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Whole-genome approach implicates CD44 in cellular resistance to carboplatin.

Shukla SJ, Duan S, Wu X, Badner JA, Kasza K, Dolan ME - Hum. Genomics (2009)

Bottom Line: We further analysed the IC(50) phenotype 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 IC(50) (p < 3.6 x 10(-5); false discovery rate <5 per cent).Next, we performed linear regression on the baseline expression and carboplatin IC(50) values of the eight associated genes, which identified the most significant correlation between CD44 expression and IC(50) (r(2)= 0.20; p = 6 x 10(-4)).Knockdown of CD44 expression through small interfering RNA resulted in increased cellular sensitivity to carboplatin (p < 0.01).

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.

ABSTRACT
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 x 10(-7) to 9 x 10(-4)), was found for cell growth inhibition following 72-hour treatment at each carboplatin concentration (10, 20, 40 and 80 microM) and IC(50) (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 x 10(-5)) encompasses 65 genes within the 1 LOD confidence interval for the carboplatin IC 50 . We further analysed the IC(50) phenotype 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 IC(50) (p < 3.6 x 10(-5); false discovery rate <5 per cent). Next, we performed linear regression on the baseline expression and carboplatin IC(50) values of the eight associated genes, which identified the most significant correlation between CD44 expression and IC(50) (r(2)= 0.20; p = 6 x 10(-4)). The quantitative real-time polymerase chain reaction further confirmed a statistically significant difference in CD44 expression levels between carboplatin-resistant and -sensitive cell lines (p = 5.9 x 10(-3)). Knockdown of CD44 expression through small interfering RNA resulted in increased cellular sensitivity to carboplatin (p < 0.01). Our whole-genome approach using molecular experiments identified CD44 as being important in conferring cellular resistance to carboplatin.

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Box plots and heritability (h2) values for 34 families are shown for 10, 20, 40 and 80 μM carboplatin. Centre d'Etude du Polymorphisme Humain (CEPH) family identification pertaining to the box plot is located on the x-axis. The middle line within the box represents the mean percentage survival of each family, while the box edges and whiskers represent the standard error of the mean and twice the standard error of the mean, respectively.
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Figure 2: Box plots and heritability (h2) values for 34 families are shown for 10, 20, 40 and 80 μM carboplatin. Centre d'Etude du Polymorphisme Humain (CEPH) family identification pertaining to the box plot is located on the x-axis. The middle line within the box represents the mean percentage survival of each family, while the box edges and whiskers represent the standard error of the mean and twice the standard error of the mean, respectively.

Mentions: Lymphoblastoid cell lines derived from 34 large CEPH pedigrees (447 total cell lines) were evaluated for cell growth inhibition following exposure to increasing concentrations of carboplatin for 72 hours. The mean (± SD) percentage cell survival pertaining to the 10, 20, 40 and 80 μM carboplatin doses were 65.7 ± 8.7, 52.7 ± 9.87, 39.8 ± 9.59 and 27.1 ± 9.17 per cent, respectively. IC50 was determined for 94 per cent (422/447) of cell lines because of the requirement to have survival values above and below 50 per cent. The mean IC50 (± SD) concentration was 25.8 ± 13 μM, with a range of 8.28-91.3 μM. Intra- and interfamily variations for all of the carboplatin concentrations are shown in the box plots in Figure 2.


Whole-genome approach implicates CD44 in cellular resistance to carboplatin.

Shukla SJ, Duan S, Wu X, Badner JA, Kasza K, Dolan ME - Hum. Genomics (2009)

Box plots and heritability (h2) values for 34 families are shown for 10, 20, 40 and 80 μM carboplatin. Centre d'Etude du Polymorphisme Humain (CEPH) family identification pertaining to the box plot is located on the x-axis. The middle line within the box represents the mean percentage survival of each family, while the box edges and whiskers represent the standard error of the mean and twice the standard error of the mean, respectively.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2683878&req=5

Figure 2: Box plots and heritability (h2) values for 34 families are shown for 10, 20, 40 and 80 μM carboplatin. Centre d'Etude du Polymorphisme Humain (CEPH) family identification pertaining to the box plot is located on the x-axis. The middle line within the box represents the mean percentage survival of each family, while the box edges and whiskers represent the standard error of the mean and twice the standard error of the mean, respectively.
Mentions: Lymphoblastoid cell lines derived from 34 large CEPH pedigrees (447 total cell lines) were evaluated for cell growth inhibition following exposure to increasing concentrations of carboplatin for 72 hours. The mean (± SD) percentage cell survival pertaining to the 10, 20, 40 and 80 μM carboplatin doses were 65.7 ± 8.7, 52.7 ± 9.87, 39.8 ± 9.59 and 27.1 ± 9.17 per cent, respectively. IC50 was determined for 94 per cent (422/447) of cell lines because of the requirement to have survival values above and below 50 per cent. The mean IC50 (± SD) concentration was 25.8 ± 13 μM, with a range of 8.28-91.3 μM. Intra- and interfamily variations for all of the carboplatin concentrations are shown in the box plots in Figure 2.

Bottom Line: We further analysed the IC(50) phenotype 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 IC(50) (p < 3.6 x 10(-5); false discovery rate <5 per cent).Next, we performed linear regression on the baseline expression and carboplatin IC(50) values of the eight associated genes, which identified the most significant correlation between CD44 expression and IC(50) (r(2)= 0.20; p = 6 x 10(-4)).Knockdown of CD44 expression through small interfering RNA resulted in increased cellular sensitivity to carboplatin (p < 0.01).

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.

ABSTRACT
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 x 10(-7) to 9 x 10(-4)), was found for cell growth inhibition following 72-hour treatment at each carboplatin concentration (10, 20, 40 and 80 microM) and IC(50) (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 x 10(-5)) encompasses 65 genes within the 1 LOD confidence interval for the carboplatin IC 50 . We further analysed the IC(50) phenotype 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 IC(50) (p < 3.6 x 10(-5); false discovery rate <5 per cent). Next, we performed linear regression on the baseline expression and carboplatin IC(50) values of the eight associated genes, which identified the most significant correlation between CD44 expression and IC(50) (r(2)= 0.20; p = 6 x 10(-4)). The quantitative real-time polymerase chain reaction further confirmed a statistically significant difference in CD44 expression levels between carboplatin-resistant and -sensitive cell lines (p = 5.9 x 10(-3)). Knockdown of CD44 expression through small interfering RNA resulted in increased cellular sensitivity to carboplatin (p < 0.01). Our whole-genome approach using molecular experiments identified CD44 as being important in conferring cellular resistance to carboplatin.

Show MeSH
Related in: MedlinePlus