Solid-state nanopore analysis of human genomic DNA shows unaltered global 5-hydroxymethylcytosine content associated with early-stage breast cancer
5-Hydroxymethylcytosine (5hmC), the first oxidized form of the well-known epigenetic modification 5-methylcytosine, is an independent regulator of gene expression and therefore a potential marker for disease. Here, we report on methods developed for a selective solid-state nanopore assay that enable...
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Published in | Nanomedicine Vol. 35; p. 102407 |
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Main Authors | , , , , , , |
Format | Journal Article |
Language | English |
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01.07.2021
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Abstract | 5-Hydroxymethylcytosine (5hmC), the first oxidized form of the well-known epigenetic modification 5-methylcytosine, is an independent regulator of gene expression and therefore a potential marker for disease. Here, we report on methods developed for a selective solid-state nanopore assay that enable direct analysis of global 5hmC content in human tissue. We first describe protocols for preparing genomic DNA derived from both healthy breast tissue and stage 1 breast tumor tissue and then use our approach to probe the net abundance of the modified base in each cohort. Then, we employ empirical data to adjust for the impact of nanopore diameter on the quantification. Correcting for variations in nanopore diameter among the devices used for analysis reveals no detectable difference in global 5hmC content between healthy and tumor tissue. These results suggest that 5hmC changes may not be associated with early-stage breast cancer and instead are a downstream consequence of the disease.
A selective solid-state nanopore assay is used to examine global 5-hydroxymethylcytosine (5hmC) content in human genomic DNA. 5hmC has been shown to be strongly downregulated in diverse cancers, but it is less clear whether the decrease is a cause or an effect of disease initiation. To investigate this, we compare DNA from healthy breast tissue with that derived from stage 1 breast tumor tissue. We show that no statistical difference is observed between the two even after implementing technical corrections to maximize quantitative accuracy. Our results suggest that 5hmC downregulation is not a driver of tumorigenesis but a result, indicating that the potential for the modification as a cancer biomarker may be diminished in early stage disease. [Display omitted] |
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AbstractList | 5-hydroxymethylcytosine (5hmC), the first oxidized form of the well-known epigenetic modification 5-methylcytosine, is an independent regulator of gene expression and therefore a potential marker for disease. Here, we report on methods developed for a selective solid-state nanopore assay that enable direct analysis of global 5hmC content in human tissue. We first describe protocols for preparing genomic DNA derived from both healthy breast tissue and stage 1 breast tumor tissue and then use our approach to probe the net abundance of the modified base in each cohort. Then, we employ empirical data to adjust for the impact of nanopore diameter on the quantification. Correcting for variations in nanopore diameter among the devices used for analysis reveals no detectable difference in global 5hmC content between healthy and tumor tissue. These results suggest that 5hmC changes may not be associated with early-stage breast cancer and instead are a downstream consequence of the disease.
A selective solid-state nanopore assay is used to examine global 5-hydroxymethylcytosine (5hmC) content in human genomic DNA. 5hmC has been shown to be strongly downregulated in diverse cancers, but it is less clear whether the decrease is a cause or an effect of disease initiation. To investigate this, we compare DNA from healthy breast tissue with that derived from stage 1 breast tumor tissue. We show that no statistical difference is observed between the two even after implementing technical corrections to maximize quantitative accuracy. Our results suggest that 5hmC downregulation is not a driver of tumorigenesis but a result, indicating that the potential for the modification as a cancer biomarker may be diminished in early stage disease. 5-Hydroxymethylcytosine (5hmC), the first oxidized form of the well-known epigenetic modification 5-methylcytosine, is an independent regulator of gene expression and therefore a potential marker for disease. Here, we report on methods developed for a selective solid-state nanopore assay that enable direct analysis of global 5hmC content in human tissue. We first describe protocols for preparing genomic DNA derived from both healthy breast tissue and stage 1 breast tumor tissue and then use our approach to probe the net abundance of the modified base in each cohort. Then, we employ empirical data to adjust for the impact of nanopore diameter on the quantification. Correcting for variations in nanopore diameter among the devices used for analysis reveals no detectable difference in global 5hmC content between healthy and tumor tissue. These results suggest that 5hmC changes may not be associated with early-stage breast cancer and instead are a downstream consequence of the disease. 