The proposed ODE model describes dynamics of IFNalpha-induced signaling in Huh7.5 cells for a time scale up to 32 hours after stimulation with IFNalpha. The model consists of an IFN receptor model, formation/degradation and cytoplasmic/nuclear shuttling of STAT1-homodimers, STAT1-STAT2-heterodimers and STAT1-STAT2-IRF9 (ISGF3) complexes. On top, formation of feedback proteins STAT1, STAT2, IRF9, USP18, SOCS1, SOCS3 and IRF2 and corresponding influences on IFNalpha signaling dynamics was incorporated. The model was calibrated by dose response and time course measurements over 32 hours as well as time courses for USP18 inhibition and overexpression experiments. As a special focus, the model is able to describe dose-dependent sensitization and desensitization of IFNalpha signaling in form of double treatment experiments at 0h and 24h.
Tiwari Krishna tiwarik@babraham.ac.uk Babraham Institute Rosenblatt Marcus University of Freiburg 2019-04-15T11:53:40Z 2019-04-15T14:39:56Z 2019-04-15T11:53:40Z Rosenblatt Marcus University of Freiburg tiwarik@babraham.ac.uk Tiwari Krishna Babraham Institute 2019-04-15T14:39:56Z 2020-08-11T15:41:04Z v v 2019-04-15T17:15:41Z genOccGASbsBySTAT1dimn pSTAT1dimn genOccGASbsBySTAT1dimn pSTAT1dimn 2019-04-15T17:14:18Z genOccGAS_ISREbsBySTAT1STAT2n pSTAT1pSTAT2n genOccGAS_ISREbsBySTAT1STAT2n pSTAT1pSTAT2n 2020-08-11T15:41:49Z Rec SOCS1 degRecBySOCS degRecBySOCS Rec SOCS1 2020-08-11T15:41:49Z BindIFN IFN Rec SOCS1 SOCS3 USP18 kinhBySOCS kinhByUSP18 BindIFN IFN Rec 1 kinhBySOCS SOCS1 1 kinhByUSP18 USP18 SOCS3 2020-08-11T15:41:49Z SOCS1 aRecIFN degaRecIFNBySOCS aRecIFN degaRecIFNBySOCS SOCS1 2020-08-11T15:41:49Z USP18 aRecIFN degByUSP18 aRecIFN degByUSP18 USP18 2020-08-11T15:41:49Z SOCS1 USP18 aRecIFN degBySOCSandUSP18 aRecIFN degBySOCSandUSP18 SOCS1 USP18 2020-08-11T15:41:49Z ComplFormSTAT1STAT2c STAT1c STAT2c aRecIFN ComplFormSTAT1STAT2c aRecIFN STAT1c STAT2c 2020-08-11T15:41:49Z ComplFormSTAT1dimc STAT1c aRecIFN ComplFormSTAT1dimc aRecIFN STAT1c STAT1c 2020-08-11T15:41:49Z ISGF3n genOccGAS_ISREbsByISGF3n genOccGAS_ISREbsByISGF3n ISGF3n 2020-08-11T15:41:49Z SOCS3mRNA synthSOCS3 synthSOCS3 SOCS3mRNA 2020-08-11T15:41:49Z OccGAS_ISREbs kmSTAT1 synthSTAT1mRNA synthSTAT1mRNA OccGAS_ISREbs kmSTAT1 OccGAS_ISREbs 2020-08-11T15:41:49Z OccGAS_ISREbs synthSTAT2mRNA synthSTAT2mRNA OccGAS_ISREbs 2020-08-11T15:41:49Z OccGAS_ISREbs kmIRF9 synthIRF9mRNA synthIRF9mRNA OccGAS_ISREbs kmIRF9 OccGAS_ISREbs 2020-08-11T15:41:49Z OccGAS_ISREbs synthIRF2mRNA synthIRF2mRNA OccGAS_ISREbs 2020-08-11T15:41:49Z OccGAS_ISREbs synthUSP18mRNA synthUSP18mRNA OccGAS_ISREbs 2020-08-11T15:41:49Z OccGAS_ISREbs synthSOCS1mRNA synthSOCS1mRNA OccGAS_ISREbs 2020-08-11T15:41:49Z IRF2 SOCS1mRNA hlSOCS1mRNA hlSOCS1mRNA SOCS1mRNA 1 IRF2 2020-08-11T15:41:49Z OccGASbs