ArticleBMC medical genomics2019
RNA-seq from archival FFPE breast cancer samples: molecular pathway fidelity and novel discovery.
Article in BMC medical genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 67 citations in OpenAlex.
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- Comparative analysis of library preparation approaches for FFPE gene expression profiling and related recommendations.Scientific reports · 2025Article
- The analysis of transcriptomic signature of TNBC-searching for the potential RNA-based predictive biomarkers to determine the chemotherapy sensitivity.Journal of applied genetics · 2025Article
- Systematic comparison of quantity and quality of RNA recovered with commercial FFPE tissue extraction kits.Journal of translational medicine · 2025Article
- Epigenetic regulation of individual components of combined hepatocellular-cholangiocarcinoma.PloS one · 2025Article
- Evaluating cell type deconvolution in FFPE breast tissue: application to benign breast disease.NAR genomics and bioinformatics · 2024Review
- EMBER creates a unified space for independent breast cancer transcriptomic datasets enabling precision oncology.NPJ breast cancer · 2024Article
- LINCATRA: Two-cycle method to amplify RNA for transcriptome analysis from formalin-fixed paraffin-embedded tissue.Heliyon · 2024Article
- Optimization of FFPE preparation and identification of gene attributes associated with RNA degradation.NAR genomics and bioinformatics · 2024Article
- Verification of molecular subtyping of bladder cancer in the GUSTO clinical trial.The journal of pathology. Clinical research · 2024Article
- Linking gene expression to clinical outcomes in pediatric Crohn's disease using machine learning.Scientific reports · 2024Article
- Archival skin biopsy specimens as a tool for miRNA-based diagnosis: Technical and post-analytical considerations.Molecular therapy. Methods & clinical development · 2023Article
- A Novel Metastatic Estrogen Receptor-Expressing Breast Cancer Model with Antiestrogen Responsiveness.Cancers · 2023Article
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Authors and funding
13 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundFormalin-fixed, paraffin-embedded (FFPE) tissues for RNA-seq have advantages over fresh frozen tissue including abundance and availability, connection to rich clinical data, and association with patient outcomes. However, FFPE-derived RNA is highly degraded and chemically modified, which impacts its utility as a faithful source for biological inquiry.
methodsTrue archival FFPE breast cancer cases (n = 58), stored at room temperature for 2-23 years, were utilized to identify key steps in tissue selection, RNA isolation, and library choice. Gene expression fidelity was evaluated by comparing FFPE data to public data obtained from fresh tissues, and by employing single-gene, gene set and transcription network-based regulon analyses.
resultsWe report a single 10 μm section of breast tissue yields sufficient RNA for RNA-seq, and a relationship between RNA quality and block age that was not linear. We find single-gene analysis is limiting with FFPE tissues, while targeted gene set approaches effectively distinguish ER+ from ER- breast cancers. Novel utilization of regulon analysis identified the transcription factor KDM4B to associate with ER+ disease, with KDM4B regulon activity and gene expression having prognostic significance in an independent cohort of ER+ cases.
conclusionOur results, which outline a robust FFPE-RNA-seq pipeline for broad use, support utilizing FFPE tissues to address key questions in the breast cancer field, including the delineation between indolent and life-threatening disease, biological stratification and molecular mechanisms of treatment resistance.
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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.