Multiplexed Single-Molecule Epigenetic Analysis of Plasma-Isolated Nucleosomes for Cancer Diagnostics

Fedyuk, V.; Erez, N.; Furth, N.; Beresh, O.; Jones, D.; Shinde, A.; Andreishcheva, K.; Zakai, B. B.; Mavor, Y.; Peretz, T.; Hubert, A.; Cohen, J. E.; Salah, A.; Temper, M.; Grinshpun, A.; Maoz, M.; Zick, A.; Ron, G.; Shema, E.

doi:10.1101/2021.11.01.466724

bioRxiv · 10.1101/2021.11.01.466724

Multiplexed Single-Molecule Epigenetic Analysis of Plasma-Isolated Nucleosomes for Cancer Diagnostics

Fedyuk, V.·Erez, N.·Furth, N.·Beresh, O.·Jones, D.·Shinde, A.·Andreishcheva, K.·Zakai, B. B.·Mavor, Y.·Peretz, T.·Hubert, A.·Cohen, J. E.·Salah, A.·Temper, M.·Grinshpun, A.·Maoz, M.·Zick, A.·Ron, G.·Shema, E.

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Abstract

The analysis of cell-free DNA (cfDNA) in plasma represents a rapidly advancing field in medicine, providing information on pathological processes in the body. Blood cfDNA is in the form of nucleosomes, which maintain their tissue- and cancer-specific epigenetic state. We developed EPINUC, a single-molecule multi-parametric assay to comprehensively profile the Epigenetics of Plasma Isolated Nucleosomes, DNA methylation and cancer-specific protein biomarkers. Our system allows high-resolution detection of six active and repressive histone modifications, their ratios and combinatorial patterns, on millions of individual nucleosomes by single-molecule imaging. In addition, it provides sensitive and quantitative data on plasma proteins, including detection of non-secreted tumor-specific proteins such as mutant p53. Applying this analysis to a cohort of plasma samples detected colorectal cancer at high accuracy and sensitivity, even at early stages. Finally, combining EPINUC with direct single-molecule DNA sequencing revealed the tissue-of-origin of colorectal, pancreatic, lung and breast tumors. EPINUC provides multi-layered clinical-relevant information from limited liquid biopsy material, establishing a novel approach for cancer diagnostics.

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Fedyuk, V., Erez, N., Furth, N., Beresh, O., Jones, D., Shinde, A., Andreishcheva, K., Zakai, B. B., Mavor, Y., Peretz, T., Hubert, A., Cohen, J. E., Salah, A., Temper, M., Grinshpun, A., Maoz, M., Zick, A., Ron, G., Shema, E.. 2021-11-03. Multiplexed Single-Molecule Epigenetic Analysis of Plasma-Isolated Nucleosomes for Cancer Diagnostics. https://doi.org/10.1101/2021.11.01.466724

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