Whole-genome approach implicates <it>CD44 </it>in cellular resistance to carboplatin

• Main Authors: Shukla Sunita J, Duan Shiwei, Wu Xiaolin, Badner Judith A, Kasza Kristen, Dolan M
• Format: Article
• Language: English
• Published: BMC 2009-01-01
• Series: Human Genomics
• Subjects: <it>CD44</it>; <it>carboplatin</it>; <it>CEPH</it>; <it>HapMap</it>; <it>expression</it>; <it>linkage</it>
• Online Access: http://www.humgenomics.com/content/3/2/128

<p>Abstract</p> <p>Carboplatin is a chemotherapeutic agent used in the management of many cancers, yet treatment is limited by resistance and toxicities. To achieve a better understanding of the genetic contribution to carboplatin resistance or toxicities, lymphoblastoid cell lines from 34 large Centre d'Etude du Polymorphisme Humain pedigrees were utilised to evaluate interindividual variation in carboplatin cytotoxicity. Significant heritability, ranging from 0.17-0.36 (p = 1 × 10^-7to 9 × 10^-4), was found for cell growth inhibition following 72-hour treatment at each carboplatin concentration (10, 20, 40 and 80 μM) and IC₅₀(concentration for 50 per cent cell growth inhibition). Linkage analysis revealed 11 regions with logarithm of odds (LOD) scores greater than 1.5. The highest LOD score on chromosome 11 (LOD = 3.36, p = 4.2 × 10^-5) encompasses 65 genes within the 1 LOD confidence interval for the carboplatin IC₅₀. We further analysed the IC₅₀phenotype with a linkage-directed association analysis using 71 unrelated HapMap and Perlegen cell lines and identified 18 single nucleotide polymorphisms within eight genes that were significantly associated with the carboplatin IC₅₀(p < 3.6 × 10^-5; false discovery rate < 5 per cent). Next, we performed linear regression on the baseline expression and carboplatin IC₅₀values of the eight associated genes, which identified the most significant correlation between <it>CD44 </it>expression and IC₅₀(<it>r</it>²= 0.20; p = 6 × 10^-4). The quantitative real-time polymerase chain reaction further confirmed a statistically significant difference in <it>CD44 </it>expression levels between carboplatin-resistant and -sensitive cell lines (p = 5.9 × 10^-3). Knockdown of <it>CD44 </it>expression through small interfering RNA resulted in increased cellular sensitivity to carboplatin (p < 0.01). Our whole-genome approach using molecular experiments identified <it>CD44 </it>as being important in conferring cellular resistance to carboplatin.</p>