You are currently viewing At AACR 2024 Learn How Pepper Tackles ‘Undruggable’ Targets: ML-Driven Transomics Identifies Four Leading Candidates to Treat HCC

At AACR 2024 Learn How Pepper Tackles ‘Undruggable’ Targets: ML-Driven Transomics Identifies Four Leading Candidates to Treat HCC

  • Post category:Blog

April 5-10, San Diego

Pepper Bio is on a mission to decipher the root causes of diseases and identify effective treatments—thereby illuminating the fastest, safest path to drug discovery. COMPASS, our ML-driven platform, is built on the world’s first and largest proprietary transomics database, integrating genomic, transcriptomic, proteomic, and phosphoproteomic data. Our approach offers a comprehensive understanding of biological systems based not just on expression but also on the activity of key molecular actors. This allows us to develop more effective drugs that are less toxic to patients. 

Developing an approved treatment for complex diseases is challenging, underscored by a bleak 4% average success rate for new drugs. Successful drug development hinges on two critical factors: understanding what drives the disease and the full impact of a drug on a patient. Our technology is specifically designed to address both these crucial aspects.

As the “Google Maps for drug discovery,” we harness transomics and proprietary ML to construct a comprehensive and functional map of disease and drug mechanisms. This identifies core targets responsible for diseases and matches them with the correct drugs.

In the last year, we’ve continued to achieve key milestones. With support from our investors, including NFX and Merck, we announced $6.5M seed funding in November 2023 to build out our oncology pipeline and advance the capabilities of COMPASS. Furthermore, we’ve successfully completed three pharmaceutical partnerships, including working with a top-five pharmaceutical company.

Debuting at AACR’s Annual meeting are our accomplishments toward treating hepatocellular carcinoma (HCC). Carried out in collaboration with Stanford Medicine’s Dean Felsher Lab, we have identified four drug candidates to treat MYC-driven HCC.

HCC is an aggressive form of liver cancer with limited treatment options. In about 30% of cases, patients have too much MYC—a gene causing cancer when it’s abnormally active. These patients have 70% shorter survival, highlighting the unmet need. Turning off MYC is therefore an appealing strategy to treat HCC, but targeting MYC directly has been a challenge. Pepper’s platform provides new hope for these patients, as we have successfully identified targets that mimic the effect of turning MYC off.

We partnered with Stanford Medicine’s Dean Felsher who has spent decades studying how MYC triggers cancerous changes inside and outside a cell. The Felsher Lab has developed a state-of-the-art MYC HCC model. Their model can be tuned to turn MYC off, which causes the liver cancer cells to die. Working together with their team, we collected omics data from their state-of-the-art models both before and after turning off MYC. 

With this data as input, our proprietary COMPASS target prioritization algorithm ranked targets that would mimic the effect of turning off MYC without the need to target MYC directly. Targets were then filtered to select those with an available pharmacological compound suitable for repurposing. The compounds were used to evaluate the targets in an in vivo model of HCC.

Among the evaluated targets, 73% significantly decreased tumor growth. Importantly, we identified four leading candidates to treat HCC for our drug development pipeline. 

These results highlight COMPASS’s ability to identify novel therapeutics for difficult-to-treat diseases. We will continue to pursue these treatments in HCC and have ongoing work on additional difficult-to-treat MYC-driven cancers. 

With our sights set on the long term, our technology is uniquely poised to advance neurodegenerative, oncology, and inflammatory diseases. In addition to our own pipeline, we also establish milestone-based partnerships with pharmaceutical companies to deliver critical insights that inform drug discovery decision-making from target identification, drug prioritization, to biomarker identification.

Pepper Bio’s technology is building a future where the label “untreatable disease” becomes obsolete.

If you’d like to learn more about our technology and pipeline, our Chief Development Officer, Simon Fricker, and Head of Biology, Christopher Nicholson, will share our findings and approach to treating HCC on Sunday, April 7, from 1:30 p.m. to 5:00 p.m. PST. More information is below. 

Title: Identification of novel targets for MYC-driven hepatocellular carcinoma by transomics

Session title: Late-breaking research: Bioinformatics, Computational Biology, Systems Biology and Convergent Science

Session date and time: Sunday, April 7 | 1.30 p.m. – 5.00 p.m

Location: Poster Section 51

Poster board number: 5Abstract presentation number: LB005