Chromosomal copy number alterations are associated with persistent lymph node metastasis after chemoradiation in locally advanced rectal cancer

Abstract

Background: Lymph node metastasis is an important indicator of oncologic outcome for patients with rectal cancer. Identifying predictive biomarkers of lymph node metastasis could therefore be clinically useful.

Objective: The aim of this study was to assess whether chromosomal copy number alterations can assist in predicting persistent lymph node metastasis in patients with locally advanced rectal cancer treated with preoperative chemoradiation therapy.

Design: This is a nonrandomized, prospective phase II study.

Setting: This study took place in a multi-institutional setting.

Patients: Ninety-five patients with stage II (cT3-4, cN0) or stage III (any cT, cN1-2) rectal cancer were included.

Intervention: Patients were treated with preoperative chemoradiation therapy followed by total mesorectal excision. Pretreatment biopsy tumor DNA and surgical margin control DNA were extracted and analyzed by oligonucleotide array-based comparative genomic hybridization. Chromosomal copy number alterations were correlated with persistent lymph node metastasis. Finally, a model for predicting persistent lymph node metastasis was built.

Main outcome measures: The primary outcomes assessed were whether chromosomal copy number alterations are associated with persistent lymph node metastasis in patients with rectal cancer and the accuracy of oligonucleotide array-based comparative genomic hybridization for predicting lymph node metastasis.

Results: Twenty-five of 95 (26%) patients had lymph node metastasis after chemoradiation. Losses of 28 chromosomal regions, most notably in chromosome 4, were significantly associated with lymph node metastasis. Our predictive model contained 65 probes and predicted persistent lymph node metastasis with 68% sensitivity, 93% specificity, and positive and negative predictive values of 77% and 89%. The use of this model accurately predicted lymph node status (positive or negative) after chemoradiation therapy in 82 of 95 patients (86%).

Limitations: The patient cohort was not completely homogeneous, which may have influenced their clinical outcome. In addition, although we performed rigorous, statistically sound internal validation, external validation will be important to further corroborate our findings.

Conclusions: Copy number alterations can help identify patients with rectal cancer who are at risk of lymph node metastasis after chemoradiation.

Trial registration: ClinicalTrials.gov NCT00335816.

Figures

Figure 1

Copy number alterations detected by aCGH (a) overall and (b) stratified by lymph node status (ypN1-2, n=25 versus ypN0, n=70). Loss of chromosome 4 depicted in the dashed box was found to be the most significantly different CNA region between lymph node positive (ypN1-2) and lymph node negative (ypN0) patients. Sample identification - Red: Loss; Green: Gain.

Figure 2

Predictive CNA model for persistent lymph node metastasis. 65 probes were used to build a predictive model using Support Vector Machine (SVM) to predict persistent lymph node metastasis. Sample identification - Red: Loss; Green: Gain. Yellow: Lymph node positive (ypN1-2); Blue: Lymph node negative (ypN0).