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Hallermayr A, Keßler T, Fujera M, Liesfeld B, Bernstein S, von Ameln S, Schanze D, Steinke-Lange V, Pickl JMA, Neuhann TM, Holinski-Feder E. Impact of cfDNA Reference Materials on Clinical Performance of Liquid Biopsy NGS Assays. Cancers (Basel) 2023; 15:5024. [PMID: 37894392 PMCID: PMC10605119 DOI: 10.3390/cancers15205024] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/29/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Liquid biopsy enables the non-invasive analysis of genetic tumor variants in circulating free DNA (cfDNA) in plasma. Accurate analytical validation of liquid biopsy NGS assays is required to detect variants with low variant allele frequencies (VAFs). METHODS Six types of commercial cfDNA reference materials and 42 patient samples were analyzed using a duplex-sequencing-based liquid biopsy NGS assay. RESULTS We comprehensively evaluated the similarity of commercial cfDNA reference materials to native cfDNA. We observed significant differences between the reference materials in terms of wet-lab and sequencing quality as well as background noise. No reference material resembled native cfDNA in all performance metrics investigated. Based on our results, we established guidelines for the selection of appropriate reference materials for the different steps in performance evaluation. The use of inappropriate materials and cutoffs could eventually lead to a lower sensitivity for variant detection. CONCLUSION Careful consideration of commercial reference materials is required for performance evaluation of liquid biopsy NGS assays. While the similarity to native cfDNA aids in the development of experimental protocols, reference materials with well-defined variants are preferable for determining sensitivity and precision, which are essential for accurate clinical interpretation.
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Affiliation(s)
- Ariane Hallermayr
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, 80336 Munich, Germany
- European Liquid Biopsy Society, 20246 Hamburg, Germany
| | - Thomas Keßler
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
- European Liquid Biopsy Society, 20246 Hamburg, Germany
| | - Moritz Fujera
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
| | - Ben Liesfeld
- Limbus Medical Technologies GmbH, 18055 Rostock, Germany; (B.L.); (S.B.)
| | - Samuel Bernstein
- Limbus Medical Technologies GmbH, 18055 Rostock, Germany; (B.L.); (S.B.)
| | - Simon von Ameln
- Immune-Oncological Centre Cologne (IOZK), 50674 Cologne, Germany;
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Otto-von-Guericke University, 39120 Magdeburg, Germany;
| | - Verena Steinke-Lange
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, 80336 Munich, Germany
- European Liquid Biopsy Society, 20246 Hamburg, Germany
| | - Julia M. A. Pickl
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, 80336 Munich, Germany
| | - Teresa M. Neuhann
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
| | - Elke Holinski-Feder
- MGZ—Medizinisch Genetisches Zentrum, 80335 Munich, Germany; (T.K.); (M.F.); (V.S.-L.); (T.M.N.); (E.H.-F.)
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, 80336 Munich, Germany
- European Liquid Biopsy Society, 20246 Hamburg, Germany
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2
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Schwenk V, Leal Silva RM, Scharf F, Knaust K, Wendlandt M, Häusser T, Pickl JMA, Steinke-Lange V, Laner A, Morak M, Holinski-Feder E, Wolf DA. Transcript capture and ultradeep long-read RNA sequencing (CAPLRseq) to diagnose HNPCC/Lynch syndrome. J Med Genet 2023; 60:747-759. [PMID: 36593122 PMCID: PMC10423559 DOI: 10.1136/jmg-2022-108931] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/10/2022] [Indexed: 01/03/2023]
Abstract
PURPOSE Whereas most human genes encode multiple mRNA isoforms with distinct function, clinical workflows for assessing this heterogeneity are not readily available. This is a substantial shortcoming, considering that up to 25% of disease-causing gene variants are suspected of disrupting mRNA splicing or mRNA abundance. Long-read sequencing can readily portray mRNA isoform diversity, but its sensitivity is relatively low due to insufficient transcriptome penetration. METHODS We developed and applied capture-based target enrichment from patient RNA samples combined with Oxford Nanopore long-read sequencing for the analysis of 123 hereditary cancer transcripts (capture and ultradeep long-read RNA sequencing (CAPLRseq)). RESULTS Validating CAPLRseq, we confirmed 17 cases of hereditary non-polyposis colorectal cancer/Lynch syndrome based on the demonstration of splicing defects and loss of allele expression of mismatch repair genes MLH1, PMS2, MSH2 and MSH6. Using CAPLRseq, we reclassified two variants of uncertain significance in MSH6 and PMS2 as either likely pathogenic or benign. CONCLUSION Our data show that CAPLRseq is an automatable and adaptable workflow for effective transcriptome-based identification of disease variants in a clinical diagnostic setting.
