Sarcoma classification by DNA methylation profiling in clinical everyday life: the Charité experience

(2022) 14:149 Roohani et al. Clinical Epigenetics https://doi.org/10.1186/s13148-022-01365-w Open Access RESEARCH Sarcoma classification by DNA methylation profiling in clinical everyday life: the Charité experience Siyer Roohani1* , Felix Ehret1,2,3 , Eilís Perez4, David Capper3,4, Armin Jarosch5, Anne Flörcken3,6, Sven Märdian7, Daniel Zips1,3 and David Kaul1,3    Abstract Background: Sarcomas are a heterogeneous group of rare malignant tumors with more than 100 subtypes. Accurate diagnosis remains challenging due to a lack of characteristic molecular or histomorphological hallmarks. A DNA methylation-based tumor profiling classifier for sarcomas (known as sarcoma classifier) from the German Cancer Research Center (Deutsches Krebsforschungszentrum) is now employed in selected cases to guide tumor classification and treatment decisions at our institution. Data on the usage of the classifier in daily clinical routine are lacking. Methods: In this single-center experience, we describe the clinical course of five sarcoma cases undergoing thorough pathological and reference pathological examination as well as DNA methylation-based profiling and their impact on subsequent treatment decisions. We collected data on the clinical course, DNA methylation analysis, histopathology, radiological imaging, and next-generation sequencing. Results: Five clinical cases involving DNA methylation-based profiling in 2021 at our institution were included. All patients’ DNA methylation profiles were successfully matched to a methylation profile cluster of the sarcoma classifier’s dataset. In three patients, the classifier reassured diagnosis or aided in finding the correct diagnosis in light of contradictory data and differential diagnoses. In two patients with intracranial tumors, the classifier changed the diagnosis to a novel diagnostic tumor group. Conclusions: The sarcoma classifier is a valuable diagnostic tool that should be used after comprehensive clinical and histopathological evaluation. It may help to reassure the histopathological diagnosis or indicate the need for thorough reassessment in cases where it contradicts previous findings. However, certain limitations (non-classifiable cases, misclassifications, unclear degree of sample purity for analysis and others) currently preclude wide clinical application. The current sarcoma classifier is therefore not yet ready for a broad clinical routine. With further refinements, this promising tool may be implemented in daily clinical practice in selected cases. Keywords: Sarcoma, Bone, Soft tissue, DNA methylation, Methylation profiling, Profiling, Classifier, Clinical experience *Correspondence: 1 Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Radiation Oncology, Augustenburger Platz 1, 13353 Berlin, Germany Full list of author information is available at the end of the article Introduction Sarcomas are a heterogeneous group of rare malignant tumors with more than 100 subtypes listed in the current World Health Organization (WHO) classification [1]. Half of all sarcoma entities lack characteristic molecular and histomorphological hallmarks frequently leading to © The Author(s) 2022. 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The Creative Commons Public Domain Dedication waiver (http://creativeco mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Roohani et al. Clinical Epigenetics (2022) 14:149 Page 2 of 9 misclassification and discrepancies among pathologists [2–5]. A DNA methylation-based profiling classifier (sarcoma classifier) from the German Cancer Research Center (Deutsches Krebsforschungszentrum (DKFZ)) is now employed in selected cases at our institution as a valuable tool to guide tumor classification and subsequent treatment decision in challenging cases [5, 6]. Initially introduced as a successful tool for the classification of central nervous system (CNS) tumors, the classification system was extended to sarcomas [7, 8]. Data on the daily clinical experience with the sarcoma classifier are lacking. Herein, we describe the clinical course of five sarcoma cases undergoing thorough pathological and reference pathological examination as well as methylation-based profiling and their impact on subsequent treatment decisions. histology included malignant peripheral nerve sheath tumor (MPNST) or synovial sarcoma. DNA methylation analysis detected a profile matching synovial sarcoma (calibrated score: 0.99, Fig. 3). No copy number variations were identified. Molecular examination conducted by the reference pathologist revealed a translocation on chromosome 18 (SS18/SYT) suggestive of synovial sarcoma. After metastatic spread was ruled out by computed tomography (CT), the MTB recommended second surgery with wide resection, since the initial resection was performed with close margins. A wide resection was then conducted, after which the patient received radiotherapy with 2 Gy daily to a total dose of 50 Gy followed by a boost of 2 Gy daily up to 16 Gy. On the day of the last follow-up in April 2022, no radiological evidence of disease was present and the patient was in good condition. Materials and methods Five cases with DNA methylation-based sarcoma classification between January and December 2021 were reviewed [6]. DNA methylation signals were processed using the R/Bioconductor package minfi (version 1.4.0.) as previously described [6, 9]. For visualization and dimensionality reduction, t-distributed stochastic neighbor embedding (t-SNE) was computed via the R package Rtsne (version 0.15) using the 25,000 most variable CpG sites according to standard deviation, 5000 iterations, and a perplexity value of 10 [10, 11]. Medical records were searched for clinical data on histopathological, immunohistochemical, and molecular pathological analyses from the institutional and reference pathology departments, medical tumor board (MTB) reports, imaging data, surgery reports, chemotherapy and radiotherapy treatment plans, past medical history, and outcome data. (...truncated)