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Heydt C, Ihle MA, Merkelbach-Bruse S. Overview of Molecular Detection Technologies for MET in Lung Cancer. Cancers (Basel) 2023; 15:cancers15112932. [PMID: 37296895 DOI: 10.3390/cancers15112932] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
MET tyrosine kinase receptor pathway activation has become an important actionable target in solid tumors. Aberrations in the MET proto-oncogene, including MET overexpression, the activation of MET mutations, MET mutations that lead to MET exon 14 skipping, MET gene amplifications, and MET fusions, are known to be primary and secondary oncogenic drivers in cancer; these aberrations have evolved as predictive biomarkers in clinical diagnostics. Thus, the detection of all known MET aberrations in daily clinical care is essential. In this review, current molecular technologies for the detection of the different MET aberrations are highlighted, including the benefits and drawbacks. In the future, another focus will be on the standardization of detection technologies for the delivery of reliable, quick, and affordable tests in clinical molecular diagnostics.
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Affiliation(s)
- Carina Heydt
- Faculty of Medicine, Institute of Pathology, University Hospital Cologne, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Michaela Angelika Ihle
- Faculty of Medicine, Institute of Pathology, University Hospital Cologne, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
| | - Sabine Merkelbach-Bruse
- Faculty of Medicine, Institute of Pathology, University Hospital Cologne, University of Cologne, Kerpener Str. 62, 50937 Cologne, Germany
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2
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Ihle MA, Heydt C. [Biomarker MET in tumor pathology]. Pathologie (Heidelb) 2023; 44:193-196. [PMID: 36944766 PMCID: PMC10160147 DOI: 10.1007/s00292-023-01189-2] [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] [Subscribe] [Scholar Register] [Accepted: 12/19/2022] [Indexed: 03/23/2023]
Affiliation(s)
- Michaela Angelika Ihle
- Institut für Pathologie. Medizinische Fakultät und Uniklinik Köln, Universität zu Köln, 50937, Köln, Deutschland.
| | - Carina Heydt
- Institut für Pathologie. Medizinische Fakultät und Uniklinik Köln, Universität zu Köln, 50937, Köln, Deutschland
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Wagener-Ryczek S, Heydt C, Süptitz J, Michels S, Falk M, Alidousty C, Fassunke J, Ihle MA, Tiemann M, Heukamp L, Wolf J, Büttner R, Merkelbach-Bruse S. Mutational spectrum of acquired resistance to reversible versus irreversible EGFR tyrosine kinase inhibitors. BMC Cancer 2020; 20:408. [PMID: 32397977 PMCID: PMC7216404 DOI: 10.1186/s12885-020-06920-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 04/30/2020] [Indexed: 12/16/2022] Open
Abstract
Background Over the past years, EGFR tyrosine kinase inhibitors (TKI) revolutionized treatment response. 1st-generation (reversible) EGFR TKI and later the 2nd –generation irreversible EGFR TKI Afatinib were aimed to improve treatment response. Nevertheless, diverse resistance mechanisms develop within the first year of therapy. Here, we evaluate the prevalence of acquired resistance mechanisms towards reversible and irreversible EGFR TKI. Methods Rebiopsies of patients after progression to EGFR TKI therapy (> 6 months) were targeted to histological and molecular analysis. Multiplexed targeted sequencing (NGS) was conducted to identify acquired resistance mutations (e.g. EGFR p.T790M). Further, Fluorescence in situ hybridisation (FISH) was applied to investigate the status of bypass mechanisms like, MET or HER2 amplification. Results One hundred twenty-three rebiopsy samples of patients that underwent first-line EGFR TKI therapy (PFS ≥6 months) were histologically and molecularly profiled upon clinical progression. The EGFR p.T790M mutation is the major mechanism of acquired resistance in patients treated with reversible as well as irreversible EGFR TKI. Nevertheless a statistically significant difference for the acquisition of T790M mutation has been identified: 45% of afatinib- vs 65% of reversible EGFR TKI treated patients developed a T790M mutation (p-value 0.02). Progression free survival (PFS) was comparable in patients treated with irreversible EGFR irrespective of the sensitising primary mutation or the acquisition of p.T790M. Conclusions The EGFR p.T790M mutation is the most prominent mechanism of resistance to reversible and irreversible EGFR TKI therapy. Nevertheless there is a statistically significant difference of p.T790M acquisition between the two types of TKI, which might be of importance for clinical therapy decision.
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Affiliation(s)
- Svenja Wagener-Ryczek
- Institute of Pathology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne, Germany.
