Lineage fate decisions of hematopoietic cells depend on intrinsic factors and extrinsic signals provided by the bone marrow microenvironment, where they reside. Abnormalities in composition and function of hematopoietic niches have been proposed as key contributors of acute lymphoblastic leukemia (ALL) progression. Our previous experimental findings strongly suggest that pro-inflammatory cues contribute to mesenchymal niche abnormalities that result in maintenance of ALL precursor cells at the expense of normal hematopoiesis. Here, we propose a molecular regulatory network interconnecting the major communication pathways between hematopoietic stem and progenitor cells (HSPCs) and mesenchymal stromal cells (MSCs) within the BM. Dynamical analysis of the network as a Boolean model reveals two stationary states that can be interpreted as the intercellular contact status. Furthermore, simulations describe the molecular patterns observed during experimental proliferation and activation. Importantly, our model predicts instability in the CXCR4/CXCL12 and VLA4/VCAM1 interactions following microenvironmental perturbation due by temporal signaling from Toll like receptors (TLRs) ligation. Therefore, aberrant expression of NF-κB induced by intrinsic or extrinsic factors may contribute to create a tumor microenvironment where a negative feedback loop inhibiting CXCR4/CXCL12 and VLA4/VCAM1 cellular communication axes allows for the maintenance of malignant cells. Bird Shannyn birdgirl@arcticmail.com University of Nebraska-Lincoln 2016-10-06T11:06:43Z 2017-03-31T14:40:05Z

Phosphorylation cascade PI3K -> PIP3 -> Akt

Name: PI3-kinase subunit beta/Protein kinase B

Gene Name: PIK3CB/AKT1

UNIPROT ID: P42338/P31749

Gene ID: 5291/207

2016-10-06T11:45:03Z

Name: C-X-C chemokine receptor type 4

Gene Name: CXCR4

UNIPROT ID: P61073

Gene ID: 7852

2016-10-06T11:45:03Z

Name: B-catenin

Gene Name: CTNNB1

UNIPROT ID: P35222

Gene ID: 1499

2016-10-31T12:48:03Z

Name: Necrosis factor-kB

Gene Name: NFKB1

UNIPROT ID: P19838

Gene ID: 4790

2016-10-06T12:11:46Z

Name: Necrosis factor-kB

Gene Name: NFKB1

UNIPROT ID: P19838

Gene ID: 4790

2016-11-01T10:08:01Z

Name: Reactive oxygen species

product of cellular metabolism

2016-10-06T11:45:03Z

Name: Growth factor indeptendent 1

Gene Name: GFI1

UNIPROT ID: Q99684

Gene ID: 2672

2016-11-01T11:56:48Z

Name: Granulocyte-colony stimulating factor

Gene Name: CSF3

UNIPROT ID: P09919

Gene ID: 1440

2016-10-06T11:45:03Z

Phosphorylation cascade PI3K -> PIP3 -> Akt

Name: PI3-kinase subunit beta/Protein kinase B

Gene Name: PIK3CB/AKT1

UNIPROT ID: P42338/P31749

Gene ID: 5291/207

2016-10-06T12:11:46Z

Very late antigen-4 (VLA-4, an integrin dimer composed of alpha 4 and beta 1 subunits)

Name: Integrin alpha-4/Integrin beta-1

Gene Name: ITGA4/ITGB1

UNIPROT ID: P13612/P05556

Gene ID: 3676/3688

2016-10-06T11:45:03Z

Name: B-catenin

Gene Name: CTNNB1

UNIPROT ID: P35222

Gene ID: 1499

2016-10-06T12:11:46Z

Name: Glycogen synthase kinase 3B

Gene Name: GSK3B

UNIPROT ID: P49841

Gene ID: 2932

2016-10-06T11:45:03Z

Gene: Forkhead box O3

Gene Name: FOXO3

UNIPROT ID: O43524

Gene ID: 2309

2016-10-06T11:45:03Z

Name: Connexin 43

Gene ID: 2697

Gene Name: GJA1

UNIPROT ID: P17302

2016-10-06T11:45:03Z

Name: Toll-like receptor 4

Gene Name: TLR4

UNIPROT ID: O00206

Gene ID: 7099

2016-11-02T09:53:07Z

Name: Interleukin-1 (alpha and beta forms)

