PMC:3585731 / 37015-41605 JSON TXT

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testone

2_test

{"project":"2_test","denotations":[{"id":"23469174-22695613-90505454","span":{"begin":2345,"end":2347},"obj":"22695613"},{"id":"23469174-19106158-90505455","span":{"begin":2828,"end":2830},"obj":"19106158"},{"id":"23469174-17850214-90505456","span":{"begin":2842,"end":2844},"obj":"17850214"},{"id":"23469174-22037377-90505457","span":{"begin":3080,"end":3082},"obj":"22037377"},{"id":"23469174-20539307-90505458","span":{"begin":3663,"end":3665},"obj":"20539307"},{"id":"23469174-15131264-90505459","span":{"begin":3669,"end":3671},"obj":"15131264"},{"id":"23469174-22695613-90505460","span":{"begin":3675,"end":3677},"obj":"22695613"},{"id":"23469174-19118012-90505461","span":{"begin":4455,"end":4457},"obj":"19118012"}],"text":"Model of RIP1, Akt and JNK Dependent Signaling in Necroptotic L929 Cells\nIn this study we investigated RIP1 kinase-dependent signaling pathways using mouse fibrosarcoma L929 cells that die by necroptosis when treated with the pan-caspase inhibitor zVAD.fmk. Altogether, our results suggest that Akt kinase is specifically engaged in signaling downstream from RIP1 kinase, which leads to a selective increase in its phosphorylation on Thr308, but not Ser473. According to our model (Fig. 9), necroptosis-associated phosphorylation of Akt requires two distinct signals. The first input, which is induced by growth factors, leads to the plasma membrane localization of Akt. Expression of a constitutively membrane-targeted Akt construct, Myr-Akt, overcomes the requirement for growth factors. At the same time, expression of Myr-Akt alone is not sufficient for the induction of necroptosis. A second, RIP1 kinase-dependent input is required for Thr308 phosphorylation of Akt in response to caspase inhibition and is essential for the propagation of the necroptotic signal.\n10.1371/journal.pone.0056576.g009 Figure 9 Model of RIP1, Akt and JNK dependent signaling in necroptotic L929 cells.\nAkt phosphorylation at Thr308 during necroptosis requires inputs from both growth factors and RIP1 kinase. Downstream from Akt, JNK activation leads to TNFα synthesis. Activation of Akt during necroptosis also leads the phosphorylation of several known Akt substrates, such as mTOR, which contribute to the execution of necroptotic death in L929 cells. Using Akt inhibitors, knockdown of Akt isoforms, and the expression of Akt mutants, we showed that necroptotic activation of Akt is indispensable for this form of cell death in L929 cells. We also investigated downstream Akt-dependent pathways that contribute to necroptosis. First, we demonstrated that selective necroptotic phosphorylation of Thr308 of Akt is sufficient to increase its activity towards a number of known substrates and Akt effector pathways such as the mTORC1 pathway, which, in turn, contributes to cell death. Second, our data suggested that Akt activation provides a pivotal link connecting RIP1 kinase to known downstream signaling and execution events in necroptotic L929 cells, namely, JNK activation and autocrine TNFα synthesis, a critical event in necroptosis in L929 cells [15].\nIn order to further test our model, we examined Akt phosphorylation after inhibition of a downstream kinase in the pathway, JNK. However, we found that SP600125, which protected L929 cells from death and inhibited TNFα production (Fig. 2A,B S2A S10A), inhibited both basal and post-treatment phosphorylation levels of Akt at both Ser473 and Thr308 (Fig. S10B). It has been published that SP600125 is a somewhat non-specific inhibitor that may inhibit the p110δ subunit of PI3K [41] and PDK1 [42]. Both of these off-target effects could inhibit basal Akt phosphorylation levels, precluding the use of SP600125 in this system.\nTherefore, to examine the role of JNK, we switched to a more specific JNK inhibitor, JNK inhibitor VIII [43], and siRNAs against JNK1 and JNK2 (Fig. S10B–G). As expected, specific inhibition or knockdown of JNK1/2 allowed phosphorylation of Akt on Thr308 while inhibiting the phosphorylation of c-Jun at Ser63 (Fig. S10B,E), agreeing with our model. It did not, however, lead to a reduction in TNFα production or cell death (Fig. S10C,D,F,G), suggesting that earlier data with SP600125 protection (Fig. 2) could reflect off-target effects of this molecule, rather than JNK inhibition. Previous reports also suggested a critical role for c-Jun in necroptosis and autocrine TNFα synthesis [13], [14], [15] and we confirmed these conclusions using c-Jun siRNA knockdown (Fig. S10H–J). Notably, in this case, Thr308 phosphorylation was reduced after the induction of necroptosis. Thus, autocrine TNFα production, dependent on c-Jun, may create a feedback loop that contributes to the delayed activation of Akt. It is also important to note that we observed an overall increase in the protein level of c-Jun after treatment of L929 cells with zVAD.fmk or TNFα, which was both Akt and mTOR-dependent (Fig. 6E,F). These new data led us to an unexpected, but important conclusion that c-Jun is critical for necroptosis, while JNK activity may serve as a useful marker of pathway activation, but may be either redundant (e.g. phosphorylation of c-Jun on a site other than Ser63 may occur [44]) or dispensable functionally. In addition, researchers need to use caution when using SP600125 due to potantial off-target effects."}