| | - Carina Heydt
- Institute of Pathology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne, Germany
| | - Juliane Süptitz
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Sebastian Michels
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Markus Falk
- Insitute for Haematopathology, Hamburg, Hamburg, Germany
| | - Christina Alidousty
- Institute of Pathology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne, Germany
| | - Jana Fassunke
- Institute of Pathology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne, Germany
| | - Michaela Angelika Ihle
- Institute of Pathology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne, Germany
| | - Markus Tiemann
- Insitute for Haematopathology, Hamburg, Hamburg, Germany
| | - Lukas Heukamp
- Insitute for Haematopathology, Hamburg, Hamburg, Germany.,NEO New Oncology GmbH, Cologne, Germany
| | - Jürgen Wolf
- Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Reinhard Büttner
- Institute of Pathology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne, Germany
| | - Sabine Merkelbach-Bruse
- Institute of Pathology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne, Germany
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Kron A, Alidousty C, Scheffler M, Merkelbach-Bruse S, Seidel D, Riedel R, Ihle MA, Michels S, Nogova L, Fassunke J, Heydt C, Kron F, Ueckeroth F, Serke M, Krüger S, Grohe C, Koschel D, Benedikter J, Kaminsky B, Schaaf B, Braess J, Sebastian M, Kambartel KO, Thomas R, Zander T, Schultheis AM, Büttner R, Wolf J. Impact of TP53 mutation status on systemic treatment outcome in ALK-rearranged non-small-cell lung cancer. Ann Oncol 2019; 29:2068-2075. [PMID: 30165392 PMCID: PMC6225899 DOI: 10.1093/annonc/mdy333] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background We analyzed whether co-occurring mutations influence the outcome of systemic therapy in ALK-rearranged non-small-cell lung cancer (NSCLC). Patients and methods ALK-rearranged stage IIIB/IV NSCLC patients were analyzed with next-generation sequencing and fluorescence in situ hybridization analyses on a centralized diagnostic platform. Median progression-free survival (PFS) and overall survival (OS) were determined in the total cohort and in treatment-related sub-cohorts. Cox regression analyses were carried out to exclude confounders. Results Among 216 patients with ALK-rearranged NSCLC, the frequency of pathogenic TP53 mutations was 23.8%, while other co-occurring mutations were rare events. In ALK/TP53 co-mutated patients, median PFS and OS were significantly lower compared with TP53 wildtype patients [PFS 3.9 months (95% CI: 2.4–5.6) versus 10.3 months (95% CI: 8.6–12.0), P < 0.001; OS 15.0 months (95% CI: 5.0–24.9) versus 50.0 months (95% CI: 22.9–77.1), P = 0.002]. This difference was confirmed in all treatment-related subgroups including chemotherapy only [PFS first-line chemotherapy 2.6 months (95% CI: 1.3–4.1) versus 6.2 months (95% CI: 1.8–10.5), P = 0.021; OS 2.0 months (95% CI: 0.0–4.6) versus 9.0 months (95% CI: 6.1–11.9), P = 0.035], crizotinib plus chemotherapy [PFS crizotinib 5.0 months (95% CI: 2.9–7.2) versus 14.0 months (95% CI: 8.0–20.1), P < 0.001; OS 17.0 months (95% CI: 6.7–27.3) versus not reached, P = 0.049] and crizotinib followed by next-generation ALK-inhibitor [PFS next-generation inhibitor 5.4 months (95% CI: 0.1–10.7) versus 9.9 months (95% CI: 6.4–13.5), P = 0.039; OS 7.0 months versus 50.0 months (95% CI: not reached), P = 0.001). Conclusions In ALK-rearranged NSCLC co-occurring TP53 mutations predict an unfavorable outcome of systemic therapy. Our observations encourage future research to understand the underlying molecular mechanisms and to improve treatment outcome of the ALK/TP53 co-mutated subgroup.
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Affiliation(s)
- A Kron
- Network Genomic Medicine, Cologne, Germany; Lung Cancer Group Cologne, Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany
| | - C Alidousty
- Network Genomic Medicine, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - M Scheffler
- Network Genomic Medicine, Cologne, Germany; Lung Cancer Group Cologne, Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany
| | - S Merkelbach-Bruse
- Network Genomic Medicine, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - D Seidel
- Center for Integrated Oncology Köln Bonn, Cologne, Germany; CECAD Cluster of Excellence, University of Cologne, Cologne, Germany
| | - R Riedel
- Network Genomic Medicine, Cologne, Germany; Lung Cancer Group Cologne, Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany
| | - M A Ihle
- Network Genomic Medicine, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - S Michels
- Network Genomic Medicine, Cologne, Germany; Lung Cancer Group Cologne, Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany
| | - L Nogova
- Network Genomic Medicine, Cologne, Germany; Lung Cancer Group Cologne, Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany
| | - J Fassunke
- Network Genomic Medicine, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - C Heydt
- Network Genomic Medicine, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - F Kron
- Network Genomic Medicine, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany
| | - F Ueckeroth
- Network Genomic Medicine, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - M Serke
- Network Genomic Medicine, Cologne, Germany; Department of Pneumology, Lungenklinik Hemer des Deutschen Gemeinschafts-Diakonieverbandes GmbH, Hemer, Germany
| | - S Krüger
- Network Genomic Medicine, Cologne, Germany; Department of Pneumology, Florence Nightingale Hospital, Düsseldorf, Germany
| | - C Grohe
- Network Genomic Medicine, Cologne, Germany; Department of Pneumology, Evangelische Lungenklinik Berlin (Paul Gerhardt Diakonie), Berlin, Germany
| | - D Koschel
- Network Genomic Medicine, Cologne, Germany; Department of Pneumology, Fachkrankenhaus Coswig, Coswig, Germany
| | - J Benedikter
- Network Genomic Medicine, Cologne, Germany; Department of Pneumology, Klinikum Bogenhausen, Munich, Germany
| | - B Kaminsky
- Network Genomic Medicine, Cologne, Germany; Department of Pneumology, Krankenhaus Bethanien, Solingen, Germany
| | - B Schaaf
- Network Genomic Medicine, Cologne, Germany; Lung Cancer Center, Klinikum Dortmund GmbH, Dortmund, Germany
| | - J Braess
- Network Genomic Medicine, Cologne, Germany; Department of Oncology and Hematology, Krankenhaus Barmherzige Brueder, Regensburg, Germany
| | - M Sebastian
- Network Genomic Medicine, Cologne, Germany; Department of Oncology and Hematology, University Hospital Frankfurt (Johannes-Wolfgang Goethe Institute), Frankfurt am Main, Germany
| | - K-O Kambartel
- Network Genomic Medicine, Cologne, Germany; Department of Pneumology, Bethanien Hospital Moers-Lungenzentrum, Moers, Germany
| | - R Thomas
- Network Genomic Medicine, Cologne, Germany; Cologne Center for Genomics, University Hospital of Cologne, Cologne, Germany
| | - T Zander
- Network Genomic Medicine, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany
| | - A M Schultheis
- Network Genomic Medicine, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - R Büttner
- Network Genomic Medicine, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - J Wolf
- Network Genomic Medicine, Cologne, Germany; Lung Cancer Group Cologne, Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany; Center for Integrated Oncology Köln Bonn, Cologne, Germany.
