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Chromosome 3p14 homozygous deletions and sequence analysis of FRA3B
F Boldog1, R M Gemmill, J West
1Division of Medical Oncology, University of Colorado Health Sciences Center, Denver 80262, USA.
Abstract:
Loss of heterozygosity (LOH) involving 3p occurs in many carcinomas but is complicated by the identification of four distinct homozygous deletion regions. One putative target, 3p14.2, contains the common fragile site, FRA3B, a hereditary renal carcinoma-associated 3;8 translocation and the candidate tumor suppressor gene, FHIT. Using a approximately 300 kb comsid/lambda contig, we identified homozygous deletions in cervix, breast, lung and colorectal carcinoma cell lines. The smallest deletion (CC19) was shown not to involve FHIT coding exons and no DNA sequence alterations were present in the transcript. We also detected discontinuous deletions as well as deletions in non-tumor DNAs, suggesting that FHIT is not a selective target. Further, we demonstrate that some reported FHIT aberrations represent normal splicing variation. DNA sequence analysis of 110 kb demonstrated that the region is high in A-T content, LINEs and MER repeats, whereas Alu elements are reduced. We note an intriguing similarity in repeat sequence composition between FRA3B and a 152 kb segment from the Fragile-X region. We also identified similarity between a FRA3B segment and a small polydispersed circular DNA. In contrast to the selective loss of a tumor suppressor gene, we propose an alternative hypothesis, that some putative targets including FRA3B may undergo loss as a consequence of genomic instability. This instability is not due to DNA mismatch repair deficiency, but may correlate in part with p53 inactivation.
Insights
Loss of heterozygosity in 3p deletions, common in carcinomas, may not selectively target the FHIT gene. Genomic instability, potentially linked to p53 inactivation, could explain these losses.
Area of Science:
- Genetics
- Molecular Biology
- Oncology
Background:
- Loss of heterozygosity (LOH) on chromosome 3p is frequent in various carcinomas.
- Four distinct homozygous deletion regions complicate the identification of specific targets.
- The 3p14.2 region, containing FRA3B and the FHIT gene, is a key area of investigation.
Purpose of the Study:
- To investigate homozygous deletions in the 3p14.2 region across different carcinoma cell lines.
- To determine if the FHIT gene is a selective target of these deletions.
- To explore alternative hypotheses for the observed LOH patterns.
Main Methods:
- Analysis of a 300 kb contig to identify homozygous deletions in cervix, breast, lung, and colorectal carcinoma cell lines.
- DNA sequence analysis of the 3p14.2 region.
- Comparison of repeat sequence composition with other genomic regions.
Main Results:
- Homozygous deletions were identified, but the smallest deletion (CC19) did not involve FHIT coding exons.
- No DNA sequence alterations were found in the FHIT transcript.
- Discontinuous deletions and deletions in non-tumor DNA were observed, suggesting FHIT is not a selective target.
- Some reported FHIT aberrations were identified as normal splicing variations.
- The 3p14.2 region exhibits high A-T content and specific repeat compositions, with similarities to Fragile-X and circular DNA elements.
- Genomic instability, possibly related to p53 inactivation, is proposed as an alternative explanation for deletions.
Conclusions:
- The FHIT gene is likely not the sole or selective target of 3p homozygous deletions in carcinomas.
- Genomic instability, rather than selective tumor suppressor gene loss, may drive these deletions.
- p53 inactivation may play a role in the genomic instability observed in these regions.