Aberrant alteration of chromosomal DNA drives the development and progression of cancer. There are a variety of alterations that promote tumorigenesis including aneuploidy, chromosomal translocation, gene amplification, and point mutations.
The ability to identify these abnormalities in cancer patients is central to disease diagnosis, staging, and treatment. The current methods that are used clinically to identify chromosomal changes rely on molecular analyses of tissue from tumor biopsies. While biopsy samples provide a wealth of information about the molecular abnormalities in tumors, they often require invasive procedures which may be prone to sampling error. The ability to detect chromosomal changes that cause cancer in peripheral blood samples may allow earlier and more accurate diagnosis.
In a recent study in Science Translational Medicine, researchers at Johns Hopkins University show that it is possible to get detailed information about the molecular characteristics of a tumor’s chromosomal DNA from peripheral blood samples. The authors exploit the fact that dead or dying tumor cells frequently dump their contents into the bloodstream. A major component of these intracellular contents is the chromosomal DNA that contains the deleterious alterations that drive tumor growth. The authors isolated this circulating cell-free DNA (CFDNA) from both cancer patients (colon and breast cancer, specifically) and healthy volunteers and used whole genome sequencing (WGS) to assess for chromosomal abnormalities. The authors saw chromosomal abnormalities such as, chromosomal copy number changes and genomic rearrangements, in the CFDNA specifically from cancer patients and not from healthy volunteers. Interestingly, the chromosomal abnormalities that the authors detected corresponded to common mutations seen in these types of cancers. Previous studies have shown that it is possible to observe oncogenic changes in chromosomal DNA from the peripheral blood of cancer patients. However, these methods required prior knowledge of what chromosomal changes might be present—that is, the investigators could only find the specific mutations that they were looking for. The current study demonstrates that it is possible to measure chromosomal changes in tumors using blood samples without advanced knowledge of the mutations that caused the cancer. This opens up the possibility of being able to fully characterize the unique molecular defects in a patient’s tumor and allowing for individual tailoring of therapy. The authors also compare chromosome arm alterations from colorectal cancer cell lines and xenografts to the blood from the colon cancer patients. They found that both showed ≥5 chromosomal alterations compared to healthy volunteers (less than 2.4 alterations).
Although this technology is promising, substantial obstacles must be overcome before WGS on peripheral blood becomes a widely-used clinical technique. First, the sensitivity of WGS depends on the amount of mutant CFDNA obtained for sequencing. Chromosomal abnormalities that are present in small amounts may be missed (i.e. small tumors). Of note, the patients analyzed in this study all had advanced disease. Further investigations into whether this technique can identify chromosomal abnormalities during early stage disease or in instances of diagnostic uncertainty are warranted. Second, it is not clear to what extent the chromosomal abnormalities detected in peripheral blood represent the molecular defects in actual tumors. Are there additional mutations contained in tumor tissues that do not show up in the blood? Further study is necessary comparing peripheral blood sequencing analyses to those performed on biopsy samples obtained from the same patient. This will be especially important for applications which seek to use the information garnered from WGS of peripheral blood to guide treatment decisions. Finally, the sequencing techniques used in this study are expensive and preclude routine clinical use at this time. Although, based on the current trend of rapidly deceasing costs associated with next-generation DNA sequencing technologies it is plausible that clinical testing of this sort will become affordable in the near future.