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CD44 gene polymorphisms in breast cancer risk and prognosis: a study in North Indian population.

Tulsyan S, Agarwal G, Lal P, Agrawal S, Mittal RD, Mittal B - PLoS ONE (2013)

Bottom Line: In-silico analysis for prediction of functional effects was done using F-SNP and FAST-SNP.On performing univariate analysis with clinicopathological characteristics and treatment response, we found significant association of genotype (CT+TT) of rs13347 polymorphism with earlier age of onset (P = 0.029, OR = 0.037).On performing multivariate analysis, increased significance of variant genotype (P = 0.017, OR = 4.29) and allele (P = 0.025, OR = 3.34) of rs353639 was found with clinical tumour size.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India.

ABSTRACT

Background: Cell surface biomarker CD44 plays an important role in breast cancer cell growth, differentiation, invasion, angiogenesis and tumour metastasis. Therefore, we aimed to investigate the role of CD44 gene polymorphisms in breast cancer risk and prognosis in North Indian population.

Materials & methods: A total of 258 breast cancer patients and 241 healthy controls were included in the case-control study for risk prediction. According to RECIST, 114 patients who received neo-adjuvant chemotherapy were recruited for the evaluation of breast cancer prognosis. We examined the association of tagging SNP (rs353639) of Hapmap Gujrati Indians in Houston (GIH population) in CD44 gene along with a significant reported SNP (rs13347) in Chinese population by genotyping using Taqman allelic discrimination assays. Statistical analysis was done using SPSS software, version 17. In-silico analysis for prediction of functional effects was done using F-SNP and FAST-SNP.

Results: No significant association of both the genetic variants of the CD44 gene polymorphisms was found with breast cancer risk. On performing univariate analysis with clinicopathological characteristics and treatment response, we found significant association of genotype (CT+TT) of rs13347 polymorphism with earlier age of onset (P = 0.029, OR = 0.037). However, significance was lost in multivariate analysis. For rs353639 polymorphism, significant association was seen with clinical tumour size, both at the genotypic (AC+CC) (P = 0.039, OR = 3.02) as well as the allelic (C) (P = 0.042, OR = 2.87) levels. On performing multivariate analysis, increased significance of variant genotype (P = 0.017, OR = 4.29) and allele (P = 0.025, OR = 3.34) of rs353639 was found with clinical tumour size. In-silico analysis using F-SNP, showed altered transcriptional regulation for rs353639 polymorphism.

Conclusions: These findings suggest that CD44 rs353639 genetic variants may have significant effect in breast cancer prognosis. However, both the polymorphisms- rs13347 and rs353639 had no effect on breast cancer susceptibility.

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Related in: MedlinePlus

Linkage disequilibrium (LD) plot of CD44 gene in Hapmap- GIH population.
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pone-0071073-g001: Linkage disequilibrium (LD) plot of CD44 gene in Hapmap- GIH population.

Mentions: TaggerSNP rs 353639 was found to represent the known SNPs in the haplotype blocks 3 and 4 in the CD44 gene of GIH population (Figure S1). It was also found to represent the haplotype block 5 in Caucasian (CEU in Hapmap) population (Figure S1). Previously significantly reported SNP (rs13347) in Chinese population also represents the haplotype block 9 (Figure 1).


CD44 gene polymorphisms in breast cancer risk and prognosis: a study in North Indian population.

Tulsyan S, Agarwal G, Lal P, Agrawal S, Mittal RD, Mittal B - PLoS ONE (2013)

Linkage disequilibrium (LD) plot of CD44 gene in Hapmap- GIH population.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3733640&req=5

pone-0071073-g001: Linkage disequilibrium (LD) plot of CD44 gene in Hapmap- GIH population.
Mentions: TaggerSNP rs 353639 was found to represent the known SNPs in the haplotype blocks 3 and 4 in the CD44 gene of GIH population (Figure S1). It was also found to represent the haplotype block 5 in Caucasian (CEU in Hapmap) population (Figure S1). Previously significantly reported SNP (rs13347) in Chinese population also represents the haplotype block 9 (Figure 1).

Bottom Line: In-silico analysis for prediction of functional effects was done using F-SNP and FAST-SNP.On performing univariate analysis with clinicopathological characteristics and treatment response, we found significant association of genotype (CT+TT) of rs13347 polymorphism with earlier age of onset (P = 0.029, OR = 0.037).On performing multivariate analysis, increased significance of variant genotype (P = 0.017, OR = 4.29) and allele (P = 0.025, OR = 3.34) of rs353639 was found with clinical tumour size.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India.

ABSTRACT

Background: Cell surface biomarker CD44 plays an important role in breast cancer cell growth, differentiation, invasion, angiogenesis and tumour metastasis. Therefore, we aimed to investigate the role of CD44 gene polymorphisms in breast cancer risk and prognosis in North Indian population.

Materials & methods: A total of 258 breast cancer patients and 241 healthy controls were included in the case-control study for risk prediction. According to RECIST, 114 patients who received neo-adjuvant chemotherapy were recruited for the evaluation of breast cancer prognosis. We examined the association of tagging SNP (rs353639) of Hapmap Gujrati Indians in Houston (GIH population) in CD44 gene along with a significant reported SNP (rs13347) in Chinese population by genotyping using Taqman allelic discrimination assays. Statistical analysis was done using SPSS software, version 17. In-silico analysis for prediction of functional effects was done using F-SNP and FAST-SNP.

Results: No significant association of both the genetic variants of the CD44 gene polymorphisms was found with breast cancer risk. On performing univariate analysis with clinicopathological characteristics and treatment response, we found significant association of genotype (CT+TT) of rs13347 polymorphism with earlier age of onset (P = 0.029, OR = 0.037). However, significance was lost in multivariate analysis. For rs353639 polymorphism, significant association was seen with clinical tumour size, both at the genotypic (AC+CC) (P = 0.039, OR = 3.02) as well as the allelic (C) (P = 0.042, OR = 2.87) levels. On performing multivariate analysis, increased significance of variant genotype (P = 0.017, OR = 4.29) and allele (P = 0.025, OR = 3.34) of rs353639 was found with clinical tumour size. In-silico analysis using F-SNP, showed altered transcriptional regulation for rs353639 polymorphism.

Conclusions: These findings suggest that CD44 rs353639 genetic variants may have significant effect in breast cancer prognosis. However, both the polymorphisms- rs13347 and rs353639 had no effect on breast cancer susceptibility.

Show MeSH
Related in: MedlinePlus