Genome-wide epigenomic profiling for biomarker discovery

Abstract

A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interesting layer of information for disease stratification and for personalized medicine. Traditionally, epigenomic profiling required large amounts of cells, which are rarely available with clinical samples. Also, the cellular heterogeneity complicates analysis when profiling clinical samples for unbiased genome-wide biomarker discovery. Recent years saw great progress in miniaturization of genome-wide epigenomic profiling, enabling large-scale epigenetic biomarker screens for disease diagnosis, prognosis, and stratification on patient-derived samples. All main genome-wide profiling technologies have now been scaled down and/or are compatible with single-cell readout, including: (i) Bisulfite sequencing to determine DNA methylation at base-pair resolution, (ii) ChIP-Seq to identify protein binding sites on the genome, (iii) DNaseI-Seq/ATAC-Seq to profile open chromatin, and (iv) 4C-Seq and HiC-Seq to determine the spatial organization of chromosomes. In this review we provide an overview of current genome-wide epigenomic profiling technologies and main technological advances that allowed miniaturization of these assays down to single-cell level. For each of these technologies we evaluate their application for future biomarker discovery. We will focus on (i) compatibility of these technologies with methods used for clinical sample preservation, including methods used by biobanks that store large numbers of patient samples, and (ii) automation of these technologies for robust sample preparation and increased throughput.

Omics Biomarkers in Ophthalmology

“…Over the past years, several techniques have been developed to profile epigenetic marks on a genome-wide scale and to determine the spatial organization of chromatin. 11 Until now, ophthalmic research has been restricted to investigations on DNA methylation profiles, which are commonly assessed using DNA methylation arrays or bisulfite sequencing. 12 Transcriptomics refers to the large-scale analysis of the transcriptome-the set of all mRNA molecules transcribed from the genome.…”

A plug and play microfluidic platform for standardized sensitive low-input Chromatin Immunoprecipitation

“…Determining protein binding sites on DNA by means of ChIP-seq is key to our understanding of gene regulation (Jenuwein and Allis 2001;Barski et al 2007;Berger 2007;Kouzarides 2007;Dekker 2008;Park 2009;Portela and Esteller 2010). Furthermore, it has important potential for identification of epigenetic biomarkers for disease stratification and personalized medicine (Heyn and Esteller 2012;Dirks et al 2016). To facilitate such studies, the compatibility of ChIP-Seq with low cell quantity input is highly beneficial to enable the use of relevant biological specimens, for example mouse early embryonic tissues or human biopsies.…”

“…Moreover, given the highly parallelized, automated workflow, the PnP-ChIP workflow will find its way to specialized epigenetic laboratories and core facilities enabling large-scale projects and consortia. In view of the reproducibility and sensitivity, the robustness of the procedure and the low-input requirements, we anticipate that the PnP-ChIP-Seq will be a first step to discovery and screening of hPTM-based biomarkers in the clinic (Martens et al 2010;Ross-Innes et al 2012;Saeed et al 2012;Jansen et al 2013;Stelloo et al 2015;Cejas et al 2016;Dirks et al 2016). Whether in a research setting or in the clinic, implementation of PnP-ChIP-Seq will benefit from the fact that our workflow is based on commercially available Fluidigm C1 tm microfluidic platform.…”

“…Furthermore, a myriad of diseases is caused or characterized by alteration of epigenetic patterns (Portela and Esteller 2010). Therefore, epigenetic changes represent a highly interesting layer of information for disease stratification and for personalized medicine (Heyn and Esteller 2012;Dirks et al 2016). A plethora of studies have highlighted the role of various histone post-translational modifications (hPTMs) in regulation of chromatin structure necessary for DNA accessibility during gene expression (Jenuwein and Allis 2001;Barski et al 2007;Berger 2007;Kouzarides 2007;Dekker 2008).…”

“…However, the ChIP-Seq workflow requires large amounts of material, is labor intensive and lacks robustness sue to experimental variation (Ho et al 2011;Chen et al 2012;Landt et al 2012). These drawbacks make the application of ChIP-seq challenging, in particular in settings where material is limited (Dirks et al 2016).…”