Detection of PAX8-PPARG Fusion Transcripts in Archival Thyroid Carcinoma Samples by Conventional RT-PCR.

The t(2;3)(q13;p25) occurs in a subgroup of follicular-patterned thyroid tumors and leads to a fusion of the genes encoding for the thyroid-specific transcription factor paired box 8 (PAX8) and the peroxisome proliferator-activated receptor gamma (PPAR). Although initially discovered in follicular carcinomas (FTC), the fusion transcripts were also detected in a small fraction of follicular adenomas and rarely in follicular variants of papillary carcinomas (FV-PTC). In most RT-PCR based studies, fresh or snap-frozen tissue samples were used. The aim of the present study was to develop a method for the detection of chimeric PAX8PPARG transcripts in formalin-fixed paraffin-embedded (FFPE) thyroid tumor samples by conventional RT-PCR. For this purpose, RNA from FFPE samples of 21 FTC, seven FV-PTC, and one bone metastasis derived from an FTC was subjected to RT-PCR with subsequent gel electrophoretic separation of the products. Fusion transcripts were detected in 2/21 primary FTC (9.5%) and in the bone metastasis, but they were undetectable in all seven FV-PTC under investigation. The RT-PCR approach described herein allows to detect all known variants of PAX8PPARG fusion transcripts and is applicable to FFPE tissues. Thus, it can be used to screen archival thyroid tumor samples for the gene fusion. (c) 2011 Wiley Periodicals, Inc.