From Proteomics to Personalized Medicine: The Importance of Isoflavone Dose and Estrogen Receptor Status in Breast Cancer Cells
Abstract
:1. Introduction
2. Materials and Methods
2.1. Cell Culture
2.2. MTT Assay
2.3. Sample Preparation for Proteomics Analysis
2.3.1. Protein Extraction
2.3.2. Protein Concentration Determination
2.3.3. Trypsin Digestion on Paramagnetic Beads
2.4. Protein Identification and Quantification by Nano-LC-UDMSE
2.5. Database Search
2.6. Statistical Analysis
2.7. Bioinformatics Analysis
3. Results and Discussion
3.1. Proteome Profiling by Data-Independent Nano-LC UDMSE Analysis
3.2. The Impact of Estrogen Receptor Status on Isoflavone Altered Pathways
3.3. The Impact of Isoflavone Dose on Protein Profile in MCF-7 Cells
4. Conclusions and Further Perspectives
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Test Compound | MCF-7 | MDA-MB-231 | |
---|---|---|---|
SC20 | IC20 | IC20 | |
Gen (μM) | 5.62 | 22.44 | 11.04 |
Dai (μM) | 19.01 | 52.24 | 36.39 |
SSE (μg/mL) | 22.59 | 166.34 | 26.36 |
MCF-7 Cells | MDA-MB-231 Cells | ||||||||
UniProt | Protein Name | p Value | log2FC | UniProt | Protein Name | p Value | log2FC | ||
Cellular Component Organization | Lipid Catabolism | ||||||||
Microtubule Cytoskeleton Organization | Lipid Catabolic Process | ||||||||
Gen IC20 | Q96N67 | Dedicator of cytokinesis protein 7 | 0.0342 | 5.06 | Gen IC20 | Q9NTX5 | Ethylmalonyl-CoA decarboxylase | 0.0015 | 7.97 |
P16591 | Tyrosine-protein kinase Fer | 0.0007 | 4.98 | Q7Z5M8 | Abhydrolase domain containing 12B | 0.0000 | 4.85 | ||
O43663 | Protein regulator of cytokinesis 1 | 0.0000 | 1.28 | Q9NY59 | Sphingomyelin phosphodiesterase 3 | 0.0067 | 1.67 | ||
Cytoskeleton Dependent Cytokinesis | Phospholipid catabolic process | ||||||||
Gen IC20 | P62745 | Rho-related GTP-binding protein RhoB | 0.0051 | −9.20 | Dai IC20 | Q13093 | Platelet-activating factor acetylhydrolase | 0.0022 | 9.76 |
Q9NZ56 | Formin-2 | 0.0057 | −9.11 | Q7Z5M8 | Abhydrolase domain containing 12B | 0.0004 | 3.61 | ||
O95630 | STAM-binding protein | 0.0150 | −1.21 | Q9NY59 | Sphingomyelin phosphodiesterase 3 | 0.0238 | 1.25 | ||
Dai IC20 | P62745 | Rho-related GTP-binding protein RhoB | 0.0201 | −6.44 | Degradation of Extracellular Matrix | ||||
Q9NZ56 | Formin-2 | 0.0013 | −6.34 | Gen IC20 | P42574 | Caspase-3 | 0.0002 | −2.95 | |
Q13464 | Rho-associated protein kinase 1 | 0.0049 | −3.44 | P07858 | Cathepsin B | 0.0001 | −2.71 | ||
Supramolecular fiber organization | Q13443 | Disintegrin and metalloproteinase domain-containing protein 9 | 0.0001 | −1.05 | |||||
Gen IC20 | P62745 | Rho-related GTP-binding protein RhoB | 0.0051 | −9.20 | Dai IC20 | P42574 | Caspase-3 | 0.0034 | −2.43 |
Q9NZ56 | Formin-2 | 0.0057 | −9.11 | O15230 | Laminin subunit alpha-5 | 0.0014 | −1.67 | ||
P23258 | Tubulin gamma-1 chain | 0.0473 | −2.80 | P07711 | Cathepsin L1 | 0.0123 | −1.66 | ||
SSE IC20 | P62745 | Rho-related GTP-binding protein RhoB | 0.0168 | −7.24 | SSE IC20 | P42574 | Caspase-3 | 0.0141 | −3.28 |
Q9NZ56 | Formin-2 | 0.0075 | −7.14 | P07858 | Cathepsin B | 0.0049 | −2.53 | ||
P23258 | Tubulin gamma-1 chain | 0.0207 | −6.03 | P09238 | Stromelysin-2 (Matrix metalloproteinase-10) | 0.0011 | −1.00 | ||
Signaling by Receptor Tyrosine Kinases | mRNA Splicing | ||||||||
Gen IC20 | P13942 | Collagen alpha-2(XI) chain | 0.0209 | 7.06 | 17S U2 snRNP | ||||
Q96N67 P16591 | Dedicator of cytokinesis protein 7 Tyrosine-protein kinase Fer | 0.0342 0.0007 | 5.06 4.98 | Gen IC20 | P14678 | Small nuclear ribonucleoprotein-associated proteins B and B’ | 0.0000 | −2.44 | |
P62318 | Small nuclear ribonucleoprotein Sm D3 | 0.0171 | −1.20 | ||||||
Dai IC20 | P19388 | DNA-directed RNA polymerases I_ II_ and III subunit RPABC1 | 0.0031 | −8.48 | Q7L014 | Probable ATP-dependent RNA helicase DDX46 | 0.0004 | −1.16 | |
Q9H6T0 | Epithelial splicing regulatory protein 2 | 0.0003 | −3.74 | RNA Polymerase II Transcription Termination | |||||
Q13464 | Rho-associated protein kinase 1 | 0.0049 | −3.44 | SSE IC20 | P14678 | Small nuclear ribonucleoprotein-associated proteins B and B’ | 0.0034 | −2.60 | |
Cell Cycle | P62318 | Small nuclear ribonucleoprotein Sm D3 | 0.0028 | −1.92 | |||||
Gen SC20 | P23258 | Tubulin gamma-1 chain | 0.0396 | −11.85 | P26368 | Splicing factor U2AF 65 kDa subunit | 0.0003 | −1.54 | |
P50402 | Emerin | 0.0437 | −11.60 | ||||||
P19388 | DNA-directed RNA polymerases I_ II_ and III subunit RPABC1 | 0.0472 | −11.12 |
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Ilieș, M.; Uifălean, A.; Pașca, S.; Dhople, V.M.; Lalk, M.; Iuga, C.A.; Hammer, E. From Proteomics to Personalized Medicine: The Importance of Isoflavone Dose and Estrogen Receptor Status in Breast Cancer Cells. J. Pers. Med. 2020, 10, 292. https://doi.org/10.3390/jpm10040292
Ilieș M, Uifălean A, Pașca S, Dhople VM, Lalk M, Iuga CA, Hammer E. From Proteomics to Personalized Medicine: The Importance of Isoflavone Dose and Estrogen Receptor Status in Breast Cancer Cells. Journal of Personalized Medicine. 2020; 10(4):292. https://doi.org/10.3390/jpm10040292
Chicago/Turabian StyleIlieș, Maria, Alina Uifălean, Sergiu Pașca, Vishnu Mukund Dhople, Michael Lalk, Cristina Adela Iuga, and Elke Hammer. 2020. "From Proteomics to Personalized Medicine: The Importance of Isoflavone Dose and Estrogen Receptor Status in Breast Cancer Cells" Journal of Personalized Medicine 10, no. 4: 292. https://doi.org/10.3390/jpm10040292