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Helbig D, Ihle MA, Pütz K, Tantcheva-Poor I, Mauch C, Büttner R, Quaas A. Oncogene and therapeutic target analyses in atypical fibroxanthomas and pleomorphic dermal sarcomas. Oncotarget 2017; 7:21763-74. [PMID: 26943575 PMCID: PMC5008321 DOI: 10.18632/oncotarget.7845] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 02/21/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Until now, almost nothing is known about the tumorigenesis of atypical fibroxanthoma (AFX) and pleomorphic dermal sarcoma (PDS). Our hypothesis is that AFX is the non-infiltrating precursor lesion of PDS. MATERIALS AND METHODS We performed the world-wide most comprehensive immunohistochemical and mutational analysis in well-defined AFX (n=5) and PDS (n=5). RESULTS In NGS-based mutation analyses of selected regions by a 17 hotspot gene panel of 102 amplicons we could detect TP53 mutations in all PDS as well as in the only analyzed AFX and PDS of the same patient. Besides, we detected mutations in the CDKN2A, HRAS, KNSTRN and PIK3CA genes.Performing immunohistochemistry for CTNNB1, KIT, CDK4, c-MYC, CTLA-4, CCND1, EGFR, EPCAM, ERBB2, IMP3, INI-1, MKI67, MDM2, MET, p40, TP53, PD-L1 and SOX2 overexpression of TP53, CCND1 and CDK4 was seen in AFX as well as in PDS. IMP3 was upregulated in 2 AFX (weak staining) and 4 PDS (strong staining).FISH analyses for the genes FGFR1, FGFR2 and FGFR3 revealed negative results in all tumors. CONCLUSIONS UV-induced TP53 mutations as well as CCND1/CDK4 changes seem to play essential roles in tumorigenesis of PDS. Furthermore, we found some more interesting mutated genes in other oncogene pathways (activating mutations of HRAS and PIK3CA). All AFX and PDS investigated immunohistochemically presented with similar oncogene expression profiles (TP53, CCND1, CDK4 overexpression) and the single case with an AFX and PDS showed complete identical TP53 and PIK3CA mutation profiles in both tumors. This reinforces our hypothesis that AFX is the non-infiltrating precursor lesion of PDS.
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Affiliation(s)
- Doris Helbig
- Department of Dermatology, University Hospital Cologne, Cologne, Germany
| | | | - Katharina Pütz
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | - Cornelia Mauch
- Department of Dermatology, University Hospital Cologne, Cologne, Germany
| | - Reinhard Büttner
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Alexander Quaas
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
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Helbig D, Quaas A, Mauch C, Merkelbach-Bruse S, Büttner R, Emberger M, Wobser M, Rüsseler V, Pütz K, Binot E, Rehker J, Budczies J, Ihle MA. Copy number variations in atypical fibroxanthomas and pleomorphic dermal sarcomas. Oncotarget 2017; 8:109457-109467. [PMID: 29312620 PMCID: PMC5752533 DOI: 10.18632/oncotarget.22691] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 11/13/2017] [Indexed: 11/25/2022] Open
Abstract
Atypical fibroxanthomas (AFX) and pleomorphic dermal sarcomas (PDS) are frequent cutaneous sarcomas typically arising on sun-exposed skin in elderly patients. In contrast to AFX, which generally do not recur after complete excision, PDS locally recur in up to 50% and metastasize in up to 20%. We recently detected characteristic UV-induced TP53 mutations as potential driver mutation in almost all PDS investigated as well as activating PIK3CA and RAS gene mutations in around one third of our tumors representing targets for personalized treatments in patients with unresectable or metastasized PDS. In the present study, we identified amplifications and deletions in a small part of the PDS (6 of 27 cases) but not in AFX suggesting that copy number variations (CNV) might not be an initial event in tumor development but rather important during tumor progression. In addition to BRAF, KNSTRN, IDH1 and PDGFRA amplification, CNV analyses revealed deletions in the CDKN2A, KIT and PDGFRA genes. In cases where an appropriate FISH assay was established, the CNV results could be verified by FISH analysis. Amplification of BRAF, KIT or PDGFRA and/or losses of CDKN2A might represent bad prognostic markers, although larger studies are needed to clarify their association with prognosis or progression in PDS.
