Multiple clonal chromosome aberrations in two thymomas

Molecular analysis of thymoma

Histologic classification of thymomas has significant limitations with respect to both subtype definitions and consistency. In order to better understand the biology of the disease processes, we performed whole genome gene expression analysis. RNA was extracted from fresh frozen tumors from 34 patients with thymomas and followup data was available. Using the Illumina BeadStudio® platform and Human Ref-8 Beadchip, gene expression data was analyzed with Partek Genomics Suite®, and Ingenuity Pathways Analysis (IPA). Unsupervised clustering of gene expression data, representing one of the largest series in literature, resulted in identification of four molecular clusters of tumors (C1–C4), which correlated with histology (P = 0.002). However, neither histology nor clusters correlated with clinical outcomes. Correlation of gene expression data with clinical data showed that a number of genes were associated with either advanced stage at diagnosis or development of recurrence or metastases. The top pathways associated with metastases were amino acid metabolisms, biosynthesis of steroids and glycosphingolipids, cell cycle checkpoint proteins and Notch signaling. The differential expression of some of the top genes related to both metastases and stage was confirmed by RT-PCR in all cases of metastases and matched nonmetastatic cases. A number of potential candidates for therapeutics were also identified.

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

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.

Familial occurrence of thymoma and autoimmune diseases with the constitutional translocation t(14;20)(q24.1;p12.3)

Thymomas are low-grade epithelial cancers of the thymus whose prevalence varies between 0.1/100,000 and 0.4/100,000. Familial occurrence of thymoma is very rare. We studied a family bearing the constitutional chromosome translocation t(14;20)(q24;p12), 3 of whose members had a thymoma. In this family, among 27 patients, 11 had the translocation: 3 had thymoma and 4 others had 5 different autoimmune diseases: type 1 diabetes mellitus, Graves' disease, pernicious anemia, primitive Sjögren disease, and autoimmune pancytopenia. FISH studies allowed us to be more specific about the translocation breakpoints. The 14q24 breakpoint was in intron 5 of RAD51L1, and the 20p12 breakpoint was 100 kb telomeric to BMP2. RAD51L1 is a tumor-suppressor gene belonging to the RAD51 family, already implicated in many tumors (uterine leiomyomas, pseudo-Meigs syndromes, pulmonary chondroid hamartomas) and involved in recombinational repair of DNA double-strand breaks. BMP2 belongs to the TGFbeta superfamily, and the BMP2-BMP4 genes are involved in thymocyte differentiation by blocking progression from CD4-CD8- to CD4+CD8+ while maintaining a sufficient pool of immature precursors. Dysregulation of RAD51L1 and/or BMP2 may explain this familial occurrence of thymomas and autoimmune diseases. Using QRT-PCR, we studied the expression of BMP2 in 20 sporadic thymomas and found various levels of expression that may be associated with autoimmune diseases.

Deletion (6)(p22p25) is a recurrent anomaly of thymoma: report of a second case and review of the literature

A patient with type AB thymoma and del(6)(p22p25) as the sole cytogenetic anomaly is described. This is the second report of a del(6)(p22p25) in a thymoma. The same deletion was previously found in association with a type A thymoma. Both patients presented with benign tumors. These data suggest that partial deletion of the short arm of chromosome 6 is a nonrandom change associated with benign thymomas.

Translocation (11;15;19): a highly specific chromosome rearrangement associated with poorly differentiated thymic carcinoma in young patients

Thymic carcinoma is a rare epithelial neoplasm of the thymus. The presence of a specific chromosomal abnormality may augment diagnosis and therapeutic stratification. We report a 15-year-old boy diagnosed with thymic carcinoma who presented with a large anterior mediastinal mass, pleural effusion, and bone metastasis. The pleural fluid, cytology, bony lesions, and bone marrow were examined and chromosomal studies were performed. Histologic and immunohistochemical studies confirmed a poorly differentiated squamous cell type of thymic carcinoma. The karyotype of the pleural fluid at the time of diagnosis revealed a complex three-way translocation t(11;15;19)(p15;q12;p13.3). The constitutional karyotype was 46,XY. Five months after diagnosis, a bone marrow aspirate demonstrated tetraploidy with all translocation chromosomes in duplicate, as well as an unbalanced rearrangement involving chromosome 1: 92,XXYY,t(11;15;19)(p15;q12;p13.3)x2[15]/92,XXYY,idem,add(1)(qter)[5]. Despite aggressive multiagent chemotherapy, the patient's condition progressed with bone marrow disease and he died 6 months after diagnosis. Several case reports of a similar chromosomal abnormality have been reported for thymic carcinoma in young patients with poor outcome. This karyotypic abnormality appears to mark a cohort of patients with thymic carcinoma who have a poor prognosis despite aggressive chemotherapy.

