Histo-molecular differentiation of renal cancer subtypes by mass spectrometry imaging and rapid proteome profiling of formalin-fixed paraffin-embedded tumor tissue sections

Möginger, Uwe; Marcussen, Niels; Jensen, Ole N.

doi:10.1101/2020.02.19.956433

Cited by 2 publications

(2 citation statements)

References 65 publications

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“…Proteomic expression profiling has highlighted the accumulation of mitochondrial proteins in renal oncocytoma. Some of these proteins correspond to traditional IHC markers used to distinguish renal oncocytoma from ChRCC [81,82].…”

Section: Molecular Diagnosismentioning

confidence: 99%

Renal oncocytoma: a challenging diagnosis

Mirkheshti

Naveed²,

Legesse

et al. 2022

Current Opinion in Oncology

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Purpose of reviewThe aim of the review is to provide an update on the current and evolving approaches to diagnosing the challenging clinical entity of renal oncocytoma. Recent findingsRenal oncocytoma is being increasingly recognized among patients with renal masses, and it can be found in up to 50% of benign small renal masses (SRMs) less than 4 cm. Renal oncocytomas have benign clinical biology but distinguishing them from some of the other renal masses with more malignant potential can be challenging due to overlapping imaging, histologic, and immunophenotypic characteristics. Increasing integration of various imaging modalities, histologic characteristics, cytogenetics, and molecular and metabolic signatures is helping better define and characterize renal masses.

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Section: Molecular Diagnosismentioning

confidence: 99%

Renal oncocytoma: a challenging diagnosis

Mirkheshti

Naveed²,

Legesse

et al. 2022

Current Opinion in Oncology

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“…In particular, the analysis of tumor tissues with pronounced cellular and morphological heterogeneity benefits from the spatially resolved MSI technology [3,4]. Common applications for MSI in cancer studies include tumor typing and subtyping [5][6][7], studying resection margins and tumor heterogeneity [8,9], and finding biomarkers for tumor diagnosis, prognosis or prediction [10][11][12].…”

mentioning

confidence: 99%

Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: A case study of an urothelial cancer cohort analyzed in the Galaxy framework

Föll

Volkmann

Enderle-Ammour

et al. 2021

Preprint

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Background: Mass spectrometry imaging (MSI) derives spatial molecular distribution maps directly from clinical tissue specimens. This allows for spatial characterization of molecular compositions of different tissue types and tumor subtypes, which bears great potential for assisting pathologists with diagnostic decisions or personalized treatments. Unfortunately, progress in translational MSI is often hindered by insufficient quality control and lack of reproducible data analysis. Raw data and analysis scripts are rarely publicly shared. Here, we demonstrate the application of the Galaxy MSI tool set for the reproducible analysis of an urothelial carcinoma dataset. Methods: Tryptic peptides were imaged in a cohort of 39 formalin-fixed, paraffin-embedded human urothelial cancer tissue cores with a MALDI-TOF/TOF device. The complete data analysis was performed in a fully transparent and reproducible manner on the European Galaxy Server. Annotations of tumor and stroma were performed by a pathologist and transferred to the MSI data to allow for supervised classifications of tumor vs. stroma tissue areas as well as for muscle-infiltrating and non-muscle invasive urothelial carcinomas. For putative peptide identifications, m/z features were matched to the MSiMass list. Results: Rigorous quality control in combination with careful pre-processing enabled reduction of m/z shifts and intensity batch effects. High classification accuracy was found for both, tumor vs. stroma and muscle-infiltrating vs. non-muscle invasive tumors. Some of the most discriminative m/z features for each condition could be assigned a putative identity: Stromal tissue was characterized by collagen type I peptides and tumor tissue by histone and heat shock protein beta-1 peptides. Intermediate filaments such as cytokeratins and vimentin were discriminative between the tumors with different muscle-infiltration status. To make the study fully reproducible and to advocate the criteria of FAIR (findability, accessibility, interoperability, and reusability) research data, we share the raw data, spectra annotations as well as all Galaxy histories and workflows. Data are available via ProteomeXchange with identifier PXD026459 and Galaxy results via https://github.com/foellmelanie/Bladder_MSI_Manuscript_Galaxy_links. Conclusion: Here, we show that translational MSI data analysis in a fully transparent and reproducible manner is possible and we would like to encourage the community to join our efforts.

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Histo-molecular differentiation of renal cancer subtypes by mass spectrometry imaging and rapid proteome profiling of formalin-fixed paraffin-embedded tumor tissue sections

Cited by 2 publications

References 65 publications

Renal oncocytoma: a challenging diagnosis

Renal oncocytoma: a challenging diagnosis

Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: A case study of an urothelial cancer cohort analyzed in the Galaxy framework

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