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Affiliation(s)
- Doris Helbig
- Department of Dermatology, University Hospital Cologne, Cologne, Germany
| | - Alexander Quaas
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Cornelia Mauch
- Department of Dermatology, University Hospital Cologne, Cologne, Germany
| | | | - Reinhard Büttner
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | - Marion Wobser
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Vanessa Rüsseler
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Katharina Pütz
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Elke Binot
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Jan Rehker
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Jan Budczies
- Institute of Pathology, Charité University Hospital, Berlin, Germany
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Fassunke J, Ihle MA, Lenze D, Lehmann A, Hummel M, Vollbrecht C, Penzel R, Volckmar AL, Stenzinger A, Endris V, Jung A, Lehmann U, Zeugner S, Baretton G, Kreipe H, Schirmacher P, Kirchner T, Dietel M, Büttner R, Merkelbach-Bruse S. EGFR T790M mutation testing of non-small cell lung cancer tissue and blood samples artificially spiked with circulating cell-free tumor DNA: results of a round robin trial. Virchows Arch 2017; 471:509-520. [DOI: 10.1007/s00428-017-2226-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 07/22/2017] [Accepted: 08/22/2017] [Indexed: 01/08/2023]
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Huss S, Pasternack H, Ihle MA, Merkelbach-Bruse S, Heitkötter B, Hartmann W, Trautmann M, Gevensleben H, Büttner R, Schildhaus HU, Wardelmann E. Clinicopathological and molecular features of a large cohort of gastrointestinal stromal tumors (GISTs) and review of the literature: BRAF mutations in KIT/PDGFRA wild-type GISTs are rare events. Hum Pathol 2017; 62:206-214. [PMID: 28159677 DOI: 10.1016/j.humpath.2017.01.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 12/27/2022]
Abstract
In KIT/PDGFRA wild-type gastrointestinal stromal tumors (wt-GISTs), BRAF mutations are regarded as alternative pathogenic events driving tumorigenesis. In our study, we aimed at analyzing a large cohort (n=444) of GISTs for BRAF mutations using molecular and immunohistochemical methods. More than 3000 GIST samples from caucasian patients were available in our GIST and Sarcoma Registry NRW. Of these, we selected 172 wt-GISTs to evaluate the frequency of BRAF mutations. Furthermore, 272 GISTs with a representative KIT and PDGFRA mutational status were selected. BRAF mutational status was evaluated by high-resolution melting analysis, Sanger sequencing, and VE1 immunohistochemistry. A BRAF mutation (p.V600E) was found in 7 cases (3.9%) of the wt-GIST cohort. In 2 cases, multiple synchronous tumors harbored the same somatic BRAF mutation. VE1 immunohistochemical staining had a sensitivity of 81.8% and a specificity of 97.5% to detect BRAF p.V600E mutations. Analyzing our cases and the cases reported in the literature (n=37), the percentage of intermediate and high-risk BRAF-mutated wt-GISTs (17/31; 54.8%) was comparable to that recorded for large GIST cohorts irrespective of the mutational status. BRAF mutations are rare events in wt-GISTs, and VE1 immunohistochemistry appears to be a valuable pre-screening tool for the detection of BRAF p.V600E mutations. BRAF mutations in GISTs do not seem to have a prognostic value per se. However, as BRAF inhibition represents a therapeutic option to control disease, we suggest the assessment of the BRAF mutational status, especially in the setting of advanced GIST disease.
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Affiliation(s)
- Sebastian Huss
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Albert-Schweitzer-Campus 1, 48156 Münster, Germany.
| | - Helen Pasternack
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck and the Research Center Borstel, Leibniz Center for Medicine and Biosciences, Ratzeburger Allee 160, 23538 Luebeck, Germany.
| | - Michaela Angelika Ihle
- Institute of Pathology, University Hospital Cologne, Kerpener Strasse 62, 50937 Cologne, Germany.
| | - Sabine Merkelbach-Bruse
- Institute of Pathology, University Hospital Cologne, Kerpener Strasse 62, 50937 Cologne, Germany.
| | - Birthe Heitkötter
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Albert-Schweitzer-Campus 1, 48156 Münster, Germany.
| | - Wolfgang Hartmann
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Albert-Schweitzer-Campus 1, 48156 Münster, Germany.
| | - Marcel Trautmann
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Albert-Schweitzer-Campus 1, 48156 Münster, Germany.
| | - Heidrun Gevensleben
- Institute of Pathology, University Hospital Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany.
| | - Reinhard Büttner
- Institute of Pathology, University Hospital Cologne, Kerpener Strasse 62, 50937 Cologne, Germany.
| | - Hans-Ulrich Schildhaus
- Institute of Pathology, University Hospital Göttingen, Robert-Koch-Straße 40, 37075 Göttingen, Germany.
| | - Eva Wardelmann
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Albert-Schweitzer-Campus 1, 48156 Münster, Germany.
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Michels S, Scheel AH, Scheffler M, Schultheis AM, Gautschi O, Aebersold F, Diebold J, Pall G, Rothschild S, Bubendorf L, Hartmann W, Heukamp L, Schildhaus HU, Fassunke J, Ihle MA, Künstlinger H, Heydt C, Fischer R, Nogovà L, Mattonet C, Hein R, Adams A, Gerigk U, Schulte W, Lüders H, Grohé C, Graeven U, Müller-Naendrup C, Draube A, Kambartel KO, Krüger S, Schulze-Olden S, Serke M, Engel-Riedel W, Kaminsky B, Randerath W, Merkelbach-Bruse S, Büttner R, Wolf J. Clinicopathological Characteristics of RET Rearranged Lung Cancer in European Patients. J Thorac Oncol 2016; 11:122-7. [PMID: 26762747 DOI: 10.1016/j.jtho.2015.09.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/11/2015] [Accepted: 09/14/2015] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Rearrangements of RET are rare oncogenic events in patients with non-small cell lung cancer (NSCLC). While the characterization of Asian patients suggests a predominance of nonsmokers of young age in this genetically defined lung cancer subgroup, little is known about the characteristics of non-Asian patients. We present the results of an analysis of a European cohort of patients with RET rearranged NSCLC. METHODS Nine hundred ninety-seven patients with KRAS/EGFR/ALK wildtype lung adenocarcinomas were analyzed using fluorescence in situ hybridization for RET fusions. Tumor specimens were molecularly profiled and clinicopathological characteristics of the patients were collected. RESULTS Rearrangements of RET were identified in 22 patients, with a prevalence of 2.2% in the KRAS/EGFR/ALK wildtype subgroup. Co-occurring genetic aberrations were detected in 10 patients, and the majority had mutations in TP53. The median age at diagnosis was 62 years (range, 39-80 years; mean ± SD, 61 ± 11.7 years) with a higher proportion of men (59% versus 41%). There was only a slight predominance of nonsmokers (54.5%) compared to current or former smokers (45.5%). CONCLUSIONS Patients with RET rearranged adenocarcinomas represent a rare and heterogeneous NSCLC subgroup. In some contrast to published data, we see a high prevalence of current and former smokers in our white RET cohort. The significance of co-occurring aberrations, so far, is unclear.
