# Single-cell and imaging data integration software to spatially resolve the tumor microenvironment

> **NIH NIH U01** · JOHNS HOPKINS UNIVERSITY · 2021 · $407,184

## Abstract

Project Summary
The tumor microenvironment (TME) plays a critical role in cancer progression and therapeutic response. New
single cell and imaging technologies provide unprecedented measurements of cell type composition, subtypes
of common cell types in disparate states, interactions between neighboring cells, and T cell function. However,
each of these components of the TME are captured by disparate measurement technologies. Both new
computational methods and software for multi-platform data integration are essential to characterize the TME.
Therefore, we propose a unified R/Bioconductor package TMEMap for multi-platform single cell data
integration. Aim 1 will integrate single cell RNA-sequencing and single cell TCR-sequencing data to distinguish
T cell function in distinct T cell subtypes and states. Aim 2 will integrate combined single cell RNA-sequencing
and protein from CITE-seq with imaging proteomics for digital pathology to map cellular interactions in the
TME. Aim 3 will further the disseminate this software with through GenePattern Notebook. This workflow will
be developed in collaboration with clinical investigators to ensure usability and interpretability of the
visualization methods using clinical biospecimens from synergistic studies. Altogether, this software will
provide a strong foundation for future work embedding these methods in a database for multi-platform single
cell data to automatically perform comprehensive TME characterization in large scale NCI profiling efforts such
as the Human Tumor Atlas Network.

## Key facts

- **NIH application ID:** 10234200
- **Project number:** 5U01CA253403-02
- **Recipient organization:** JOHNS HOPKINS UNIVERSITY
- **Principal Investigator:** Elana Fertig
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $407,184
- **Award type:** 5
- **Project period:** 2020-09-01 → 2023-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10234200

## Citation

> US National Institutes of Health, RePORTER application 10234200, Single-cell and imaging data integration software to spatially resolve the tumor microenvironment (5U01CA253403-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10234200. Licensed CC0.

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