The effect of an extra chromosome 21 on gene expression variation–a new insight to trisomy 21
Date Issued
2007
Date
2007
Author(s)
Chou, Ching-Yu
DOI
zh-TW
Abstract
Introduction: Down syndrome (DS) is the most frequent genetic disorder with mental retardation and caused by trisomy 21. With more publications focusing on over-expression on genes of chromosome 21 and expression variation in normal human and organisms, the research for significance of gene expression variation in DS is lacking. We use microarray to study the effect of extra chromosome 21 to gene expression variation in amniocytes of trisomy 21. We also observe if this change of variation occurred in fetal brain tissues that the microarray datasets were shared on the websites. We hoped to get a new insight of genomic biology in trisomy 21.
Method and materials: We use 5 amniocyte cultures of trisomy 21 and 6 cases of normal amniocytes. Total RNA was extracted, mixed with human reference RNA and hybridized with microarray chips (Agilent Technologies, USA). Normalization used LOWESS method. The variances of 21073 genes of 2 groups was calculated and graded into different groups. The gene numbers of different variance was compared between the DS and normal control. And χ2 method was used to test the significance. The expression of genes that vary among amniocytes of trisomy 21 and normal control was evaluated using ANOVA model and p-value was modified with the concept of pFDR. Further validation of 4 genes (CXCL12, GABRA5, ATP5G3 and ZZZ3) with significantly difference in variance was performed by quantitative RT-PCR. The same statistical methods were also applied on the dataset of Mao’s fetal trisomy 21 brain tissues on the websites.
To determine how many genes are expected to be in common by chance if genes were chosen randomly, we undertook two simulation studies with 2000 datasets generated by randomly using and the same analysis for 100 datasets in our study.
Results: Average expression ratio of Down syndrome over normal control in genes on chromosome 21 was 1.35. And other genes of non-chromosome 21 keep the ratio at 1. The numbers of genes with variance more than 1 is much increased in cells of trisomy 21 in our amniocytes dataset and Mao’s fetal brain dataset(p<0.01). When performing the F-test, 37 hypothesizes will be rejected. And 15 genes will be picked up after excluding weak signals. The difference of variance does not come from random. CXCL12 was validated to have different variance in two groups by QRT-PCR(p=0.003).
Conclusion: In human trisomy 21 tissues including amniocytes and fetal brain tissues, the gene expression variation increased generally as compared to normal tissues. There exist a set of genes with increased variance in gene expression and can be validated by QRT-PCR. Increased variation of gene expression in trisomy 21 may lead to variable level of mRNA and then variable phenotypes of Down syndrome.
Subjects
唐氏症
基因變異性
生物晶片
羊水細胞
Down syndrome
gene expression variation
microarray
amniocyte
Type
other
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