Review of Patient Gene Profiles Obtained through a Non-Negative Matrix Factorization-Based Framework to Determine the Role Inflammation Plays in Neuroblastoma Pathogenesis
Abstract
:1. Introduction
- (i)
- MYCN signaling promoting NB cell proliferation and activating MDM2 expression.
- (ii)
- Wnt signaling, which is involved in stemness and increases the level of MYCN.
- (iii)
- ALK signaling, which activates the expression of PI3K/AKT/mTOR, RAS-MAPK, and MYCN.
- (iv)
- p53-MDM2 pathway, which promotes angiogenesis, MYCN translation and drug resistance.
- (v)
- PI3K/AKT/mTOR pathway which promotes survival and chemoresistance of NB cells.
- (vi)
- RAS-MAPK signaling, which is activated by EGFR, promotes neuroblastoma cell survival.
- (vii)
2. Results and Discussions
- i.
- B-cell activation.
- ii.
- Axon growth guidance mediated by netrins, which act as growth factors and promote growth activity in target cells (netrin-mediated axon guidance) [19].
3. Materials and Methods
Non-Negative Matrix Factorization for Automatic Gene Extraction
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
ACTA2 | actin alpha 2, smooth muscle |
ACTG2 | actin gamma 2, smooth muscle |
AKT | Akt kinase |
ALK | ALK receptor tyrosine kinase |
ALOX5AP | arachidonate 5-lipoxygenase activating protein |
AP1 | K-box region and MADS-box transcription factor family protein |
BLNK | B cell linker |
BTK | Bruton tyrosine kinaseC5AR1 |
C5AR1 | complement C5a receptor 1 |
CCL1 | C-C motif chemokine ligand 1 |
CCL11 | C-C motif chemokine ligand 11 |
CCL13 | C-C motif chemokine ligand 13 |
CCL18 | C-C motif chemokine ligand 18 |
CCL2 | C-C motif chemokine ligand 2 |
CCL21 | C-C motif chemokine ligand 21 |
CCL4 | C-C motif chemokine ligand 4 |
CCL5 | C-C motif chemokine ligand 5 |
CCL8 | C-C motif chemokine ligand 8 |
CCR1 | C-C motif chemokine receptor 1 |
CCR2 | C-C motif chemokine receptor 2 |
CCR5 | C-C motif chemokine receptor 5 |
CCR7 | C-C motif chemokine receptor 7 |
CD14 | CD14 molecule |
CD19 | CD19 molecule |
CD247 | CD247 molecule |
CD28 | CD28 molecule |
CD3D | CD3 delta subunit of T-cell receptor |
CD3E | CD3 epsilon subunit of T-cell receptor complex |
CD3G | CD3 gamma subunit of T-cell receptor complex |
CD74 | CD74 molecule |
CD86 | CD86 molecule |
COL10A1 | collagen type X alpha 1 chain |
COL11A1 | collagen type XI alpha 1 chain |
COL12A1 | collagen type XII alpha 1 chain |
COL14A1 | collagen type XIV alpha 1 chain |
COL15A1 | collagen type XV alpha 1 chain |
COL4A5 | collagen type IV alpha 5 chain |
COL5A1 | collagen type V alpha 1 chain |
COL5A2 | collagen type V alpha 2 chain |
COL5A3 | collagen type V alpha 3 chain |
COL6A2 | collagen type VI alpha 2 chain |
COL6A3 | collagen type VI alpha 3 chain |
COL8A1 | collagen type VIII alpha 1 chain |
COL8A2 | collagen type VIII alpha 2 chain |
CX3CR1 | C-X3-C motif chemokine receptor 1 |
CXCL10 | C-X-C motif chemokine ligand 10 |
CXCR1 | C-X-C motif chemokine receptor 1 |
EGFR | epidermal growth factor receptor |
FACIT | collageni associati a fibrille con triple eliche interrotte |
FLNA | filamin A |
FOS | Fos proto-oncogene, AP-1 transcription factor subunit |
FPR1 | formyl peptide receptor 1 |
FPR3 | formyl peptide receptor 3 |
HLA-DMB | major histocompatibility complex, class II, DM beta |
HLA-DPA1 | major histocompatibility complex, class II, DP alpha 1 |
HLA-DQA1 | major histocompatibility complex, class II, DQ alpha 1 |
HLA-DQA2 | major histocompatibility complex, class II, DQ alpha 2 |
HLA-DRA | major histocompatibility complex, class II, DR alpha |
INF I | interferon I |
ITGAL | integrin subunit alpha L |
ITGB7 | integrin subunit beta 7 |
ITPR3 | inositol 1,4,5-trisphosphate receptor type 3 |
JUNB | JunB proto-oncogene, AP-1 transcription factor subunit |
LCK | LCK proto-oncogene, Src family tyrosine kinase |
LCP2 | lymphocyte cytosolic protein 2 |
LY96 | lymphocyte antigen 96 |
MAP3K8 | mitogen-activated protein kinase kinase kinase 8 |
MAPK | map kinase |
MDM2 | MDM2 proto-oncogene |
MHC-I | histocompatibility-1, MHC |
MHC-II | histocompatibility-2, MHC |
