Background

There remains an urgent need for new diagnostic tests capable of detecting cancer earlier than existing tests to enable timely treatment before local or systemic spread has occurred. Essential characteristics of such new tests includes the need to be easily repeatable and non-invasive. This would also allow for the tumour burden to be followed in real-time enabling the assessment of the response to therapy during disease progression or after recurrence. The current gold standard in cancer diagnosis involves radiological detection followed by a tissue biopsy. Such biopsies can be painful, are invasive, can be practically impossible to do depending upon the cancer and are associated with a risk of infection. Furthermore, most tumours are genetically heterogeneous and sampling errors associated with biopsies may mean missing the full range of mutations present and this is particularly true for metastatic tumours. Finally, tumour biopsies also represent a temporal snap-shot of the tumour’s genetic composition that can change over time.

Technology Overview

Due to the challenges stated above there has been significant research investment into finding cancer diagnostics capable of detecting tumour biomarkers in the blood and other body fluids. Most of these tests have been focused on identifying point mutations. This has proven to be technically challenging due to the fact that 1) tumours are heterogeneous in the occurrence of point mutations; 2) tumour DNA sequences may be present in body fluids at less than one genome equivalent per volume where the chances of detecting a single mutation becomes problematic; 3) normal DNA is always present in blood causing high background and; 4) error rates of PCR and sequencing limits detection to approximately 1% mutant DNA in normal DNA. To that end most studies to date have been tested on advanced metastatic disease patients were hundreds of grams of tumour exists and lack evidence to support detection of only a few grams worth of tumours.

To overcome these challenges Queen’s researchers have developed a liquid biopsy assay, called _m_DETECT, which leverages detection of highly correlated regions of DNA methylation using Next Generation Sequencing (NGS). In contrast to point mutations, DNA hypermethylation is a common event, and while some inter-tumoural variability is observed the large number of these events makes them much more readily detectable in the context of circulating tumour DNA. The researchers have identified and developed a number of signatures using the _m_DETECT method for many tumour types including to date: various breast cancer subtypes (BC) such as triple negative (TNBC), HER2+, ER+/PR+ and signatures for prostate (PC), lung, colorectal, uveal melanoma (UM), and pancreatic cancers. To date the researchers have validated signatures for metastatic UM, metastatic TNBC, and PC from patient blood samples with the demonstrated ability to detect very small tumours (< 0.5cm³).

It is very challenging to detect cancer at its earliest stage or during initial relapse stages within the blood. The demonstrated ability of _m_DETECT to detect cancer at ultralow limits of detection, form patients with tumors < 0.5 cm², with very high accuracy make it a revolutionary step forward in cancer diagnostics.

Stage of Development

Cross-validated data in metastatic TNBC patients with prospective studies ongoing in prostate cancer and in lung cancer for early pembrolizumab responders.

Further Details

A DNA methylation-based liquid biopsy for triple-negative breast cancer. Cristall K, Bidard FC, Pierga JY, Rauh MJ, Popova T, Sebbag C, Lantz O, Stern MH, Mueller CR. NPJ Precis Oncol. 2021 Jun 16;5(1):53. https://pubmed.ncbi.nlm.nih.gov/34135468/

Benefits

The _m_DETECT method has broad applicability to many or all cancers and is performed using cell-free DNA extracted from whole blood. It is easily scalable and takes advantage of existing technologies found in many pathology laboratories unlike other diagnostic technologies in development. For example, a limited number of centres are equipped and possess the expertise to conduct diagnostic tests on circulating tumour cells.

Figure 1: Signature for Very Low Limit of Detection

_m_DETECT takes advantage of targeted multiplexed probes from across the genome as well as within larger methylated regions which greatly increases the assay sensitivity. To that end the researchers have demonstrable benefits over existing gold-standard diagnostic assays diagnostic at a very low limit of detection of < 0.03 genome equivalents. This has translated into the ability to detect tumours of very small volume < 0.5 cm³. Furthermore, the use of methylated signatures overcomes limitations in existing liquid biopsy methods in development that are focused on point mutations.

Figure 2: Detecting Tumour Growth in Metastatic Patients

_m_DETECT was initially validated in uveal melanoma testing blood samples from a cohort of 40 patients with metastatic disease. The signature was found to reliably, specifically and sensitively detect tumour DNA in the blood. When compared to a gold standard PCR-based test it easily outperformed it and was able to detect the presence of cancer in patients having tumours as small as 0.5 cm³ as well as increases in tumour sizes in the same patients could be identified.

_m_DETECT has also been validated in metastatic TNBC (mTNBC). Applied to serum from 30 mTNBC patients and 30 controls the _m_DETECT signature gave AUC of 0.97 for detection of a tumour with a sensitivity of 93% for a specificity of 100%. _m_DETECT had superior performance to an NGS TP53 26 mutation-based test or to the conventional CA15-3 biomarker. An initial signature for PC was able to detect cancer in unstable patients compared to stable patients with a sensitivity of 100% and specificity of 85.71% (the AUC: 0.9821, p=0.0018).

Applications

Its non-invasiveness, repeatability and very low limit of detection will enable _m_DETECT assays to be applied for early cancer detection, population cancer screening, cancer recurrence, or general diagnosis. As a targeted method _m_DETECT is requires lower levels of sequencing, < 100-fold compared to pan-cancer screening tests, and the test also works as well in serum as plasma. Early results from ongoing studies in blood from lung cancer patients looking for early pembrolizumab responders support potential as companion diagnostic.

Opportunity

Seeking licensing partners and/or research development partners.

Novel NGS-Based Liquid Biopsy Diagnostic for Cancer Detection: mDETECT

Patents

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