Systems models of biological networks show promise for informing drug target selection/qualification, identifying lead compounds and factors regulating disease progression, rationalizing combinatorial regimens, and explaining sources of intersubject variability and adverse drug reactions. However, most models of biological systems are qualitative and are not easily coupled with dynamical models of drug exposure-response relationships. In this proof-of-concept study, logic-based modeling of signal transduction pathways in U266 multiple myeloma (MM) cells is used to guide the development of a simple dynamical model linking bortezomib exposure to cellular outcomes. Bortezomib is a commonly used first-line agent in MM treatment; however, knowledge of the signal transduction pathways regulating bortezomib-mediated cell cytotoxicity is incomplete. A Boolean network model of 66 nodes was constructed that includes major survival and apoptotic pathways and was updated using responses to several chemical probes. Simulated responses to bortezomib were in good agreement with experimental data, and a reduction algorithm was used to identify key signaling proteins. Bortezomib-mediated apoptosis was not associated with suppression of nuclear factor κB (NFκB) protein inhibition in this cell line, which contradicts a major hypothesis of bortezomib pharmacodynamics. A pharmacodynamic model was developed that included three critical proteins (phospho-NFκB, BclxL, and cleaved poly (ADP ribose) polymerase). Model-fitted protein dynamics and cell proliferation profiles agreed with experimental data, and the model-predicted IC50 (3.5 nM) is comparable to the experimental value (1.5 nM). The cell-based pharmacodynamic model successfully links bortezomib exposure to MM cellular proliferation via protein dynamics, and this model may show utility in exploring bortezomib-based combination regimens. Bird Shannyn birdgirl@arcticmail.com University of Nebraska-Lincoln 2016-09-14T09:01:51Z 2018-03-27T15:46:39Z

Name: Tumor necrosis factor alpha

Gene Name: TNF

UNIPROT ID: P01375

Gene ID: 7124

2017-03-09T18:20:42Z

Name: dummy factor

2017-03-22T14:50:28Z

Name: Tumor necrosis factor receptor alpha

Gene Name: TRAF2

UNIPROT ID: Q12933

Gene ID: 7132

2017-03-09T18:20:42Z

Name: Bortezomib

proteasome inhibitor

Used in the treatment of multiple myeloma

2017-03-22T14:50:28Z

Name: protein tyrosine phosphatase

Gene Name: PTPN6

UNIPROT ID: P29350

Gene ID: 5777

2017-03-09T18:20:42Z

Name: retinoblastoma

Gene Name: RB1

UNIPROT ID: P06400

Gene ID: 5925

This node refers to pRB in its hyperphosphorylated state.

