Multi-Omics Characterization of the Spontaneous Mesenchymal–Epithelial Transition in the PMC42 Breast Cancer Cell Lines
Abstract
:1. Introduction
2. Materials and Methods
2.1. Cell Lines and Cell Culture
2.2. Preparation of Metaphase Spread and Karyotyping
2.3. DNA Extraction, Whole Exome Sequencing and Processing of Sequencing Data
2.4. RNA Extraction, cDNA Synthesis and RT-qPCR
2.5. Whole Transcriptome Sequencing and Analysis of PMC42 Cell Lines
2.6. Data-Independent Acquisition (DIA) Mass Spectrometry of PMC42 Cell Lines
2.7. Fluorescence Activated Cell Sorting (FACS)
2.8. Immunocytochemistry
2.9. Seahorse Metabolic Analyser
2.10. Statistical Analysis
3. Results
3.1. Comparison of PMC42 Cell Lines with Other BC Cell Lines (Luminal, Basal A and Basal B)
3.2. CD44+CD24−/low Phenotype Association with Breast Molecular Subtypes and Other EMT Markers
3.3. Comparative RNA-seq Analysis of PMC42 Cell Lines
3.4. Comparative Proteome Quantification of Alterations in the PMC42 Cell Line System
3.5. Karyotypic Heterogeneity Exists within and across the Sister Breast Cancer Cell Lines PMC42-ET and PMC42-LA
3.6. Cancer Driver Mutations in PMC42 Cell Lines
3.7. Inference of CNV from Exome Sequencing Data
3.8. TGFBR2 Ablation and Influence on EMT Induction in PMC42-LA
3.9. Inter-Data Relationships from CNV and RNA-seq with Proteome Data
3.10. The Differences in PMC42 Karyotypes are Reflected in Their Transcriptome and Proteome Ratios
3.11. Bioenergetic Profiles of PMC42 Cells in Comparison with Other Breast Cancer Cell Lines
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Chromosome No. | p-Value across ET vs. LA |
---|---|
22 | 5.28847 × 10−45 |
5 | 1.50398 × 10−28 |
13 | 7.71473 × 10−23 |
11 | 9.42164 × 10−20 |
3 | 3.33503 × 10−18 |
7 | 8.49205 × 10−14 |
8 | 3.73987 × 10−8 |
9 | 1.08547 × 10−6 |
10 | 0.012162341 |
X | 0.0151172 |
14 | 0.022502942 |
18 | 0.083804992 |
12 | 0.260603283 |
1 | 0.278286015 |
15 | 0.531258862 |
2 | 0.678929758 |
6 | 0.717332498 |
16 | 0.748135128 |
4 | 0.75812698 |
17 | 0.771687988 |
20 | 0.814301536 |
21 | 0.823855275 |
19 | 0.928168854 |
Cytokines and Growth Factors (CGF) | Transcription Factor (TF) | Homeodomain Proteins (HP) | Cell Differentiation Markers (CM) | Protein Kinases (PK) | Translocated Cancer Genes (TCG) | Oncogenes | Tumour Suppressors | |
---|---|---|---|---|---|---|---|---|
Tumour suppressors | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 4* |
Oncogenes | 1 | 4 | 1 | 1 | 1 | 8 | 10& | |
Translocated cancer genes | 0 | 4 | 1 | 0 | 1 | 8* | ||
Protein kinases | 0 | 0 | 0 | 0 | 17# | |||
Cell differentiation markers | 2 | 0 | 0 | 8! | ||||
Homeodomain proteins | 0 | 4 | 4@ | |||||
Transcription factor | 0 | 28$ | ||||||
Cytokines and Growth Factors | 6^ |
Cytokines and Growth Factors | Transcription Factor | Homeodomain Proteins | Cell Differentiation Markers | Protein Kinases | Translocated Cancer Genes | Oncogenes | Tumour Suppressors | |
---|---|---|---|---|---|---|---|---|
Tumour suppressors | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 3* |
Oncogenes | 0 | 3 | 1 | 0 | 1 | 7 | 8& | |
Translocated cancer genes | 0 | 3 | 1 | 0 | 1 | 7* | ||
Protein kinases | 0 | 0 | 0 | 0 | 15# | |||
Cell differentiation markers | 1 | 0 | 0 | 6! | ||||
Homeodomain proteins | 0 | 3 | 3@ | |||||
Transcription factor | 0 | 24$ | ||||||
Cytokines and Growth Factors | 5^ |
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Bhatia, S.; Monkman, J.; Blick, T.; Duijf, P.H.; Nagaraj, S.H.; Thompson, E.W. Multi-Omics Characterization of the Spontaneous Mesenchymal–Epithelial Transition in the PMC42 Breast Cancer Cell Lines. J. Clin. Med. 2019, 8, 1253. https://doi.org/10.3390/jcm8081253
Bhatia S, Monkman J, Blick T, Duijf PH, Nagaraj SH, Thompson EW. Multi-Omics Characterization of the Spontaneous Mesenchymal–Epithelial Transition in the PMC42 Breast Cancer Cell Lines. Journal of Clinical Medicine. 2019; 8(8):1253. https://doi.org/10.3390/jcm8081253
Chicago/Turabian StyleBhatia, Sugandha, James Monkman, Tony Blick, Pascal HG Duijf, Shivashankar H. Nagaraj, and Erik W. Thompson. 2019. "Multi-Omics Characterization of the Spontaneous Mesenchymal–Epithelial Transition in the PMC42 Breast Cancer Cell Lines" Journal of Clinical Medicine 8, no. 8: 1253. https://doi.org/10.3390/jcm8081253