Highlights from the Molecular Medicine Tri-Conference
In planning for this year’s Molecular Medicine Tri-Conference (MMTC), I was looking forward to a number of sessions that focused on liquid biopsy and was not disappointed.
Liquid biopsy and circulating tumor cells (CTCs) are areas of intense activity for many of Invetech’s clients and the sessions offered a number of opportunities to learn more about this emerging technology from recognized industry leaders. I was also inspired by many other hot topic conference sessions, including next generation sequencing and molecular diagnostics being adopted into standard clinical protocols. Below are some highlights from what is always a fascinating event.
Bringing liquid biopsy to clinical practice
What better place to start my liquid biopsy journey than hearing from the man who coined the term.
About six years ago, Dr. Klaus Pantel first used the phrase “liquid biopsy” in a paper in which biomarkers such as circulating tumor DNA (ctDNA), miRNA, tumor-educated platelets, exosomes and CTCs were shown to contribute to tumor biology and demonstrated the clinical utility of these biomarkers in early detection and screening for cancer recurrence.
Dr. Pantel discussed the many technologies utilizing liquid biopsy that are increasingly used today for applications that include detection of cancer recurrence, estimating the risk for metastatic relapse or progression, stratification and real-time monitoring of therapies, identification of therapeutic targets and resistance mechanisms and understanding the biology of metastatic development.
However, Dr. Pantel proposed that the most impactful application for liquid biopsy may be the real-time detection of metastatic cells many years after the original primary tumor resection, and characterizing new mutation profiles for the detected cells. After treatment, the primary tumor will change composition, and profiling blood-based biomarkers by liquid biopsy methods can reveal representative information about these metastatic cells that may spread to new sites in the body.
Using liquid biopsy to monitor patients for early detection of cancer recurrence—and any changes to these cells that may affect therapy decisions—can be critically important for improving cancer survival. For example, detecting Estrogen Receptor (ER) negative CTCs from an ER positive primary tumor patient provides actionable information for therapy decisions as ER negative CTCs may survive endocrine therapy and allow the spread of the primary tumor to other areas of the body.
Moreover, other liquid biopsy approaches, such as cell-free DNA (cfDNA), can inform the decision between chemotherapy and immunotherapy and track therapy efficacy. If a particular therapy is effective, then most primary tumor cells and/or metastatic sites are killed and release DNA into the blood; whereas if a therapy fails, then most primary tumor cells and/or metastatic sites survive and can disseminate into the blood and little circulating DNA is found.
Spit matters! Sample for diagnostic analysis that does not require blood draw
Dr. Stephen D. Andrews and Dr. Manasi Jain of Abogen gave a thoroughly engaging presentation about liquid biopsy applications utilizing saliva—which they have determined to be a valuable source of cfDNA/cfRNA, proteins, microorganisms, hormones and cells. Their key findings are that saliva is a lot more similar to blood as an analysis sample than commonly realized and yet is only used in a limited number of applications.
Abogen’s proprietary technology is the first to enable the collection, preservation and isolation of ALL components found in saliva. Their company mission is to shift the medical paradigm away from blood collections and frequent hospital visits for routine testing to a more patient-friendly home-based collection of oral fluids.
What’s really impressive is that this non-invasive technology has been developed to be temperature insensitive, with collected saliva components remaining stable for months at a wide range of temperatures to enable many different sample collection scenarios. Abogen’s technology enables more than 85 percent of the currently run standard blood tests to be performed accurately in addition to epigenetics, cfDNA, cellular and cancer diagnostics, as well as distinguishing between bacterial and viral infections.
Exosomes: The holy grail of liquid biopsy
Dr. Johan Skog of ExosomeDx discussed how interrogating all blood marker components is essential to realize the full potential of liquid biopsy applications, which includes cfDNA, CTCs and exosomes. Exosomes, for example, contain an optimal source of stable RNA, tumor specific proteins, and DNA, and so are mini representations of the tumor-specific biology.
Dr. Skog stressed that the platform including assay and detection system used for exosome applications matters as some assays yield 100-fold less DNA and RNA and are less sensitive when compared to ExosomeDx’s platform. Their research demonstrates that specific disease exosomes showed different ID signatures for patients with treatment versus progressive disease and differential changes of exosomal transcriptome in responders versus non-responders. If you capture more quality DNA and RNA, more markers can be identified and assessed, resulting in a higher negative predictive value for the testing results.
The conclusion was that exosomes can add valuable information for more complete monitoring of the treatment response.
