# PURE-seq integrates FACS and PIP-seq for single-cell genomics of ultra-rare cells

## TL;DR

PURE-seq is a new method that combines FACS and PIP-seq to efficiently sequence ultra-rare cells, enabling detailed study of rare cell populations like cancer cells and aging stem cells.

## Contribution

PURE-seq integrates FACS and PIP-seq to directly sequence ultra-rare cells at a rarity of 1 in 1,000,000.

## Key findings

- PURE-seq successfully isolated and sequenced circulating tumor cells from metastatic melanoma patient blood.
- Transcriptomic analysis identified Egr1 as a putative master regulator of murine hematopoietic stem and progenitor cell aging.

## Abstract

Single-cell transcriptomics is valuable for uncovering individual cell properties, particularly in heterogeneous systems. However, this technique often results in the reanalysis of many well-characterized cells, increasing costs and diluting rare cell populations. To address this, we develop PIP-seq for Rare-cell Enrichment and Sequencing (PURE-seq). PURE-seq allows direct FACS sorting of cells into PIP-seq reactions, minimizing handling and reducing cell loss. PURE-seq reliably sequences ultrarare cells, with 1 hour of sorting capturing tens of target cells at a rarity of 1 in 1,000,000. Leveraging this extreme sensitivity, we use PURE-seq to isolate and single-cell sequence circulating tumor cells from metastatic melanoma patient blood, obtaining detailed single cancer cell gene expression profiles. Additionally, we use PURE-seq to examine hematopoietic stem and progenitor cells from young, old and middle-aged mice. Transcriptomic analysis identifies Egr1 as a putative master regulator of murine hematopoietic stem and progenitor cell aging, demonstrating PURE-seq’s utility as a discovery platform for basic science applications. PURE-seq offers a simple and highly sensitive method for single-cell sequencing ultra-rare cells.

Rare cells are often biologically and clinically important, but their low abundance makes them challenging to study using single-cell transcriptomics. Here, the authors develop PURE-seq which integrates FACS and PIP-seq to directly sequence ultra-rare cells. It captures cells at 1 in 1,000,000 rarity, which the authors demonstrate by profiling circulating tumor cells and identifying Egr1 as a regulator of mouse hematopoietic stem cell aging.