pmc-enju-pas

bionlp-st-ge-2016-coref

{"project":"bionlp-st-ge-2016-coref","denotations":[{"id":"T18387","span":{"begin":4039,"end":4047},"obj":"Antecedent"},{"id":"T18386","span":{"begin":4131,"end":4136},"obj":"Anaphor"}],"relations":[{"id":"R12163","pred":"boundBy","subj":"T18386","obj":"T18387"}],"namespaces":[{"prefix":"_base","uri":"https://bionlp.dbcls.jp/ontology/ge.owl#"}],"text":"Model of RIP1, Akt and JNK Dependent Signaling in Necroptotic L929 Cells\nIn this study we investigated RIP1 kinase-dependent signaling pathways using mouse fibrosarcoma L929 cells that die by necroptosis when treated with the pan-caspase inhibitor zVAD.fmk. Altogether, our results suggest that Akt kinase is specifically engaged in signaling downstream from RIP1 kinase, which leads to a selective increase in its phosphorylation on Thr308, but not Ser473. According to our model (Fig. 9), necroptosis-associated phosphorylation of Akt requires two distinct signals. The first input, which is induced by growth factors, leads to the plasma membrane localization of Akt. Expression of a constitutively membrane-targeted Akt construct, Myr-Akt, overcomes the requirement for growth factors. At the same time, expression of Myr-Akt alone is not sufficient for the induction of necroptosis. A second, RIP1 kinase-dependent input is required for Thr308 phosphorylation of Akt in response to caspase inhibition and is essential for the propagation of the necroptotic signal.\n10.1371/journal.pone.0056576.g009 Figure 9 Model of RIP1, Akt and JNK dependent signaling in necroptotic L929 cells.\nAkt phosphorylation at Thr308 during necroptosis requires inputs from both growth factors and RIP1 kinase. Downstream from Akt, JNK activation leads to TNFα synthesis. Activation of Akt during necroptosis also leads the phosphorylation of several known Akt substrates, such as mTOR, which contribute to the execution of necroptotic death in L929 cells. Using Akt inhibitors, knockdown of Akt isoforms, and the expression of Akt mutants, we showed that necroptotic activation of Akt is indispensable for this form of cell death in L929 cells. We also investigated downstream Akt-dependent pathways that contribute to necroptosis. First, we demonstrated that selective necroptotic phosphorylation of Thr308 of Akt is sufficient to increase its activity towards a number of known substrates and Akt effector pathways such as the mTORC1 pathway, which, in turn, contributes to cell death. Second, our data suggested that Akt activation provides a pivotal link connecting RIP1 kinase to known downstream signaling and execution events in necroptotic L929 cells, namely, JNK activation and autocrine TNFα synthesis, a critical event in necroptosis in L929 cells [15].\nIn order to further test our model, we examined Akt phosphorylation after inhibition of a downstream kinase in the pathway, JNK. However, we found that SP600125, which protected L929 cells from death and inhibited TNFα production (Fig. 2A,B S2A S10A), inhibited both basal and post-treatment phosphorylation levels of Akt at both Ser473 and Thr308 (Fig. S10B). It has been published that SP600125 is a somewhat non-specific inhibitor that may inhibit the p110δ subunit of PI3K [41] and PDK1 [42]. Both of these off-target effects could inhibit basal Akt phosphorylation levels, precluding the use of SP600125 in this system.\nTherefore, to examine the role of JNK, we switched to a more specific JNK inhibitor, JNK inhibitor VIII [43], and siRNAs against JNK1 and JNK2 (Fig. S10B–G). As expected, specific inhibition or knockdown of JNK1/2 allowed phosphorylation of Akt on Thr308 while inhibiting the phosphorylation of c-Jun at Ser63 (Fig. S10B,E), agreeing with our model. It did not, however, lead to a reduction in TNFα production or cell death (Fig. S10C,D,F,G), suggesting that earlier data with SP600125 protection (Fig. 2) could reflect off-target effects of this molecule, rather than JNK inhibition. Previous reports also suggested a critical role for c-Jun in necroptosis and autocrine TNFα synthesis [13], [14], [15] and we confirmed these conclusions using c-Jun siRNA knockdown (Fig. S10H–J). Notably, in this case, Thr308 phosphorylation was reduced after the induction of necroptosis. Thus, autocrine TNFα production, dependent on c-Jun, may create a feedback loop that contributes to the delayed activation of Akt. It is also important to note that we observed an overall increase in the protein level of c-Jun after treatment of L929 cells with zVAD.fmk or TNFα, which was both Akt and mTOR-dependent (Fig. 6E,F). These new data led us to an unexpected, but important conclusion that c-Jun is critical for necroptosis, while JNK activity may serve as a useful marker of pathway activation, but may be either redundant (e.g. phosphorylation of c-Jun on a site other than Ser63 may occur [44]) or dispensable functionally. In addition, researchers need to use caution when using SP600125 due to potantial off-target effects."}

