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Schimmelpfennig C, Rade M, Füssel S, Löffler D, Blumert C, Bertram C, Borkowetz A, Otto DJ, Puppel SH, Hönscheid P, Sommer U, Baretton GB, Köhl U, Wirth M, Thomas C, Horn F, Kreuz M, Reiche K. Characterization and evaluation of gene fusions as a measure of genetic instability and disease prognosis in prostate cancer. BMC Cancer 2023; 23:575. [PMID: 37349736 DOI: 10.1186/s12885-023-11019-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/27/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Prostate cancer (PCa) is one of the most prevalent cancers worldwide. The clinical manifestations and molecular characteristics of PCa are highly variable. Aggressive types require radical treatment, whereas indolent ones may be suitable for active surveillance or organ-preserving focal therapies. Patient stratification by clinical or pathological risk categories still lacks sufficient precision. Incorporating molecular biomarkers, such as transcriptome-wide expression signatures, improves patient stratification but so far excludes chromosomal rearrangements. In this study, we investigated gene fusions in PCa, characterized potential novel candidates, and explored their role as prognostic markers for PCa progression. METHODS We analyzed 630 patients in four cohorts with varying traits regarding sequencing protocols, sample conservation, and PCa risk group. The datasets included transcriptome-wide expression and matched clinical follow-up data to detect and characterize gene fusions in PCa. With the fusion calling software Arriba, we computationally predicted gene fusions. Following detection, we annotated the gene fusions using published databases for gene fusions in cancer. To relate the occurrence of gene fusions to Gleason Grading Groups and disease prognosis, we performed survival analyses using the Kaplan-Meier estimator, log-rank test, and Cox regression. RESULTS Our analyses identified two potential novel gene fusions, MBTTPS2,L0XNC01::SMS and AMACR::AMACR. These fusions were detected in all four studied cohorts, providing compelling evidence for the validity of these fusions and their relevance in PCa. We also found that the number of gene fusions detected in a patient sample was significantly associated with the time to biochemical recurrence in two of the four cohorts (log-rank test, p-value < 0.05 for both cohorts). This was also confirmed after adjusting the prognostic model for Gleason Grading Groups (Cox regression, p-values < 0.05). CONCLUSIONS Our gene fusion characterization workflow revealed two potential novel fusions specific for PCa. We found evidence that the number of gene fusions was associated with the prognosis of PCa. However, as the quantitative correlations were only moderately strong, further validation and assessment of clinical value is required before potential application.
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Affiliation(s)
- Carolin Schimmelpfennig
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Michael Rade
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Susanne Füssel
- Department of Urology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Dennis Löffler
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Conny Blumert
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Catharina Bertram
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Angelika Borkowetz
- Department of Urology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Dominik J Otto
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Sven-Holger Puppel
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Pia Hönscheid
- Institute of Pathology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Ulrich Sommer
- Institute of Pathology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Gustavo B Baretton
- Institute of Pathology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Ulrike Köhl
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
- Institute of Clinical Immunology, Medical Faculty, University Hospital, University of Leipzig, Leipzig, Germany
| | - Manfred Wirth
- Department of Urology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Christian Thomas
- Department of Urology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Friedemann Horn
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Markus Kreuz
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Kristin Reiche
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany.
- Institute of Clinical Immunology, Medical Faculty, University Hospital, University of Leipzig, Leipzig, Germany.
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Martini C, Logan JM, Sorvina A, Gordon C, Beck AR, S-Y Ung B, Caruso MC, Moore C, Hocking A, Johnson IRD, Li KL, Karageorgos L, Hopkins AM, Esterman AJ, Huzzell C, Brooks RD, Lazniewska J, Hickey SM, Bader C, Parkinson-Lawrence E, Weigert R, Sorich MJ, Tewari P, Martin C, O'Toole S, Bates M, Ward M, Mohammed B, Keegan H, Watson W, Prendergast S, Heffernan S, NiMhaolcatha S, O'Connor R, Malone V, Carter M, Ryan K, Brady N, Clarke A, Sokol F, Prabhakaran S, Stahl J, Klebe S, Samaratunga H, Delahunt B, Selemidis S, Moretti KL, Butler LM, O'Leary JJ, Brooks DA. Aberrant protein expression of Appl1, Sortilin and Syndecan-1 during the biological progression of prostate cancer. Pathology 2023; 55:40-51. [PMID: 36089417 DOI: 10.1016/j.pathol.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/19/2022] [Accepted: 08/01/2022] [Indexed: 01/27/2023]
Abstract
Diagnosis and assessment of patients with prostate cancer is dependent on accurate interpretation and grading of histopathology. However, morphology does not necessarily reflect the complex biological changes occurring in prostate cancer disease progression, and current biomarkers have demonstrated limited clinical utility in patient assessment. This study aimed to develop biomarkers that accurately define prostate cancer biology by distinguishing specific pathological features that enable reliable interpretation of pathology for accurate Gleason grading of patients. Online gene expression databases were interrogated and a pathogenic pathway for prostate cancer was identified. The protein expression of key genes in the pathway, including adaptor protein containing a pleckstrin homology (PH) domain, phosphotyrosine-binding (PTB) domain, and leucine zipper motif 1 (Appl1), Sortilin and Syndecan-1, was examined by immunohistochemistry (IHC) in a pilot study of 29 patients with prostate cancer, using monoclonal antibodies designed against unique epitopes. Appl1, Sortilin, and Syndecan-1 expression was first assessed in a tissue microarray cohort of 112 patient samples, demonstrating that the monoclonal antibodies clearly illustrate gland morphologies. To determine the impact of a novel IHC-assisted interpretation (the utility of Appl1, Sortilin, and Syndecan-1 labelling as a panel) of Gleason grading, versus standard haematoxylin and eosin (H&E) Gleason grade assignment, a radical prostatectomy sample cohort comprising 114 patients was assessed. In comparison to H&E, the utility of the biomarker panel reduced subjectivity in interpretation of prostate cancer tissue morphology and improved the reliability of pathology assessment, resulting in Gleason grade redistribution for 41% of patient samples. Importantly, for equivocal IHC-assisted labelling and H&E staining results, the cancer morphology interpretation could be more accurately applied upon re-review of the H&E tissue sections. This study addresses a key issue in the field of prostate cancer pathology by presenting a novel combination of three biomarkers and has the potential to transform clinical pathology practice by standardising the interpretation of the tissue morphology.
