Genomic Characterization of Preclinical Prostate Cancer Cell Line Models
Abstract
:1. Introduction
2. Results
2.1. Database Confirmation of Detected Coding Region Alterations
2.1.1. PC-3 Cells
2.1.2. 22RV1 Cells
2.1.3. Du-145 Cells
2.1.4. LNCaP Parental and Derivative Cell Lines
2.1.5. VCaP Parental and Derivative Cell Line
2.2. Clinically Actionable Alterations in Selected Pathways
2.2.1. AR Pathway
2.2.2. Apoptosis Pathway
2.2.3. DDR Pathway
2.2.4. PTEN/PI3K/AKT Pathway
2.2.5. Tumor Suppression Pathway
2.3. Therapeutic Targeting of Cell Line-Specific Markers
2.4. The Cancer Dependency Map Celligner Tool
3. Discussion
4. Materials and Methods
4.1. Cell Culture
4.2. DNA Extractions
4.3. Custom Illumina AmpliSeq Panel Construction
4.4. Library Preparation and Targeted Next-Generation Sequencing
4.5. Variant Identification and Analysis
4.6. Compounds
4.7. CellTiter-Glo Luminescent Cell Viability Assay
4.8. Population Data
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Figg Lab Panel | BRCAnalysis CDX | FoundationONE CDX | ProstateNext | Invitae PCa Panel | Color Hereditary Prostate | Fulgent | ||
---|---|---|---|---|---|---|---|---|
Androgen Receptor Signaling | AR | x | ||||||
Apoptosis | BCL2 | x | ||||||
BCL2L1 | x | |||||||
MCL1 | x | |||||||
DNA Damage Repair | ATM | x | x | x | x | x | x | |
BARD1 | x | x | x | |||||
BRCA1 | x | x | x | x | x | x | x | |
BRCA2 | x | x | x | x | x | x | x | |
BRIP1 | x | x | x | x | ||||
CDK12 | x | x | ||||||
CHEK2 | x | x | x | x | x | |||
NBN | x | x | x | x | ||||
PALB2 | x | x | x | x | x | |||
RAD51B | x | x | ||||||
PTEN/PI3K/AKT pathway | AKT1 | x | x | |||||
MAP3K1 | x | |||||||
PIK3CA | x | x | ||||||
PTEN | x | x | ||||||
Tumor Suppression | TP53 | x | x | x | x | x | ||
MDM2 | x |
AR | ATM | AKT1 | BARD1 | BCL2 | BCL2L1 | BRCA1 | BRCA2 | BRIP1 | CDK12 | CHEK2 | MAP3K1 | NBN | MCL1 | MDM2 | PALB2 | PIK3CA | PTEN | RAD51B | TP53 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PC-3 | INS-1 | DEL-7 | SNV-8 | SNV-12 | SNV-1 | SNV-2 | SNV-12 | SNV-5 | SNV-1 | SNV-11 | INS-1 | SNV-2 | SNV-1 | SNV-11 | DEL-1 | SNV-2 | DEL-1 | |||
SNV-1 | MNV-1 | MNV-1 | DEL-1 | DEL-1 | INS-2 | SNV-1 | DEL-1 | |||||||||||||
DEL-1 | DEL-1 | |||||||||||||||||||
22RV1 | INS-4 | DEL-12 | SNV-9 | SNV-12 | SNV-1 | DEL-1 | SNV-15 | SNV-13 | SNV-2 | SNV-3 | SNV-1 | SNV-7 | SNV-10 | INS-1 | SNV-2 | SNV-3 | SNV-7 | SNV-3 | SNV-2 | SNV-3 |
SNV-3 | SNV-8 | MNV-1 | MNV-1 | DEL-3 | DEL-1 | DEL-1 | DEL-1 | DEL-1 | DEL-1 | DEL-1 | DEL-1 | DEL-1 | DEL-2 | DEL-3 | DEL-2 | |||||
DEL-1 | INS-1 | DEL-1 | DEL-3 | INS-1 | INS-1 | INS-1 | INS-1 | |||||||||||||
Du-145 | SNV-3 | DEL-11 | SNV-9 | SNV-3 | SNV-15 | SNV-10 | SNV-5 | SNV-1 | SNV-1 | SNV-9 | INS-1 | INS-1 | SNV-2 | SNV-2 | SNV-4 | SNV-3 | SNV-7 | SNV-4 | ||