bionlp-st-ge-2016-test-proteins

bionlp-st-ge-2016-uniprot

GO-BP

GO-MF

{"project":"GO-MF","denotations":[{"id":"T18473","span":{"begin":2474,"end":2477},"obj":"http://purl.obolibrary.org/obo/GO_0004705"},{"id":"T18472","span":{"begin":2253,"end":2256},"obj":"http://purl.obolibrary.org/obo/GO_0004705"},{"id":"T18471","span":{"begin":23,"end":26},"obj":"http://purl.obolibrary.org/obo/GO_0004705"},{"id":"T18480","span":{"begin":2836,"end":2840},"obj":"http://purl.obolibrary.org/obo/GO_0004740"},{"id":"T18479","span":{"begin":2822,"end":2826},"obj":"http://purl.obolibrary.org/obo/GO_0016303"},{"id":"T18478","span":{"begin":4293,"end":4296},"obj":"http://purl.obolibrary.org/obo/GO_0004705"},{"id":"T18477","span":{"begin":3544,"end":3547},"obj":"http://purl.obolibrary.org/obo/GO_0004705"},{"id":"T18476","span":{"begin":3060,"end":3063},"obj":"http://purl.obolibrary.org/obo/GO_0004705"},{"id":"T18475","span":{"begin":3045,"end":3048},"obj":"http://purl.obolibrary.org/obo/GO_0004705"},{"id":"T18474","span":{"begin":3009,"end":3012},"obj":"http://purl.obolibrary.org/obo/GO_0004705"},{"id":"T32326","span":{"begin":1316,"end":1319},"obj":"http://purl.obolibrary.org/obo/GO_0004705"},{"id":"T32325","span":{"begin":1137,"end":1140},"obj":"http://purl.obolibrary.org/obo/GO_0004705"}],"text":"Model of RIP1, Akt and JNK Dependent Signaling in Necroptotic L929 Cells\nIn this study we investigated RIP1 kinase-dependent signaling pathways using mouse fibrosarcoma L929 cells that die by necroptosis when treated with the pan-caspase inhibitor zVAD.fmk. Altogether, our results suggest that Akt kinase is specifically engaged in signaling downstream from RIP1 kinase, which leads to a selective increase in its phosphorylation on Thr308, but not Ser473. According to our model (Fig. 9), necroptosis-associated phosphorylation of Akt requires two distinct signals. The first input, which is induced by growth factors, leads to the plasma membrane localization of Akt. Expression of a constitutively membrane-targeted Akt construct, Myr-Akt, overcomes the requirement for growth factors. At the same time, expression of Myr-Akt alone is not sufficient for the induction of necroptosis. A second, RIP1 kinase-dependent input is required for Thr308 phosphorylation of Akt in response to caspase inhibition and is essential for the propagation of the necroptotic signal.\n10.1371/journal.pone.0056576.g009 Figure 9 Model of RIP1, Akt and JNK dependent signaling in necroptotic L929 cells.\nAkt phosphorylation at Thr308 during necroptosis requires inputs from both growth factors and RIP1 kinase. Downstream from Akt, JNK activation leads to TNFα synthesis. Activation of Akt during necroptosis also leads the phosphorylation of several known Akt substrates, such as mTOR, which contribute to the execution of necroptotic death in L929 cells. Using Akt inhibitors, knockdown of Akt isoforms, and the expression of Akt mutants, we showed that necroptotic