# Activity based profiling of Phosphoprotein phosphatases in cancer using mass spectrometry-based proteomics

> **NIH NIH R33** · DARTMOUTH COLLEGE · 2020 · $392,248

## Abstract

PROJECT SUMARRY
Targeting dysregulated phosphorylation signaling by kinase inhibitors is a proven strategy and a focus in the
development of anti-cancer treatments. However, variability in patient responses and drug resistance limit
efficacy and often lead to therapy failure. The underlying mechanisms that determine drug efficacy are
multifaceted and include the drug target itself, as well as associated signaling pathways. For instance, mutation
or amplification of the targeted kinase, functional compensation by related kinases, reprograming of kinase
signaling, and alterations in phosphatase signaling networks that antagonize substrate phosphorylation or
directly modulate kinase activity are common.
Tremendous progress has been made in deciphering the cancer kinome and its response to anti-cancer
treatment. These studies were enabled by an array of innovative technologies, including a chemical proteomics
strategy that utilizes kinase inhibitors immobilized on beads and mass spectrometry (MS).
The majority of protein dephosphorylation is carried out by phosphoprotein phosphatases (PPPs). The PPP
family consists of nine catalytic subunits that bind to regulatory and scaffolding subunits and assemble into
hundreds of multi-subunit enzymes and function as distinct, selective signaling entities. Excitingly, the role and
regulation of PPPs in cellular signaling in normal and cancerous tissue is beginning to emerge.
While kinome profiling provides global information on phosphorylation reactions, no such technology exists for
phosphatases; thus, we lack knowledge of the understudied, but equally important, dephosphorylation reaction
in cancer. To address this gap in capability, we have established a chemical proteomics strategy called “PIB-
MS” for efficient affinity-capture, identification, and quantification of all endogenously expressed PPPs and their
associated proteins (“PPPome”) in a single mass spectrometry analysis from limited protein amounts of cell,
tissue, and tumor lysate. In this application, we further develop and mature this technology and assess its
performance to identify and quantify the PPPome in breast cancer cell lines, upon perturbation by drug treatment,
and breast cancer PDX tumor models, and in primary human breast cancer tumors. We will assess the
performance of this technology in an inter-laboratory comparison to achieve broad implementation.
Statement of Potential Impact. PPPs have emerged as critical signaling entities in cancer. However, currently
no approach exists for rapid, quantitative, and comprehensive assessment of the endogenous PPPome and its
dynamic changes associated with cellular stress, short- and long-term treatment with anti-cancer drugs, or
development of drug resistance. PIB-MS is a highly innovative technology that provides these capabilities for the
analysis of cell lines, mouse models of disease, and primary human tumors. PIB-MS will accelerate and enhance
the molecular analysis of cancer in basic, tran...

## Key facts

- **NIH application ID:** 9917701
- **Project number:** 5R33CA225458-02
- **Recipient organization:** DARTMOUTH COLLEGE
- **Principal Investigator:** Scott A. Gerber
- **Activity code:** R33 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $392,248
- **Award type:** 5
- **Project period:** 2019-07-01 → 2022-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9917701

## Citation

> US National Institutes of Health, RePORTER application 9917701, Activity based profiling of Phosphoprotein phosphatases in cancer using mass spectrometry-based proteomics (5R33CA225458-02). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/9917701. Licensed CC0.

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