Researchers develop epigenetic ‘cell-free’ DNA blood test for prostate cancer.


Researchers from the Vanderbilt University, the University of Toronto and Chronix Biomedical have demonstrated a method for detecting ‘cell-free’ tumour DNA in the bloodstream.  The team believe that the technique will be transformative in providing improved cancer diagnostics that can both predict treatment outcomes and monitor patient responses to therapy.

In a large retrospective study of blood samples, the researchers showed that the method, called a liquid biopsy, could accurately distinguish prostate cancer from normal controls without prior knowledge of the genetic signature of the tumours, and with over three times the sensitivity of current prostate-specific antigen (PSA) screening.  The study is published in the journal Clinical Chemistry.

The team believe that based on the reported data and work in progress that the liquid biopsy will revolutionize cancer diagnostics, not only before a patient begins therapy but also following patient responses to therapy.

The current study collected serum from more than 200 patients with prostate cancer and more than 200 controls. The samples included PSA levels and prostate tissue biopsy grading, called the Gleason score.

The researchers reported that the technique distinguished prostate cancer from normal controls with 84-percent accuracy, and cancer from benign hyperplasia and prostatitis with an accuracy of 91 percent.  Because the method quantifies the inherent chromosomal instability of cancer and can be followed as a function of time without having to do an invasive tissue biopsy, it is called a liquid biopsy.

It’s been known for many years that dying cells, including tumour cells, shed DNA into the bloodstream.  But only recently has technology, notably next-generation sequencing, made it possible to reliably distinguish and quantify cancer-specific DNA from normal controls by the identification and chromosomal location of billions of specific DNA fragments present in blood as cell-free DNA.

The current prostate cancer study identified 20 hotspots of greatest chromosomal instability as additions or deletions in less than 0.5 percent of the total DNA present in human chromosomes.  This is because the group’s liquid biopsy technique takes a broader approach. It examines the entire genome rather than known specific gene point mutations.

Robust mutation panels vastly improve monitoring since cancer cells are constantly deleting chromosomal DNA and liquid biopsies with only one or two mutations will allow cancer cell escape variants to go undetected.  Since the entire genome was surveyed, the researchers were able to identify a non-coding region of the genome as a hotspot, which may be generating previously unrecognized chromosomal control elements in prostate cancer.

The other 19 hotspots were rich in genes involved in replication and cell control processes that are highly relevant to cancer.

Since cell-free DNA has a relatively short half-life in the circulation, sequencing of cell-free DNA soon after therapy may be used to detect minimal residual disease in solid tumours.

The team further predict that liquid biopsies will quantify immediate tumour responses to therapy.

Source:  Vanderbilt University 

 

Circos plot showing the frequencies of prostate cancer samples positive for the respective region. The outer circle depicts all preselected consolidated regions. The inner circle depicts the 20 regions selected for the final model. Regions of copy-number loss are shown in red, gains in green. The scale of each circle is 0-0.5. The outer scale shows chromosome positions in Mbp (HG18).  Chromosomal Instability in Cell-Free DNA Is a Serum Biomarker for Prostate Cancer.  Narod et al 2014.

Circos plot showing the frequencies of prostate cancer samples positive for the respective region. The outer circle depicts all preselected consolidated regions.
The inner circle depicts the 20 regions selected for the final model. Regions of copy-number loss are shown in red, gains in green. The scale of each circle is 0-0.5. The outer scale shows chromosome positions in Mbp (HG18). Chromosomal Instability in Cell-Free DNA Is a Serum Biomarker for Prostate Cancer. Narod et al 2014.

 

 

 

One comment

  • Steven McLauder

    You have to use 10-20 mL of blood to extract enough cell-free DNA (cfDNA)!! The recovery efficiency of cfDNA is too low with current Qiagen or silica-matrix-based methods. No matter how good your downstream technology eg, ddPCR, BEAMing, ICE-COLD PCR, NGS, or how good the library-prep kit is, you just can not detect something already lost during cfDNA extraction!!! The lost is lost…Here is the catch: cancer management from a drop of blood, that’s the future!! Are we there yet? According to 2015 ASCO abstract, CirculoGene Diagnostics has a way to do tumor NGS mutation detection from as low as 20 uL of plasma!! Maybe it’s time for last-generation of liquid biopsy and nanodiagnostics.

    Like

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