Copy number alteration and uniparental disomy analysis categorizes Japanese papillary thyroid carcinomas into distinct groups

Genomic profile of columnar cell variant of papillary thyroid carcinoma

BACKGROUND AND AIMS

Columnar cell variant (CCV) is a rare papillary thyroid carcinoma subtype. The majority of CCV occur in older patients and are large, invasive tumours that pursue an aggressive clinical course. Rare well-circumscribed CCV occur in younger female patients and are comparatively indolent.

METHODS AND RESULTS

We retrospectively identified CCV with material available to perform targeted next-generation sequencing and correlated molecular results with clinicopathological features and outcome. Our cohort was comprised of nine CCV. Nearly all were aggressive tumours; however, one was predominantly well-circumscribed and arose in a thyroglossal duct cyst of a 26-year-old woman who had no evidence of disease at last follow-up. Seven (78%) cases demonstrated activating oncogenic driver alterations in BRAF, including BRAF V600E, an activating N486_P490del deletion, and BRAF-AGK fusions. Activating RAS mutations were seen in two (22%) cases. Additionally, three (33%) cases had TERT promoter mutations, four (44%) had loss of the tumour suppressor CDKN2A and one (11%) case had a loss of function TP53 mutation. Most cases (89%) also demonstrated copy number alterations, including recurrent gain of chromosome 1q (five cases) and losses of chromosome 9p (three cases) and 22q (four cases). The one case without secondary pathogenic mutations or copy number alterations was the tumour in the 26-year-old woman.

CONCLUSIONS

We found that CCV is primarily a BRAF-driven tumour, with most also harbouring secondary oncogenic mutations and multiple chromosomal gains and losses. Moreover, our findings suggest that molecular analysis could potentially be used to help risk stratify CCV.

The Role of Cell Growth-Related Gene Copy Number Variation in Autoimmune Thyroid Disease

Autoimmune thyroid disease (AITD) is a recurrent and refractory clinical endocrine disease. Some studies have shown that the incidence of AITD is not only related to iodine, a kind of environmental factor, but that susceptibility genes also play a crucial role in its pathogenesis. Since research on susceptibility genes is still underway, the aims of this study were to assess the association between copy number variations (CNVs) and AITD, to identify genes related to susceptibility to AITD, and to explore the risk factors in the occurrence of AITD. Blood samples from five AITD patients and five controls from each area were assessed by chromosome microarray to identify candidate genes. The copy number (CN) of the candidate genes and urinary iodine levels were determined in adults, including 158 AITD patients and 181 controls, from areas having different iodine statuses. The cell growth-related genes, glypican 5 (GPC5), B9 domain containing 2 (B9D2), and ankyrin repeat and suppressor of cytokine signaling [SOCS] box-containing protein family 11 (ASB11), were selected as the candidate genes. The distribution of GPC5, B9D2, and ASB11 CNVs in AITD patients and controls was significantly different, and high urinary iodine levels and GPC5 CNVs are risk factors for AITD. There was no significant association between urinary iodine level and CNVs of the candidate genes. High urinary iodine levels and GPC5 CNVs are risk factors for AITD, but an association with the occurrence of AITD was not found.

Copy Number Variation of Immune-Related Genes and Their Association with Iodine in Adults with Autoimmune Thyroid Diseases

BACKGROUND

Autoimmune thyroid diseases (AITD) are complex conditions that are caused by an interaction between genetic susceptibility and environmental triggers. Iodine is already known to be an environmental trigger for AITD, but genes associated with susceptibility need to be further assessed. Therefore, the aims of this study were to assess the association between copy number variations (CNVs) and AITD, to identify genes related with susceptibility to AITD, and to investigate the interaction between iodine status and CNVs in the occurrence of AITD.

METHODS

Blood samples from 15 patients with AITD and 15 controls were assessed by chromosome microarray to identify candidate genes. The copy number of candidate genes and urinary iodine level was determined in adults from areas of different iodine statuses including 158 patients and 181 controls.

RESULTS

The immune-related genes, SIRPB1 and TMEM91, were selected as candidate genes. The distribution of SIRPB1 CNV in AITD patients and controls was significantly different and was considered a risk factor for AITD. There was no significant association between urinary iodine level and candidate gene CNVs.

CONCLUSION

SIRPB1 CNV and an excess of iodine were risk factors for AITD, but an association with the occurrence of AITD was not found.

Association between the KRAS Gene Polymorphisms and Papillary Thyroid Carcinoma in a Chinese Han Population

Several studies have reported the association between MAPK signaling pathway gene polymorphisms and papillary thyroid carcinoma (PTC). KRAS gene, an oncogene from the mammalian RAS gene family plays an important role in the MAPK pathway. This study aimed to identify the potential association of KRAS gene polymorphisms with susceptibility to PTC in a Han Chinese population. A total of 861 patients with PTC, 562 disease controls with nodular goiter and 897 healthy controls were recruited. Four tagSNP polymorphisms (rs12427141, rs712, rs7315339 and rs7960917) of KRAS gene were genotyped by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS). Statistical analyses and haplotype estimations were conducted using Haploview and Unphased softwares. Only significant differences were observed in genotypic frequencies of the rs7315339 polymorphism (χ² =7.234, df=2, p=0.027) between PTC and disease controls. Statistically significant differences in both allelic and genotypic genotypes frequencies for rs712 (Genotype, χ²=8.258, p=0.016) and rs12427141 (Allele, χ²=3.992, p=0.046; Genotype, χ²=8.140, p=0.017) were observed between PTC patients and controls. Haplotype analyses revealed higher frequencies of GA and TA haplotypes (p=0.039 and p=0.003, respectively) from rs712- rs12427141 (two-SNP) or TGA and TTG haplotype containing the alleles from rs7960917, rs712 and rs12427141, as well as the GAT haplotype containing the alleles from rs712, rs12427141 and rs7315339 in PTC patients than in healthy controls (p=0.042, p=0.037, p=0.027, respectively). Inversely, the haplotype TTA from rs7960917, rs712 and rs12427141 or the haplotype TAC from rs712, rs12427141 and rs7315339 was significantly less frequent in the PTC patients than in normal control (p=0.003, p=0.003, respectively). These findings suggest the role of these KRAS gene variants in susceptibility to PTC. Moreover, significant differences of the KRAS gene polymorphisms may occur between nodular goiter and PTC.

