A pilot study of chromosomal aberrations and epigenetic changes in peripheral blood samples to identify patients with melanoma

Abstract

Prognosis is markedly improved when melanoma is diagnosed early. Improved methods are needed for earlier detection and screening. We hypothesized that epigenetic analysis of blood samples could discriminate patients with melanoma from patients with other cutaneous lesions and from healthy volunteers. After institutional review board approval and consent, whole blood was obtained from 59 patients with melanoma, 20 patients with other skin cancers, 20 patients with benign skin conditions, and 20 healthy volunteers. Fifteen conformation biomarkers from five gene loci were analyzed on chromatin with the EpiSwitch technology using a modified chromatin conformation capture assay. Differentiation between patients with melanoma and those with nonmelanoma skin cancers was correct 85% of the time, resulting in a sensitivity of 88% and a specificity of 82%. Differentiation of patients with melanoma from healthy controls was correct 80% of the time, resulting in a sensitivity of 85% and a specificity of 75%. The noninvasive test was more accurate in early-stage melanoma (1/10 and 1/16 stage I and stage II patients were misclassified, respectively) and became less accurate with more advanced disease (3/14 and 4/19 stage III and IV patients were misclassified, respectively). We report the results of a noninvasive test using chromosomal aberrations and epigenetic changes identified in peripheral blood that, in this pilot study, distinguished patients with early-stage melanoma from other cohorts.

Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions

“…We used Oxford Biodynamics’ EpiSwitch™ platform to investigate two interaction regions, one at oncogene MYC , and the other at tumor suppressor TP53 in K562 cells and in clinical samples. The EpiSwitch method follows similar steps as in conventional 3C, with several modifications such as including genetically modified TaqI for chromatin digestion and incubation with high efficiency DNA ligase to increase the efficiency of the method, as described previously 25, 26 .…”

“…All samples were processed for chromosome conformation capture analysis as per manufacturer’s instructions using EpiSwitch™ proprietary reagents and procedure developed for blood, tissue and cell lines analysis (Oxford BioDynamics Plc., Oxford, UK) as described previously 25, 26 . Briefly, following washes with PBS, cells were fixed with formaldehyde for 15 minutes and quenched with glycine.…”

Chromosome conformation signatures define predictive markers of inadequate response to methotrexate in early rheumatoid arthritis

“…To identify an initial set of common epigenetic profiles in early RA patients, 123 genetic loci (Additional file 1 : Table S5) previously associated with RA [ 35 , 54 – 57 ] were selected and annotated with chromosome conformation interactions predicted using the EpiSwitch in silico annotation package [ 44 – 46 ]. The in silico prediction generated 13,322 high-confidence chromosome interaction candidates, with an average of 99 per loci (99 ± 64; mean ± SD) (Additional file 1 : Table S5).…”

“…Chromatin with intact chromosome conformations from 50 µl of each blood sample was extracted using the EpiSwitch assay following the manufacturer’s instructions (Oxford BioDynamics Ltd.) [ 43 , 45 , 46 ]. The methods used to perform an EpiSwitch microarray and EpiSwitch PCR detection are described in detail in Supplementary Methods.…”

Enhancer Activity Requires CBP/P300 Bromodomain-Dependent Histone H3K27 Acetylation

“…3C Assay 1 million LP-1 cells were treated with 500 nM GNE-049 or DMSO for 4 hr. Subsequent processing steps were performed at Oxford Biodynamics (OBD) as described in Jakub et al (2015).…”