# Imaging the native 3D architecture of pancreatic and breast tumor patient tissue at single-cell resolution

> **NIH NIH UH2** · WASHINGTON UNIVERSITY · 2021 · $360,281

## Abstract

PROJECT SUMMARY
Cancer remains the second-leading cause of adult death in the United States, yet the mechanisms by which
cancerous growths are initiated and how crucial transitions such as metastasis and therapeutic resistance occur
are not well understood. Significant progress has been made in the multiplexed analysis of solid tumors through
the use of single-cell sequencing and spatio-molecular mapping techniques. However, despite the unique
insights into tumor heterogeneity these methods have afforded, they are limited to two-dimensional (2D) thin
analyses which provide little information on the native three-dimensional architecture of the tumor. Serial
reconstruction can provide some three-dimensional context, but such approaches are both inefficient in terms of
sample throughput and are inherently destructive to the tissue architecture. We propose a cross-disciplinary,
approach to quantitatively characterize the native three-dimensional architecture of human solid tumor tissue
from triple negative breast cancer (TNBC) and pancreatic ductal adenocarcinoma (PDAC) patients using a
combination of the state-of-the art, yet mature technologies of tissue clearing, immunofluorescence and in situ
hybridization labeling, and high-resolution lightsheet fluorescence microscopy. Analysis of these tissue volumes
will enable the elucidation of the spatial interactome of different tumor, immune and stromal cells that give rise
to tumor heterogeneity as well as their interactions with components of the tumor microenvironment. Our Specific
Aims are (1) to image the three-dimensional spatial distribution of tumor, immune and stromal cells in relation to
vasculature, lymphatics and the extracellular matrix in native solid tumor tissue from human pancreatic and
breast malignancies using a combination of tissue clearing, immunofluorescence, in situ hybridization and 3D
lightsheet microscopy, and (2) to develop a computational pipeline to build three-dimensional spatial maps of
protein expression and RNA transcript localization in intact solid tumor tissue from human pancreatic and breast
malignancies.
The innovation of the proposed work lies in our cross-disciplinary strategy of combining the cutting-
edge tissue clearing, multiplexed labelling and high-resolution lightsheet microscopy to better understand the
native three-dimensional architecture of solid tumors. Specifically, by classifying and quantitating previously
unknown three-dimensional features of solid tumor tissue we will be able to relate the spatial organization of the
tumor to genomic and proteomic data taken from the same specimen. The significance of this proposal is that
successful three-dimensional characterization of human tumor tissues will enable key insights to be derived on
both intra- and inter-tumor heterogeneity thus facilitating the identification of cell-cell and cell-microenvironment
interactions that could serve as potential therapeutic targets thus providing new routes to treatment...

## Key facts

- **NIH application ID:** 10300193
- **Project number:** 1UH2CA263954-01
- **Recipient organization:** WASHINGTON UNIVERSITY
- **Principal Investigator:** James Alexander Fitzpatrick
- **Activity code:** UH2 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $360,281
- **Award type:** 1
- **Project period:** 2021-08-03 → 2023-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10300193

## Citation

> US National Institutes of Health, RePORTER application 10300193, Imaging the native 3D architecture of pancreatic and breast tumor patient tissue at single-cell resolution (1UH2CA263954-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10300193. Licensed CC0.

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