Deletions at the chromosome 3 common eliminated region 1 on 3p21.3 in human breast tumors

Background

Chromosome 3 is abnormal in a variety of human cancers. An assay, based on a non-random elimination of human chromosome segments in mouse-human microcell hybrids during tumor growth in SCID mice, has been developed. It is called the Elimination test (Et), and is designed for the identification of chromosomal regions containing putative TSGs. A commonly lost segment, termed chromosome 3 common eliminated region 1 (C3CER1) (also referred to as CER1), was identified using the Et. This region spans ~2.4 Mb at 3p21.3 and contains 33 active genes, including the putative TSGs: LF, LIMD1 and RIS1. It was recently reported that the LIMD1 gene product functions in connection with pRB to suppress cell proliferation. Here, we addressed the question of whether the C3CER1 region at 3p21.3 is preferentially lost in actual human breast tumors, and whether the fragile nature of FRA3B induces terminal deletions leading to 3p14.2-pter losses or whether the eventual 3p21.3 losses are interstitial. We also analysed whether the LIMD1 gene was mutated in human breast tumors.

Methods

To evaluate the loss of C3CER1 in human tumor tissues we performed loss of heterozygosity (LOH) analysis of 159 breast tumors. We compared the deletion frequency of the C3CER1 area with two other regions on 3p; that is, the FHIT/FRA3B region at 3p14.2 and VHL at 3p25.3. The tumor material was screened for mutations with the SSCP method, and samples with abnormal mobility in SSCP gels were sequenced in an ABI 3100 genetic analyser. We are conducting multipoint FISH analysis to confirm microdeletions in the breast tumor specimens.

Results

LOH was detected in the C3CER1 region in 84% of informative tumors. Thirty-nine percent of LOH-positive tumors showed LOH at all informative C3CER1 markers. The other 61% had a discontinuous LOH pattern suggesting interstitial deletions or breakpoints. In the VHL and FHIT regions, deletions were observed in 69% and 30% of tumors, respectively. We found polymorphism in the first three exons of LIMD1, but sequencing revealed no mutations leading to changes in the protein product.

Conclusion

Of the three 3p regions analysed, the highest deletion frequency was observed at the C3CER1 region. We demonstrate that the interstitial deletions including C3CER1 prevail over 3p14.2-pter losses. The LIMD1 gene is not frequently mutated in breast cancer biopsies.