Kinase inhibitor pulldown assay (KiP) for clinical proteomics.

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For breast cancer treatment, the identification and quantification of the protein kinase ERBB2 is critical for therapeutic decisions. While immunohistochemistry (IHC) is the current clinical diagnostic approach, it is only semiquantitative. Mass spectrometry-based proteomics offers quantitative assays that, unlike IHC, can be used to accurately evaluate hundreds of kinases simultaneously. The enrichment of less abundant kinase targets for quantification, along with depletion of interfering proteins, improves sensitivity and thus promotes more effective downstream analyses. Multiple kinase inhibitors were therefore deployed as a capture matrix for kinase inhibitor pulldown (KiP) assays designed to profile the human protein kinome as broadly as possible. Optimized assays were initially evaluated in 16 patient derived xenograft models (PDX) where KiP identified multiple differentially expressed and biologically relevant kinases. From these analyses, an optimized single-shot parallel reaction monitoring (PRM) method was developed to improve quantitative fidelity. The PRM KiP approach was then reapplied to low quantities of proteins typical of yields from core needle biopsies of human cancers. The initial prototype targeting 100 kinases recapitulated intrinsic subtyping of PDX models obtained from comprehensive proteomic and transcriptomic profiling. Luminal and HER2 enriched OCT-frozen patient biopsies subsequently analyzed through KiP-PRM also clustered by subtype. Finally, stable isotope labeled peptide standards were developed to define a prototype clinical method. Data are available via ProteomeXchange with identifiers PXD044655 and PXD046169.", "claims": [{"id": "claim-method", "statement": "For differential expression of druggable kinases between basal and luminal breast tumors, a Student’s t-test was performed for each gene across each dataset (KiP PRM, Profiling, Phosphoprofiling, and RNA). 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While immunohistochemistry (IHC) is the current clinical diagnostic app", "eutic decisions. While immunohistochemistry (IHC) is the current clinical diagnostic approach", "mics offers quantitative assays that, unlike IHC, can be used to accurately evaluate hundreds"], "order_basis": "paper_text_order:310", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ls obtained from comprehensive proteomic and transcriptomic profiling. Luminal and HER2 enriched OCT-fro", "nd luminal tumors within and across methods. RNAseq data was accessed as described previously [2", "EBV-associated lymphoproliferative lesions. RNAseq data analysis included all available WHIM da", "tive phosphorylation status of each protein. 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