# Molecular Sub-typing Breast Cancer Patients using a Liquid Biopsy

> **NIH NIH R21** · UNIVERSITY OF KANSAS LAWRENCE · 2022 · $222,005

## Abstract

Abstract
Breast cancer (BC) continues to be a devastating disease representing 30% of newly diagnosed cancer cases
amongst females in the US (276,480 newly diagnosed cases in 2020) and the second leading cancer cause of
death in females. The challenge with BC is its heterogeneity in terms of molecular alterations. For example,
Stage I/II BC patients are typically subjected to molecular subtyping using expression analysis of a mRNA gene
panel, for example the PAM50 panel. The 4 major molecular subtypes include Luminal A, Luminal B, HER2-
enriched, and Basal-like subtypes with each one associated with a certain treatment regimen to optimize clinical
outcomes for those patients. These tests are performed from a solid tissue biopsy to satisfy the mass
requirements of the molecular subtyping assay (100 ng of RNA). The assay to determine the molecular subtype
of the BC patients uses reporter probes and fluorescent dyes to provide high multiplexing capabilities, but
requires single-molecule fluorescence readout of mRNA/reporter probe assemblies stretched on a glass slide.
Liquid biopsy samples, for example extracellular vesicles (EVs), are an attractive alternative to solid-tissue
biopsies for managing cancer-related diseases. The attractive nature of liquid biopsies is the minimally invasive
nature of their acquisition and that they can report on the status of the primary tumor as well as metastatic sites.
However, a challenge with liquid biopsy samples is the limited mass of nucleic acid material they supply. For
example, 108 EVs secured from a Stage I/II BC patient would provide ~1.5 ng of mRNA.
In this R21 project, an innovative mRNA identification/quantification technology will be generated that can
accommodate the mass limits associated with liquid biopsy samples. The technology consists of a dual in-plane
nanopore sensor comprised of microfluidic and nanofluidic structures fabricated in a plastic, for example PMMA,
using replication-based techniques such as injection molding. The sensor consists of properly engineered input
microstructures to allow for high sampling efficiency to provide an exquisite limit-of-detection (<5 ng of RNA).
The nanofluidic elements consist of a nanochannel (50 × 50 nm, width × depth, length >5 µm) flanked on either
side by an in-plane pore (10 – 30 nm effective diameter). Using resistive pulse sensing (RPS), unique reporter
probes can be identified by their characteristic current transient amplitudes, temporal profiles, and/or dwell times.
In addition, because two pores are placed in series, the molecular-dependent electrophoretic mobility of the
reporter probes can be deduced, which will add an additional layer of identification information to expand the
multiplexing capability of the RPS readout (>27plex). The reporter probes consist of gene-specific sequences,
and a DNA backbone to which is hybridized RNA segments bearing 1 of 3 different proteins (avidin, streptavidin,
or neutravidin). The utility of the dual in-pl...

## Key facts

- **NIH application ID:** 10497497
- **Project number:** 1R21CA272351-01
- **Recipient organization:** UNIVERSITY OF KANSAS LAWRENCE
- **Principal Investigator:** Steven Allan Soper
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $222,005
- **Award type:** 1
- **Project period:** 2022-09-01 → 2025-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10497497

## Citation

> US National Institutes of Health, RePORTER application 10497497, Molecular Sub-typing Breast Cancer Patients using a Liquid Biopsy (1R21CA272351-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10497497. Licensed CC0.

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