March 2024

Arpeggio Pipeline: Sarcoma

Cancer is a disease of survival: cells grow when they shouldn’t. So unsurprisingly, many proteins and enzymes that prevent cell death are abnormally active in tumors. In fact, apoptosis evasion is considered one of the “hallmarks of cancer”, so it was with great excitement in 2012 that scientists discovered ferroptosis: a new form of regulated cell death that is strongly evaded by cancer. Ferroptosis results from an increase in toxic lipid peroxides owing to high levels of iron and specific poly-unsaturated fatty acids. Cancer tends to upregulate iron transporters to grow faster, so it is no surprise that it is quite susceptible to ferroptosis and very dependent on its suppression.  

After a decade of ferroptosis research, we now know many of the important genes that prevent ferroptosis, many of which cancer relies on to grow, proliferate, and survive. The most well-studied enzyme is GPX4: a protein that reduces toxic lipid peroxides into inert lipid alcohols, evading ferroptosis. Many scientists across the country have linked GPX4 to certain cancer contexts such as mesenchymal lineages in pancreatic cancer, osteosarcomas, and triple negative breast cancer.

At Arpeggio, we’ve used our GRETATM technology to identify an extremely selective and potent GPX4 inhibitor. Like apoptosis, ferroptosis leaves an extremely identifiable transcriptional fingerprint on a cell. Certain genes like HMOX1, OSGIN1, and DUSP1 are unique transcriptional responses to the induction of ferroptosis. We can leverage this transcriptional signature to screen for compounds that uniquely and selectively turn on this pathway in cancer (Figure 1).

Figure 1. Arpeggio’s proprietary chemotranscriptome database. Each dot represents a cell’s transcriptome following treatment with a unique small molecule. The highlighted region indicates molecules that induce the ferroptosis pathway where our small molecule GPX4 inhibitor emerged. The x- and y-axis are UMAP dimensions used to visualize and compress the more than 20,000 mRNA levels in our cell’s transcriptome.

After a large chemotranscriptomic small molecule screen using GRETATM, we identified a hit compound that both binds and inhibits GPX4 (a protein many drug discovery and development consider “undruggable" due to its greasy globular protein structure). After medicinal chemistry optimization, our current lead small molecule induces robust tumor growth inhibition in multiple mouse models of cancer including pancreatic cancer and sarcoma. Early toxicology studies of our lead GPX4 inhibitor indicate a safe and tolerated profile with no signs of body weight loss or impairment in either kidney or liver function (Figure 2).

Figure 2. Syngeneic model of ARP-0864, an orally bioavailable GPX4 inhibitor, leads to sustained tumor growth inhibition in a very refractory and IO-resistant sarcoma mouse model.

Recent studies have emerged suggesting that ferroptosis plays a synergistic role in activating the immune system to fight cancer. CD8+ T-cells are an extremely well-studied subset of our immune system that are responsible for clearing and attacking foreign bodies like viruses but, when activated by medicine such as Keytruda, can also recognize and fight cancer. CD8+ T-cells fight cancer, in part, by expressing high extracellular levels of IFN-y (Figure 3). Recent work suggests that IFN-y actually suppresses system-Xc expression, which depletes cancer cells of glutathione and ultimately renders them more susceptible to Ferroptosis. Using our first-in-class GPX4 inhibitor, we’ve demonstrated robust anti-tumor activity in combination with anti-PDL1 in mouse models harboring an intact immune system, paving the way for a novel combination opportunity to bring medicine to millions of patients who do not respond to drugs like Keytruda.  

Figure 3. Adapted from Feng et al, recent evidence suggests a strong link between ferroptosis, the tumor microenvironment, and potential synergy with checkpoint blockade drugs such as Keytruda.
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