Caris Life Sciences and Debiopharm Collaborate in the Development of Companion Diagnostic

Doctor consulting with a patient, working on diagnostic examination.
Doctor consulting with a patient, working on diagnostic examination.

Caris Life Sciences and Debiopharm have entered into a strategic collaboration with for the development of a companion diagnostic (CDx) test using its newly-launched Whole Transcriptome Sequencing (WTS) assay for mRNA analysis called MI Transcriptome™. The assay, which was granted Breakthrough Device Designation by the U.S. Food and Drug Administration (FDA) in early May, reliably detects rare fibroblast growth factor receptor (FGFR1, FGFR2 and FGFR3) fusion events.

MI Transcriptome uses the capabilities of high-throughput sequencing to gain insight into the RNA profiles of patients’ tumors.

RNA-based sequencing analysis is considered the best method to detect clinically relevant aberrations, because the presence of RNA transcripts ensures that the alterations have been transcribed from DNA to RNA.

W. Michael Korn, MD., Chief Medical Officer, Caris Life Sciences. In this role, Korn guides Caris’ research efforts and clinical strategies for innovative precision medicine tools and tumor profiling services. His executive oversight responsibilities include medical affairs, evidence cultivation and the Caris Research Institute, which has produced more than 150 posters/presentations at major medical conferences and over 50 peer-reviewed publications since 2014.

“This agreement supports our vision for optimizing the detection of rare fusion events using RNA, and building value on our multi-platform tumor profiling approach,” noted W. Michael Korn, MD, Chief Medical Officer at Caris Life Sciences.

“We continue to develop novel technologies to provide the most comprehensive molecular profiling possible,” Korn added.

Agreement

Under the terms of the agreement, MI Transcriptome™ will be used to identify eligible patients for Debiopharm’s FUZE Phase II Pivotal Trial of Debio 1347, an investigational novel orally available small molecule highly selective FGFR 1, 2, 3 ATP competitive inhibitor that Debiopharm is evaluating for the treatment of patients with non-central nervous system solid tumors that have a specific FGFR gene fusion.

Results from the phase I clinical trial showed that patients with solid tumors with activating alterations in FGFR may benefit from treatment with Debio 1347. Debio 1347 is expected to become a tailored treatment which will be developed with a companion diagnostic.

The investigational agent received Fast Track designation from FDA earlier this year.

Eligible patients

In addition to developing MI Transcriptome CDx, Caris will use its MI Trials service to improve the identification of patients eligible to enroll in the FUZE trial, analyzing the tens of thousands of patients profiled by Caris Life Sciences each year. The FUZE study is an open-label, blinded, multicenter, pan-cancer international Phase II Basket Trial that plans to enroll 125 patients across more than 20 countries.

“This collaboration represents a key milestone in the advancement of a new tumor-agnostic approach,” said Angela Zubel, Chief Development Officer at Debiopharm International.

“We believe that a whole transcriptome assay is particularly relevant to detect oncogene fusions and to identify tumor expression profiles that could benefit from Debio 1347 therapy,” she added.

“When investigating novel targeted therapies in small, genetically-defined subpopulations which can be found in a broad range of cancers, it is critical that molecular screening be conducted in the broadest possible group of potential trial participants,” commented Keith Flaherty, Director of Clinical Research at the Massachusetts General Hospital Cancer Center.

“Kinase fusions across multiple histologies have become very important targets in precision oncology but we know that detection methods based purely on DNA can unfortunately miss some patients who might otherwise benefit from these therapies,” said David Hyman, Chief of Early Drug Development at Memorial Sloan Kettering Cancer Center. “We are excited to see the increasing adoption of RNA-based, unbiased screening technologies in the clinic.”

Different fusion or rearrangement types

As opposed to DNA-only based methods, MI Transcriptome™ RNA profiling has the ability to detect any fusion event independent of breakpoint locations and fusion partners. It can distinguish between different fusion or rearrangement types and has the potential to discover previously uncharacterized events, which is critical to identifying every potential patient who may benefit from targeted therapies.

MI Transcriptome™ also uses the capabilities of high-throughput transcript sequencing to gain insight into the gene expression profiles of patients’ tumors and builds upon Caris’ offering of the most comprehensive tumor profiling approach, which assesses DNA, RNA and proteins for every patient.

Clinical trials

  • Debio 1347-101 Phase I Trial in Advanced Solid Tumours With Fibroblast Growth Factor Receptor (FGFR) Alterations | NCT01948297
  • A Study of Debio 1347 Plus Fulvestrant in Patients With Metastatic Breast Cancer | NCT03344536
  • Basket Trial in Solid Tumors Harboring a Fusion of FGFR1, FGFR2 or FGFR3- (FUZE Clinical Trial) | NCT03834220