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Peters S, Loi S, André F, Chandarlapaty S, Felip E, Finn SP, Jänne PA, Kerr KM, Munzone E, Passaro A, Pérol M, Smit EF, Swanton C, Viale G, Stahel RA. Antibody-drug conjugates in lung and breast cancer: Current evidence and future directions - a position statement from the ETOP IBCSG Partners Foundation. Ann Oncol 2024:S0923-7534(24)00108-X. [PMID: 38648979 DOI: 10.1016/j.annonc.2024.04.002] [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: 02/14/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024] Open
Abstract
Following the approval of the first antibody-drug conjugates (ADCs) in the early 2000s, development has increased dramatically, with 14 ADCs now approved and >100 in clinical development. In lung cancer, trastuzumab deruxtecan (T-DXd) is approved in human epidermal growth factor receptor 2 (HER2)-mutated, unresectable or metastatic non-small cell lung cancer, with ADCs targeting HER3 (patritumab deruxtecan), trophoblast cell-surface antigen 2 (datopotamab deruxtecan and sacituzumab govitecan [SG]) and mesenchymal-epithelial transition factor (telisotuzumab vedotin) in late-stage clinical development. In breast cancer, several agents are already approved and widely used, including trastuzumab emtansine, T-DXd and SG, and multiple late-stage trials are ongoing. Thus, in the coming years, we are likely to see significant changes to treatment algorithms. As the number of available ADCs increases, biomarkers (of response and resistance) to better select patients are urgently needed. Biopsy sample collection at the time of treatment selection and incorporation of translational research into clinical trial designs are therefore critical. Biopsy samples taken peri- and post-ADC treatment combined with functional genomics screens could provide insights into response/resistance mechanisms as well as the impact of ADCs on tumour biology and the tumour microenvironment, which could improve understanding of the mechanisms underlying these complex molecules. Many ADCs are undergoing evaluation as combination therapy, but a high bar should be set to progress clinical evaluation of any ADC-based combination, particularly considering the high cost and potential toxicity implications. Efforts to optimise ADC dosing/duration, sequencing and the potential for ADC rechallenge are also important, especially considering sustainability aspects. The ETOP IBCSG Partners Foundation are driving strong collaborations in this field and promoting the generation/sharing of databases, repositories and registries to enable greater access data. This will allow the most important research questions to be identified and prioritised, which will ultimately accelerate progress and help to improve patient outcomes.
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Affiliation(s)
- S Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne University, Lausanne, Switzerland
| | - S Loi
- Department of Clinical Medicine and Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - F André
- Breast Cancer Unit, Medical Oncology Department, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - S Chandarlapaty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - E Felip
- Medical Oncology Department, Vall d'Hebron University Hospital and Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - S P Finn
- Department of Histopathology and Cancer Molecular Diagnostics, St James's Hospital and Trinity College, Dublin, Ireland
| | - P A Jänne
- Department of Medical Oncology, Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - K M Kerr
- Department of Pathology, Aberdeen Royal Infirmary, Aberdeen, United Kingdom
| | - E Munzone
- Division of Medical Senology, European Institute of Oncology IRCCS, Milan
| | - A Passaro
- Division of Thoracic Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - M Pérol
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - E F Smit
- Department of Pulmonary Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - C Swanton
- Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, UK
| | - G Viale
- Department of Pathology, European Institute of Oncology IRCCS, Milan, Italy
| | - R A Stahel
- Coordinating Center, ETOP IBCSG Partners Foundation, Bern, Switzerland.
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Murchan P, Baird AM, Ó Broin P, Sheils O, Finn SP. Surrogate Biomarker Prediction from Whole-Slide Images for Evaluating Overall Survival in Lung Adenocarcinoma. Diagnostics (Basel) 2024; 14:462. [PMID: 38472935 DOI: 10.3390/diagnostics14050462] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Recent advances in computational pathology have shown potential in predicting biomarkers from haematoxylin and eosin (H&E) whole-slide images (WSI). However, predicting the outcome directly from WSIs remains a substantial challenge. In this study, we aimed to investigate how gene expression, predicted from WSIs, could be used to evaluate overall survival (OS) in patients with lung adenocarcinoma (LUAD). METHODS Differentially expressed genes (DEGs) were identified from The Cancer Genome Atlas (TCGA)-LUAD cohort. Cox regression analysis was performed on DEGs to identify the gene prognostics of OS. Attention-based multiple instance learning (AMIL) models were trained to predict the expression of identified prognostic genes from WSIs using the TCGA-LUAD dataset. Models were externally validated in the Clinical Proteomic Tumour Analysis Consortium (CPTAC)-LUAD dataset. The prognostic value of predicted gene expression values was then compared to the true gene expression measurements. RESULTS The expression of 239 prognostic genes could be predicted in TCGA-LUAD with cross-validated Pearson's R > 0.4. Predicted gene expression demonstrated prognostic performance, attaining a cross-validated concordance index of up to 0.615 in TCGA-LUAD through Cox regression. In total, 36 genes had predicted expression in the external validation cohort that was prognostic of OS. CONCLUSIONS Gene expression predicted from WSIs is an effective method of evaluating OS in patients with LUAD. These results may open up new avenues of cost- and time-efficient prognosis assessment in LUAD treatment.
