Stanford Medicine researchers have developed a two-part molecule that turns a major driver of B-cell lymphoma against the cancer cells that depend on it. In mice, twice-daily treatment with the experimental compound caused aggressive lymphoma tumors to disappear within 11 days.
The work advances a strategy the research team has been developing for years. Instead of simply shutting down a cancer-promoting protein, the scientists designed a small molecule that connects it to another protein capable of activating the cell’s built-in death program. The researchers believe this type of molecular rewiring could eventually have applications beyond lymphoma, including other cancers and some autoimmune diseases.
“We’re trying to essentially fight cancer with its cause — taking the driving force of the cancer and then rewiring it to activate cell death mechanisms,” said Gerald Crabtree, MD, the David Korn, MD, Professor in Pathology and a professor of developmental biology.
Crabtree shares senior authorship of the study, which was published in Cell, with Nathanael Gray, PhD, the Krishnan-Shah Family Professor and a professor of chemical and systems biology; Stephen Hinshaw, PhD, assistant professor of molecular and cellular physiology; and Michael Green, PhD, director of translational and laboratory research, lymphoma/myeloma at the MD Anderson Cancer Center. Graduate student Meredith Nix and postdoctoral scholar Sai Gourisankar, PhD, are the lead authors of the research.
How BCL6 Helps Lymphoma Cells Survive
Diffuse large B-cell lymphoma is the most common form of non-Hodgkin lymphoma, a type of blood cancer. In many cases, the disease is driven by a protein known as BCL6.
In healthy immune cells, BCL6 attaches to DNA and temporarily shuts down genes that would normally stop cell growth or initiate cell death. This temporary suppression gives immune cells time to multiply during an immune response.
Once the immune threat has passed, other proteins modify BCL6 so that it can no longer silence those genes. The excess immune cells can then die through apoptosis, a controlled form of programmed cell death that allows the body to remove unneeded, damaged or cancerous cells without causing inflammation or harming nearby tissue.
Problems arise when BCL6 remains permanently active. In lymphoma cells, the protein can stay stuck in the “on” position, continually suppressing death-related genes and allowing malignant cells to keep multiplying.
Crabtree, Gray and their colleagues wanted to do more than simply remove that suppression. Their goal was to push those same cell-death genes into a highly active state. To accomplish this, they turned to a technique known as chemically induced proximity, which uses chemical connections to bring together molecules that normally interact only rarely, if at all.
A Two-Sided Molecule Rewires the Cancer Protein
The researchers created a molecule called TCIP3 that functions somewhat like a two-sided key.
“One side binds to BCL6,” Nix explained. “The other side binds either of two proteins called P300 and CBP that add chemical tags called acetyl marks onto nearby proteins.”
When an acetyl tag is added to BCL6, the protein loses its ability to suppress the cell-death genes downstream from it. P300 and CBP also place acetyl tags on nearby histones, the structures that help package DNA inside cells. Those modifications cause the histones to loosen their grip on DNA, opening up access for transcription factors that are needed to turn genes on.
That produces a different effect from existing drugs that target BCL6 by blocking or degrading it.
“We’re not just relieving the repression conferred by BCL6; we’re also actively driving the expression of these cell death genes, which is why we’re able to get really potent compounds,” Nix said, comparing the difference to easing off a car’s brake versus flooring the accelerator.
Why TCIP3 Acts Like “Molecular Glue”
To investigate why TCIP3 was so effective, the researchers examined the compound at the atomic level. They crystallized the molecular complex and exposed it to X-rays — allowing them to see precisely how TCIP3 connects the proteins.
The structural analysis uncovered an unexpected feature. Once TCIP3 brought the proteins together, they formed several additional chemical contacts with one another. Those interactions helped stabilize the entire complex, strengthening the effect of the hybrid molecule beyond what the researchers had initially expected.
“We used structural studies and biophysical measurements to determine that TCIP3 acts as a kind of molecular glue, anchoring these proteins together,” Gourisankar said.
Using that structural information, the chemists were able to make the connection between the molecule’s two halves more rigid. This helped preserve the favorable interactions instead of allowing the molecule to flex and lose energy. The resulting TCIP3 compound killed lymphoma cells grown in the laboratory at very low concentrations.
Lymphoma Tumors Disappeared in Mice
The team then tested TCIP3 in mice implanted with human lymphoma cells. After allowing the cells to develop into tumors, the researchers treated the animals with TCIP3 twice a day.
“By 11 days, the tumors that had been treated with TCIP3 were completely gone, whereas the tumors in the control animals remained,” Nix said.
The treated mice showed no obvious signs of toxicity, and blood tests did not reveal an increase in inflammatory signals. At the same time, TCIP3 was also eliminating germinal centers — clusters of rapidly dividing immune cells that depend heavily on BCL6 and represent the same type of cells that become abnormal in lymphoma.
That effect pointed to another possible application for the technology. Germinal center cells also play an important role in certain autoimmune diseases, including rheumatoid arthritis and myasthenia gravis. Because of that connection, the researchers think molecules similar to TCIP3 could eventually be explored as treatments for those conditions as well.
A Broader Strategy for Reprogramming Cancer
TCIP3 is not yet ready for use in people. The compound still requires further chemical refinement and must be tested in additional animal species before researchers can consider moving toward human clinical trials.
Even so, the broader strategy may have wide potential. The researchers are using bivalent, or two-headed, molecules to redirect the activity of cancer-driving proteins instead of merely blocking them. They are now looking for additional cancer-promoting proteins that could be vulnerable to the same type of molecular matchmaking.
“This could be a powerful approach to tackling other cell death repressors or transcription factors that control genes we want to activate in cancer,” Nix said.
Researchers from MD Anderson Cancer Center and the AI-powered drug discovery platform Deep Origin contributed to the study.
The study was funded by the National Institutes of Health (grants CA276167, CA163915, R01CA3044298, MH126720-01, S10OD028697-01, R01CA201380 and 1K99CA296700-01), the Howard Hughes Medical Institute, the Mary Kay Foundation, the Williams Foundation, the Victor Family Fund, Ed and Beatriz Schweitzer, the David L. Sze and Kathleen Donahue Interdisciplinary Fellowship, and a PhRMA Foundation Predoctoral Fellowship in Drug Discovery.
Crabtree is a founder and scientific advisor for Shenandoah Therapeutics, which has a license from Stanford University for the TCIP technology described in the study. Gray is a founder, scientific advisor and board member for Shenandoah Therapeutics.
