Detecting cancer during its early stages drastically enhances treatment success. This was acknowledged by researchers from UCSC led by Assistant Professor of Biomolecular Engineering, Daniel Kim with their recent work that took a significant step forward in cancer detection. By harnessing the untapped potential of RNA "dark matter," they've taken liquid biopsy technologies to a new level of accuracy and efficiency.
Liquid biopsies, which rely on a simple blood draw, allow for non-invasive cancer detection by sequencing either DNA or RNA from a patient's blood. Daniel Kim's lab focuses on the less explored realm of the genome—the RNA "dark matter." This research indicates that this genetic material is found in the blood of individuals with cancers like pancreatic, lung, and esophageal during the early stages of the disease.
The RNA liquid biopsy platform developed in Kim's lab aims to detect both protein-coding RNA and the lesser-studied RNA "dark matter." Interestingly, while most research is centered around DNA-based liquid biopsies, Kim’s method stands out for its concentration on noncoding and repetitive RNA.
The human genome's vast portion, around 75%, produces noncoding RNA, which doesn't code for proteins. Many of these RNAs originate from repetitive elements and can migrate from their originating cells into the bloodstream. Kim's studies indicate that these repetitive RNAs become especially prominent in the presence of early-stage cancer, marking them as strong early-stage disease indicators.
Using a platform named COMPLETE-seq, Kim's team looks at all recognized RNA areas and five million noncoding repetitive elements, providing a comprehensive analysis. Kim notes that these repetitive RNAs offer abundant information, enhancing the sensitivity of cancer detection.
Existing liquid biopsies often falter at early-stage detection due to the tumor's minute size. Yet, when repetitive RNA was incorporated into the liquid biopsy platform, the detection rates improved dramatically. For instance, colorectal cancer detection sensitivity increased to an impressive 91%.
Highlighting the importance of this research, Kim said, “The value of our study is that we've now shown the potential of these repeat elements for diagnosing disease, so hopefully there'll be a lot of interest in leveraging repetitive RNAs to boost the sensitivity of these multi-cancer early detection tests.”
The research not only centered on pancreatic cancer but also explored other types. The broader vision is to establish an RNA liquid biopsy test for early-stage multi-cancer detection, utilizing the valuable information from repetitive RNAs. Kim envisions his platform diagnosing cancer early on, paving the way for tailored treatments and potentially diagnosing other diseases that influence the repetitive RNA environment, like Alzheimer's.
The team also employed nanopore sequencing, allowing them to acquire long reads of the cell-free RNAs in the blood. Remarkably, they believe they are the first to use nanopore sequencing for RNA liquid biopsies to diagnose cancer. This approach might enable cancer screenings in areas where advanced equipment is scarce.
Read the published study here.
Liquid biopsies, which rely on a simple blood draw, allow for non-invasive cancer detection by sequencing either DNA or RNA from a patient's blood. Daniel Kim's lab focuses on the less explored realm of the genome—the RNA "dark matter." This research indicates that this genetic material is found in the blood of individuals with cancers like pancreatic, lung, and esophageal during the early stages of the disease.
The RNA liquid biopsy platform developed in Kim's lab aims to detect both protein-coding RNA and the lesser-studied RNA "dark matter." Interestingly, while most research is centered around DNA-based liquid biopsies, Kim’s method stands out for its concentration on noncoding and repetitive RNA.
The human genome's vast portion, around 75%, produces noncoding RNA, which doesn't code for proteins. Many of these RNAs originate from repetitive elements and can migrate from their originating cells into the bloodstream. Kim's studies indicate that these repetitive RNAs become especially prominent in the presence of early-stage cancer, marking them as strong early-stage disease indicators.
Using a platform named COMPLETE-seq, Kim's team looks at all recognized RNA areas and five million noncoding repetitive elements, providing a comprehensive analysis. Kim notes that these repetitive RNAs offer abundant information, enhancing the sensitivity of cancer detection.
Existing liquid biopsies often falter at early-stage detection due to the tumor's minute size. Yet, when repetitive RNA was incorporated into the liquid biopsy platform, the detection rates improved dramatically. For instance, colorectal cancer detection sensitivity increased to an impressive 91%.
Highlighting the importance of this research, Kim said, “The value of our study is that we've now shown the potential of these repeat elements for diagnosing disease, so hopefully there'll be a lot of interest in leveraging repetitive RNAs to boost the sensitivity of these multi-cancer early detection tests.”
The research not only centered on pancreatic cancer but also explored other types. The broader vision is to establish an RNA liquid biopsy test for early-stage multi-cancer detection, utilizing the valuable information from repetitive RNAs. Kim envisions his platform diagnosing cancer early on, paving the way for tailored treatments and potentially diagnosing other diseases that influence the repetitive RNA environment, like Alzheimer's.
The team also employed nanopore sequencing, allowing them to acquire long reads of the cell-free RNAs in the blood. Remarkably, they believe they are the first to use nanopore sequencing for RNA liquid biopsies to diagnose cancer. This approach might enable cancer screenings in areas where advanced equipment is scarce.
Read the published study here.