DEL-2 | SNV-6 | DEL-1 | DEL-2 | DEL-3 | DEL-2 | DEL-1 | DEL-1 | DEL-1 | DEL-1 | DEL-2 | DEL-3 | DEL-1 | ||||||||
INS-2 | INS-1 | INS-1 | INS-1 | |||||||||||||||||
LNCaP | SNV-1 | DEL-15 | SNV-9 | SNV-12 | SNV-4 | SNV-8 | SNV-6 | SNV-2 | SNV-2 | SNV-7 | SNV-1 | INS- 1 | SNV-2 | SNV-1 | SNV-5 | SNV-2 | SNV-6 | SNV-3 | ||
INS-1 | SNV-9 | MNV-1 | MNV- 1 | DEL-1 | DEL-2 | DEL-1 | INS-1 | DEL-1 | DEL-1 | SNV-1 | DEL-1 | DEL-2 | DEL-2 | DEL-3 | INS-1 | DEL-1 | ||||
INS-1 | DEL-1 | DEL-1 | INS-1 | DEL-2 | ||||||||||||||||
LNCaP-ABL | SNV-3 | DEL-19 | SNV-9 | SNV-13 | SNV-1 | SNV-6 | SNV-11 | SNV-8 | SNV-4 | SNV-5 | SNV-9 | DEL-3 | INS-1 | SNV-2 | SNV-2 | SNV-11 | SNV-4 | SNV-6 | SNV-5 | |
INS-1 | SNV-14 | MNV-1 | MNV-1 | DEL-1 | DEL-1 | DEL-2 | DEL-1 | INS-2 | DEL-1 | SNV-2 | SNV-1 | DEL-2 | DEL-2 | DEL-2 | DEL-4 | INS-1 | DEL-1 | |||
INS-3 | DEL-1 | DEL-1 | INS-1 | DEL-3 | ||||||||||||||||
LNCaP-95 | SNV-1 | DEL-18 | SNV-9 | SNV-12 | SNV-1 | SNV-9 | SNV-12 | SNV-10 | SNV-4 | SNV-5 | SNV-10 | SNV-4 | INS-1 | SNV-5 | SNV-3 | SNV-6 | SNV-2 | SNV-6 | SNV-4 | |
INS-1 | SNV-17 | MNV-1 | MNV-1 | DEL-2 | DEL-2 | DEL-2 | DEL-3 | INS-1 | DEL-2 | DEL-3 | SNV-1 | DEL-2 | DEL-1 | DEL-2 | DEL-4 | DEL-4 | DEL-1 | |||
DEL-1 | INS-1 | DEL-1 | DEL-1 | INS-1 | INS-1 | INS-1 | INS-1 | |||||||||||||
VCaP | DEL-2 | DEL-7 | SNV-8 | SNV-12 | SNV-1 | SNV-14 | SNV-12 | SNV-4 | SNV-3 | SNV-1 | SNV-7 | INS-1 | SNV-2 | SNV-1 | SNV-3 | SNV-3 | SNV-3 | SNV-4 | ||
SNV-8 | MNV-1 | MNV-1 | DEL-3 | DEL-1 | DEL-1 | INS-1 | DEL-2 | DEL-1 | ||||||||||||
INS-2 | DEL-1 | DEL-1 | ||||||||||||||||||
VCaP-CR | DEL-2 | DEL-7 | SNV-7 | SNV-12 | SNV-1 | SNV-14 | SNV-12 | SNV-4 | SNV-3 | SNV-1 | SNV-7 | INS-1 | SNV-2 | SNV-1 | SNV-3 | SNV-3 | SNV-3 | SNV-4 | ||
SNV-8 | MNV-1 | MNV-1 | DEL-3 | DEL-1 | DEL-1 | INS-1 | DEL-2 | DEL-1 | ||||||||||||
INS-2 | DEL-1 | DEL-1 |
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Beatson, E.L.; Risdon, E.N.; Napoli, G.C.; Price, D.K.; Chau, C.H.; Figg, W.D. Genomic Characterization of Preclinical Prostate Cancer Cell Line Models. Int. J. Mol. Sci. 2024, 25, 6111. https://doi.org/10.3390/ijms25116111
Beatson EL, Risdon EN, Napoli GC, Price DK, Chau CH, Figg WD. Genomic Characterization of Preclinical Prostate Cancer Cell Line Models. International Journal of Molecular Sciences. 2024; 25(11):6111. https://doi.org/10.3390/ijms25116111
Chicago/Turabian StyleBeatson, Erica L., Emily N. Risdon, Giulia C. Napoli, Douglas K. Price, Cindy H. Chau, and William D. Figg. 2024. "Genomic Characterization of Preclinical Prostate Cancer Cell Line Models" International Journal of Molecular Sciences 25, no. 11: 6111. https://doi.org/10.3390/ijms25116111