A single mitochondrial DNA deletion accurately detects significant prostate cancer in men in the PSA 'grey zone'.

PURPOSE: To determine the clinical performance of a blood-based test for clinically significant (CS) prostate cancer (PCa) (grade group ≥ 2) intended for use in men with prostate serum antigen levels in the 'grey zone' (PSA < 10 ng/ml). The test quantifies a previously described 3.4 kb mitochondrial DNA (mtDNA) deletion. METHODS: In a first prospective study of an MRI-guided re-biopsy population (n = 126), the 3.4 kb deletion and 18S rRNA gene were amplified from plasma. A diagnostic threshold was selected from the coordinates of the receiver operating characteristic curve and tested in a second population of men who were (n = 92) biopsy naïve when the mtDNA deletion was assayed and for whom those diagnosed with cancer on initial biopsy were treated with radical prostatectomy. RESULTS: The 3.4 kb deletion was a good predictor of CS PCa in the image-guided re-biopsy population [AUC 0.84, (95% CI 0.73-0.95)] and the selected threshold corresponded to a sensitivity of 87% [95% CI, 70-96%], specificity of 68% [95% CI, 47-85%] and negative predictive value (NPV) of 97%. Applying this threshold to the second population showed this deletion to be a strong predictor of CS cancer [AUC 0.98, (95% CI 0.94-1.02)], independent of PSA or age [sensitivity 100% (95% CI, 93-100%), specificity 90% (95%CI 73-98%) and NPV 100%]. CONCLUSION: The 3.4 kb deletion in plasma is an accurate predictor of CS cancer for men in the PSA 'grey zone'. Used in advance of biopsy for improved patient selection, this deletion may reduce the number of biopsies needed to diagnose CS prostate cancers.

Mitochondrial DNA deletions accurately detect endometriosis in symptomatic females of child-bearing age.

AIM: Accurate noninvasive diagnostic aids for endometriosis are needed. We evaluated mitochondrial DNA deletions as potential biomarkers for endometriosis. METHODS: The diagnostic accuracy of deletions was evaluated by quantitative polymerase chain reaction (QPCR) using well-characterized clinical specimens from all subtypes and stages of endometriosis in a case-control format (n = 182). RESULTS: Deletions (1.2 and 3.7 kb) detected in blood differentiated between endometriosis and controls (area under the curve [AUC] 0.71-0.90). Differences in deletion levels were statistically significant (p < 0.05) for all disease subtypes and stages. Neither deletion was correlated with patient or specimen age or hormone status. The 1.2 kb deletion was not correlated with menstrual stage; the 3.7 kb deletion was significantly correlated between two of the groups. CONCLUSION: Biomarkers of the mitochondrial genome, including the deletions described here, offer a promising and largely unexplored avenue in the pursuit of diagnostic markers for endometriosis that can be effectively translated to clinical application.

Facile whole mitochondrial genome resequencing from nipple aspirate fluid using MitoChip v2.0.

BACKGROUND: Mutations in the mitochondrial genome (mtgenome) have been associated with many disorders, including breast cancer. Nipple aspirate fluid (NAF) from symptomatic women could potentially serve as a minimally invasive sample for breast cancer screening by detecting somatic mutations in this biofluid. This study is aimed at 1) demonstrating the feasibility of NAF recovery from symptomatic women, 2) examining the feasibility of sequencing the entire mitochondrial genome from NAF samples, 3) cross validation of the Human mitochondrial resequencing array 2.0 (MCv2), and 4) assessing the somatic mtDNA mutation rate in benign breast diseases as a potential tool for monitoring early somatic mutations associated with breast cancer. METHODS: NAF and blood were obtained from women with symptomatic benign breast conditions, and we successfully assessed the mutation load in the entire mitochondrial genome of 19 of these women. DNA extracts from NAF were sequenced using the mitochondrial resequencing array MCv2 and by capillary electrophoresis (CE) methods as a quality comparison. Sequencing was performed independently at two institutions and the results compared. The germline mtDNA sequence determined using DNA isolated from the patient's blood (control) was compared to the mutations present in cellular mtDNA recovered from patient's NAF. RESULTS: From the cohort of 28 women recruited for this study, NAF was successfully recovered from 23 participants (82%). Twenty two (96%) of the women produced fluids from both breasts. Twenty NAF samples and corresponding blood were chosen for this study. Except for one NAF sample, the whole mtgenome was successfully amplified using a single primer pair, or three pairs of overlapping primers. Comparison of MCv2 data from the two institutions demonstrates 99.200% concordance. Moreover, MCv2 data was 99.999% identical to CE sequencing, indicating that MCv2 is a reliable method to rapidly sequence the entire mtgenome. Four NAF samples contained somatic mutations. CONCLUSION: We have demonstrated that NAF is a suitable material for mtDNA sequence analysis using the rapid and reliable MCv2. Somatic mtDNA mutations present in NAF of women with benign breast diseases could potentially be used as risk factors for progression to breast cancer, but this will require a much larger study with clinical follow up.

Mitochondrial genome deletion aids in the identification of false- and true-negative prostate needle core biopsy specimens.

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.

The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation.

