Loxo Oncology work with Illumina to develop Cdx NGS assay for Larotrectinib (NTRK) and LOXO-292 (RET)

Anthony Magliocco MD

In an important announcement Industry sequencing leader Illumina and LOXO Oncology, released that they are working on developing a companion diagnostic for larotrectinib, a NTRK inhibitor and LOXO-292 which targets ret.

 

It appears that they intend to use the TST170 as a basis and perhaps a DX version of the Nexseq 500

This is an important development for 2 reasons. The first is the molecular alterations in question are relatively rare, but they can occur in any tumor type regardless of the tissue of origin. The second is the identification of a standard instrument platform and multi-gene assay panel that is already in clinical use (Moffitt has recently deployed a version of TST170 for patient care as Moffitt STAR) will undoubtedly expedite the capability to scale this test for widespread deployment accross laboratories

The fact that TST170 is so comprehensive potentially offers the opportunity for other oncology drug developers to consider using this versatile assay as a companion diagnostic as well.

https://ir.loxooncology.com/press-releases/loxo-oncology-and-illumina-to-partner-on-developing-next-generation-sequencing-based-pan-cancer-companion-diagnostics

STAMFORD, Conn. and SAN DIEGO, April 10, 2018 (GLOBE NEWSWIRE) —  Loxo Oncology (Nasdaq:LOXO) and Illumina, Inc. (Nasdaq:ILMN) today announced a global strategic partnership to develop and commercialize a multi-gene panel for broad tumor profiling, resulting in a distributable, next-generation sequencing (NGS) based companion diagnostic (CDx) with a pan-cancer indication. The co-development partnership will seek approval for a version of the Illumina TruSight Tumor 170 as a companion diagnostic (CDx) for Loxo Oncology’s larotrectinib, which targets NTRK gene fusions, and LOXO-292, which targets RET gene alterations, across tumor types.

TruSight Tumor 170 is a comprehensive, state-of-the-art, next-generation sequencing test that interrogates point mutations, fusions, amplifications and splice variants in 170 genes associated with common solid tumors. The CDx version of TruSight Tumor 170 will allow local laboratories to provide referring physicians with comprehensive genomic information, so that patients can be matched to the most appropriate therapeutic options. This version of TruSight Tumor 170 will run on the NextSeq 550Dx platform.

“We are leveraging our leadership in next-generation sequencing to deliver in-vitro diagnostic solutions to improve the management of cancer patients in the clinic,” said Garret Hampton, Ph.D., executive vice president of clinical genomics at Illumina. “To this end, we are partnering with leading biotechnology companies, such as Loxo Oncology, to develop companion diagnostics for best-in-class therapeutics. Distributable diagnostic solutions, such as a CDx version of TruSight Tumor 170, in combination with the NextSeq 550Dx platform, will enable labs to perform precision medicine testing in-house.”

Under the partnership, the companies will collaborate to validate a CDx version of TruSight Tumor 170 for NTRK fusions and RET fusions/mutations as a Class III FDA-approved diagnostic in conjunction with larotrectinib and LOXO-292, respectively. The companies are also planning to broaden the clinical utility of the full panel by obtaining regulatory approval for the other assay content, to be marketed as a tumor profiling test. Illumina will lead regulatory activities related to the Class III plans for NTRK and RET, the Class II plans for the tumor profiling content, and CE marking.

“We are very excited to announce this collaboration with Illumina, the world’s leader in NGS technology,” said Jacob Van Naarden, chief business officer of Loxo Oncology. “We have piloted numerous NGS assays, and the Illumina TruSight Tumor 170 assay has consistently demonstrated robust performance with its assessment of both DNA and RNA, including highly sensitive gene fusion detection. The broad 170-gene assay content has the potential to deliver meaningful insights from a single tumor specimen, identifying patients with NTRK fusions, RET fusions, RET mutations, and many other actionable tumor alterations. Furthermore, we believe that this collaboration will improve patient access to high-quality NGS testing because pathologists will be able to run TruSight Tumor 170 locally and receive reimbursement.”

