Morsani Molecular Lab at Moffitt Cancer Center is Central to its Personalized Oncology Mission

By Anthony M Magliocco MD

Moffitt Cancer Center, the largest and only NCI designated comprehensive cancer center in Florida and one of the largest in the country has been rapidly expanding its capabilities in molecular diagnostics with a clear focus on supporting its burgeoning personalized oncology programs which are led by internationally recognized expert Dr Howard McLeod.

It became clear several years ago that a huge revolution was coming in the area of personalized oncology and cancer treatments. That revolution is now here.

Explosive advances and numerous FDA approvals for new targeted therapies have emerged for treating and controlling once universal killers such as metastatic melanoma and advanced lung cancer.

These targeted therapy medicines, include vemurafenib targeting mutant BRAF, Erlotinib for EGFR mutant lung cancer, and crizontinib targeting ALK translocations. Further truly dramatic results have been seen with immunotherapy treatments such as the anti PDL-1 immune checkpoint inhibitor pembrolizumab for treatment of a variety of advanced cancers that over express the protein PDL-1 or carry MSI. More recently approvals of NTRK inibitors Larotrectinib and the PARP inhibitor Olaparib for BRCA mutant cancer have further increased demand for specialized testing as both of these treatments have companion diagnostic requirements

 

Immune cells (red and blue) surround a invasive cancer cells (green)

The approval of many new targeted treatments requiring companion biomarker evaluation is providing impetus to develop more advanced diagnostic technology including new cellular imaging methods

These rapid advances in treatment options hinge on the availability of routine, high quality, clinical grade, molecular analysis and diagnosis to properly identify patients who will be most likely to benefit from these costly and frequently toxic treatments.

The Morsani Molecular Laboratories were created to facilitate the rapid development and implementation of new molecular diagnostic assays into the routine CLIA laboratory at Moffitt

Moffitt leadership and its generous philanthropic doners and foundation laid the important cornerstone of the Moffitt Morsani Molecular Laboratories. Under the direction of Dr Magliocco, the laboratories had a singular mission to rapidly develop and deploy the advanced clinical grade diagnostic services necessary to support Moffitts rapidly maturing personalized medicine program.

The Laboratories were initially opened in 2012 and were first equipped with Mass array instruments and conventional Sanger sequencing, pyrosequencing and routine PCR ability. The decision was made to recruit PhD scientists who would help develop the new assays to a CLIA standard and then launch them into a “routine” production laboratory.

The demand from the Moffitt clincal services was high, especially from thoracic oncology, a ground breaking team offering a multitude of clinical trail options for Moffitt patients. This demand required that the assays be CLIA grade, complex and delivered in a rapid way.

This was very challenging. Launching a highly multiplex assay into a CLIA lab is not a trivial matter. The assay must be calibrated to show sensitivity, specificity, analytical performance, range, precision, accuracy and many other technical components. Further, any new assay must also be put through its paces to show its robustness and reproducibility when handled by different scientists and technologists.

Launching new assays into CLIA labs is not trivial and requires extensive expertise and investments

We initially chose to launch the LungCarta (TM) Mass Array Panel from Sequenom. This was very challenging to validate as it contained individual assays run in multiplex to assay over 213 distinct mutations. as these were separate mutations and assays, the decision was made to only validate the most clinically important ones, namely BRAF V600E, KRAS, EGFR, and PIK3CA. The next issue was obtaining appropriate clinical reference materials to validate these assays. Fortunately with Moffitt’s very high clinical volume, previous experience with single-plex testing, and availability of Total Cancer Care Protocol tumor bank which houses data and specimens from over 400,000 patients it was possible to obtain the necessary control and case materials to validate and launch the assays into clinical service.

The development of a CLIA assay requires access to appropriately characterized reference materials to enable clinical validation of the process and assay results.

Although the complete 213 mutation panel was run, only the CLIA validated assay results were reported to the treating physician. The remaining results were ported into Moffitt’s data warehouse for storage and use in properly approved research studies. Following the launch of the LungCarta assay, the Morsani Molecular laboratory also launched assays for melanoma, and a specially constructed Glioma panel assay.

 

In 2014, clinical demands for even more complex sequencing arose for proper management of Myelodysplastic Syndrome (MDS) mounted. The hematology team needed access to over 30 genes and potentially thousands of mutations. It was time for the big guns, time for next generation sequencing. At the same time Moffitt molecular pathologists also saw increasing needs for more complex sequencing for solid tumors as well. After careful discussions and further evaluations it was decided to begin next generation sequencing. Following some debate, the consensus was to start with Illumina, given their long history in next gen sequencing and also the experience with the technology in Moffitt’s core genetic research laboratory. It was decided to develop an off the shelf 26 gene panel TST26 that covered most of the key mutations in lung cancer and in melanoma. In addition Moffitt CLIA scientists, molecular pathologists, and clinicians worked with Illumina to design a 32 gene myeloid NGS panel.

Bringing on NGS brought new challenges of a complex wet lab and also a very complex bioinformatics dry lab. At Moffitt we worked with PierianDx who helped design bioinformatics pipelines and an efficient validation program for both the wet and dry lab as well as an information system – a genome workbench- which allows molecular pathologists to rapidly review cases and access a knowledge database to enable rapid sign out. We also required access to numerous control samples to validate the assays. Again these came from Moffitts vast biospecimen resources and also Horizon Discovery, a company specializing the the provision of reference materials for clinical validations. To date Moffitt has run over 10,000 NGS assays.