5-Hydroxymethylcytosine (5hmC), the first oxidized form of the well-known epigenetic modification 5-methylcytosine, is an independent regulator of gene expression and therefore a potential marker for disease. Here, we report on methods developed for a selective solid-state nanopore assay that enable direct analysis of global 5hmC content in human tissue. We first describe protocols for preparing genomic DNA derived from both healthy breast tissue and stage 1 breast tumor tissue and then use our approach to probe the net abundance of the modified base in each cohort. Then, we employ empirical data to adjust for the impact of nanopore diameter on the quantification. Correcting for variations in nanopore diameter among the devices used for analysis reveals no detectable difference in global 5hmC content between healthy and tumor tissue. These results suggest that 5hmC changes may not be associated with early-stage breast cancer and instead are a downstream consequence of the disease. A selective solid-state nanopore assay is used to examine global 5-hydroxymethylcytosine (5hmC) content in human genomic DNA. 5hmC has been shown to be strongly downregulated in diverse cancers, but it is less clear whether the decrease is a cause or an effect of disease initiation. To investigate this, we compare DNA from healthy breast tissue with that derived from stage 1 breast tumor tissue. We show that no statistical difference is observed between the two even after implementing technical corrections to maximize quantitative accuracy. Our results suggest that 5hmC downregulation is not a driver of tumorigenesis but a result, indicating that the potential for the modification as a cancer biomarker may be diminished in early stage disease. [Display omitted] |
ArticleNumber | 102407 |
Author | Zahid, Osama K. Wang, Fanny Rivas, Felipe Sethi, Komal Reiss, Katherine Bearden, Samuel Hall, Adam R. |
AuthorAffiliation | 1 Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA 2 Department of Engineering, Wake Forest University, Winston-Salem, NC 27101, USA 3 Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA |
AuthorAffiliation_xml | – name: 3 Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA – name: 1 Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA – name: 2 Department of Engineering, Wake Forest University, Winston-Salem, NC 27101, USA |
Author_xml | – sequence: 1 givenname: Osama K. surname: Zahid fullname: Zahid, Osama K. organization: Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA – sequence: 2 givenname: Felipe surname: Rivas fullname: Rivas, Felipe organization: Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA – sequence: 3 givenname: Fanny surname: Wang fullname: Wang, Fanny organization: Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA – sequence: 4 givenname: Komal surname: Sethi fullname: Sethi, Komal organization: Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA – sequence: 5 givenname: Katherine surname: Reiss fullname: Reiss, Katherine organization: Department of Engineering, Wake Forest University, Winston-Salem, NC, USA – sequence: 6 givenname: Samuel surname: Bearden fullname: Bearden, Samuel organization: Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA – sequence: 7 givenname: Adam R. surname: Hall fullname: Hall, Adam R. email: arhall@wakehealth.edu organization: Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA |
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Keywords | Epigenetics Hydroxymethylcytosine Solid-state nanopore Cancer |
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Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Credit Author Statement Osama K. Zahid: Methodology, Formal analysis, Investigation, Writing - Review & Editing Felipe Rivas: Formal analysis, Investigation Fanny Wang: Formal analysis, Investigation, Writing - Review & Editing Komal Sethi: Investigation, Writing - Review & Editing Katherine Reiss: Investigation, Writing - Review & Editing Samuel Bearden: Investigation, Writing - Review & Editing Adam R. Hall: Conceptualization, Methodology, Formal analysis, Resources, Writing - Original Draft, Writing - Review & Editing, Visualization, Supervision, Project administration, Funding acquisition O.K.Z., F.W., and F.R. performed experiments, analyzed data, and contributed to manuscript preparation. O.K.Z. also developed protocols. K.S. and K.R. contributed to construct length measurements. K.S. and S.B. performed SS-nanopore measurements on the diameter dependence of the assay. A.R.H. designed and oversaw the project, analyzed data, and wrote the manuscript. All authors reviewed the manuscript. Author Contributions |
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Snippet | 5-Hydroxymethylcytosine (5hmC), the first oxidized form of the well-known epigenetic modification 5-methylcytosine, is an independent regulator of gene... 5-hydroxymethylcytosine (5hmC), the first oxidized form of the well-known epigenetic modification 5-methylcytosine, is an independent regulator of gene... |
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SubjectTerms | 5-Methylcytosine - analogs & derivatives Breast Neoplasms - genetics Breast Neoplasms - metabolism Cancer DNA, Neoplasm - genetics DNA, Neoplasm - metabolism Epigenetics Female Genome, Human Humans Hydroxymethylcytosine MCF-7 Cells Nanopore Sequencing Neoplasm Staging Solid-state nanopore |
Title | Solid-state nanopore analysis of human genomic DNA shows unaltered global 5-hydroxymethylcytosine content associated with early-stage breast cancer |
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