A team of biologists believes it’s on the path to developing a new early diagnosis test for different cancers using tiny particles in the blood known as exosomes they’ve discovered contain huge chunks of DNA.
The team, from The University of Texas MD Anderson Cancer Centre, says we should be able to sequence the material from a blood sample to identify any number of genetic mutations that indicate cancer is present. They believe it will open up a whole new field of research, considering that the exosome samples tested were found to contain genomic DNA spanning across all chromosomes. “This novel finding contradicts the current opinion that circulating DNA is highly fragmented,” they commented.
Exosomes are tiny particles about the size of a virus shed by almost every cell in the body. The Texas team, led by Raghu Kalluri, decided to investigate the particles to see if they could potentially carry additional information about any cancerous cells in the body.
“We found they contain proteins, RNA, but while looking at these proteins and RNA we kept identifying some other things present in there — large fragments of DNA, which was really surprising to us. We didn’t expect something that’s present mainly in the nucleus of the cell to be present in these little particles,” says Kalluri.
“We began looking at these fragments and found there were large quantities of them. So we began analysing them further and further and found these little particles contain the entire genomic DNA present in the nucleus, which is extremely exciting because now these little particles floating in the blood represent DNA coming from all kinds of tissues in the body — it means you can probe the DNA to find out what’s going on in those tissues, but you don’t have to go to the tissue to get.”
Today, preliminary tests to confirm the presence of cancer do include blood tests, but these look for things like cell count and sometimes tumour markers (proteins produced by particular tumours). The latter can also be found in non cancerous conditions though, so it’s possible to get a false positive. Otherwise, to confirm the presence of cancer tissue samples are taken from tumours. At this stage though, as Kalluri points out, the cancer may have already significantly progressed. Identifying cancer at its early stages, when a tumour is difficult if not impossible to detect through imaging, is the aim of the new test Kalluri is proposing.
“In many cases, current protocols require a tumour sample to determine whether gene mutations and deletions exist and therefore determine whether the tumour itself is cancerous or benign. To procure tumour tissue, one needs to know that a tumour exists and if so, is it accessible for sample collection or removal? Finally, there are always risks and significant costs associated with surgical procedures to acquire tumour tissue.
“We looked at the particles to see if patients who had tumours in them have exosomes that contain the tumour derived DNA in them. What we found is that these particles contain the entire DNA that is present within the cancer cells. Now we can probe that DNA for mutations.”
In the clinical study, written up in the Journal of Biological Chemistry, Kalluri and his team found that mutations commonly associated with pancreatic tumours — namely, mutations of KRAS, a protein that’s key to normal tissue cell communications, and the p53 gene — were indeed identified in the DNA of these particles.
Kalluri says if the results are replicable, “then we have a way of identifying the entire spectrum of mutations of cancer cells by looking at these particles in the blood. Detection can happen early and we can track them and see how they respond to therapy — we’re very excited this is going to launch a new area of research”.
Speaking to Wired.co.uk, Clinical Immunologist John Maher at King’s College London’s Guy’s and St Thomas’ NIHR Biomedical Research Centre says the concept is an interesting one, but the promise of a new diagnostics method still relies on how well it performs when tested in a “real life” population.
“In this study only two patients and two healthy individuals were tested but in reality, you would be testing a population in which only a tiny minority of subjects with disease will be present, which provides a much more stringent challenge.”
“The same principle applies even more strongly to the Andraka test where false positive test results could become an issue in that setting,” adds Maher, referring to the 28 pence pancreatic cancer test developed by teenager Jack Andraka, which is 200 times more sensitive that current diagnostics tests. The test relies on a strip of filter paper, dipped in a solution of carbon nanotubes and a special antibody, being able to trap a cancer biomarker protein called mesothelin. Like the blood test being proposed in Texas, Andraka believes his test can be tweaked to detect any cancer — we just need to get the right antibody.
Maher is himself currently working on a new method of pancreatic cancer detection, using genetically engineered T-cells. Last year he was awarded a grant by Pancreatic Cancer UK for pre-clinical trials, and this year he will begin clinical trials in head and neck cancer patients.
In the Journal of Biological Chemistry paper, Kalluri and his team admit that further investigation will be needed to isolate cancer cell-specific exosomes.
“Nevertheless, our study provides unequivocal evidence for the presence of double stranded genomic DNA in the exosomes that spans across all the chromosomes,” continues the paper. “Whether our discovery will enable the use of genomic DNA from circulating exosomes to sequence a significant portion of human genome for diagnostic and therapeutic purpose remains to be detemined.
“Exosomes may enable themselves as powerful DNA diagnostic tool and likely also provide new methods to predict prognosis of cancer patients and improve treatment via a personalised medicine approach.”
A company called Exosome Diagnostics is in fact already working toward using exosomes in personalised medicine. The private firm specialises in the extraction of RNA and DNA from exosomes — it was already known that bits of DNA were contained within the particles, including mitochondrial DNA and single stranded DNA, but not to the extent discovered by the Texan team. The genetic data is gathered from patient blood for analysis and sequenced so that doctors can “perform real-time biomarker analysis on patient plasma and serum samples”.
“The company’s proprietary exosome technology makes use of the presence and natural stability of RNA in exosomes to detect and measure levels of genes responsible for cancer and other diseases.”
The company is hoping to commercialise the diagnostics test and take it further to monitor disease, just as Kalluri is suggesting with his approach. Last summer it partnered with Cedars-Sinai Medical Centre to use its “biofluid extraction kits” to look for biomarkers in extremely premature babies.
“We were thrilled to see the publication from the group at MD Anderson,” Hannah Mamuszka, VP of Business Development at Exosome Diagnostics told Wired.co.uk. “We believe exosomes represent a new paradigm in personalised medicine, and we were excited to see that a world leading institution such as MD Anderson is actively generating data in the field. The implications of being able to monitor a patient’s mutational status in a blood sample, without requiring tissue biopsies, are significant. In addition to reducing cost, detection in a biofluid allows for frequent monitoring for resistance development and disease progression.
“Moving personalised medicine from tissue into biofluids is a significant advance. Exosomes represent the leading biological medium to create a new generation of high-performance, non-invasive gene-based diagnostics for earlier disease detection and better direction for targeted drug therapies.”