Hybrid Fusion FISH™ and Liquid Biopsies: The Future of Economically Sustainable Cancer Diagnostics For Targeted Therapies and Precision Medicine

Review Article: Part 1 of Series

Preventive cancer screening is far more effective than treatment of disease. Early detection and active surveillance is a proactively sustainable approach for preemptive diagnosis. More importantly, finding cost-effective, globally impactful and highly efficient screening tests should be the primary focus of modern cancer care as opposed to novel therapies and new clinical treatments. Through preventive measures, many of the public, social, medical and economic health burdens can be drastically reduced. Finding a cure and preventing the onset of disease are cooperatively essential in medicine, but it’s the preventive aspect that significantly makes an overall positive impact within our healthcare system. Simple screening tests that are understandable to the average consumer coupled to modernized and cost-efficient accessibility are the solution to reducing cancer’s epidemiological presence in the US and the world.

“Cancers that can be prevented or detected earlier by screening account for at least half of all new cancer cases.” – American Cancer Society, Cancer Facts and Figures 2010 Annual Report

The molecular precursors of cancer can be simplified for the average consumer: Humans have cells, and within these cells are nuclei, the portion of the cell that houses the entirety of a person’s DNA (genes). These genes are the “countable units” that are implicated in cancer. In the normal state, every cell possesses two copies of each gene. In the abnormal state, cells may possess more than two copies (“amplification” of a gene), less than two copies (“deletion” of a gene), or an overlap between two genes (“translocation” of a gene). These three events are abnormal phenomena in cancer genetics that may indicate precancerous and cancerous states and are the root cause in the overall cancer pathology and progression. Such abnormal genetic events can be readily identified and assessed over time.

Cancer is a highly heterogeneic disease, meaning that it manifests and progresses through various genetic mutations (“hetero”) over time and its molecular origin is derived from abnormal genetic DNA (“geneic”). There are very specific genes within the nuclei of cells that become abnormal during disease — these subsets of genes can be quantified and characterized for particular cancers. Therefore, one barrier is identifying which genes are abnormal early on for an effective diagnosis that leads to a higher probability of beneficial outcomes. The following are examples of well-known genetic aberrations that are seen in specific cancers.

A second barrier is identifying those specific cancerous cells that are creeping around in circulation of a patient’s body. Typically, a solid tumor biopsy may be conducted at the suspected source of the cancer, but this is invasive, expensive and painful to the patient. Alternatively, obtaining blood is non-invasive and cost-effective for sample efficiency and viability. Out of tens of millions of cells, there are typically only a few cancer cells that may be found circulating in the blood. These are called “circulating tumor cells” (CTCs), and these cells are the earliest precursors of distant metastases within the blood that can effectively characterize the source of the cancer. To put it simply, approximately 90% of cancer-related deaths occur as a result of metastases, the spread of the local benign cancer to distant organs via circulation. Therefore, identifying these cells early on for molecular characterization is critical (and far often too late leading to more complex treatment protocols).

The overarching solution, then, is to overcome these two barriers with a) a cost-effective solution, b) an easy-to-interpret diagnostic test, and c) high clinical validity and therapeutic utility. Genetic characterization of cancer cells can be overcome through a novel technology known as “Hybrid Fusion FISH™” (fluorescence in situ hybridization). In technical terms, it’s a molecular method whereby small, highly-specific genetic probes that are fluorescently labeled with visually distinct fluorophores target cancer-related genes within the nuclei of cells. Simply put, these “colored dots” will travel to the nuclei of cells and bind to cancer genes in a specific manner such that we can see both a) the quantitative number of dots that are bound and b) the qualitative colors of these dots. Here’s an illustrative example using the chronic lymphocytic leukemia (CLL) Hybrid Fusion FISH™ panel of genes presented above.

The barrier to avoid painful and invasive biopsies that are traditionally conducted to diagnose and track cancer can be overcome through the advent of “liquid biopsies”. These are non-invasive methods to characterize blood for the presence of solid tumors. Liquid biopsies can provide telling information for disease prediction, progression, residual disease monitoring, treatment efficacy and more. More importantly, it’s highly repeatable and can model disease over time, offering the physician tremendous insight to pursue a precise and personalized course of action — a notion often reflected as “precision medicine” and “personalized diagnostics”.