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Affiliation(s)
- Sebastian Michels
- Center for Integrated Oncology Köln Bonn, Cologne, Germany; Lung Cancer Group Cologne, Department I for Internal Medicine, University Hospital of Cologne, Cologne, Germany; Network Genomic Medicine, Cologne, Germany
| | - Andreas Hans Scheel
- Network Genomic Medicine, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Matthias Scheffler
- Center for Integrated Oncology Köln Bonn, Cologne, Germany; Lung Cancer Group Cologne, Department I for Internal Medicine, University Hospital of Cologne, Cologne, Germany; Network Genomic Medicine, Cologne, Germany
| | - Anne Maria Schultheis
- Network Genomic Medicine, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Oliver Gautschi
- Department for Medical Oncology, Lucerne Cantonal Hospital, Lucerne, Switzerland
| | | | - Joachim Diebold
- Institute of Pathology, Lucerne Cantonal Hospital, Lucerne, Switzerland
| | - Georg Pall
- Department for Internal Medicine, Haematology and Oncology, University Hospital Innsbruck, Innsbruck, Austria
| | - Sacha Rothschild
- Department for Oncology, University Hospital Basel, Basel, Switzerland
| | - Lukas Bubendorf
- Department for Cytopathology, University Hospital Basel, Basel, Switzerland
| | - Wolfgang Hartmann
- Gerhard-Domagk-Institute of Pathology, University Hospital of Münster, Münster, Germany
| | - Lukas Heukamp
- Network Genomic Medicine, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | | | - Jana Fassunke
- Network Genomic Medicine, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Michaela Angelika Ihle
- Network Genomic Medicine, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Helen Künstlinger
- Network Genomic Medicine, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Carina Heydt
- Network Genomic Medicine, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Rieke Fischer
- Center for Integrated Oncology Köln Bonn, Cologne, Germany; Lung Cancer Group Cologne, Department I for Internal Medicine, University Hospital of Cologne, Cologne, Germany; Network Genomic Medicine, Cologne, Germany
| | - Lucia Nogovà
- Center for Integrated Oncology Köln Bonn, Cologne, Germany; Lung Cancer Group Cologne, Department I for Internal Medicine, University Hospital of Cologne, Cologne, Germany; Network Genomic Medicine, Cologne, Germany
| | - Christian Mattonet
- Center for Integrated Oncology Köln Bonn, Cologne, Germany; Lung Cancer Group Cologne, Department I for Internal Medicine, University Hospital of Cologne, Cologne, Germany; Network Genomic Medicine, Cologne, Germany
| | - Rebecca Hein
- Institute of Medical Statistics, Informatics and Epidemiology, University Hospital of Cologne, Cologne, Germany
| | - Anne Adams
- Institute of Medical Statistics, Informatics and Epidemiology, University Hospital of Cologne, Cologne, Germany
| | - Ulrich Gerigk
- Thoracic Centre, Malteser Hospital Bonn/Rhein-Sieg, Bonn, Germany
| | - Wolfgang Schulte
- Departent for Pulmonology Cardiology and Allergology, Johanniter Hospital, Bonn, Germany
| | - Heike Lüders
- Evangelic Lung Clinic Berlin, Department of Pneumology, Berlin, Germany
| | - Christian Grohé
- Evangelic Lung Clinic Berlin, Department of Pneumology, Berlin, Germany
| | - Ullrich Graeven
- Department for Hematology, Oncology and Gastroenterology, Maria Hilf Hospital Mönchengladbach, Mönchengladbach, Germany
| | | | - Andreas Draube
- Department for Internal Medicine, St. Vinzenz Hospital Cologne, Cologne, Germany
| | - Karl-Otto Kambartel
- Department for Pulmonology and Allergology, Bethanien Hospital Moers, Moers, Germany
| | - Stefan Krüger
- Department for Pulmonology/Allergology/Sleep Medicine and Respiratory Care, Florence-Nightingale-Hospital, Düsseldorf, Germany
| | - Susanne Schulze-Olden
- Department for Pulmonology/Allergology/Sleep Medicine and Respiratory Care, Florence-Nightingale-Hospital, Düsseldorf, Germany
| | - Monika Serke
- Department for Pulmonology and Thoracic Oncology, Lung Clinic Hemer, Hemer, Germany
| | | | - Britta Kaminsky
- Clinic for Pulmonology and Allergology, Bethanien Hospital, Solingen, Germany
| | - Winfried Randerath
- Clinic for Pulmonology and Allergology, Bethanien Hospital, Solingen, Germany
| | - Sabine Merkelbach-Bruse
- Network Genomic Medicine, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Reinhard Büttner
- Network Genomic Medicine, Cologne, Germany; Institute of Pathology, University Hospital of Cologne, Cologne, Germany
| | - Jürgen Wolf
- Center for Integrated Oncology Köln Bonn, Cologne, Germany; Lung Cancer Group Cologne, Department I for Internal Medicine, University Hospital of Cologne, Cologne, Germany; Network Genomic Medicine, Cologne, Germany.
