Chromatin barcodes as biomarkers for melanoma

Abstract

The major barrier to effective cancer therapy is the presence of genetic and phenotypic heterogeneity within cancer cell populations that provides a reservoir of therapeutically resistant cells. As the degree of heterogeneity present within tumours will be proportional to tumour burden, the development of rapid, robust, accurate and sensitive biomarkers for cancer progression that could detect clinically occult disease before substantial heterogeneity develops would provide a major therapeutic benefit. Here, we explore the application of chromatin conformation capture technology to generate a diagnostic epigenetic barcode for melanoma. The results indicate that binary states from chromatin conformations at 15 loci within five genes can be used to provide rapid, non-invasive multivariate test for the presence of melanoma using as little as 200 μl of patient blood.

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.…”

Novel insights into chromosomal conformations in cancer

“…Three MITF-related chromosome loops (with BRN2, CDKN1A and TBX3) have been found in both cell lines and patient blood samples. This study was the first confirmation of long-range chromosome loops in melanoma and provided valuable prospects for diagnosis by examination of circulating immune cells [ 86 ]. A study investigating neurofibromatosis found a 1-Mb fragment containing the neurofibromatosis type I (NF1) gene that interacts with another nearby 1-Mb fragment recorded in the HindIII and NcoI-maps ([ 87 ]) using Hi-C data.…”

“…In melanoma, MITF-related loops identified in circulating tumor cells can be used to noninvasively detect cancer [ 86 ] and predict a poor prognosis [ 109 ], as shown in humans. In gliomas, 11q23.3 was identified as a susceptibility locus that is closely related to abnormal chromosome conformations [ 99 ], and rs965513 was identified as a risk factor in papillary thyroid carcinoma [ 97 ].…”

3D genome organization in health and disease: emerging opportunities in cancer translational medicine

“…The development of Episwitch , a proprietary 3C-based platform developed by Oxford biodynamics is a promising entry into this field. 106,107 The platform utilizes blood as the specimen to identify chromosomal conformations in the target genes of interest and reports the results in few hours. This method could open up new possibilities for less invasive blood-based biomarkers for monitoring.…”