Differential Expression of miRNAs in Papillary Thyroid Carcinoma Compared to Multinodular Goiter Using Formalin Fixed Paraffin Embedded Tissues Michael T. Tetzlaff & Aihua Liu & Xiaowei Xu & Stephen R. Master & Don A. Baldwin & John W. Tobias & Virginia A. Livolsi & Zubair W. Baloch Published online: 9 August 2007 # Humana Press Inc. 2007 Abstract microRNAs (miRNAs) are approximately 22 nt RNAs that negatively regulate target gene expression. Their dysregulation has been implicated in the pathogenesis of a number of human cancers, including papillary thyroid carcinoma (PTC). Whereas previous studies using microarray technologies have largely relied on the ability to procure fresh tissue at the time of surgery to characterize miRNA signatures in PTC, we exploited the ability to procure sufficient miRNA from formalin-fixed paraffin-embedded (FFPE) tissue to describe a series of miRNAs whose expression is dysregulated in PTC compared to benign proliferative multinodular goiter (MNG). We identified 13 miRNAs upregulated and 26 miR- NAs downregulated in PTC versus MNG. These include miRNA-21, miRNA-31, miRNA-221, and miRNA-222. Their dysregulation was further validated by real time RT- PCR analysis in an independent set of FFPE tissues. Many of these have previously been described in fresh tissue studies as altered in PTC, confirming the utility of this approach. These results further highlight the applicability of miRNA expres- sion patterns as potential markers of human cancer, and our results suggest that FFPE tissues are suitable resources for such miRNA expression analyses. The ability to utilize FFPE tissue in the molecular characterization of human malignancy will unlock a rich resource for future cancer studies. Keywords miRNA . thyroid . cancer . microarray Introduction Papillary thyroid carcinoma (PTC) and follicular thyroid carcinoma (FTC) are the most common subtypes of thyroid malignancies and account for approximately 80% and 11% of all thyroid cancers, respectively [1]. Many genomic alterations have been described for thyroid carcinomas, and these tend to cluster with the discrete histological subtypes. The most common of these is a mutation in the B-RAF oncogene (T1799A transversion/V600E substitution), which is present in approximately 44% (29–83%) of PTCs [2–11]. Numerous other somatically acquired mutations and gene rearrangements have been identified in thyroid cancer, albeit with less frequency. Follicular adenomas and carcino- mas contain translocations fusing PAX8 with peroxisome proliferator activated receptor-γ (PPARγ)[12–16]. Activat- ing mutations in Ras occur primarily in follicular adenomas and carcinomas of the thyroid, as well as in the follicular variant of papillary thyroid carcinoma (PTC-fv) [17–22]. RET/PTC gene rearrangements occur in radiation-associated and sporadic papillary thyroid carcinomas, as well as in follicular adenomas [23–29]. Although all these genetic changes could serve as potential indicators of malignant Endocr Pathol (2007) 18:163–173 DOI 10.1007/s12022-007-0023-7 Electronic supplementary material The online version of this article (doi:10.1007/s12022-007-0023-7) contains supplementary material, which is available to authorized users. M. T. Tetzlaff (*) : A. Liu : X. Xu : S. R. Master : D. A. Baldwin : V. A. Livolsi : Z. W. Baloch Department of Pathology and Laboratory Medicine, Hospital for the University of Pennsylvania, 3400 Spruce Street, 7 Founders Pavilion, Philadelphia, PA 19040, USA e-mail: tetzlafm@uphs.upenn.edu Z. W. Baloch e-mail: baloch@mail.med.upenn.edu J. W. Tobias Penn Bioinformatics Core, University of Pennsylvania, 1313 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA