Q&A with Pravin J. Mishra, PhD
Director, Research and Development Center
Intermountain Precision Genomics
Intermountain Healthcare

MedicalLab Management: What are your laboratory’s therapeutic initiatives and goals, including the use of next generation sequencing?
Pravin Mishra: Intermountain Healthcare is internationally recognized as a highly regarded health care system, and in perpetuating this reputation, Intermountain initiated a precision medicine program to provide our patients with individualized cancer treatment. In order to deliver novel insights into the biology of disease, identify de novo targets, and benefit patients, our laboratory is motivated to interrogate new methodologies and technologies incorporating a bench-to-bedside approach (ie, research to clinic).

Cancer is known to be predominantly a genetic disease, and the recent development in next generation sequencing (NGS) technologies has made it possible to not only help patients with a clearer vision of the existing knowledge base, but also in the discovery of new cancer cell mutations. Thus, the overall goals of the Research and Development Center revolve around finding new avenues for more effective cancer therapies. These avenues include the utilization of genomics, epigenomics, proteomics, metabolomics, pharmacogenomics, immunology-based approaches, and other cutting edge technologies, such as genetic editing.

MLM: Is your practice targeting specific cancers using DNA extraction?
Dr. Mishra: We provide end-to-end service for all types of cancer (solid and liquid), including processes spanning DNA extraction to comprehensive interpretation and reporting. In the next few months, Intermountain Precision Genomics plans to offer this type of service for patients diagnosed with myeloid malignancies (including myeloproliferative neoplasms, myelodysplastic syndromes, and chronic myelomonocytic leukemia) and acute myeloid leukemia (AML) stages.

MLM: In terms of your practice, what does the relationship among NGS, molecular characterization, and liquid biopsies represent?
Dr. Mishra: A contemporary analogy could be the now fairly universal use of GPS systems in our vehicles. These navigation systems are so remarkably precise because they are fed a constant stream of multiple, real-time layers of information (eg, coordinates, images, traffic information, etc), or, to use a popular term: big data.

In health care, and in cancer treatment specifically, the best-case scenario is to comprise the multiple layers of information derived from the above-mentioned practices (genomics, epigenomics, and other fruitful ‘omic’ streams) in manipulating both solid and liquid biopsies in conjunction with other molecular assays and analytics, and then stream that information to clinicians in some semblance of real time. This would realize the promise of precise and patient-specific methods for treating cancer with a reduction in drug driven side effects, radiation, and mortality rates.

I see health care moving away from intuition-based to evidence-based therapy prescription, and as precision medicine practices continue to develop rapidly, we are witnessing the integration of artificial intelligence navigation with algorithm-based drug development and therapy prescription.

MLM: How have you integrated NGS technology into your lab?
Dr. Mishra: We have access to the latest technologies to support DNA and RNA sequencing efforts, including high-throughput genomic sequencing, droplet-digital PCR, QPCR, robotics, and imaging. We also recently purchased and implemented instruments to perform whole genome sequencing. In the lab, we validate findings and perform orthogonal comparison for our new assays using mass spectrometry and other instruments, which also allow us to develop small panels, such as a cancer panel that covers more than 300 somatic mutations in 4 key oncogenes observed in lung, colorectal, and metastatic tumors, including EGFR, KRAS, NRAS, and BRAF.

MLM: Where does your lab stand operationally regarding the utilization of liquid biopsies from a clinical standpoint?
Dr. Mishra: We are optimizing NGS and PCR based assays, both for prognosis and for tumor monitoring purposes. To put this assay into production, along with establishing clinical utility, we will soon be confirming our assay’s sensitivity, specificity, and reproducibility. Our oncologists understand the vast potential of precision medicine, and I am seeing this trend in other health care systems as well.

Just two decades ago, the majority of cancer types were discovered and treated in a completely different way. As we are detecting and learning about more targets, we are approaching and treating cancer in a more customized, educated way. It is only a matter of time before all cancer treatment facilities begin adapting their procedures to explore liquid biopsies (many are already in some stage of this transition), deriving molecular information from those samples, and providing their patients with minimally invasive procedures to treat their cancer.

