# Development of new technologies  for high-sensitivity detection of a B-cell tumor marker in DNA

> **NIH NIH R21** · WAYNE STATE UNIVERSITY · 2021 · $365,463

## Abstract

There is a critical need for the development of cheap, safe, and accurate tools for cancer
surveillance. Patients diagnosed with cancer require an accurate assessment of tumor burden
through the course of their treatment, and the need for tumor surveillance is even more acute for
many indolent B-cell malignancies such as follicular lymphoma and chronic lymphocytic leukemia.
Current imaging techniques such as ultrasound sonography, computed tomography and positron
emission tomography are expensive, have limited reliability and expose patients to excessive
radiation. We will help satisfy this need by creating a bench-top assay for a known biomarker for
many B-cell cancers that should eventually lead to the development of a kit that may be used to
detect the presence of this marker in circulating tumor DNA (ctDNA). The levels of this biomarker,
uracil, are low in the genomes of normal human cells, but are greatly elevated in the DNA of a
majority of B-cell lymphomas and leukemias. The long-term goal of this project is to apply this
technology to the detection of uracils in ctDNA in blood plasma of B-cell cancer patients as a tumor
surveillance tool. In the first aim, we will increase the sensitivity of a click chemistry-based technology
to quantify uracils by synthesizing and testing turn-on fluorescent tags that react with abasic sites in
DNA. The use of these novel probes will eliminate many steps in the current assays, increase the
yield of DNA and drastically lower the background signal. A variety of turn-on chemistries are
available and we will use a click chemistry pair that has known on/off fluorescence intensity ratio of
>>100. In the second aim, we will engineer a novel protein from M. smegmatis, UdgX, which
specifically and covalently links at sites of uracils in DNA, as a probe for this rare base. This protein
will be fused to a FLAG tag and a fluorescent protein, and used to directly label uracil-containing
DNA. The fluorescence signal of the protein-DNA complex may be enhanced further using anti-FLAG
antibodies conjugated to appropriate fluorescent tags, through ELISA or tyramide chemistry. The limit
of detection of both the techniques will be determined using synthetic DNA containing uracils and
genomic DNA from B-cell lymphoma-derived cell lines with high uracil content. The overall goal of this
project is to increase the sensitivity of current uracil detection methods 10- to 50-fold, which should
allow us to detect uracils in the blood plasma of a majority of B-NHL patients and eventual develop an
assay kit that will be useful to monitor B-cell cancer patients through a routine blood draw.

## Key facts

- **NIH application ID:** 10217428
- **Project number:** 1R21CA252858-01A1
- **Recipient organization:** WAYNE STATE UNIVERSITY
- **Principal Investigator:** ASHOK S BHAGWAT
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $365,463
- **Award type:** 1
- **Project period:** 2021-04-08 → 2023-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10217428

## Citation

> US National Institutes of Health, RePORTER application 10217428, Development of new technologies  for high-sensitivity detection of a B-cell tumor marker in DNA (1R21CA252858-01A1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10217428. Licensed CC0.

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