2016-10-18T15:05:40Z

Name: Caspase 9

Gene Name: CASP9

UNIPROT ID: P55211

Gene ID: 842

2016-09-16T08:18:47Z

Name: p53 tumor suppressor

Gene Name: TP53

UNIPROT ID: P04637

Gene ID: 7157

2016-09-16T08:18:47Z

Name: ataxia telangiectasia mutated

Gene Name: ATM

UNIPROT ID: Q13315

Gene ID: 472

2016-09-16T08:18:47Z

Name: TNF receptor superfamily member 6

Gene Name: FAS

UNIPROT ID: P25445

Gene ID: 355

2017-03-23T15:36:47Z

Name: MEK kinase 2

Gene Name: MAP3K2

UNIPROT ID: Q9Y2U5

Gene ID: 10746

2016-09-16T08:18:47Z
2016-10-18T15:13:58Z

Name: Apoptosis

Programmed cell death

2016-09-16T08:18:47Z

Name: Phospho-nuclear factor kappa B

2017-03-17T12:34:43Z

Name: B-cell linked protein extra large

Gene Name: BCL2L1

UNIPROT ID: Q07817

Gene ID: 598

2016-10-18T15:05:40Z

Name: cyclin-dependent kinase inhibitor 1A

Gene Name: CDKN1A

UNIPROT ID: P38936

Gene ID: 1026

2017-03-22T13:36:51Z

Name: MEK kinase

Gene Name: MAP3K1

UNIPROT ID: Q13233

Gene ID: 4214

2016-10-18T15:11:39Z

Name: Cyclin E

Gene Name: CCNE1

UNIPROT ID: P24864

Gene ID: 898

2016-10-18T15:05:40Z

Name: Caspase 8

Gene Name: CASP8

UNIPROT ID: Q14790

Gene ID: 841

2017-03-23T15:36:47Z

Name: Janus associated kinase 1

Gene Name: JAK2

UNIPROT ID: O60674

Gene ID: 3717

2016-10-18T15:05:40Z

Name: c-jun transcription factor

Gene Name: JUN

UNIPROT ID: P05412

Gene ID: 3725

2016-09-16T08:18:47Z

Name: Cyclin dependent kinase 4

Gene Name: CDK4

UNIPROT ID: P11802

Gene ID: 1019

2016-10-18T15:13:58Z

Name: c-Jun N-terminal kinase

Gene Name: MAPK8

UNIPROT ID: P45983

Gene ID: 5599

2016-09-16T08:18:47Z

Name: cellular stress induced by proteasome inhibition

2016-10-18T16:35:07Z

Name: cyclin-dependent kinase inhibitor 1B

Gene Name: CDKN18

UNIPROT ID: P46527

Gene ID: 1027

2016-09-14T09:48:27Z

Name: NFκB-inducing kinase

Gene Name: MAP3K14

UNIPROT ID: Q99558

Gene ID: 9020

2016-10-18T15:05:40Z

Name: mitogen-activated protein kinase

Gene Name: MAPK1

UNIPROT ID: P28482

Gene ID: 5594

2016-10-18T15:11:39Z

Name: Cyclin dependent kinase 6

Gene Name: CDK6

UNIPROT ID: Q00534

Gene ID: 1021

2016-10-18T15:13:58Z

Name: receptor interacting protein

Gene Name: RIPK1

UNIPROT ID: Q13546

Gene ID: 8737

2017-03-09T18:20:42Z

Name: Cytochrome c

Gene Name: CYCS

UNIPROT ID: P99999

Gene ID: 54205

2016-09-16T08:18:47Z

Name: Ras related protein

Gene Name: AKT1

UNIPROT ID: P31749

Gene ID: 207

2016-09-16T08:18:47Z

Name: murine double minute 2

Gene Name: MDM2

UNIPROT ID: Q00987

Gene ID: 4193

2016-10-18T15:05:40Z

Name: Cyclin D

Gene Name: CCND1

UNIPROT ID: P24385

Gene ID: 595

2016-10-18T15:05:40Z

Name: Proteasome

2017-03-17T12:34:43Z

Name: mitogen-activated protein kinase kinase 1

Gene Name: MAP2K1

UNIPROT ID: Q02750

Gene ID: 5604

2016-10-18T15:11:39Z

Name: inhibitor of apoptosis protein

Gene Name: BIRC2

UNIPROT ID: Q13490

Gene ID: 329

2016-10-18T15:11:39Z

Name: Fas ligand

Gene Name: FASLG

UNIPROT ID: P48023

Gene ID: 356

2017-03-23T15:36:47Z

Name: Bcl2-associated X protein

Gene Name: BAX

UNIPROT ID: Q07812

Gene ID: 581

2017-03-17T14:43:29Z

Name: second mitochondriaderived activator of caspases

Gene Name: DIABLO

UNIPROT ID: Q9NR28

Gene ID: 56616

2016-09-16T08:18:47Z

Name: glycoprotein 130

Gene Name: IL6ST

UNIPROT ID: P40189

Gene ID: 3572

2017-03-17T09:57:24Z

Name: MAP kinase kinase 4

Gene Name: MAP2K4

UNIPROT ID: P45985

Gene ID: 6416

2016-09-16T08:18:47Z

Name: FLICE-like inhibitory protein

Gene Name: CFLAR

UNIPROT ID: O15519

Gene ID: 8837

2016-10-18T15:05:40Z

Name: BCL2-associated agonist of cell death

Gene Name: BAD

UNIPROT ID: Q92934

Gene ID: 572

2016-09-14T09:48:27Z

Name: signal transducer and activator of transcription 3

Gene Name: STAT3

UNIPROT ID: P40763

Gene ID: 6774

2016-10-18T15:05:40Z

Name: mitochondria

2016-09-16T08:18:47Z

Name: Phospho-inhibitor of NFκB

Gene: NFKBIA

UniProtID: P25963

Gene ID: 4792

pIκB is the phosphorylated form of the NFκB inhibitor, IκB.

