells under both serum and serum free conditions.\nWe next examined whether bFGF contributes to zVAD.fmk-induced necroptosis under normal serum conditions (10% FBS). We used two bFGF receptor tyrosine kinase inhibitors (PD173074 and PD166866), and determined that inhibition of bFGF signaling strongly inhibited zVAD.fmk-induced necroptosis under normal serum conditions (Fig. 1D). In contrast, neither bFGF receptor inhibitor was able to attenuate TNFα-induced necroptosis (Fig. 1D), consistent with growth factors being dispensable for this pathway (Fig. 1A). Overall, these data suggest that the induction of necroptosis by zVAD.fmk is promoted by bFGF under both serum and serum free conditions. The induction of necroptosis, however, is not a simple consequence of growth factor signaling since not all growth factors allowed death to occur. Instead, specific signaling events mediated by particular growth factors appear to contribute to necroptotic death."}

GO-CC

{"project":"GO-CC","denotations":[{"id":"T28528","span":{"begin":2753,"end":2757},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T28527","span":{"begin":2254,"end":2258},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T28526","span":{"begin":2158,"end":2163},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3170","span":{"begin":3853,"end":3858},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3169","span":{"begin":3289,"end":3294},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3168","span":{"begin":2037,"end":2042},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3167","span":{"begin":1334,"end":1339},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3166","span":{"begin":1248,"end":1253},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3165","span":{"begin":978,"end":983},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3164","span":{"begin":926,"end":931},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3163","span":{"begin":379,"end":384},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T3162","span":{"begin":119,"end":124},"obj":"http://purl.obolibrary.org/obo/GO_0005623"}],"text":"Basic Fibroblast Growth Factor Promotes Necroptosis in L929 Cells\nIt has been established that mouse fibrosarcoma L929 cells undergo necroptotic cell death following stimulation with TNFα [10], [17]. In addition, inhibition of caspase-8 activity alone, either through siRNA knockdown or by using the pan-caspase inhibitor, zVAD.fmk, is sufficient to trigger necroptosis in these cells [10], [14]. Interestingly, while necroptosis was initially identified as a back-up form of cell death triggered by pro-apoptotic stimuli in the presence of apoptosis inhibitors [17], recent analysis of physiological cell death during mouse development has suggested that the loss of apoptotic regulators, such as caspase-8 and FADD [18], [19], [20], leads to robust induction of necroptosis and death of E10.5 embryos even though apoptosis is not normally induced in wild type embryos. These data are reminiscent of the observations in L929 cells where the loss of caspase activity in healthy cells is sufficient to trigger necroptosis and prompted us to explore the extrinsic or intrinsic cellular factors that promote necroptosis once caspase-8 activity, which cleaves and inactivates RIP1 kinase and the RIP1 deubiquitinase CYLD [21], [22], is removed in L929 cells. Consistent with a previous report [16], we found that serum starvation of L929 cells prevented necroptosis in response to zVAD.fmk (Fig. 1A). The addition of growth factors, such as bFGF, restored zVAD.fmk induced death under serum free conditions (Fig. 1B). Interestingly, this does not reflect a generic requirement for growth factor signaling, as only some growth factors (bFGF and IGF-1, but not EGF and PDGF) promoted death (Fig. 1B). Furthermore, growth factor-dependent necroptosis required the inhibition of caspase activity, as bFGF alone did not induce cell death (Fig. 1C). In contrast, TNFα triggered necroptosis equally efficiently in the absence of serum (Fig. 1A), suggesting that either growth factors and zVAD.fmk or TNFα are required for necroptotic death in L929 cells.\n10.1371/journal.pone.0056576.g001 Figure 1 bFGF and IGF-1 promote necroptosis in concert with zVAD.fmk.\n(A) L929 cells were treated with TNFα or zVAD.fmk under normal serum (10% FBS) or serum free conditions. Cell viability was determined after 24 hr using the CellTiter-Glo Viability assay. The concentrations of all necroptosis-inducing agents are listed in the Materials and Methods section or indicated in the figures. (B) Cells were treated with zVAD.fmk, the indicated growth factors, and Nec-1 under serum free conditions for 24 hrs followed by measurement of cell viability. (C) Cells under serum free conditions were treated with FGF, zVAD.fmk, or both for 24 hrs followed by viability assay. (D) Cell death was induced by zVAD.fmk or TNFα under full serum condition in the presence of 2 µM PD173074 and 20 µM PD166866. In all graphs, average±SD was plotted. Previously we described the development of 7-Cl-O-Nec-1 (Nec-1) as a potent and selective inhibitor of RIP1 kinase and necroptosis (Fig. S1A) [23], [24]. Recently, its selectivity has been further validated against a panel of more than 400 human kinases [15]. This inhibitor efficiently blocked growth factor/zVAD.fmk-induced necroptosis under serum free conditions in L929 cells and both zVAD.fmk and TNFα-induced necroptosis under full serum conditions (Fig. 1B, S1B). To further validate the role of RIP1, we used an inactive analog, 7-Cl-O-Nec-1i (Nec-1i) (Fig. S1A), which contains an extra N-methyl group that leads to almost complete loss of RIP1 kinase inhibitory activity in vitro [23]. Nec-1i was unable to protect L929 cell death under serum condtions treated with zVAD.fmk or TNFα (Fig. S1B) or serum free conditions treated with bFGF/zVAD.fmk (Fig. S1C). This confirms that RIP1 kinase is responsible for necroptosis in L929 cells under both serum and serum free conditions.\nWe next examined whether bFGF contributes to zVAD.fmk-induced necroptosis under normal serum conditions (10% FBS). We used two bFGF receptor tyrosine kinase inhibitors (PD173074 and PD166866), and determined that inhibition of bFGF signaling strongly inhibited zVAD.fmk-induced necroptosis under normal serum conditions (Fig. 1D). In contrast, neither bFGF receptor inhibitor was able to attenuate TNFα-induced necroptosis (Fig. 1D), consistent with growth factors being dispensable for this pathway (Fig. 1A). Overall, these data suggest that the induction of necroptosis by zVAD.fmk is promoted by bFGF under both serum and serum free conditions. The induction of necroptosis, however, is not a simple consequence of growth factor signaling since not all growth factors allowed death to occur. Instead, specific signaling events mediated by particular growth factors appear to contribute to necroptotic death."}

sentences

simple1

BioNLP16_DUT

BioNLP16_Messiy

DLUT931

bionlp-st-ge-2016-test-ihmc

bionlp-st-ge-2016-spacy-parsed

bionlp-st-ge-2016-test-tees

test3

PMC:3585731 / 5289-10103 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:3585731 / 5289-10103 JSON TXT