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Varadi M, Nagy N, Reis H, Hadaschik B, Niedworok C, Modos O, Szendroi A, Ablat J, Black PC, Keresztes D, Csizmarik A, Olah C, Gaisa NT, Kiss A, Timar J, Toth E, Csernak E, Gerstner A, Mittal V, Karkampouna S, Kruithof de Julio M, Gyorffy B, Bedics G, Rink M, Fisch M, Nyirady P, Szarvas T. Clinical sequencing identifies potential actionable alterations in a high rate of urachal and primary bladder adenocarcinomas. Cancer Med 2023; 12:9041-9054. [PMID: 36670542 PMCID: PMC10134276 DOI: 10.1002/cam4.5639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/20/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVE Administration of targeted therapies provides a promising treatment strategy for urachal adenocarcinoma (UrC) or primary bladder adenocarcinoma (PBAC); however, the selection of appropriate drugs remains difficult. Here, we aimed to establish a routine compatible methodological pipeline for the identification of the most important therapeutic targets and potentially effective drugs for UrC and PBAC. METHODS Next-generation sequencing, using a 161 cancer driver gene panel, was performed on 41 UrC and 13 PBAC samples. Clinically relevant alterations were filtered, and therapeutic interpretation was performed by in silico evaluation of drug-gene interactions. RESULTS After data processing, 45/54 samples passed the quality control. Sequencing analysis revealed 191 pathogenic mutations in 68 genes. The most frequent gain-of-function mutations in UrC were found in KRAS (33%), and MYC (15%), while in PBAC KRAS (25%), MYC (25%), FLT3 (17%) and TERT (17%) were recurrently affected. The most frequently affected pathways were the cell cycle regulation, and the DNA damage control pathway. Actionable mutations with at least one available approved drug were identified in 31/33 (94%) UrC and 8/12 (67%) PBAC patients. CONCLUSIONS In this study, we developed a data-processing pipeline for the detection and therapeutic interpretation of genetic alterations in two rare cancers. Our analyses revealed actionable mutations in a high rate of cases, suggesting that this approach is a potentially feasible strategy for both UrC and PBAC treatments.
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Affiliation(s)
- Melinda Varadi
- Department of Urology, Semmelweis University, Budapest, Hungary
| | - Nikolett Nagy
- Department of Urology, Semmelweis University, Budapest, Hungary
| | - Henning Reis
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany.,Institute of Pathology, West German Cancer Center, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Boris Hadaschik
- Department of Urology, West German Cancer Center, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Christian Niedworok
- Department of Urology, West German Cancer Center, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Orsolya Modos
- Department of Urology, Semmelweis University, Budapest, Hungary
| | - Attila Szendroi
- Department of Urology, Semmelweis University, Budapest, Hungary
| | - Jason Ablat
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - Peter C Black
- Vancouver Prostate Centre, University of British Columbia, Vancouver, Canada
| | - David Keresztes
- Department of Urology, Semmelweis University, Budapest, Hungary.,Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Anita Csizmarik
- Department of Urology, Semmelweis University, Budapest, Hungary
| | - Csilla Olah
- Department of Urology, West German Cancer Center, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Nadine T Gaisa
- Institute of Pathology, RWTH Aachen University, Aachen, Germany
| | - Andras Kiss
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Jozsef Timar
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary
| | - Erika Toth
- National Institute of Oncology, Budapest, Hungary
| | | | | | - Vinay Mittal
- Thermo Fisher Scientific, Ann Arbor, Michigan, USA
| | - Sofia Karkampouna
- Department for BioMedical Research, Urology Research Laboratory, University of Bern, Bern, Switzerland
| | - Marianna Kruithof de Julio
- Department for BioMedical Research, Urology Research Laboratory, University of Bern, Bern, Switzerland.,Department of Urology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Balazs Gyorffy
- Research Centre for Natural Sciences, Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary.,2nd Department of Pediatrics and Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - Gabor Bedics
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Michael Rink
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Margit Fisch
- Department of Urology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Nyirady
- Department of Urology, Semmelweis University, Budapest, Hungary
| | - Tibor Szarvas
- Department of Urology, Semmelweis University, Budapest, Hungary.,Department of Urology, West German Cancer Center, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
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Neumann JM, Niehaus K, Neumann N, Knobloch HC, Bremmer F, Krafft U, Kellner U, Nyirády P, Szarvas T, Bednarz H, Reis H. A new technological approach in diagnostic pathology: mass spectrometry imaging-based metabolomics for biomarker detection in urachal cancer. J Transl Med 2021; 101:1281-1288. [PMID: 34021261 PMCID: PMC8367814 DOI: 10.1038/s41374-021-00612-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 11/18/2022] Open
Abstract
