LONDON – Oxford Biodynamics plc has published initial proof of concept showing its Episwitch epigenetic biomarker technology can diagnose amyotrophic lateral sclerosis (ALS) from a blood sample, in 24 hours.

That compares to an average of one year from symptom onset that it takes to perform the multiple investigations currently needed to reach a definitive diagnosis.

The research, carried out in collaboration with clinicians at Massachusetts General Hospital and John Radcliffe Hospital, Oxford, U.K., also provides an indication that epigenetics could be a means to explore biological pathways and mechanisms that are involved in the pathogenesis of the fatal neurodegenerative disorder.

In addition, the biomarker has potential prognostic power in a multifactorial disease where rate of progression varies significantly from patient to patient, and it could be used to stratify patients in clinical studies of drugs for treating ALS.

"Talking to our clinical collaborators, they want to start using [the test] for patient stratification in trials," said Alexandre Akoulitchev, chief scientific officer of U.K.-based Oxford Biodynamics. "We are starting to see some clinical utility, and there is a lot of interest," he told BioWorld.

Episwitch works by assessing and tracking changes in the 3D organization of chromosomes that occur in disease states. Those epigenetic changes in conformation lead to disease-associated changes in gene expression.

The 3D chromosome conformation signatures (CCS) are detected using proprietary pattern recognition algorithms to look for DNA sequences that are packed physically close to each other, but are linearly far apart on the DNA strand.

Initial hits are subject to screening and statistical analysis, before validation, DNA sequencing to identify which genes are involved, and cross-validation on sample cohorts.

An initial pool of 13,000 markers, comparing blood samples of six ALS patients and six healthy controls, narrowed that down to 153 markers. Those were subsequently tested on 24 ALS and 24 control samples, reducing the number of CCS markers to eight.

The eight CCSs were then assessed in 74 unblinded samples from patients with a confirmed diagnosis of ALS. Sensitivity for ALS was 83.33 percent (CI 51.59 to 97.91 percent). Specificity was 76 percent (CI 46.17 to 94.96 percent).

The researchers next tested the eight CCSs on a blinded cohort of 16 patients. Here, sensitivity was 87.5 percent and specificity was 75 percent.

As there is currently no definitive, clinically validated measure for confirming ALS, physicians perform a series of exclusion tests. As Akoulitchev noted, that leads to a delay in diagnosis in what is a rapidly progressing disease. "On average, there is 27 months survival [post-diagnosis]. Earlier diagnosis would mean offering better care while patients are still able," he said.

The delay in diagnosis also limits recruitment of patients with early stage ALS into clinical trials.

Interestingly, the CCSs discovered by Oxford Biodynamics map to eight gene loci with known or emerging associations with the development of ALS. One example is the superoxide dismutase1 (SOD1) gene, mutations of which are known to cause ALS and are linked to prognosis.

ALS caused by the A5V mutation of SOD1 is generally associated with shorter life expectancy than other SOD1 mutations.

Another example is the TARDBP gene, where 60 or so mutations have been found that cause ALS. Most of the mutations lead to misfolding of the protein, resulting in aggregates that have been found in the motor neurons of ALS patients.

In addition to gene loci with established links to ALS, the analysis confirmed involvement of recently implicated genes.

It was "fascinating" to see how the gene loci identified by Episwitch mapped onto individual genes that are linked to ALS. "For us, this was the most amazing thing, because we just follow the data in a non-biased way," Akoulitchev said. "Epigenetics and genetics go hand in hand, and this shows epigenetics gives insights into the genetics."

In addition to providing the basis of a potential diagnostic, this highlights how CCS analysis could be of use in the identification of disease mechanisms for target discovery.

Demonstrating that the eight CCSs can differentiate ALS patients from healthy controls is the first step in developing a commercial diagnostic. Akoulitchev said the next stage will be to deliver evidence of utility in clinical trials of potential ALS therapies. Further data will come from the retrospective analysis of completed clinical studies.

In addition to ALS, Oxford Biodynamics has data indicating the Episwitch technology could form the basis of blood tests for rheumatoid arthritis, diabetes and breast, prostate and pancreatic cancers.

Although it has disclosed little detail of the precise projects and most clients are not named, Oxford Biodynamics has contracts with pharma companies and research institutes in which it is applying Episwitch for patient stratification, to identify drug responders and to monitor response to treatment.