Analysis of a new homozygous deletion in the tumor suppressor region at 3p12.3 reveals two novel intronic noncoding RNA genes

Abstract

Homozygous deletions or loss of heterozygosity (LOH) at human chromosome band 3p12 are consistent features of lung and other malignancies, suggesting the presence of a tumor suppressor gene(s) (TSG) at this location. Only one gene has been cloned thus far from the overlapping region deleted in lung and breast cancer cell lines U2020, NCI H2198, and HCC38. It is DUTT1 (Deleted in U Twenty Twenty), also known as ROBO1, FLJ21882, and SAX3, according to HUGO. DUTT1, the human ortholog of the fly gene ROBO, has homology with NCAM proteins. Extensive analyses of DUTT1 in lung cancer have not revealed any mutations, suggesting that another gene(s) at this location could be of importance in lung cancer initiation and progression. Here, we report the discovery of a new, small, homozygous deletion in the small cell lung cancer (SCLC) cell line GLC20, nested in the overlapping, critical region. The deletion was delineated using several polymorphic markers and three overlapping P1 phage clones. Fiber-FISH experiments revealed the deletion was approximately 130 kb. Comparative genomic sequence analysis uncovered short sequence elements highly conserved among mammalian genomes and the chicken genome. The discovery of two EST clusters within the deleted region led to the isolation of two noncoding RNA (ncRNA) genes. These were subsequently found differentially expressed in various tumors when compared to their normal tissues. The ncRNA and other highly conserved sequence elements in the deleted region may represent miRNA targets of importance in cancer initiation or progression.

Alterations of ROBO1/DUTT1 and ROBO2 loci in early dysplastic lesions of head and neck: clinical and prognostic implications

“…Downregulation of the ncRNAs was reported in renal cell carcinoma (66.67%, 4/6) and breast carcinoma (60%, 6/10), but their overexpression was observed in lung carcinoma (75%) (Angeloni et al 2006). Relatively lower expression of the ncRNAs than ROBO1/DUTT1 seen in both normal and HNSCC samples suggests the presence of diVerent promoters of these genes.…”

“…Their overexpression has been seen in lung cancers whereas reduced expression in kidney and breast carcinoma indicating diVerential role of these ncRNAs in development of cancers (Angeloni et al 2006). Both transcripts were transcribed in the same direction as ROBO1/DUTT1, suggesting their product could be co-regulated and possibly related to ROBO1/ DUTT1 function.…”

A Roundabout Way to Cancer

“…One additional consequence of epigenetic silencing of Slit2 and Slit3 is downregulation of microRNA (miR)-218-1 and miR-218-2, which are located within intron 15 of human Slit2 and intron 14 of human Slit3 , respectively (Angeloni et al, 2006; Tie et al, 2010). This miR negatively regulates Robo1 expression in gastric, head and nasopharyngeal cancers (Alajez et al, 2011; Tie et al, 2010), but its downregulation due to Slit methylation in many tumor types provides one explanation for the observation that Robo1 appears to be infrequently silenced in the majority of tumor samples (Grone et al, 2006; Ito et al, 2006; Xu et al, 2010).…”

ROBO1 deletion as a novel germline alteration in breast and colorectal cancer patients

“…Interestingly, the heterozygous deletion on intron 4 of the long ROBO1 transcript is within the homozygous deletion in the short ROBO1 transcript [NM_133631/ENST00000495273; hg17 spanning from intron 3 to intron 4 in the long transcript, converted by hg19 using Batch Coordinate ConversionliftOver tool (https://genome.ucsc.edu/cgi-bin/hgLiftOvert)] reported by Angeloni et al [27]. The authors also identified two lncRNAs on intron 4 of the long transcript (intron 2 of the short transcript) with the potential to modulate ROBO1 expression.…”