The intrinsic substrate specificity of the human tyrosine kinome

Tomer M Yaron-Barir; Brian A Joughin; Emily M Huntsman; Alexander Kerelsky; Daniel M Cizin; Benjamin M Cohen; Amit Regev; Junho Song; Neil Vasan; Ting-Yu Lin; Jose M Orozco; Christina Schoenherr; Cari Sagum; Mark T Bedford; R Max Wynn; Shih-Chia Tso; David T Chuang; Lei Li; Shawn S-C Li; Pau Creixell; Konstantin Krismer; Mina Takegami; Harin Lee; Bin Zhang; Jingyi Lu; Ian Cossentino; Sean D Landry; Mohamed Uduman; John Blenis; Olivier Elemento; Margaret C Frame; Peter V Hornbeck; Lewis C Cantley; Benjamin E Turk; Michael B Yaffe; Jared L Johnson

doi:10.1038/s41586-024-07407-y

The intrinsic substrate specificity of the human tyrosine kinome

Nature. 2024 May 8. doi: 10.1038/s41586-024-07407-y. Online ahead of print.

Authors

Tomer M Yaron-Barir^{1

2

3}, Brian A Joughin^{4

5

6

7}, Emily M Huntsman^{1

2}, Alexander Kerelsky^{1

2}, Daniel M Cizin^{1

2}, Benjamin M Cohen^{1

2}, Amit Regev¹, Junho Song¹, Neil Vasan⁸, Ting-Yu Lin^{1

9}, Jose M Orozco^{10

11}, Christina Schoenherr¹², Cari Sagum¹³, Mark T Bedford¹³, R Max Wynn^{14

15}, Shih-Chia Tso¹⁴, David T Chuang^{14

15}, Lei Li¹⁶, Shawn S-C Li¹⁷, Pau Creixell^{4

5

6

7

18}, Konstantin Krismer^{4

5

6

19}, Mina Takegami^{4

5

6

7}, Harin Lee²⁰, Bin Zhang²⁰, Jingyi Lu²⁰, Ian Cossentino²⁰, Sean D Landry²⁰, Mohamed Uduman²⁰, John Blenis^{1

21

22}, Olivier Elemento², Margaret C Frame¹², Peter V Hornbeck²⁰, Lewis C Cantley^{23

24

25}, Benjamin E Turk²⁶, Michael B Yaffe^{27

28

29

30

31}, Jared L Johnson^{32

33

34}

Affiliations

¹ Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
² Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
³ Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
⁴ David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁵ Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁶ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁷ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁸ Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA.
⁹ Department of Discovery Technologies, Calico Life Sciences, South San Francisco, CA, USA.
¹⁰ Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
¹¹ Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
¹² Cancer Research United Kingdom Scotland Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
¹³ Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
¹⁴ Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
¹⁵ Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
¹⁶ School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, China.
¹⁷ Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada.
¹⁸ Cancer Research UK Cambridge Institute, University of Cambridge Li Ka Shing Centre, Cambridge, UK.
¹⁹ Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
²⁰ Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA.
²¹ Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA.
²² Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA.
²³ Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA. Lewis_Cantley@dfci.harvard.edu.
²⁴ Department of Cell Biology, Harvard Medical School, Boston, MA, USA. Lewis_Cantley@dfci.harvard.edu.
²⁵ Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. Lewis_Cantley@dfci.harvard.edu.
²⁶ Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA. ben.turk@yale.edu.
²⁷ David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. myaffe@mit.edu.
²⁸ Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA. myaffe@mit.edu.
²⁹ Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. myaffe@mit.edu.
³⁰ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. myaffe@mit.edu.
³¹ Division of Acute Care Surgery, Trauma, and Surgical Critical Care, and Division of Surgical Oncology, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA. myaffe@mit.edu.
³² Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA. jaredl_johnson@dfci.harvard.edu.
³³ Department of Cell Biology, Harvard Medical School, Boston, MA, USA. jaredl_johnson@dfci.harvard.edu.
³⁴ Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA. jaredl_johnson@dfci.harvard.edu.

PMID: 38720073
DOI: 10.1038/s41586-024-07407-y

Abstract

Phosphorylation of proteins on tyrosine (Tyr) residues evolved in metazoan organisms as a mechanism of coordinating tissue growth¹. Multicellular eukaryotes typically have more than 50 distinct protein Tyr kinases that catalyse the phosphorylation of thousands of Tyr residues throughout the proteome^1-3. How a given Tyr kinase can phosphorylate a specific subset of proteins at unique Tyr sites is only partially understood^4-7. Here we used combinatorial peptide arrays to profile the substrate sequence specificity of all human Tyr kinases. Globally, the Tyr kinases demonstrate considerable diversity in optimal patterns of residues surrounding the site of phosphorylation, revealing the functional organization of the human Tyr kinome by substrate motif preference. Using this information, Tyr kinases that are most compatible with phosphorylating any Tyr site can be identified. Analysis of mass spectrometry phosphoproteomic datasets using this compendium of kinase specificities accurately identifies specific Tyr kinases that are dysregulated in cells after stimulation with growth factors, treatment with anti-cancer drugs or expression of oncogenic variants. Furthermore, the topology of known Tyr signalling networks naturally emerged from a comparison of the sequence specificities of the Tyr kinases and the SH2 phosphotyrosine (pTyr)-binding domains. Finally we show that the intrinsic substrate specificity of Tyr kinases has remained fundamentally unchanged from worms to humans, suggesting that the fidelity between Tyr kinases and their protein substrate sequences has been maintained across hundreds of millions of years of evolution.