Molecular Characterization and Subtyping of Breast Cancer Cell Lines Provide Novel Insights into Cancer Relevant Genes
Abstract
:1. Introduction
2. Materials and Methods
2.1. Cell Lines and Sample Preparation
2.2. Immunoblotting
2.3. mRNA-Sequencing and Expression Analysis
2.4. Quantitative PCR
2.5. Mutation Calling
2.6. Fusion Calling and Analysis of Fusion Transcripts
2.7. SNP Array
2.8. Transfection of siRNAs
3. Results
3.1. Molecular Subtyping of BC Cell Lines Separate Basal-like from Luminal BC Models
3.2. Mutations in BC Cell Lines Frequently Affect TP53 and BRCA2
3.3. Identification of Novel Fusion Transcripts in BC Cell Lines
3.4. Identification of IRX Genes and KLF15 as Candidate Tumor Suppressor Genes in BC
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Cell Line | Origin | Stage | Histologic Subtype | Sex | Age | Site of Sampling | P/M | Refs |
---|---|---|---|---|---|---|---|---|
BT-474 | breast ductal carcinoma | invasive | ductal | f | 60 | breast | P | [17] |
CAL-120 | breast adenocarcinoma | invasive | na | f | 43 | PE | M | * |
CAL-148 | breast adenocarcinoma | invasive | ductal | f | 58 | PE | M | [18] |
CAL-51 | breast adenocarcinoma | invasive | ductal | f | 45 | PE | M | [19] |
CAL-85-1 | breast adenocarcinoma | invasive | ductal | f | 35 | breast | M | [18] |
COLO-824 | breast carcinoma | invasive | na | f | 52 | PE | M | * |
DU-4475 | breast ductal carcinoma | invasive | ductal | f | 62 | skin | M | [20] |
EFM-19 | breast ductal carcinoma | invasive | ductal | f | 50 | PE | M | [21] |
EFM-192A 1 | breast adenocarcinoma | invasive | na | f | 46 | PE | M | * |
EFM-192B 1 | breast adenocarcinoma | invasive | na | f | 46 | PE | M | * |
EFM-192C 1 | breast adenocarcinoma | invasive | na | f | 46 | PE | M | * |
ETCC-006 2 | breast ductal carcinoma | in situ | ductal | f | 47 | breast | P | [22] |
ETCC-007 2 | breast ductal carcinoma | in situ | ductal | f | 47 | breast | P | [22] |
EVSA-T | breast carcinoma | invasive | na | f | 58 | ascites | M | [23] |
HCC-1143 3 | breast ductal carcinoma | invasive | ductal | f | 52 | breast | P | [24] |
HCC-1599 3 | breast ductal carcinoma | invasive | ductal | f | 44 | breast | P | [24] |
HCC-1937 3 | breast ductal carcinoma | invasive | ductal | f | 24 | breast | P | [24] |
HDQ-P1 | breast ductal carcinoma | invasive | ductal | f | 50 | breast | P | [25] |
HS-578T | breast carcinosarcoma | invasive | ductal | f | 74 | breast | P | [26] |
IPH-926 | breast lobular carcinoma | invasive | lobular | f | 72 | ascites | M | [27] |
JIMT-1 | breast ductal carcinoma | invasive | ductal | f | 62 | PE | M | [28] |
KPL-1 4 | breast adenocarcinoma | invasive | na | f | 69 | PE | M | [10] |
MCF-7 | breast adenocarcinoma | invasive | na | f | 69 | PE | M | [10] |
MDA-MB-231 | breast carcinoma | invasive | na | f | 51 | PE | M | [29] |
MDA-MB-453 | breast carcinoma | invasive | na | f | 48 | PF | M | [29] |
MDA-MB-468 | breast carcinoma | invasive | na | f | 51 | PE | M | [29] |
MFM-223 | breast ductal carcinoma | invasive | ductal | f | >45 | PE | M | [30] |
