Perturbation-based Phosphoproteomics to Study Drug Response Heterogeneity

Objetivo

Every tumor is a distinct disease entity, characterized by a unique cellular and molecular profile specific to each individual patient, resulting in varying responses to targeted therapies. Genomics technologies currently pioneer personalized medicine approaches to match patients to optimal therapies, yet most therapeutics aim to alter the activity of proteins rather than genes. At the same time, understanding of the functional consequences of genetic aberrations on drug action has remained elusive. My goal is to bridge this gap by directly assessing how drugs act on a patient’s tumor proteome, a close proxy of cellular function. Leveraging ultra-sensitive mass spectrometry-based phosphoproteomics, my first objective is to develop and benchmark a first-of-its-kind framework for measuring the response of peripheral blood mononuclear cells to drug perturbations (PerturbPhos). We will apply PerturbPhos to a cohort of acute myeloid leukemia (AML) patients to demonstrate that drug-induced perturbations are personal and reflect the individual’s disease background. Moreover, I hypothesize that ex vivo perturbations functionalize a patient’s phosphoproteome, which will allow us to investigate patient-specific mechanisms of drug action and associate many previously uncharacterized phosphorylation sites in the human proteome with drug response. We will perform a CRISPR-mediated based editor screen to functionally validate the latter at scale. The third objective is to demonstrate, on the example of AML patients, that computational integration of PerturbPhos profiles with clinical data, public databases and literature can rationalize treatment recommendations. Collectively, these results will shed mechanistic light on drug response heterogeneity, underscore the potential of proteomics to provide actionable insights for treating individual cancer patients and advocate for adopting a multi-omics perspective in precision medicine.