Cargando…
Liquid biopsy epigenomic profiling for cancer subtyping
Although circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we d...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
Nature Publishing Group US
2023
|
| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10695830/ https://www.ncbi.nlm.nih.gov/pubmed/37865722 http://dx.doi.org/10.1038/s41591-023-02605-z |
| _version_ | 1785154440527872000 |
|---|---|
| author | Baca, Sylvan C. Seo, Ji-Heui Davidsohn, Matthew P. Fortunato, Brad Semaan, Karl Sotudian, Shahabbedin Lakshminarayanan, Gitanjali Diossy, Miklos Qiu, Xintao El Zarif, Talal Savignano, Hunter Canniff, John Madueke, Ikenna Saliby, Renee Maria Zhang, Ziwei Li, Rong Jiang, Yijia Taing, Len Awad, Mark Chau, Cindy H. DeCaprio, James A. Figg, William D. Greten, Tim F. Hata, Aaron N. Hodi, F. Stephen Hughes, Melissa E. Ligon, Keith L. Lin, Nancy Ng, Kimmie Oser, Matthew G. Meador, Catherine Parsons, Heather A. Pomerantz, Mark M. Rajan, Arun Ritz, Jerome Thakuria, Manisha Tolaney, Sara M. Wen, Patrick Y. Long, Henry Berchuck, Jacob E. Szallasi, Zoltan Choueiri, Toni K. Freedman, Matthew L. |
| author_facet | Baca, Sylvan C. Seo, Ji-Heui Davidsohn, Matthew P. Fortunato, Brad Semaan, Karl Sotudian, Shahabbedin Lakshminarayanan, Gitanjali Diossy, Miklos Qiu, Xintao El Zarif, Talal Savignano, Hunter Canniff, John Madueke, Ikenna Saliby, Renee Maria Zhang, Ziwei Li, Rong Jiang, Yijia Taing, Len Awad, Mark Chau, Cindy H. DeCaprio, James A. Figg, William D. Greten, Tim F. Hata, Aaron N. Hodi, F. Stephen Hughes, Melissa E. Ligon, Keith L. Lin, Nancy Ng, Kimmie Oser, Matthew G. Meador, Catherine Parsons, Heather A. Pomerantz, Mark M. Rajan, Arun Ritz, Jerome Thakuria, Manisha Tolaney, Sara M. Wen, Patrick Y. Long, Henry Berchuck, Jacob E. Szallasi, Zoltan Choueiri, Toni K. Freedman, Matthew L. |
| author_sort | Baca, Sylvan C. |
| collection | PubMed |
| description | Although circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1 ml of patient plasma. Using an immunoprecipitation-based approach targeting histone modifications and DNA methylation, we measured 1,268 epigenomic profiles in plasma from 433 individuals with one of 15 cancers. Our assay provided a robust proxy for transcriptional activity, allowing us to infer the expression levels of diagnostic markers and drug targets, measure the activity of therapeutically targetable transcription factors and detect epigenetic mechanisms of resistance. This proof-of-concept study in advanced cancers shows how plasma epigenomic profiling has the potential to unlock clinically actionable information that is currently accessible only via direct tissue sampling. |
| format | Online Article Text |
| id | pubmed-10695830 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2023 |
| publisher | Nature Publishing Group US |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-106958302023-12-06 Liquid biopsy epigenomic profiling for cancer subtyping Baca, Sylvan C. Seo, Ji-Heui Davidsohn, Matthew P. Fortunato, Brad Semaan, Karl Sotudian, Shahabbedin Lakshminarayanan, Gitanjali Diossy, Miklos Qiu, Xintao El Zarif, Talal Savignano, Hunter Canniff, John Madueke, Ikenna Saliby, Renee Maria Zhang, Ziwei Li, Rong Jiang, Yijia Taing, Len Awad, Mark Chau, Cindy H. DeCaprio, James A. Figg, William D. Greten, Tim F. Hata, Aaron N. Hodi, F. Stephen Hughes, Melissa E. Ligon, Keith L. Lin, Nancy Ng, Kimmie Oser, Matthew G. Meador, Catherine Parsons, Heather A. Pomerantz, Mark M. Rajan, Arun Ritz, Jerome Thakuria, Manisha Tolaney, Sara M. Wen, Patrick Y. Long, Henry Berchuck, Jacob E. Szallasi, Zoltan Choueiri, Toni K. Freedman, Matthew L. Nat Med Brief Communication Although circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1 ml of patient plasma. Using an immunoprecipitation-based approach targeting histone modifications and DNA methylation, we measured 1,268 epigenomic profiles in plasma from 433 individuals with one of 15 cancers. Our assay provided a robust proxy for transcriptional activity, allowing us to infer the expression levels of diagnostic markers and drug targets, measure the activity of therapeutically targetable transcription factors and detect epigenetic mechanisms of resistance. This proof-of-concept study in advanced cancers shows how plasma epigenomic profiling has the potential to unlock clinically actionable information that is currently accessible only via direct tissue sampling. Nature Publishing Group US 2023-10-21 2023 /pmc/articles/PMC10695830/ /pubmed/37865722 http://dx.doi.org/10.1038/s41591-023-02605-z Text en © The Author(s) 2023, corrected publication 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
