Transcriptional and Metabolic Investigation in 5′-Nucleotidase Deficient Cancer Cell Lines
Abstract
:1. Introduction
2. Material and Methods
2.1. Cell Models and Culture
2.2. RNA Sequencing
2.3. Quantitative RT-PCR
2.4. Targeted Metabolomics
3. Results
3.1. Gene Expression in 5′-Nucleotidase-Deficient Cancer Cells
3.2. Pathway-Directed Analysis of Gene Expression Profiles
3.3. Transcriptional Regulation by Adenosine and AMP
3.4. Metabolic Modifications in Cell Models
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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RNA Sequencing | qRT-PCR | |||||||
---|---|---|---|---|---|---|---|---|
Gene | cN-II+/CD73+ | cN-II−/ CD73+ | cN-II+/ CD73− | cN-II−/ CD73− | cN-II+/ CD73+ | cN-II−/ CD73+ | cN-II+/ CD73− | cN-II−/ CD73− |
ALKBH2 | 1.1 | 0.2 | 0.0003 a | 0.001 a | 0.8 ± 0.2 | 1.09 ± 0.05 a | 0.66 ± 0.04 | 1.4 ± 0.2 a |
ALOX5AP | 3.2 | 0.7 a | 0.7 | 0.2 | 0.6 ± 0.3 | 0.7 ± 0.2 | 0.23 ± 0.01 | 0.8 ± 0.5 |
EMB | 0.4 | 10.8 a | 2.5 a | 14.6 a | 0.7 ± 0.2 | 16.1 ± 3.9 a | 2.9 ± 0.7 | 22.2 ± 8.6 a |
ENTPD3 | 0.4 | 2.1 a | 0.4 | 4.4 a | 0.8 ± 0.2 | 3.8 ± 1.1 a | 1.2 ± 0.4 | 13.9 ± 2.3 a |
HLA-F | 1.3 | 0.1 a | 0.8 | 0.4 | 0.7 ± 0.2 | 0.6 ± 0.2 | 0.55 ± 0.08 | 0.6 ± 0.3 |
LAIR1 | 1.4 | 0.0003 a | 0.08 a | 0.2 | 0.8 ± 0.2 | 1.1 ± 0.2 a | 0.30 ± 0.09 a | 0.83 ± 0.08 |
LOX | 5.6 | 9.5 | 9.5 | 12.6 a | 0.8 ± 0.1 | 2.3 ± 0.7 a | 2.0 ± 0.3 a | 4.1 ± 0.7 a |
PLA2G4A | 0.02 | 1.5 a | 0.02 | 1.6 a | 1.1 ± 0.4 | 79 ± 10 a | 3.1 ± 1.2 | 111 ± 10 a |
ROBO1 | n.d. | 1.6 a | n.d. | 2.0 a | 1.0 ± 0.2 | 90 ± 16 a | 5.2 ± 2.2 | 225 ± 17 a |
SERPINA3 | 2.5 | 0.8 a | 0.2 a | 0.1 a | 0.6 ± 0.3 | 0.6 ± 0.2 | 0.17 ± 0.04 a | 0.3 ± 0.2 |
SPDEF | 0.1 | 15.0 a | 0.6 | 18.2 | 0.9 ± 0.3 | 14.5 ± 0.7 a | 2.0 ± 0.6 | 17.7 ± 2.2 a |
ZNF185 | 1.6 | 0.1 a | 0.9 | n.d.a | 0.9 ± 0.1 | 1.3 ± 0.2 a | 1.30 ± 0.03 a | 0.82 ± 0.07 |
ZNF3 | 1.4 | 0.1 a | 0.009 | 0.5 | 0.8 ± 0.1 | 0.8 ± 0.1 | 0.9 ± 0.1 | 0.8 ± 0.1 |
NCI-H292 | RL | |||||
---|---|---|---|---|---|---|
Gene | cN-II+/ CD73+ | cN-II−/ CD73+ | cN-II+/ CD73− | cN-II−/ CD73− | cN-II+ | cN-II− |
ALOX5AP | 0.6 ± 0.4 | 0.4 ± 0.2 | 0.6 ± 0.1 | 0.5 ± 0.3 | 0.9 ± 0.2 | 1.2 ± 0.3 |
EMB | 1.4 ± 0.5 | 2.5 ± 0.7 a | 2.4 ± 0.1 a | 2.5 ± 0.5 a | 1.0 ± 0.2 | 1.4 ± 0.1 |