By 2017, clinical demands continued to mount for even more complex testing. There were new drugs approved that needed to evaluate fusions, “exon skipping” mutations, and even MSI and tumor mutational burden. With these demands, we turned to illuminas TST170 assay, a new type of sequencing assay that had both DNA and RNA. In addition the assay was designed with “actionable targets” in mind. Meaning, that targeted agents in clinical trials were scrutinized to determine the collection of genes and mutations that would likely be most informative for treatment selection in solid tumor oncology. This approach makes the assay very useful and practical for deployment in a busy cancer center where multiple trials are underway and complex patients with unusual cancers are presenting. Moffitts Morsani molecular team worked hard and spent several months validating the assay to bring it to acceptable CLIA standard finally launching it as “Moffitt STAR” an assay to screen for actionable mutations.

Since its launch, demand has been exceptionally high with hundreds of physician orders in the first week alone.

 

Moffitt laboratories continue to work closely with the worlds leading oncologists and pharma and technology companies to ensure that Moffitt Patients always have access to the latest diagnostic tools to enable them access to the most current treatment options.

That is what makes Moffitt an exceptional hospital for cancer patients seeking innovative treatments and explains why Moffitt has some of the best cancer outcome response rates in the country.

 

New Window into Brain Metastasis Using Modified CTC and cfDNA Technologies

Anthony M Magliocco MD

Many cancers metastasize to the central nervous system including the brain and its coverings, the leptomeninges. These cancers are difficult to treat and monitor. The so called “liquid biopsy” is making excellent progress in monitoring disease progression and response using blood samples in patients with disseminated solid tumors. In this technique, either circulating tumor cells (CTCs), or cell free DNA (cfDNA) can be harvested and captured for analysis.

These new “real time” monitoring methods create a new opportunity to monitor cancer progression and evolution while patients are actually under therapy- for example are the number of circulating tumor cells increasing, or is their phenotype evolving into something different.

For example, metastatic breast cancer cells may change their receptor status to go from estrogen receptor positive to negative, or they may acquire a new targetable change, for example acquiring HER2 over expression.

Images of circulating tumor cells captured in the Cell Search System

Intact tumor cells might also allow for examination of activation of signalling cascades and perhaps a pharmacodynamic read out.  One of the challenges of CTCs is their extreme fragility- with current method they generally need to be captured and examined within 48-72 hours. These cells also tend to be exquisitely rare, especially in early stage disease raising questions as to how representative they may be of the systemic disease.

 

Cell Free DNA cfDNA

A complementary assay method,  the measurement of cell free DNA (or cfDNA), provides a new application for monitoring cfDNA in patients. It has found widespread use monitoring lung cancer patients for the development of tyrosine kinase resistance while under therapy.  A common mechanism of resistance is the the switch or evolution to EGFR T790M mutation that portends the looming end of response to first generation TKI drugs and an opportunity to intervene with a switch to the 3rd generation Osimertinib therapy.

Liquid Biopsy is a powerful method to enable real time monitoring of solid tumor evolution and response to therapy using a blood sample to cature CTCs and cfDNA. Unfortunately, this does not typically work for CNS tumors due to the blood brain barrier

Unfortunately tumors occurring or metastasizing to the CNS are not easily followed by blood tests due to the presence of the blood brain barrier. However, these tumors are in contact with the cerebrospinal fluid, a specialized liquid that circulates around the brain cushioning it.

This fluid can be extracted in small amounts for analysis using a spinal tap, or in some cases of patients with malignancy an in-dwelling catheter is placed to enable CSF to be drained off to reduce the central nervous system pressure. This CSF fluid is traditionally sent to pathology for cytopathology analysis. Unfortunately standardized cytopathology methods do not lend themselves to evaluation of rare cells and molecular events in CSF.

 

Because CSF is very similar to blood, we reasoned that liquid biopsy methods used for blood samples might be potentially adapted for use on CSF samples. Recently, the Moffitt teams of the Neuro Oncology group, led by Dr Peter Forsyth and the Morsani Molecular Laboratory teamed up to attempt to modify the liquid biopsy procedures currently used for blood to adapt for CSF.

The current CTC platform in use at the Morsani Molecular Laboratory at Moffitt is the CellSearch system which is designed for magnetic capture of EPCAM expressing carcinoma cells in blood followed by evaluation of keratin expression in an automated scanning step with exclusion of non- specific cells using stains for nuclei and lymphocytes.

The adaptation of this system for analysis of melanoma in CSF was not trivial, as the volume of CSF is significantly less requiring adjustments on the liquid handling approaches. Further, the Neuroncology team was particularly interested in metastatic and primary melanomas of the central nervous system. This required changing capture antibodies to CD146 which targets melanoma and visualization with MelPE.

The Moffitt Morsani Molecular Laboratory has Developed New Methods to Monitor Melanoma in the CSF using both CTCs and cfDNA approaches

We also determined that DNA could be extracted and sequenced from CSF using both the NGS sequencing methods and MassArray systems. Further, we determined that melanoma cells captured from CSF can be grown ex-vivo and cultured for further analysis.

These advances create new opportunities to apply advances from personalized oncology to patients with metastatic melanoma in the CSF and central nervous system enabling potential real time adaptation of treatment strategies based on directly monitoring tumor molecular responsiveness to therapy in real time \\.

REFERENCES

Fedorenko IV, Evernden B, Kenchappa RS, et al. A rare case of leptomeningeal carcinomatosis in a patient with uveal melanoma: case report and review of literature. Melanoma research. 2016;26(5):481-486. doi:10.1097/CMR.0000000000000274.

Neuro-Oncology, Volume 19, Issue suppl_6, 6 November 2017, Pages vi46,https://doi.org/10.1093/neuonc/nox168.183 Published: 06 November 2017