A group of CAT scans of the human brain

A group of CAT scans of the human brain

What if circulating tumor methylated DNA from brain cancer could be detected?

Can ctmDNA be an early detection tool for glioblastoma multiforme?

Gliblastoma Multiforme is a terrible form of brain cancer. With a reported 5-year survival rate of only 4.4%, at just the 3-year mark anyone surviving that long is considered a 'long term survivor'. It is for this reason that GBM was first chosen along with pancreatic cancer to be intensely studied as part of a pilot project for The Cancer Genome Atlas, a major multi-year US National Institutes of Health initiative. The first paper on GBM from this TCGA pilot was published in September of 2008, with exciting news about three new signficant genes mutated in GBM (NF1, ERBB2 and PIK3R1).

In addition to these genes mutated at the DNA level, TCGA findings at the global gene-expresssion and genome-wise methylation point to several major disrupted pathways in GBM, including a mechanism of resistance by the hypermethylation of the MGMT gene along with common alkylating chemotherapy is highly correlated with mismatch repair deficiency, or MMRD leading to high recurrence of a specific MMRD mutation signature.

The challenge of the blood-brain barrier

The release of circulating tumor cells or tumor-derived DNA into the bloodstream from brain cancer is blocked by the biology of the blood-brain barrier. Protecting the brain from circulating pathogens, it also blocks 98% of all small-molecule drugs. Liposome-based nanoparticles are a promising novel method of drug delivery.

And yet there is evidence that brain-derived circulating tumor cells, tumor-derived exosomal vessicles, and circulating tumor DNA do cross the barrier where they can be detected in the bloodstream of affected individuals.

Liquid biopsy's entire spectrum

In 2014 it was shown that CTCs (Circulating Tumor Cells) can be isolated from GBM patients using a newer iteration of the CellSearch technology using negative selection. CTCs were identified in 13/33 patients in at least one blood specimen, and the researchers characterized the mesenchymal differentiation status with RNA in-situ hybridization.

The technology used for this characterization in 2014, called iChip, has since gone through several iterations, and a commercialization effort from this group has been started as a commercial company called TorpedoDx.

A complement to CTCs are extracellular vessicles (EVs), including exosomes. These small cargo-containing EVs contain miniscule amounts of protein, microRNAs and messenger RNAs, and can be enriched and analyzed for cancer-specific markers. This 2008 paper pointed the way for further work using digital droplet PCR and BEAMing to detect nucleic acids from exosome for prognosis of a collection of different types of advanced cancers.

A third analyte for liquid biopsy detection is circulating tumor DNA. This seminal study of ctDNA of several cancer types by Bettegowda et al. in 2014 also studied glioma and found it in less than 10% of the cases examined, and quantified the amount of circulating tumor DNA at less than 10 copies per 5 mL of plasma.

Can circulating tumor methylated DNA be an answer?

Singlera has a novel approach to early detection of cancer using circulating tumor methylated DNA (ctmDNA). While the amount of circulating tumor DNA crossing the blood-brain barrier is limited, it is a tantalizing thought to look at ctmDNA from affected GBM patient plasma samples.

While Singlera's methylation haplotype technology from circulating DNA could be applied to CTCs and extracellular vessicles, this may not be a useful approach as the simple presence of CTCs (a process called enumeration) is considered diagnostic for GBM, and EVs contain microRNAs and other RNAs for direct analysis.

Do you have an interest in early-detection of GBM from patient plasma, and have an idea for a research collaboration? Feel free to contact us directly.