ArticleProceedings of the National Academy of Sciences of the United States of America2010
Pathology tissue-chromatin immunoprecipitation, coupled with high-throughput sequencing, allows the epigenetic profiling of patient samples.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed, 73 citations in OpenAlex.
- Improved ChIP Sequencing for H3K27ac Profiling and Super-Enhancer Analysis Assisted by Fluorescence-Activated Sorting of Formalin-Fixed Paraffin-Embedded Tissues.Biological procedures online · 2025Article
- A High-Throughput PIXUL-Matrix-Based Toolbox to Profile Frozen and Formalin-Fixed Paraffin-Embedded Tissues Multiomes.Laboratory investigation; a journal of technical methods and pathology · 2024Article
- Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag.Nature communications · 2023Article
- Titration-based normalization of antibody amount improves consistency of ChIP-seq experiments.BMC genomics · 2023Article
- FFPE-ATAC: A Highly Sensitive Method for Profiling Chromatin Accessibility in Formalin-Fixed Paraffin-Embedded Samples.Current protocols · 2022Article
- A Highly Sensitive Method to Efficiently Profile the Histone Modifications of FFPE Samples.Bio-protocol · 2022Article
- The Current State of Chromatin Immunoprecipitation (ChIP) from FFPE Tissues.International journal of molecular sciences · 2022Review
- Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples.Genome research · 2022Article
- FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers.Nucleic acids research · 2021Article
- Modeling population size independent tissue epigenomes by ChIL-seq with single thin sections.Molecular systems biology · 2021Article
- Genome-Wide Chromatin Analysis of FFPE Tissues Using a Dual-Arm Robot with Clinical Potential.Cancers · 2021Article
- Article
- The K219T-Lamin mutation induces conduction defects through epigenetic inhibition of SCN5A in human cardiac laminopathy.Nature communications · 2019Article
- Direct measurement of the mechanical properties of a chromatin analog and the epigenetic effects of para-sulphonato-calix[4]arene.Scientific reports · 2019Article
- Blastic plasmacytoid dendritic cell neoplasm: genomics mark epigenetic dysregulation as a primary therapeutic target.Haematologica · 2019Article
- Enhanced and controlled chromatin extraction from FFPE tissues and the application to ChIP-seq.BMC genomics · 2019Article
- Epigenomic profiling of archived FFPE tissues by enhanced PAT-ChIP (EPAT-ChIP) technology.Clinical epigenetics · 2018Article
- PAT-H-MS coupled with laser microdissection to study histone post-translational modifications in selected cell populations from pathology samples.Clinical epigenetics · 2017Article
- The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies.International journal of genomics · 2017Review
- Tumour heterogeneity: principles and practical consequences.Virchows Archiv : an international journal of pathology · 2016Review
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Authors and funding
14 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Epigenetic alterations in the pattern of DNA and histone modifications play a crucial role in cancer development. Analysis of patient samples, however, is hampered by technical limitations in the study of chromatin structure from pathology archives that usually consist of heavily fixed, paraffin-embedded material. Here, we present a methodology [pathology tissue-ChIP (PAT-ChIP)] to extract and immunoprecipitate chromatin from paraffin-embedded patient samples up to several years old. In a pairwise comparison with canonical ChIP, PAT-ChIP showed a high reproducibility of results for several histone marks and an identical ability to detect dynamic changes in chromatin structure upon pharmacological treatment. Finally, we showed that PAT-ChIP can be coupled with high-throughput sequencing (PAT-ChIP-Seq) for the genome-wide analysis of distinct chromatin modifications. PAT-ChIP therefore represents a versatile procedure and diagnostic tool for the analysis of epigenetic alterations in cancer and potentially other diseases.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.