Gene Name: IL1A/IL1B

UniProt ID: P01583/P01584

Gene ID: 3552/3553

2016-10-06T11:45:03Z

Name: Lipopolysaccharide, O-antigen

synthesized by Gram-negative bacteria

2016-10-06T11:45:03Z

Name: C-X-C chemokine receptor type 7

Gene Name: ACKR3

UNIPROT ID: P25106

Gene ID: 57007

2016-10-06T11:45:03Z

Name: Extracellular signal-regulated kinase

Gene Name: MAPK1

UNIPROT ID: P28482

Gene ID: 5594

2016-10-06T11:45:03Z

Name: Extracellular signal-regulated kinase

Gene Name: MAPK1

UNIPROT ID: P28482

Gene ID: 5594

2016-10-06T11:45:03Z

Name: Toll-like receptor 4

Gene Name: TLR4

UNIPROT ID: O00206

Gene ID: 7099

2016-10-06T11:45:03Z

Name: Stromal-cell derived factor 1

Gene Name: CXCL12

UNIPROT ID: P48061

Gene ID: 6387

2016-10-06T11:45:03Z

Gene: Forkhead box O3

Gene Name: FOXO3

UNIPROT ID: O43524

Gene ID: 2309

2016-10-06T11:45:03Z

Name: Reactive oxygen species

product of cellular metabolism

2016-10-06T11:45:03Z

Name: Glycogen synthase kinase 3B

Gene Name: GSK3B

UNIPROT ID: P49841

Gene ID: 2932

2016-10-06T11:45:03Z

Name: Vascular cell adhesion molecule-1

Gene Name: VCAM1

UNIPROT ID: P19320

Gene ID: 7412

2016-11-02T10:04:48Z

VLA4_H, TLR_H, ROS_H and GCSF are positive regulators of PI3KAkt_H. CXCR4_H activates PI3KAkt_H in conjunction with CXCR7_H. FoxO3a_H inhibits PI3KAkt_H and expresses dominance over VLA4_H, TLR_H, ROS_H, GCSF, and CXCR4_H.

G-CSF increases Akt phosphorylaton and activation.

CXCR4 and CXCR7 are capable of activating the PI3K pathway via G-protein and β-arrestin. Blocking either receptor is sufficient to inhibit Akt phosphorylation, but co-stimulation does not indicate an additive effect.

TLR stimulation results in the phosphorylation of Akt by a p38α- and MK2/3-dependent manner.

ROS accumulation inhibits the PI3K pathway repressor, PTEN.

Inhibition of FoxO3a leads to a hyperphosphorylation of Akt.

Linkage of β1 integrins with some of their ligands leads to activation of PI3K through the direct interaction with the focal adhesion kinase (FAK) or Pyk2, depending on cell type.

CXCR4 and CXCR7 are capable of activating the PI3K pathway via G-protein and β-arrestin. Blocking either receptor is sufficient to inhibit Akt phosphorylation, but co-stimulation does not indicate an additive effect.

S_8 1 S_23 1 S_2 1 S_18 1 S_23 1 S_21 1 S_23 1 S_24 1 S_23 1 S_10 1 S_23 1

CXCL12_M activates CXCR7_H. Gfi1_H, GCSF, and CXCR7_H all inhibit CXCR4_H and express dominance over CXCL12_M.

CXCL12 binds to CXCR4.

Elevated G-CSF secretion triggers neutrophil elastase and cathepsin-G production in the bone marrow. Both proteases cleave CXCR4, inhibiting its chemotactic property.

CXCR7 binds with higher affinity to CXCL12, inhibiting G-protein signaling by CXCR4. Additionally, CXCR7 can fom a heterodimer with CXCR4, promoting its internalization and degradation.

