Abstract
Enhancing the effectiveness of utilizing circulating cell-free DNA (cfDNA) for disease screening remains a challenge, necessitating improved sensitivity, specificity, cost-efficiency, and patient adherence. We present here LAMP-MS, an innovative technology that integrates linear amplification with single-base quantitative nucleic acid mass spectrometry on silicon chips. This approach overcomes several limitations in utilizing cfDNA 5-methylcytosine (5 mC) status for colorectal cancer (CRC) screening. LAMP-MS enables unbiased amplification of as little as 1 ng of cfDNA, site-specifically quantify methylation levels of multiple 5 mC sites, thereby facilitating cost-effective, high-resolution quantitative detection of cfDNA methylation markers. We have validated the accuracy of DNA methylation determination using DNA probes and cfDNA from patient plasma samples, confirmed by mass spectrometric peak areas. Additionally, we have further shown this Mass Array technology could be expanded to also quantify RNA m6A modification sites. Combining the ability to work with ultra-low input materials and a visually interpretable output, LAMP-MS stands out as a promising method for real-world applications in clinics and laboratories for nucleic acid methylation detection and quantification.
| Original language | English (US) |
|---|---|
| Article number | e202413872 |
| Journal | Angewandte Chemie - International Edition |
| Volume | 64 |
| Issue number | 1 |
| DOIs | |
| State | Published - Jan 2 2025 |
Funding
This work was supported by National Key R&D Program of China (2021YFA1100400), General Program of National Natural Science Foundation of China (32471340), Natural science foundation of Science and Technology Commission of Shanghai Municipality (STCSM, 21ZR1480300), and Fudan University Start\u2010up funding to L.H. J. L. was supported by National Natural Science Foundation of China, No. 82121002. Z. L. was supported by National Natural Science Foundation of China, General Program, No. 82172557. National Natural Science Foundation of China, General Program, No. 81870456. C.H. is a Howard Hughes Medical Institute Investigator. We thank the staff of Bionova (Shanghai) Medical Technology Co., Ltd. for assistance in cfDNA preparation and high\u2010throughput sequencing data analysis. We thank staff in Hushan Hospital for collecting blood samples. We thank The Professional Technical Service Platform for Critical Diseases in Shanghai, China (No.22142202400) for MALDI\u2010TOF analysis of synthesized DNA probes during LAMP\u2010MS strategy validation stage. We thank GenWish for MASS\u2010Array analysis of patient cfDNA during LAMP\u2010MS application stage. This work was supported by National Key R&D Program of China (2021YFA1100400), General Program of National Natural Science Foundation of China (32471340), Natural science foundation of Science and Technology Commission of Shanghai Municipality (STCSM, 21ZR1480300), and Fudan University Start-up funding to L.H. J. L. was supported by National Natural Science Foundation of China, No. 82121002. Z. L. was supported by National Natural Science Foundation of China, General Program, No. 82172557. National Natural Science Foundation of China, General Program, No. 81870456. C.H. is a Howard Hughes Medical Institute Investigator. We thank the staff of Bionova (Shanghai) Medical Technology Co., Ltd. for assistance in cfDNA preparation and high-throughput sequencing data analysis. We thank staff in Hushan Hospital for collecting blood samples. We thank The Professional Technical Service Platform for Critical Diseases in Shanghai, China (No.22142202400) for MALDI-TOF analysis of synthesized DNA probes during LAMP-MS strategy validation stage. We thank GenWish for MASS-Array analysis of patient cfDNA during LAMP-MS application stage.
Keywords
- DNA 5 mC
- LAMP-MS
- RNA mA
- cell-free DNA (cfDNA)
- colorectal cancer (CRC) screening
ASJC Scopus subject areas
- Catalysis
- General Chemistry