Correlation between polymorphisms of BRAF gene and papillary thyroid carcinoma

BACKGROUND

Papillary thyroid carcinoma (PTC), which accounts for 80% of all thyroid cancers, has an increasing incidence over these years. Single nucleotide polymorphisms (SNPs) of BRAF were considered to be one of well-established risk factors leading to development of PTC. The aim of this study was to investigate whether the common mutations of BRAF could elevate significantly the risk of PTC in a Chinese population.

METHODS

Four SNPs (rs11762469, rs17623204, rs1267636 and rs3748093) of BRAF were selected through our filter by Haploview 4.2 software with HapMap databases. We used the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) to genotype the four SNPs in blood samples of 618 subjects (206 patients with PTC and 412 healthy controls). The correlation between BRAF polymorphisms and PTC risk was assessed using student t-test and chi-square test.

RESULTS

The results showed that mutation in rs3748093 was significantly associated with an increased risk of PTC in allele model (A allele vs. T allele, OR = 1·68, 95% CI = 1·16-2·43, P = 0·006), dominant model (TA + AA vs TT, OR = 1·64, 95% CI = 1·08-2·48, P = 0·019) and homozygote model (AA vs. TT, OR = 2·94, 95% CI = 1·00-8·61, P = 0·040). However, the other three SNPs (rs11762469, rs17623204 and rs1267636) were shown to have no association with the risk of PTC.

CONCLUSIONS

Our results indicated that polymorphism of rs3748093*A was significantly correlated with an increased risk of PTC in a Chinese population. Further investigation on the aetiological mechanism of PTC is needed to validate our results.

Establishment, characterization and comparison of seven authentic anaplastic thyroid cancer cell lines retaining clinical features of the original tumors

BACKGROUND

Anaplastic thyroid cancer (ATC) is thought to often be transformed from pre-existing differentiated thyroid cancer. It is one of the most aggressive malignancies and has a dismal prognosis due to its resistance to multimodal therapies. Basic exploratory studies using authentic ATC cell lines that retain its clinical features are necessary. We investigated the characteristics of seven ATC cell lines newly established at our institute to confirm their possible utility for basic studies.

METHODS

Seven distinct cell lines from six patients were established. Their molecular characteristics and sensitivities to cytotoxic anti-cancer drugs were investigated and compared with each other, and with the clinical features of the original tumors.

RESULTS

All cells showed extensive chromosomal abnormality and Pax8 expression, indicating human thyroid follicular cell origin. Vascular endothelial growth factor was secreted from all cells, suggesting possible candidacy for targeted therapy. Vimentin was expressed, but E-cadherin expression was lost in all cells but OCUT-1C, which showed different features from those of OCUT-1F derived from the same tumor, suggesting a mixture of cancer cell clones with various degrees of differentiation within a single ATC tumor. Cells were likely to show sensitivity for taxanes, indicating the usefulness of taxanes as the first-line chemotherapy. OCUT-2, a cell line with both B-Raf and PI3 KCA mutation, demonstrated the importance of molecular target-oriented therapy.

CONCLUSIONS

Basic studies using authentic ATC cell lines retaining the clinical features of the original tumor are useful models for investigating the mechanism of anaplastic transformation and exploring novel therapeutic strategies.

Molecular pathogenesis of B-cell posttransplant lymphoproliferative disorder: what do we know so far?

Posttransplant lymphoproliferative disorder (PTLD) is a potentially fatal disease that arises in 2%-10% of solid organ and hematopoietic stem cell transplants and is most frequently of B-cell origin. This very heterogeneous disorder ranges from benign lymphoproliferations to malignant lymphomas, and despite the clear association with Epstein-Barr Virus (EBV) infection, its etiology is still obscure. Although a number of risk factors have been identified (EBV serostatus, graft type, and immunosuppressive regimen), it is currently not possible to predict which transplant patient will eventually develop PTLD. Genetic studies have linked translocations (involving C-MYC, IGH, BCL-2), various copy number variations, DNA mutations (PIM1, PAX5, C-MYC, RhoH/TTF), and polymorphisms in both the host (IFN-gamma, IL-10, TGF-beta, HLA) and the EBV genome to B-cell PTLD development. Furthermore, the tumor microenvironment seems to play an important role in the course of disease representing a local niche that can allow antitumor immune responses even in an immunocompromised host. Taken together, B-cell PTLD pathogenesis is very complex due to the interplay of many different (patient-dependent) factors and requires thorough molecular analysis for the development of novel tailored therapies. This review aims at giving a global overview of the currently known parameters that contribute to the development of B-cell PTLD.