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Künstlinger H, Fassunke J, Schildhaus HU, Brors B, Heydt C, Ihle MA, Mechtersheimer G, Wardelmann E, Büttner R, Merkelbach-Bruse S. FGFR2 is overexpressed in myxoid liposarcoma and inhibition of FGFR signaling impairs tumor growth in vitro. Oncotarget 2016; 6:20215-30. [PMID: 26036639 PMCID: PMC4652999 DOI: 10.18632/oncotarget.4046] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 04/22/2015] [Indexed: 01/14/2023] Open
Abstract
Myxoid liposarcomas account for more than one third of liposarcomas and about 10% of all adult soft tissue sarcomas. The tumors are characterized by specific chromosomal translocations leading to the chimeric oncogenes FUS-DDIT3 or EWS1R-DDIT3. The encoded fusion proteins act as aberrant transcription factors. Therefore, we implemented comparative expression analyses using whole-genome microarrays in tumor and fat tissue samples. We aimed at identifying differentially expressed genes which may serve as diagnostic or prognostic biomarkers or as therapeutic targets. Microarray analyses revealed overexpression of FGFR2 and other members of the FGF/FGFR family. Overexpression of FGFR2 was validated by qPCR, immunohistochemistry and western blot analysis in primary tumor samples. Treatment of the myxoid liposarcoma cell lines MLS 402 and MLS 1765 with the FGFR inhibitors PD173074, TKI258 (dovitinib) and BGJ398 as well as specific siRNAs reduced cell proliferation, induced apoptosis and delayed cell migration. Combination of FGFR inhibitors with trabectedin further increased the effect. Our study demonstrates overexpression of FGFR2 and a functional role of FGFR signaling in myxoid liposarcoma. As FGFR inhibition showed effects on proliferation and cell migration and induced apoptosis in vitro, our data indicate the potential use of FGFR inhibitors as a targeted therapy for these tumors.
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Affiliation(s)
- Helen Künstlinger
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Jana Fassunke
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | - Benedikt Brors
- Computational Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carina Heydt
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | | | - Eva Wardelmann
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Reinhard Büttner
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
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11
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Angelika Ihle M, Merkelbach-Bruse S, Hartmann W, Bauer S, Ratner N, Sonobe H, Nishio J, Larsson O, Åman P, Pedeutour F, Taguchi T, Wardelmann E, Buettner R, Schildhaus HU. HR23b expression is a potential predictive biomarker for HDAC inhibitor treatment in mesenchymal tumours and is associated with response to vorinostat. J Pathol Clin Res 2016; 2:59-71. [PMID: 27499916 PMCID: PMC4907056 DOI: 10.1002/cjp2.35] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 12/13/2015] [Accepted: 12/17/2015] [Indexed: 12/13/2022]
Abstract
Histone deacetylases (HDAC) are key players in epigenetic regulation of gene expression and HDAC inhibitor (HDACi) treatment seems to be a promising anticancer therapy in many human tumours, including soft tissue sarcomas. HR23b has been shown to be a potential biomarker for sensitivity to HDACi therapy in cutaneous T‐cell lymphoma and hepatocellular carcinoma. We aimed to evaluate HR23b as a candidate biomarker for HDACi response in sarcomas and gastrointestinal stromal tumours (GIST). Therefore, HR23b expression was analysed comprehensively by western blot in sarcoma and GIST cell lines covering all major clinically relevant subtypes. MTT assay and ApoTox‐GloTM Triplex assay were performed after treatment with vorinostat, belinostat, mocetinostat and entinostat. HR23b protein expression was measured under HDACi treatment. Furthermore, HR23b expression levels were immunohistochemically determined in a large set of 523 clinical samples from sarcoma and GIST patients. Western blot analyses showed that sarcomas differ significantly in their expression of HR23b protein. All HDACi were able to regulate proliferation and apoptosis in vitro. Sensitivity to vorinostat correlated significantly with HR23b protein expression. Immunohistochemical prevalence screening in clinical samples of relevant adult‐type tumours revealed that 12.5% of sarcomas (among them malignant peripheral nerve sheath tumours, pleomorphic liposarcomas, leiomyosarcomas, dedifferentiated liposarcomas, synovial sarcomas and angiosarcomas) and 23.2% of GIST show high HR23b expression. Therefore, HDACi have antiproliferative and proapoptotic effects in sarcomas depending on the expression level of HR23b. These findings suggest that HR23b represents a candidate biomarker for HDACi sensitivity in certain sarcoma types and in GIST.