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Affiliation(s)
- Pierre Murchan
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- The SFI Centre for Research Training in Genomics Data Science, University of Galway, H91 CF50 Galway, Ireland
- Trinity St. James's Cancer Institute (TSJCI), St. James's Hospital, D08 RX0X Dublin, Ireland
| | - Anne-Marie Baird
- Trinity St. James's Cancer Institute (TSJCI), St. James's Hospital, D08 RX0X Dublin, Ireland
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D02 A440 Dublin, Ireland
| | - Pilib Ó Broin
- School of Mathematical & Statistical Sciences, University of Galway, H91 TK33 Galway, Ireland
| | - Orla Sheils
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Trinity St. James's Cancer Institute (TSJCI), St. James's Hospital, D08 RX0X Dublin, Ireland
| | - Stephen P Finn
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Trinity St. James's Cancer Institute (TSJCI), St. James's Hospital, D08 RX0X Dublin, Ireland
- Department of Histopathology, St. James's Hospital, James's Street, D08 X4RX Dublin, Ireland
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Keogh RJ, Barr MP, Keogh A, McMahon D, O’Brien C, Finn SP, Naidoo J. Genomic Landscape of NSCLC in the Republic of Ireland. JTO Clin Res Rep 2024; 5:100627. [PMID: 38333230 PMCID: PMC10850121 DOI: 10.1016/j.jtocrr.2023.100627] [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: 07/04/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 02/10/2024] Open
Abstract
Introduction The identification of genomic "targets" through next-generation sequencing (NGS) of patient's NSCLC tumors has resulted in a rapid expansion of targeted treatment options for selected patients. This retrospective study aims to identify the proportion of patients with advanced NSCLC in the Republic of Ireland whose tumors harbor actionable genomic alterations through broad NGS panel testing. Methods Institutional review board approval was obtained before study initiation. Patients with NSCLC whose tumors underwent genomic testing through the largest available NGS panel at a nationally funded Cancer Molecular Diagnostics laboratory (St. James's Hospital) between June 2017 and June 2022 were identified. Patient demographics and tumor-related data were collected by retrospective review from all cancer centers in Ireland, referring to the Cancer Molecular Diagnostics laboratory. A total of 203 (9%) tumor samples were excluded due to insufficient neoplastic cell content. Genomic data were collected through retrospective search of Ion Reporter software. The spectrum and proportion of patients with oncogenic driver mutations were evaluated using descriptive statistics (SPSS version 29.0). Results In total, 2052 patients were identified. Patients were referred from 23 different hospital sites and all four geographic regions (Leinster = 1091, 53%; Munster = 763, 37.2%; Connacht = 191, 9.3%; Ulster = 7, 0.3%). Median age was 69 (range: 26-94) years; 53% were male. The most common tumor histologic subtype was adenocarcinoma (77%, n = 1577). An actionable genomic alteration was identified in 1099 cases (53%), the most common of which was KRAS (n = 657, 32%). Less frequently, NSCLC tumors harbored the following: MET exon 14 skipping (n = 53, 2.6%), MET amplification (n = 26, 1.3%), EGFR (n = 181, 8.8%), HER2 (n = 35, 1.7%), and BRAF (n = 72, 3.5%) mutations. Fusions were detected in 76 patients (3.7%) including ALK (n = 44, 58%), RET (n = 11, 14.5%), ROS1 (n = 16, 21%), and FGFR3 (n = 5, 6.6%), whereas no NTRK fusion was identified. Co-alterations were detected in 114 patients (5.6%), the most common of which was KRAS/PIK3CA (n = 19, 17%), EGFR/PIK3CA (n = 10, 8.5%), and KRAS/IDH1 (n = 9, 8%). Other co-alterations of interest identified included KRAS G12A/ROS1 fusion (n = 1) and KRAS G12C/BRAF G469A (n = 2). Conclusions This is the first retrospective study to comprehensively characterize the genomic landscape of NSCLC in Ireland, using the broadest available NGS panel. Actionable alterations were identified in 53.4% of the patients, and KRAS was the most common oncogenic driver alteration. Our study revealed a lower prevalence of patients whose tumor harbors ALK, ROS1, and RET fusions, compared with similar data sets.
