Cookies

Like most websites The Translational Scientist uses cookies. In order to deliver a personalized, responsive service and to improve the site, we remember and store information about how you use it. Learn more.
Tools & Techniques Diagnostics & prognostics, Cancer, Personalized medicine

All the RAGE

This article was first published in our sister publication, The Pathologist. For more content relating to disease diagnostics, visit www.thepathologist.com

Although immunotherapy is a promising form of cancer therapy, not all patients respond well – and current methods to assess an individual’s immune cell behavior often fall short. Immune cells that recognize cancer are rare, making it difficult to identify those that will mount an effective response. But that’s exactly what Repertoire and Gene Expression by Sequencing (RAGE-Seq) – a new cellular barcode tracker – aims to do. Developed by scientists at the Garvan Institute of Medical Research, the new technology can spot the rare lymphocytes that are most reactive against cancer cells, all from within the patient’s own immune system (1).

Current approaches allow us to read the long stretches of RNA that encode immune cell receptors, but each comes with its own limitation. Bulk sequencing can identify lymphocyte expansion very sensitively, but tells us little about the cell’s phenotype or how receptors are paired in a cell. Plate-based methods, on the other hand, can be used to reconstruct gene expression and receptors from single cells, but are low-throughput and expensive.

“The key to finding the lymphocytes of interest lies in the structure of their antigen receptor,” says Alex Swarbrick, Head of the Tumor Progression Laboratory at Garvan and lead researcher of the RAGE-Seq study. “This tells us about the type of lymphocyte, whether they have proliferated and undergone clonal expansion in response to antigens, and other features, such as whether splicing or somatic hypermutation has occurred in B cell receptors.”

RAGE-Seq [...] works much like a barcode tracker that scans the relevant receptors to show which cells might be most effective against a particular cancer.

The breakthrough that has enabled such analysis came when the researchers combined three distinct technologies: high-throughput single-cell RNA-Seq, targeted capture of lymphocyte receptors, and long-read sequencing of cDNA libraries. “The key bottlenecks were in optimizing targeted capture from single cell libraries and developing the computational methods to match short-read Illumina sequencing with long-read Nanopore sequencing of the same cells,” Swarbrick says. After establishing a way to enrich the RNA that encodes immune cell receptors from single cells, the team then developed a computational tool that generates full-length sequences of antigen receptors at nucleotide resolution and analyzes them to infer B-cell clonal evolution. In this way, RAGE-Seq allows deep characterization of the subsets of lymphocytes in a sample, working much like a barcode tracker that scans the relevant receptors to show which cells might be most effective against a particular cancer.

Using RAGE-Seq to sample 7,138 cells from the tumor and metastasized sentinel lymph node of a breast cancer patient, the researchers were able to identify clones in both tissues that shared unique gene expression features. Both T cell receptor clonality and gene expression signatures have previously been linked to patients’ response to immune checkpoint inhibitors. Applying RAGE-Seq to biopsies before and after treatment could, therefore, help identify biomarkers or cell states that predict therapy response. Swarbrick says, “We think RAGE-Seq will lead to new discoveries in cancer immunotherapy and autoimmunity, allowing us to guide treatment strategies based on the individual.”

Enjoy our FREE content!

Log in or register to gain full unlimited access to all content on the The Translational Scientist site. It’s FREE and always will be!

Login

Or register now - it’s free and always will be!

You will benefit from:

  • Unlimited access to ALL articles
  • News, interviews & opinions from leading industry experts
Register

Or Login via Social Media

By clicking on any of the above social media links, you are agreeing to our Privacy Notice.

  1. M Singh et al., “High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes”, Nat Commun, 10, 3120 (2019). PMID: 31311926.

About the Author

Luke Turner

While completing my undergraduate degree in Biology, I soon discovered that my passion and strength was for writing about science rather than working in the lab. My master’s degree in Science Communication allowed me to develop my science writing skills and I was lucky enough to come to Texere Publishing straight from University. Here I am given the opportunity to write about cutting edge research and engage with leading scientists, while also being part of a fantastic team!

Register to The Translational Scientist

Register to access our FREE online portfolio, request the magazine in print and manage your preferences.

You will benefit from:

  • Unlimited access to ALL articles
  • News, interviews & opinions from leading industry experts

Register