Identification of differentially expressed genes in papillary thyroid cancers

Abstract

Purpose: Techniques designed to identify differentially expressed genes (DEGs) in tumors have become important in modern pathology. Genefishing technique using the annealing control primer (ACP) system has recently been developed to screen for DEG transcripts. We tried to identify DEGs involved in papillary thyroid cancer (PTC) by using Genefishing technique.

Materials and methods: We utilized a new differential display method, designated with Genefishing technique, to analyze DEGs in 21 cases of PTCs.

Results: Comparing the gene expression profiles between PTC and normal thyroid, we detected 17 genes that were differentially expressed in PTCs and performed cloning with sequencing in 10 genes. We confirmed the expression patterns of 2 DEGs by RT-PCR assay and identified the same results in 17 out of 21 (81%) PTCs. The 2 DEGs over-expressed in PTCs were identified as DC-STAMP and type I collagen A1. They are novel genes identified first in PTCs.

Conclusion: We confirmed 2 DEGs in PTCs as DC-STAMP and type I collagen A1 by using Genefishing technique. Although the detailed functions of those 2 genes and their products remain to be determined, the genes will provide insights into mechanisms of carcinogenesis or tumor progression in PTCs.

Keywords: Papillary thyroid cancer; dendritic cell-specific transmembrane protein; differentially expressed genes; type I collagen A1.

Fig. 1

GeneFishing™ DEG screening results. There are 8 genes overexpressed in normal thyroid (arrowhead) and nine genes overexpressed in PTC (arrow). 1. normal, 2. PTC. DEG, differentially expressed gene; PTC, papillary thyroid cancer.

Fig. 2

The mRNAs of the 10 DEGs showing distinct results were extracted, amplified using the TOPO® TA Cloning kit and were sequenced. DEGs, differentially expressed genes; TA, Taq-amplified.

Fig. 3

RT-PCR primer sets of DEG3 and DEG14. RT-PCR, reverse transcriptase-polymerase chain reaction; DEG, differentially expressed gene.

Fig. 4

The DEG3 and DEG14 were subjected to confirmation with RT-PCR and confirmed ACP observation. RT-PCR, reverse transcriptase-polymerase chain reaction; ACP, annealing control primer.

Fig. 5

In 21 PTC samples by RT-PCR, DEG3 and DEG14 were observed to be up-regulated in most tumors. Bothe DEGs in 2 cases of follicular subtype (No. 10 and No. 14) were not up-regulated. PTC, papillary thyroid cancer; RT-PCR, reverse transcriptase-polymerase chain reaction; DEG, differentially expressed gene.