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Affiliation(s)
- Rachel J. Keogh
- Department of Medical Oncology, Beaumont RCSI Cancer Centre, Dublin, Ireland
| | - Martin P. Barr
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, Dublin, Ireland
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Anna Keogh
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
- Department of Histopathology, St James’s Hospital, Dublin, Ireland
| | - David McMahon
- Department Medical Oncology, St James’s Hospital, Dublin, Ireland
| | - Cathal O’Brien
- Cancer Molecular Diagnostics Laboratory, St James’s Hospital, Dublin, Ireland
| | - Stephen P. Finn
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, Dublin, Ireland
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
- Department of Histopathology, St James’s Hospital, Dublin, Ireland
- Cancer Molecular Diagnostics Laboratory, St James’s Hospital, Dublin, Ireland
| | - Jarushka Naidoo
- Department of Medical Oncology, Beaumont RCSI Cancer Centre, Dublin, Ireland
- Beaumont Hospital, Dublin, Ireland
- RCSI University of Health Sciences, Dublin, Ireland
- Sidney Kimmel Comprehensive Cancer Centre at Johns Hopkins University, Baltimore, Maryland
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Hannon G, Bogdanska A, Keogh A, Finn SP, Gobbo OL, Prina-Mello A. Biodistribution and histological analysis of iron oxide-dextran nanoparticles in wistar rats. Nanotoxicology 2023; 17:562-580. [PMID: 37982374 DOI: 10.1080/17435390.2023.2276413] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/11/2023] [Indexed: 11/21/2023]
Abstract
Iron oxide nanoparticles (IONP) are showing promise in many biomedical applications. One of these- magnetic hyperthermia- utilizes externally applied alternating magnetic fields and tumor-residing magnetic nanoparticles to generate localized therapeutic temperature elevations. Magnetic hyperthermia is approved in Europe to treat glioblastoma and is undergoing clinical assessment in the United States to treat prostate cancer. In this study, we performed biodistribution and histological analysis of a new IONP (RCL-01) in Wistar rats. These nanoparticles are currently undergoing clinical assessment in locally advanced pancreatic ductal adenocarcinoma to determine the feasibility of magnetic hyperthermia treatment in this disease. The study presented here aimed to determine the fate of these nanoparticles in vivo and whether this results in organ damage. Wistar rats were injected intravenously with relatively high doses of IONP (30 mgFe/kg, 45 mgFe/kg and 60 mgFe/kg) and compared to a vehicle control to determine the accumulation of iron in organs and whether this resulted in histological changes in these tissues. Dose-dependent increases of iron were observed in the liver, spleen and lungs of IONP-treated animals at 7 days postinjection; however, this did not result in significant histological changes in these tissues. Immunofluorescent imaging determined these nanoparticles are internalized by macrophages in tissue, suggesting they are readily phagocytosed by the reticuloendothelial system for eventual recycling. Notably, no changes in iron or dextran staining were found in the kidneys across all treatment groups, providing evidence for potential renal clearance.
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Affiliation(s)
- Gary Hannon
- Nanomedicine and Molecular Imaging Group, Trinity Translational Medicine Institute, Ireland
- Laboratory of Biological Characterization of Advanced Materials (LBCAM), Trinity Translational Medicine Institute, Trinity College Dublin, Ireland
| | - Anna Bogdanska
- Nanomedicine and Molecular Imaging Group, Trinity Translational Medicine Institute, Ireland
- Laboratory of Biological Characterization of Advanced Materials (LBCAM), Trinity Translational Medicine Institute, Trinity College Dublin, Ireland
| | - Anna Keogh
- Department of Histopathology, Trinity College Dublin, Ireland
| | - Stephen P Finn
- Department of Histopathology, Trinity College Dublin, Ireland
| | - Oliviero L Gobbo
- School of Pharmacy and Pharmaceutical Sciences, Ireland
- Trinity St James's Cancer Institute, Ireland
| | - Adriele Prina-Mello
- Nanomedicine and Molecular Imaging Group, Trinity Translational Medicine Institute, Ireland
- Laboratory of Biological Characterization of Advanced Materials (LBCAM), Trinity Translational Medicine Institute, Trinity College Dublin, Ireland
- Advanced Materials and Bioengineering Research (AMBER) Centre, CRANN Institute, Trinity College Dublin, Ireland
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Homicsko K, Zygoura P, Norkin M, Tissot S, Shakarishvili N, Popat S, Curioni-Fontecedro A, O'Brien M, Pope A, Shah R, Fisher P, Spicer J, Roy A, Gilligan D, Rusakiewicz S, Fortis E, Marti N, Kammler R, Finn SP, Coukos G, Dafni U, Peters S, Stahel RA. PD-1-expressing macrophages and CD8 T cells are independent predictors of clinical benefit from PD-1 inhibition in advanced mesothelioma. J Immunother Cancer 2023; 11:e007585. [PMID: 37880184 PMCID: PMC10603330 DOI: 10.1136/jitc-2023-007585] [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] [Accepted: 09/03/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Few tissue biomarkers exist to date that could enrich patient with cancer populations to benefit from immune checkpoint blockade by programmed cell death protein 1/ligand-1 (PD-/L-1) inhibitors. PD-L1 expression has value in this context in some tumor types but is an imperfect predictor of clinical benefit. In malignant pleural mesothelioma, PD-L1 expression is not predictive of the benefit from PD-1 blockade. We aimed to identify novel markers in malignant pleural mesothelioma to select patients better. METHODS We performed a multiplex-immune histochemistry analysis of tumor samples from the phase III PROMISE-meso study, which randomized 144 pretreated patients to receive either pembrolizumab or standard second-line chemotherapy. Our panel focused on CD8+T cell, CD68+macrophages, and the expression of PD-1 and PD-L1 on these and cancer cells. We analyzed single and double positive cells within cancer tissues (infiltrating immune cells) and in the stroma. In addition, we performed cell neighborhood analysis. The cell counts were compared with clinical outcomes, including responses, progression-free and overall survivals. RESULTS We confirmed the absence of predictive value for PD-L1 in this cohort of patients. Furthermore, total CD8 T cells, CD68+macrophages, or inflammatory subtypes (desert, excluded, inflamed) did not predict outcomes. In contrast, PD-1-expressing CD8+T cells (exhausted T cells) and PD-1-expressing CD68+macrophages were both independent predictors of progression-free survival benefit from pembrolizumab. Patients with tumors simultaneously harboring PD1+T cells and PD-1+macrophages benefited the most from immune therapy. CONCLUSION We analyzed a large cohort of patients within a phase III study and found that not only PD-1+CD8 T cells but also PD-1+CD68+ macrophages are predictive. This data provides evidence for the first time for the existence of PD-1+macrophages in mesothelioma and their clinical relevance for immune checkpoint blockade.