Urachal adenocarcinomas (UrC) are rare but aggressive. Despite being of profound therapeutic relevance, UrC cannot be differentiated by histomorphology alone from other adenocarcinomas of differential diagnostic importance. As no reliable tissue-based diagnostic biomarkers are available, we aimed to detect such by integrating mass-spectrometry imaging-based metabolomics and digital pathology, thus allowing for a multimodal approach on the basis of spatial information. To achieve this, a cohort of UrC (n = 19) and colorectal adenocarcinomas (CRC, n = 27) as the differential diagnosis of highest therapeutic relevance was created, tissue micro-arrays (TMAs) were constructed, and pathological data was recorded. Hematoxylin and eosin (H&E) stained tissue sections were scanned and annotated, enabling an automized discrimination of tumor and non-tumor areas after training of an adequate algorithm. Spectral information within tumor regions, obtained via matrix-assisted laser desorption/ionization (MALDI)-Orbitrap-mass spectrometry imaging (MSI), were subsequently extracted in an automated workflow. On this basis, metabolic differences between UrC and CRC were revealed using machine learning algorithms. As a result, the study demonstrated the feasibility of MALDI-MSI for the evaluation of FFPE tissue in UrC and CRC with the potential to combine spatial metabolomics data with annotated histopathological data from digitalized H&E slides. The detected Area under the curve (AUC) of 0.94 in general and 0.77 for the analyte taurine alone (diagnostic accuracy for taurine: 74%) makes the technology a promising tool in this differential diagnostic dilemma situation. Although the data has to be considered as a proof-of-concept study, it presents a new adoption of this technology that has not been used in this scenario in which reliable diagnostic biomarkers (such as immunohistochemical markers) are currently not available.
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Affiliation(s)
- Judith Martha Neumann
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Nils Neumann
- Research Institute for Cognition and Robotics (CoR-Lab), Bielefeld University, Bielefeld, Germany
| | - Hans Christoph Knobloch
- Department of Urology, University Medical Center Göttingen, University of Göttingen, Göttingen, Germany
| | - Felix Bremmer
- Institute of Pathology, University Medical Center Göttingen, University of Göttingen, Göttingen, Germany
| | - Ulrich Krafft
- Department of Urology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Udo Kellner
- Institut für Pathologie, Johannes Wesling Klinikum Minden, Minden, Germany
| | - Peter Nyirády
- Department of Urology, Semmelweis University Budapest, Budapest, Hungary
| | - Tibor Szarvas
- Department of Urology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Department of Urology, Semmelweis University Budapest, Budapest, Hungary
| | - Hanna Bednarz
- Proteome and Metabolome Research, Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany.
- Medical School OWL, Bielefeld University, Bielefeld, Germany.
| | - Henning Reis
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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Hager T, Kraywinkel K, Szarvas T, Hadaschik B, Schmid KW, Reis H. Urachal Cancer in Germany and the USA: An RKI/SEER Population-Based Comparison Study. Urol Int 2020; 104:803-809. [PMID: 32784300 DOI: 10.1159/000509481] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/07/2020] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Urachal cancer (UrC) is a rare but aggressive cancer. Due to its low incidence, structured epidemiological data have only rarely been reported. To date, no valid data on UrC are available for the German population. METHODS Data on incidence and relative 5-year survival of urachal lesions (ICD-10: C67.7) were collected from all population-based cancer registries in Germany, provided by the Robert Koch-Institut (RKI). Data were anonymized and included age, sex, and general histology (ICD-O-3). For comparison, a similar inquiry of the "Surveillance, Epidemiology, and End Results program" (SEER-18) database for the USA was conducted. RESULTS From 2011 to 2015, a total of 154 and 152 cases of UrC were reported for Germany (RKI) and the USA (SEER-18 area), respectively. Age-standardized incidence was 0.32/1,000,000 age-standardized cases/year in both cohorts, and elderly persons were more often affected. The major histological type was adenocarcinoma (64.9 and 81.6%). Relative 5-year survival was 54.8% (CI: 45.0-64.6) in Germany (RKI) and 64.4% (54.1-72.1) in the USA (SEER-18 cohort). Discusssion/Conclusion: The collected data demonstrate low incidence rates and similar epidemiological and clinicopathological characteristics of UrC for both registries. This is the first report of structured epidemiological data for UrC for the German population.
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Affiliation(s)
- Thomas Hager
- Institute of Pathology, University Medicine Essen, University of Duisburg-Essen, Essen, Germany
| | | | - Tibor Szarvas
- Department of Urology, University Medicine Essen, University of Duisburg-Essen, Essen, Germany.,Clinic of Urology, Semmelweis University, Budapest, Hungary
| | - Boris Hadaschik
- Department of Urology, University Medicine Essen, University of Duisburg-Essen, Essen, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Medicine Essen, University of Duisburg-Essen, Essen, Germany
| | - Henning Reis
- Institute of Pathology, University Medicine Essen, University of Duisburg-Essen, Essen, Germany,
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