Chromosome 3p14 homozygous deletions and sequence analysis of FRA3B.
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.
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Division of Medical Oncology, University of Colorado Health Sciences Center, Denver 80262, USA.
Gemmill
R M
RM
West
J
J
Robinson
M
M
Robinson
L
L
Li
E
E
Roche
J
J
Todd
S
S
Waggoner
B
B
Lundstrom
R
R
Jacobson
J
J
Mullokandov
M R
MR
Klinger
H
H
Drabkin
H A
HA
D017766:Acid Anhydride Hydrolases; D001483:Base Sequence; D043283:Chromosome Fragile Sites; D002873:Chromosome Fragility; D002893:Chromosomes, Human, Pair 3; D004247:DNA; D017353:Gene Deletion; D019073:HT29 Cells; D006367:HeLa Cells; D006720:Homozygote; D006801:Humans; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D009363:Neoplasm Proteins; D011506:Proteins / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D014407:Tumor Cells, Cultured; D000099170:Bis(5'-adenosyl)triphosphatase
D017766:Acid Anhydride Hydrolases; D004247:DNA; D009363:Neoplasm Proteins; D011506:Proteins; D000099170:Bis(5'-adenosyl)triphosphatase