FDA Approved PARP Inhibitor Rucaparib For Maintainance Treatment for Recurrent Ovarian Cancer Boosting Need for Clinical NGS Testing

By Anthony M Magliocco MD

On April 6, 2018, the Food and Drug Administration approved rucaparib (Rubraca®, Clovis Oncology Inc.), a poly ADP-ribose polymerase (PARP) inhibitor, for the maintenance treatment of recurrent epithelial ovarian, fallopian tube, or primary peritoneal cancer who are in a complete or partial response to platinum-based chemotherapy.      

Approval was based on ARIEL3 (NCT01968213), a randomized, double-blind, placebo-controlled trial in 561 patients with recurrent epithelial ovarian, fallopian tube, or primary peritoneal cancer who had been treated with at least two prior treatments of platinum-based chemotherapy and were in complete or partial response to the most recent platinum-based chemotherapy. Patients were randomized (2:1) to rucaparib 600 mg orally twice daily (n=372) or placebo (n=189) and were treated until disease progression or unacceptable toxicity. 

Tumor tissue samples were examined with a next-generation sequencing assay to determine whether DNA contained a deleterious somatic or germline BRCA mutation (tBRCA). This test was also used to determine the percentage of genomic loss of heterozygosity (LOH). Positive homologous recombination deficiency (HRD) status was defined as tBRCA-positive and/or LOH high. Three patient outcomes analyses were performed on the following groups: all patients, HRD subgroup, and tBRCA subgroup.

NGS ASSAY WAS REQUIRED TO IDENTIFY BRCA MUTATIONS

 

ARIEL3 demonstrated a statistically significant improvement in estimated median progression-free survival (PFS) assessed by investigator for patients randomized to rucaparib compared with placebo in all patients (median PFS 10.8 vs. 5.4 months, HR 0.36; 95% CI:0.30, 0.45; p<0.0001), in the HRD subgroup (median PFS 13.6 vs. 5.4 months, HR 0.32; 95% CI: 0.24, 0.42; p<0.0001), and in the tBRCA subgroup (median PFS 16.6 vs. 5.4 months, HR 0.23; 95% CI: 0.16, 0.34; p <0.0001).

 

The FDA also concurrently approved the complementary diagnostic test, FoundationFocusTM CDx BRCA LOH, for tumor samples to determine HRD status. 

In ARIEL3, the most common adverse reactions in at least 20% of patients treated with rucaparib included nausea, fatigue (including asthenia), abdominal pain/distension, rash, dysgeusia, anemia, ALT/AST elevation, constipation, vomiting, diarrhea, thrombocytopenia, nasopharyngitis/URI, stomatitis, decreased appetite, and neutropenia. Myelodysplastic syndrome and/or acute myeloid leukemia occurred in 7 of 372 (1.9%) patients treated with rucaparib and in 1 of 189 (0.5%) patients assigned to placebo. Discontinuation due to adverse reactions occurred in 15% of patients receiving rucaparib and 2% of those assigned to placebo. 

The recommended rucaparib dose is 600 mg (two 300 mg tablets) taken orally twice daily with or without food.

FDA granted this application priority review. A description of FDA expedited programs is in the Guidance for Industry: Expedited Programs for Serious Conditions-Drugs and Biologics, available at:

 

This approval is another example of the exploding need to broad access to next generation sequencing in routine clinical care of cancer patients forming the foundational basis of personalized oncology

” This most recent approval of yet another therapeutic advance that is reliant on NGS for patient selection further increases the urgency for access to routine NGS for all cancer patients”  – Anthony M Magliocco MD

The Moffitt Morsani Laboratories have developed and launched a new NGS assay ‘Moffitt STAR(TM)” that covers the key actionable target genes including BRCA1 and BRCA2