2017-03-17T12:34:43Z

Name: phosphor-signal transducer and activator of transcription 3

Gene Name: STAT3

UNIPROT ID: P40763

Gene ID: 6774

2016-10-18T15:05:40Z

Name: myelocytomatosis viral oncogene homolog

Gene Name: MYC

UNIPROT ID: P01106

Gene ID: 4609

2016-10-18T15:05:40Z

Name: small G-protein

UNIPROT ID: P01112

Gene ID: 3265

Gene Name: RAS

2016-10-18T15:05:40Z

Name: phosphoinositide-3-kinase

Gene Name: PI3KR1

UNIPROT ID: P27986

Gene ID: 5295

2016-10-18T15:05:40Z

Name: BH3 interacting domain death agonist

Gene Name: BID

UNIPROT ID: P55957

Gene ID: 637

2016-09-16T08:18:47Z

Name: Inhibitor of kappa B kinase

Gene Name: IKBKB

UNIPROT ID: O14920

Gene ID: 3551

2017-03-20T14:52:00Z

Name: x-linked inhibitor of apoptosis

Gene Name: XIAP

UNIPROT ID: P98170

Gened ID: 331

2016-10-18T15:05:40Z

Name: Interleukin 6

Gene Name: IL6

UNIPROT ID: P05231

Gene ID: 3569

2017-03-17T09:57:24Z

Name: proto-oncogene c-RAF

Gene Name: RAF1

UNIPROT ID: P04049

Gene ID: 5894

2016-10-18T15:05:40Z

Name: phosphatase and tensin homolog

Gene Name: PTEN

UNIPROT ID: P60484

Gene ID: 5728

2016-09-14T09:48:27Z

Name: Cyclin dependent kinase 2

Gene Name: CDK2

UNIPROT ID: P24941

Gene ID: 1017

2017-03-22T13:36:51Z

Name: DNA-dependent protein kinase catalytic subunit

Gene Name: PRKDC

UNIPROT ID: P78527

Gene ID: 5591

2016-09-16T08:18:47Z

Name: DNA damage

2016-10-18T16:35:07Z

Name: Janus associated kinase 1

Gene Name: JAK1

UNIPROT ID: P23458

Gene ID: 3716

2017-03-17T09:57:24Z

Name: TNF receptor-associated factor 3

Gene Name: TRAF3

UNIPROT ID: Q13114

Gene ID: 7187

2016-09-14T09:48:27Z

Name: cleaved poly (ADP-ribose) polymerase

Gene Name: PARP1

UNIPROT ID: P09874

Gene ID: 142

2017-03-23T19:47:20Z

Name: extracellular regulated MAP kinase

Gene Name: MAPK3

UNIPROT ID: P27361

Gene ID: 5595

2016-10-18T15:12:03Z

Name: Phosphatidylinositol (3,4,5)-triphosphate

2016-10-18T15:05:40Z

Name: protein kinase B

Gene Name: AKT1

UNIPROT ID: P31749

Gene ID: 207

2016-10-18T15:11:39Z

Name: B-cell leukemia/lymphoma 2

Gene Name: BCL2

UNIPROT ID: P10415

Gene ID: 596

2016-10-18T15:05:40Z

Name: Caspase 3

Gene Name: CASP3

UNIPROT ID: P42574

Gene ID: 836

2016-09-29T12:40:13Z

CDK2 activates pRB in conjunction with CDK4 and CDK6. CDK4 activates pRB in conjunction with CDK6.

CDK2 (in complex with Cyclin E) phosphorylates pRB to progress the cell into S phase. Formation of the CDK2:CyclinE complex is dependent on the partial phosphorylation of pRB (in this model pRB represents the phosphorylated form of pRB) by CDK4 and CDK6.

CDK6 (in complex with Cyclin D) phosphorylates pRB.

CDK4 (in complex with Cyclin D) phosphorylates pRB.

S_57 1 S_26 1 S_19 1 S_19 1 S_26 1

Cytc activates Cas9. AKT and XIAP are negative regulators of Cas9 that express dominance over Cytc.

The BIR3 domain of XIAP forms a heterodimer with Cas9 monomers, thus preventing Cas9 catalytic activity.

The release of Cytc leads to the proteolytic activation of procaspase-9 by Apaf-1, which produces Cas9.

