High resolution chromosome 3p allelotyping of human lung cancer and preneoplastic/preinvasive bronchial epithelium reveals multiple, discontinuous sites of 3p allele loss and three regions of frequent breakpoints

Allele loss involving chromosome arm 3p is one of the most frequent and ear liest known genetic events in lung cancer pathogenesis and may affect sever al potential tumor suppressor gene regions. To Further study the role of ch romosome 3p allele loss in the pathogenesis of lung cancer, we performed hi gh resolution toss of heterozygosity (LOH) studies on 97 lung cancer and 54 preneoplastic/preinvasive microdissected respiratory epithelial samples us ing a panel of 28 3p markers. Allelic losses of 3p were detected in 96% of the lung cancers and in 78% of the preneoplastic/ preinvasive lesions. The allele losses were often multiple and discontinuous, with areas of LOH inte rspersed with areas of retention of heterozygosity, Most small cell lung ca rcinomas (91%) and squamous cell carcinomas (95%) demonstrated larger 3p se gments of allele loss, whereas most (71%) of the adenocarcinomas and preneo plastic/preinvasive lesions had smaller chromosome areas of 3p allele loss. There was a progressive increase in the frequency and size of 3p allele lo ss regions with increasing severity of histopathological preneoplastic/prei nvasive changes. In analyses of the specific parental allele lost comparing 42 preneoplastic/preinvasive foci with those lost in the lung cancer in th e same patient (n = 10), the same parental allele was lost in 88% of 244 co mparisons for 28 3p markers (P = 1.2 x 10(-36) for this occurring by chance ). This indicates the occurrence of allele-specific loss in these foci simi lar to that seen in the tumor by a currently unknown mechanism. Analysis of all of the data indicated multiple regions of localized 3p allele loss inc luding telomere-D3S1597, D3S1111-D3S2432, D3S2432-D3S1537, D3S1537, D3S1537 -D3S1612, D3S4604/Luca19.1-D3S4622/Luca4.1, D3S4624/Luca2.1, D3S4624/ Luca2 .1-D3S1582, D3S1766, D3S1234-D3S1300 (FHIT/FRA3B region centered on D3S1300 ), D3S1284-D3S1577 (U2020/DUTT1 region centered on D351274), and D3S1511-ce ntromere. A panel of six markers in the 600-kb 3p21.3 deletion region showe d loss in 77% of the lung cancers, 70% of normal or preneoplastic/preinvasi ve lesions associated with lung cancer, and 49% of 47 normal, mildly abnorm al, or preneoplastic/preinvasive lesions found in smokers without lung canc er; however, loss was seen in 0% of 18 epithelial samples from seven never smokers. The 600-kh 3p21.3 region and the 3p14.2 (FHIT/FRA3B) and 3p12 (U20 20/DUTT1) regions were common, independent sites of breakpoints (retention of heterozygosity by some markers and LOH by other markers in the immediate region), We conclude that 3p allele loss Is nearly universal in lung cance r pathogenesis; involves multiple, discrete, 3p LOH sites that often show a "discontinuous LOH" pattern in individual tumors; occurs in preneoplastic/ preinvasive lesions in smokers with and without lung cancer (multiple lesio ns often Lose the same parental allele); frequently involves breakpoints in at least three very small defined genomic regions; and appears to have all ele Loss and breakpoints first occurring in the 600-kb 3p21.3 region. These findings are consistent with previously reported LOH studies in a variety of tumors showing allele loss occurring by mitotic recombination and induce d by oxidative damage.