Abstract 462: Chromatin signatures of DLBCL subtypes

Abstract

Diffuse Large B-cell Lymphoma (DLBCL) is a common and aggressive type of Non-Hodgkin's Lymphoma. Gene expression profiling long ago identified two distinct subtypes: Activated B-Cell (ABC) and Germinal Center B-Cell (GCB), reflecting the biology associated with the cell of origin of the lymphoma (Alizadeh et al, Nature 2000). These subtypes are histologically non distinguishable, yet are associated with distinct outcomes. Emerging clinical data also suggests that they are predictive of outcome for novel therapeutics, including a BTK inhibitor, a proteasome inhibitor and an immune modulatory agent. Reliable diagnosis of the DLBLC subtype may therefore become a requirement for choosing the best treatment for DLBCL patients. Since gene regulation is known to be associated with changes in chromatin structures, we decided to investigate the chromatin conformation around key regulators of ABC/ GCB biology using a Chromatin Conformation Capture Assay (3C). For this assay, chromatin loops are cross-linked; the DNA is digested and re-ligated, joining topologically proximal ends that may be very distant along the length of the chromosome into distinct novel fusion products. After reversing the cross-links, the presence of these novel DNA fusions can be detected by PCR, resulting in a binary read-out. Composites of these PCR products form a signature that may be characteristic of disease, disease state or subtype. The EpiSwitchTM technology has been optimized to identify these epigenetic patterns not only in tissue, but also from blood borne tumor DNA. To investigate characteristic changes in chromatin conformation in ABC- and GCB- DLBCL cell lines, we focused on key genes known to be differentially expressed in the two sub-types, including Bcl-6, IRF-4 and LMO-2 (Wright et al. PNAS 2003,). We mapped several interactions indicating that these loci are subject to epigenetic regulation. We also applied the assay to blood from DLBCL patients and from healthy volunteers to exclude background signals from normal B-cell maturation. The assay was able to detect the same signatures as seen in cell lines. These results demonstrate the potential of this technology to detect DLBCL subtype specific chromatin conformation associated biomarkers in patient blood. Citation Format: Ron McCord, Megan Field, Philip Jordan, Ewan Hunter, Alexandre Akoulitchev, Kirsten E. Mundt. Chromatin signatures of DLBCL subtypes. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 462. doi:10.1158/1538-7445.AM2014-462

Initial Identification of a Blood-Based Chromosome Conformation Signature for Aiding in the Diagnosis of Amyotrophic Lateral Sclerosis

“…EpiSwitch is a high throughput technology platform that pairs high resolution chromosome conformational capture results with regression analysis and machine learning to develop disease classifications [ 8 ]. Screening and selection of statistically significant differences in conditional and stable profiles of genome architecture associated with samples from patients suffering from a disease, in comparison to healthy control samples, serves as a way to select epigenetic biomarkers that can diagnose and stratify pathological conditions [ [8] , [9] , [10] , [11] , [12] , [13] ]. In this study, EpiSwitch was used on blood samples in a three-step process to identify, evaluate, and validate statistically-significant differences in chromosomal conformations between ALS patients and healthy controls ( Fig.…”

“…In light of this, the Northeast ALS Consortium (NEALS) Biofluid Repository was established to provide researches and industry partners with biologic samples collected from the patients using standard operating procedures (SOPs) and linked to clinical information for use in research studies [ 7 ]. In this pilot study, samples from the NEALS Biofluid Repository were analyzed using EpiSwitch , a high-resolution technology to identify structural-functional epigenetic changes in genomic architecture associated with pathological phenotypes developed by Oxford BioDynamics [ [8] , [9] , [10] , [11] , [12] , [13] ]. As multiple genomic regions contribute to phenotypic differences through changes in genomic architecture, this approach allows for the development of a chromosomal conformation signature (CCS) of alterations in genomic architecture between two states (disease vs. non-diseased, pre-treatment vs. post-treatment).…”