ArticlePloS one2016
Transcriptome Sequencing (RNAseq) Enables Utilization of Formalin-Fixed, Paraffin-Embedded Biopsies with Clear Cell Renal Cell Carcinoma for Exploration of Disease Biology and Biomarker Development.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Pre-analytical Best Practices for RNA Sequencing from Small Biopsies and Cytologic Specimens.Molecular diagnosis & therapy · 2026Review
- Reconstruction of Single-Cell Spatial Transcriptomes in Archival Kidney Biopsies.Kidney international reports · 2026Article
- Formalin-fixed paraffin-embedded (FFPE) samples help to investigate transcriptomic responses in wildlife disease.Molecular ecology resources · 2025Article
- Reliable RNA-seq analysis from FFPE specimens as a means to accelerate cancer-related health disparities research.PloS one · 2025Article
- Alternative Polyadenylation Regulatory Factors Signature for Survival Prediction in Kidney Renal Cell Carcinoma.Cancer informatics · 2024Article
- Comprehensive RNA-seq reveals molecular changes in kidney malignancy among people living with HIV.Molecular therapy. Nucleic acids · 2022Article
- A multiomics disease progression signature of low-risk ccRCC.Scientific reports · 2022Article
- AGAP2-AS1 as a prognostic biomarker in low-risk clear cell renal cell carcinoma patients with progressing disease.Cancer cell international · 2021Article
- Silencing circular RNA circ_0054537 and upregulating microRNA-640 suppress malignant progression of renal cell carcinoma via regulating neuronal pentraxin-2 (NPTX2).Bioengineered · 2021Article
- Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors.NPJ genomic medicine · 2021Article
- Predicting the clinical outcome of oral potentially malignant disorders using transcriptomic-based molecular pathology.British journal of cancer · 2021Article
- Variable expression of eighteen common housekeeping genes in human non-cancerous kidney biopsies.PloS one · 2021Article
- SMIXnorm: Fast and Accurate RNA-Seq Data Normalization for Formalin-Fixed Paraffin-Embedded Samples.Frontiers in genetics · 2021Article
- MIXnorm: normalizing RNA-seq data from formalin-fixed paraffin-embedded samples.Bioinformatics (Oxford, England) · 2020Article
- Ubiquitin specific peptidase 19 is a prognostic biomarker and affect the proliferation and migration of clear cell renal cell carcinoma.Oncology reports · 2020Article
- Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research.Scientific reports · 2019Article
- RNA-seq from archival FFPE breast cancer samples: molecular pathway fidelity and novel discovery.BMC medical genomics · 2019Article
- A comparative analysis of RNA sequencing methods with ribosome RNA depletion for degraded and low-input total RNA from formalin-fixed and paraffin-embedded samples.BMC genomics · 2019Article
- Insights into rheumatic diseases from next-generation sequencing.Nature reviews. Rheumatology · 2019Review
- The Transcriptomic Toolbox: Resources for Interpreting Large Gene Expression Data within a Precision Medicine Context for Metabolic Disease Atherosclerosis.Journal of personalized medicine · 2019Article
Corrections and comments
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10 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissues are an underused resource for molecular analyses. This proof of concept study aimed to compare RNAseq results from FFPE biopsies with the corresponding RNAlater® (Qiagen, Germany) stored samples from clear cell renal cell carcinoma (ccRCC) patients to investigate feasibility of RNAseq in archival tissue. From each of 16 patients undergoing partial or full nephrectomy, four core biopsies, such as two specimens with ccRCC and two specimens of adjacent normal tissue, were obtained with a 16g needle. One normal and one ccRCC tissue specimen per patient was stored either in FFPE or RNAlater®. RNA sequencing libraries were generated applying the new Illumina TruSeq® Access library preparation protocol. Comparative analysis was done using voom/Limma R-package. The analysis of the FFPE and RNAlater® datasets yielded similar numbers of detected genes, differentially expressed transcripts and affected pathways. The FFPE and RNAlater datasets shared 80% (n = 1106) differentially expressed genes. The average expression and the log2 fold changes of these transcripts correlated with R2 = 0.97, and R2 = 0.96, respectively. Among transcripts with the highest fold changes in both datasets were carbonic anhydrase 9 (CA9), neuronal pentraxin-2 (NPTX2) and uromodulin (UMOD) that were confirmed by immunohistochemistry. IPA revealed the presence of gene signatures of cancer and nephrotoxicity, renal damage and immune response. To simulate the feasibility of clinical biomarker studies with FFPE samples, a classifier model was developed for the FFPE dataset: expression data for CA9 alone had an accuracy, specificity and sensitivity of 94%, respectively, and achieved similar performance in the RNAlater dataset. Transforming growth factor-ß1 (TGFB1)-regulated genes, epithelial to mesenchymal transition (EMT) and NOTCH signaling cascade may support novel therapeutic strategies. In conclusion, in this proof of concept study, RNAseq data obtained from FFPE kidney biopsies are comparable to data obtained from fresh stored material, thereby expanding the utility of archival tissue specimens.
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