Molecular diagnostics company Biodesix has entered into a biomarker research collaboration with Checkmate Pharmaceuticals, a Cambridge, MA-based biopharmaceutical company focused on developing novel approaches to cancer immunotherapy.

The collaboration will leverage MALDI-TOF mass spectrometry analysis of the circulating proteome of advanced melanoma patients treated with Checkmate’s candidate CMP-001 in combination with pembrolizumab (Keytruda). The mass spec analysis will be performed using the Diagnostic Cortex artificial intelligence-based biomarker discovery platform from Biodesix, which enables the development of clinically-relevant proteomic liquid biopsy tests.

“The market for proteomic analysis is picking up speed and growing with the rise of immunotherapies in both clinical practice and drug development,” said David Brunel, CEO of Biodesix. “The circulating proteome can provide unique insights into the host response to the tumor and its microenvironment. With the latest therapies using the immune system to treat cancer, the role of inflammation in cancer biology has taken on a new relevance.”

According to Brunel, the Diagnostic Cortex technology that will be used in the Checkmate collaboration uses machine learning and deep learning using proprietary algorithms to recognize spectral differences and relationships among the proteins identified by the mass spectrometry peaks in order to design classifiers to be used for the development of diagnostics.  

Checkmate’s CMP-001 is a first-in-class CpG-A oligonucleotide that activates the innate immune system via Toll-like receptor 9 (TLR9). The combination therapy with pembrolizumab has the potential to improve the response rate of cancer patients receiving checkpoint inhibitor therapies and to increase the magnitude and duration of the patients’ anti-tumor responses, providing added clinical benefit. The intention of the collaboration is to discover relevant biomarkers associated with a favorable response to CMP-001 and then developing a serum-based diagnostic test for identifying patients more likely to benefit from the combination therapy.

While immunotherapies for treating cancer can make a significant positive impact for a portion of patients, a large number of patients either do not respond or experience significant side-effects. Companion and complementary diagnostics, therefor, play an important role in helping clinicians providing treatment only to those most likely to benefit.

To date, genomic testing has provided the bulk of information for targeting therapies, but advances in proteomics could bring these biomarkers to the table for potentially new molecular diagnostics in the future.

“Interrogating the proteome can provide the information necessary to tailor therapies to individual patients based on their likelihood of benefit,” Brunel added. “However, the benefits of proteomic analysis need to be better understood by biopharma and clinicians alike in order for the market for these services to grow and become synergistic with genetic testing.”

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