Chromosome 6 suffers frequent and multiple aberrations in thymoma

Thymoma is the most frequent tumor arising in human thymus. In this study, we performed a detailed mapping of deleted regions on chromosome 6 shown previously to harbor the most frequent genetic aberrations in this cancer. We analyzed 40 thymomas using 41 microsatellites. Two hundred ninety-four (23.5%) of 1253 informative genotypes showed loss of heterozygosity (LOH), only 39 (2.4%) were positive for microsatellite instability (MSI). Genetic aberrations on chromosome 6 were found in 31 of 40 cases (77.5%) in five hot spots. The most frequent LOHs (48.6%) occurred in region 6q25.2 within a 0.7-Mb interval flanked by markers D6S441 and D6S290. Another hot spot showing LOH in 32.4% of tumors was located between markers D6S442 and D6S1708 (0.4 Mb apart) on 6q25.2-25.3, just 1.1 Mb from the D6S441-D6S290 deletions. The third hot spot (30%) showing LOH appeared in region 6p21.31 including the MHC locus (markers D6S1666-D6S1560, 1 Mb apart). The fourth hot spot (26.3%) was detected on 6q14.1-14.3 (D6S1596-D6S284, 5.2 Mb apart). Some tumors (21.6%) showed LOHs within a fifth hot spot on 6q21 (D6S447-D6S1592, 0.3 Mb apart). Thus, several tumor suppressor genes on chromosome 6 seem to be involved in the pathogenesis of thymoma.

Ring chromosome 6 may represent a cytogenetic subgroup in benign thymoma

Cytogenetic and fluorescence in situ hybridization analysis of a thymoma revealed the presence of an abnormal clone with a karyotype 46,XY,r(6)(p2?q35?).ish r(6)(p2?q35?)(WCP6+,dJ476O18-,dJ62I11-, PAC59C23+,PAC57H24-),der(21)t(6;21)(p25;q22)(dJ62I11+,cosC9a1-). Histologically, the tumor was encapsulated and classified as thymoma type AB (World Health Organization classification) or mixed thymoma (Muller-Hermelink classification), composed of well-formed lobules with sharp demarcation of both the spindly type A and lymphocyte-rich type B components. This finding, together with literature data, strongly suggests that terminal deletion of the short arm of chromosome 6 is a recurrent aberration in thymoma.

Pseudodicentric (16;12)(q11;p11.2) in a type AB (mixed) thymoma

Genetic alterations of thymomas are rarely described in the literature. In this study, a previously unreported instance of aberrant karyotypic change consisting of 45,XX,pseu dic(16;12) (q11;p11.2) [cp23]/87-90,idemx2[cp4] in a Masaoka Stage II mixed thymoma or type AB thymoma affecting a 56-year-old Chinese woman is detailed. Abnormalities involving 12p containing important tumor suppressor-like genes have been documented especially in hematological malignancies. Recently, recurrent losses involving 16q, a locus known to harbor several tumor suppressor genes, have been described in type C thymomas (squamous cell carcinoma), suggesting a possible relationship between type AB thymoma and type C thymoma. Whether these genes are involved in the pathogenesis of type AB thymoma remain to be clarified and it is currently unclear if cytogenetic studies may eventually play a role in the classification of thymic tumors.

A novel t(1;8)(p13;p11) in a thymic carcinoma with unusual giant cell features and renal metastasis

Cytogenetic analysis of a thymic carcinoma metastatic to the left kidney revealed the presence of a t(1;8)(p13;p11). In addition to a previously undescribed translocation, this tumor histologically showed unusual giant cell features.

Cytogenetic profile of a thymoma. A case report and review of the literature

Cytogenetic analysis of mixed lymphocyte and epithelial thymoma in a nonmyasthenic female patient revealed deletion of part of the short arm of chromosome 6. To our knowledge, this cytogenetic abnormality in a benign thymoma has not been previously described in the literature, which is reviewed.

Recurrent genetic aberrations in thymoma and thymic carcinoma

Apart from single reported aberrant karyotypes, genetic alterations in thymic epithelial neoplasms have not been investigated so far. In this study, 12 World Health Organization classification type A thymomas (medullary thymomas), 16 type B3 thymomas (well-differentiated thymic carcinomas), and nine type C thymomas, all of them primary thymic squamous cell carcinomas, were analyzed by comparative genomic hybridization and fluorescence in situ hybridization. With the exception of one single case, type A thymomas did not reveal chromosomal gains or losses in comparative genomic hybridization. In contrast, all type B3 thymomas showed chromosomal imbalances, with gain of 1q, loss of chromosome 6, and loss of 13q occurring in 11 (69%), six (38%), and five (31%) of 16 cases, respectively. In primary thymic squamous cell carcinoma, the most frequent chromosomal losses were observed for 16q (six of nine cases, 67%), 6 (4 of 9, 44%), and 3p and 17p (three of nine each, 33%), whereas recurrent gains of chromosomal material were gains of 1q (5 of 9, 56%), 17q, and 18 (three of nine each, 33%). This study shows that the distinct histological thymoma types A and B3 exhibit distinct genetic phenotypes, whereas type B3 thymoma and primary thymic squamous cell carcinoma partially share genetic aberrations. In addition to the possible tumorigenic role, the deletion in type B3 thymoma of chromosome 6, harboring the HLA locus, might play a role in the pathogenesis of paraneoplastic autoimmunity characteristic of thymoma.

Thymoma with a t(15;22)(p11;q11)

Cytogenetic analysis of a thymoma revealed the presence of a t(15;22)(p11;q11) as the only chromosome abnormality. From the few thymomas so far analyzed, no characteristic chromosome change seems to be emerging.