# Spatially resolved multi-omics sequencing of FFPE tissues at cellular level

> **NIH NIH R61** · UNIVERSITY OF PENNSYLVANIA · 2024 · $227,906

## Abstract

Project Summary
Studying tumors in a spatial context will advance our understanding of intratumoral heterogeneity and how the
complex interactions between cancer and surrounding non-cancer cells results in the growth of malignant
subclones, which promises to address outstanding questions in cancer biology and improve the diagnosis and
treatment of specific cancer subtypes. In both basic and translational cancer studies, the majority of biopsies
are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples, and a growing
number of FFPE specimens are newly archived every year. Accordingly, spatial omics profiling in archived
FFPE tissue can be invaluable for cancer research and potential novel biomarker or molecular regulators
discovery. In this project, we propose to develop a first-of-its-kind technology for spatially resolved co-mapping
of epigenome, transcriptome, and proteins in FFPE tissues at the cell level. Specifically, we will (Aim 1) develop
spatial epigenome sequencing to measure not only gene expression but also epigenetic underpinning of cell
type and state directly in FFPE tissues, (Aim 2) develop a novel deterministic barcoding strategy for joint
profiling of accessible chromatin or histone modifications, mRNAs, and proteins in the same FFPE tissue
section. This novel technology addresses the lack of capability for spatial multi-omics that can be integrated,
scaled, and applied to FFPE tissue mapping. As FFPE samples are widely available and represent the most
abundant format of archivable clinical tumor tissue samples, we envision that this work will open up new
opportunities to revisit the huge resource of clinical tissue banks to study the mechanisms of pathophysiology
and to discover new targets for diagnosis and treatment of human diseases.

## Key facts

- **NIH application ID:** 10915826
- **Project number:** 1R61CA287408-01A1
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** Yanxiang Deng
- **Activity code:** R61 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $227,906
- **Award type:** 1
- **Project period:** 2024-09-17 → 2027-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10915826

## Citation

> US National Institutes of Health, RePORTER application 10915826, Spatially resolved multi-omics sequencing of FFPE tissues at cellular level (1R61CA287408-01A1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10915826. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*