| spellingShingle | Brief Communication Baca, Sylvan C. Seo, Ji-Heui Davidsohn, Matthew P. Fortunato, Brad Semaan, Karl Sotudian, Shahabbedin Lakshminarayanan, Gitanjali Diossy, Miklos Qiu, Xintao El Zarif, Talal Savignano, Hunter Canniff, John Madueke, Ikenna Saliby, Renee Maria Zhang, Ziwei Li, Rong Jiang, Yijia Taing, Len Awad, Mark Chau, Cindy H. DeCaprio, James A. Figg, William D. Greten, Tim F. Hata, Aaron N. Hodi, F. Stephen Hughes, Melissa E. Ligon, Keith L. Lin, Nancy Ng, Kimmie Oser, Matthew G. Meador, Catherine Parsons, Heather A. Pomerantz, Mark M. Rajan, Arun Ritz, Jerome Thakuria, Manisha Tolaney, Sara M. Wen, Patrick Y. Long, Henry Berchuck, Jacob E. Szallasi, Zoltan Choueiri, Toni K. Freedman, Matthew L. Liquid biopsy epigenomic profiling for cancer subtyping |
| title | Liquid biopsy epigenomic profiling for cancer subtyping |
| title_full | Liquid biopsy epigenomic profiling for cancer subtyping |
| title_fullStr | Liquid biopsy epigenomic profiling for cancer subtyping |
| title_full_unstemmed | Liquid biopsy epigenomic profiling for cancer subtyping |
| title_short | Liquid biopsy epigenomic profiling for cancer subtyping |
| title_sort | liquid biopsy epigenomic profiling for cancer subtyping |
| topic | Brief Communication |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10695830/ https://www.ncbi.nlm.nih.gov/pubmed/37865722 http://dx.doi.org/10.1038/s41591-023-02605-z |
| work_keys_str_mv | AT bacasylvanc liquidbiopsyepigenomicprofilingforcancersubtyping AT seojiheui liquidbiopsyepigenomicprofilingforcancersubtyping AT davidsohnmatthewp liquidbiopsyepigenomicprofilingforcancersubtyping AT fortunatobrad liquidbiopsyepigenomicprofilingforcancersubtyping AT semaankarl liquidbiopsyepigenomicprofilingforcancersubtyping AT sotudianshahabbedin liquidbiopsyepigenomicprofilingforcancersubtyping AT lakshminarayanangitanjali liquidbiopsyepigenomicprofilingforcancersubtyping AT diossymiklos liquidbiopsyepigenomicprofilingforcancersubtyping AT qiuxintao liquidbiopsyepigenomicprofilingforcancersubtyping AT elzariftalal liquidbiopsyepigenomicprofilingforcancersubtyping AT savignanohunter liquidbiopsyepigenomicprofilingforcancersubtyping AT canniffjohn liquidbiopsyepigenomicprofilingforcancersubtyping AT maduekeikenna liquidbiopsyepigenomicprofilingforcancersubtyping AT salibyreneemaria liquidbiopsyepigenomicprofilingforcancersubtyping AT zhangziwei liquidbiopsyepigenomicprofilingforcancersubtyping AT lirong liquidbiopsyepigenomicprofilingforcancersubtyping AT jiangyijia liquidbiopsyepigenomicprofilingforcancersubtyping AT tainglen liquidbiopsyepigenomicprofilingforcancersubtyping AT awadmark liquidbiopsyepigenomicprofilingforcancersubtyping AT chaucindyh liquidbiopsyepigenomicprofilingforcancersubtyping AT decapriojamesa liquidbiopsyepigenomicprofilingforcancersubtyping AT figgwilliamd liquidbiopsyepigenomicprofilingforcancersubtyping AT gretentimf liquidbiopsyepigenomicprofilingforcancersubtyping AT hataaaronn liquidbiopsyepigenomicprofilingforcancersubtyping AT hodifstephen liquidbiopsyepigenomicprofilingforcancersubtyping AT hughesmelissae liquidbiopsyepigenomicprofilingforcancersubtyping AT ligonkeithl liquidbiopsyepigenomicprofilingforcancersubtyping AT linnancy liquidbiopsyepigenomicprofilingforcancersubtyping AT ngkimmie liquidbiopsyepigenomicprofilingforcancersubtyping AT osermatthewg liquidbiopsyepigenomicprofilingforcancersubtyping AT meadorcatherine liquidbiopsyepigenomicprofilingforcancersubtyping AT parsonsheathera liquidbiopsyepigenomicprofilingforcancersubtyping AT pomerantzmarkm liquidbiopsyepigenomicprofilingforcancersubtyping AT rajanarun liquidbiopsyepigenomicprofilingforcancersubtyping AT ritzjerome liquidbiopsyepigenomicprofilingforcancersubtyping AT thakuriamanisha liquidbiopsyepigenomicprofilingforcancersubtyping AT tolaneysaram liquidbiopsyepigenomicprofilingforcancersubtyping AT wenpatricky liquidbiopsyepigenomicprofilingforcancersubtyping AT longhenry liquidbiopsyepigenomicprofilingforcancersubtyping AT berchuckjacobe liquidbiopsyepigenomicprofilingforcancersubtyping AT szallasizoltan liquidbiopsyepigenomicprofilingforcancersubtyping AT choueiritonik liquidbiopsyepigenomicprofilingforcancersubtyping AT freedmanmatthewl liquidbiopsyepigenomicprofilingforcancersubtyping |