Single Cell Analysis with the BD AbSeq Assay

New tools are enabling researchers to explore individual cells with unprecedented clarity by allowing RNA and protein expression levels to be simultaneously analyzed. In this blog, Brian Lilhanand, Global Platform Leader, Single Cell Multiomics, at BD, discusses how BD’s new AbSeq Assay can provide this targeted profiling and benefit immunology researchers. 

Ruairi Mackenzie (RM): Analysis workflows are focusing on the single-cell level more than ever – what advances have allowed us to explore the lone cell?

Brian Lilhanand (BL): The advent of lower cost next-generation sequencing technology has enabled more researchers to add single-cell genomics tools like the BD Rhapsody single cell analysis system to their labs.

 These tools make single-cell analysis more accessible; the BD Rhapsody system includes  reagents, instruments, software, and targeted gene panels and offers additional single-cell analysis capabilities with the BD AbSeq assay.  This helps researchers develop a more complete picture of the role genes and proteins play in biological systems. 

RM: Protein expression and RNA levels don’t always match up. Why is that the case and why is it a challenge for researchers?

BL: High-throughput sequencing has allowed researchers to examine hundreds to thousands of RNA targets and greatly advanced our understanding of complex biological systems. However, understanding gene regulation and single-cell heterogeneity often requires information about both RNA and protein expression. There are few technologies that allow concurrent examination of both types of molecules in a single experiment with a single readout.

Due to several cell regulation pathways, levels of RNA versus levels of protein are not always correlative. One prime example is that of the T-cell marker PD1, which has emerged as an important immunotherapy target.  For PD1, the RNA expression is almost undetectable in T-cells.  Yet, depending on the subtype of immune cells, the protein expression varies widely.

Using Rhapsody gene expression panels with the BD AbSeq assay, researchers can identify high- and low-expressors at the protein level in conjunction with RNA expression, even if gene expression is low. For assays where cell-surface molecules like PD1 are targeted for drug delivery, the ability to identify and study cells based on protein expression will be vital to understanding drug responses.

RM: The BD AbSeq assay brings together RNA and protein expression data – why is that especially important for immunologists?

BL: By bringing together well characterized, high quality antibodies from the BD Pharmingen portfolio with oligonucleotide barcodes, the AbSeq assay enables researchers to simultaneously analyze RNA and proteins in thousands of individual cells to help immunology.

Advanced protein profiling methods, such as the BD AbSeq assay, have been developed to accommodate more parameters, on scale with that of single-cell RNA-seq, and represent a major step forward for immunology and other fields. This simultaneous analysis in single cells could enable researchers to gain a better understanding of the regulatory mechanism responsible for turning genes on and off and uncover a more complete characterization of how gene expression shapes cellular phenotypes.

This is important for immunologists because the assay enables deeper and more precise understanding of the role each cell plays in the immune system, and with more than 100 different combinations of human antibody-oligonucleotides, and more in development, researchers are empowered to advance their understanding of complex diseases without needing to run multiple experiments.

RM: What are the next steps for the BD AbSeq assay; can more omics be integrated?

BL: Single-cell analysis is an obvious starting point for BD Biosciences in fulfilment of our corporate purpose – advancing the world of health. We want to continue driving single-cell analysis into new research areas like immunology and expanding our offerings in these areas with additional human and mouse antibody-oligonucleotide combinations in the coming months and years. 

With the addition of FlowJo and SeqGeq informatics packages to the portfolio, BD are working to better integrate omics from an informatics perspective – a significant challenge in research today.  The ability to both collect, analyze and interpret single cell flow, RNAseq and AbSeq data together will be a powerful capability that enables new discoveries.

Our goal has been to make single-cell genomics accessible to all researchers given its enormous potential for better understanding the cells that drive disease. 

Brian Lilhanand was speaking to Ruairi J Mackenzie, Science Writer for Technology Networks.