Detailed molecular mapping of stored tumor tissue at single-cell level
Spatially resolved multi-omics sequencing of FFPE tissues at cellular level
['FUNDING_OTHER'] · UNIVERSITY OF PENNSYLVANIA · NIH-11193898
This project will create a way to map gene activity, gene regulation, and proteins inside preserved tumor biopsies so researchers and clinicians can see which cells are driving cancer.
Quick facts
| Phase | ['FUNDING_OTHER'] |
|---|---|
| Study type | Nih_funding |
| Sex | All |
| Sponsor | UNIVERSITY OF PENNSYLVANIA (nih funded) |
| Locations | 1 site (PHILADELPHIA, UNITED STATES) |
| Trial ID | NIH-11193898 on ClinicalTrials.gov |
What this research studies
Researchers are building a new laboratory method to read multiple molecular layers — chromatin accessibility (epigenome), RNA (gene expression), and proteins — from formalin-fixed, paraffin-embedded (FFPE) tumor samples that hospitals commonly store. They will develop a spatial epigenome sequencing approach and a deterministic barcoding strategy to jointly profile accessible chromatin or histone marks, mRNAs, and proteins from the same tissue section at single-cell resolution. The approach is designed to preserve the location of different cell types and malignant subclones within archived biopsies so those spatial relationships can inform diagnosis and biomarker discovery. The work is a technology development effort led at the University of Pennsylvania to enable broader use of stored tumor tissue in cancer research.
Who could benefit from this research
Good fit: Patients who have archived FFPE tumor biopsy samples in hospital pathology departments or tissue banks and who are willing to allow their stored samples to be used for research would be the ideal contributors.
Not a fit: Patients without available archived biopsy tissue or those seeking an immediate change in their clinical care are unlikely to gain direct benefit from this methods-focused project.
Why it matters
Potential benefit: If successful, this could help identify new biomarkers and reveal which tumor cells drive disease, supporting more precise diagnoses and future targeted treatments.
How similar studies have performed: Related spatial transcriptomics and proteomics methods have shown promise, but combining epigenome, transcriptome, and protein mapping in FFPE samples at cellular resolution is largely novel and untested.
Where this research is happening
PHILADELPHIA, UNITED STATES
- UNIVERSITY OF PENNSYLVANIA — PHILADELPHIA, UNITED STATES (ACTIVE)
Researchers
- Principal investigator: DENG, YANXIANG — UNIVERSITY OF PENNSYLVANIA
- Study coordinator: DENG, YANXIANG
About this research
- This is an active NIH-funded research project — typically early-stage science, not a clinical trial accepting patient enrollment.
- Some NIH-funded labs run parallel clinical studies or seek volunteers for related work. To check, contact the principal investigator or institution listed above.
- For full project details, budget, and progress reports, visit the official NIH RePORTER page below.
Conditions: Cancer Biology