Modifications of microbiome-derived cell-free RNA in plasma discriminates colorectal cancer samples

Authors

• Cheng-Wei Ju, Department of Chemistry, The University of Chicago, Chicago, IL, USA.
• Ruitu Lyu, Department of Chemistry, The University of Chicago, Chicago, IL, USA.
• Han Li, Department of Chemistry, The University of Chicago, Chicago, IL, USA.
• Jiangbo Wei, Department of Chemistry, The University of Chicago, Chicago, IL, USA.
• Alberto J. Parra Vitela, Advocate Health - Midwest
• Urszula Dougherty, Department of Pathology, The University of Chicago, Chicago, IL, USA.
• Akushika Kwesi, Department of Pathology, The University of Chicago, Chicago, IL, USA.
• Alexander Luna, Department of Pathology, The University of Chicago, Chicago, IL, USA.
• Xuanhao Zhu, Department of Chemistry, The University of Chicago, Chicago, IL, USA.
• Shenghai Shen, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China.
• Yunzheng Liu, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
• Liangliang Wang, The Laboratory of Microbiome and Microecological Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
• Xiaolong Cui, Department of Chemistry, The University of Chicago, Chicago, IL, USA.
• Yuzhi Xu, Department of Chemistry, New York University, New York, NY, USA.
• Bochen Jiang, Department of Chemistry, The University of Chicago, Chicago, IL, USA.
• Yiyi Ji, Department of Chemistry, The University of Chicago, Chicago, IL, USA.
• Peng Xia, Department of Chemistry, The University of Chicago, Chicago, IL, USA.
• Diana C. West-Szymanski, Department of Chemistry, The University of Chicago, Chicago, IL, USA.
• Chenxi Sun, Department of Chemistry, The University of Chicago, Chicago, IL, USA.
• Yuhao Zhong, Department of Chemistry, The University of Chicago, Chicago, IL, USA.
• Chang Ye, Department of Chemistry, The University of Chicago, Chicago, IL, USA.
• Angelica Moran, Department of Pathology, The University of Chicago, Chicago, IL, USA.
• Christopher Lehmann, Department of Pathology, The University of Chicago, Chicago, IL, USA.
• Eric Pamer, Department of Pathology, The University of Chicago, Chicago, IL, USA.
• Wei Zhang, Department of Preventive Medicine and The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
• Marc Bissonnette, Department of Pathology, The University of Chicago, Chicago, IL, USA. mbissonn@bsd.uchicago.edu.
• Li-Sheng Zhang, Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China. zhangls@ust.hk.
• Chuan He, Department of Chemistry, The University of Chicago, Chicago, IL, USA. chuanhe@uchicago.edu.

Recommended Citation

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

Affiliations

Advocate Lutheran General Hospital

Abstract

Circulating cell-free RNA (cfRNA) in plasma represents a promising avenue for cancer detection. We report low-input multiple methylation sequencing, a method for profiling modification patterns in cfRNA, enabling the detection of diverse transfer RNAs and small noncoding RNAs derived from both the human genome and the microbiome. RNA modification patterns in microbiome-derived cfRNA accurately reflect host microbiota activity and hold potential for the early detection of colorectal cancer.

Document Type

Article

PubMed ID

40629040