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Diagnosis of malignant body fluids via cancer-universal methylation in cell-free DNA
Zhanrui Mao, … , Lin Tong, Wenqiang Yu
Zhanrui Mao, … , Lin Tong, Wenqiang Yu
Published April 8, 2024
Citation Information: JCI Insight. 2024;9(7):e175482. https://doi.org/10.1172/jci.insight.175482.
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Clinical Research and Public Health Genetics Oncology

Diagnosis of malignant body fluids via cancer-universal methylation in cell-free DNA

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Abstract

BACKGROUND Differentiating malignant from nonmalignant body fluids remains a clinical challenge because of the unsatisfying performance of conventional cytology. We aimed to improve the sensitivity and ubiquity of cancer cell detection by assaying universal cancer–only methylation (UCOM) markers in supernatant cell-free DNA (cfDNA).METHODS An observational prospective cohort including 1,321 nonmalignant and malignant body fluids of multiple cancers was used to develop and validate a cfDNA UCOM methylation diagnostic assay. All samples were divided into 2 portions for cytology and supernatant cfDNA methylation analysis.RESULTS The significant hypermethylation of a potentially novel UCOM marker, TAGMe, together with the formerly reported PCDHGB7, was identified in the cfDNA of malignant body fluid samples. The combined model, cell-free cancer-universal methylation (CUE), was developed and validated in a prospective multicancer cohort with markedly elevated sensitivity and specificity, and was further verified in a set containing additional types of malignant body fluids and metastases. In addition, it remained hypersensitive in detecting cancer cells in cytologically negative malignant samples.CONCLUSION cfDNA methylation markers are robust in detecting tumor cells and are applicable to diverse body fluids and tumor types, providing a feasible complement to current cytology-based diagnostic analyses.TRIAL REGISTRATION This study was registered at Chictr.org.cn (ChiCTR2200060532).FUNDING National Natural Science Foundation of China (32270645, 31872814, 32000505, 82170088), the National Key R&D Program of Ningxia Hui Autonomous region (2022BEG01003), Shanghai Municipal Key Clinical Specialty (shslczdzk02201), Science and Technology Commission of Shanghai Municipality (20DZ2261200, 20DZ2254400), and Major Special Projects of Basic Research of Shanghai Science and Technology Commission (18JC1411101).

Authors

Zhanrui Mao, Shihua Dong, Yu Yan, Chengyang Wang, Wei Li, Lu Wang, Chengchen Qian, Yuanlin Song, Lin Tong, Wenqiang Yu

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Figure 2

UCOM markers demonstrated to identify tumor cells using cfDNA in malignant pleural effusion (MPE).

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UCOM markers demonstrated to identify tumor cells using cfDNA in maligna...
(A) Significant cfDNA hypermethylation of PCDHGB7 was detected in MPE samples from lung cancer patients by pyrosequencing. (B) MSRE-qPCR–based results highly correlated with the methylation percentages using cfDNA pyrosequencing. Spearman’s r correlation and P value were calculated using GraphPad Prism 9.3.0. (C) MSRE-qPCR simultaneously revealed PCDHGB7 cfDNA hypermethylation in MPE samples. (D) ROC analysis demonstrates complementary performance of the marker identified in this study, TAGMe, and PCDHGB7 across multiple cancer types in TCGA database. P values were calculated by pair-wise comparison of ROC curves test with SPSS 20.0. *P < 0.05; ***P < 0.001; ****P < 0.0001.NS, not significant. (E) cfDNA hypermethylation of TAGMe was also validated in MPE samples by MSRE-qPCR. (F) ROC analysis demonstrated the performance of the 3 assays. (G) Complementary results for 2 markers were found in the same sample. (H) The sensitivity can be maximized by a 2-marker detection in a single-positive-for-positive method. Black circles: nonmalignant samples; pink circles: malignant samples with positive cytology; green squares: malignant samples in which cytology failed to detect tumor cells. BLCA, bladder cancer; BRCA, breast cancer; CESC, cervical cancer; CHOL, bile duct cancer; COADREAD, colon and rectal cancer; ESCA, esophageal cancer; GBM, glioblastoma; HNSC, head and neck cancer; KIRC, kidney clear cell carcinoma; KIRP, kidney papillary cell carcinoma; LIHC, liver cancer; LUNG, lung cancer; PAAD, pancreatic cancer; PRAD, prostate cancer; UCEC, endometrioid cancer. P values in A, C, and E were calculated using a 2-tailed, nonparametric Mann-Whitney test as determined by GraphPad Prism 9.3.0.

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