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Comparative Study
. 2007 Feb 20:8:53.
doi: 10.1186/1471-2164-8-53.

Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex genetic alterations in cervical cancer

Judith N Kloth  1 , Jan Oosting, Tom van Wezel, Karoly Szuhai, Jeroen Knijnenburg, Arko Gorter, Gemma G Kenter, Gert Jan Fleuren, Ekaterina S Jordanova
Affiliations
Comparative Study

Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex genetic alterations in cervical cancer

Judith N Kloth et al. BMC Genomics. .

Abstract

Background: Cervical carcinoma develops as a result of multiple genetic alterations. Different studies investigated genomic alterations in cervical cancer mainly by means of metaphase comparative genomic hybridization (mCGH) and microsatellite marker analysis for the detection of loss of heterozygosity (LOH). Currently, high throughput methods such as array comparative genomic hybridization (array CGH), single nucleotide polymorphism array (SNP array) and gene expression arrays are available to study genome-wide alterations. Integration of these 3 platforms allows detection of genomic alterations at high resolution and investigation of an association between copy number changes and expression.

Results: Genome-wide copy number and genotype analysis of 10 cervical cancer cell lines by array CGH and SNP array showed highly complex large-scale alterations. A comparison between array CGH and SNP array revealed that the overall concordance in detection of the same areas with copy number alterations (CNA) was above 90%. The use of SNP arrays demonstrated that about 75% of LOH events would not have been found by methods which screen for copy number changes, such as array CGH, since these were LOH events without CNA. Regions frequently targeted by CNA, as determined by array CGH, such as amplification of 5p and 20q, and loss of 8p were confirmed by fluorescent in situ hybridization (FISH). Genome-wide, we did not find a correlation between copy-number and gene expression. At chromosome arm 5p however, 22% of the genes were significantly upregulated in cell lines with amplifications as compared to cell lines without amplifications, as measured by gene expression arrays. For 3 genes, SKP2, ANKH and TRIO, expression differences were confirmed by quantitative real-time PCR (qRT-PCR).

Conclusion: This study showed that copy number data retrieved from either array CGH or SNP array are comparable and that the integration of genome-wide LOH, copy number and gene expression is useful for the identification of gene specific targets that could be relevant for the development and progression in cervical cancer.

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Figures

Figure 1
Figure 1
Chromosomal gains and losses in cervical cancer cell lines. A) Array CGH results are depicted by lines to the right of the chromosomes as gains and on the left as losses. Thick solid lines represent regions with amplifications of more than 1 copy loss. B) SNP-LOH results show LOH as lines on the left side of the chromosomes. The letters above the lines indicate the cell lines: a) CSCC7, b) CSCC1, c) CC11-, d) CC11+, e) CaSki, f) CC8, g) CC10b, h) CC10a, i) SiHa and j) HeLa.
Figure 2
Figure 2
Complex genomic alterations of chromosome 20 (A) and chromosome 8 (B) of SiHa and chromosome 3 of CaSki (C). Below each chromosome ideogram, SNP array data are shown in blue and array CGH data in red. The blue line directly beneath the ideogram depicts LOH, whereas the blue line shifting around the baseline (0) shows copy number retrieved from SNP array data. The dotted blue and red lines represent the confidence intervals for the copy number of the SNP and the CGH array, respectively.
Figure 3
Figure 3
FISH of metaphase preparations depicting copy number alterations. A) CaSki – 5 chromosomes 5 (centromere 5-blue; TRIO-green; SKP2-red); one isochromosome 5p (yellow arrow), 2 translocations of RP11-1150G22, encompassing TRIO (green arrow) and 2 translocations of RP11-624K2, encompassing SKP2 (red arrow). B) CaSki – 3 chromosomes 8 (centromere 8-red, TUSC3-green) with loss of one copy the BACs encompassing TUSC3, RP11-44L18/184C1 (green arrow). C) HeLa – 4 chromosomes 20 (centromere 20-blue, ZNF-217-red, CYP24A1-green); one isochromosome 20q (yellow arrow).
Figure 4
Figure 4
LOH at 6p21.3 is demonstrated for microsatellite marker C125. Tumour samples from which cell lines CC11 and CC10 originated were analyzed for LOH. In black the particular alleles are depicted and in grey the marker is shown.
Figure 5
Figure 5
Box plots show differences in gene expression measured by qRT-PCR of SKP2 (p = 0.003, ANOVA); TRIO (p < 0.001, ANOVA) and ANKH (p < 0.001, ANOVA) in cell lines with and without amplification of 5p and normal cervical epithelial cell cultures (NPE). Ampl: amplification.
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References

    1. Narayan G, Pulido HA, Koul S, Lu XY, Harris CP, Yeh YA, Vargas H, Posso H, Terry MB, Gissmann L, Schneider A, Mansukhani M, Rao PH, Murty VV. Genetic analysis identifies putative tumor suppressor sites at 2q35-q36.1 and 2q36.3-q37.1 involved in cervical cancer progression. Oncogene. 2003;22:3489–3499. doi: 10.1038/sj.onc.1206432. - DOI - PubMed
    1. Melsheimer P, Klaes R, Doeberitz MV, Bastert G. Prospective clinical study comparing DNA flow cytometry and HPV typing as predictive tests for persistence and progression of CIN I/II. Cytometry. 2001;46:166–171. doi: 10.1002/cyto.1101. - DOI - PubMed
    1. Kersemaekers AM, van de Vijver MJ, Kenter GG, Fleuren GJ. Genetic alterations during the progression of squamous cell carcinomas of the uterine cervix. Genes Chromosomes Cancer. 1999;26:346–354. doi: 10.1002/(SICI)1098-2264(199912)26:4<346::AID-GCC9>3.0.CO;2-D. - DOI - PubMed
    1. Fan X, Chen JJ. Regulation of cell cycle progression and apoptosis by the papillomavirus E6 oncogene. Crit Rev Eukaryot Gene Expr. 2004;14:183–202. doi: 10.1615/CritRevEukaryotGeneExpr.v14.i3.30. - DOI - PubMed
    1. Nishimura M, Furumoto H, Kato T, Kamada M, Aono T. Microsatellite instability is a late event in the carcinogenesis of uterine cervical cancer. Gynecol Oncol. 2000;79:201–206. doi: 10.1006/gyno.2000.5940. - DOI - PubMed

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