Using Copy Number Alterations to Identify New Therapeutic Targets for Bladder Carcinoma
Abstract
:1. Introduction
2. Results and Discussion
3. Materials and Methods
3.1. Tumor Specimens
3.2. Array Comparative Genomic Hybridization (Array-CGH)
3.3. Fluorescence in Situ Hybridization (FISH)
4. Conclusions
Acknowledgments
Author Contributions
Conflicts of Interest
Abbreviations
TCC: transitional cell carcinomas |
NMIBC: non-muscle-invasive bladder cancer |
MIBC: muscle-invasive bladder cancer |
CSC: cancer stem cell |
CGH: comparative genomic hybridization |
CNA: copy number alteration |
LGNI: low grade non-infiltrating |
HGIN: high grade infiltrating |
FISH: fluorescence in situ hybridization |
References
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Genes | Nature [10] | Clin Cancer Res [11] | Biopsies | CSC Subpopulation | Biopsies | CSC Subpopulation | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
% Loss HGIN | % Gain HGIN | % Loss IN | % Gain IN | % Loss LGNI | % Loss HGIN | % Loss LGNI | % Loss HGIN | % Gain LGNI | % Gain HGIN | % Gain LGNI | % Gain HGIN | |
CCND1 * | - | 10 A° | - | 11 A | - | - | 10 M | 20 M | 20 A 30 M | 12.5 A 12.5 NM 12.5 M | 40 A 20 M | 20 A 20 NM |
E2F3/SOX4 | - | 20 A° | - | 18 A | - | - | - | - | - | 12.5 NM | - | 20 NM |
EGFR | - | 11 A° | - | 7 A | - | - | 10 M | - | 20 NM 10 M | 12.5 M | 30 NM | 20 M |
PPARG | - | 17 A° | - | 14 A | - | - | - | - | - | 12.5 A 25 NM 25 M | - | 40 M |
PVRL4 * | - | 19 A° | - | 17 A | - | - | 10 CL 20 NM | 20 NM | 10 NM 10 M | 75 M | 30 NM 10 M | 40 M |
YWHAZ * | - | 22 A° | - | 22 A | - | - | - | - | 10 NM | 25 NM | 10 NM | 40 NM |
MDM2 | - | 9 A° | - | 9 A | - | - | 10 M | - | 20 M | - | 10 M | 20 NM 20 M |
HER2 | - | 7 A° | - | 5 A | - | - | 20 M | - | 20 M 10 NM | 37.5 M | 10 M | - |
YAP1 | - | 4 A° | - | ni | 10 M | 12.5 M | - | - | - | 12.5 M | - | 25 M |
CCNE1 | - | 12 A° | - | 9 A | - | 12.5 M | - | - | - | 25 M | - | 60 M |
MYC | - | 13 A° | - | 13 A | - | 12.5 M | 10 NM 10 M | - | - | 12.5 M | 10 M | 40 M |
FGFR3 * | - | 3 A° | - | 4 A | - | 12.5 M | 20 M | 20 M | 10 A 40 M | 12.5 M | 10 A 10 M | 20 M |
MYCL1 * | - | 6 A° | 6 A | - | - | - | - | 10 M | 12.5 M | 10 NM | - | |
BCL2L1 | - | 11 A° | - | 10 A | - | - | 10 CL 20 NM | - | 50 M | 12.5 A 12.5 NM 37.5 M | 10 A 20 NM 10 M | 20 NM |
BEND3 * | - | ni | - | 3 A | - | 37.5 NM | - | - | 10 M | 25 NM | 20 NM 10 M | - |
BIRC3 | - | ni | - | 4 A | 20 M | 37.5 M | 10 NM 10 M | 20 M | - | - | 10 M | 20 NM 20 M |
GDI2 * | - | ni | - | 9 A | 30 M | 12.5 M | 10 M | 10 NM 10 M | 25 M | 10 NM | 60 M | |
PRKCI | - | ni | 4 A | - | - | - | - | - | 12.5 M | - | - | |
SOX4 | - | ni | 18 A | - | - | - | - | - | 12.5 NM | - | 20 NM | |
CDKN2A | 47 D° | - | 43 D | 30 CL 10 M | 12.5 CL 12.5 NM 25 M | 30 CL | 20 CL 40 M | - | - | - | - | |
PTEN | 13 D° | - | 13 D | - | - | - | - | - | 10 M | - | - | 20 NM |
NCOR1 | 25 D° | - | 24 D | - | - | 25 M | - | 20 M | - | - | - | - |
CREBBP | 13 D° | - | 16 D | - | 20 M | 25 M | 10 M | - | - | 37.5 M | - | - |
RB1 | 14 D° | - | 17 D | - | - | 12.5 M | 40 M | 20 M | - | 12.5 M | - | - |
ARID1A | ni | - | 5 D | - | 10 M | - | - | - | - | - | - | - |
FHIT | ni | - | 13 D | - | 10 M | 12.5 M | 10 M | 20 M | - | 12.5 M | - | - |
IKZF2 | ni | - | 15 D | - | - | 50 M | - | 20 M | 10 M | - | - | - |
LRP1B | ni | - | 17 D | - | - | 37.5 M | - | 20 M | - | - | - | - |
