Phosphoproteomic profiling of T cell acute lymphoblastic leukemia reveals targetable kinases and combination treatment strategies

Valentina Cordo’,Sander R Piersma,Adolfo A Ferrando,Connie R Jimenez,Rico Hagelaar,Vera M Poort,Mariska T Meijer,Guido J R Zaman,Alex A Henneman,Koichi Oshima,Thang V Pham,Jules P P Meijerink,Richard R De Goeij-De Haas

doi:10.1038/s41467-022-28682-1

Abstract

Protein kinase inhibitors are amongst the most successful cancer treatments, but targetable kinases activated by genomic abnormalities are rare in T cell acute lymphoblastic leukemia. Nevertheless, kinases can be activated in the absence of genetic defects. Thus, phosphoproteomics can provide information on pathway activation and signaling networks that offer opportunities for targeted therapy. Here, we describe a mass spectrometry-based global phosphoproteomic profiling of 11 T cell acute lymphoblastic leukemia cell lines to identify targetable kinases. We report a comprehensive dataset consisting of 21,000 phosphosites on 4,896 phosphoproteins, including 217 kinases. We identify active Src-family kinases signaling as well as active cyclin-dependent kinases. We validate putative targets for therapy ex vivo and identify potential combination treatments, such as the inhibition of the INSR/IGF-1R axis to increase the sensitivity to dasatinib treatment. Ex vivo validation of selected drug combinations using patient-derived xenografts provides a proof-of-concept for phosphoproteomics-guided design of personalized treatments.

Highlights

Protein kinase inhibitors are amongst the most successful cancer treatments, but targetable kinases activated by genomic abnormalities are rare in T cell acute lymphoblastic leukemia
Recurrent activating mutations detected in kinasecoding genes or kinase regulators involve the PI3K-AKT axis (AKT1, PIK3CD, and PIK3R1), the Janus kinases (JAKs)-STAT (IL7R, JAK1, and JAK3 which is mutated in about 16% of T cell acute lymphoblastic leukemia (T-ALL) cases6), or the Ras signaling pathways (PTPN11, NF1, N-RAS, and K-RAS), while in some early T cell precursor (ETP)-ALL cases, Fms-like tyrosine kinase (FLT3) mutations and/or overexpression are found[7]
Following phospho-tyrosine peptide immunoprecipitation, we identified about 3800 phosphosites while the titanium dioxide (TiO2)based enrichment yielded over 17,000 phosphosites

Summary

Introduction

Protein kinase inhibitors are amongst the most successful cancer treatments, but targetable kinases activated by genomic abnormalities are rare in T cell acute lymphoblastic leukemia. We describe a mass spectrometry-based global phosphoproteomic profiling of 11 T cell acute lymphoblastic leukemia cell lines to identify targetable kinases. Proteome analyses can provide additional insights into active signaling pathways and kinases that could be exploited for targeted therapy. Mass spectrometry (MS)-based phosphoproteomics importantly contributed to the identification of signaling pathways and protein networks that can be targeted for cancer therapy[18–20]. We present an exploratory MS-based, unbiased, global profiling of tyrosine, serine, and threonine phosphorylation in a panel of T-ALL cell lines and patient-derived xenografts (PDXs) to identify relevant kinase signaling and to predict novel dependencies. We demonstrate how the application of phosphoproteomics can guide the ex vivo identification of synergistic combination treatments, and the selection of the most appropriate therapeutical strategy for personalized medicine

Methods

Results

Conclusion