Effects of Anticancer Agent P-bi-TAT on Gene Expression Link the Integrin Thyroid Hormone Receptor to Expression of Stemness and Energy Metabolism Genes in Cancer Cells
Abstract
:1. Introduction
2. Results
2.1. Mechanisms of Anticancer Activities of P-bi-TAT Revealed by Genome-Wide Expression Profiling of a Primary Culture of Human GBM Cells (PC-GBM)
2.2. Examples of Specific GBM Driver Genes Important to Regulation of Cell Division, Energy Metabolism and Signal Transductions of Cancer Survival Pathways Whose Expression Is Affected by P-bi-TAT
2.3. P-bi-TAT Markedly Affects the Transcriptional Architecture of the Energy-Metabolism-Sustaining Life-Support Infrastructure of Cancer Cells
2.4. Expression of ATP Synthase Genes Is Altered by Exposure of GBM Cells to P-bi-TAT
2.5. Expression of NADH Dehydrogenase Genes in Response to Exposure of GBM Cells to P-bi-TAT
2.6. Concordant Patterns of Expression Changes of Energy Metabolism Genes in Human Cancer Cell Lines in Response to P-bi-TAT
2.7. Concordance of Biological Activities and Molecular Mechanisms of Actions of P-bi-TAT
2.8. Naïve Pluripotency Network Genes of Human Preimplantation Embryo Comprise a Marked Majority of the P-bi-TAT Target Genes in Human GBM Cells
3. Discussion
4. Materials and Methods
4.1. P-bi-TAT
4.2. Cells and Cell Culture Conditions; Treatment with P-bi-TAT
4.3. Cell Proliferation Assay
4.4. Analysis of the P-bi-TAT Effects on Angiogenesis
4.5. Microarray
5. Conclusions
- Energy metabolism gene expression pathways represent an intrinsic component of stemness and cancer survival networks engaged in malignant cells;
- The association between cancer cells’ stemness state, survival networks and energy metabolism pathways revealed by thyrointegrin antagonist actions was observed in primary GBM cells and appears less evident in cancer cells adapted to in vitro cell culture conditions;
- This apparent dichotomy likely reflects different states of cancer cells’ adaptations to strikingly distinct in vivo and in vitro microenvironmental conditions favoring deployments of different energy metabolism mechanisms. Some important examples of such microenvironmental factors include availability of nutrients, degrees of oxygen accessibility and milieu acidification reaching extreme hypoxic and acidic conditions in vivo;
- In addition to fundamental and mechanistic considerations, documented effects of P-bi-TAT on gene expression of cancer stemness, survival and energy metabolism networks highlight a powerful therapeutic interference opportunity with growth and survival of malignant cells.
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Classification Category | Number of Differentially Regulated Genes | Number of Cancer Survival Genes | Percent of Cancer Survival Genes | p Value |
---|---|---|---|---|
Pancreatic cancer (SUIT2) | 1293 | 860 | 67 | 1.47 × 10−19 |
Top upregulated (p = 0.001) | 50 | 40 | 80 | 0.000124 |
Top downregulated (p = 0.001) | 15 | 12 | 80 | 0.030497 |
Top differentially regulated (p = 0.001) | 65 | 52 | 80 | 1.32 × 10−5 |
Glioblastoma multiforme (GBM) | 5362 | 3403 | 63 | 1.91 × 10−52 |
Top upregulated (6-fold) | 66 | 47 | 71 | 0.002467 |
Top downregulated (2.5-fold) | 106 | 64 | 60 | 0.039735 |
Top differentially regulated | 172 | 111 | 65 | 0.002074 |
Consensus (SUIT2 and GBM) | 737 | 501 | 68 | 2.5 × 10−14 |
Top upregulated (4.9-fold) | 68 | 57 | 84 | 2.91 × 10−7 |
Top downregulated (2.5-fold) | 61 | 43 | 70 | 0.004617 |
Top differentially regulated | 129 | 100 | 78 | 3.88 × 10−8 |
Classification Category | Downregulated Genes |
---|---|
Electron transport chain | ATP5A1, ATP5I, COX6B1, ATP5G2, NDUFA8, NDUFA3, NDUFV2, NDUFA6, NDUFA2, COX5A, NDUFS7, COX6A1, COX4I1, SLC25A6, NDUFB3, ATP5G1, COX7A2, ND6, NDUFAB1, COX7B, NDUFB7, UQCRC1, COX5B, COX8A, NDUFV1, ATP5G3, SURF1, NDUFB2, NDUFS2, ATP5D, NDUFV3, NDUFA10, UCP2, NDUFS8, NDUFB8 |