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Affiliation(s)
| | | | - Wolfgang Hartmann
- Institute of Pathology, University Hospital CologneCologneGermany; Gerhard Domagk Institute of Pathology, University Hospital MünsterMünsterGermany
| | - Sebastian Bauer
- Sarcoma Center, West German Cancer Center, University of Essen Essen Germany
| | - Nancy Ratner
- US Department of Pediatrics Cincinnati Children's Hospital Medical Centre Cincinnati OH USA
| | - Hiroshi Sonobe
- Department of Laboratory Medicine Chugoku Central Hospital Fukuyama Hiroshima Japan
| | - Jun Nishio
- Faculty of Medicine, Department of Orthopaedic Surgery Fukuoka University Fukuoka Japan
| | - Olle Larsson
- Department of Oncology and Pathology The Karolinska Institute Stockholm Sweden
| | - Pierre Åman
- Sahlgrenska Cancer Centre, University of Gothenburg Gothenburg Sweden
| | - Florence Pedeutour
- Faculty of Medicine, Laboratory of Genetics of Solid Tumours Institute for Research on Cancer and Aging Nice France
| | - Takahiro Taguchi
- Division of Human Health & Medical Science, Graduate School of Kuroshio Science Kochi University Nankoku Kochi Japan
| | - Eva Wardelmann
- Institute of Pathology, University Hospital CologneCologneGermany; Gerhard Domagk Institute of Pathology, University Hospital MünsterMünsterGermany
| | | | - Hans-Ulrich Schildhaus
- Institute of Pathology, University Hospital CologneCologneGermany; Institute of Pathology, University Hospital GöttingenGöttingenGermany
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12
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Heydt C, Kumm N, Fassunke J, Künstlinger H, Ihle MA, Scheel A, Schildhaus HU, Haller F, Büttner R, Odenthal M, Wardelmann E, Merkelbach-Bruse S. Massively parallel sequencing fails to detect minor resistant subclones in tissue samples prior to tyrosine kinase inhibitor therapy. BMC Cancer 2015; 15:291. [PMID: 25886408 PMCID: PMC4404105 DOI: 10.1186/s12885-015-1311-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Accepted: 04/01/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Personalised medicine and targeted therapy have revolutionised cancer treatment. However, most patients develop drug resistance and relapse after showing an initial treatment response. Two theories have been postulated; either secondary resistance mutations develop de novo during therapy by mutagenesis or they are present in minor subclones prior to therapy. In this study, these two theories were evaluated in gastrointestinal stromal tumours (GISTs) where most patients develop secondary resistance mutations in the KIT gene during therapy with tyrosine kinase inhibitors. METHODS We used a cohort of 33 formalin-fixed, paraffin embedded (FFPE) primary GISTs and their corresponding recurrent tumours with known mutational status. The primary tumours were analysed for the secondary mutations of the recurrences, which had been identified previously. The primary tumours were resected prior to tyrosine kinase inhibitor therapy. Three ultrasensitive, massively parallel sequencing approaches on the GS Junior (Roche, Mannheim, Germany) and the MiSeq(TM) (Illumina, San Diego, CA, USA) were applied. Additionally, nine fresh-frozen samples resected prior to therapy were analysed for the most common secondary resistance mutations. RESULTS With a sensitivity level of down to 0.02%, no pre-existing resistant subclones with secondary KIT mutations were detected in primary GISTs. The sensitivity level varied for individual secondary mutations and was limited by sequencing artefacts on both systems. Artificial T > C substitutions at the position of the exon 13 p.V654A mutation, in particular, led to a lower sensitivity, independent from the source of the material. Fresh-frozen samples showed the same range of artificially mutated allele frequencies as the FFPE material. CONCLUSIONS Although we achieved a sufficiently high level of sensitivity, neither in the primary FFPE nor in the fresh-frozen GISTs we were able to detect pre-existing resistant subclones of the corresponding known secondary resistance mutations of the recurrent tumours. This supports the theory that secondary KIT resistance mutations develop under treatment by "de novo" mutagenesis. Alternatively, the detection limit of two mutated clones in 10,000 wild-type clones might not have been high enough or heterogeneous tissue samples, per se, might not be suitable for the detection of very small subpopulations of mutated cells.
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Affiliation(s)
- Carina Heydt
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Niklas Kumm
- Institute of Pathology, University Hospital Erlangen, Krankenhausstraße 8-10, 91054, Erlangen, Germany.
| | - Jana Fassunke
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Helen Künstlinger
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Michaela Angelika Ihle
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Andreas Scheel
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Hans-Ulrich Schildhaus
- Institute of Pathology, University Hospital Göttingen, Robert-Koch-Strasse 40, 37075, Göttingen, Germany.
| | - Florian Haller
- Institute of Pathology, University Hospital Erlangen, Krankenhausstraße 8-10, 91054, Erlangen, Germany.
| | - Reinhard Büttner
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Margarete Odenthal
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
| | - Eva Wardelmann
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Albert-Schweitzer-Campus 1, Gebäude D17, 48149, Münster, Germany.
| | - Sabine Merkelbach-Bruse
- Institute of Pathology, University Hospital Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
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Ihle MA, Trautmann M, Kuenstlinger H, Huss S, Heydt C, Fassunke J, Wardelmann E, Bauer S, Schildhaus HU, Buettner R, Merkelbach-Bruse S. miRNA-221 and miRNA-222 induce apoptosis via the KIT/AKT signalling pathway in gastrointestinal stromal tumours. Mol Oncol 2015; 9:1421-33. [PMID: 25898773 DOI: 10.1016/j.molonc.2015.03.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/30/2015] [Indexed: 02/09/2023] Open
Abstract
Aberrantly expressed microRNAs (miRNAs) are involved in many diseases including cancer. In gastrointestinal stromal tumours (GISTs) expression of miR-221 and miR-222 is reduced compared to control tissue and other sarcomas but the functional effects of this downregulation are not fully understood. This study aimed at evaluating the miR-221 and miR-222 expression profiles in different GIST subtypes and the functional role of these miRNAs. Expression of miR-221 and miR-222 was analysed in six KIT exon 9 and three KIT exon 11 mutated and nine wildtype GISTs by qPCR. Viability and apoptosis were examined in three different, KIT positive GIST cell lines (GIST882, GIST-T1 and GIST48) after overexpression of these miRNAs. The modulation of KIT and the PI3K/AKT pathways was determined by Western blot. Wildtype and KIT mutated GISTs revealed reduced miRNA expression compared to adequate control tissue. miRNA expression was lower for wildtype compared to mutated GISTs. Transient transfection of miR-221 and miR-222 reduced viability and induced apoptosis by inhibition of KIT expression and its phosphorylation and activation of caspases 3 and 7 in all three GIST cell lines. p-AKT, AKT and BCL2 expression was reduced after miRNA transfection whereas only slight influence on p-MTOR, MTOR and BCL2L11 (BIM) was detected. Our results demonstrate that miR-221 and miR-222 which are downregulated in wildtype and mutated GISTs, induce apoptosis in vitro by a signalling cascade involving KIT, AKT and BCL2. Therefore, overexpression of these miRNAs seems to functionally counteract oncogenic signalling pathways in GIST.