Moffitt STAR NGS panel covers the key mutations

PierianDx Customer, Moffitt Cancer Center, Launches Clinical NGS Assay, STAR

VISIT MOFFITT CANCER CENTER WEBSITE

http://www.moffitt.org

 

New Mechanism Involving NFkappaB Drives Metastasis in Cancer with Chromosomal Instability

By Anthony M Magliocco MD

An interesting and important new study recently published in Nature gives new insights into possible targetable molecular mechanism linking chromosomal instability observed in some cancers and progession and metastasis.

https://www.nature.com/articles/nature25432

A subset of cancers develop chromosomal instability via disjunction errors during mitosis. This can lead to highly aneuploid and abnormal karyotypes more prevalent in certain cancers than other. For example, ovarian cancer is notorious for developing a  disrupted and unstable karyotype.

Metastatic Cancer

It appears that chromosomal instability in itself does not promote metastasis, however, in an intriguing observation it was noted that tumors with chromosomal instability also developed micronuclei when under mechanical stress.

These micronuclei are more prone to cytoplasmic rupture. Free DNA in the cytoplasm triggers a non-canonical NFkappaB cascade which may lead to mesenchymal transformation and a propensity to metastasis.

Interestingly cancers with high aneuploidy do not generally develop a high mutational burden such as cancers like melanoma. Nor do they tend to have targetable driver mutations.

“Cytosolic DNA from micronuclear rupture appears to trigger non-cannonical NFKappaB signaling which could lead to tumor metastasis”

 

DNA in the cytoplasm triggers NFKappaB as part of a host response to viral infection, but cancer may subvert this mechanism. In addition,  NFkappaB non-cannonical activation by cytosolic DNA from ruptured micronuclei may lead to a variety of effects immune activation which could assist with tumor metastasis.

These new insights into the consequences of chromosomal instability create opportunities for developing new therapeutic strategies for these types of cancer that lack specific driver mutations and significant neoantigen loads

 

Moffitt Cancer Center Morsani Molecular Lab Researchers Create New Laboratory Test to Better Diagnose Metastatic Bladder Cancer

Moffitt researchers reported the discovery of a new 19 gene expression signature that appears to have value in improving the accuracy of urothelial cancer diagnosis at the USCAP 2018 meeting in Vancouver.

The correct diagnosis of urothelial cancer, especially when metastatic can be very challenging for the surgical pathologist Urothelial carcinoma (UC) can mimic a poorly squamous cell carcinoma (SCC) and it may be difficult to distinguish the two especially in metastatic sites.

Metastatic cancer imaged with PET scan

 

It is important to distinguish the two cancers for proper patient management. These two cancers have an overlapping immunohistochemical profile (both positive for CK5/6, CK7, p63 and p40). GATA3 although relatively specific for UC, can also be expressed in SCC.

It is important to distinguish urothelial carcinoma from other epithelial cancers to ensure proper diagnosis and patient managment

Gene expression analysis is a powerful method that can measure the expression level of thousands of mRNA messages simultaneously in a tissue biopsy specimen. Analysis of data from this technique, when coupled with bioinformatics analysis can produce powerful classification algorithms which could be used in a CLIA laboratory to improve the accuracy of current diagnostic approaches.

Affymetrix chips for rapid gene expression

The Moffitt researchers analyzed 161 UC, 38 head and neck cases, and 268 lung cancer SCC cases from Moffitts Total Cancer Care (TCC) database to create the initial algorithm. The data was collected on the a specially modified HuRSTA chip containing 60607 probe sets covering 26356 genes. An algorithm was developed from the 19 top most differentially expressed genes using principal component analysis (PCA). The PCA model performed at above 98% sensitivity and specificity correctly identifying the histological origin of the specimens on self validation.

PCA analysis separating tumor types using 19 gene signature

The signature was further validated on publicly available external datasets at GEO datasets, with 96 cases of H&N SCC from GSE31056, 18 lung SCCs from GSE10245 and 93 UC from GSE31684, total of 207 cases.This signature correctly identified 112 of the 114 publicly available SCCs with gene data (96 H&N and 16 lung) as SCC and all of 93 publicly available UCs with gene data as UC

The identification of a gene classification algorithm will enable improved classification of these challenging lesions, particularly in the metastatic setting.