S_22 1 S_18 1 S_7 1 S_8 1

GSK3B_H inhibits Bcatenin_H.

GSK3β-mediated phosphorylation leads to β-catenin ubiquitination and subsequent degradation via proteasome-dependent proteolysis.

S_25 1

TLR_M activates NfkB_M. ROS_M activates NfkB_M in conjunction with ERK_M. IL1 activates NfkB_M in conjunction with PI3KAkt_M.

TLR4 recognition of its ligand stimulates Myd88 recruitment, which leads to the activation of NF-kB.

The NF-kB pathway is activated by Myd88-dependent IL-1R signaling. Studies observing endothelial cells have noted that NF-kB activation requires PI3K, which is recruited through the interaction of p85 with IL-1R.

ROS activation of the NF-kB pathway requires ERK for IκBα phosphorylation and degradation.

ROS activation of the NF-kB pathway requires ERK for IκBα phosphorylation and degradation.

The NF-kB pathway is activated by Myd88-dependent IL-1R signaling. Studies observing endothelial cells have noted that NF-kB activation requires PI3K, which is recruited through the interaction of p85 with IL-1R.

S_15 1 S_16 1 S_9 1 S_6 1 S_19 1

ROS_H and TLR_H activate NfkB_H. IL1 activates NfkB_H in conjunction with PI3KAkt_H. FoxO3a_H inhibits NfkB_H and expresses dominance over IL1, ROS_H, and TLR_H.

The NF-kB pathway is activated by IL-1R signaling in a PI3K-dependent mechanism.

TLR1,2,4-10 recognition of their ligands stimulates Myd88 recruitment, which leads to the activation of NF-kB.

ROS accumulation results in increased activation of the NF-kB pathway. This activity is caused by two possible mechanisms: the promotion of disulfide-bonds formation favoring NEMO dimerization and S-gluthationylation of IKK-β.

FoxO3a inhibits transloation of the NF-kB subunit RelA.

The NF-kB pathway is activated by IL-1R signaling in a PI3K-dependent mechanism.

S_21 1 S_23 1 S_16 1 S_1 1 S_23 1 S_24 1 S_23 1

TLR_M and IL1 are positive regulators of ROS_M. FoxO3a_M inhibits ROS_M and expresses dominance over IL1 and TLR_M.

FoxO3a upregulates enzymes such as superoxide dismutase, glutathion peroxidases, and catalase which regulate ROS levels.

Stimulation with LPS increases intracellular ROS levels.

Mesenchymal stem cells treated with IL-1β upregulate intracellular ROS levels.

S_16 1 S_15 1 S_13 1

TLR_H and GCSF activate Gfil_H. Gfi1_H inhibits itself and expresses dominance over TLR_H and GCSF.

Gfi1 contains consensus sites for its own promoter region, suggestin cis regulation. These sites are conserved in mice, rates, and humans.

Gfi1 mRNA concentration increases after treatment with G-CSF. This increase is dependent on the integrity of the carboxil terminal region of the G-CSF receptor.

Gfi1 is upregulated after LPS stimulation of bone marrow and macrophages. Gfil regulates some NF-kB targets by binding to p65.

S_8 1 S_7 1 S_21 1 S_7 1

IL1 is a positive regulator for GCSF.

Treatment with IL-1α showed an increase in G-CSF expression. Since IL-1α and IL-1β bind and activate the same receptor, it is assumed that G-CSF can be induced in mesenchymal stem cells or other stromal components expressing IL-1R1.

S_16 1

GCSF, ROS_M, and TLR_M are all positive regulators of PI3KAkt_M.

G-CSF binding to its receptor increases Akt and Erk phosphorylaton and activation.

TLR stimulation results in the phosphorylation of Akt in serine 473.

ROS accumulation inhibits the PI3K pathway repressor, PTEN.

S_8 1 S_6 1 S_15 1

VCAM1_M activates VLA4_H in conjunction with CXCR4_H.

