Radiation Research

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Radiation Research 166(3):519-531. 2006
doi: 10.1667/RR0547.1

Microarray Comparative Genomic Hybridization Reveals Genome-Wide Patterns of DNA Gains and Losses in Post-Chernobyl Thyroid Cancer

Robert R. Kimmel1a, Lue Ping Zhaoc, Doan Nguyenb, Somnit Leeb, Mark Aronszajnd, Chun Chengc, Vladislav P. Troshine, Alexander Abrosimovf, Jeffrey Delrowb, R. Michael Tuttleg, Anatoli F. Tsybf, Kenneth J. Kopeckyc, Scott Davisch, and Paul E. Neimanbi

aClinical Research Division,

bDivision of Basic Science,

cDivision of Public Health Sciences,

dBiocomputing Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, Washington;

eInstitute of Pathology, Bryansk, Russian Federation;

fRussian Academy of Medical Science, Medical Radiological Research Center, Obninsk, Russian Federation;

gDivision of Endocrinology, Memorial Sloan Kettering Cancer Center, New York, New York;

hDepartment of Epidemiology, School of Public Health and Community Medicine, University of Washington, Seattle, Washington; and

iDepartment of Medicine, University of Washington School of Medicine, Seattle, Washington

1Address for correspondence: 1100 Fairview Avenue North, C2-023, Seattle, WA 98109;

Abstract

Kimmel, R. R., Zhao, L. P., Nguyen, D., Lee, S., Aronszajn, M., Cheng, C., Troshin, V. P., Abrosimov, A., Delrow, J., Tuttle, R. M., Tsyb, A. F., Kopecky, K. J., Davis, S. and Neiman, P. E. Microarray Comparative Genomic Hybridization Reveals Genome-Wide Patterns of DNA Gains and Losses in Post-Chernobyl Thyroid Cancer. Radiat. Res. 166, 519–531 (2006).

Genetic gains and losses resulting from DNA strand breakage by ionizing radiation have been demonstrated in vitro and suspected in radiation-associated thyroid cancer. We hypothesized that copy number deviations might be more prevalent, and/or occur in genomic patterns, in tumors associated with presumptive DNA strand breakage from radiation exposure than in their spontaneous counterparts. We used cDNA microarray-based comparative genome hybridization to obtain genome-wide, high-resolution copy number profiles at 14,573 genomic loci in 23 post-Chernobyl and 20 spontaneous thyroid cancers. The prevalence of DNA gains in tumors from cases in exposed individuals was two- to fourfold higher than for cases in unexposed individuals and up to 10-fold higher for the subset of recurrent gains. DNA losses for all cases were low and more prevalent in spontaneous cases. We identified unique patterns of copy variation (mostly gains) that depended on a history of radiation exposure. Exposed cases, especially the young, harbored more recurrent gains that covered more of the genome. The largest regions, spanning 1.2 to 4.9 Mbp, were located at 1p36.32-.33, 2p23.2-.3, 3p21.1-.31, 6p22.1-.2, 7q36.1, 8q24.3, 9q34.11, 9q34.3, 11p15.5, 11q13.2-12.3, 14q32.33, 16p13.3, 16p11.2, 16q21-q12.2, 17q25.1, 19p13.31-qter, 22q11.21 and 22q13.2. Copy number changes, particularly gains, in post-Chernobyl thyroid cancer are influenced by radiation exposure and age at exposure, in addition to the neoplastic process.

Received: January 17, 2006; Accepted: April 21, 2006



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FIG. 1. Prevalence of copy number gains and losses in Bryansk and Seattle thyroid tumors. Box plots show (panel A) total (random plus recurrent) gains (FR > 1.72) in Bryansk and Seattle tumors for young and adult cases and (panel B) total losses (FR < 0.48) for young and adult cases. “Mean” refers to average for replicates. See text for significant P values for the differences between means. The distributions of (panel C) recurrent gains and (panel D) recurrent losses are shown for each tumor group. FR, fluorescence ratio; ATA, at time of accident; ATD, at time of diagnosis. Boxes in panel A define the interquartile range (IQR), which is bound by upper (0.75) and lower (0.25) quartiles; whiskers extend to include adjacent values that are 1.5 × IQR above and below the IQR