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Affiliation(s)
- Krisztian Homicsko
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne branch, Lausanne, Switzerland
| | - Panagiota Zygoura
- ETOP Statistical Center, Frontier Science Foundation - Hellas, Athens, Greece
| | - Maxim Norkin
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne branch, Lausanne, Switzerland
| | - Stephanie Tissot
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Immune Landscape Laboratory, Centre Thérapies Expérimentales (CTE), Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | | | - Sanjay Popat
- Lung Unit, Royal Marsden Hospital NHS Trust, London, UK
| | - Alessandra Curioni-Fontecedro
- Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Department of Oncology, Fribourg Hospitals, Fribourg, Switzerland
| | - Mary O'Brien
- Department of Oncology, Royal Marsden Hospital NHS Trust, London, UK
| | - Anthony Pope
- Department of Oncology, Clatterbridge Cancer Centre NHS Foundation Trust, Bebington, UK
| | - Riyaz Shah
- Department of Medical Oncology, Kent Oncology Centre, Maidstone, UK
| | - Patricia Fisher
- Department of Medical Oncology, Weston Park Hospital, Sheffield, UK
| | - James Spicer
- Comprehensive Cancer Center, King's College London, London, UK
| | - Amy Roy
- Department of Medical Oncology, University Hospitals Plymouth NHS Trust, Plymouth, UK
| | - David Gilligan
- Department of Medical Oncology, Addenbrooke's Hospital, Cambridge, UK
| | - Sylvie Rusakiewicz
- Immune Landscape Laboratory, Centre Thérapies Expérimentales (CTE), Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Ekaterina Fortis
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Immune Landscape Laboratory, Centre Thérapies Expérimentales (CTE), Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Nesa Marti
- Translational Research Coordination, ETOP IBCSG Partners Foundation, Bern, Switzerland
| | - Roswitha Kammler
- Translational Research Coordination, ETOP IBCSG Partners Foundation, Bern, Switzerland
| | - Stephen P Finn
- Molecular Diagnostics and Histopathology, Trinity College, Dublin, Ireland
| | - Georges Coukos
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne branch, Lausanne, Switzerland
| | - Urania Dafni
- ETOP Statistical Center, Frontier Science Foundation - Hellas, Athens, Greece
- National and Kapodistrian University of Athens, Athens, Greece
| | - Solange Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Agora Research Center, Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Rolf A Stahel
- President, ETOP IBCSG Partners Foundation, Bern, Switzerland
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Murphy C, Gornés Pons G, Keogh A, Ryan L, McCarra L, Jose CM, Kesar S, Nicholson S, Fitzmaurice GJ, Ryan R, Young V, Cuffe S, Finn SP, Gray SG. An Analysis of JADE2 in Non-Small Cell Lung Cancer (NSCLC). Biomedicines 2023; 11:2576. [PMID: 37761019 PMCID: PMC10526426 DOI: 10.3390/biomedicines11092576] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 09/29/2023] Open
Abstract
The JADE family comprises three members encoded by individual genes and roles for these proteins have been identified in chromatin remodeling, cell cycle progression, cell regeneration and the DNA damage response. JADE family members, and in particular JADE2 have not been studied in any great detail in cancer. Using a series of standard biological and bioinformatics approaches we investigated JADE2 expression in surgically resected non-small cell lung cancer (NSCLC) for both mRNA and protein to examine for correlations between JADE2 expression and overall survival. Additional correlations were identified using bioinformatic analyses on multiple online datasets. Our analysis demonstrates that JADE2 expression is significantly altered in NSCLC. High expression of JADE2 is associated with a better 5-year overall survival. Links between JADE2 mRNA expression and a number of mutated genes were identified, and associations between JADE2 expression and tumor mutational burden and immune cell infiltration were explored. Potential new drugs that can target JADE2 were identified. The results of this biomarker-driven study suggest that JADE2 may have potential clinical utility in the diagnosis, prognosis and stratification of patients into various therapeutically targetable options.
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Affiliation(s)
- Ciara Murphy
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (S.P.F.)
- Thoracic Oncology Research Group, Central Pathology Laboratory, Trinity St. James’s Cancer Institute (TSJCI), St. James’s Hospital, D08 RX0X Dublin, Ireland (A.K.)
| | - Glòria Gornés Pons
- Thoracic Oncology Research Group, Central Pathology Laboratory, Trinity St. James’s Cancer Institute (TSJCI), St. James’s Hospital, D08 RX0X Dublin, Ireland (A.K.)
- Faculty of Biology, University of Barcelona, 08025 Barcelona, Spain
| | - Anna Keogh
- Thoracic Oncology Research Group, Central Pathology Laboratory, Trinity St. James’s Cancer Institute (TSJCI), St. James’s Hospital, D08 RX0X Dublin, Ireland (A.K.)
