Researchers at the University of California, Santa Cruz, led by Assistant Professor of Biomolecular Engineering Daniel Kim, are pioneering liquid biopsy technologies that focus on RNA “dark matter” to detect early-stage cancer.
Published in Nature Biomedical Engineering, the study demonstrates that this novel approach significantly improves the performance of liquid biopsy for cancer diagnosis.
The ‘Dark Matter’ of RNA
While current liquid biopsy technologies largely rely on DNA sequencing, Kim’s lab focuses on the noncoding and repetitive RNA, often referred to as RNA “dark matter”.
Though they do not code for proteins, these RNAs, making up around 75% of the transcriptome, can be strong biomarkers for early-stage cancer, as they are secreted out of cancer cells into the bloodstream.
Technical Innovations
The research employs a novel RNA liquid biopsy platform called COMPLETE-seq. It detects both protein-coding RNA and RNA “dark matter” from a simple blood draw.
This comprehensive approach boosts the performance of machine learning models for cancer classification, leading to higher sensitivity in detecting cancer. For example, Kim’s lab achieved a 91% sensitivity rate for identifying colorectal cancer.
Nanopore Sequencing
Kim’s lab is among the first to use nanopore sequencing for RNA liquid biopsies.
This method can be performed on a handheld device, making it a practical option for resource-poor settings.
The researchers specifically used a device developed by Oxford Nanopore Technologies called the MinION.
This innovative technology holds promise for early-stage cancer detection, including in types such as pancreatic, lung, and esophageal cancer.
It also offers potential for identifying recurrences and could be applied to other diseases that alter the repetitive RNA landscape, like Alzheimer’s. The lab aims to collaborate with clinicians and companies for further studies across various types of cancer.
Conclusion
The research marks a significant advancement in the field of early cancer detection.
By tapping into the largely unexplored realm of RNA “dark matter”, Kim’s lab opens up new avenues for diagnosing and treating cancer at an early stage when it is most treatable.
The study received robust support from the American Cancer Society and involves contributions from Kim’s lab members and collaborators, including Ph.D. student Roman Reggiardo.
If you care about health, please read studies about vitamin D deficiency linked to chronic inflammation, and vitamin D supplements could strongly reduce cancer death.
For more information about health, please see recent studies about new way to halt excessive inflammation, and results showing higher intake of dairy foods linked to higher prostate cancer risk.
The study was published in Nature Biomedical Engineering.
Follow us on Twitter for more articles about this topic.
Copyright © 2023 Knowridge Science Report. All rights reserved.