When Hybrid Fusion FISH and liquid biopsies are coupled together in diagnostic matrimony, the result is a very powerful screening assay that can track tumor relapse, warrant the usage of targeted therapies, and qualify patient response for effective treatments (or inversely, disqualify patients from very expensive therapies that would otherwise have no beneficial effect and result in increased toxicity). The long-term goal is for the early detection and diagnosis of cancer before the manifestation of further molecular symptoms (genotypes and phenotypes). To date, catching abnormalities early is the best cure for cancer, as it is the most critical and responsive window for highly effective treatment to potentially reverse the course of disease.

The molecular intelligence that is provided from Hybrid Fusion FISH is valuable on multiple fronts. Genetic interrogation at single-cell resolution while retaining the morphology of the nucleus is a luxury that is not readily made possible by other analytical techniques such as DNA sequencing. The resulting morphometric analysis by Hybrid Fusion FISH allows the physician to keep the tissue architecture and morphology intact when viewing the signals. Additionally, clonal cell populations typically arise in cancers harboring multiple metastases, which can be identified with precision via Hybrid Fusion FISH. Such populations with distinct genetic signatures provide the over-encompassing nature of the cancer as a whole. Each distinct cell population will have a distinct susceptibility to a pharmaceutical drug. Narrowing the focus of cancer treatment through single-cell identification of genetic aberrations is the cornerstone of personalized and precision medicine heavily directing targeted therapies. Here is an example using the same CLL Hybrid Fusion FISH™ panel as presented earlier.

Example: 11 different cell populations were identified with a single Hybrid Fusion FISH CLL Assay. Each clonal population is affiliated with a good/bad prognosis with therapeutic outcomes.

Of course, there are other initial techniques to diagnose cancer such as noninvasive imaging (such as MRIs and CT scans) and protein-specific biomarkers (for example, PSA for prostate cancer). However, these techniques do not provide the molecular intelligence presented above, is rather expensive, and not as sensitive for characterization of tumors. Collectively, it does not provide for a scalable model for early detection and diagnosis of cancer on a global scale. Simply put, it is not economically feasible to provide actionable information for the masses from a preventive diagnostics’ perspective.

The logic behind CTCs is simple: they are not found freely in healthy individuals, and when they are found, the number of cells is proportional with the prognosis of disease. Isolation of such cells via targeted cell-enrichment methods enable the capture of aberrant cells which can be subsequently characterized by Hybrid Fusion FISH to provide a molecular genetics component. All of this can be accomplished in as much as 24 hours.

Today, Hybrid Fusion FISH and liquid biopsy technologies are maturing into the clinical diagnostics marketplace. Understanding that cancer has a major genetic component for the progression of disease is paramount. This will enable a new wave of applications utilizing Hybrid Fusion FISH specifically for the development of companion diagnostics that couple the screening test to a clinically viable therapeutic agent. The technology only represents the diagnostic potential of personalized medicine in oncology. Drug development by pharmaceutical companies will prove vital to act on the actionable diagnostic intelligence that is afforded by Hybrid Fusion FISH.

DISCLAIMER: This article is part 1 of a series of articles dissecting, researching and evaluating Hybrid Fusion FISH™ applications within the clinical diagnostics and research environments. Prevnos Inc. is a cancer diagnostics company that is rapidly evolving the current cytogenetics and molecular cancer genetics markets. The company is the inventor of the world’s first Hybrid Fusion FISH™ tests (consumables) and the world’s most economical fluorescence microscope termed the Retina™ FISH scope (capital equipment). The company is also the inventor of GEN+ Connect (software), which enables digital pathology for molecular cytogeneticists around the world. Furthermore, the company explores clinical research with pharmaceutical companies for companion diagnostics. Prevnos engages in various forward-thinking R&D projects including, but not limited to, targeted cell-enrichment with subsequent FISH, CTC FISH™, non-disruptive FISH probe delivery vehicles, single-cell isolative technology for FISH, tyrosine kinase inhibitor master FISH assays for lung cancer, molecular characterization for stratification of prostate cancer patients, and COMET (chromatin organization mediated electrophoretic transfer) FISH™ assays for assessing DNA viability.
To learn more, visit Prevnos at www.prevnos.com