June 7, 2023  |  Cancer research

Cracking cancer: Using long-read RNA sequencing for cancer neoantigen discovery

cracking cancer blog image

When developing effective personalized immunotherapies, such as cancer vaccines, a pivotal factor lies in uncovering tumor neoantigens that can serve as crucial therapeutic targets. Traditionally, neoantigen discovery heavily relied on short-read sequencing technology, with a predominant focus on neoantigens resulting from single-nucleotide variants (SNVs). However, recent advancements have unveiled the potential of RNA isoforms and fusions as potent neoantigens that can trigger robust immune responses. Unfortunately, the current limitations of short-read sequencing impede the detection of these variant classes. But what if there was another approach that could enable cancer researchers to detect ALL potential neoantigens in a single assay? Imagine the possibilities it could unlock.

A new approach to neoantigen discovery

A new study from researchers at the National University of Singapore applied PacBio’s accurate long-read single-cell RNA sequencing (the Iso-Seq method) to colorectal cancer (CRC) samples.

As previously discussed, the Iso-seq method captures transcriptomic events by sequencing the full length of the transcript, revealing aberrant transcript isoforms that may cause tumor-related RNA dysregulation. RNA-seq using traditional short-read technology is, on the other hand, limited in detecting RNA isoforms and complex fusions.

The team looked specifically at tumor-specific RNA isoforms as neoepitopes and prioritized those with highest HLA binding affinity as potential vaccine targets. In doing so, they stated that, “these findings demonstrate a proof-of-concept for the discovery of neoepitopes based on the tumor-specific transcriptome, as well as the invaluable application potential of long-read scRNA sequencing in the development of neoepitope-based cancer vaccines.”

neoantigen identification for cancer vaccines
Figure 1: Neoantigen discovery using short- vs PacBio long-read sequencing. The Iso-Seq method offers robust detection of isoforms, fusions, and expressed mutations.

What made the PacBio technology so valuable in this case is the ability to capture and then sequence more of the transcriptome. Since cancer neoantigens can result from all RNA variant types, such as fusions, isoform and small variants, sequencing read length AND accuracy matter. Traditional short-read sequencing looks primarily at SNV-derived neoantigens, while missing larger events such as isoforms and fusions. Inaccurate long-read technologies can detect larger variants, but their error-prone nature results in inferior SNV detection. PacBio technology offers the best of both worlds (Figure 1).

Looking to the future

This study is the first step in changing the way we look for cancer neoantigens. It provides us with a framework for identifying and selecting the most valuable target candidates for vaccine development, potentially resulting in more effective personalized vaccines. With the Revio system and MAS-Seq kit, this approach is not only doable, but cost-effective and scalable.

As cancer research and genomics at large continue to evolve, long-read sequencing, recognized as the 2022 Method of the Year, is enabling researchers to see and do more than ever before. And with this study, we find that cancer vaccine development has new dimensions.

Interested in seeing how to apply this approach to your research? Reach out to one of our experts to learn how.

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