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Affiliation(s)
| | | | | | | | | | - Tanja Häusser
- Medizinisch Genetisches Zentrum (MGZ), Munich, Germany
| | - Julia M A Pickl
- Medizinisch Genetisches Zentrum (MGZ), Munich, Germany
- Klinikum der Universität München, Munich, Germany
| | | | - Andreas Laner
- Medizinisch Genetisches Zentrum (MGZ), Munich, Germany
| | - Monika Morak
- Medizinisch Genetisches Zentrum (MGZ), Munich, Germany
- Klinikum der Universität München, Munich, Germany
| | - Elke Holinski-Feder
- Medizinisch Genetisches Zentrum (MGZ), Munich, Germany
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
| | - Dieter A Wolf
- Medizinisch Genetisches Zentrum (MGZ), Munich, Germany
- Department of Medicine II, Technical University Munich, Munich, Germany
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3
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Hallermayr A, Neuhann TM, Steinke-Lange V, Scharf F, Laner A, Ewald R, Liesfeld B, Holinski-Feder E, Pickl JMA. Highly sensitive liquid biopsy Duplex sequencing complements tissue biopsy to enhance detection of clinically relevant genetic variants. Front Oncol 2022; 12:1014592. [PMID: 36636551 PMCID: PMC9831673 DOI: 10.3389/fonc.2022.1014592] [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: 08/08/2022] [Accepted: 11/14/2022] [Indexed: 12/28/2022] Open
Abstract
Background Liquid biopsy (LB) is a promising complement to tissue biopsy for detection of clinically relevant genetic variants in cancer and mosaic diseases. A combined workflow to enable parallel tissue and LB analysis is required to maximize diagnostic yield for patients. Methods We developed and validated a cost-efficient combined next-generation sequencing (NGS) workflow for both tissue and LB samples, and applied Duplex sequencing technology for highly accurate detection of low frequency variants in plasma. Clinically relevant cutoffs for variant reporting and quantification were established. Results We investigated assay performance characteristics for very low amounts of clinically relevant variants. In plasma, the assay achieved 100% sensitivity and 92.3% positive predictive value (PPV) for single nucleotide variants (SNVs) and 91.7% sensitivity and 100% PPV for insertions and deletions (InDel) in clinically relevant hotspots with 0.5-5% variant allele frequencies (VAFs). We further established a cutoff for reporting variants (i.e. Limit of Blank, LOB) at 0.25% VAF and a cutoff for quantification (i.e. Limit of Quantification, LOQ) at 5% VAF in plasma for accurate clinical interpretation of analysis results. With our LB approach, we were able to identify the molecular cause of a clinically confirmed asymmetric overgrowth syndrome in a 10-year old child that would have remained undetected with tissue analysis as well as other molecular diagnostic approaches. Conclusion Our flexible and cost-efficient workflow allows analysis of both tissue and LB samples and provides clinically relevant cutoffs for variant reporting and precise quantification. Complementing tissue analysis by LB is likely to increase diagnostic yield for patients with molecular diseases.
