Genomic and gene expression profiling of minute alterations of chromosome arm 1p in small-cell lung carcinoma cells

Abstract

Genetic alterations occurring on human chromosome arm 1p are common in many types of cancer including lung, breast, neuroblastoma, pheochromocytoma, and colorectal. The identification of tumour suppressors and oncogenes on this arm has been limited by the low resolution of current technologies for fine mapping. In order to identify genetic alterations on 1p in small-cell lung carcinoma, we developed a new resource for fine mapping segmental DNA copy number alterations. We have constructed an array of 642 ordered and fingerprint-verified bacterial artificial chromosome clones spanning the 120 megabase (Mb) 1p arm from 1p11.2 to p36.33. The 1p arm of 15 small-cell lung cancer cell lines was analysed at sub-Mb resolution using this arm-specific array. Among the genetic alterations identified, two regions of recurrent amplification emerged. They were detected in at least 45% of the samples: a 580 kb region at 1p34.2-p34.3 and a 270 kb region at 1p11.2. We further defined the potential importance of these genomic amplifications by analysing the RNA expression of the genes in these regions with Affymetrix oligonucleotide arrays and semiquantitative reverse transcriptase-polymerase chain reaction. Our data revealed overexpression of the genes HEYL, HPCAL4, BMP8, IPT, and RLF, coinciding with genomic amplification.

Figure 1

Alignment of 1p array CGH profiles from 15 SCLC cell lines. Gains are shown to the right of the chromosome arm and losses to the left. Two recurrent amplifications are revealed, one at 1p34.2–p34.3 and the second at 1p11.2.

Figure 2

Array CGH profiles of SCLC cell lines. (A) Profile of NCI-H1672 demonstrating a large deletion at 1p31.2–p34.1. (B) Profile of NCI-H2141 demonstrating a small amplification at 1p34.3, deletion at 1p13.1–p13.3, and amplification at 1p11.2–p12. (C) Profile of HCC33 showing a small amplification at 1p34.2–p34.3 and multiple distinct deletions from 1p34.1 to p36.33.

Figure 3

(A) Array CGH profile of SCLC cell line NCI-H526 demonstrating multiple segmental alterations across the 1p arm. Three BACs used in FISH analysis are indicated. (B) FISH analysis of 548I13 vs 476E6, indicating that the presence of three copies of 548I13 and two copies of 476E6. (C) FISH analysis of 548I13 vs 385C11, indicating the presence of three copies of 548I13 and six copies of 385C11. FISH experiments were conducted as described previously (Henderson et al, 2004).

Figure 4

Integrating gene expression profiles with genomic alterations. (A) Relative expression of the genes within Region 1. (B) Relative expression of the genes within Region 2. Each Affymetrix probe set (probe set ID is indicated in brackets), which exhibited a detection P-value of less than 0.06 in >50% of samples was analysed by dividing the expression value for the gene in each experiment by the average expression value for that gene in the five normal cell lines. The resultant log 2 ratio is displayed colorimetrically according to the legend.