David Hout, PhD

Q&A on Companion Dx with Insight Genetics

By: Judy O’Rourke

     Since 2010, the National Cancer Institute (NCI) has awarded Insight Genetics, Nashville, Tenn, four contracts to develop and refine companion diagnostic tests that identify and characterize specific genetic mutations known to be active in the proliferation of lung and breast cancers. Insight’s tests support physicians in accurately diagnosing and monitoring patients’ cancers to improve personalized treatment.
Most recently, the company received NCI funding to continue analytical and clinical validation of Insight ALK Screen™, the company’s real-time qPCR-based test under development on a QIAGEN platform. It is the company’s second of two NCI awards related to the test, which detects the range of genetic abnormalities of anaplastic lymphoma kinase (ALK).
Since the first observation in 2007, a number of variations in ALK have been linked with lung cancer, specifically contributing to about 5% to 10% of lung cancers. The American Lung Association estimates that approximately 373,489 Americans are living with lung cancer, and the Centers for Disease Control and Prevention reports that lung cancer claims the most lives—accounting for almost 30% of all cancer deaths.
Using the Insight ALK Screen, clinicians can better decide which patients will benefit from targeted therapy with ALK-inhibitor drugs, for which the Food and Drug Administration requires a companion diagnostic. The most recent Clinical Practice Guidelines in Oncology from the National Comprehensive Cancer Network (NCCN) advise that advanced ALK screening be performed for all non-small cell lung cancer (NSCLC) patients.
Even with the promise of ALK inhibitors as targeted treatments for NSCLC, most patients’ response to the drugs change over time. To help physicians pinpoint and monitor the effectiveness of ALK-inhibitor therapies and spot later-stage drug resistance mutations, Insight developed Insight ALK Resistance™. The company received an NCI contract in 2011 to demonstrate the test’s ability to identify cancer cells with mutations conferring resistance to ALK-inhibitor drugs.
NCI also awarded the company a Phase I Fast Track contract of nearly $200,000 to support research and development of a panel of companion diagnostic tests for the detection of RET, ROS1, and DEPDC1, genes associated with  NSCLC.
Clinical Lab Products recently had the opportunity to catch up with David Hout, PhD, Insight Genetics’ vice president of R&D, on the company’s continuing work on Insight ALK Screen, Insight ALK Resistance, and other biomarker-specific diagnostic tools to advance cancer care.

CLP: Analytical and clinical validation of Insight ALK Screen is under way. Tell us more about the test—is it more effective (sensitive and specific) than other methods in use or in development, will it be cost-effective, and how convenient will it be for labs to use?
David Hout, PhD: Insight is currently involved in several head-to-head studies comparing the performance of Insight ALK Screen™ qPCR assay to fluorescent in situ hybridization (FISH) and immune-histochemistry (IHC), two other predominant methods of testing the field. We expect these studies will demonstrate the assay to be more sensitive than FISH (the current FDA-cleared companion diagnostic for Xalkori), resulting in the identification of more ALK-positive patients for whom current and upcoming ALK inhibitor therapies may be beneficial. With respect to IHC, we believe that the Insight ALK Screen will be comparable in performance, but the qPCR method will be more cost-efficient. In addition, the qPCR method is adaptable to multiplex testing when the time comes that an oncologist needs to screen a patient for multiple markers at one time.  

CLP: Can it be automated?
Hout: Yes. Insight Genetics is currently developing the Insight ALK screen on QIAGEN’s qPCR and extraction platform to decrease turnaround time and accelerate delivery of results to physicians.  

CLP: Could you tell us how the qPCR method differs in efficacy from fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), or reverse transcription-polymerase chain reaction (RT-PCR) methods?
Hout: Each of these methods suffers from some technical shortcomings. IHC surveys the tumor with antibodies specific for ALK protein expression, which is the drug target. However, using IHC on EML4-ALK positive specimens has encountered difficulty due to low expression levels of the fusion protein. Higher affinity antibodies against ALK have improved performance, but false negatives may still arise due to cytoplasmic irregularities.  
     FISH surveys the DNA of a tumor for irregularities using a labeled probe, which makes this kind of assay very specific. A drawback to this method is that the sensitivity of this test is low and its interpretation is subjective (resulting in a high percentage of false-negatives) and requires analysis by a highly skilled cytogeneticist.
     Allele-specific RT-PCR surveys RNA expression of specific fusion events in the ALK gene. It is relatively inexpensive and highly sensitive, but allele-specific RT-PCR is limited because it does not detect all ALK Fusions, and in its inability to comprehensively detect uncharacterized NSCLC ALK fusions, with both leading to false negatives.
     Recent studies compared all three ALK detection methodologies and provided evidence that allele-specific RT-PCR was the most sensitive and least-subjective methodology. The Insight ALK Screen utilizes the advantages of allele-specific RT-PCR over the other methods while increasing sensitivity through proprietary detection of oncogenic ALK expression, much like the advantage of IHC, but at lower cost, faster time to result, and capability to multiplex with other tests.

CLP: How far along the R&D continuum is the company from releasing this test?
Hout: Insight Genetics and QIAGEN are collaborating on assay performance evaluation and clinical validation of the test, which will be marketed by QIAGEN as a companion diagnostic. QIAGEN plans to offer an RUO/CE ALK assay and will work toward an FDA-cleared IVD kit.  

CLP: Tell us more about R&D of a panel of companion diagnostics for the detection of RET, ROS1, and DEPDC1 mutations in NSCLC. What percentage of these patients are diagnosed with NSCLC, and how will you fill the void for identifying biomarkers so that patients can receive effective treatment?
Hout: Three mutually exclusive oncogenes, EGFR, KRAS, and ALK make up between 30% to 60% of all NSCLC cases.  Alternatively, oncogenic drivers such as ROS1 and RET fusions along with DEPDC1 over expression also have been identified as clearly recurrent, collectively constituting up to 9% of all NSCLC cases. Preclinical studies have demonstrated ROS1-driven cancers to be exquisitely sensitive to small-molecule tyrosine kinase inhibitors (TKIs) as well as Hsp90 inhibitors that are now under development by several pharma and biotech firms.
     Similarly, ambiguous TKI treatments also have been used against non-NSCLC RET and DEPDC1-driven cancers in ongoing Phase I and Phase II clinical trials with good efficacy. These trials should encourage numerous pharmaceutical companies to follow suit and conduct similar clinical trials using therapeutics specifically targeting RET- and DEPDC1-driven NSCLC cases. Unfortunately, no commercial diagnostic tests are readily available to reliably and efficiently diagnose ROS1, RET fusions, or DEPDC1 over-expression in NSCLC patients, so the objective of Insight Genetics’ R&D is to meet this need.

CLP: Are you working with Bayer (Nexavar® (sorafenib) for RET) or Pfizer (Xalkori® (crizotinib) that inhibits ROS1 and ALK) during the R&D process?
Hout: Insight Genetics is in discussion with several potential pharmaceutical partners that could benefit from the novel ALK and ROS1 assays in development at our company, but there are no developments we can disclose at this time.

CLP: Is there anything else you would like to share?
Hout: Less than 1% of current drugs have a companion diagnostic, and 60% of the drugs in clinical trials have a companion diagnostic in mind. To this end, Insight Genetics is developing novel approaches that will greatly improve patient care and also help differentiate pharmaceutical drugs in a time of high growth for targeted therapeutics.  

Judy O’Rourke is editor of CLP. For more information, e-mail her at [email protected]