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Affiliation(s)
- Ariane Hallermayr
- MGZ – Medizinisch Genetisches Zentrum, Munich, Germany,Pettenkofer School of Public Health, Munich, Germany,Institute for Medical Information Processing, Biometry, and Epidemiology –IBE, Ludwig-Maximilians-Universität (LMU) Munich, Munich, Germany
| | | | - Verena Steinke-Lange
- MGZ – Medizinisch Genetisches Zentrum, Munich, Germany,Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany
| | | | - Andreas Laner
- MGZ – Medizinisch Genetisches Zentrum, Munich, Germany
| | - Roland Ewald
- Limbus Medical Technologies GmbH, Rostock, Germany
| | - Ben Liesfeld
- Limbus Medical Technologies GmbH, Rostock, Germany
| | - Elke Holinski-Feder
- MGZ – Medizinisch Genetisches Zentrum, Munich, Germany,Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany
| | - Julia M. A. Pickl
- MGZ – Medizinisch Genetisches Zentrum, Munich, Germany,Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany,*Correspondence: Julia M. A. Pickl,
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4
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Hallermayr A, Wohlfrom T, Steinke-Lange V, Benet-Pagès A, Scharf F, Heitzer E, Mansmann U, Haberl C, de Wit M, Vogelsang H, Rentsch M, Holinski-Feder E, Pickl JMA. Somatic copy number alteration and fragmentation analysis in circulating tumor DNA for cancer screening and treatment monitoring in colorectal cancer patients. J Hematol Oncol 2022; 15:125. [PMID: 36056434 PMCID: PMC9438339 DOI: 10.1186/s13045-022-01342-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 05/20/2022] [Accepted: 08/19/2022] [Indexed: 11/10/2022] Open
Abstract
Background Analysis of circulating free DNA (cfDNA) is a promising tool for personalized management of colorectal cancer (CRC) patients. Untargeted cfDNA analysis using whole-genome sequencing (WGS) does not need a priori knowledge of the patient´s mutation profile. Methods Here we established LIquid biopsy Fragmentation, Epigenetic signature and Copy Number Alteration analysis (LIFE-CNA) using WGS with ~ 6× coverage for detection of circulating tumor DNA (ctDNA) in CRC patients as a marker for CRC detection and monitoring.
Results We describe the analytical validity and a clinical proof-of-concept of LIFE-CNA using a total of 259 plasma samples collected from 50 patients with stage I-IV CRC and 61 healthy controls. To reliably distinguish CRC patients from healthy controls, we determined cutoffs for the detection of ctDNA based on global and regional cfDNA fragmentation patterns, transcriptionally active chromatin sites, and somatic copy number alterations. We further combined global and regional fragmentation pattern into a machine learning (ML) classifier to accurately predict ctDNA for cancer detection. By following individual patients throughout their course of disease, we show that LIFE-CNA enables the reliable prediction of response or resistance to treatment up to 3.5 months before commonly used CEA. Conclusion In summary, we developed and validated a sensitive and cost-effective method for untargeted ctDNA detection at diagnosis as well as for treatment monitoring of all CRC patients based on genetic as well as non-genetic tumor-specific cfDNA features. Thus, once sensitivity and specificity have been externally validated, LIFE-CNA has the potential to be implemented into clinical practice. To the best of our knowledge, this is the first study to consider multiple genetic and non-genetic cfDNA features in combination with ML classifiers and to evaluate their potential in both cancer detection and treatment monitoring. Trial registration DRKS00012890. Supplementary Information The online version contains supplementary material available at 10.1186/s13045-022-01342-z.
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Affiliation(s)
- Ariane Hallermayr
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Pettenkofer School of Public Health, Munich, Germany.,Institute for Medical Information Processing, Biometry, and Epidemiology -IBE, LMU Munich, Munich, Germany
| | | | - Verena Steinke-Lange
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Medizinische Klinik Und Poliklinik IV, Campus Innenstadt, Klinikum Der Universität München, Munich, Germany
| | - Anna Benet-Pagès
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine (Austria), Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria
| | - Ulrich Mansmann
- Institute for Medical Information Processing, Biometry, and Epidemiology -IBE, LMU Munich, Munich, Germany
| | - Christopher Haberl
- Department of Oncology and Hematology, Barmherzige Brüder, Klinikum St. Elisabeth, Straubing, Germany
| | - Maike de Wit
- Department of Hematology, Oncology and Palliative Medicine, Vivantes Klinikum Neukoelln, Berlin, Germany.,Department of Oncology, Vivantes Auguste-Viktoria-Klinikum, Berlin, Germany
| | - Holger Vogelsang
- Department of General, Visceral, Thoracic and Endocrine Surgery, Klinikum Garmisch-Partenkirchen, Teaching Hospital, Ludwig Maximilian University Munich, Garmisch-Partenkirchen, Germany
| | - Markus Rentsch
- Department of General, Visceral and Thorax Surgery, Klinikum Ingolstadt, Ingolstadt, Germany.,Department of General, Visceral, Vascular and Transplant Surgery, University Hospital Munich, Ludwig-Maximilians University of Munich, Campus Großhadern, Munich, Germany
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Medizinische Klinik Und Poliklinik IV, Campus Innenstadt, Klinikum Der Universität München, Munich, Germany
| | - Julia M A Pickl
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany. .,Medizinische Klinik Und Poliklinik IV, Campus Innenstadt, Klinikum Der Universität München, Munich, Germany.
