A susceptibility locus for papillary thyroid carcinoma on chromosome 8q24

Abstract

Papillary thyroid carcinoma (PTC) displays higher heritability than most other cancers. To search for genes predisposing to PTC, we performed a genome-wide linkage analysis in a large family with PTC and melanoma. Among several peaks the highest was at 8q24, with a maximum nonparametric linkage (NPL) score of 7.03. Linkage analysis was then broadened to comprise 25 additional PTC families that produced a maximum NPL score of 3.2, P = 0.007 at the 8q24 locus. Fine mapping with microsatellite markers was compatible with linkage to the 8q24 locus in 10 of the 26 families. In the large family, a approximately 320 Kb haplotype was shared by individuals with PTC, melanoma, or benign thyroid disease, but not by unaffected individuals. A 12 Kb haplotype of 8 SNP markers within the larger haplotype was shared by 9 of the 10 families in which the 8q24 locus was compatible with linkage. The shared haplotype is located within 2 known overlapping protein-coding genes, thyroglobulin (TG) and Src-like adaptor (SLA). Resequencing of the coding and control regions of TG and SLA did not disclose putative mutations in PTC patients. Embedded in the TG-SLA region are three likely noncoding RNA genes, one of which (AK023948) harbors the 8-SNP haplotype. Resequencing of AK023948 and one of the other RNA genes did not reveal candidate mutations. Gene expression analysis indicated that AK023948 is significantly down-regulated in most PTC tumors. The putative noncoding RNA gene AK023948 is a candidate susceptibility gene for PTC.

Figure 1

Haplotypes of microsatellite markers in members of family #1. A unique haplotype (boxed) co-segregates with PTC, melanoma, and some benign thyroid diseases.

Figure 2

NPL and LOD score plots of chromosome 8 from 26 PTC families. Multi-point nonparametric linkage analysis is shown with two different sets of SNPs separately. The linkage peak region was further re-analyzed with tag SNPs only; the tag SNPs (r=1.0) were chosen by using tagger program (http://www.broad.mit.edu/mpg/tagger/). The LOD score plots (a) and NPL score plots (b) with 3 sets of SNP markers are shown.

Figure 3

The thyroglobulin (TG) gene cluster and shared haplotype in the 8q24 locus. The cluster consists of the large TG gene (48 exons total); the SLA gene encoded by the opposite strand in TG introns 41, 42 and 43; and three cDNAs encoded in introns of SLA. The relative positions of the SNP markers forming a shared haplotype in 9 families was based on UCSC Genome Browser (http://genome.ucsc.edu/). The 8 SNPs forming the shared haplotype are: 1: rs9942754; 2: rs2702969; 3: rs2702968; 4: rs2702967; 5: rs2739136; 6: rs17695552; 7: rs2702966; 8: rs2741205.

Figure 4

Gene expression analysis in PTC. (a) Semi-quantitative RT-PCR of AK023852, AK023948, SLA, and TG in 5 sporadic PTC samples from which tumor (T) and paired unaffected thyroid tissue (N) were analyzed. GAPDH was used as an internal control. (b) Quantitative real time RT-PCR of AK023948 in familial and sporadic PTC samples. GAPDH was used as control. The expression ratio (T/N) of PTC tumor (T) versus paired unaffected normal (N) was calculated by the comparative threshold cycle method (mean and the standard deviation are shown).