Excluding TTC4 as a target for loss on chromosome 1p31 in human breast cancer

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We have previously reported a region of high loss of heterozygosity in human breast cancer on chromosome 1p31.1. Recently a new member of the human tetratricopeptide repeat-containing gene family, TTC4, was mapped to a YAC 879a6 which encompasses the smallest region of overlapping loss (SRO) reported by our group. This therefore became a candidate for a new breast cancer tumour suppressor gene. We used multiple pairs of PCR primers from the gene to screen CEPH and Zeneca YACs covering the region, but were unable to amplify a product from any of them, including two independent isolates of YAC 879a6. We have isolated both a BAC (31C23) and YAC (13EA7) using primers from the 3' untranslated region of TTC4. In single and double FISH experiments both 13EA7 and 31C23 located on chromosome 1p but distal to 879a6 at 1p31.3. This localisation was confirmed by screening a panel of monochromosome hybrids. Comparison of TTC4 sequence with the genome database identified a match between the 3' untranslated region of the gene and EST WI-9676. However, this EST was assigned to chromosome 7 by radiation hybrid mapping, transcript and YAC contig mapping. We therefore identified YACs from these contigs using primers from WI-9676 and sequenced the resulting PCR products. These revealed a number of nucleotide alterations that suggested that the sequence on chromosome 7 is a pseudogene. Finally pseudogene-specific primers were used to identify two new BACs, one of which (51H8) was localised to 7p13-14 by FISH. In conclusion, we have therefore reassigned TTC4 by FISH to 1p31.3, excluding it as a target for inactivation in human breast cancer at 1p31.1, and identified a TTC4 pseudogene that maps to chromosome 7p13-14.