synthSOCS3mRNA synthSOCS3mRNA OccGASbs 2020-08-11T15:41:49Z STAT1mRNA kmsynthSTAT1 synthSTAT1 synthSTAT1 STAT1mRNA kmsynthSTAT1 STAT1mRNA 2020-08-11T15:41:49Z STAT2mRNA synthSTAT2 synthSTAT2 STAT2mRNA 2020-08-11T15:41:49Z IRF9mRNA synthIRF9 synthIRF9 IRF9mRNA 2020-08-11T15:41:49Z USP18mRNA synthUSP18 synthUSP18 USP18mRNA 2020-08-11T15:41:49Z SOCS1mRNA synthSOCS1 synthSOCS1 SOCS1mRNA 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2019-04-16T08:57:26Z 2020-08-17T14:00:27Z 2020-08-17T14:05:13Z 2020-08-17T14:07:20Z 2020-08-17T14:07:20Z 2020-08-17T14:07:21Z 2020-08-17T14:07:21Z 2020-08-17T14:07:22Z 10 IRF2mRNA 10 IRF9mRNA 10 STAT1mRNA 10 STAT2mRNA 10 USP18mRNA 10 SOCS1mRNA 10 SOCS3mRNA 2019-04-15T14:20:15Z compartment Constant_flux__irreversible v 2019-04-15T14:23:40Z compartment k1 Rec 2019-04-15T14:27:17Z compartment Receptor_degradation_by_SOCS1_1 Rec SOCS1 degRecBySOCS 2019-04-15T16:31:54Z compartment Active_receptor_complex_formation_1 BindIFN IFN Rec SOCS1 SOCS3 USP18 kinhBySOCS kinhByUSP18 2019-04-15T19:44:50Z compartment k1 aRecIFN 2019-04-15T19:45:04Z compartment Active_receptor_complex_degradation_by_SOCS1_1 SOCS1 aRecIFN degaRecIFNBySOCS 2019-04-15T19:45:18Z compartment Active_receptor_complex_degradation_by_USP18_1 USP18 aRecIFN degByUSP18 2019-04-15T19:45:28Z compartment Active_receptor_complex_degradation_by_USP18_and_SOCS1__synergy__1 SOCS1 USP18 aRecIFN degBySOCSandUSP18 2019-04-15T19:17:06Z compartment k1 USP18 2019-04-15T19:01:23Z compartment Heterodimer_complex_formation_1 ComplFormSTAT1STAT2c STAT1c STAT2c aRecIFN 2019-04-15T19:01:48Z compartment k1 pSTAT1pSTAT2c 2019-04-15T19:01:33Z compartment k1 pSTAT1pSTAT2n 2019-04-15T19:05:14Z compartment k1 pSTAT1pSTAT2c IRF9c 2019-04-15T19:05:57Z compartment k1 ISGF3c 2019-04-15T19:05:38Z compartment k1 ISGF3n 2019-04-15T19:02:00Z compartment Homodimer_complex_formation_1 ComplFormSTAT1dimc STAT1c aRecIFN 2019-04-15T19:02:28Z compartment k1 pSTAT1dimc 2019-04-15T19:02:19Z compartment k1 pSTAT1dimn 2019-04-15T19:08:54Z compartment OccGAS_ISREbs_formation_by_ISGF3_1 ISGF3n genOccGAS_ISREbsByISGF3n 2019-04-15T19:08:34Z compartment OccGAS_ISREbs_formation_by_heterodimer_0 genOccGAS_ISREbsBySTAT1STAT2n pSTAT1pSTAT2n 2019-04-15T19:08:22Z compartment k1 OccGAS_ISREbs 2019-04-15T19:09:19Z compartment Occupy_GAS_binding_site_0 genOccGASbsBySTAT1dimn pSTAT1dimn 2019-04-15T19:08:12Z compartment k1 OccGASbs 2019-04-15T19:13:42Z compartment k1 STAT1c 2019-04-15T19:14:10Z compartment k1 STAT1n 2019-04-15T19:14:20Z compartment k1 STAT1c 2019-04-15T19:15:42Z compartment k1 STAT2c 2019-04-15T19:15:50Z compartment k1 STAT2n 2019-04-15T19:15:59Z compartment k1 STAT2c 2019-04-15T19:04:08Z compartment k1 IRF9n 2019-04-15T19:04:26Z compartment k1 IRF9c 2019-04-15T19:03:58Z compartment k1 IRF9c 