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Affiliation(s)
- Carmela Martini
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia.
| | - Jessica M Logan
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Alexandra Sorvina
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Colin Gordon
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Andrew R Beck
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Ben S-Y Ung
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Maria C Caruso
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Courtney Moore
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Ashleigh Hocking
- Department of Anatomical Pathology, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Ian R D Johnson
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Ka Lok Li
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Litsa Karageorgos
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Ashley M Hopkins
- College of Medicine and Public Health, Flinders University, Flinders Drive, Bedford Park, Adelaide, SA, Australia
| | - Adrian J Esterman
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Chelsea Huzzell
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Robert D Brooks
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Joanna Lazniewska
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Shane M Hickey
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Christie Bader
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | | | - Roberto Weigert
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Michael J Sorich
- College of Medicine and Public Health, Flinders University, Flinders Drive, Bedford Park, Adelaide, SA, Australia
| | - Prerna Tewari
- Department of Histopathology, Trinity College Dublin, Dublin, Ireland
| | - Cara Martin
- Department of Histopathology, Trinity College Dublin, Dublin, Ireland
| | - Sharon O'Toole
- Department of Histopathology, Trinity College Dublin, Dublin, Ireland
| | - Mark Bates
- Department of Histopathology, Trinity College Dublin, Dublin, Ireland
| | - Mark Ward
- Department of Histopathology, Trinity College Dublin, Dublin, Ireland
| | - Bashir Mohammed
- Department of Histopathology, Trinity College Dublin, Dublin, Ireland
| | - Helen Keegan
- Department of Histopathology, Trinity College Dublin, Dublin, Ireland
| | - William Watson
- University College Dublin, School of Medicine, Conway Institute, University College Dublin, Dublin, Ireland
| | - Sophie Prendergast
- Department of Pathology, The Coombe Women and Infants University Hospital, Dublin, Ireland
| | - Sheena Heffernan
- Department of Pathology, The Coombe Women and Infants University Hospital, Dublin, Ireland
| | - Sarah NiMhaolcatha
- Department of Pathology, The Coombe Women and Infants University Hospital, Dublin, Ireland
| | - Roisin O'Connor
- Department of Pathology, The Coombe Women and Infants University Hospital, Dublin, Ireland
| | - Victoria Malone
- Department of Pathology, The Coombe Women and Infants University Hospital, Dublin, Ireland
| | - Marguerite Carter
- Department of Pathology, The Coombe Women and Infants University Hospital, Dublin, Ireland
| | - Katie Ryan
- Department of Pathology, The Coombe Women and Infants University Hospital, Dublin, Ireland
| | - Nathan Brady
- Department of Pathology, The Coombe Women and Infants University Hospital, Dublin, Ireland
| | - Andres Clarke
- Department of Pathology, The Coombe Women and Infants University Hospital, Dublin, Ireland
| | - Filip Sokol
- Department of Pathology, The Coombe Women and Infants University Hospital, Dublin, Ireland
| | - Sarita Prabhakaran
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia; Department of Anatomical Pathology, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Jürgen Stahl
- Department of Cytopathology and Histopathology, Clinpath Pathology, Adelaide, SA, Australia
| | - Sonja Klebe
- Department of Anatomical Pathology, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia; Department of Surgical Pathology, SA Pathology at Flinders Medical Centre, Adelaide, SA, Australia
| | | | - Brett Delahunt
- Department of Pathology and Molecular Medicine, Wellington School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand
| | - Stavros Selemidis
- School of Health and Biomedical Sciences, STEM College, RMIT University, Bundoora, Melbourne, Vic, Australia
| | - Kim L Moretti
- Discipline of Surgery, University of Adelaide, Adelaide, SA, Australia; University of South Australia, Adelaide, SA, Australia; Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Vic, Australia
| | - Lisa M Butler
- South Australian ImmunoGENomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia; Solid Tumour Program, Precision Cancer Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - John J O'Leary
- Department of Histopathology, Trinity College Dublin, Dublin, Ireland
| | - Douglas A Brooks
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
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