Genomic imbalances in precancerous tissues signal oral cancer risk

Abstract

Oral cancer develops through a series of histopathological stages: through mild (low grade), moderate, and severe (high grade) dysplasia to carcinoma in situ and then invasive disease. Early detection of those oral premalignant lesions (OPLs) that will develop into invasive tumors is necessary to improve the poor prognosis of oral cancer. Because no tools exist for delineating progression risk in low grade oral lesions, we cannot determine which of these cases require aggressive intervention. We undertook whole genome analysis by tiling-path array comparative genomic hybridization for a rare panel of early and late stage OPLs (n = 62), all of which had extensive longitudinal follow up (>10 years). Genome profiles for oral squamous cell carcinomas (n = 24) were generated for comparison. Parallel analysis of genome alterations and clinical parameters was performed to identify features associated with disease progression. Genome alterations in low grade dysplasias progressing to invasive disease more closely resembled those observed for later stage disease than they did those observed for non-progressing low grade dysplasias. This was despite the histopathological similarity between progressing and non-progressing cases. Strikingly, unbiased computational analysis of genomic alteration data correctly classified nearly all progressing low grade dysplasia cases. Our data demonstrate that high resolution genomic analysis can be used to evaluate progression risk in low grade OPLs, a marked improvement over present histopathological approaches which cannot delineate progression risk. Taken together, our data suggest that whole genome technologies could be used in management strategies for patients presenting with precancerous oral lesions.

Figure 1

Summary of chromosomal alterations for all 86 cases. Samples are grouped into non-progressing low grade dysplasias, progressing low grade dysplasias, high grade lesions (severe dysplasia and CIS lesions), and oral squamous cell carcinomas. A blue box indicates the presence of at least one segmental change on the chromosome arm and a red box represents a whole arm alteration. Copy number changes due to polymorphic regions were not included in the analysis. Case numbers are listed to the left, while chromosome arms are listed at the top.

Figure 2

Box plot showing percentage of genome altered. As in Figure 1, samples are grouped into non-progressing LGDs, progressing LGDs, HGD/CIS lesions, and OSCCs. Genome altered was calculated by dividing the number of clones deemed changed (gain or loss), by aCGH-Smooth, by the total number of clones assayed for each sample. Chromosomes X and Y were excluded from this analysis.

Figure 3

Whole genome tiling path array CGH karyogram of an oral low grade dysplasia which subsequently progressed to cancer. Whole genome tiling path array CGH karyogram of an oral low grade dysplasia which subsequently progressed to cancer (Oral51). Each dark blue dot on the karyogram represents the average signal ratio for an individual BAC clone from the array. Clones were plotted vertically against known chromosomal position. Log2 signal intensity ratios for each clone were plotted horizontally, with colored vertical lines denoting log2 signal ratios from -1 to 1. Where the signal intensity ratio equals zero (purple line), equivalent DNA copy number between the sample and the reference DNA was inferred. Alternatively, DNA copy number increases were inferred where log2 > 0 (red line) and losses were inferred where log2 < 0 (green line). Numerous whole chromosome, whole arm, and segmental changes are apparent. Examples of these alterations were magnified and are represented in orange boxes. High level segmental amplicons for chromosome 2 and 4 are depicted in this manner. Lower copy number segmental (chromosome 8) and whole arm (chromosome 12) gains are similarly shown. The magnified image for Chromosome 9 shows a complex genomic rearrangement that includes multiple segmental losses and a high level segmental amplification event.