CXCL12 binding to CXCR4 enhances VLA-4 affinity to its ligands.

VLA-4 integrin binds to the integrin receptor VCAM-1.

S_26 1 S_2 1

NfkB_M, GSK3B_M, and FoxO3a_M all inhibit Bcatenin_M.

FOXO transcription factors compete with T-cell factor for binding to β-catenin, which inhibits β-catenin/T-cell factor transcription activity.

GSK3β-mediated phosphorylation leads to β-catenin ubiquitination and subsequent degradation via proteasome-dependent proteolysis.

NFkB recruits IKKβ. IKKβ directly phosphorylates p65, promoting its nuclear translocation. This induces expression of Smurf1 and Smurf2 (Smad ubiquitin regulatorand factor1 and 2), which increase β-catenin degradation.

S_13 1 S_4 1 S_12 1

PI3KAkt_M inhibits GSK3B_M.

Akt activation leads to the phosphorylation and inactivation of GSK3β.

S_9 1

Bcatenin_M and ROS_M activate FoxO3a_M. PI3KAkt_M and ERK_M are negative regulators of FoxO3a_M which are dominant over ROS_M and Bcatenin_M.

Akt phosphorylates FoxO3a, causing its cytoplasmic localization and down-regulation of its target genes.

ERK phosphorylates FoxO3a, causing its inactivation and subsequent degradation via MDM2.

β-catenin interacts directly with FoxO1, FoxO3a, and FoxO3 to increase its transcriptional activity.

ROS accumulation stimulates FOXO localization, increasing the expression of ROS-regulating enzymes such as catalase.

S_6 1 S_9 1 S_19 1 S_11 1 S_9 1 S_19 1

Cx43_M activates itself.

Cx43 Cx43_M activates itself.

S_14 1

TLR_M is activated by ITLR.

TLR_M is activated by ITLR.

S_17 1

ROS_M, NfkB_M, ROS_H, and NfkB_H all activate IL1. PI3KAkt_M is a negative regulator of IL1 which expresses dominance over NfkB_M and ROS_M. PI3KAkt_H is a negative regulator of IL1 which expresses dominance over NfkB_H and ROS_H.

The PI3K/Akt pathway regulates the maturation of IL-1β through the inhibition of caspase-1. The PI3K/Akt pathway also up-regulates antagonist molecules for the IL-1β receptor, preventing IL-1β signaling.

The PI3K/Akt pathway upregulates antagonist molecules for the IL-1β receptor, preventing IL-1β signaling.

IL-1β contains binding sites for NF-κB pathway elements.

ROS- dependent signaling upregulates pro-IL-1β transcription and IL-1β exportation in macrophage stimulated with LPS.

ROS accumulation in mesenchymal stem cells increases IL-1β expression and secretion.

From the analysis of the IL-1β promoter region in rainbow trout, IL-1β appears to contain consensus sites for NF-κB, NF-IL6, AP1, AP4, CHOP/CEBPa, SP1, PU.1, and Gfi1. NF-κB binding sites have been confirmed in humans and mice.

S_4 1 S_9 1 S_6 1 S_9 1 S_24 1 S_1 1 S_5 1 S_1 1

ITLR activates itself.

ITLR activates itself.

S_17 1

CXCL12_M and NfkB_H both activate CXCR7_H.

CXCR7 is an alternative CXCL12 receptor that has higher binding affinity than CXCR4.

The promoter region of CXCR7 contains three consensus sites for NF-κB binding.

S_22 1 S_5 1

TLR_M, ROS_M, and GCSF activate ERK_M.

G-CSF promotes the phosphorylation of Akt and ERK1/2.

Mesenchymal stem cells treated with LPS increased ERK phosphorylation by 40%.

Oxidative stress promotes the phosphorylation and activation of ERK1/2.

