Epistem Bioinformatics Services
Experts in Preclinical Biomarker Discovery
and Clinical Biomarker Validation

Epistem's pharmacogenomics division have provided biomarker discovery and validation studies with many sponsors. The bespoke nature of many of Epistem's services mean that bioinformatics analysis is always tailored to the nature of the study. Indeed many of Epistem's CRO services also filter into pharmacogenomics often relying on creative methods of analysis.

Epistem offer a stand-alone bioinformatics analysis for many standard big‑data generating projects. Dr Elliott Harrison, Head Bioinformatician at Epistem, has summarised some data we have generated, using a case study where a PI3 kinase inhibitor signature was identified, and progressed as a biomarker in clinical samples.

To demonstrate proof of concept, plucked anagen hairs from four healthy normal volunteers were cultured in the presence or absence of a panPI3K inhibitor for 24 hours. RNA was extracted and amplified using Epistem's RNA-Amp™ amplification technology. cDNA was synthesised and hybridised to whole genome microarrays.

bioinform-fig-1

PCA analysis demonstrated clear clustering of untreated and PI3K inhibitor treated hair samples even at the lower incubation time (A). Bioinformatic analysis identified a set of probes differentially expressed when exposed to the PI3K inhibitor and further identified a subset of genes differentially expressed in common with other PI3K inhibitors (B).

We used this probe set as a multivariate signature to define a score for PI3K inhibition (or PI3K/mTOR inhibition) to validate its potential as a clinical biomarker in hair. The signature was also assessed in non-hair assays and included commercially available PI3K inhibitors to demonstrate multi‑model predictability.

bioinform-fig-2

A multivariate signature identified from an ex vivo hair study was assessed in mouse xenografts (A) and the breast cancer cell line MCF7, harbouring the oncogenic PIK3CA E545K mutation (B). A reduction in the PI3K (mTOR) score is evident in xenografts and MCF7 cells treated with a known PI3K inhibitor. In hair (C and D), a dose‑dependent repression of the PI3K score was observed with a PI3Kβ selective inhibitor and with the sponsor's pan‑PI3K inhibitor in all four donor subjects.

The signature was also assessed in a clinical setting. RNA was extracted and amplified from plucked anagen hairs from individuals enrolled onto the sponsor's clinical trial. cDNA was synthesised and hybridised to whole genome microarrays.

bioinform-fig-3

Bioinformatics analysis of multiple hairs from patients treated with a PI3K inhibitor demonstrated that the PI3K signature effectively discriminated the pre- and post‑treatment samples as shown in the PCA (A). The average score for each patient clearly shows repression of the PI3K inhibitor signature in most patients (B).

Drilling down further into the PI3K inhibition gene signature our bioinformaticians identified a number of biologically relevant genes to test as clinical biomarkers. Microarray data from both the ex vivo hair study and the clinical hair data demonstrated that genes identified in the ex vivo experiment predicted PI3K inhibitor response in the clinical samples.

bioinform-fig-4

Analysis of gene expression clearly demonstrates dose‑dependent reduction of Gene 1 and Gene 2 at all incubation times in the ex vivo cultures. This reduction is concordant with that observed in clinical samples of hair where both Gene 1 and Gene 2 expression is suppressed following 4 hr treatment with the PI3K inhibitor

This case study demonstrates the validation of a clinical biomarker from the very first proof of concept stages. This study exemplifies some of the creative thinking and know‑how utilised by Epistem's pharmacogenomics and bioinformatics unit.

Get in touch

Find out how Epistem can assist with your research…

* Required Fields

Speak to one of our scientists
Request a copy of our poster
Request copies of our flyers

Epistem Bioinformatics Services

At Epistem, we now offer a stand-alone or integrated bioinformatics service to add value to your preclinical or clinical project.

Epistem provides a unique plucked hair biomarker platform for targeting intracellular signalling pathways in oncology, inflammation, fibrosis and other therapeutic areas. Plucked hair provides a minimally invasive surrogate tissue to assess epithelial tissue drug-induced changes. Effects on mRNA and protein expression levels can be analysed and can be applied to preclinical and clinical samples.

Epistem also presented a poster at this year's AACR: 'Plucked anagen scalp hair: A reproducible surrogate tissue to monitor drug induced transcriptional changes and provide pharmacodynamicbiomarker and target engagement information from cancer patients'. If you would like a copy of the poster please get in touch using the contact us box.

About Epistem

Epistem's contract research service is committed to providing reliable, innovative and transferable pre-clinical models and services to support decision making throughout the drug discovery and development pipeline.

Tel: +44 (0)161 850 7600  Email: info@epistem.co.uk