AKT inhibits Cas9 by blocking Cytc release into the cytosol as well as inhibiting Cytc activation of Cas9.

S_29 1 S_53 1 S_65 1

p53 is activated by DNAPK and JNK. In conjunction with prot, MDM expresses dominance over DNAPK and JNK as well as inhibits p53.

MDM induces proteasome degradation of p53.

MDM induces proteasome degradation of p53.

Experimental evidence demonstrates that p53 is incapable of binding to DNA in the absence of DNAPK, insinuating that DNAPK is required for p-53 activation in response to DNA damage.

JNK converts p53 from a transactivator to a repressor of Wip1, a p53 signaling inhibitor.

S_58 1 S_31 1 S_33 1 S_20 1 S_31 1 S_33 1

Cas3 and DNAdam are positive regulators of ATM.

ATM is activated in response to DNA damage, specifically in the form of double-strand breaks.

ATM activity is up-regulated with apoptotic progression. As a result, activation of ATM occurs concurrently with caspase-3 activation.

S_67 1 S_59 1

FasL and p53 activate Fas.

p53 upregulates Fas following DNA damage.

FasL binds to its receptor, Fas.

S_3 1 S_36 1

MEKK2 is activated by RAC.

RAC indirectly activates the same downstream target as MEKK2.

S_30 1

GROWTH is activated by pRB.

Unphosphorylated pRB inhibits progression from G1 to S phase by blocking transcription of S phase proteins. When pRB is phophorylated (pRB in this model represents the phosphorylated form), the cell cycle is able to progress from G1 to S phase.

S_1 1

Apoptosis is activated by C1_PARP.

CI_PARP activation induces apoptosis.

S_62 1

Prot activates pNFkB in conjunction with pIkB. pIkB, pSTAT3, and X also activates pNFkB.

c-Src-mediated transcriptional activation of NFκB requires tyrosine phosphorylation of IκBα.

Only phosphorylated Stat3 is able to interact with phosphorylated NF-kappa-B p65.

X activates pNFkB.

Inhibition of Prot prevents cleavage of IκBα and decreases NFκB activity.

S_47 1 S_33 1 S_46 1 S_18 1 S_46 1

pNFkB and pSTAT3 are positive regulators of Bclxl. BAD, Bax, and p53 are negative regulators of Bclxl and are dominant over pNFkB and pSTAT3.

NFKB binds to Bclxl.

BclxL expression can be inhibited by blocking STAT3 activation from JAKs, demonstrating that STAT3 plays a role in Bclxl expression.

Bclxl is an antiapoptotic protein while p53 is a known tumor suppressor protein that can mediate cell death.

BAD binds to and inhibits Bclxl.

Bclxl is a antiapoptotic protein while BAX promotes mitochondrial apoptosis. In multiple myeloma cells, there is higher expression of Bclxl and lower expression of BAX.

S_9 1 S_37 1 S_43 1 S_3 1 S_47 1 S_37 1 S_43 1 S_3 1

p21 is activated by p53 and inactivated by AKT, CDK4, MDM, and MYC. AKT, CDK4, MDM, and MYC all express dominance over p53.

MDM iinhibits p53, the positive regulator of p21.

AKT phosphorylates p27, leading to its relocalization to the cytoplasm.

p53 transcriptionally activates p21 expression.

The CYCD:CDK4 complex sequesters unbound p27 and prevents its inhibitory effect on CYCE:CDK2.

MYC inhibits p21 transcription by repressing the p21 promoter.

S_3 1 S_19 1 S_31 1 S_65 1 S_48 1

MEK1 activates MEKK.

MEK1 phosphorylates MEKK.

S_34 1

CYCE is activated by MYC.

MYC indirectly upregulates CYCE activity through activation of E2F.

S_48 1

Fas activates Cas8 in conjunction with FasL. FLIP is a negative regulator of Cas8 that expresses dominance over Fas.

Binding of FasL to Fas promotes oligomerization of Cas8 through activation of FADD.

FLIP is recruited and partially processed by death-induced signaling complexes. A portion of the FLIP protein is retained, which in turn inhibits recruitment of caspase-8.

Binding of FasL to Fas promotes oligomerization of Cas8 through activation of FADD.

