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

Eikrem, Øystein; Beisland, Christian; Hjelle, Karin M.; Flatberg, Arnar; Scherer, Andreas; Landolt, Lea; Skogstrand, Trude; Leh, Sabine; Beisvåg, Vidar; Marti, Hans-Peter

doi:10.1371/journal.pone.0149743

Cited by 52 publications

(57 citation statements)

References 43 publications

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“…The copy numbers of 587 ccRCC tissues and 901 paired normal kidney tissues from the TCGA database (KIRC CNV) were obtained. GSE76207 (14) and GSE102101 (15) were obtained from the GEO database (http://www.ncbi.nlm. nih.gov/geo/), and respectively contained 16 and 10 paired tumor and normal kidney tissues.…”

Section: Methodsmentioning

confidence: 99%

Ubiquitin specific peptidase 19 is a prognostic biomarker and affect the proliferation and migration of clear cell renal cell carcinoma

Fei

et al. 2020

Oncol Rep

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Ubiquitin specific peptidase 19 (USP19) is a member of the USP family and exhibits diverse roles in various biological processes, such as cell differentiation, cell cycle progression and apoptosis. There is limited knowledge regarding the role and impact of USP19 in cancer, particularly clear cell renal cell carcinoma (ccRCC). To examine the function of USP19 in ccRCC, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases were examined to determine USP19 mRNA expression levels. USP19 mRNA levels were significantly lower in ccRCC tissues than in normal tissues. USP19 downregulation was associated with ccRCC progression and poor prognostic outcomes in TCGA cohort. Furthermore, the functional involvement of USP19 in ccRCC was examined using Cell Counting Kit-8, soft agar, Transwell and wound healing assays in vitro following overexpression or knockdown of USP19 in the Caki-1 cell line. USP19 overexpression inhibited ccRCC proliferation and migration, whereas USP19 knockdown promoted ccRCC proliferation and migration in vitro. Consistent with these results, it was further demonstrated that USP19 downregulation promoted tumor growth in vivo in a xenograft model. Mechanistically, it was found that USP19 exerted its inhibitory effect on ccRCC proliferation and migration by suppressing the activation of ERK. Collectively, the present findings identified a role for USP19 as a tumor suppressor in ccRCC and demonstrated that USP19 is a potential prognostic biomarker that could be applied in ccRCC therapy.

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Section: Methodsmentioning

confidence: 99%

Ubiquitin specific peptidase 19 is a prognostic biomarker and affect the proliferation and migration of clear cell renal cell carcinoma

Fei

et al. 2020

Oncol Rep

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“…On the other hand, a low percentage relates to higher degradation and lower quality. The DV 200 shows a considerably higher reliability in comparison to RIN regarding RNA quality determination and thus allows the preparation of valuable libraries out of poor source material ( Eikrem et al, 2016 ).…”

Section: Standard Proposals For General Sequencing Workflowsmentioning

confidence: 99%

Standardization and quality management in next-generation sequencing

Endrullat

Glökler

Franke

et al. 2016

Applied & Translational Genomics

167

102

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DNA sequencing continues to evolve quickly even after > 30 years. Many new platforms suddenly appeared and former established systems have vanished in almost the same manner. Since establishment of next-generation sequencing devices, this progress gains momentum due to the continually growing demand for higher throughput, lower costs and better quality of data. In consequence of this rapid development, standardized procedures and data formats as well as comprehensive quality management considerations are still scarce. Here, we listed and summarized current standardization efforts and quality management initiatives from companies, organizations and societies in form of published studies and ongoing projects. These comprise on the one hand quality documentation issues like technical notes, accreditation checklists and guidelines for validation of sequencing workflows. On the other hand, general standard proposals and quality metrics are developed and applied to the sequencing workflow steps with the main focus on upstream processes. Finally, certain standard developments for downstream pipeline data handling, processing and storage are discussed in brief. These standardization approaches represent a first basis for continuing work in order to prospectively implement next-generation sequencing in important areas such as clinical diagnostics, where reliable results and fast processing is crucial. Additionally, these efforts will exert a decisive influence on traceability and reproducibility of sequence data.

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“…10 Beyond this reconstruction approach, there is potential value in being able to work in the opposite direction to 'deconvolute' bulk-tissue data, 29 e.g. in the analysis of formalin-fixed paraffin-embedded kidney biopsy samples, 30,31 to ascertain what cell types are present in the samples and how they are altered by disease processes. This can succeed qualitatively by identifying cell-type specific transcripts that differ in abundance in a patient sample versus some appropriate reference.…”

Section: Discussionmentioning

confidence: 99%

Cell-Type Selective Markers Represented in Whole-Kidney RNA-Seq Data

Clark

Chen

Chou

et al. 2018

Preprint

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Bulk-tissue RNA-Seq is seeing increasing use in the study of physiological and pathophysiological processes in the kidney. However, the presence of multiple cell types in kidney complicates the data interpretation. Here we address the question, “What cell types are represented in whole-kidney RNA-Seq data?” to identify circumstances in which bulk-kidney RNA-Seq can be successfully interpreted. We carried out RNA-Seq in mouse whole kidneys and microdissected renal tubule segments. To aid in the interpretation of the data, we compiled a database of cell-type selective protein markers for 43 cell types believed to be present in kidney tissue. The whole-kidney RNA-Seq analysis identified transcripts corresponding to 17742 genes, distributed over 5 orders of magnitude of expression level. Markers for all 43 curated cell types were detectable. Analysis of the cellular makeup of mouse and rat kidney, calculated from published literature, suggests that proximal tubule cells account for more than half of the mRNA in a kidney. Comparison of RNA-Seq data from microdissected proximal tubules with whole-kidney data supports this view. RNA-Seq data for cell-type selective markers in bulk-kidney samples provide a valid means to identify changes in minority-cell abundances in kidney tissue. Because proximal tubules make up a substantial fraction of whole-kidney samples, changes in proximal tubule gene expression can be assessed presumptively by bulk-kidney RNA-Seq, although results could potentially be obscured by the presence of mRNA from other cell types. The dominance of proximal tubule cells in whole-kidney samples also has implications for the interpretation of single-cell RNA-Seq data.

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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

Cited by 52 publications

References 43 publications

Ubiquitin specific peptidase 19 is a prognostic biomarker and affect the proliferation and migration of clear cell renal cell carcinoma

Ubiquitin specific peptidase 19 is a prognostic biomarker and affect the proliferation and migration of clear cell renal cell carcinoma

Standardization and quality management in next-generation sequencing

Cell-Type Selective Markers Represented in Whole-Kidney RNA-Seq Data

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