Mitochondrial Genome Deletion Aids in the Identification of False- and True-Negative Prostate Needle Core Biopsy Specimens

Abstract

We report the usefulness of a 3.4-kb mitochondrial genome deletion (3.4 mtdelta) for molecular definition of benign, malignant, and proximal to malignant (PTM) prostate needle biopsy specimens. The 3.4 mtdelta was identified through long-extension polymerase chain reaction (PCR) analysis of frozen prostate cancer samples. A quantitative PCR assay was developed to measure the levels of the 3.4 mtdelta in clinical samples. For normalization, amplifications of a nuclear target and total mitochondrial DNA were included. Cycle threshold data from these targets were used to calculate a score for each biopsy sample. In a pilot study of 38 benign, 29 malignant, and 41 PTM biopsy specimens, the difference between benign and malignant core biopsy specimens was well differentiated (P & .0001), with PTM indistinguishable from malignant samples (P = .833). Results of a larger study were identical. In comparison with histopathologic examination for benign and malignant samples, the sensitivity and specificity were 80% and 71%, respectively, and the area under a receiver operating characteristic (ROC) curve was 0.83 for the deletion. In a blinded external validation study, the sensitivity and specificity were 83% and 79%, and the area under the ROC curve was 0.87. The 3.4 mtdelta may be useful in defining malignant, benign, and PTM prostate tissues.

Accurate prediction of repeat prostate biopsy outcomes by a mitochondrial DNA deletion assay

“…Because the Cts of our previous assays were generally high, 9 we optimized the assay to improve efficiency and specificity. We redesigned the primers for the deletion and this dropped the annealing temperature from 66 to 64.4 1C.…”

“…9 This could resolve negative prostate biopsies into true-and falsenegative categories. However, of the 96 patients in the validation study that provided proximal biopsy samples, only 48 had accompanying malignant biopsy cores for comparative analysis of test performance.…”

“…This suggests that the marker could predict the outcome for the patient with a rising PSA and negative initial biopsies with a high degree of accuracy. 9 This study was designed to establish the 3.4-kb deletion biomarker cutoff that had the highest predictive accuracy for the results of subsequent biopsies. The findings should form the basis for the subsequent evaluation of this marker on prostate re-biopsy outcomes.…”

Tissue-based biomarkers in prostate cancer

“…The mutations in mitochondrial DNA of histologically normal tissue may indicate a ‘cancerization’ or field effect similar to that of methylation studies. [94, 95] In the initial reports of this assay in 101 patients with an initially negative biopsy who underwent repeat biopsy within 1 year demonstrated sensitivity, specificity, and negative predictive value of 84%, 54%, and 91%, respectively. [96] This study demonstrated that the assay was able to predict the presence of a missed tumor in 17 out of 20 men a year before diagnosis.…”

Addressing the need for repeat prostate biopsy: new technology and approaches

“…An early study involving a cohort of 183 men including those with benign, malignant or proximaltomalignant biopsy samples, generated a remarkable AUC of 0.87 using this test in the validation phase of this study. 58 In a followup study of 101 patients undergoing repeat biopsy procedures, 20 were found to have prostate cancer within 1 year of the initial biopsy; analysis of biopsy samples for prostate cancer using the PCMT generated a sensitivity and specificity of 84% and 54%, respectively, (AUC 0.75) and a negative predictive value of 91%. 59 Larger validation studies are required before the widespread use of this assay can be recommended.…”