S_5 1 S_36 1 S_42 1

IL6 activates JAK2 in conjunction with gp130. SHP1 is a negative regulator of JAK2 that expresses dominance over IL6.

SHP1 binds to the EPO receptor and dephosphorylates the associated JAK2 proteins.

IL6 binding to its receptor induces gp130-homodimerization. This in turn leads to JAK2 phosphorylation.

IL6 binding to its receptor induces gp130-homodimerization. This in turn leads to JAK2 phosphorylation.

S_54 1 S_40 1 S_39 1

cJun is activated by JNK.

JNK phosphorylates cJun on its N-terminal transactivation domain at Ser63 and Ser73.

S_20 1

CYCD activates CDK4. p21 and p27 are negative regulators for CDK4 that express dominance over CYCD.

p21 is a CDK inhibitor.

CYCD forms a complex with CDK4.

p27 is a CDK inhibitor.

S_32 1 S_23 1 S_11 1

MKK4 is a positive regulator of JNK. Prot inactivates JNK and is dominant over MKK4.

MKK4 phosphorylates JNK.

Treatment with proteasome inhibitors led to a steady increase in JNK activity, implying that Prot is a negative regulator of JNK.

S_41 1 S_33 1

DNAdam activates STRESS. prot inhibits STRESS.

DNA damage causes cellular stress.

Proteolytic activities of proteasomes are important for repairing DNA damage. Prot prevents the buildup of DNA damage and cellular stress caused by that damage.

S_59 1 S_59 1 S_33 1

p53 activates p27. AKT, CDK4, and MYC express dominance over p53 and inhibit p27.

AKT phosphorylates p27, leading to its relocalization to the cytoplasm.

p53 binds to the p27 promoter to activates p27 expression.

The CYCD:CDK4 complex sequesters unbound p27 and prevents its inhibitory effect on CYCE:CDK2.

MYC is an upstream regulator of CDKs and functionally antagonizes p27 activity.

S_3 1 S_19 1 S_48 1 S_65 1

TRAF3 inactivates NIK.

TRAF3 inhibits NIK by interacting with a TRAF2–cIAP complex to direct cIAP-mediated K48-linked polyubiquitylation of NIK.

S_61 1

MAPK is activated by MEK1.

MAPK phosphorylates MEK1.

S_34 1

CYCD activates CDK6.

CYCD forms a complex with CDK6.

S_32 1

TNFa activates RIP in conjunction with TNFaR. Bort also activates RIP.

TNFAR indirectly activates RIP.

TNFA indirectly activates RIP through binding of its receptor, TNFAR.

Bort induces phosphorylation of RIP.

S_27 1 S_21 1 S_17 1

Cytc is activated by MITO.

The formation of pores in the mitochondrial membrane by BAX leads to the release of Cytc.

S_45 1

RAC is activated by STRESS.

STRESS indirectly induces RAC activation.

S_22 1

MDM is activated by AKT and p53. ATM inhibits MDM and is dominant over AKT and p53.

Akt signaling promotes the phosphorylation and movement of the MDM into the nucleus.

p53 transcriptionally upregulates MDM.

ATM phosphorylates serine 394 of MDM. This reduces MDM's ability to induce p53 degradation.

S_65 1 S_4 1 S_3 1 S_4 1

CYCD is activated by AKT, ERK, and MYC.

ERK indirectly upregulates CYCD expression.

AKT up regulates CYCD expression by phosphorylating and inactivating glycogen synthase kinase 3β. This prevents the degradation of CYCD.

MYC knockout cells saw a 12-fold reduction in CYCD-CDK4 activity, indicating that MYC is important for CYCD's role in promoting cell division.

S_63 1 S_65 1 S_48 1

Bort inactivates prot.

Bortezomib is a potent, selective, and reversible inhibitor of the proteasome

S_27 1

MEK1 is activated by RAF.

RAF phosphorylates MEK1.

S_55 1

TNFAR activates CIAP.

Activation of TNFAR leads to the recruitment of CIAP to the receptor.

S_21 1

FasL is activated by cJun and Fas.

cJun has been shown to directly activate the FasL promoter.

Fas indirectly upregulates FasL expression.

S_16 1 S_5 1

p53 and BID are positive regulators of Bax. Bclxl and BCL2 are negative regulators of Bax that express dominance over p53 and BID.

p53 neutralizes the inhibitory effects of Bclxl and BCL2 on Bax.

