Low-Input Methylation Sequencing For Profiling Epitranscriptomic Signatures And Early Colorectal Cancer Diagnosis

SUMMARY

A method that analyzes cfRNA methylation in plasma to distinguish human RNA from microbiome RNA, accurately detecting colorectal cancer through specific methylation markers even in ultralow input samples.

The Unmet Need: Effective biomarkers for early detection of colorectal cancer

• Current advancements in molecular diagnostics have emphasized non-invasive techniques, especially through the analysis of cell-free RNA circulating in blood plasma. This approach holds significant promise for early disease detection, as it leverages biological markers that are present even before clinical symptoms emerge. However, the field is challenged by the inherently low abundance of these biomarkers and the susceptibility of RNA molecules to degradation. There is a growing need for more nuanced methods to capture subtle biochemical modifications that could serve as reliable indicators of disease.

• Current methodologies are hampered by limited sensitivity and specificity when it comes to detecting crucial epitranscriptomic modifications in low-input samples. Conventional sequencing approaches often fail to accurately identify subtle methylation patterns and other modifications, leading to potential misclassification of RNA species originating from the host versus microbiome. Additionally, high background noise and technical variability make it difficult to achieve consistent results, particularly in distinguishing early disease markers from normal biological variation. These obstacles highlight the pressing requirement for refined analytical tools tailored to overcome the limitations of present-day diagnostic technologies.

The Proposed Solution: A novel sequencing method that uses ultralow-input cfRNA samples and detects epitranscriptomic modifications to improve early-stage colorectal cancer diagnosis sensitivity and specificity

• The faculty inventor developed a high-resolution sequencing approach that targets cell-free RNA from plasma to reveal detailed epitranscriptomic modifications. It utilizes ultralow-input methods and enables the detection of specific methylation markers. This process allows for precise mapping of modifications within both tRNA and rRNA, distinguishing between human and microbiome-derived RNA species. Such detailed profiling provides insightful information on cell-type origins and potential biomarkers for early disease detection.

ADVANTAGES

ADVANTAGES

• Non-invasive and highly sensitive
• Effective use of ultralow-input samples allowing robust analysis of diverse RNA modifications
• Enhanced differentiation between human and microbiome RNA
• Simultaneous detection of multiple methylation modifications
• Robust diagnostic performance validated by rigorous computational models

APPLICATIONS

• Early colorectal cancer diagnosis
• Liquid biopsy diagnostic kit
• RNA methylation biomarker assay
• Microbiome diagnostic profiling

PUBLICATIONS

• Ju, CW., Lyu, R., Li, H. et al. Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples. Nat Biotechnol (2025). https://doi.org/10.1038/s41587-025-02731-8

May 6, 2025

Proof of concept

Patent Pending

Licensing,Co-development

Chuan He