Multiplexed, single-molecule, epigenetic analysis of plasma-isolated nucleosomes for cancer diagnostics

Vadim Fedyuk; Nir Erez; Noa Furth; Olga Beresh; Ekaterina N Andreishcheva; Abhijeet Shinde; Daniel Jones; Barak Bar Zakai; Yael Mavor; Tamar Peretz; Ayala Hubert; Jonathan Cohen; Azzam Salah; Mark Temper; Albert Grinshpun; Myriam Maoz; Aviad Zick; Guy Ron; Efrat Shema

doi:10.1038/s41587-022-01447-3

Multiplexed, single-molecule, epigenetic analysis of plasma-isolated nucleosomes for cancer diagnostics

Vadim Fedyuk, Nir Erez, Noa Furth, Olga Beresh, Ekaterina N Andreishcheva, Abhijeet Shinde, Daniel Jones, Barak Bar Zakai, Yael Mavor, Tamar Peretz, Ayala Hubert, Jonathan Cohen, Azzam Salah, Mark Temper, Albert Grinshpun, Myriam Maoz, Aviad Zick, Guy Ron, Efrat Shema^*

^*Corresponding author for this work

Department of Immunology and Regenerative Biology

Research output: Contribution to journal › Article › peer-review

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Abstract

The analysis of cell-free DNA (cfDNA) in plasma provides 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 a single-molecule multiparametric assay to comprehensively profile the epigenetics of plasma-isolated nucleosomes (EPINUC), DNA methylation and cancer-specific protein biomarkers. Our system allows for high-resolution detection of six active and repressive histone modifications and their ratios and combinatorial patterns on millions of individual nucleosomes by single-molecule imaging. In addition, our system provides sensitive and quantitative data on plasma proteins, including detection of non-secreted tumor-specific proteins, such as mutant p53. EPINUC analysis of a cohort of 63 colorectal cancer, 10 pancreatic cancer and 33 healthy plasma samples detected cancer with 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 multilayered information of potential clinical relevance from limited (<1 ml) liquid biopsy material.<br />

Original language	English
Pages (from-to)	212-221
Number of pages	10
Journal	Nature Biotechnology
Volume	41
Issue number	2
DOIs	https://doi.org/10.1038/s41587-022-01447-3
Publication status	Published - Feb 2023

Bibliographical note

Funding Information:
We thank R. Rozenzweing, O. Fasust, M. Maurer and R. Irwin for their contributions in establishing a protocol for MBD2 labeling. We thank L. Segev for help with writing and integrating the μManager scripts for performing EPINUC–seq. We are grateful for the important comments made by I. Ulitsky while reading the manuscript. E.S. is an incumbent of the Lisa and Jeffrey Aronin Family Career Development chair. This research was supported by grants from the European Research Council (ERC801655 and ERC_PoC_963863), Emerson Collective, The Israeli Science Foundation (1881/19), The Israel Cancer Research Fund: Research Career Development Award, The German-Israeli Foundation for Scientific Research and Development and Minerva. We also obtained generous support from the Swiss Society Institute for Cancer Prevention Research and the Henry Chanoch Krenter Institute for Biomedical Imaging and Genomics.

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Fedyuk, V., Erez, N., Furth, N., Beresh, O., Andreishcheva, E. N., Shinde, A., Jones, D., Bar Zakai, B., Mavor, Y., Peretz, T., Hubert, A., Cohen, J., Salah, A., Temper, M., Grinshpun, A., Maoz, M., Zick, A., Ron, G., & Shema, E. (2023). Multiplexed, single-molecule, epigenetic analysis of plasma-isolated nucleosomes for cancer diagnostics. Nature Biotechnology, 41(2), 212-221. https://doi.org/10.1038/s41587-022-01447-3

@article{5f6d85c901be42059a2a4b7a3f0a2738,

title = "Multiplexed, single-molecule, epigenetic analysis of plasma-isolated nucleosomes for cancer diagnostics",

abstract = "The analysis of cell-free DNA (cfDNA) in plasma provides 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 a single-molecule multiparametric assay to comprehensively profile the epigenetics of plasma-isolated nucleosomes (EPINUC), DNA methylation and cancer-specific protein biomarkers. Our system allows for high-resolution detection of six active and repressive histone modifications and their ratios and combinatorial patterns on millions of individual nucleosomes by single-molecule imaging. In addition, our system provides sensitive and quantitative data on plasma proteins, including detection of non-secreted tumor-specific proteins, such as mutant p53. EPINUC analysis of a cohort of 63 colorectal cancer, 10 pancreatic cancer and 33 healthy plasma samples detected cancer with 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 multilayered information of potential clinical relevance from limited (<1 ml) liquid biopsy material.",

author = "Vadim Fedyuk and Nir Erez and Noa Furth and Olga Beresh and Andreishcheva, {Ekaterina N} and Abhijeet Shinde and Daniel Jones and {Bar Zakai}, Barak and Yael Mavor and Tamar Peretz and Ayala Hubert and Jonathan Cohen and Azzam Salah and Mark Temper and Albert Grinshpun and Myriam Maoz and Aviad Zick and Guy Ron and Efrat Shema",

