Genome-wide genetic aberrations of thymoma using cDNA microarray based comparative genomic hybridization

Abstract

Background: Thymoma is a heterogeneous group of tumors in biology and clinical behavior. Even though thymoma is divided into five subgroups following the World Health Organization classification, the nature of the disease is mixed within the subgroups.

Results: We investigated the molecular characteristics of genetic changes variation of thymoma using cDNA microarray based-comparative genomic hybridization (CGH) with a 17 K cDNA microarray in an indirect, sex-matched design. Genomic DNA from the paraffin embedded 39 thymoma tissues (A 6, AB 11, B1 7, B2 7, B3 8) labeled with Cy-3 was co-hybridized with the reference placenta gDNA labeled with Cy-5. Using the CAMVS software, we investigated the deletions on chromosomes 1, 2, 3, 4, 5, 6, 8, 12, 13 and 18 throughout the thymoma. Then, we evaluated the genetic variations of thymoma based on the subgroups and the clinical behavior. First, the 36 significant genes differentiating five subgroups were selected by Significance Analysis of Microarray. Based on these genes, type AB was suggested to be heterogeneous at the molecular level as well as histologically. Next, we observed that the thymoma was divided into A, B (1, 2) and B3 subgroups with 33 significant genes. In addition, we selected 70 genes differentiating types A and B3, which differ largely in clinical behaviors. Finally, the 11 heterogeneous AB subtypes were able to correctly assign into A and B (1, 2) types based on their genetic characteristics.

Conclusion: In our study, we observed the genome-wide chromosomal aberrations of thymoma and identified significant gene sets with genetic variations related to thymoma subgroups, which might provide useful information for thymoma pathobiology.

Figure 1

Microarray-CGH profiles using CAMVS (Chromosome analyzer and Map Viewer using S plus). Each black line displays the overall genetic pattern of each thymoma patient and the central orange horizontal line represents the common genetic alterations of 8,411 genes in all patients. (A) Overall microarray-CGH profile of 39 thymoma patients showing the losses on chromosomes 1, 2, 3, 4, 5, 6, 8, 12, 13 and 18. (B) The common genetic alteration patterns in type A with losses of chromosomes 2, 4, 6q, and 13. (C) The common genetic alteration patterns in type B1 with losses of chromosomes 1p, 2q, 3q, 4, 5, 6q, 8, 13, and 18 and a gain of chromosome 9q.

Figure 2

(A) The common genetic alteration patterns in type B2 with losses of chromosomes 1p, 2q, 3q, 4, 5, 6q, 8, 13, and 18. (B) The common genetic alteration patterns in type B3 with losses of chromosomes 2q, 4, 5, 6, 8, 12q, 13, 18 and a gain of chromosome 1q. (C) The common genetic alteration patterns in type AB with losses of chromosomes 2, 4, 5, 6q, 8, 13 and 18.

Figure 3

Genetic pattern profiles of thymoma subgroups by the hierarchical clustering of 36 selected genes. Color scale bar showing the level of log R/G ratio. The thymoma subgroup of each patient is displayed in a different color as below.

Figure 4

Comparison of genetic aberration patterns between subtypes of thymoma. (A) Hierarchical clustering with 50 selected genes showing different genetic patterns between types A and B (1, 2, 3). (B) Hierarchical clustering of 70 genes showing different genetic patterns in types A and B3. (C) Hierarchical clustering of 48 genes showing the different genetic patterns between types B (1, 2) and B3. (D) Hierarchical clustering with 33 genes showing three molecular characteristic subgroups of thymoma as types A, B(1,2) and B3.

Figure 5

Prediction analysis of thymoma subgroups. (A) Cross-validated probabilities of the selected 136–44 genes at threshold 2.78 in the training set using 18 cases of thymoma subgroups, six cases each of A, B (1, 2), B3, showing 90% accuracy. (B) Prediction analysis of 11 ambiguous type AB samples as a training set showed the similar result as Figure 2, designating three as type A and eight as type B.