We searched for chromosome 3p homo-and hemizygous losses in 23 lung cancer cell lines, 53 renal cell and 22 breast carcinoma biopsies using 31 microsatellite markers located in frequently deleted 3p regions. In addition, two sequence-tagged site markers (NLJ-003 and NL3-001) located in the Alu-PCR clone 20 region (AP20) and lung cancer (LUCA) regions, respectively, were used for quantitative real-time PCR (QPCR). We found frequent (10-18%) homozygous deletions (HDs) in both 3p21.3 regions in the biopsies and lung cancer cell lines. In addition, we discovered that amplification of 3p is a very common (15-42.5%) event in these cancers and probably in other epithelial malignancies. QPCR showed that aberrations of either NLJ-003 or NL3-001 were detected in more than 90% of all studied cases. HDs were frequently detected simultaneously both in NLJ-003 or NL3-001 loci in the same tumour (Po3-10 À7 ). This observation suggests that tumour suppressor genes (TSG) in these regions could have a synergistic effect. The exceptionally high frequency of chromosome aberrations in NLJ-003 and NL3-001 loci suggests that multiple TSG(s) involved in different malignancies are located very near to these markers. Precise mapping of 15 independent HDs in the LUCA region allowed us to establish the smallest HD region in 3p21.3C located between D3S1568 (CACNA2D2 gene) and D3S4604 (SEMA3F gene). This region contains 17 genes. Mapping of 19 HDs in the AP20 region resulted in the localization of the minimal region to the interval flanked by D3S1298 and D3S3623 markers. Only four genes were discovered in this interval, namely, APRG1, ITGA9, HYA22 and VILL.

(2012) Genetic and epigenetic analysis of non-small cell lung cancer with NotImicroarrays, Epigenetics, 7:5, 502-513,

To ascertain the involvement of human chromosome 3p and its established critical TSG regions in various epithelial malignancies, 21 polymorphic and 2 nonpolymorphic 3p markers were allelotyped in nonpapillary RCC, NSCLC, CC and BC from a total of 184 patients. LOH was observed with high frequency in all types of cancer studied: RCC (52/57, 91%), BC (41/51, 80%), NSCLC (30/40, 75%) and CC (27/36, 75%). Interstitial deletions, believed to signal TSG inactivation, were verified using the "L-allele rule" and real-time quantitative PCR. Significant correlation was observed between DNA copy numbers for 2 nonpolymorphic STS markers and LOH data for adjacent polymorphic loci. Interstitial deletions in 3p were demonstrated for all cancer types studied. However, the distribution of different types of deletion was characteristic for tumors from various locations. Large terminal deletions were predominantly seen in RCC and NSCLC (51% and 40%, respectively), correlating with clear cell RCC and squamous cell carcinomas of the lung. In addition to the LUCA region at 3p21.3 (centromeric), we found that the AP20 region (3p21.3, telomeric) was frequently affected in all 4 cancers, suggesting that this newly defined critical region contains multiple TSGs. Moreover, at least 3 candidate cancer-specific loci were identified. The telomeric 3p26.1-p25.3 region was predominantly deleted in RCC and NSCLC. The D3S1286 and D3S3047 markers (3p25.2-p24.3) were deleted nonrandomly in NSCLC. High-frequency LOH was detected in a segment mapped closely distal to the LUCA site (3p21.3), around the D3S2409 and D3S2456 markers. © 2002 Wiley-Liss, Inc. Key words: chromosome 3p; tumor-suppressor gene; loss of heterozygosity; allelotyping; renal cell carcinomaVarious tumor-suppressing pathways and cancer-causing genes have been extensively studied over the past decade. 1 Several regions on the short arm of chromosome 3 are commonly affected in different epithelial tumors, and chromosome 3p contains several TSGs. 2,3 Frequent deletions with complicated profiles have been revealed in 3p by cytogenetic and allelotyping studies. 2,4 Tumorsuppression activity has been observed in functional chromosome transfer studies with subchromosomal fragments from distinct 3p regions. 2,5-7 Moreover, several genes from these regions were identified as TSG candidates. 3,8 -12 Our study was undertaken to evaluate distinct critical TSG regions of 3p involved in the origin and/or development of common major human cancers, with the aim of identifying the most promising regions to scan for novel candidate TSGs and for risk assessment. Some large areas of 3p, including long segments of the commonly involved 3p21 region, have not been tested before because identification of the most deleted regions is dependent on the choice of markers and only a limited set of markers has been used. For example, an additional important DNA segment has been identified at 3p21.31 with the application of tri-and tetranucleotide markers instead of the traditionally used CA repeats. 13 Further...

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