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5
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Scharf F, Leal Silva RM, Morak M, Hastie A, Pickl JMA, Sendelbach K, Gebhard C, Locher M, Laner A, Steinke-Lange V, Koehler U, Holinski-Feder E, Wolf DA. Constitutional chromothripsis of the APC locus as a cause of genetic predisposition to colon cancer. J Med Genet 2021; 59:976-983. [PMID: 34911816 PMCID: PMC9554066 DOI: 10.1136/jmedgenet-2021-108147] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/11/2021] [Indexed: 11/21/2022]
Abstract
Purpose Approximately 20% of patients with clinical familial adenomatous polyposis (FAP) remain unsolved after molecular genetic analysis of the APC and other polyposis genes, suggesting additional pathomechanisms. Methods We applied multidimensional genomic analysis employing chromosomal microarray profiling, optical mapping, long-read genome and RNA sequencing combined with FISH and standard PCR of genomic and complementary DNA to decode a patient with an attenuated FAP that had remained unsolved by Sanger sequencing and multigene panel next-generation sequencing for years. Results We identified a complex 3.9 Mb rearrangement involving 14 fragments from chromosome 5q22.1q22.3 of which three were lost, 1 reinserted into chromosome 5 and 10 inserted into chromosome 10q21.3 in a seemingly random order and orientation thus fulfilling the major criteria of chromothripsis. The rearrangement separates APC promoter 1B from the coding ORF (open reading frame) thus leading to allele-specific downregulation of APC mRNA. The rearrangement also involves three additional genes implicated in the APC–Axin–GSK3B–β-catenin signalling pathway. Conclusions Based on comprehensive genomic analysis, we propose that constitutional chromothripsis dampening APC expression, possibly modified by additional APC–Axin–GSK3B–β-catenin pathway disruptions, underlies the patient’s clinical phenotype. The combinatorial approach we deployed provides a powerful tool set for deciphering unsolved familial polyposis and potentially other tumour syndromes and monogenic diseases.
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Affiliation(s)
| | | | - Monika Morak
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Alex Hastie
- BioNano Genomics Inc, San Diego, California, USA
| | | | | | | | | | - Andreas Laner
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | | | - Udo Koehler
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany .,Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
| | - Dieter A Wolf
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany .,Department of Medicine II, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
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6
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Hallermayr A, Benet-Pagès A, Steinke-Lange V, Mansmann U, Rentsch M, Holinski-Feder E, Pickl JMA. Liquid Biopsy Hotspot Variant Assays: Analytical Validation for Application in Residual Disease Detection and Treatment Monitoring. Clin Chem 2021; 67:1483-1491. [PMID: 34392332 DOI: 10.1093/clinchem/hvab124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/12/2021] [Accepted: 06/15/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Analysis of circulating tumor DNA (ctDNA) in plasma is a powerful approach to guide decisions in personalized cancer treatment. Given the low concentration of ctDNA in plasma, highly sensitive methods are required to reliably identify clinically relevant variants. METHODS We evaluated the suitability of 5 droplet digital PCR (ddPCR) assays targeting KRAS, BRAF, and EGFR variants for ctDNA analysis in clinical use. RESULTS We investigated assay performance characteristics for very low amounts of variants, showing that the assays had very low limits of blank (0% to 0.11% variant allele frequency, VAF) and limits of quantification (0.41% to 0.7% VAF). Nevertheless, striking differences in detection and quantification of low mutant VAFs between the 5 tested assays were observed, highlighting the need for assay-specific analytical validation. Besides in-depth evaluation, a guide for clinical interpretation of obtained VAFs in plasma was developed, depending on the limits of blank and limits of quantification values. CONCLUSION It is possible to provide comprehensive clinical reports on actionable variants, allowing minimal residual disease detection and treatment monitoring in liquid biopsy.