MLM: What benefits to your practice do you expect from the utilization of liquid biopsies?
Dr. Mishra: Liquid biopsy is a noninvasive procedure (a blood draw, for example), and studies suggest the potential of replacing tumor tissue biopsy with liquid biopsy without compromising molecular details. Given the profundity of evidence-based medicine, I expect it would be fairly straightforward for oncology laboratorians and pathologists to convince clinical oncologists to request sequencing of cell-free circulating tumor DNA rather than biopsy a tissue derived specimen. To wit, liquid biopsy sequencing holds clear advantages over tissue biopsies:

• Liquid-biopsy-derived DNA is usually fresh and not fixed or otherwise compromised, as can be the case with tissue biopsy.
• There are multiple ways to assess tumor samples using liquid biopsies:
  • Use of cell-free DNA (cfDNA), which may be derived from normal cells
  • Use of circulating tumor DNA (ctDNA), which is circulating DNA in the bloodstream derived from necrotic or apoptotic cancer cells
  • Use of circulating tumor cells (CTCs), which are viable cancer cells in the blood stream
  • Use of cell-free RNA (cfRNA), which includes microRNAs, also an excellent source of genetic information

These are notable resources that can be detected not only in blood, but also in urine, saliva, and cerebrospinal fluids. To take advantage of this, at Intermountain Precision Genomics, we are engaged in developing assays around all types of liquid biopsies. Easy access to patient bodily fluids will help us (and the scientific community at large) to investigate a greater variety of biomarkers and begin understanding the source of cancer and its evolution at a more rapid pace. Liquid biopsy as a rapid genotyping approach is more reliable than tissue biopsy and has significant potential to change the way we practice medicine.

MLM: What challenges or additional services are you hoping to address via NGS and liquid biopsy technology?
Dr. Mishra: Transitioning to blood-based biopsy testing, and thereby reducing or eliminating the need for surgical procedures to acquire tissue samples, will help us address several key elements of tumor biology in an expedited way, including clonal evolution, tumor heterogeneity, and tumor resistance. Of particular note, liquid-biopsy-based tumor monitoring will allow for rapid tumor surveillance, and this close observation enables a nimble response to disease recurrence and greater insight into therapy response. At present, we are developing customized assays to longitudinally monitor tumor progression, and to learn more about biomarkers of response as well as mechanisms of drug resistance.

MLM: What challenges remain to improve utilization of liquid biopsies in clinical cancer care?
Dr. Mishra: Ultimately, liquid biopsies help to identify treatment failures at an early stage and therefore would spare patients costly hospital visits, unnecessary side effects, CT/PET scan based imaging, and radiation exposure. Technological advances in detecting and isolating CTCs/cfDNA/cfRNA efficiently will allow us to validate/transition existing variants of unknown significance and de novo targets into actionable (therapeutically targetable variant) categories. With plummeting technology costs, relatively easy access to and availability of bodily fluid, we would be able to comprehensively understand metastatic mechanisms and learn more about migratory/developmental pattern of this disease. In a few years, such information collectively will advance the precision medicine field and help cancer patients at any stage of this vicious disease.

Pravin J. Mishra, MS, PhD, is director of the Research and Development Center at Intermountain Precision Genomics, part of Intermountain Healthcare, where he oversees laboratory operations and leads discovery and innovation efforts in precision medicine and oncology. Pravin earned his PhD in molecular medicine and oncology from George Washington University and has developed subject expertise in oncology, stem cells, cancer genomics, drug discovery, and developmental therapeutics. His research efforts at NIH led to the discovery of signature biomarkers that can predict late-stage melanoma patient survival and he has published several key findings in cancer, genomics, and wound healing, including a highly cited study of mesenchymal stem cells’ role in tumor growth. Pravin is the recipient of the National Cancer Institute Director’s Award, awarded by Nobel Award-winner Dr. Harold Varmus.