activation of Akt is indispensable for this form of cell death in L929 cells. We also investigated downstream Akt-dependent pathways that contribute to necroptosis. First, we demonstrated that selective necroptotic phosphorylation of Thr308 of Akt is sufficient to increase its activity towards a number of known substrates and Akt effector pathways such as the mTORC1 pathway, which, in turn, contributes to cell death. Second, our data suggested that Akt activation provides a pivotal link connecting RIP1 kinase to known downstream signaling and execution events in necroptotic L929 cells, namely, JNK activation and autocrine TNFα synthesis, a critical event in necroptosis in L929 cells [15].\nIn order to further test our model, we examined Akt phosphorylation after inhibition of a downstream kinase in the pathway, JNK. However, we found that SP600125, which protected L929 cells from death and inhibited TNFα production (Fig. 2A,B S2A S10A), inhibited both basal and post-treatment phosphorylation levels of Akt at both Ser473 and Thr308 (Fig. S10B). It has been published that SP600125 is a somewhat non-specific inhibitor that may inhibit the p110δ subunit of PI3K [41] and PDK1 [42]. Both of these off-target effects could inhibit basal Akt phosphorylation levels, precluding the use of SP600125 in this system.\nTherefore, to examine the role of JNK, we switched to a more specific JNK inhibitor, JNK inhibitor VIII [43], and siRNAs against JNK1 and JNK2 (Fig. S10B–G). As expected, specific inhibition or knockdown of JNK1/2 allowed phosphorylation of Akt on Thr308 while inhibiting the phosphorylation of c-Jun at Ser63 (Fig. S10B,E), agreeing with our model. It did not, however, lead to a reduction in TNFα production or cell death (Fig. S10C,D,F,G), suggesting that earlier data with SP600125 protection (Fig. 2) could reflect off-target effects of this molecule, rather than JNK inhibition. Previous reports also suggested a critical role for c-Jun in necroptosis and autocrine TNFα synthesis [13], [14], [15] and we confirmed these conclusions using c-Jun siRNA knockdown (Fig. S10H–J). Notably, in this case, Thr308 phosphorylation was reduced after the induction of necroptosis. Thus, autocrine TNFα production, dependent on c-Jun, may create a feedback loop that contributes to the delayed activation of Akt. It is also important to note that we observed an overall increase in the protein level of c-Jun after treatment of L929 cells with zVAD.fmk or TNFα, which was both Akt and mTOR-dependent (Fig. 6E,F). These new data led us to an unexpected, but important conclusion that c-Jun is critical for necroptosis, while JNK activity may serve as a useful marker of pathway activation, but may be either redundant (e.g. phosphorylation of c-Jun on a site other than Ser63 may occur [44]) or dispensable functionally. In addition, researchers need to use caution when using SP600125 due to potantial off-target effects."}

