Results of the MDR analysis of the gene pair models differentiating the patient subgroups according to age at time of GD onset.

<p>Results of the MDR analysis of the gene pair models differentiating the patient subgroups according to age at time of GD onset.</p

General clinical characteristics of patients with GD included in this study.

<p>General clinical characteristics of patients with GD included in this study.</p

Differences between the risk of GD onset in young patients compared to older patients according to the coexistence of pairs of polymorphisms.

<p>OR: odds ratio; OR = 1.0 (ref.): referent category.</p

Summary of the MDR results.

<p>Summary of the MDR results.</p

Odds ratio analysis of young patients compared to older patients with adjustment for smoking.

<p>Young/older: number of patients with age of onset of GD ≤ 30 years/number of patients with age of onset of GD > 30 years adjusted by smoking status; carriers: carriers of minor alleles.</p

Frequency of the alleles and distribution of the genotypes of the four genes in patients with GD stratified by age at GD onset.

<p>Frequency of the alleles and distribution of the genotypes of the four genes in patients with GD stratified by age at GD onset.</p

BRAFV600E-Associated Gene Expression Profile: Early Changes in the Transcriptome, Based on a Transgenic Mouse Model of Papillary Thyroid Carcinoma

<div><p>Background</p><p>The molecular mechanisms driving the papillary thyroid carcinoma (PTC) are still poorly understood. The most frequent genetic alteration in PTC is the <i>BRAF</i>V600E mutation–its impact may extend even beyond PTC genomic profile and influence the tumor characteristics and even clinical behavior.</p><p>Methods</p><p>In order to identify <i>BRAF</i>-dependent signature of early carcinogenesis in PTC, a transgenic mouse model with <i>BRAF</i>V600E-induced PTC was developed. Mice thyroid samples were used in microarray analysis and the data were referred to a human thyroid dataset.</p><p>Results</p><p>Most of <i>BRAF</i>(+) mice developed malignant lesions. Nevertheless, 16% of <i>BRAF</i>(+) mice displayed only benign hyperplastic lesions or apparently asymptomatic thyroids. After comparison of non-malignant <i>BRAF</i>(+) thyroids to <i>BRAF</i>(−) ones, we selected 862 significantly deregulated genes. When the mouse <i>BRAF</i>-dependent signature was transposed to the human HG-U133A microarray, we identified 532 genes, potentially indicating the <i>BRAF</i> signature (representing early changes, not related to developed malignant tumor). Comparing <i>BRAF</i>(+) PTCs to healthy human thyroids, PTCs without <i>BRAF</i> and <i>RET</i> alterations and <i>RET</i>(+), <i>RAS</i>(+) PTCs, 18 of these 532 genes displayed significantly deregulated expression in all subgroups. All 18 genes, among them 7 novel and previously not reported, were validated as <i>BRAF</i>V600E-specific in the dataset of independent PTC samples, made available by The Cancer Genome Atlas Project.</p><p>Conclusion</p><p>The study identified 7 <i>BRAF</i>-induced genes that are specific for <i>BRAF V600E</i>-driven PTC and not previously reported as related to <i>BRAF</i> mutation or thyroid carcinoma: <i>MMD</i>, <i>ITPR3</i>, <i>AACS</i>, <i>LAD1</i>, <i>PVRL3</i>, <i>ALDH3B1</i>, and <i>RASA1</i>. The full signature of <i>BRAF</i>-related 532 genes may encompass other <i>BRAF</i>-related important transcripts and require further study.</p></div

Hierarchical clustering of mouse samples.

<p>Thirty-eight mouse samples based on 1020 probe sets significantly differentiating between <i>BRAF</i>(+) and <i>BRAF</i>(−) non-malignant mouse samples (marked with blue and cyan respectively). PTCs (red); borderline thyroid lesions (BL; magenta); benign hyperplastic thyroid lesions (BHL; dark green); asymptomatic thyroid glands (AT; green).</p

Boxplots of 18 genes chosen for validation.

<p>Expression distribution for each gene from our microarray data (on the left), The Cancer Genome Atlas Project data (on the right). The expression levels of analyzed genes are presented in <i>BRAF</i>(+) PTCs, <i>RET</i>(+), <i>RAS</i>(+), PTC(-) and healthy thyroids (HT) from left to right, respectively (as presented at the bottom of the figure). FDR values are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143688#pone.0143688.t004" target="_blank">Table 4</a>.</p

Microarray-derived dataset- human cohort.

<p>PTC(-)- PTCs without any mutation detected</p><p>Microarray-derived dataset- human cohort.</p