Truncated BID translocates to the mitochondria where it then induces a conformational change and oligomerization of BAX.

Bclxl inhibits Bax by competing for binding to membranes.

BCL2 induces conformational changes in the mitochondrial membrane to bind membrane-inserted BAX monomers in order to inhibit BID-mediated activation of BAX.

S_3 1 S_10 1 S_66 1 S_51 1 S_10 1 S_66 1

Smac is activated by mitochondria.

The formation of pores in the mitochondrial membrane by BAX leads to the sequential activation of the caspase cascade.

S_45 1

Cas3 inactivates gp130.

Downregulation of gp130 by proteasome inhibitor PS-341 is dependent on caspase activation and is suspected to be mediated by caspase-3 specifically.

S_67 1

Mkk4 is activated by MEKK2.

MEKK2 phosphorylates MKK4.

S_6 1

FLIP is activated by pNFkB.

NFκB activation upregulates FLIP.

S_9 1

AKT is a negative regulator of BAD.

AKT phosphorylates BAD.

S_65 1

STAT3 is inactivated by Cas3.

STAT3 plays a role in cell survival, while Cas 3 promotes apoptosis.

S_67 1

Mitochondria is activated by Bax.

BAX induces apoptotic pores in the mitochondrial outer membrane to induce cell death.

S_37 1

pIkB is activated by IKK.

IKK phosphorylates IkB.

S_52 1

JAK2 activates pSTAT3 in conjunction with JAK1 and STAT3. JAK1 activates pSTAT3 in conjunction with JAK2 and STAT3. IKK and JNK are negative regulators of pSTAT3 which are dominant over JAK2.

IKK is a negative regulator of pSTAT3 which expresses dominance over JAK1 and JAK2.

JAK2 and JAK1 phosphorylate STAT3 at Tyr705, resulting in translocation of activated STAT3 dimers to the nucleus.

JAK2 and JAK1 phosphorylate STAT3 at Tyr705, resulting in translocation of activated STAT3 dimers to the nucleus.

JAK2 and JAK1 phosphorylate STAT3 at Tyr705, resulting in translocation of activated STAT3 dimers to the nucleus.

JNK induces ser-727 phosphorylation of STAT3 and can negatively regulate the tyrosine phosphorylation of STAT3.

S_60 1 S_15 1 S_44 1 S_15 1 S_60 1 S_44 1 S_52 1 S_20 1

ERK, MEKK, and pSTAT3 are positive regulators of MYC.

Inhibition of STAT3 signaling suppresses MYC expression, suggesting that STAT3 positively regulates MYC experssion.

MEKK expression stimulated the transactivation of MYC.

ERK stabilizes MYC through phosphorylation of MYC at Ser62.

S_63 1 S_12 1 S_47 1

IL6 activates RAS in conjunction with gp130. SHP1 is a positive regulator of RAS.

SHP1 is required for Ras-dependent activation of the MAPK pathway, but not required for activation of RAF.

IL6 binding to its receptor induces gp130-homodimerization. This in turn leads to RAS activation.

IL6 binding to its receptor induces gp130-homodimerization. This in turn leads to RAS activation.

S_54 1 S_40 1 S_39 1

IL6 activates PI3K in conjunction with gp130.

IL6 binding to its receptor induces gp130-homodimerization. This in turn leads to activation of the PI3K/AKT pathway.

IL6 binding to its receptor induces gp130-homodimerization. This in turn leads to activation of the PI3K/AKT pathway.

S_54 1 S_40 1

Cas8, Fas, and STRESS are positive regulators of BID. BCL2 and Bclxl are negative regulators of BID that express dominance over Cas8, Fas, and STRESS.

STRESS activates BID.

Fas indirectly activates BID through caspase-8.

Cas8 cleaves and activates BID.

Bclxl inhibits BID-mediated activation of Bax by competing for binding to membranes.

BCL2 induces conformational changes in the mitochondrial membrane to bind membrane-inserted BAX monomers in order to inhibit BID-mediated activation of BAX.

S_14 1 S_66 1 S_10 1 S_22 1 S_66 1 S_10 1 S_5 1 S_66 1 S_10 1

RIP activates IKK in conjunction with NIK. AKT also activates IKK.

Akt phosphorylates IKKα on T23.

