# Deciphering Cellular Heterogeneity with Single Cell Calling Cards

> **NIH NIH F30** · WASHINGTON UNIVERSITY · 2020 · $50,520

## Abstract

PROJECT SUMMARY
Multicellular life is defined by its organization of diverse cell types into higher-order tissues and organs. Millions
of cells take part in a complex synthesis of gene expression, signaling cascades, and environmental sensing to
maintain normal physiology. Disturbances in these processes can lead to illness like cancer, which results from
aberrant cell growth and dysregulation. Understanding how cells behave at an individual level is therefore crucial
to understanding both normal and abnormal physiological states. Previous investigations into cellular diversity
have been limited by available technology. Bulk RNA sequencing (RNA-seq) averages transcriptomic data
across all cells present in a sample; while this is sufficient for relatively homogeneous organs, it is inappropriate
for complex tissues. Single-cell RNA-seq is now revealing previously unappreciated heterogeneity in systems
long thought to have been uniform, such as stem cells, neutrophils, and skeletal muscle. In a typical experiment,
tissues are dissociated into a single cell suspension; individual cells are isolated, either into a microwell or in a
microfluidic droplet; cells are lysed; and mRNA is uniquely barcoded and collected. Throughput of these
techniques ranges from a hundred to several thousands of transcriptomes obtained in a single workflow. As a
result, investigators have discovered several new and rare cellular subtypes in heterogeneous tissues like the
retina.
While the ability to catalog cell types is rapidly increasing, the capacity to infer meaningful information about
these cell types lags behind. Open problems include dissecting the gene regulatory networks governing cell
states and deciding whether rare cell types are biologically meaningful. How do rare cell states arise and how
are they developmentally related to common cell types? This proposal aims to develop a new technology, single
cell calling cards, to address these concerns. The calling card method relies on fusing a transcription factor (TF)
to a transposase which directs the insertion of a transposon into the genome near TF binding sites. These marks
are recovered from genomic DNA and subsequently analyzed. Aim 1 of this proposal merges our existing method
with single-cell RNA-seq to create single cell calling cards, which can simultaneously characterize cell identity
and record TF binding sites. Calling card insertions are permanent and can be used to study TF localization
throughout development. Moreover, they can serve as genealogical markers. Aim 2 develops new from single
cell calling cards data to delineate phylogenetic relationships between cell types. Successful completion of these
aims will yield new technologies to study how, and when, diverse cell fates arise.

## Key facts

- **NIH application ID:** 9857630
- **Project number:** 5F30HG009986-03
- **Recipient organization:** WASHINGTON UNIVERSITY
- **Principal Investigator:** Arnav Moudgil
- **Activity code:** F30 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $50,520
- **Award type:** 5
- **Project period:** 2018-02-01 → 2021-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9857630

## Citation

> US National Institutes of Health, RePORTER application 9857630, Deciphering Cellular Heterogeneity with Single Cell Calling Cards (5F30HG009986-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9857630. Licensed CC0.

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