Cloning of a breast cancer homozygous deletion junction narrows the region of search for a 3p21.3 tumor suppressor gene

Abstract

Chromosome 3p abnormalities and allele loss are frequent in lung and breast cancers, and several lung cancer cell lines exhibit homozygous deletions of 3p indicating potential sites of tumor suppressor genes at regions 3p21.3, 3p14.2 and 3p12. We have identi®ed and characterized a new 3p21.3 homozygous deletion in a breast cancer cell line and the primary tumor that overlaps those previously described in small cell lung cancer (SCLC). This homozygous deletion is approximately 220 kb in length and represents a somatically acquired change in the primary breast cancer. Cloning and sequencing of the breakpoint demonstrated that this resulted from an interstitial deletion and precisely pinpoints this deletion within the three SCLC homozygous deletions previously reported. This deletion signi®cantly narrows the minimum common deleted region to 120 kb and is distinct from the previously reported region that suppresses tumor formation of the murine A9 ®brosarcoma cells. These ®ndings suggest that a common homozygous deletion region on 3p21.3 is important in both lung and breast cancers. It is likely that this very well characterized region either contains one tumor suppressor gene common to both tumor types or two closely linked tumor suppressor genes speci®c for each tumor.

Evaluation of the 3p21.3 tumour-suppressor gene cluster

“…High-resolution studies of tumours refined the areas of allelic losses in 3p into several distinct regions representing likely locations of tumour-suppressor genes (TSGs). These candidate regions include 3p12-13, 3p14.2, 3p21.3, 3p24-25 and 3p25-26 (Hung et al, 1995;Sekido et al, 1998;Sundaresan et al, 1998;Wistuba et al, 2000). Investigation of these regions has identified resident TSGs, for example VHL at 3p25 and FHIT at 3p14.2, or likely candidates such as DUTT1/ROBO1 at 3p12.…”

“…Following construction of a B700 kb clone contig covering this deletion overlap and its flanks the transcribed sequences were characterized (Wei et al, 1996;Lerman and Minna, 2000). Additional discovery of a nesting homozygous deletion in a breast cancer cell line (Sekido et al, 1998) divided the minimal candidate region into a 120 kb region containing 8 genes (HYAL2, FUS1, Ras-associated factor 1 (RASSF1), BLU/ZMYND10, nitrogen permease regulator protein 2-like (NPR2L), 101F6, PL6 and CACNA2D2) and a B250 kb region containing a further 11 genes ( Figure 1). Thus one or more lung and breast cancer TSGs likely resides in the minimal 120 kb critical deletion region or the larger 250 kb region.…”

HYAL1LUCA-1, a candidate tumor suppressor gene on chromosome 3p21.3, is inactivated in head and neck squamous cell carcinomas by aberrant splicing of pre-mRNA

“…The position of HYAL1 within this 30 kb homozygous deletion and the larger overlapping homozygous deletions in the NCI H740 and GLC20 SCLC lines leaves this gene a strong candidate TSG. A recent study identi®ed a 220 kb homozygous deletion on 3p21.3 in a breast carcinoma line (Sekido et al, 1998). The telomeric breakpoint resides approximately 4 kb centromeric to the HYAL1 open reading frame, and overlaps with the centromeric region of the SCLC deletions.…”

Frequent hypermethylation of the RASSF1A gene in prostate cancer

“…Recently, we and others (Dammann et al, 2000;Burbee et al, 2001) have cloned and characterized the Ras association domain family 1 (RASSF1) gene at 3p21.3, from which loss of genetic material is one of the most frequent events in several types of human solid tumors (Kok et al, 1997;Sekido et al, 1998;Lerman et al, 2000;Wistuba et al, 2000). One of the two major isoforms transcribed from this locus, RASSF1A, was absent in human lung and breast tumors due to promoter methylation (Dammann et al, 2000Agathanggelou et al, 2001;Burbee et al, 2001).…”