mTOR | mechanistic target of rapamycin kinase |
MYC | MYC proto-oncogene |
MYH11 | myosin heavy chain 11 |
MYH9 | myosin heavy chain 9 |
NFATC2 | nuclear factor of activated T cells 2 |
P53 | tumor protein p53 |
PGE2 | prostaglandin E2 |
PI3K | phosphatidylinositol 3-kinase |
PIK3CG | phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma |
PIK3R2 | phosphoinositide-3-kinase regulatory subunit 2 |
PIK3R5 | phosphoinositide-3-kinase regulatory subunit 5 |
PRRX1 | paired related homeobox 1 |
PTGS2 | prostaglandin-endoperoxide synthase 2 |
PTPRC | protein tyrosine phosphatase receptor type C |
RAC2 | Rac family small GTPase 2 |
RAS | RAS p21 protein activator 1 |
SYK | spleen associated tyrosine kinase |
TLR2 | Toll like receptor 2 |
TLR3 | Toll like receptor 3 |
TLR7 | Toll like receptor 7 |
TrKB | neurotrophic receptor tyrosine kinase 2 |
VAV1 | vav guanine nucleotide exchange factor |
VWF | von Willebrand factor |
WAS | WASP actin nucleation promoting factor |
WNT | Wnt family signaling pathway |
ZAP70 | zeta chain of T cell receptor associated protein kinase 70 |
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Gene Set | Description | Size | Expect | Ratio | p Value | FDR |
---|---|---|---|---|---|---|
P00053 | T-cell activation | 75 | 4.8985 | 4.4912 | 4.9299 × 10−10 | 5.5708 × 10−8 |
P00031 | Inflammation mediated by chemokine and cytokine signaling pathway | 200 | 13.063 | 2.7559 | 3.6630 × 10−9 | 2.0696 × 10−7 |
P00034 | Integrin signaling pathway | 166 | 10.842 | 2.1214 | 0.00030327 | 0.011423 |
P00010 | B-cell activation | 58 | 3.7882 | 2.9038 | 0.00099971 | 0.028242 |
P00054 | Toll receptor signaling pathway | 50 | 3.2657 | 2.1435 | 0.041004 | 0.79098 |
P00009 | Axon guidance mediated by netrin | 30 | 1.9594 | 2.5518 | 0.041999 | 0.79098 |
P00050 | Plasminogen activation cascade | 15 | 0.97970 | 3.0622 | 0.069606 | 1 |
P00033 | Insulin/IGF pathway–protein kinase B signaling cascade | 35 | 2.2860 | 2.1873 | 0.073811 | 1 |
P00011 | Blood coagulation | 38 | 2.4819 | 2.0146 | 0.097796 | 1 |
P00047 | PDGF signaling pathway | 125 | 8.1642 | 1.4698 | 0.11051 | 1 |
T-cell activation | CD247, CD28, CD3D, CD3E, CD3G, CD74, CD86, FOS, HLA-DMB, HLA-DPA1, HLA-DQA1, HLA-DQA2, HLA-DRA, LCK, LCP2, NFATC2, PIK3CG, PIK3R2, PTPRC, VAV1, WAS, ZAP70 |
Inflammation mediated by chemokine and cytokine signaling pathway | ACTA2, ACTG2, ALOX5AP, C5AR1, CCL11, CCL13, CCL18, CCL2, CCL21, CCL4, CCL5, CCL8, CCR1, CCR2, CCR5, CCR7, COL12A1, COL14A1 COL6A2, COL6A2, COL6A3, CX3CR1, CXCL10, FPR1, FPR3, ITGAL, ITGB7, ITPR3, JUNB, MYH11, MYH9, NFATC2, PIK3CG, PTGS2, RAC2, VAV1, VWF |
Integrin signaling pathway | COL10A1, COL11A1 COL12A1, COL14A1, COL15A1, COL1A2, COL4A5, COL5A1, COL5A2, COL5A2, COL6A2, COL6A3, COL8A1, COL8A1, FLNA, ITGAL, ITGAX, ITGAX, ITGB7, ITGBL1, PIK3CG, PIK3R2, PTGS2, RAC2 |
B-cell activation | BLNK, BTK, CD19, FOS, ITPR3, NFATC2, PIK3CG, PTPRC, RAC2, SYK, VAV1 |
Toll receptor signaling pathway | CD14, LY96, MAP3K8, PTGS2, TLR2, TLR3, TLR7 |
Axon guidance mediated by netrin | NFATC2, PIK3CG, PIK3R2, PIK3R5, RAC2 |
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Boccarelli, A.; Del Buono, N.; Esposito, F. Review of Patient Gene Profiles Obtained through a Non-Negative Matrix Factorization-Based Framework to Determine the Role Inflammation Plays in Neuroblastoma Pathogenesis. Int. J. Mol. Sci. 2024, 25, 4406. https://doi.org/10.3390/ijms25084406
Boccarelli A, Del Buono N, Esposito F. Review of Patient Gene Profiles Obtained through a Non-Negative Matrix Factorization-Based Framework to Determine the Role Inflammation Plays in Neuroblastoma Pathogenesis. International Journal of Molecular Sciences. 2024; 25(8):4406. https://doi.org/10.3390/ijms25084406
Chicago/Turabian StyleBoccarelli, Angelina, Nicoletta Del Buono, and Flavia Esposito. 2024. "Review of Patient Gene Profiles Obtained through a Non-Negative Matrix Factorization-Based Framework to Determine the Role Inflammation Plays in Neuroblastoma Pathogenesis" International Journal of Molecular Sciences 25, no. 8: 4406. https://doi.org/10.3390/ijms25084406