PDE4D | ni | - | 22 D | - | - | 25 M | - | 20 M | - | - | - | - |
WWOX | ni | - | 15 D | - | - | 12.5 M | - | - | - | - | - | - |
HGIN | HER2 % of Amplified Cells | PPARG > Two Signals | CDKN2A < Two Signals |
19 | 22% | 32% m = 2.36 | 100% m = 0.08 |
20 | 6% | - | 85% m = 1.02 |
21 | 84% | 56.4% m = 3 | 58% m = 1.19 |
22 | 80% | 50% m = 2.8 | 6% m = 2.94 |
23 | 30% | 63.6% m = 2.97 | 10% m = 2.27 |
24 | 2.5% | 48% m = 2.66 | - |
25 | 3.3% | 42% m = 2.4 | 100% m = 0.02 |
26 | 20% | 28% m = 2.34 | 7% m = 2.72 |
27 | 37.5% | 87.5% m = 3.7 | 43% m = 1.83 |
LGNI | HER2 % of Amplified Cells | PPARG > Two Signals | CDKN2A < Two Signals |
28 | 8% | 4% m = 2.02 | 100% m = 0.17 |
29 | 10% | - | 61% m = 1.28 |
30 | 13% | 10% m = 1.6 | 100% m = 0 |
31 | 32% | 2% m = 1.72 | 58% m = 1.21 |
32 | 14% | 38% m = 2.52 | 99% m = 0.03 |
33 | 30% | 4% m = 1.76 | - |
Histotype | CASE n° | Biopsies | Cancer Stem Cells | ||||
---|---|---|---|---|---|---|---|
HER2 | PPARγ | CDKN2A | HER2 | PPARγ | CDKN2A | ||
LGNI | 1 | disomy | disomy | disomy | disomy | disomy | disomy |
2 | disomy | disomy | complete loss | disomy | disomy | complete loss | |
3 | disomy | disomy | disomy | mosaic loss | disomy | disomy | |
4 | non mosaic gain | disomy | disomy | mosaic loss | disomy | disomy | |
5 | mosaic gain | disomy | mosaic loss | mosaic gain | disomy | disomy | |
6 | mosaic gain | disomy | disomy | disomy | disomy | disomy | |
7 | disomy | disomy | disomy | disomy | disomy | disomy | |
8 | disomy | disomy | complete loss | disomy | disomy | complete loss | |
9 | disomy | disomy | disomy | disomy | disomy | disomy | |
10 | disomy | disomy | complete loss | disomy | disomy | complete loss | |
HGIN | 11 | disomy | non mosaic gain | mosaic loss | disomy | disomy | disomy |
12 | mosaic gain | mosaic gain | complete loss | disomy | mosaic gain | mosaic loss | |
13 | disomy | disomy | mosaic loss | disomy | disomy | mosaic loss | |
14 | mosaic gain | disomy | non mosaic loss | disomy | disomy | complete loss | |
15 | disomy | non mosaic gain | disomy | disomy | mosaic gain | disomy | |
16 | disomy | amplification | disomy | - | - | - | |
17 | disomy | disomy | disomy | - | - | - | |
18 | mosaic gain | disomy | disomy | - | - | - |
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Conconi, D.; Sala, E.; Bovo, G.; Strada, G.; Dalprà, L.; Lavitrano, M.; Bentivegna, A. Using Copy Number Alterations to Identify New Therapeutic Targets for Bladder Carcinoma. Int. J. Mol. Sci. 2016, 17, 271. https://doi.org/10.3390/ijms17030271
Conconi D, Sala E, Bovo G, Strada G, Dalprà L, Lavitrano M, Bentivegna A. Using Copy Number Alterations to Identify New Therapeutic Targets for Bladder Carcinoma. International Journal of Molecular Sciences. 2016; 17(3):271. https://doi.org/10.3390/ijms17030271
Chicago/Turabian StyleConconi, Donatella, Elena Sala, Giorgio Bovo, Guido Strada, Leda Dalprà, Marialuisa Lavitrano, and Angela Bentivegna. 2016. "Using Copy Number Alterations to Identify New Therapeutic Targets for Bladder Carcinoma" International Journal of Molecular Sciences 17, no. 3: 271. https://doi.org/10.3390/ijms17030271
APA StyleConconi, D., Sala, E., Bovo, G., Strada, G., Dalprà, L., Lavitrano, M., & Bentivegna, A. (2016). Using Copy Number Alterations to Identify New Therapeutic Targets for Bladder Carcinoma. International Journal of Molecular Sciences, 17(3), 271. https://doi.org/10.3390/ijms17030271