Unsupervised analysis of follicular thyroid tumours transcriptome by oligonucleotide microarray gene expression profiling

Abstract

Introduction: Mechanisms driving the invasiveness of follicular thyroid cancer (FTC) are not fully understood. In our study, we undertook an unsupervised analysis of the set of follicular thyroid tumours (adenomas (FTA) and carcinomas) to verify whether the malignant phenotype influences major sources of variability in our dataset. Material and methods:The core set of samples consisted of 52 tumours (27 FTC, 25 FTA). Total RNA was analysed by oligonucleotide microarray (HG-U133 Plus 2.0). Principal Component Analysis (PCA) was applied as a main method of unsupervised analysis. Results: An analysis of biological character of genes correlated to the first six PCs was performed. When genes correlated to the first PC were used to cluster FTC and FTA, they appeared in two branches; one, relatively enriched in adenomas, with homogenous expression of subset of genes, and the other containing mainly carcinomas, with down-regulation of these genes and heterogeneous up-regulation in a smaller cluster of transcripts. Genes highly up-regulated in adenomas included some thyroid-specific transcripts. The second cluster of genes, up-regulated in carcinomas, contained mainly immunity-related transcripts. Immune response genes were found in the first, third and sixth principal components, improving the discrimination between carcinomas and adenomas. Conclusions: Our unsupervised analysis indicates that invasiveness of follicular tumours might be considered as the major source of variability in transcriptome analysis. However, the distance between both groups is small and the clusters are overlapping, thus, unsupervised analysis is not sufficient to properly classify them. (Endokrynol Pol 2013; 64 (5): 328-334)

Gene Expression (mRNA) Markers for Differentiating between Malignant and Benign Follicular Thyroid Tumours

“…The samples and microarray data have been already used in our previous studies and are reused in the current study [18,27]. Surgical procedures on patients were conducted in Polish and German centres, at the MSC Institute—Oncology Center in Gliwice, University of Leipzig, University of Halle, and Mainz University Hospital.…”

“…However, reproducibility of results obtained between mentioned publications was rather low. This could be a consequence of slight molecular differences between FTC and FTA [18,19] or the insufficient sample size used in these studies. Genetic alterations, such as RAS gene family somatic mutations or PAX8/PPARG translocations, although very promising in initial studies, were not found to be specific for follicular carcinoma, as these genetic alterations occurred in both FTCs and FTAs with similar frequencies [20,21,22].…”

“…We performed a two-step analysis: first a statistical testing of a large gene expression microarray dataset of FTC and FTA previously generated in our laboratory [18,27], and next, a meta-analysis of all available datasets, to select the most robustly represented markers [4,5,6,7,8,9,10,11,12,13,14,15,16,17] (Figure 1). Such approach allowed us to select independent genes coming from own dataset and from a meta-analysis.…”

Molecular Analysis by Gene Expression of Mitochondrial ATPase Subunits in Papillary Thyroid Cancer: Is ATP5E Transcript a Possible Early Tumor Marker?

“…In accordance with these findings, it has been shown that most cancer cells have mutations in the TCA cycle enzymes, such as succinate dehydrogenase and fumarate hydratase, leading to metabolic changes that have already been observed at the RNA level [ 84 , 85 ]. Transcriptome changes in carcinogenesis have been widely studied and a great amount of data has been published [ 86 – 89 ]. However, most of these data require confirmation by means of a highly accurate method of quantitative real-time PCR.…”