cancers Article Characterization of Genetic Heterogeneity in Recurrent Metastases of Renal Cell Carcinoma Carolin Sauter-Meyerhoff 1 , Regina Bohnert 1 , Pascale Mazzola 1 , Viktoria Stühler 2 , Siarhei Kandabarau 1 , Florian A. Büttner 1 , Stefan Winter 1 , Lisa Herrmann 2 , Steffen Rausch 2 , Jörg Hennenlotter 2 , Falko Fend 3 , Marcus Scharpf 3 , Arnulf Stenzl 2 , Stephan Ossowski 4 , Jens Bedke 2,5 , Matthias Schwab 1,5,6,7, * ,† and Elke Schaeffeler 1,7,†   Citation: Sauter-Meyerhoff, C.; Bohnert, R.; Mazzola, P.; Stühler, V.; Kandabarau, S.; Büttner, F.A.; Winter, S.; Herrmann, L.; Rausch, S.; Hennenlotter, J.; et al. Characterization of Genetic Heterogeneity in Recurrent Metastases of Renal Cell Carcinoma. Cancers 2021, 13, 6221. https:// doi.org/10.3390/cancers13246221 Academic Editor: José I. Lopez Received: 3 November 2021 Accepted: 4 December 2021 Published: 10 December 2021 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). 1 Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; carolin.meyerhoff@ikp-stuttgart.de (C.S.-M.); regina.bohnert@ikp-stuttgart.de (R.B.); pascale.mazzola@med.uni-tuebingen.de (P.M.); siarhei.kandabarau@ikp-stuttgart.de (S.K.); florian.buettner@ikp-stuttgart.de (F.A.B.); stefan.winter@ikp-stuttgart.de (S.W.); elke.schaeffeler@ikp-stuttgart.de (E.S.) 2 Department of Urology, University Hospital Tuebingen, 72076 Tuebingen, Germany; viktoria.stuehler@med.uni-tuebingen.de (V.S.); lisa.herrmann@student.uni-tuebingen.de (L.H.); steffen.rausch@med.uni-tuebingen.de (S.R.); joerg.hennenlotter@med.uni-tuebingen.de (J.H.); arnulf.stenzl@med.uni-tuebingen.de (A.S.); jens.bedke@med.uni-tuebingen.de (J.B.) 3 Institute of Pathology and Neuropathology, University Hospital Tuebingen, 72076 Tuebingen, Germany; falko.fend@med.uni-tuebingen.de (F.F.); marcus.scharpf@med.uni-tuebingen.de (M.S.) 4 Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tuebingen, Germany; stephan.ossowski@med.uni-tuebingen.de 5 German Cancer Consortium (DKTK), Partner Site Tuebingen, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany 6 Departments of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tuebingen, 72076 Tuebingen, Germany 7 Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, 72076 Tuebingen, Germany * Correspondence: matthias.schwab@ikp-stuttgart.de; Tel.: +49-711-8101-3700 † These authors contributed equally. Simple Summary: Survival rates in metastatic renal cell carcinoma (RCC) are still low despite novel therapies available. Thus, knowledge of molecular characteristics of distant metastases is important for personalized treatment strategies. Therefore, we investigated the genetic landscape of metastases, including synchronous and/or recurrent metastases to elucidate potential drug target genes and clin- ically relevant mutations. Furthermore, differences in mutational composition in different metastatic sites and over the course of the disease and treatment will demonstrate the importance of somatic profiling for precision medicine in RCC, thereby improving disease management in the future. Abstract: Metastatic renal cell carcinoma (RCC) exhibits poor prognosis. Better knowledge of distant metastases is crucial to foster personalized treatment strategies. Here, we aimed to investigate the genetic landscape of metastases, including synchronous and/or recurrent metastases to elucidate potential drug target genes and clinically relevant mutations in a real-world setting of patients. We assessed 81 metastases from 56 RCC patients, including synchronous and/or recurrent metastases of 19 patients. Samples were analysed through next-generation sequencing with a high coverage (~1000× mean coverage). We therefore established a novel sequencing panel comprising 32 genes with impact on RCC development. We observed a high frequency of mutations in known RCC driver genes (e.g., >40% carriers of VHL and PBRM1 mutations) in metastases irrespective of the metastatic site. The somatic mutational composition was significantly associated with cancer-specific survival (p(logrank) = 0.03). Moreover, we identified in 34 patients at least one drug target gene as well as clinically relevant mutations listed in the VICC Meta-Knowledgebase in 7%. In addition to significantly higher mutational burden in recurrent metastases compared to earlier ones, synchronous and/or recurrent metastases of individual patients, even after a time-period >2 yrs, shared a high proportion of somatic events. Our data demonstrate the importance of somatic profiling in metastases for precision medicine in RCC. Cancers 2021, 13, 6221. https://doi.org/10.3390/cancers13246221 https://www.mdpi.com/journal/cancers