- Department of Histopathology and Morbid Anatomy, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Lisa Ryan
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (S.P.F.)
| | - Lorraine McCarra
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (S.P.F.)
| | - Chris Maria Jose
- School of Medicine, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Shagun Kesar
- School of Medicine, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Siobhan Nicholson
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (S.P.F.)
| | - Gerard J. Fitzmaurice
- Surgery, Anaesthesia and Critical Care Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (V.Y.)
| | - Ronan Ryan
- Surgery, Anaesthesia and Critical Care Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (V.Y.)
| | - Vincent Young
- Surgery, Anaesthesia and Critical Care Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (V.Y.)
| | - Sinead Cuffe
- HOPE Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland
| | - Stephen P. Finn
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (S.P.F.)
- Thoracic Oncology Research Group, Central Pathology Laboratory, Trinity St. James’s Cancer Institute (TSJCI), St. James’s Hospital, D08 RX0X Dublin, Ireland (A.K.)
- Department of Histopathology and Morbid Anatomy, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Steven G. Gray
- Thoracic Oncology Research Group, Central Pathology Laboratory, Trinity St. James’s Cancer Institute (TSJCI), St. James’s Hospital, D08 RX0X Dublin, Ireland (A.K.)
- Department of Clinical Medicine, Trinity College Dublin, D02 PN40 Dublin, Ireland
- School of Biological Sciences, Technological University Dublin, D07 XT95 Dublin, Ireland
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Opitz I, Bille A, Dafni U, Nackaerts K, Ampollini L, de Perrot M, Brcic L, Nadal E, Syrigos K, Gray SG, Aerts J, Curioni-Fontecedro A, Rüschoff JH, Monkhorst K, Weynand B, Silini EM, Bavaghar-Zaeimi F, Jakopovic M, Llatjos R, Tsimpoukis S, Finn SP, von der Thüsen J, Marti N, Dimopoulou G, Kammler R, Peters S, Stahel RA, Falcoz PE, Brunelli A, Baas P. European Epidemiology of Pleural Mesothelioma-Real-Life Data From a Joint Analysis of the Mesoscape Database of the European Thoracic Oncology Platform and the European Society of Thoracic Surgery Mesothelioma Database. J Thorac Oncol 2023; 18:1233-1247. [PMID: 37356802 DOI: 10.1016/j.jtho.2023.06.011] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 06/27/2023]
Abstract
INTRODUCTION Pleural mesothelioma (PM) is an aggressive malignancy with increasing prevalence and poor prognosis. Real-life data are a unique approach to reflect the reality of PM epidemiology, treatment, and prognosis in Europe. METHODS A joint analysis of the European Thoracic Oncology Platform Mesoscape and the European Society of Thoracic Surgeons (ESTS) databases was performed to better understand the characteristics and epidemiology of PM, including histologic subtype, staging, and treatment. Overall survival (OS) was assessed, adjusting for parameters of clinical interest. RESULTS The analysis included 2766 patients (Mesoscape: 497/10 centers/ESTS: 2269/77 centers). The primary histologic subtype was epithelioid (71%), with 57% patients on stages III to IV. Within Mesoscape, the patients received either multimodality (59%) or palliative intention treatment (41%). The median follow-up was 47.2 months, on the basis of 1103 patients (Mesoscape: 491/ESTS: 612), with 823 deaths, and median OS was 17.4 months. In multivariable analysis, female sex, epithelioid subtype, and lower stage were associated with longer OS, when stratifying by cohort, age, and Eastern Cooperative Oncology Group Performance Status. Within Mesoscape, multimodality treatment including surgery was predictive of longer OS (hazard ratio = 0.56, 95% confidence interval: 0.45-0.69), adjusting for sex, histologic subtype, and Eastern Cooperative Oncology Group Performance Status. Overall, surgical candidates with a macroscopic complete resection had a significantly longer median OS compared with patients with R2 (25.2 m versus 16.4 m; log-rank p < 0.001). CONCLUSIONS This combined European Thoracic Oncology Platform/ESTS database analysis offers one of the largest databases with detailed clinical and pathologic outcome. Our finding reflects a benefit for selected patients that undergo multimodality treatment, including macroscopic complete resection, and represents a valuable resource to inform the epidemiology and treatment options for individual patients.
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Affiliation(s)
- Isabelle Opitz
- Department of Thoracic Surgery, University Hospital Zurich, Zurich, Switzerland.