Platelet cloaking, cancer cells and CTCs
The concept of platelet cloaking as presented by Dr. John O’Leary, Chair, Pathology at Trinity College Dublin, was both fascinating and provocative. The observations by Dr. O’Leary’s team demonstrated CTCs coated with platelets, which enables the cells to be refractive to therapy. As a result, the coated CTCs can more effectively initiate a metastatic cascade to enable recurrence of a primary tumor elsewhere in a patient.
Dr. O’Leary has observed platelet cloaking of CTCs in every cancer patient, although not every CTC is cloaked in these patients. Those cloaked cells are more protected against shear forces in the blood which normally destroy many ‘naked’ CTCs, and so the survival rate of these cells is increased, even in the absence of therapy. The cloak further inhibits immune surveillance by making the CTCs invisible to natural killer cells with a kind of “immune decoy mechanism.”
The current standard method of identifying CTCs via common markers, such as pan-cytokeratin positive and CD45 negative, presents challenges when CTCs are platelet cloaked. There can be a loss of epithelial markers such as cytokeratins, and selecting for those markers can miss detecting the biology/metastatic potential of the CTCs. In clinical samples of CTCs stained for platelet visualization, Dr. O’Leary commented that cloaked CTCs become more ‘sticky’, and clusters of these cells may represent a more aggressive form of cancer. Using a method to visualize CTCs that are cloaked with platelets—in addition to standard protocols—could enable identification, characterization and enumeration of clinically relevant CTCs, and enable better understanding of a patient’s status and prognosis.
The discovery of this phenomenon helps explain some treatment failures and the challenges of being able to identify certain CTCs. Interestingly, recent studies of patients with platelet cloaks treated with aspirin showed mitigation of the platelet cloaking and reduced metastatic potential of the CTCs.
Translating rapid whole genome sequences into precision medicine for babies in intensive care nurseries
Dr. Stephen Kingsmore of Rady Children’s Hospital in San Diego presented a compelling case study about translating whole genome sequencing into routine precision medicine, in this instance for critically ill infants.
Genetic diseases are the number one cause of death in newborns in intensive care units. Rapid genome sequencing (STATseq) developed by Dr. Kingsmore’s team has demonstrated the potential to routinely diagnose genetic diseases in newborns within 26 hours. The future challenge will be scaling the STATseq protocol to enable sequencing of thousands of acutely ill newborns, followed by implementation of precision care plans that improve outcomes. This is uncharted territory in current clinical practice.
The case study presented described a critically ill 30-day old infant at the Rady Children’s neonatal intensive-care unit (NICU) suffering from acute liver failure, on a respirator and failing to thrive. Genetic disease was suspected with a prognosis of one week to live. A traditional diagnostic approach of cascading testing protocols requiring a week or more to inform diagnosis and treatment would not be practical in such a scenario. Instead, the Rady Genomics Medicine Team applied their in-house developed accelerated sequencing and analysis protocol that enabled actionable information and treatment within 26 hours.
Genomes for both parents plus baby were sequenced and analyzed within 24 hours after collection of the blood samples. What followed was largely a computational phase narrowing down a wealth of sequence information to two clinically relevant mutations. Within 26 hours, the diagnosis was completed showing that the infant was heterozygous for mutations on the Prf1 gene, causing Hemophagocytic Lymphohistiocytosis (HLH Syndrome). Treatment protocols were implemented and the child is now 32 months old with normal liver function and no recurring symptoms of HLH.
Additional highlights that merit mention include the panel discussion on commercialization of various liquid biopsy technologies with Dr. Steven Soper (BioFluidica), Dr. Murali Prahalad (Epic Sciences), Dr. Veena Singh (Biocept) and Dr. Farideh Bischoff (Silicon Biosystems).
Dr. Cloud Paweletz‘s presentation on using blood to monitor cancer and the panel discussion Dr. Paweletz chaired that discussed clinical implementation of cfDNA.
Lastly, I would like to mention the infectious disease Point of Care cartridge technology presented by Dr. Anna Dixon (Atlas Genetics Limited) that addresses an important need/niche for faster results to enable same visit treatment for young adults.
As a former laboratorian, and now a molecular biologist at Invetech, attending this important molecular medicine conference provided me with actionable learnings about emerging technologies in molecular medicine and diagnostics. Leading researchers are bringing these technologies to commercialization, providing new approaches to the diagnosis and prognosis of important genetic and infectious diseases, as well as cancer.
Rebecca Newman is an Associate Principal Scientist at Invetech based in our Melbourne office.