SK-BR-3 | breast adenocarcinoma | invasive | na | f | 43 | PE | M | [31] |
T-47D | breast ductal carcinoma | invasive | ductal | f | 54 | PE | M | [32] |
Name | Sequence (5′→3′) | Product Size [bp] |
---|---|---|
FGFR2_ex9_fwd 1 | TGTATGGTGGTAACAGTCATCC | 240 and 246 |
CRYBG1_ex18_rev 2 | CTGAACAGAGCGTATTTGTGTG | |
RTN4IP1_ex8_fwd 3 | GGAAAGGAGTCCATTATCGCTG | 206 |
CRYBG1_ex3_rev 2 | TGATCTGGTGGGACTCTCTAAC | |
ABL1_fwd | TGACTTTGAGCCTCAGGGTCTGAGTGAAGCC | 216 (mRNA) 779 (gene) |
ABL1_rev | CCATTTTTGGTTTGGGCTTCACACCATTCC |
Cell Line | ER | PR | AR | HER2 | TNBC | Cluster | PAM50 Subtype |
---|---|---|---|---|---|---|---|
BT-474 | ++ | ++ | ++ | +++ | A | luminal | |
CAL-120 | yes | B | basal-like | ||||
CAL-148 | + | + | yes | A | luminal | ||
CAL-51 | + | yes | B | basal-like | |||
CAL-85-1 | + | yes | B | basal-like | |||
COLO-824 | + | yes | B | basal-like | |||
DU-4475 | yes | B | luminal | ||||
EFM-19 | +++ | ++ | ++ | ++ | A | luminal | |
EFM-192A | + | +++ | A | luminal | |||
EFM-192B | + | +++ | A | luminal | |||
EFM-192C | ++ | + | + | +++ | A | luminal | |
ETCC-006 | yes | B | basal-like | ||||
ETCC-007 | + | yes | B | luminal | |||
EVSA-T | ++ | A | luminal | ||||
HCC-1143 | + | yes | B | basal-like | |||
HCC-1599 | + | yes | B | basal-like | |||
HCC-1937 | + | yes | B | basal-like | |||
HDQ-P1 | + | yes | B | luminal | |||
HS-578T | yes | B | luminal | ||||
IPH-926 | ++ | A | luminal | ||||
JIMT-1 | ++ | B | luminal | ||||
KPL-1 | +++ | +++ | + | A | luminal | ||
MCF-7 | +++ | + | A | luminal | |||
MDA-MB-231 | yes | B | basal-like | ||||
MDA-MB-453 | +++ | ++ | A | luminal | |||
MDA-MB-468 | yes | B | basal-like | ||||
MFM-223 | +++ | yes | A | luminal | |||
SK-BR-3 | ++ | A | luminal | ||||
T-47D | +++ | +++ | ++ | ++ | A | luminal |
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Pommerenke, C.; Nagel, S.; Haake, J.; Koelz, A.L.; Christgen, M.; Steenpass, L.; Eberth, S. Molecular Characterization and Subtyping of Breast Cancer Cell Lines Provide Novel Insights into Cancer Relevant Genes. Cells 2024, 13, 301. https://doi.org/10.3390/cells13040301
Pommerenke C, Nagel S, Haake J, Koelz AL, Christgen M, Steenpass L, Eberth S. Molecular Characterization and Subtyping of Breast Cancer Cell Lines Provide Novel Insights into Cancer Relevant Genes. Cells. 2024; 13(4):301. https://doi.org/10.3390/cells13040301
Chicago/Turabian StylePommerenke, Claudia, Stefan Nagel, Josephine Haake, Anne Leena Koelz, Matthias Christgen, Laura Steenpass, and Sonja Eberth. 2024. "Molecular Characterization and Subtyping of Breast Cancer Cell Lines Provide Novel Insights into Cancer Relevant Genes" Cells 13, no. 4: 301. https://doi.org/10.3390/cells13040301
APA StylePommerenke, C., Nagel, S., Haake, J., Koelz, A. L., Christgen, M., Steenpass, L., & Eberth, S. (2024). Molecular Characterization and Subtyping of Breast Cancer Cell Lines Provide Novel Insights into Cancer Relevant Genes. Cells, 13(4), 301. https://doi.org/10.3390/cells13040301