Biomarkers of Cancer
Larry H. Bernstein, MD, FCAP, Curator
LPBI
Biomarker Discovery Gets a Fix on Cancer
GEN Feb 1, 2016 (Vol. 36, No. 3) http://www.genengnews.com/gen-articles/biomarker-discovery-gets-a-fix-on-cancer/5674/
Just Because Cancer Is a Moving Target—Emerging Here, Eluding Treatment There—Doesn’t Mean It Can’t Be Tracked
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Epic Sciences’ “no cell left behind” platform can identify circulating tumor cells in an unbiased manner, without enrichment or depletion on any parameter. For example, as indicated in this image, it has been used to detect the AR-V7-positive cells among the cells collected in a simple blood draw. The AR-V7 splice variant is linked to resistance of androgen receptor-targeting drugs in metastatic castration-resistant prostate cancer patients.
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Just as signposts provide information, direction, and guidance, so too cancer biomarkers can better reveal the complex, dynamic, and heterogeneous landscape of malignancies.
Such information is critical for creating better cancer diagnostics, prognostics, and therapeutics, but the journey to find just the right biomarker is often a long and winding road.
Biomarker discovery and utilization is being explored by means of various methods and technologies. These include the isolation and characterization of rare circulating cancer cells, the use of multiplexing to extract information from limited amounts of sample, and even the application of evolutionary biology to detect early cell changes.
These approaches are all being developed by companies interested in improving cancer diagnostics, prognostics, and therapeutics. For example, one of the companies cited in this article is scrutinizing circulating tumor cells (CTCs) to predict resistance to cancer drugs. (This work was presented at a scientific retreat convened by the Prostate Cancer Foundation.) Other companies represented in this article are developing novel cancer diagnostic approaches. (These were detailed at the recent Cambridge Health Diagnostics Summit.)
While a typical blood sample from a cancer patient can contain 30 million nucleated cells, it’s estimated that perhaps only 5 of those cells may be destined to form tumors. “Most present-day diagnostic technologies cannot precisely detect those rare CTCs,” observed Ryan Dittamore, vice president, translational research and clinical affairs, Epic Sciences. “Identifying robust predictive biomarkers that can be utilized in real-time with a test compatible with diagnostic workflows is one of the greatest challenges to precision medicine.
“Epic Sciences is focused on developing sensitive diagnostic tests to characterize CTCs molecularly in order to match therapies to a patient’s cancer biology.” As Dittamore indicated at the Prostate Cancer Foundation event, the company evaluated its CTC approach in a study undertaken with Howard Scher, M.D., chief of the genitourinary oncology service at Memorial Sloan Kettering.
“We focused on a form of prostate cancer called metastatic castration-resistant prostate cancer,” explained Dittamore. “In the study, we confirmed the value of the prostatic cancer biomarker AR-V7 in 193 patient samples. In men with this androgen receptor (AR) splice variant, treatment with taxanes may be more effective than treatment with AR-signaling-directed agents (enzalutamide or abiraterone).”
In Epic Sciences’ “no cell left behindTM” approach, all nucleated cells from a blood sample are placed on a slide. CTCs are stained using biomarker monoclonal antibodies and assessed via immunofluorescence and high-resolution digital pathology scanning.
“We’ve industrialized this process,” asserted Dittamore, “and can evaluate millions of patient cells in every assay. Once identified, we can then isolate individual CTCs for further single-cell evaluation, such as with next-generation sequencing.” Overall, the company’s approach can achieve the following tasks: quantifying the number of cancer cells, characterizing biomarker expression (specifying, for example, subcellular localization and genomic alterations), and assessing disease heterogeneity and clonality of cancer cell types.
Commercializating the tests will come later, indicated Dittamore. “We will continue refining and expanding tests with our numerous collaborators in academia and pharma, many of whom are using our biorepository capabilities to bank samples for later study of biomarkers for other types of cancer.
The ultimate goal of molecular diagnostics is to get as much information as possible, as quickly as possible, with as little sample as possible. Unfortunately, it is often necessary to make do with samples that are limited in number and extent—consider, for example, formalin-fixed, paraffin-embedded (FFPE) specimens—even though one would like to extract comprehensive information. To help solve this problem, Qiagen has developed a new platform that marries and automates two proven techniques: multiplex PCR and capillary electrophoresis.
“We created a novel and automated clinical platform called Modaplex for real-time sampling, size separation of PCR products, amplification curve building, and Ct (cycle threshold) calculations,” summarized Lilly Kong, DVM, Qiagen’s senior director, assay development. “As a result, from a very limited amount of sample, we can utilize a multimodal, multiplex, essentially ‘all in one well’ means to quickly obtain actionable results.”
Dr. Kong said that Qiagen has developed multiple oncological biomarker tests including RAS, cMET, FGFR, Cell Cycle, and DLBCL signatures. “We can multiplex up to 40 targets in a single reaction,” she asserted. “Traditional assays allow testing of only one or a few assays at a time. Further, this is an architecture that uses a modular approach.”
Dr. Kong described development of an assay evaluating cMET and epidermal growth factor receptor (EGFR) expression and copy number variation. These two players are important because the MET proto-oncogene encodes for the receptor tyrosine kinase, cMET, which is widely expressed by many cells.
Under pathological conditions, cMET confers survival and invasive properties of cancer cells while potentially blocking EGFR therapies. “This multimodal 21-plex assay,” Dr. Kong indicated, “succeeded in evaluateing nine mRNA targets and nine genomic DNA targets with appropriate standards and external process controls.”
Qiagen also examined cMET simple nucleotide polymorphisms (SNPs) in a 16-plex reaction tube. “The modular approach enables combinations of important biomarker assays that can test for disparate target types, such as SNPs, expression biomarkers, miRNAs, and fusion genes,” Dr. Kong detailed. “Further, one FFPE slide is sufficient for about 10 assays with 10–50 ng input per reaction. The automation is user-friendly while sensitivity, specificity, and precision are equal to or exceed singleplex assays.”
Although Modaplex started with oncological applications, many other panels are in development. For example, Qiagen is working on pathogen detection applications as well as in-process monitoring applications for biologicals manufacturing.
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