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ChIP and MIRA for clinical diagnosis

Final Report Summary - DIA-CHIP (ChIP and MIRA for clinical diagnosis)

DIA-ChIP ( aimed to develop state-of-the-art molecular techniques for the routine high-throughput analysis of clinical samples for advanced molecular diagnosis and biomedical research. Most of the project aims were achieved, and this was only possible through a collaborative partnership between academic, SME and public health partners interacting through the IAPP, and the secondments and recruitments that the scheme supported.

New molecular diagnostics in clinical pathology need to be robust, cost effective and offer significant advantages over existing techniques. With the move towards personalised medicine the specificity of diagnosis will need to be enhanced significantly, yet in the short to medium term will need to be compatible with current gold standards of analysis. In this project the focus one of the most important cancer affecting the female European population - Endometrial Cancer (Cancer of the womb).

The analysis of archival clinical material, especially in practice, is largely limited to immune histochemistry and quantification the native biomolecules (DNA, RNA, protein). The advent of functional characterisation of these molecules i.e. DNA-protein interactions and DNA status will provide information to enhance diagnostic histopathology.

Application to archival material will provide access to a hugely valuable resource and will contribute significantly to scientific understanding of disease processes by allowing the examination of large patient cohorts, and by facilitating direct comparison to model systems. Also by examining patient samples in concert with model human cell culture systems, alternatives to animal model systems will be developed.

DIA-ChIP enabled the establishment of a strategic partnership between 5 groups, which was critical in realising the project. The partners developed strong long-term collaborative links and are already engaged in post-project research projects and intellectual exchange that continue to strengthen each of the partners, ensuring long-term co-operation between all sectors (Business, Academic, Public Health).

The project delivered on all its aims, whilst at the same time accommodating rapid technology developments. The project was devised and funded somewhat ahead of its time. Immediately following funding there was a global explosion in the area of epigenomics. Coupled with this was the rapid development of ChIP-seq technology and DNA sequencing technologies and with this the almost complete displacement of microarray based ‘ChIP on chip’ approaches. The aim of undertaking genome wide microarray based screening was therefore replaced by a ChIP-seq approach, and post-project collaboration with Active Motif, who acquired a DNA sequencing based genome wide ChIP business during the course of DIAChIP, is continuing with the availability of FFPE ChIP protocols developed in DIAChIP and refined in collaboration with M. Fanelli, who attended and presented at the DIAChIP workshop.

DNA methylation detection technology was used to examine the methylation status of clinical endometrial cancer samples, with a particular focus on targets including the estrogen receptor (ER) and defined downstream target genes of this important nuclear hormone receptor transcription factor. Regulation of molecular variants of ER have been characterised for the first time in endometrial cell lines and in clinical samples. Analysis was conducted from high (bisulphite sequencing) to low (MedIP) on samples. Technology developments during the project saw MeDIP displacing MIRA as the technique of choice for low resolution analysis. Indeed Active Motif adopted this technique commercially with the launch of a MeDIP kit.

Novel solid phase platform CHROMATRAP for Chromatin Immunopreciptitation (ChIP) was adopted from the new partner Porvair Ltd. This platform was developed to deliver a high throughput 96 reaction format enabled due to Porvair’s manufacturing capabilities. Evaluation of this new platform was initiated during the project, and initial positive results have led Porvair to invest more into the further refinement which is ongoing.

A very successful DiaChIP workshop was held in June 2012, and attended by 65 researchers from across Europe. Advances in technology and science were presented along with two hands-on workshops in the laboratory of the coordinator which were led by the industrial partners Active Motif and Porvair

The impact of the project has been to advance technologies for utilisation in epigenomics research, a novel area of research which was in its infancy at the start of DiaChIP and which has now developed into major international initiatives. Scientific manuscripts are in preparation, delayed only by the necessity to build up a large cohort of clinical samples to fully verify initial findings.

The inter-sectorial secondments have greatly benefitted those involved, giving specific insights into sectors where the individuals involved had limited previous experience. The project has led to the establishment of lasting relationships between partners.