Kyoto University develops new protein "Crunch" which removes unwanted cells in the body by inducing phagocytosis

Living organisms maintain homeostasis through phagocytic cells such as macrophages consuming cells that have undergone cell death. A research group led by Professor Jun Suzuki and former Researcher Yuki Yamato from the Institute for Integrated Cell-Material Sciences (iCeMS) at Kyoto University has developed a new protein called "Crunch" (connector for removal of unwanted cell habitat) that removes unwanted but living cells in the body through phagocytosis, including cells that cause cancer and autoimmune diseases. They have also succeeded in removing melanoma transplanted into mice. Suzuki stated: "By changing the recognition sites of Crunch, we can remove various types of cells. In the future, we want to address unmet medical needs by targeting fibrotic organs and other conditions for which no effective treatments exist. Currently, to commercialize Crunch, we expect to establish a biotech startup in collaboration with Takashi Toraishi, former co-CEO of Rakuten Medical, no later than next month. We aim to advance to clinical trials within three years."

Suzuki's group has previously identified scramblases that expose phosphatidylserine, an "eat-me" signal of dead cells, on cell surfaces. The group has been working on an approach to remove unwanted cells by activating scramblases with drugs and other agents to expose eat-me signals.

However, as their research progressed, they considered that target cells could be removed through phagocytosis without exposing eat-me signals by recognizing specific cell surface changes in unwanted cells. This idea occurred around 2020 during the COVID pandemic. "During the COVID period, as anxiety spread throughout society, I strongly felt that I wanted to do something useful for society as a basic researcher. While it's important to plant seeds for decades in the future, when I was thinking about whether there was something that could be immediately useful, I came up with the idea of removing unwanted cells. At the time, I was also thinking it would be nice if we could remove viruses too (laughs)." The synthetic protein Crunch for safely and selectively eliminating unwanted cells consists of three functional modules: a target recognition site that binds to target cells, an EGF-like domain that enhances structural stability, and an SHBG-like domain that binds to phagocytic receptors (such as MerTK). It serves to bridge unwanted cells and phagocytic cells while activating phagocytic signals.

The base is Protein S, which is used for phagocytosis of dead cells. By replacing the phosphatidylserine-recognizing region (Gla domain) of Protein S with a domain that recognizes antigens specific to target cells, it can recognize and remove target cells.

Melanoma (malignant melanoma) was transplanted into mice, and seven days later, Crunch with a single-chain variable fragment (scTYRP1) targeting TYRP1 expressed on melanoma was injected into the mice. As a result, melanoma cell proliferation was significantly suppressed. Macrophages play the most active role as phagocytic cells. "M1 macrophages usually play the leading role because they exhibit high antigen presentation capabilities, but M2 macrophages specialize in phagocytosis. In cancer cells, M1 macrophages change to M2, which reduces their attack capability. However, in this case, Crunch attaches to cancer cells and gets phagocytosed by M2 macrophages, achieving high efficacy."

Additionally, in a mouse model causing systemic lupus erythematosus (SLE)-type autoimmune disease lacking Fas, a cell death receptor, they verified whether Crunch using a single-chain variable fragment against CD19 (scCD19) could remove B cells and improve the pathological condition. As a result, they found that the number of B cells in the blood decreased significantly. Consistent with this result, the number of leukocytes infiltrating the kidneys decreased, antibody deposition also decreased, and the urine protein-to-creatinine ratio normalized. Furthermore, they found that concentrations of anti-DNA antibodies and antinuclear antibodies in the blood also decreased, confirming the therapeutic effect of Crunch.

Since Crunch is removed from the body within half a day, research is being conducted to extend its half-life depending on the types of cells to be targeted for removal. By using Crunch to remove specific cells existing in organs or specific compartments (such as synapses) of large cells like neurons, the functions of target cells and compartments can be investigated. By loading Crunch with the target recognition sites of antibodies and CAR-T cells already in use, or the recognition sites for target proteins of antibodies and CAR-T cells that did not achieve sufficient efficacy in clinical trials, this could lead to the development of new therapeutic strategies aimed at removing unwanted cells.

Journal Information
Publication: Nature Biomedical Engineering
Title: Phagocytic clearance of targeted cells with a synthetic ligand
DOI: 10.1038/s41551-025-01483-9