# Clinical translation of a NexGen platform for quantifying protein networks in human biospecimens

> **NIH NIH R01** · FRED HUTCHINSON CANCER CENTER · 2024 · $837,288

## Abstract

PROJECT SUMMARY
 In this competitive renewal for the Academic-Industrial Partnership (R01CA235575) between the Fred
Hutchinson Cancer Center and AstraZeneca, we will continue to advance the clinical translation of multiple re-
action monitoring mass spectrometry (MRM-MS) protein assays into the clinical trial setting. The MRM-MS tech-
nology is agnostic to the patient population. In the first funding cycle, our AIP successfully (a) optimized the MRM
assay technology for use on small clinical biospecimens; (b) developed and optimized reagents and SOPs for
controlling sample processing variation, calibrating assay results across samples & labs, maximizing sensitivity
of the platform for analysis of small volume clinical biospecimens, & improving methods for greater multiplexing;
(c) developed novel methods to account for microheterogeneity in tissue biospecimens; (d) achieved analytical
validation of MRM-based assay panels in our CLIA environment; (e) translated MRM-MS protein assays into
clinical trials, & (f) licensed the technology for commercialization. Data that we generated during the first funding
cycle uncovered an exciting opportunity and a new technological challenge. Specifically, some of the MRM-
based assays that we translated into clinical trials enabled quantification of phosphosignaling in the DNA Dam-
age Response (DDR) network. These assays are of high interest to our biopharmaceutical partners since the
DDR network is a major target for cancer drugs. Excitingly, our data indicate that analyzing DDR network signal-
ing through serial collections of peripheral blood mononuclear cells (PBMCs) before and after treatment can
provide meaningful pharmacodynamic data via a simple blood draw (vs invasive tissue sampling). Yet, the chal-
lenge lies in the low basal DDR signaling levels in PBMCs, hindering precise treatment effect quantification. To
address this, we've formed a collaboration with Rules Based Medicine (RBM) to develop a prototype "DDR boost
tube," an extension of RBM's TruCulture® immune activation blood tubes. DDR Boost tubes are blood culture
tubes containing a DNA damaging agent. Our preliminary data demonstrate that incubating blood ex vivo in the
DDR Boost tubes activates DDR signaling in PBMCs, boosting basal signaling levels, & improving pharmacody-
namic measurements. In cycle 2 of funding, we will translate the integrated technologies (DDR Boost tubes +
streamlined MRM assay) into clinical trials via the following Specific Aims: Aim 1: Optimize the design of DDR
Boost tubes to maximize MRM signal-to-noise ratios & develop a streamlined DDR MRM assay panel that seam-
lessly integrates with the tubes. Aim 2: Investigate biospecimen preanalytical variables affecting DDR measure-
ments using the optimized DDR Boost tubes & develop an evidence-based Standard Operating Procedure for
clinical trial laboratory manuals. Aim 3. Validate the DDR Boost tubes in a prospective clinical trial. Successful
completion of this project...

## Key facts

- **NIH application ID:** 10979669
- **Project number:** 2R01CA235575-07
- **Recipient organization:** FRED HUTCHINSON CANCER CENTER
- **Principal Investigator:** AMANDA G PAULOVICH
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $837,288
- **Award type:** 2
- **Project period:** 2019-07-18 → 2029-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10979669

## Citation

> US National Institutes of Health, RePORTER application 10979669, Clinical translation of a NexGen platform for quantifying protein networks in human biospecimens (2R01CA235575-07). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10979669. Licensed CC0.

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