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Affiliation(s)
- Ariane Hallermayr
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Pettenkofer School of Public Health, Munich, Germany.,Institute for Medical Information Processing, Biometry, and Epidemiology - IBE, LMU Munich, Munich, Germany
| | - Anna Benet-Pagès
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Verena Steinke-Lange
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
| | - Ulrich Mansmann
- Institute for Medical Information Processing, Biometry, and Epidemiology - IBE, LMU Munich, Munich, Germany
| | - Markus Rentsch
- Department of General, Visceral and Thorax Surgery, Klinikum Ingolstadt, Germany.,Department of General, Visceral, Vascular and Transplant Surgery, University Hospital Munich, Ludwig-Maximilians University of Munich, Campus Großhadern, Munich, Germany
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
| | - Julia M A Pickl
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
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Pickl JMA, Tichy D, Kuryshev VY, Tolstov Y, Falkenstein M, Schüler J, Reidenbach D, Hotz-Wagenblatt A, Kristiansen G, Roth W, Hadaschik B, Hohenfellner M, Duensing S, Heckmann D, Sültmann H. Ago-RIP-Seq identifies Polycomb repressive complex I member CBX7 as a major target of miR-375 in prostate cancer progression. Oncotarget 2018; 7:59589-59603. [PMID: 27449098 PMCID: PMC5312160 DOI: 10.18632/oncotarget.10729] [Citation(s) in RCA: 36] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/09/2016] [Indexed: 01/02/2023] Open
Abstract
Prostate cancer is a heterogeneous disease. MiR-375 is a marker for prostate cancer progression, but its cellular function is not characterized. Here, we provide the first comprehensive investigation of miR-375 in prostate cancer. We show that miR-375 is enriched in prostate cancer compared to normal cells. Furthermore, miR-375 enhanced proliferation, migration and invasion in vitro and induced tumor growth and reduced survival in vivo showing that miR-375 has oncogenic properties in prostate cancer. On the molecular level, we provide the targetome and genome-wide transcriptional changes of miR-375 expression by applying a generalized linear model for Ago-RIP-Seq and RNA-Seq, and show that miR-375 is involved in tumorigenic networks and Polycomb regulation. Integration of tissue and gene ontology data prioritized miR-375 targets and identified the tumor suppressor gene CBX7, a member of Polycomb repressive complex 1, as a major miR-375 target. MiR-375-mediated repression of CBX7 was accompanied by increased expression of its homolog CBX8 and activated transcriptional programs linked to malignant progression in prostate cancer cells. Tissue analysis showed association of CBX7 loss with advanced prostate cancer. Our study indicates that miR-375 exerts its tumor-promoting role in prostate cancer by influencing the epigenetic regulation of transcriptional programs through its ability to directly target the Polycomb complex member CBX7.
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Affiliation(s)
- Julia M A Pickl
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Diana Tichy
- Department of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vladimir Y Kuryshev
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Yanis Tolstov
- Section of Molecular Urooncology, Department of Urology, University of Heidelberg School of Medicine, Heidelberg, Germany
| | - Michael Falkenstein
- Section of Molecular Urooncology, Department of Urology, University of Heidelberg School of Medicine, Heidelberg, Germany
| | - Julia Schüler
- Oncotest GmbH, Institute for Experimental Oncology, Freiburg, Germany
| | - Daniel Reidenbach
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- Bioinformatics Group, Core Facility Genomics & Proteomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Glen Kristiansen
- Institute of Pathology, Center for Integrated Oncology, University of Bonn, Bonn, Germany
| | - Wilfried Roth
- NCT Tissue Bank of The National Center of Tumor Diseases (NCT) and Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Boris Hadaschik
- Department of Urology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Stefan Duensing
- Section of Molecular Urooncology, Department of Urology, University of Heidelberg School of Medicine, Heidelberg, Germany
| | - Doreen Heckmann
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Holger Sültmann
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
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