S_15 1 S_6 1 S_8 1

VLA4_H, ROS_H, Gfi1_H, GCSF, and CXCR7_H activate ERK_H. CXCR4_H activates ERK_H in conjunction with PI3KAkt_H. GSK3B_H and FoxO3a_H inhibit ERK_H and express dominance over VLA4_H, ROS_H, Gfi1_H, GCSF, CXCR7_H, and CXCR4_H.

Phosphorylation of ERK1/2 after CXCL12-CXCR4 binding is prevented by PI3K-inhibitor treatment.

Cells from Gfi1-/- mice showed a decreased activation of the ERK pathway.

G-CSF promotes the phosphorylation of Akt and ERK1/2.

GSK3β prevents LPS-inducted ERK1/2 phosphorylation.

CXCR4 binding to CXCR7, promotes ERK1/2 phosphorylation and activation.

Oxidative stress activates MAP kinases, increasing ERK1/2 phosphorylation.

Interaction between VLA-4 and its ligand leads to the up-regulation of the ERK pathway.

Phosphorylation of ERK1/2 after CXCL12-CXCR4 binding is prevented by PI3K-inhibitor treatment.

FoxO3a increases Spred2 expression, which prevents ERK phosphorylation.

S_10 1 S_25 1 S_23 1 S_8 1 S_25 1 S_23 1 S_2 1 S_1 1 S_25 1 S_23 1 S_18 1 S_25 1 S_23 1 S_7 1 S_25 1 S_23 1 S_24 1 S_25 1 S_23 1

TLR_H is activated by ITLR.

TLR_H is activated by ITLR.

S_17 1

Cx43_M activates CXCL12_M. NfkB_M, GCSF, and Bcatenin_M are all negative regulators of CXCL12_M which express dominance over Cx43_M.

Cx43 gap junctions mediate the conduction of calcium ions, allowing for intercelular contact. This in turn enables MSC to secrete CXCL12.

G-CSF promotes the degradation of CXCL12 mRNA by the increase of metalloproteinase-9.

β-catenin inhibits CXCL12 transcription by binding to the promotor region.

Activation of the NF-kB pathway down-regulates CXCL12 expression through an unknown mechanism that utilizes RelB.

S_14 1 S_8 1 S_11 1 S_4 1

FoxO3a_H is activated by ROS_H and Bcatenin_H. ERK_H and PI3KAkt_H inhibit FoxO3a_H and express dominance over ROS_H and Bcatenin_H.

Akt phosphorylates FoxO3a, causing its cytoplasmic localization and down-regulation of its target genes.

β-catenin interacts directly with FoxO1, FoxO3a, and FoxO3 to increase its transcriptional activity.

ROS accumulation stimulates FOXO localization, increasing the expression of ROS-regulating enzymes such as catalase.

ERK phosphorylates FoxO3a, causing its inactivation and subsequent degradation via MDM2.

S_24 1 S_1 1 S_20 1 S_3 1 S_1 1 S_20 1

IL1 activates ROS_H in conjunction with TLR_H. FoxO3a_H is a negative regulator of ROS_H which expresses dominance over IL1.

Stimulation with LPS increases intracellular ROS levels.

FoxO3a upregulates enzymes such as superoxide dismutase and catalase which regulate ROS levels.

Mesenchymal stem cells treated with IL-1β upregulate intracellular ROS levels.

S_16 1 S_21 1 S_23 1

PI3KAkt_H inhibits GSK3B_H.

Akt activates leads to the phosphorylation and inactivation of GSK3β.

S_1 1

NfkB_M and PI3KAkt_M activate VCAM1_M. Bcatenin_M inhibits VCAM1_M.

Treatment with a specific PI3K inhibitor implicated that the PI3KAkt_M pathway is involved in the up-regulation of VCAM-1 expression.

NF-κB up-regulaties VCAM-1 expression, likely through directly binding to NF-κB sites in the promoter region of the VCAM-1 gene.

Treatment with the canonical Wnt pathway ligand, Wnt3a, down-regulation of VCAM-1 expression.

S_4 1 S_9 1 S_9 1 S_4 1 S_11 1