GO-CC

{"project":"GO-CC","denotations":[{"id":"T32328","span":{"begin":1534,"end":1539},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T32327","span":{"begin":1181,"end":1186},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T18490","span":{"begin":2014,"end":2020},"obj":"http://purl.obolibrary.org/obo/GO_0031931"},{"id":"T18489","span":{"begin":702,"end":710},"obj":"http://purl.obolibrary.org/obo/GO_0016020"},{"id":"T18488","span":{"begin":641,"end":649},"obj":"http://purl.obolibrary.org/obo/GO_0016020"},{"id":"T18487","span":{"begin":634,"end":649},"obj":"http://purl.obolibrary.org/obo/GO_0005886"},{"id":"T18482","span":{"begin":1723,"end":1728},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T18481","span":{"begin":174,"end":179},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T18486","span":{"begin":4102,"end":4107},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T18485","span":{"begin":2533,"end":2538},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T18484","span":{"begin":2338,"end":2343},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T18483","span":{"begin":2238,"end":2243},"obj":"http://purl.obolibrary.org/obo/GO_0005623"}],"text":"Model of RIP1, Akt and JNK Dependent Signaling in Necroptotic L929 Cells\nIn this study we investigated RIP1 kinase-dependent signaling pathways using mouse fibrosarcoma L929 cells that die by necroptosis when treated with the pan-caspase inhibitor zVAD.fmk. Altogether, our results suggest that Akt kinase is specifically engaged in signaling downstream from RIP1 kinase, which leads to a selective increase in its phosphorylation on Thr308, but not Ser473. According to our model (Fig. 9), necroptosis-associated phosphorylation of Akt requires two distinct signals. The first input, which is induced by growth factors, leads to the plasma membrane localization of Akt. Expression of a constitutively membrane-targeted Akt construct, Myr-Akt, overcomes the requirement for growth factors. At the same time, expression of Myr-Akt alone is not sufficient for the induction of necroptosis. A second, RIP1 kinase-dependent input is required for Thr308 phosphorylation of Akt in response to caspase inhibition and is essential for the propagation of the necroptotic signal.\n10.1371/journal.pone.0056576.g009 Figure 9 Model of RIP1, Akt and JNK dependent signaling in necroptotic L929 cells.\nAkt phosphorylation at Thr308 during necroptosis requires inputs from both growth factors and RIP1 kinase. Downstream from Akt, JNK activation leads to TNFα synthesis. Activation of Akt during necroptosis also leads the phosphorylation of several known Akt substrates, such as mTOR, which contribute to the execution of necroptotic death in L929 cells. Using Akt inhibitors, knockdown of Akt isoforms, and the expression of Akt mutants, we showed that necroptotic activation of Akt is indispensable for this form of cell death in L929 cells. We also investigated downstream Akt-dependent pathways that contribute to necroptosis. First, we demonstrated that selective necroptotic phosphorylation of Thr308 of Akt is sufficient to increase its activity towards a number of known substrates and Akt effector pathways such as the mTORC1 pathway, which, in turn, contributes to cell death. Second, our data suggested that Akt activation provides a pivotal link connecting RIP1 kinase to known downstream signaling and execution events in necroptotic L929 cells, namely, JNK activation and autocrine TNFα synthesis, a critical event in necroptosis in L929 cells [15].\nIn order to further test our model, we examined Akt phosphorylation after inhibition of a downstream kinase in the pathway, JNK. However, we found that SP600125, which protected L929 cells from death and inhibited TNFα production (Fig. 2A,B S2A S10A), inhibited both basal and post-treatment phosphorylation levels of Akt at both Ser473 and Thr308 (Fig. S10B). It has been published that SP600125 is a somewhat non-specific inhibitor that may inhibit the p110δ subunit of PI3K [41] and PDK1 [42]. Both of these off-target effects could inhibit basal Akt phosphorylation levels, precluding the use of SP600125 in this system.\nTherefore, to examine the role of JNK, we switched to a more specific JNK inhibitor, JNK inhibitor VIII [43], and siRNAs against JNK1 and JNK2 (Fig. S10B–G). As expected, specific inhibition or knockdown of JNK1/2 allowed phosphorylation of Akt on Thr308 while inhibiting the phosphorylation of c-Jun at Ser63 (Fig. S10B,E), agreeing with our model. It did not, however, lead to a reduction in TNFα production or cell death (Fig. S10C,D,F,G), suggesting that earlier data with SP600125 protection (Fig. 2) could reflect off-target effects of this molecule, rather than JNK inhibition. Previous reports also suggested a critical role for c-Jun in necroptosis and autocrine TNFα synthesis [13], [14], [15] and we confirmed these conclusions using c-Jun siRNA knockdown (Fig. S10H–J). Notably, in this case, Thr308 phosphorylation was reduced after the induction of necroptosis. Thus, autocrine TNFα production, dependent on c-Jun, may create a feedback loop that contributes to the delayed activation of Akt. It is also important to note that we observed an overall increase in the protein level of c-Jun after treatment of L929 cells with zVAD.fmk or TNFα, which was both Akt and mTOR-dependent (Fig. 6E,F). These new data led us to an unexpected, but important conclusion that c-Jun is critical for necroptosis, while JNK activity may serve as a useful marker of pathway activation, but may be either redundant (e.g. phosphorylation of c-Jun on a site other than Ser63 may occur [44]) or dispensable functionally. In addition, researchers need to use caution when using SP600125 due to potantial off-target effects."}

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 / 37015-41605 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:3585731 / 37015-41605 JSON TXT