# Core 2: Tissue Imaging and Profiling Core

> **NIH NIH U54** · INSTITUTE FOR SYSTEMS BIOLOGY · 2022 · $369,373

## Abstract

Core 2. Imaging and Spatial Profiling Core Project Summary:
Central technologies of the ST-Analytics U54 program are tissue imaging and profiling platforms, including two
sets of tools for highly multiplex, multi-omic analysis of tumor tissue specimens including clinical archival FFPE
and lightly preserved frozen tissues, and associated image analysis & informatics software. These Core
resource technologies are used extensively by both ST Analytics Projects.
 The first spatial profiling tool is the well-established commercial Nanostring Digital Spatial Profiling (DSP)
system, which permits analysis of regions of interest (ROIs) containing as few as 10-20 cells for detecting around
1000 genes or around 50 proteins (Lee 2017, Lu 2021). Adjacent slices from an FFPE block are prepared. The
first is subjected to H&E staining for pathological analysis, while the second is stained with fluorescent antibodies
to identify ROIs (for example, immune cell rich or cancer cell rich regions). Those ROIs are then interrogated at
the transcriptome or proteome level. We have extensive experience with this tool for analysis of FFPE preserved
patient tumor tissues (Lu 2021).
 The second profiling tools are those recently developed and reported by the Fan group (Deng 2021,
2021, Liu 2020). These powerful tools permit highly multiplex (up to 300-plex) proteomics and genome--wide
transcriptome mapping at a resolution of 10 micrometers in tissue slices prepared from FFPE blocks. They also
permit spatially resolved ATAC-seq and ChIP-seq type epigenetic profiling (Chen 2017; Chen 2018) at a similar
spatial resolution in lightly fixed tissue slices. In particular, this epigenetic profiling capacity is unique to these
tools. Similar to DSP, adjacent tissue slices can be H&E stained, and low-plex fluorescent imaging can be
employed on the same slice for identification of nuclei as well as immune rich and immune poor regions for
alignment validation. These methods can enable high throughput and cost-effective profiling of tissues, and
some technology development to that end is described. The Core will continue to develop new spatial profiling
tools to meet the emergent needs in the two projects as they advance in the next 5 years, thus serving as a
Technoloy Innovation Hub for the U54 center and for the CSBC consortium as well.

## Key facts

- **NIH application ID:** 10526107
- **Project number:** 1U54CA274509-01
- **Recipient organization:** INSTITUTE FOR SYSTEMS BIOLOGY
- **Principal Investigator:** Rong Fan
- **Activity code:** U54 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $369,373
- **Award type:** 1
- **Project period:** 2022-09-22 → 2027-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10526107

## Citation

> US National Institutes of Health, RePORTER application 10526107, Core 2: Tissue Imaging and Profiling Core (1U54CA274509-01). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/10526107. Licensed CC0.

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