BACKGROUND: Nuclear mitochondrial pseudogenes (numts) are a potential source of contamination during mitochondrial DNA PCR amplification. This possibility warrants careful experimental design and cautious interpretation of heteroplasmic results. RESULTS: Here we report the cloning and sequencing of numts loci, amplified from human tissue and rho-zero (rho0) cells (control) with primers known to amplify the mitochondrial genome. This paper is the first to fully sequence 46 paralogous nuclear DNA fragments that represent the entire mitochondrial genome. This is a surprisingly small number due primarily to the primer sets used in this study, because prior to this, BLAST searches have suggested that nuclear DNA harbors between 400 to 1,500 paralogous mitochondrial DNA fragments. Our results indicate that multiple numts were amplified simultaneously with the mitochondrial genome and increased the load of pseudogene signal in PCR reactions. Further, the entire mitochondrial genome was represented by multiple copies of paralogous nuclear sequences. CONCLUSION: These findings suggest that mitochondrial genome disease-associated biomarkers must be rigorously authenticated to preclude any affiliation with paralogous nuclear pseudogenes. Importantly, the common perception that mitochondrial template "swamps" numts loci precluding detectable amplification, depends on the region of the mitochondrial genome targeted by the PCR reaction and the number of pseudogene loci that may co-amplify. Cloning and relevant sequencing data will facilitate the correct interpretation. This is the first complete, wet-lab characterization of numts that represent the entire mitochondrial genome.

Somatic mitochondrial DNA mutations in prostate cancer and normal appearing adjacent glands in comparison to age-matched prostate samples without malignant histology.

Studies of somatic mitochondrial DNA mutations have become an important aspect of cancer research because these mutations might have functional significance and/or serve as a biosensor for tumor detection. Here we report somatic mitochondrial DNA mutations from three specific tissue types (tumor, adjacent benign, and distant benign) recovered from 24 prostatectomy samples. Needle biopsy tissue from 12 individuals referred for prostate biopsy, yet histologically benign (symptomatic benign), were used as among individual control samples. We also sampled blood (germplasm tissue) from each patient to serve as within individual controls relative to the somatic tissues sampled (malignant, adjacent, and distant benign). Complete mitochondrial genome sequencing was attempted on each sample. In contrast to both control groups [within patient (blood) and among patient (symptomatic benign)], all of the tissue types recovered from the malignant group harbored significantly different mitochondrial DNA (mtDNA) mutations. We conclude that mitochondrial genome mutations are an early indicator of malignant transformation in prostate tissue. These mutations occur well before changes in tissue histo-pathology, indicative of prostate cancer, are evident to the pathologist.

Mitochondria, prostate cancer, and biopsy sampling error.

Mitochondria and their associated genome are emerging as sophisticated indicators of prostate cancer biology. Alterations in the mitochondrial genome (mtgenome) have been implicated in cell proliferation, metastatic behavior, androgen independence, as a signal for apoptosis, and as a predictor of biochemical recurrence. Somatic mutation patterns in complete mtgenomes are associated with prostate specific antigen levels (PSA) in prostate cancer patients and a large-scale mtgenome deletion (3.4 kb) is consistent with a prostate "cancerization" field effect. This review will focus on the biological characteristics of mitochondria and their direct clinical application to prostate cancer. Mitochondrial science is currently influencing clinical prostate cancer diagnostics and the rapid progress in this area indicates future, break-through contributions in the general field of oncology.

Paired ductal carcinoma in situ and invasive breast cancer lesions in the D-loop of the mitochondrial genome indicate a cancerization field effect.

Alterations in the mitochondrial genome have been chronicled in most solid tumors, including breast cancer. The intent of this paper is to compare and document somatic mitochondrial D-loop mutations in paired samples of ductal carcinoma in situ (DCIS) and invasive breast cancer (IBC) indicating a potential breast ductal epithelial cancerization field effect. Paired samples of these histopathologies were laser-captured microdissected (LCM) from biopsy, lumpectomy, and mastectomy tissues. Blood samples were collected as germplasm control references. For each patient, hypervariable region 1 (HV1) in the D-loop portion of the mitochondrial genome (mtGenome) was sequenced for all 3 clinical samples. Specific parallel somatic heteroplasmic alterations between these histopathologies, particularly at sites 16189, 16223, 16224, 16270, and 16291, suggest the presence of an epithelial, mitochondrial cancerization field effect. These results indicate that further characterization of the mutational pathway of DCIS and IBC may help establish the invasive potential of DCIS. Moreover, this paper indicates that biofluids with low cellularity, such as nipple aspirate fluid and/or ductal lavage, warrant further investigation as early and minimally invasive detection mediums of a cancerization field effect within breast tissue.

3.4 kb mitochondrial genome deletion serves as a surrogate predictive biomarker for prostate cancer in histopathologically benign biopsy cores.

Recently, we described a 3.4-kb mitochondrial genome deletion having significance for identifying malignant and benign prostate tissues (p < 0.001). This biomarker was also present in normal appearing tissue, in close proximity to a tumour indicating a "field effect." In the present study, we report 4 cases (3 malignant, 1 benign) which suggest that this field effect may occur before tumourigenesis; this effect may also identify the presence of a small tumour focus/foci, which are difficult to detect with single or multiple biopsy procedures.