| | - Andrea Bille
- Department of Thoracic Surgery, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Urania Dafni
- ETOP IBCSG Partners Foundation Statistical Center, Frontier Science Foundation-Hellas & University of Athens, Athens, Greece
| | - Kristiaan Nackaerts
- Department of Respiratory Oncology, University Hospitals KU Leuven, Leuven, Belgium
| | - Luca Ampollini
- Thoracic Surgery, Department of Medicine and Surgery, University Hospital of Parma, Parma, Italy
| | - Marc de Perrot
- Division of Thoracic Surgery, Toronto General Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Luka Brcic
- Institute of Pathology, Medical Faculty University of Zagreb, Zagreb, Croatia; Current: Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Ernest Nadal
- Department of Medical Oncology, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, L'Hospitalet, Barcelona, Spain
| | - Konstantinos Syrigos
- Medical School of Athens, National and Kapodistrian University, Sotiria General Hospital, Athens, Greece
| | - Steven G Gray
- Thoracic Oncology, St James's Hospital and Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
| | - Joachim Aerts
- Thoracic Oncology Department, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Jan H Rüschoff
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Kim Monkhorst
- Division of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Birgit Weynand
- Department of Pathology, University Hospitals KU Leuven, Leuven, Belgium
| | | | - Fatemeh Bavaghar-Zaeimi
- Division of Thoracic Surgery, Toronto General Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Marko Jakopovic
- Department for Lung Diseases, University Hospital Centre Zagreb & University of Zagreb, Zagreb, Croatia
| | - Roger Llatjos
- Department of Pathology, Hospital Universitari de Bellvitge, L'Hospitalet, Barcelona, Spain
| | - Sotirios Tsimpoukis
- Medical School of Athens, National and Kapodistrian University, Sotiria General Hospital, Athens, Greece
| | - Stephen P Finn
- Department of Histopathology and Cancer Molecular Diagnostics, St James's Hospital and Trinity College, Dublin, Ireland
| | - Jan von der Thüsen
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nesa Marti
- Translational Research Coordination, ETOP IBCSG Partners Foundation Coordinating Center, Bern, Switzerland
| | - Georgia Dimopoulou
- ETOP IBCSG Partners Foundation Statistical Center, Frontier Science Foundation-Hellas, Athens, Greece
| | - Roswitha Kammler
- Translational Research Coordination, ETOP IBCSG Partners Foundation Coordinating Center, Bern, Switzerland
| | - Solange Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV) and Lausanne University, Lausanne, Switzerland
| | | | | | - Alessandro Brunelli
- European Society of Thoracic Surgeons and Department of Thoracic Surgery, St. James's University Hospital, Leeds, United Kingdom
| | - Paul Baas
- Department of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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8
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Keogh RJ, Barr MP, Keogh A, McMahon D, Baird AM, Cotter S, Breen D, Fitzmaurice GJ, Fitzpatrick D, O'Brien C, Finn SP, Naidoo J. Lung Cancer in the Republic of Ireland. J Thorac Oncol 2023; 18:851-857. [PMID: 37348994 DOI: 10.1016/j.jtho.2023.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 06/24/2023]
Affiliation(s)
- Rachel J Keogh
- Department of Medical Oncology, Cork University Hospital, Wilton, Cork, Republic of Ireland
| | - Martin P Barr
- Thoracic Oncology Research Group, Trinity St James's Cancer Institute, St James's Hospital, Dublin, Republic of Ireland; School of Medicine, Trinity St James's Cancer Institute, St James's Hospital, Dublin, Republic of Ireland
| | - Anna Keogh
- School of Medicine, Trinity St James's Cancer Institute, St James's Hospital, Dublin, Republic of Ireland; Department of Histopathology, St James's Hospital, Dublin, Republic of Ireland
| | - David McMahon
- Department of Medical Oncology, St James's Hospital, Dublin, Republic of Ireland
| | - Anne-Marie Baird
- School of Medicine, Trinity St James's Cancer Institute, St James's Hospital, Dublin, Republic of Ireland; Irish Lung Cancer Community, Republic of Ireland
| | - Seamus Cotter
- Irish Lung Cancer Community, Republic of Ireland; Cancer Trials Ireland, Dublin, Republic of Ireland
| | - David Breen
- Interventional Respiratory Unit, Galway University Hospitals, Galway, Republic of Ireland
| | - Gerard J Fitzmaurice
- Thoracic Oncology Research Group, Trinity St James's Cancer Institute, St James's Hospital, Dublin, Republic of Ireland; School of Medicine, Trinity St James's Cancer Institute, St James's Hospital, Dublin, Republic of Ireland; Department of Cardiothoracic Surgery, St James's Hospital, Dublin, Republic of Ireland
| | | | - Cathal O'Brien
- Cancer Molecular Diagnostics Laboratory, St James's Hospital, Dublin, Republic of Ireland
| | - Stephen P Finn
- Thoracic Oncology Research Group, Trinity St James's Cancer Institute, St James's Hospital, Dublin, Republic of Ireland; School of Medicine, Trinity St James's Cancer Institute, St James's Hospital, Dublin, Republic of Ireland; Department of Histopathology, St James's Hospital, Dublin, Republic of Ireland; Cancer Molecular Diagnostics Laboratory, St James's Hospital, Dublin, Republic of Ireland
| | - Jarushka Naidoo
- Cancer Trials Ireland, Dublin, Republic of Ireland; Beaumont Hospital, Dublin, Republic of Ireland; RCSI University of Health Sciences, Dublin, Republic of Ireland.
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9
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van Gulik AL, Sluydts E, Vervoort L, Kockx M, Kortman P, Ylstra B, Finn SP, Bubendorf L, Bahce I, Sie D, Radonic T, Lissenberg-Witte B, Thunnissen E. False positivity in break apart fluorescence in-situ hybridization due to polyploidy. Transl Lung Cancer Res 2023; 12:676-688. [PMID: 37197629 PMCID: PMC10183404 DOI: 10.21037/tlcr-22-516] [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: 07/12/2022] [Accepted: 03/08/2023] [Indexed: 05/19/2023]
Abstract
Background In-situ hybridization (ISH) is a diagnostic tool in the detection of chromosomal anomalies, which has important implications for diagnosis, classification and prediction of cancer therapy in various diseases. Certain thresholds of number of cells showing an aberrant pattern are commonly used to declare a sample as positive for genomic rearrangements. The phenomenon of polyploidy can be misleading in the interpretation of break apart fluorescence in-situ hybridization (FISH). The aim of this study is to investigate the impact of cell size and ploidy on FISH results. Methods In sections of varying thickness of control liver tissue and non-small cell lung cancer cases, nuclear size was measured and the number of MET chromogenic ISH and ALK FISH (liver) or ALK and ROS1 FISH (lung cancer) signals was manually counted and quantified. Results In liver cell nuclei the number of FISH/chromogenic ISH signals increases with nuclear size related to physiological polyploidy and is related to section thickness. In non-small cell lung cancer cases tumour cells with higher ploidy levels and nuclear size have an increased chance of single signals. Furthermore, additional lung cancer samples with borderline ALK FISH results were examined with a commercial kit for rearrangements. No rearrangements could be demonstrated, proving a false positive ALK FISH result. Conclusions In case of polyploidy there is an increased likelihood of false positivity when using break apart FISH probes. Therefore, we state that prescribing one single cut-off in FISH is inappropriate. In polyploidy, the currently proposed cut-off should only be used with caution and the result should be confirmed by an additional technique.