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Affiliation(s)
| | - Marcel Trautmann
- Institute of Pathology, University of Cologne, Medical Centre, Cologne, Germany
| | - Helen Kuenstlinger
- Institute of Pathology, University of Cologne, Medical Centre, Cologne, Germany
| | - Sebastian Huss
- Institute of Pathology, University of Cologne, Medical Centre, Cologne, Germany
| | - Carina Heydt
- Institute of Pathology, University of Cologne, Medical Centre, Cologne, Germany
| | - Jana Fassunke
- Institute of Pathology, University of Cologne, Medical Centre, Cologne, Germany
| | - Eva Wardelmann
- Institute of Pathology, University of Cologne, Medical Centre, Cologne, Germany
| | - Sebastian Bauer
- Sarcoma Centre, West German Cancer Centre, University of Essen, Essen, Germany
| | | | - Reinhard Buettner
- Institute of Pathology, University of Cologne, Medical Centre, Cologne, Germany
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14
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Heydt C, Fassunke J, Künstlinger H, Ihle MA, König K, Heukamp LC, Schildhaus HU, Odenthal M, Büttner R, Merkelbach-Bruse S. Comparison of pre-analytical FFPE sample preparation methods and their impact on massively parallel sequencing in routine diagnostics. PLoS One 2014; 9:e104566. [PMID: 25105902 PMCID: PMC4126727 DOI: 10.1371/journal.pone.0104566] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/11/2014] [Indexed: 11/19/2022] Open
Abstract
Over the last years, massively parallel sequencing has rapidly evolved and has now transitioned into molecular pathology routine laboratories. It is an attractive platform for analysing multiple genes at the same time with very little input material. Therefore, the need for high quality DNA obtained from automated DNA extraction systems has increased, especially to those laboratories which are dealing with formalin-fixed paraffin-embedded (FFPE) material and high sample throughput. This study evaluated five automated FFPE DNA extraction systems as well as five DNA quantification systems using the three most common techniques, UV spectrophotometry, fluorescent dye-based quantification and quantitative PCR, on 26 FFPE tissue samples. Additionally, the effects on downstream applications were analysed to find the most suitable pre-analytical methods for massively parallel sequencing in routine diagnostics. The results revealed that the Maxwell 16 from Promega (Mannheim, Germany) seems to be the superior system for DNA extraction from FFPE material. The extracts had a 1.3-24.6-fold higher DNA concentration in comparison to the other extraction systems, a higher quality and were most suitable for downstream applications. The comparison of the five quantification methods showed intermethod variations but all methods could be used to estimate the right amount for PCR amplification and for massively parallel sequencing. Interestingly, the best results in massively parallel sequencing were obtained with a DNA input of 15 ng determined by the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). No difference could be detected in mutation analysis based on the results of the quantification methods. These findings emphasise, that it is particularly important to choose the most reliable and constant DNA extraction system, especially when using small biopsies and low elution volumes, and that all common DNA quantification techniques can be used for downstream applications like massively parallel sequencing.
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Affiliation(s)
- Carina Heydt
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
- * E-mail:
| | - Jana Fassunke
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Helen Künstlinger
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | - Katharina König
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | | | | | - Reinhard Büttner
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
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15
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Ihle MA, Fassunke J, König K, Grünewald I, Schlaak M, Kreuzberg N, Tietze L, Schildhaus HU, Büttner R, Merkelbach-Bruse S. Comparison of high resolution melting analysis, pyrosequencing, next generation sequencing and immunohistochemistry to conventional Sanger sequencing for the detection of p.V600E and non-p.V600E BRAF mutations. BMC Cancer 2014; 14:13. [PMID: 24410877 PMCID: PMC3893431 DOI: 10.1186/1471-2407-14-13] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 01/08/2014] [Indexed: 01/11/2023] Open
Abstract
Background The approval of vemurafenib in the US 2011 and in Europe 2012 improved the therapy of not resectable or metastatic melanoma. Patients carrying a substitution of valine to glutamic acid at codon 600 (p.V600E) or a substitution of valine to leucine (p.V600K) in BRAF show complete or partial response. Therefore, the precise identification of the underlying somatic mutations is essential. Herein, we evaluate the sensitivity, specificity and feasibility of six different methods for the detection of BRAF mutations. Methods Samples harboring p.V600E mutations as well as rare mutations in BRAF exon 15 were compared to wildtype samples. DNA was extracted from formalin-fixed paraffin-embedded tissues by manual micro-dissection and automated extraction. BRAF mutational analysis was carried out by high resolution melting (HRM) analysis, pyrosequencing, allele specific PCR, next generation sequencing (NGS) and immunohistochemistry (IHC). All mutations were independently reassessed by Sanger sequencing. Due to the limited tumor tissue available different numbers of samples were analyzed with each method (82, 72, 60, 72, 49 and 82 respectively). Results There was no difference in sensitivity between the HRM analysis and Sanger sequencing (98%). All mutations down to 6.6% allele frequency could be detected with 100% specificity. In contrast, pyrosequencing detected 100% of the mutations down to 5% allele frequency but exhibited only 90% specificity. The allele specific PCR failed to detect 16.3% of the mutations eligible for therapy with vemurafenib. NGS could analyze 100% of the cases with 100% specificity but exhibited 97.5% sensitivity. IHC showed once cross-reactivity with p.V600R but was a good amendment to HRM. Conclusion Therefore, at present, a combination of HRM and IHC is recommended to increase sensitivity and specificity for routine diagnostic to fulfill the European requirements concerning vemurafenib therapy of melanoma patients.
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