# Quantitative protein network profiling to improve CAR design and efficacy

> **NIH NIH R01** · SEATTLE CHILDREN'S HOSPITAL · 2021 · $504,231

## Abstract

PROJECT SUMMARY
This grant is in response to PAR-18-206, Bioengineering Research Grants (BRG). Our goal is to adapt a
cutting-edge proteomic network analysis platform, Quantitative Multiplex co-Immunoprecipitation or QMI,
to chimeric antigen receptor (CAR) T cell signaling. We will then use CAR-QMI to characterize signal
transduction network activation downstream of the CAR, to both understand how the CAR instructs a T cell to
attack and destroy cancerous targets, and to make batch-specific predictions about efficacy and side-effect
profiles of CAR T cell products. CAR T cells are a breakthrough anti-cancer therapy that recently won FDA
approval for relapsed B cell lymphomas. A true “personalized medicine”, CAR T cells are manufactured for
each patient from that patient's own T cells by transducing T cells collected by leukopheresis with a viral vector
encoding a CAR. However, since each batch is unique, some batches perform better than others in terms of
producing remissions and/or deleterious and sometimes fatal side effects including cytokine storms and
neurotoxicity. The goal of this project is to develop a “personalized signal transduction network analysis
platform” that can screen each batch of CAR T cells and predict the efficacy and side-effect potential of that
specific batch. Because signal transduction networks integrate information from multiple input sources- for
example costimulatory and immunosuppressive cell surface receptors, patient genetic background, and T-cell
specific history of activation- we hypothesize that this readout will be a powerful predictor of function. Our
preliminary data show that small changes in CAR design parameters such as scFV binding domain affinity
produce measurable changes in signal transduction network state that correlate with functional variables such
as target killing ability and cytokine release. Further, we show that there exists considerable individual-to-
individual variation in batches of CAR T cells produced from different donors. Therefore, the two prerequisites
for an individualized predictive assay are present- variation in our measurement across the population, and the
functional relevance of our measurement to outcome parameters. Our interdisciplinary team consists of
experts in CAR development, signal transduction, proteomics, and bioinformatics. Our ambitious but
achievable goals are to expand the QMI panel to include CAR-specific components; to understand how CAR
design parameters influence both signal transduction network states and functional performance measures;
and to develop a predictive machine learning algorithm that translates QMI-derived signal transduction network
states into a functional biomarker of in vivo clinical efficacy. Successful completion these aims will (1) identify
specific proteins or protein interactions that determine clinically-relevant outcomes such as cytokine production
or cell killing ability, allowing CAR designers to rationally modify the design of CA...

## Key facts

- **NIH application ID:** 10144946
- **Project number:** 5R01CA240985-02
- **Recipient organization:** SEATTLE CHILDREN'S HOSPITAL
- **Principal Investigator:** Stephen Edward Paucha Smith
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $504,231
- **Award type:** 5
- **Project period:** 2020-04-15 → 2025-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10144946

## Citation

> US National Institutes of Health, RePORTER application 10144946, Quantitative protein network profiling to improve CAR design and efficacy (5R01CA240985-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10144946. Licensed CC0.

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