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Affiliation(s)
| | | | | | | | - Pim Kortman
- Department of Pathology, Amsterdam University Medical Center, Location VUmc, Amsterdam, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, Amsterdam University Medical Center, Location VUmc, Amsterdam, The Netherlands
| | - Stephen P. Finn
- University of Dublin, Trinity College and St. James’s Hospital, Dublin, Ireland
| | - Lukas Bubendorf
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Idris Bahce
- Department of Pulmonology, Amsterdam University Medical Center, Location VUmc, Amsterdam, The Netherlands
| | - Daoud Sie
- Amsterdam University Medical Center, Location VUmc, Tumor Genome Analysis Core, Amsterdam, The Netherlands
| | - Teodora Radonic
- Department of Pathology, Amsterdam University Medical Center, Location VUmc, Amsterdam, The Netherlands
| | - Birgit Lissenberg-Witte
- Department of Epidemiology and Data Science, Amsterdam University Medical Center, Location VUmc, Amsterdam, The Netherlands
| | - Erik Thunnissen
- Department of Pathology, Amsterdam University Medical Center, Location VUmc, Amsterdam, The Netherlands
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10
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Lin Z, Stopsack KH, Fiorentino M, Vaselkiv JB, Gerke T, Pettersson A, Flanagan S, Penney KL, Finn SP, Loda M, Mucci LA. Abstract 737: Variation in prognostic value of Gleason score for lethal prostate cancer using time-varying area under the curve. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Background: Gleason score is one of the strongest prognostic factors for prostate cancer survival in patients with primary prostate cancer. However, its predictive accuracy is less clear during extended follow-up periods.
Methods: We included men diagnosed with prostate cancer in the Physicians’ Health Study (PHS) and Health Professionals Follow-up Study (HPFS) between 1982 and 2009. We included individuals with available radical prostatectomy tissue specimens and undertook a central standardized histopathologic re-review of H&E slides including Gleason score according to the 2014 International Society of Urological Pathology Consensus. Comparing pathologic Gleason score, we estimated hazard ratios (HR) and 95% confidence intervals (CIs) for lethal prostate cancer-free survival from the time of diagnosis using the Cox proportional hazards regression through 2018. Lethal prostate cancer was defined as development of distant metastases or prostate cancer-specific death. We assessed the time-dependent predictive accuracy of Gleason score over 10, 15, 20, and 25-years post-diagnosis with time-varying area under the curve (tAUC) using the Uno estimator.
Results: Among the 1,404 prostate cancer patients, 113 developed lethal prostate cancer during a follow-up of up to 30 years (median 17.1 years). There were 11% men with Gleason score of 9-10 (grade group 5), 7.1% with 8 (grade group 4), 23% with 4+3 (grade group 3), 36% with 3+4 (grade group 2), and 23% with 6 (grade group 1). Compared to Gleason score 6, the HRs for lethal disease were 5.6 (95% CI: 1.3 to 24) for score 3+4, 13 (95% CI: 3.1 to 55) for 4+3, 17 (95% CI: 3.8 to 75) for 8, and 27 (95% CI: 6.5 to 117) for 9-10, adjusting for pathological tumor stage, age at diagnosis, and prostate-specific antigen (PSA) level at diagnosis. The overall AUC over the entire follow-up was 0.71 (95% CI: 0.63 to 0.79) for Gleason score alone and 0.76 (95% CI: 0.68 to 0.83) with the addition of stage, PSA, and age. Discrimination for lethal prostate cancer based on Gleason score alone varied over follow-up, peaking at a tAUC of 0.81 (95% CI: 0.77 to 0.85) at 10 years, and slowly declined to 0.78 (95% CI: 0.74 to 0.83) at 15 years, 0.78 (95% CI: 0.74 to 0.81) at 20 years, and 0.74 (95% CI: 0.69 to 0.80) at 25 years post-diagnosis. The tAUC had a similar trend with the addition of stage, PSA, and age, with higher point estimates at each time point.
Conclusions: The prognostic value of Gleason score for lethal prostate cancer after prostatectomy, based on genitourinary pathologist re-review, remains high for decades after diagnosis, with only a modest decline over time. Given the long natural history of prostate cancer, an understanding of the factors that contribute to remaining metastasis-free is needed to inform clinical decisions.
