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Duchnowska R, Supernat AM, Pęksa R, Łukasiewicz M, Stokowy T, Ronen R, Dutkowski J, Umińska M, Iżycka-Świeszewska E, Kowalczyk A, Och W, Rucińska M, Olszewski WP, Mandat T, Jarosz B, Bieńkowski M, Biernat W, Jassem J. Pathway-level mutation analysis in primary high-grade serous ovarian cancer and matched brain metastases. Sci Rep 2022; 12:20537. [PMID: 36446793 PMCID: PMC9708673 DOI: 10.1038/s41598-022-23788-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/04/2022] [Indexed: 11/30/2022] Open
Abstract
Brain metastases (BMs) in ovarian cancer (OC) are a rare event. BMs occur most frequently in high-grade serous (HGS) OC. The molecular features of BMs in HGSOC are poorly understood. We performed a whole-exome sequencing analysis of ten matched pairs of formalin-fixed paraffin-embedded samples from primary HGSOC and corresponding BMs. Enrichment significance (p value; false discovery rate) was computed using the Reactome, the Kyoto Encyclopedia of Genes and Genomes pathway collections, and the Gene Ontology Biological Processes. Germline DNA damage repair variants were found in seven cases (70%) and involved the BRCA1, BRCA2, ATM, RAD50, ERCC4, RPA1, MLHI, and ATR genes. Somatic mutations of TP53 were found in nine cases (90%) and were the only stable mutations between the primary tumor and BMs. Disturbed pathways in BMs versus primary HGSOC constituted a complex network and included the cell cycle, the degradation of the extracellular matrix, cell junction organization, nucleotide metabolism, lipid metabolism, the immune system, G-protein-coupled receptors, intracellular vesicular transport, and reaction to chemical stimuli (Golgi vesicle transport and olfactory signaling). Pathway analysis approaches allow for a more intuitive interpretation of the data as compared to considering single-gene aberrations and provide an opportunity to identify clinically informative alterations in HGSOC BM.
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Affiliation(s)
- Renata Duchnowska
- grid.415641.30000 0004 0620 0839Oncology Department, Military Institute of Medicine - National Research Institute, Szaserów St. 128, 04-141 Warsaw, Poland
| | - Anna Maria Supernat
- grid.11451.300000 0001 0531 3426Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Rafał Pęksa
- grid.11451.300000 0001 0531 3426Department of Pathology, Medical University of Gdańsk, Gdańsk, Poland
| | - Marta Łukasiewicz
- grid.11451.300000 0001 0531 3426Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Tomasz Stokowy
- grid.7914.b0000 0004 1936 7443Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | | | | | - Ewa Iżycka-Świeszewska
- grid.11451.300000 0001 0531 3426Department of Pathology and Neuropathology, Medical University of Gdańsk, Gdańsk, Poland
| | - Anna Kowalczyk
- grid.11451.300000 0001 0531 3426Department of Oncology and Radiotherapy, Medical University of Gdańsk, Gdańsk, Poland
| | - Waldemar Och
- Neurosurgery Department, Regional Specialist Hospital, Olsztyn, Poland
| | - Monika Rucińska
- grid.412607.60000 0001 2149 6795Department of Oncology, Collegium Medicum, University of Warmia and Mazury, Olsztyn, Poland
| | - Wojciech P. Olszewski
- grid.418165.f0000 0004 0540 2543Department of Pathology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Tomasz Mandat
- grid.418165.f0000 0004 0540 2543Department of Neurosurgery, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Bożena Jarosz
- grid.411484.c0000 0001 1033 7158Department of Neurosurgery and Paediatric Neurosurgery, Medical University of Lublin, Lublin, Poland
| | - Michał Bieńkowski
- grid.11451.300000 0001 0531 3426Department of Pathology, Medical University of Gdańsk, Gdańsk, Poland
| | - Wojciech Biernat
- grid.11451.300000 0001 0531 3426Department of Pathology, Medical University of Gdańsk, Gdańsk, Poland
| | - Jacek Jassem
- grid.11451.300000 0001 0531 3426Department of Oncology and Radiotherapy, Medical University of Gdańsk, Gdańsk, Poland
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Duchnowska R, Supernat AM, Pęksa R, Łukasiewicz M, Stokowy T, Umińska M, Iżycka-Świeszewska E, Kowalczyk A, Och W, Rucinska M, Olszewski WP, Mandat T, Jarosz B, Bieńkowski M, Biernat W, Jassem J. Genomic characterization of brain metastases (BM) in high-grade serous ovarian cancer (HGSOC). J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e13580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e13580 Background: BM are a rare occurrence in ovarian cancer (OC) and their molecular characteristics is virtually unknown. DNA damage repair (DDR) deficiency is prevalent in OC, and co-mutated TP53 and any DDR denotes high tumor mutation burden (TMB). We genetically characterized a unique series of high-grade serous ovarian cancer (HGSOC) patients who developed BM to identify alterations of potential clinical relevance. Methods: Whole-exome sequencing (2x150bp, SureSelectXT Library Prep Kit, Illumina’s NovaSeq platform) was performed in matched BM, primary tumors (PT) and normal tissue. DNA was extracted from FFPE samples using QIAamp DNA FFPE Tissue Kit (Qiagen, Germany). All mutations were checked with Catalogue of Somatic Mutations in Cancer (COSMIC) and Integrative Genomics Viewer (IGV). Results: Study group included 10 HGSOC patients (International Federation of Gynecology and Obstetrics classification (FIGO) II-IV, mean age at diagnosis 48 years, range 35-59). Median time from primary HGSOC diagnosis to BM was 38 months (range, 18 to 149). TP53 somatic mutations were found in both primary tumor (PT) and BM in 8 patients. The other 2 cases harbored TP53 mutations not reported in COSMIC catalogue: p.S60L and intronic TP53 mutation preceding p.I322 (IGV). In 9 cases TP53 mutations coexisted with germline or somatic DNA damage repair deficiency. Four cases contained BRCA1 mutations (all germline), and none harbored germline BRCA2 mutation. Other mutated genes included MLH1 (2 somatic, 2 germline), ATR (4 germline, 1 somatic), AMT (1 somatic), RAD50 (1 somatic), ERCC4 (1 somatic), FANCD2 (1 somatic) and RPA1 (1 germline). Three mutation signatures defined in the COSMIC database were indentified in BM: 6, 20 and 30. In 6 cases these mutations were shared in PT, and in another 4 their presence in PT could not be determined due to technical reasons. Median survival from BM was 31 months (range, 5 to 184). Conclusions: Genomic analysis of BM provides an opportunity to identify potentially clinically informative alterations. Mutational profiles in PT are generally reflected in BM. Detected genetic alterations suggest their potential sensitivity to PARP inhibitors and immunotherapy.
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Affiliation(s)
| | | | - Rafał Pęksa
- Department of Pathology, Medical University of Gdańsk, Gdańsk, Poland
| | - Marta Łukasiewicz
- Laboratory of Cell Biology, Intercollegiate Faculty of Biotechnology, University of Gdańsk, Gdańsk, Poland
| | - Tomasz Stokowy
- Computational Biology Unit, Institute of Informatics, University of Bergen, Bergen, Norway
| | - Monika Umińska
- Oncology Unit, Copernicus Hospital Gdańsk, Gdańsk, Poland
| | - Ewa Iżycka-Świeszewska
- Department of Pathology and Neuropathology Medical University of Gdańsk; Department of Pathomorphology, Copernicus Hospitals, Gdańsk, Poland
| | - Anna Kowalczyk
- Medical University of Gdańsk, Oncology and Radiotherapy, Gdańsk, Poland
| | | | - Monika Rucinska
- Department of Oncology Collegium Medicum School of Medicine Univeristy of Warmia and Mazury, Olsztyn, Poland
| | - Wojciech P Olszewski
- Department of Pathology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | | | | | | | - Wojciech Biernat
- Medical University of Gdańsk, Department of Pathology, Gdańsk, Poland
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Łapińska-Szumczyk SM, Supernat AM, Żaczek AJ, Majewska H, Gulczyński J, Sawicki S, Biernat W, Wydra D. Rak błony śluzowej trzonu macicy u chorych po przebytej chorobie nowotworowej - aspekty kliniczne i molekularne. Ginekol Pol 2016; 87:88-93. [PMID: 27306283 DOI: 10.17772/gp/60559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Indexed: 11/12/2022] Open
Affiliation(s)
- Sylwia Maria Łapińska-Szumczyk
- Katedra i Klinika Ginekologii, Ginekologii Onkologicznej i Endokrynologii Ginekologicznej Gdańskiego Uniwersytetu Medycznego, Kliniczna 1a, 80-402 Gdańsk, Polska.
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Supernat AM, Lapinska-Szumczyk S, Majewska H, Gulczynski J, Biernat W, Wydra D, Zaczek AJ. Prognostic value of dysregulated ErbB signaling network in endometrial cancer. J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.15_suppl.e16540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Sylwia Lapinska-Szumczyk
- Department of Gynaecology, Gynaecological Oncology and Gynaecological Endocrinology, Medical University of Gdansk, Gdansk, Poland
| | - Hanna Majewska
- Department of Pathomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Jacek Gulczynski
- Department of Pathology and Neuropathology, Medical University of Gdansk, Gdansk, Poland
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Dariusz Wydra
- Department of Gynaecology, Gynaecological Oncology and Gynaecological Endocrinology, Medical University of Gdansk, Gdansk, Poland
| | - Anna Joanna Zaczek
- Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
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Supernat AM, Lapinska-Szumczyk S, Majewska H, Gulczynski J, Biernat W, Wydra D, Zaczek AJ. Tumor heterogeneity on a protein level in endometrial cancer. J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.15_suppl.e16539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Sylwia Lapinska-Szumczyk
- Department of Gynaecology, Gynaecological Oncology and Gynaecological Endocrinology, Medical University of Gdansk, Gdansk, Poland
| | - Hanna Majewska
- Department of Pathomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Jacek Gulczynski
- Department of Pathology and Neuropathology, Medical University of Gdansk, Gdansk, Poland
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Dariusz Wydra
- Department of Gynaecology, Gynaecological Oncology and Gynaecological Endocrinology, Medical University of Gdansk, Gdansk, Poland
| | - Anna Joanna Zaczek
- Department of Medical Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
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