High-throughput arrays identify distinct genetic profiles associated with lymph node involvement in rectal cancer.

Abstract

Preoperative clinical diagnosis of lymph node involvement guides treatment decisions for rectal cancer. Unfortunately, clinical staging still suffers from a lack of accuracy. The aim of this study was to evaluate objective genetic differences in primary rectal cancers with and without associated lymph node metastasis. cDNA microarrays were generated from fresh-frozen tumors. Normalized data underwent global unsupervised hierarchical clustering analysis, and discriminating genes were mapped. Top discriminating genes were compared between stage II and III rectal cancers by use of an empirical Bayes 2 group t test with the Statistical Analysis of Microarrays and the Reproducibility-Optimized Test Statistic software separately to guide data reduction and deal with the difficulties of simultaneous statistical inference. Ingenuity Pathways Analysis software was used to analyze discriminating genes in terms of function and biological processes. Fifty-five patients with stage II and 22 patients with stage III rectal adenocarcinomas not treated with chemoradiation were included. Two major unsupervised clusters emerged representing stage II and III cancers. In 1 cluster, 11 of 12 patients (92%) had stage III cancer; in the other cluster, 54 of 65 patients (83%) had stage II (p < 0.001). Five significantly differentially expressed genes characterized the stage III cluster: interleukin-8, 3-hydroxy-3-methylglutaryl coenzyme A synthase, carbonic anhydrase, ubiquitin, and cystatin (all p < 0.05). Of the 12 patients with differential expression of the 5 marker genes, only one had stage II cancer. Fifty-four of 55 stage II patients clustered with alternative expression patterns of the predictor genes. Differentially expressed genes are related to cancer-associated processes, pathways, and networks. The identified gene signatures have not yet been validated in independent patient populations. Distinct gene expression signatures from primary rectal adenocarcinomas can help differentiate the presence or absence of lymph node metastases. These data are informative, and validation of this gene signature may provide a novel approach for more appropriate individualized treatment selection.