Researchers have recently launched an extensive database detailing human protein kinases and their binding sites, marking a significant advancement for studying cellular signaling pathways.
After 25 years of diligent research, a collaborative team from MIT, Harvard University, and Yale University has unveiled a comprehensive atlas focused on human tyrosine kinases—crucial enzymes that influence a myriad of cellular functions. This new resource complements an earlier published dataset and now offers a free, publicly accessible atlas encompassing all human kinases and their distinct binding sites. These kinases play a vital role in fundamental processes essential for cell growth, division, and metabolism.
This atlas empowers researchers to harness mass spectrometry, a standard lab technique, to pinpoint the kinases involved in both normal and aberrant cell signaling within human tissues, particularly in cases of inflammation and cancer development.
“I am particularly excited about applying this tool to individual tumor samples, allowing us to analyze the signaling states within cancer and the variability of that signaling,” shares Michael Yaffe, the David H. Koch Professor of Science at MIT and director of the MIT Center for Precision Cancer Medicine. “This work has the potential to uncover new drug targets or innovative combination therapies.”
The findings, detailed in a study published in Nature, emerge from a longstanding partnership among senior authors Lewis Cantley from Harvard Medical School and the Dana-Farber Cancer Institute, Benjamin Turk at Yale, and Jared Johnson from Weill Cornell Medical College. Lead authors include Tomer Yaron-Barir at Columbia University Irving Medical Center and MIT’s Brian Joughin, with contributions from Kontstantin Krismer, Mina Takegami, and Pau Creixell.
The Kinase Kingdom Explained
Human cellular behavior is orchestrated by a complex network of protein kinases, which modify other proteins by adding or removing phosphate groups—tiny yet impactful chemical tags. These phosphate groups can activate or deactivate proteins or significantly alter their function. However, determining which of the nearly 400 human kinases phosphorylates a given protein at a specific site has been a time-consuming challenge.
Starting in the mid-1990s, the Cantley laboratory pioneered a method utilizing a library of small peptides to identify the optimal amino acid sequences, known as motifs, targeted by kinases on their substrate proteins for phosphorylation. Over the years, Yaffe, Turk, and Johnson, who were formerly postdocs in the Cantley lab, made remarkable improvements to enhance accuracy and throughput.
Johnson spearheaded an extensive experimental initiative exposing various kinases to the peptide libraries, revealing which kinases phosphorylated which peptides. Their previous Nature study, published in January 2023, mapped over 300 serine/threonine kinases to their corresponding motifs. The current paper completes the ‘kinome’ by successfully mapping 93 tyrosine kinases to their specific motifs.
Utilizing advanced computational tools, Yaron-Barir, Krismer, Joughin, Takegami, and Yaffe tested the predictive power of their findings on real proteins, uncovering previously unrecognized signaling events in normal and cancer cells and accurately predicting tyrosine kinase activity within established cell signaling frameworks.
For instance, analysis of phosphoproteomic data from human lung cancer cells treated with targeted drugs indicated that the EGFR inhibitor erlotinib downregulated sites corresponding to its motif, while afatinib, a HER2 inhibitor, influenced the HER2 motif. Notably, afatinib also upregulated MET kinase motifs, providing insights into patient data linking MET activity to afatinib resistance.
Transformative Insights
This new atlas offers researchers two primary applications. First, it can help narrow down potential kinases involved in phosphorylating a protein of interest, creating a shorter list of candidates for further study. “While experimental validation is still necessary, this represents a significant advancement in making informed predictions that can be tested,” explains Yaffe.
Secondly, the atlas enhances the utility of phosphoproteomic data. Previously, researchers struggled to interpret data gathered from tissue samples, unable to determine its implications for future research directions. With this atlas, such data can now clarify which kinases are active and the associated cellular signaling pathways.
“This tool acts as a Rosetta Stone for phosphoproteomics, enabling us to glean actionable insights from extensive datasets,” Yaffe remarks. This is particularly vital when examining cancer, as phosphoproteomic data from tumor biopsies can help clinicians identify active kinases and signaling pathways driving cancer progression or drug resistance, tailoring appropriate treatments.
Yaffe’s lab, in collaboration with the National Institutes of Health, is now leveraging the atlas to explore insights into challenging cancers, such as appendiceal cancer and neuroendocrine tumors. While the genetics of some cancers, like breast cancer’s BRCA1 and BRCA2 genes, are well understood, others lack clear genetic causes. “Using this atlas, we’re probing these enigmatic tumors for key kinases that may be influencing cancer advancement,” he states.
Biological Discoveries
The completion of the human kinase atlas also led to two significant biological insights in this latest study. The researchers identified three primary classes of phosphorylation motifs for tyrosine kinases. The first class indicates motifs that correspond to multiple kinases, showing that diverse signaling pathways can phosphorylate a protein with such motifs. The second class represents motifs that uniquely match a single kinase, which came as a surprise given the previously held belief that tyrosine kinases had limited specificity.
The final class features motifs without a clear pairing with any of the 78 traditional tyrosine kinases, instead matching with 15 atypical tyrosine kinases that can also phosphorylate serine or threonine residues. “This suggests the existence of a group of kinases we hadn’t previously recognized as significant players,” Yaffe observes, hinting at other potential mechanisms influencing kinase interactions with proteins.
Furthermore, the team found that tyrosine kinase motifs are highly conserved between humans and the worm species C. elegans, suggesting that kinases perform crucial functions across diverse multicellular organisms—any minor alterations could have detrimental consequences.
This groundbreaking research was made possible through the support of the Charles and Marjorie Holloway Foundation, the MIT Center for Precision Cancer Medicine, the Koch Institute Frontier Research Program, the Leukemia and Lymphoma Society, the National Institutes of Health, Cancer Research UK, the Brain Tumour Charity, and the National Cancer Institute’s Koch Institute Support (core) grant.
Photo credit & article inspired by: Massachusetts Institute of Technology