note = "Funding Information: We thank R. Rozenzweing, O. Fasust, M. Maurer and R. Irwin for their contributions in establishing a protocol for MBD2 labeling. We thank L. Segev for help with writing and integrating the μManager scripts for performing EPINUC–seq. We are grateful for the important comments made by I. Ulitsky while reading the manuscript. E.S. is an incumbent of the Lisa and Jeffrey Aronin Family Career Development chair. This research was supported by grants from the European Research Council (ERC801655 and ERC_PoC_963863), Emerson Collective, The Israeli Science Foundation (1881/19), The Israel Cancer Research Fund: Research Career Development Award, The German-Israeli Foundation for Scientific Research and Development and Minerva. We also obtained generous support from the Swiss Society Institute for Cancer Prevention Research and the Henry Chanoch Krenter Institute for Biomedical Imaging and Genomics. ",

year = "2023",

month = feb,

doi = "10.1038/s41587-022-01447-3",

language = "English",

volume = "41",

pages = "212--221",

journal = "Nature Biotechnology",

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Fedyuk, V, Erez, N , Furth, N , Beresh, O, Andreishcheva, EN, Shinde, A, Jones, D, Bar Zakai, B, Mavor, Y, Peretz, T, Hubert, A, Cohen, J, Salah, A, Temper, M, Grinshpun, A, Maoz, M, Zick, A, Ron, G & Shema, E 2023, 'Multiplexed, single-molecule, epigenetic analysis of plasma-isolated nucleosomes for cancer diagnostics', Nature Biotechnology, vol. 41, no. 2, pp. 212-221. https://doi.org/10.1038/s41587-022-01447-3

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T1 - Multiplexed, single-molecule, epigenetic analysis of plasma-isolated nucleosomes for cancer diagnostics

AU - Fedyuk, Vadim

AU - Erez, Nir

AU - Furth, Noa

AU - Beresh, Olga

AU - Andreishcheva, Ekaterina N

AU - Shinde, Abhijeet

AU - Jones, Daniel

AU - Bar Zakai, Barak

AU - Mavor, Yael

AU - Peretz, Tamar

AU - Hubert, Ayala

AU - Cohen, Jonathan

AU - Salah, Azzam

AU - Temper, Mark

AU - Grinshpun, Albert

AU - Maoz, Myriam

AU - Zick, Aviad

AU - Ron, Guy

AU - Shema, Efrat

N1 - Funding Information: We thank R. Rozenzweing, O. Fasust, M. Maurer and R. Irwin for their contributions in establishing a protocol for MBD2 labeling. We thank L. Segev for help with writing and integrating the μManager scripts for performing EPINUC–seq. We are grateful for the important comments made by I. Ulitsky while reading the manuscript. E.S. is an incumbent of the Lisa and Jeffrey Aronin Family Career Development chair. This research was supported by grants from the European Research Council (ERC801655 and ERC_PoC_963863), Emerson Collective, The Israeli Science Foundation (1881/19), The Israel Cancer Research Fund: Research Career Development Award, The German-Israeli Foundation for Scientific Research and Development and Minerva. We also obtained generous support from the Swiss Society Institute for Cancer Prevention Research and the Henry Chanoch Krenter Institute for Biomedical Imaging and Genomics.

PY - 2023/2

Y1 - 2023/2

N2 - The analysis of cell-free DNA (cfDNA) in plasma provides 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 a single-molecule multiparametric assay to comprehensively profile the epigenetics of plasma-isolated nucleosomes (EPINUC), DNA methylation and cancer-specific protein biomarkers. Our system allows for high-resolution detection of six active and repressive histone modifications and their ratios and combinatorial patterns on millions of individual nucleosomes by single-molecule imaging. In addition, our system provides sensitive and quantitative data on plasma proteins, including detection of non-secreted tumor-specific proteins, such as mutant p53. EPINUC analysis of a cohort of 63 colorectal cancer, 10 pancreatic cancer and 33 healthy plasma samples detected cancer with 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 multilayered information of potential clinical relevance from limited (<1 ml) liquid biopsy material.

AB - The analysis of cell-free DNA (cfDNA) in plasma provides 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 a single-molecule multiparametric assay to comprehensively profile the epigenetics of plasma-isolated nucleosomes (EPINUC), DNA methylation and cancer-specific protein biomarkers. Our system allows for high-resolution detection of six active and repressive histone modifications and their ratios and combinatorial patterns on millions of individual nucleosomes by single-molecule imaging. In addition, our system provides sensitive and quantitative data on plasma proteins, including detection of non-secreted tumor-specific proteins, such as mutant p53. EPINUC analysis of a cohort of 63 colorectal cancer, 10 pancreatic cancer and 33 healthy plasma samples detected cancer with 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 multilayered information of potential clinical relevance from limited (<1 ml) liquid biopsy material.

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DO - 10.1038/s41587-022-01447-3

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EP - 221

JO - Nature Biotechnology

JF - Nature Biotechnology

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ER -

Multiplexed, single-molecule, epigenetic analysis of plasma-isolated nucleosomes for cancer diagnostics

Abstract

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