Liquid biopsies – tests done on a simple blood sample that can detect cancer DNA – are set to become much more accurate and useful for monitoring cancer thanks to new techniques developed by researchers. Two newly published studies detail methods to greatly boost the signal of cancer DNA in blood samples, enabling faster and more reliable scanning for mutations that reveal the presence or status of tumors.
Injectable molecules substantially increase detectability of tumor DNA
Researchers at MIT and the Broad Institute have developed synthetic DNA molecules that can be injected into the bloodstream, where they selectively bind to DNA fragments released from cancer cells and concentrate them in the blood. This enables liquid biopsies to pick up genetic traces of the tumor that would previously have gone undetected.
When tested in mice with human cancer xenografts, injecting the DNA strands called amplifier strands led to a greater than 10,000 fold boost in the ability to detect human cancer DNA circulating in the mouse bloodstream. The approach also worked to amplify the signal from tumor DNA in blood samples from 2 human patients with advanced breast cancer.
The technology promises to make liquid biopsies much more sensitive and useful for a number of applications:
- Early cancer detection – amplifier strands may enable detection of tiny tumor traces in asymptomatic individuals
- Monitoring treatment response – detailed tracking of how tumor mutation patterns change in response to therapies
- Identifying emergence of treatment resistance – early detection of new mutations that enable tumors to evade medications
- Discovering metastases – improved ability to detect if cancer has started spreading to other sites in the body
The method developed by the researchers consists of short single strands of synthetic DNA, with a sequence designed to be complementary to known recurrent hotspot mutations in cancer genes. When injected into the bloodstream, billions of these short strands float through blood vessels across the body. Upon encountering a DNA fragment released from a tumor cell, the amplifier strand recognizes the sequence of the mutation and binds to it quickly and tightly.
This reaction concentrates any tumor DNA fragments in the blood sample and flags them for detection. The researchers demonstrated that by using amplifier strands targeted to just 3 known mutations in the PIK3CA gene, they could increase detection of circulating tumor DNA by at least 10,000 fold.
Follow up experiments showed that the amplifier strands appear safe with no adverse effects or inflammation when injected into mice. The DNA sequences also break down naturally within 24 hours – just long enough to enable an enhanced liquid biopsy before disappearing from the bloodstream.
The researchers highlight the versatility of the approach to create amplifier strands that recognize any known tumor mutation. This raises the prospect of using sets of amplifier strands to scan for large panels of common cancer mutations, enabling both highly sensitive screening in undiagnosed patients and detailed tracking of mutations in tumors over time.
Novel preservative enables tumor DNA in blood samples to be sequenced directly
In another breakthrough study published in parallel, researchers at Stanford University have developed a novel liquid preservative that can stabilize tumor DNA in blood samples for up to a week at room temperature. This enables the samples to skip lengthy and costly DNA extraction and processing, and instead go straight into high throughput sequencing machines.
The product named BluGenie contains chemicals that prevent the breakdown of DNA fragments in blood serum or plasma samples from multiple cancers. In head to head comparisons, BluGenie preserved DNA integrity in liquid biopsy samples for at least 5 days longer than existing commercial reagents at 25°C.
BluGenie ensures circulating tumor DNA fragments do not degrade before sequencing, helping avoid false negative results. The direct blood sequencing also retains the relative abundances of mutations in the sample, instead of introducing biases that skew the frequencies of variants during extraction and amplification steps.
This approach promises to greatly streamline processing and analysis of liquid biopsies:
- Faster turnaround times – blood samples can be batched up and sent directly for sequencing without waiting to extract DNA
- Lower costs – skips expensive nucleic acid extraction kits and person-time needed to extract DNA
- Retains original profile – prevents biases that distort the mutation fractions in a tumor
- Enables direct capture – allows direct application to blood samples of probes that pull down or enrich tumor DNA fragments
The researchers suggest BluGenie could be adapted into a simple collection device – where patients add a blood sample which mixes with the preservative solution and gets stabilized for transportation and centralized sequencing.
They also highlight the potential to identify panels of mutation biomarkers that act as indicators of cancer type or treatment resistance. Screening for these markers directly in blood samples treated with BluGenie could form the basis of routine diagnostic tests from a basic blood draw.
Outlook and next steps
The two studies demonstrate techniques that substantially improve liquid biopsies – allowing more sensitive and specific scanning for tumor DNA traces, while also streamlining workflows and reducing costs. When combined together, these approaches could form the foundations of a next generation liquid biopsy platform.
Some of the promising future directions include:
- Combining amplifier strands and direct DNA sequencing of blood samples preserved in BluGenie solution
- Adapting the techniques into simple collection devices for obtaining stabilized blood that is transported to a centralized analysis facility
- Using the approaches to screen for cancer recurrence and treatment resistance in cancer survivors
- Exploring the utility of highly sensitive scanning for early detection of aggressive tumors
- Continuing ongoing clinical studies to further validate performance
Both groups of researchers are looking towards clinical and commercial translation of their technologies through start-up companies recently spun out from their labs.
Wider availability of these enhanced liquid biopsy techniques promises to enable tracking of tumors through a simple blood test to become a routine part of cancer care and screening in the years ahead. With sensitivity boosted drastically, the evolution of tumors could be monitored in unprecedented detail – helping match patients to emerging targeted therapies and detect worrying resistance mutations at very early stages.
|Cancer detection approach
|Injectable amplifier strands
|10,000 fold enhancement of tumor DNA signal in blood
|Enables direct sequencing of blood samples without DNA extraction
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