2019-04-15T19:11:27Z compartment k1 SOCS1 2019-04-15T19:12:24Z compartment SOCS3_synthesis_1 SOCS3mRNA synthSOCS3 2019-04-15T19:12:25Z compartment k1 SOCS3 2019-04-15T19:14:01Z compartment Constant_flux__irreversible v 2019-04-15T19:14:49Z compartment STAT1mRNA_production_by_ISRE_1 OccGAS_ISREbs kmSTAT1 synthSTAT1mRNA 2019-04-15T19:14:38Z compartment k1 STAT1mRNA 2019-04-15T19:16:07Z compartment Constant_flux__irreversible v 2019-04-15T19:16:27Z compartment STAT2mRNA_production_by_ISRE_1 OccGAS_ISREbs synthSTAT2mRNA 2019-04-15T19:16:16Z compartment k1 STAT2mRNA 2019-04-15T19:04:35Z compartment Constant_flux__irreversible v 2019-04-15T19:05:01Z compartment IRF9mRNA_production_by_ISRE_1 OccGAS_ISREbs kmIRF9 synthIRF9mRNA 2019-04-15T19:04:46Z compartment k1 IRF9mRNA 2019-04-15T19:03:07Z compartment Constant_flux__irreversible v 2019-04-15T19:03:19Z compartment IRF2mRNA_production_by_ISRE_1 OccGAS_ISREbs synthIRF2mRNA 2019-04-15T19:02:53Z compartment k1 IRF2mRNA 2019-04-15T19:17:21Z compartment Constant_flux__irreversible v 2019-04-15T19:17:57Z compartment USP18mRNA_production_by_ISRE_1 OccGAS_ISREbs synthUSP18mRNA 2019-04-15T19:17:45Z compartment k1 USP18mRNA 2019-04-15T19:11:38Z compartment Constant_flux__irreversible v 2019-04-15T19:12:07Z compartment SOCS1mRNA_production_by_ISRE_1 OccGAS_ISREbs synthSOCS1mRNA 2019-04-15T19:11:37Z compartment SOCS1mRNA_decay_1 IRF2 SOCS1mRNA hlSOCS1mRNA 2019-04-15T19:10:00Z compartment Constant_flux__irreversible v 2019-04-15T19:13:10Z compartment SOCS3mRNA_production_by_ISRE_1 OccGASbs synthSOCS3mRNA 2019-04-15T19:12:52Z compartment k1 SOCS3mRNA 2019-04-15T19:02:36Z compartment k1 IRF2 2019-04-15T19:07:24Z compartment Linear_chain_for_time_delay_in_STAT1_translation_1 STAT1mRNA kmsynthSTAT1 synthSTAT1 2019-04-15T19:13:24Z compartment k1 STAT1_LC_1 2019-04-15T19:13:33Z compartment k1 STAT1_LC_2 2019-04-15T19:13:43Z compartment k1 STAT1_LC_3 2019-04-15T19:07:41Z compartment Linear_chain_for_time_delay_in_STAT2_translation_1 STAT2mRNA synthSTAT2 2019-04-15T19:15:03Z compartment k1 STAT2_LC_1 2019-04-15T19:15:11Z compartment k1 STAT2_LC_2 2019-04-15T19:15:20Z compartment k1 STAT2_LC_3 2019-04-15T19:15:27Z compartment k1 STAT2_LC_4 2019-04-15T19:15:34Z compartment k1 STAT2_LC_5 2019-04-15T19:06:06Z compartment Linear_chain_for_time_delay_in_IRF9_translation_1 IRF9mRNA synthIRF9 2019-04-15T19:03:29Z compartment k1 IRF9_LC_1 2019-04-15T19:03:46Z compartment k1 IRF9_LC_2 2019-04-15T19:07:57Z compartment Linear_chain_for_time_delay_in_USP18_translation_1 USP18mRNA synthUSP18 2019-04-15T19:16:47Z compartment k1 USP18_LC_1 2019-04-15T19:16:59Z compartment k1 USP18_LC_2 2019-04-15T19:06:36Z compartment Linear_chain_for_time_delay_in_SOCS1_translation_1 SOCS1mRNA synthSOCS1 2019-04-15T19:11:12Z compartment k1 SOCS1_LC_1