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Cell-communication molecules called kinases play a key role in the growth and spread of many cancers. But exactly which kinases are active in a particular cancer is not always clear — there are 1.8 million sites on human proteins that kinases might act on, and researchers have fully characterized less than 1 percent of them.
A Harvard Medical School team has now built an AI-enabled tool called KinoPlex that maps the three-dimensional structures and biochemical environments of all of these sites and matches them with the specific kinases that can interact with them.
In a paper published July 29 in Nature Biotechnology, the researchers demonstrate that KinoPlex can be used to determine which kinases are active in specific cancer cells.
If validated in the clinic, the tool could help doctors identify which of around 100 existing kinase-inhibiting treatments would be most effective for a particular patient. KinoPlex may also reveal targets for future cancer therapeutics.
“Kinases are rapidly becoming one of the largest targeted families in therapeutics,” said senior author Steven Gygi, professor of cell biology in the Blavatnik Institute at HMS. “By analyzing a patient’s particular cancer, their particular set of mutations, their particular phosphorylation state, we might be able to predict which drugs would provide the best therapeutic effect.”
The researchers are partnering with oncologists at several hospitals, including Brigham and Women’s Hospital and Massachusetts General Hospital, to test KinoPlex with clinical samples from cancer patients.
“We need really good diagnostic indicators for cancer, and this is very different from existing diagnostics — it’s a signature of a process, not just a level of a protein or something similar,” Gygi said. “I think it can be really useful.”
They have made KinoPlex publicly available with the help of Cell Signaling Technology, a life sciences company.
“Everything that we’ve built is available to the scientific community,” said first author David Vanderwall, a Harvard MD-PhD student in the Gygi Lab. “Anyone can start applying it to their work.”
A three-dimensional approach
Kinases work by attaching signaling molecules to different proteins, changing how those proteins behave. This process, called phosphorylation, controls cell growth, division, metabolism, DNA repair, and other activity. Mutations in kinases can contribute to cancer and other diseases.
There are roughly 500 different kinases, and each has different requirements for its binding sites. Previous work, much of which was led by corresponding author Lewis Cantley, HMS professor of cell biology at Dana-Farber Cancer Institute, has focused on identifying the biochemical signatures at these sites to determine which kinases could be a match. KinoPlex is the first approach to also incorporate the 3D structures of these areas.
The researchers measured more than 100 properties around each potential site. They found that in many cases, a binding site has the right amino acid sequence around it but is physically inaccessible to the matching kinase.
KinoPlex revealed roughly 250,000 sites with both a recognizable biochemical signature around them and a compatible 3D structure.
“What we’ve demonstrated here is that it’s not just a question of having that amino acid sequence available to be phosphorylated, but it also has to be structurally realizable,” said Vanderwall, who is in the Biological and Biomedical Sciences Program at HMS.
The researchers developed a scoring framework that allowed them to translate detected phosphorylation sites into measurements of kinase activity. They tested their method on leukemia cells, successfully identifying kinase signals associated with the cancer’s growth and survival.
Working with additional cell lines across multiple cancer types, they were able to identify which kinase signaling pathways were most relevant to each cell, suggesting which kinase-inhibiting drugs might be most effective against them.
“There are more than 90 FDA-approved drugs that target kinases,” Gygi said. “We hope this technology can support and improve those treatments.”
Authorship, funding, disclosures
Additional authors of this work include Edward L. Huttlin, Julian Mintseris, Tomer M. Yaron-Barir, Jared L. Johnson, Kevin D. Dong, Alex J. Bott, Yuchen He, Christina B. Schroeter, Geordon A. Frere, Mohamed Uduman, Harin Lee, Sean Landry, Sean A. Beausoleil, and Joao A. Paulo.
This work was supported by the National Institutes of Health (grants T32GM007753, T32GM144273, T32GM145407, GM67945, R35CA197588, P01CA120964 and P01CA117969) and a Claudia Adams Barr Program for Cancer Research award.
Gygi is on the Scientific Advisory Board of Thermo Fisher Scientific and Cell Signaling Technology. Cantley is a founder and member of the board of directors of Agios Pharmaceuticals and receives research support from Petra Pharmaceuticals; is listed as an inventor on a patent (WO2019232403A1, Weill Cornell Medicine) for combination therapy for PI3K-associated disease or disorder and the identification of therapeutic interventions to improve response to PI3K inhibitors for cancer treatment; is a co-founder and shareholder in Marendis Therapeutics and Faeth Therapeutics; has equity in and consults for Cell Signaling Technology, Volastra Therapeutics, Larkspur Bioscience, and 1Base Pharmaceuticals and consults for Loxo-Lilly. Huttlin has received consulting fees from Matchpoint Therapeutics, FL94, and Calico. Johnson is a co-founder and shareholder in Marendis Therapeutics and has received consulting fees from Scorpion Therapeutics and Volastra Therapeutics. Yaron-Barir is a co-founder and shareholder in Marendis Therapeutics and Destroke.