ENTPD3 | 0.8 ± 0.2 | 1.5 ± 0.5 a | 1.2 ± 0.3 | 1.3 ± 0.5 | n.d. | n.d. |
LAIR1 | n.d. | n.d. | n.d. | n.d. | 1.5 ± 0.7 | 0.8 ± 0.9 |
LOX | 1.6 ± 0.8 | 3.17 ± 0.06 a | 2.6 ± 0.3 | 2.7 ± 1.2 | 0.9 ± 0.4 | 0.8 ± 0.4 |
PLA2G4 | 1.4 ± 0.3 | 1.3 ± 0.2 | 1.4 ± 1.0 | 1.4 ± 0.5 | 0.7 ± 0.6 | 8.0 ± 8.2 |
ROBO1 | 1.7 ± 1.2 | 2.9 ± 0.7 | 0.7 ± 0.2 a | 0.7 ± 0.2 a | 1.2 ± 0.2 | 0.8 ± 0.1 |
SERPINA3 | n.d. | n.d. | n.d. | n.d. | n.d. | n.d. |
SPDEF | 0.8 ± 0.4 | 1.4 ± 0.3 | 1.7 ± 0.7 | 3.3 ± 2.3 a | n.d. | n.d. |
Model | Pathway Term | Genes | p-Value |
---|---|---|---|
cN-II+/CD73− | Pantothenate and CoA biosynthesis | 4 | 0.00053 |
HTLV-I infection | 6 | 0.0083 | |
Herpes simplex infection | 8 | 0.025 | |
Nicotinate and nicotinamide metabolism | 3 | 0.028 | |
Intestinal immune network for IgA production | 3 | 0.068 | |
Tuberculosis | 5 | 0.077 | |
cN-II−/CD73+ | ECM-receptor interaction | 8 | 0.0065 |
Hippo signaling pathway | 10 | 0.015 | |
Protein digestion and absorption | 7 | 0.024 | |
Complement and coagulation cascades | 6 | 0.031 | |
Pathways in cancer | 17 | 0.042 | |
Mucin type O-Glycan biosynthesis | 4 | 0.043 | |
Ras signaling pathway | 11 | 0.062 | |
Focal adhesion | 10 | 0.080 | |
Rap1 signaling pathway | 10 | 0.087 | |
cN-II−/CD73− | Complement and coagulation cascades | 8 | 0.0065 |
Cell adhesion molecules | 11 | 0.016 | |
Oxytocin signaling pathway | 11 | 0.023 | |
Proteoglycans in cancer | 13 | 0.028 | |
Staphylococcus aureus infection | 6 | 0.029 | |
Viral myocarditis | 6 | 0.036 | |
Rap1 signaling pathway | 13 | 0.039 | |
Glucagon signaling pathway | 8 | 0.040 | |
Protein digestion and absorption | 7 | 0.064 | |
Malaria | 5 | 0.072 | |
Inflammatory mediator regulation of TRP channels | 7 | 0.096 | |
Epstein–Barr virus infection | 8 | 0.099 |
MDA-MB-231 | NCI-H292 | RL | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
Gene | cN-II+/ CD73+ | cN-II−/ CD73+ | cN-II+/ CD73− | cN-II−/ CD73− | cN-II+/ CD73+ | cN-II−/ CD73+ | cN-II+/ CD73− | cN-II−/ CD73− | cN-II+ | cN-II− |
ACO1 | 1.1 ± 0.7 | 0.9 ± 0.3 | 0.9 ± 0.6 | 1.13 ± 0.09 | 1.2 ± 1.3 | 1.7 ± 0.8 | 0.7 ± 0.2 | 0.8 ± 0.2 | 2.5 ± 1.5 | 5.3 ± 0.3 |
ASS1 | 1.5 ± 0.6 | 2.0 ± 1.8 | 2.5 ± 1.0 | 2.0 ± 0.2 | 1.0 ± 0.4 | 1.0 ± 0.6 | 0.8 ± 0.2 | 0.8 ± 0.2 | 0.7 ± 0.3 | 3.0 ± 1.0 |