FIG. 2. Distribution of genomic distances between adjacent pairs of recurrent gains in tumors. Bryansk tumor (young and adult ATA) and Seattle tumor (young ATD) distributions are shown for intervals up to 3 Mbp. Frequencies of occurrence are normalized to the total number of gains in each respective group. Each distribution is non-random (P < 0.001) by permutation analysis. P values for comparison of median adjacent intervals show that only Bryansk young tumor gains differ significantly from Bryansk adults and Seattle young. ATA: at time of accident; ATD, at time of diagnosis

FIG. 3. Recurrent gain clusters in radiation-associated thyroid tumors. Size (genomic span) distributions of recurrent gain clusters are shown for all Bryansk tissue (panels A–C) and Seattle tumors, young ATD (panel D). Loci within these clusters are mapped to chromosomal ideograms (panel E) by color-coded, horizontal lines whose length is proportional to log2(fluorescence ratio). Centromeres are plotted as points. Gray scale simulates G-bands [Golden Path cytoBand. txt (44)]. Y-chromosome genes are removed from this analysis. FR, fluorescence ratio; ATA, at time of accident; ATD, at time of diagnosis

FIG. 4. DNA copy number gains and losses in non-tumor thyroid. Box plots show (panel A) total (random plus recurrent) gains (FR > 1.72) in Bryansk and Seattle non-tumor thyroid for adult cases and (panel B) total losses (FR < 0.48) in adult cases. The distributions of recurrent gains (panel C) and recurrent losses (panel D) are shown for each non-tumor group. FR, fluorescence ratio; SD, standard deviation; ATA, at time of accident; ATD, at time of diagnosis

FIG. 5. Differential PCR confirmation of adrenomedullin (ADM, GenBank accession no. AA446120) and aryl hydrocarbon receptor-interacting protein (AIP, GenBank accession no. AA454926) gene amplification in post-Chernobyl thyroid carcinoma. Normal human genomic DNA (N) and genomic tumor DNA (T) were templates in differential PCR (41). Experimental (Expt.)/Control are the ratios of band intensities within a lane. Fold Tumor vs. Normal are the fold changes for Expt./ Normal ratios in tumor DNA compared to normal DNA. Inset shows that MYC out-competes the control gene in HL60 (right lane) but not in normal DNA (left lane). Lanes 1, 2, 4, 5, 7 and 9 show the PCR products of the individual primer sets for IFNG (diploid control), ADM or AIP, using either normal (N) or tumor (T) DNA template, as indicated. These show that PCR amplification is robust in the absence of competition between primers for template. Lanes 3 and 6 for ADM (lanes 8 and 10 for AIP) show PCR products of the primer set pairs in competition with normal or tumor template, respectively. The band intensity ratios (lanes 3 and 8, or 6 and 10) for the experimental gene and IFNG control for PCR efficiency. “Tumor/Normal” is an estimated fold copy number of 2.1 for ADM (4.7 for AIP) relative to normal, (tumor ratio)/(normal ratio) in each case

table

TABLE 1 Distribution of Thyroid Cancer Cases by Gender and Age

table

TABLE 2 Distribution of Tumor and Nodal Stagea for Thyroid Cancer Cases

table

TABLE 3 Age-Specific Recurrent DNA Copy Changes in Thyroid Cancer from Radiation-Exposed and Spontaneous Cases

table

TABLE 3 Continued

Annotated lists of recurrent gains and losses for all tissue groups are available online at http://dx.doi.org/10.1667/RR0547.1.s1, http://dx.doi.org/10.1667/RR0547.1.s2, http://dx.doi.org/10.1667/RR0547.1.s3, http://dx.doi.org/10.1667/RR0547.1.s4,http://dx.doi.org/10.1667/RR0547.1.s5, http://dx.doi.org/10.1667/RR0547.1.s6,http://dx.doi.org/10.1667/RR0547.1.s7, http://dx.doi.org/10.1667/RR0547.1.s8, http://dx.doi.org/10.1667/RR0547.1.s9, andhttp://dx.doi.org/10.1667/RR0547.1.s10.

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Abstract & References : Full Text : PDF (464 KB) : Rights & Permissions 

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Abstract & References : Full Text : PDF (518 KB) : Rights & Permissions 

 
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