Cytoplasmic ribosomal proteins | RPL10A, RPL8, RPL9, RPLP2, RPLP1, RPL35, RPL7A, RPL13, RPL14, RPL18A, RPL18, RPL19, RPL21, RPL27, RPL28, RPL29, RPL32, RPL39, UBA52, RPL41, RPL36A, RPS3, RPS9, RPS5, RPS15A, RPS16, RPS20, RPS14, RPS29, RPS11, RPS15, RPS7, RPS8, RPS10, RPS19, RPS26, RPS27, RPS27A, RPS28, FAU, RPLP0, RPS6KA1, RPL11, RPL10, RPL30, RPS2, RPS6KB2 |
Oxidative phosphorylation | ATP5A1, ATP5D, ATP5G2, ATP5G1, ATP5G3, ATP5I, NDUFA11, NDUFS7, NDUFA2, ND6, NDUFA8, NDUFS2, NDUFS8, NDUFB2, NDUFV2, NDUFV3 |
Metabolism of carbohydrates | SLC25A1, PCK1, SLC25A10, GALK1, GALT, PGLS, SLC37A4, AKR1B1, AKR1A1 |
Glucose metabolism | SLC25A1, PCK1, SLC25A10, SLC37A4 |
Fatty acyl-CoA and cholesterol biosynthesis | SLC25A1, PPT2, SLC27A3, FDPS, MVD, DHCR7, PMVK, FDFT1, MVK |
Globo sphingolipid metabolism | ST3GAL1, ST6GALNAC4, ST6GALNAC6, ST6GAL1 |
Biogenic amine synthesis | DDC, ACHE, COMT |
Pathway | Cancer Model | Number of Genes | p-Value | Cancer Model | Number of Genes | p-Value |
---|---|---|---|---|---|---|
VEGFA-VEGFR2 signaling pathway | GBM | 85 | 0.011056 | SUIT2 | 29 | 0.00245 |
Androgen receptor signaling pathway | GBM | 43 | 0.000046 | SUIT2 | 13 | 0.00843 |
Brain-derived neurotrophic factor (BDNF) signaling pathway | GBM | 54 | 0.020347 | SUIT2 | 19 | 0.00678 |
Deubiquitination | GBM | 13 | 0 | SUIT2 | 4 | 0 |
Endoderm differentiation | GBM | 53 | 0.025638 | SUIT2 | 17 | 0.02808 |
Focal adhesion | GBM | 69 | 0.011855 | SUIT2 | 24 | 0.00308 |
Gastric cancer network 2 | GBM | 15 | 0.027934 | SUIT2 | 7 | 0.00467 |
Human thyroid-stimulating hormone (TSH) signaling pathway | GBM | 30 | 0.002383 | SUIT2 | 10 | 0.01235 |
IL-6 signaling pathway | GBM | 22 | 0.001737 | SUIT2 | 9 | 0.00193 |
Integrin-mediated cell adhesion | GBM | 40 | 0.013987 | SUIT2 | 14 | 0.0085 |
Interleukin-11 signaling pathway | GBM | 27 | 0.000004 | SUIT2 | 8 | 0.00831 |
MAPK signaling pathway | GBM | 16 | 0.002772 | SUIT2 | 21 | 0.00768 |
Olfactory receptor activity | GBM | 47 | 0 | SUIT2 | 6 | 4 × 10−6 |
Signaling of hepatocyte growth factor (HGF) receptor | GBM | 16 | 0.020177 | SUIT2 | 6 | 0.02432 |
TCF-dependent signaling in response to WNT | GBM | 14 | 0 | SUIT2 | 9 | 0.00539 |
TGF-beta signaling pathway | GBM | 61 | 0.000019 | SUIT2 | 17 | 0.01388 |
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Glinsky, G.V.; Godugu, K.; Sudha, T.; Rajabi, M.; Chittur, S.V.; Hercbergs, A.A.; Mousa, S.A.; Davis, P.J. Effects of Anticancer Agent P-bi-TAT on Gene Expression Link the Integrin Thyroid Hormone Receptor to Expression of Stemness and Energy Metabolism Genes in Cancer Cells. Metabolites 2022, 12, 325. https://doi.org/10.3390/metabo12040325
Glinsky GV, Godugu K, Sudha T, Rajabi M, Chittur SV, Hercbergs AA, Mousa SA, Davis PJ. Effects of Anticancer Agent P-bi-TAT on Gene Expression Link the Integrin Thyroid Hormone Receptor to Expression of Stemness and Energy Metabolism Genes in Cancer Cells. Metabolites. 2022; 12(4):325. https://doi.org/10.3390/metabo12040325
Chicago/Turabian StyleGlinsky, Gennadi V., Kavitha Godugu, Thangirala Sudha, Mehdi Rajabi, Sridar V. Chittur, Aleck A. Hercbergs, Shaker A. Mousa, and Paul J. Davis. 2022. "Effects of Anticancer Agent P-bi-TAT on Gene Expression Link the Integrin Thyroid Hormone Receptor to Expression of Stemness and Energy Metabolism Genes in Cancer Cells" Metabolites 12, no. 4: 325. https://doi.org/10.3390/metabo12040325
APA StyleGlinsky, G. V., Godugu, K., Sudha, T., Rajabi, M., Chittur, S. V., Hercbergs, A. A., Mousa, S. A., & Davis, P. J. (2022). Effects of Anticancer Agent P-bi-TAT on Gene Expression Link the Integrin Thyroid Hormone Receptor to Expression of Stemness and Energy Metabolism Genes in Cancer Cells. Metabolites, 12(4), 325. https://doi.org/10.3390/metabo12040325