BCAT1 | 0.8 ± 0.2 | 1.1 ± 0.5 | 0.667 ± 0.002 | 0.83 ± 0.03 | 1.5 ± 0.7 | 1.5 ± 0.3 | 0.9 ± 0.4 | 0.8 ± 0.4 | 1.1 ± 0.2 | 1.3 ± 0.3 |
CPS1 | 0.8 ± 0.4 | 1.7 ± 0.5 a | 0.7 ± 0.2 | 1.82 ± 0.08 a,b | 0.8 ± 0.4 | 0.7 ± 0.6 | 0.3 ± 0.1 | 0.4 ± 0.1 | 1.1 ± 0.2 | 1.4 ± 0.4 |
CTH | 0.8 ± 0.2 | 0.5 ± 0.2 | 0.47 ± 0.01 | 0.5 ± 0.1 | 2.0 ± 1.2 | 1.7 ± 0.6 | 1.6 ± 0.5 | 1.5 ± 0.5 | 1.5 ± 0.7 | 1.8 ± 0.4 |
ECHS1 | 0.7 ± 0.4 | 0.9 ± 0.5 | 0.66 ± 0.04 | 1.2 ± 0.3 | 1.1 ± 0.3 | 1.2 ± 0.5 | 1.0 ± 0.5 | 0.9 ± 0.4 | 1.0 ± 0.2 | 1.3 ± 0.3 |
FH | 0.6 ± 0.5 | 0.6 ± 0.3 | 0.567 ± 0.004 | 0.7 ± 0.2 | 1.5 ± 0.7 | 1.6 ± 0.6 | 1.3 ± 0.5 | 1.1 ± 0.6 | 0.8 ± 0.2 | 1.0 ± 0.2 |
GLUD1 | 0.9 ± 0.3 | 1.2 ± 0.4 | 0.1 ± 0.2 | 1.13 ± 0.08 | 1.2 ± 0.6 | 1.5 ± 1.3 | 0.9 ± 0.2 | 0.9 ± 0.3 | 1.1 ± 0.3 | 1.5 ± 0.3 |
GNPNAT1 | 0.8 ± 0.2 | 0.8 ± 0.4 | 0.9 ± 0.4 | 0.9 ± 0.2 | 0.9 ± 0.3 | 2.0 ± 2.0 | 1.8 ± 0.5 | 1.2 ± 0.2 | 1.0 ± 0.3 | 1.7 ± 0.3 |
IVD | 0.7 ± 0.4 | 0.7 ± 0.3 | 0.70 ± 0.06 | 0.98 ± 0.06 | 1.1 ± 0.4 | 1.1 ± 0.5 | 0.7 ± 0.3 | 0.8 ± 0.3 | 1.4 ± 0.2 | 2.5 ± 0.3 |
PDHA1 | 0.94 ± 0.09 | 1.0 ± 0.4 | 1.7 ± 0.3 a | 1.15 ± 0.09 | 1.4 ± 0.6 | 1.3 ± 0.4 | 1.0 ± 0.3 | 1.0 ± 0.4 | 1.0 ± 0.2 | 1.2 ± 0.2 |
TPI1 | 2.7 ± 2.4 | 2.1 ± 1.1 | 1.1 ± 0.2 | 1.4 ± 0.2 | 1.9 ± 1.0 | 2.0 ± 0.6 | 1.3 ± 0.3 | 1.5 ± 0.7 | 1.2 ± 0.2 | 1.5 ± 0.4 |
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Cadassou, O.; Forey, P.; Machon, C.; Petrotto, E.; Chettab, K.; Tozzi, M.G.; Guitton, J.; Dumontet, C.; Cros-Perrial, E.; Jordheim, L.P. Transcriptional and Metabolic Investigation in 5′-Nucleotidase Deficient Cancer Cell Lines. Cells 2021, 10, 2918. https://doi.org/10.3390/cells10112918
Cadassou O, Forey P, Machon C, Petrotto E, Chettab K, Tozzi MG, Guitton J, Dumontet C, Cros-Perrial E, Jordheim LP. Transcriptional and Metabolic Investigation in 5′-Nucleotidase Deficient Cancer Cell Lines. Cells. 2021; 10(11):2918. https://doi.org/10.3390/cells10112918
Chicago/Turabian StyleCadassou, Octavia, Prescillia Forey, Christelle Machon, Edoardo Petrotto, Kamel Chettab, Maria Grazia Tozzi, Jérôme Guitton, Charles Dumontet, Emeline Cros-Perrial, and Lars Petter Jordheim. 2021. "Transcriptional and Metabolic Investigation in 5′-Nucleotidase Deficient Cancer Cell Lines" Cells 10, no. 11: 2918. https://doi.org/10.3390/cells10112918