Genomic aberrations in lung adenocarcinoma in never smokers

Abstract

Background: Lung cancer in never smokers would rank as the seventh most common cause of cancer death worldwide.

Methods and findings: We performed high-resolution array comparative genomic hybridization analysis of lung adenocarcinoma in sixty never smokers and identified fourteen new minimal common regions (MCR) of gain or loss, of which five contained a single gene (MOCS2, NSUN3, KHDRBS2, SNTG1 and ST18). One larger MCR of gain contained NSD1. One focal amplification and nine gains contained FUS. NSD1 and FUS are oncogenes hitherto not known to be associated with lung cancer. FISH showed that the amplicon containing FUS was joined to the next telomeric amplicon at 16p11.2. FUS was over-expressed in 10 tumors with gain of 16p11.2 compared to 30 tumors without that gain. Other cancer genes present in aberrations included ARNT, BCL9, CDK4, CDKN2B, EGFR, ERBB2, MDM2, MDM4, MET, MYC and KRAS. Unsupervised hierarchical clustering with adjustment for false-discovery rate revealed clusters differing by the level and pattern of aberrations and displaying particular tumor characteristics. One cluster was strongly associated with gain of MYC. Another cluster was characterized by extensive losses containing tumor suppressor genes of which RB1 and WRN. Tumors in that cluster frequently harbored a central scar-like fibrosis. A third cluster was associated with gains on 7p and 7q, containing ETV1 and BRAF, and displayed the highest rate of EGFR mutations. SNP array analysis validated copy-number aberrations and revealed that RB1 and WRN were altered by recurrent copy-neutral loss of heterozygosity.

Conclusions: The present study has uncovered new aberrations containing cancer genes. The oncogene FUS is a candidate gene in the 16p region that is frequently gained in never smokers. Multiple genetic pathways defined by gains of MYC, deletions of RB1 and WRN or gains on 7p and 7q are involved in lung adenocarcinoma in never smokers.

Figure 1. Aberrations using aCGH analysis in 60 never smokers with lung adenocarcinoma.

Panel A. Heat map of gains (green color) and losses (red color) by chromosome generated by non supervised hierarchical clustering. Small blue or yellow dot indicate gains with log2(ratio)>1.5 and losses with log2(ratio)<−1.5, respectively. Blue star (*): two outliers (37875 between classes A and B and 37569 between clusters B1 and B2). Panel B. Distribution of gains (green color) and losses (red color) along the genome.

Figure 2. Amplicons on 16p11.2 in case 37817 using aCGH and FISH analyses.

Panel A. aCGH analysis. Below: chromosome 16 diagram; the blue line limits the 16p11.2 region represented above. Above: aCGH profile for the enlarged 16p11.2 region showing the complex amplification. The dots are individual oligonucleotides that are in green when they are gained; a brown color, enhanced by an horizontal line, show the region of copy-number alteration segmented by the algorithm. The p telomere is to the left, the centromere to the right. The location and color of probes used for FISH are indicated as red or green squares at the upper part of the aCGH profile. Panel B. Examples of FISH results for the 16p11.2 region. (a) Normal chromosome 16 from a normal blood mitosis, in DAPI inversed colors showing the specific heterochromatin secondary constriction of the long arm. Although separated by less than a 1 Mb, RP11-347C12 (red) is slightly more telomeric than RP11-388M20 (green), although they are fused for a large part. (b) The same probes on case 37817 cells showing a distinct pattern of amplification. (c) Combination of Vysis FUS probes with RP11-388M20 (red) that show a co-localization of the three probes on the amplicon even in decondensed HS.