RIP is suspected to activate IKK by recruiting the IKK kinase to the TNF-R1 complex.

NIK is required for IKK activation and seems to function as an IKK-activating kinase as well as a scaffold linking IKK and p100.

S_28 1 S_24 1 S_65 1

pNFkB and pSTAT3 are positive regulators of XIAP. Smac and p53 are negative regulators of XIAP which are dominant over pNFkB and pSTAT3.

NFKB and XIAP are apart of a positive feedback loop where NFKB activates XIAP, which in turn activates NFKB.

XIAP binds to and inactivates caspase-9. Smac prevents XIAP-mediated inhibition of caspase-9 activity by disrupting the interaction of the linker peptide of caspase-9 with the BIR3 domain iof XIAP.

Inhibition of STAT3 decrease XIAP expression, suggesting that STAT3 up-regulates XIAP expression.

Expression of p53 reduced XIAP protein in neurons, suggesting that p53 down-regulates XIAP expression.

S_9 1 S_3 1 S_38 1 S_47 1 S_3 1 S_38 1

IL6 is activated by pNFKB.

MM cell adhesion to bone marrow stromal cells upregulates transcription and secretion of IL6 via a NFKB-dependent pathway.

S_9 1

RAS is a postive regulator of RAF.

RAS binds to RAF and recruits it to the cell membrane. Here, RAF is phosphorylated to activate its enzymatic activity.

S_49 1

PTEN is activated by p53.

PTEN lcontains a p53 binding element directly upstream of the PTEN gene that is necessary for inducible transactivation of PTEN by p53.

S_3 1

CYCE activates CDK2. p53 is a negative regulator of CDK2 expressing dominance over CYCE.

p21 is a CDK inhibitor.

CYCE forms a complex CDK2.

S_13 1 S_11 1

DNAPK is activvated by ATM.

ATM mediates DNAPK phosphorylation at Thr-2609.

S_4 1

Cas3 and STRESS activate DNAdam.

Proteolytic activities of proteasomes are important for a number of cellular processes, including DNA repair. Inhibition of the proteasome causes by stress leads to the accumulation of DNA damage.

Cas3 cleaves a protein important for cellular repair, DNA-PKc, thus inhibiting DNA repair.

S_67 1 S_22 1

gp130 activates JAK1 in conjunction with IL6. SHP1 is a negative regulator of JAK1 that expresses dominance over IL6.

SHP1 is plays a role in the dephosphorylation of JAK1.

IL6 binding to its receptor induces gp130-homodimerization. This in turn leads to JAK1 phosphorylation.

IL6 binding to its receptor induces gp130-homodimerization. This in turn leads to JAK1 phosphorylation.

S_40 1 S_54 1

TRAF3 is inhibited by CIAP.

In response to ligands such as CD40L, CIAPs target TRAF3 for proteasomal degradation.

S_35 1

C1_PARP is activated by Cas3.

Cas3 cleaves C1_PARP.

S_67 1

ERK is activated by MAPK.

ERK is activated by MAPK.

S_25 1

PIP3 activates itself and is inactived by the dominant negative regulator PTEN.

PTEN deposphorylates PIP3.

PIP3 is involved in a positve feedback loop that sustains its own activity.

S_64 1 S_56 1

AKT is activated by PIP3.

PIP3 potentially activates AKT by recruiting it to the plasma membrane and altering its conformation to induce subsequent phosphorylation by PDK1.

S_64 1

pNFkB and pSTAT3 are positive regulators of BCL2. p53 and BAD are negative regulators of BCL2 that express dominance over pNFkB and pSTAT3.

NFKB transcriptionally regulates BCL2.

pSTAT3 directly associates with the BCL2 promoter to upregulate BCL2 expression.

p53 is a proapoptotic protein that can counteract the antiapoptotic effects of BCL2.

BAD heterodimerizes with BCL2.

S_47 1 S_3 1 S_43 1 S_9 1 S_3 1 S_43 1

Cas8 and Cas9 are positive regulators of Cas3. XIAP is a negative regulator of Cas3 that expresses dominance over Cas8 and Cas9.

XIAP can polyubiquitylate Cas3, leading to its proteasome-dependent degradation.

Cas9 cleaves and activates Cas3.

Cas8 cleaves and activates Cas3.

S_14 1 S_53 1 S_2 1 S_53 1