The Moffitt investigators will continue to evaluate this new signature and propose to develop it into a routine diagnostic assay. In addition, deeper understanding of the molecular basis of urothelial cancer and how it differs at the molecular level potentially opens new approaches to therapy.

An assay like this could be far superior than classical IHC as the complexity of gene expression will give multiple insights into not only tissue of orign but also other aspects of the cancer biology such as immune status.

Understanding the molecular basis of urothelial cancer will provide insights into novel treatment opportunity

The work was supported by the Moffitt Morsani Molecular Laboratories

Presented at the 2018 USCAP meeting in Vancouver Canada

Gene Biomarker Signature for Distinguishing Urothelial Carcinoma from Squamous Cell Carcinoma. Jasreman Dhillon, MD Yin Xiong, Ph.D. Anthony Magliocco, MD, Soner Altiok, MD, PhD, H. Lee Moffitt Cancer Center, Tampa FL

MOFFITT NGS STAR* Enters Clinical Service

Moffitt’s latest NGS sequencing assay the Moffitt STAR (Solid Tumor Actionable Result) panel was validated by the Moffitt Morsani Molecular Laboratory and launched into service this month at the busy Florida Comprehensive Cancer Center in Tampa.

The assay is based on Illumina’s TruSight Tumor 170 assay which is a next-generation sequencing assay designed to cover 170 genes that are commonly designated as drivers in solid tumors. The assay evaluates both DNA and RNA and focuses on detecting actionable mutations which include SNV, dels, insertions, amplifications, and translocations. Such alterations are the target for many new targetable therapies including anti-EGFR agents, anti BRAF therapies and treatments targeting the Tropomyosin Receptor Kinase fusions (TRK) such as Larotrectinib.

Many key actionable mutations only occur rarely, making detection by single marker tests problematic and wasteful. However, the Moffitt STAR assay now allows the Moffitt molecular laboratory to screen patient tumors for multiple targetable mutations efficiently in a single test using a relatively small amount of nucleic acid extracted from routine formalin fixed, paraffin embedded tissues (FFPE). This important advance enables the Moffitt molecular diagnostic laboratory to effectively evaluate a patient for eligibility to receive treatment with a FDA approved targeted therapy, or be considered for clinical trial enrollment. Moffitt STAR is essentially an “All in one” test that can provide multiple functions.

Moffitt NGS STAR* is an exciting new “all in one” technology advance for Moffitt Cancer Center patients enabling rapid assessment of their tumors for presence of key mutations directing selection of effective approved targeted therapies or for qualification to enroll in the latest generation of clinical trials

Evidence is also emerging the assay, despite its mid size, Moffitt STAR could also reliably measure tumor mutational load and microsatellite instability. These molecular features are often associated with potential response to the latest immune check point inhibitors such as Pembrolizumab which has recently received FDA approval for use in tumors with high microsatellite instability.

Moffitt NGS STAR also provides information on tumor mutational burden and microsatellite instability- key features which may drive patient response to the latest immuno-oncology check point inhibitor therapies

Moffitt NGS STAR can also detect mutations in BRCA genes, a molecular feature that may predict response to parp inhibitors such as olaparib.

Moffitt NGS STAR can be performed on as little as 40ng of input nucleic acid.

Development and launch of Moffitt NGS STAR was made possible through collaboration with industry partners PierianDx and Illumina Inc.

The Moffitt Cancer center is one of the largest in the United States, is consistently ranked in the top cancer centers by U.S. News & World Report. Moffitt Cancer Center has a mission to “contribute to the prevention and cure of cancer” and the vision ” to transform cancer care through service, science, and partnership”

For further details contact anthony.magliocco@moffitt.org