Citation Format: Zhike Lin, Konrad H. Stopsack, Michelangelo Fiorentino, Jane B. Vaselkiv, Travis Gerke, Andreas Pettersson, Sinead Flanagan, Kathryn L. Penney, Stephen P. Finn, Massimo Loda, Lorelei A. Mucci. Variation in prognostic value of Gleason score for lethal prostate cancer using time-varying area under the curve [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 737.
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Affiliation(s)
- Zhike Lin
- 1Harvard T.H. Chan School of Public Health, Boston, MA
| | | | | | | | - Travis Gerke
- 2The Prostate Cancer Clinical Trials Consortium (PCCTC), New York, NY
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11
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O’Sullivan É, Keogh A, Henderson B, Finn SP, Gray SG, Gately K. Treatment Strategies for KRAS-Mutated Non-Small-Cell Lung Cancer. Cancers (Basel) 2023; 15:1635. [PMID: 36980522 PMCID: PMC10046549 DOI: 10.3390/cancers15061635] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 02/14/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
Activating mutations in KRAS are highly prevalent in solid tumours and are frequently found in 35% of lung, 45% of colorectal, and up to 90% of pancreatic cancers. Mutated KRAS is a prognostic factor for disease-free survival (DFS) and overall survival (OS) in NSCLC and is associated with a more aggressive clinical phenotype, highlighting the need for KRAS-targeted therapy. Once considered undruggable due to its smooth shallow surface, a breakthrough showed that the activated G12C-mutated KRAS isozyme can be directly inhibited via a newly identified switch II pocket. This discovery led to the development of a new class of selective small-molecule inhibitors against the KRAS G12C isoform. Sotorasib and adagrasib are approved in locally advanced or metastatic NSCLC patients who have received at least one prior systemic therapy. Currently, there are at least twelve KRAS G12C inhibitors being tested in clinical trials, either as a single agent or in combination. In this study, KRAS mutation prevalence, subtypes, rates of occurrence in treatment-resistant invasive mucinous adenocarcinomas (IMAs), and novel drug delivery options are reviewed. Additionally, the current status of KRAS inhibitors, multiple resistance mechanisms that limit efficacy, and their use in combination treatment strategies and novel multitargeted approaches in NSCLC are discussed.
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Affiliation(s)
- Éabha O’Sullivan
- Thoracic Oncology Research Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James’s Hospital, D08 W9RT Dublin, Ireland
| | - Anna Keogh
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James’s Hospital, D08 RX0X Dublin, Ireland
| | - Brian Henderson
- Thoracic Oncology Research Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James’s Hospital, D08 W9RT Dublin, Ireland
| | - Stephen P. Finn
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James’s Hospital, D08 RX0X Dublin, Ireland
| | - Steven G. Gray
- Thoracic Oncology Research Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James’s Hospital, D08 W9RT Dublin, Ireland
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James’s Hospital, D08 RX0X Dublin, Ireland
| | - Kathy Gately
- Thoracic Oncology Research Group, Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James’s Hospital, D08 W9RT Dublin, Ireland
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James’s Hospital, D08 RX0X Dublin, Ireland
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12
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Digby B, Finn SP, Ó Broin P. nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs. BMC Bioinformatics 2023; 24:27. [PMID: 36694127 PMCID: PMC9875403 DOI: 10.1186/s12859-022-05125-8] [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: 07/08/2022] [Accepted: 12/22/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) are a class of covalenty closed non-coding RNAs that have garnered increased attention from the research community due to their stability, tissue-specific expression and role as transcriptional modulators via sequestration of miRNAs. Currently, multiple quantification tools capable of detecting circRNAs exist, yet none delineate circRNA-miRNA interactions, and only one employs differential expression analysis. Efforts have been made to bridge this gap by way of circRNA workflows, however these workflows are limited by both the types of analyses available and computational skills required to run them. RESULTS We present nf-core/circrna, a multi-functional, automated high-throughput pipeline implemented in nextflow that allows users to characterise the role of circRNAs in RNA Sequencing datasets via three analysis modules: (1) circRNA quantification, robust filtering and annotation (2) miRNA target prediction of the mature spliced sequence and (3) differential expression analysis. nf-core/circrna has been developed within the nf-core framework, ensuring robust portability across computing environments via containerisation, parallel deployment on cluster/cloud-based infrastructures, comprehensive documentation and maintenance support. CONCLUSION nf-core/circrna reduces the barrier to entry for researchers by providing an easy-to-use, platform-independent and scalable workflow for circRNA analyses. Source code, documentation and installation instructions are freely available at https://nf-co.re/circrna and https://github.com/nf-core/circrna .
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Affiliation(s)
- Barry Digby
- grid.6142.10000 0004 0488 0789School of Mathematical and Statistical Sciences, National University of Ireland, Galway, Ireland
| | - Stephen P. Finn
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Dublin, Ireland
| | - Pilib Ó Broin
- grid.6142.10000 0004 0488 0789School of Mathematical and Statistical Sciences, National University of Ireland, Galway, Ireland
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13
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Oner E, Gray SG, Finn SP. Cell Viability Assay with 3D Prostate Tumor Spheroids. Methods Mol Biol 2023; 2645:263-275. [PMID: 37202626 DOI: 10.1007/978-1-0716-3056-3_17] [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] [Indexed: 05/20/2023]
Abstract
WST-8 (Cell Counting Kit 8; CCK-8) is the last generation tetrazolium-based cell viability assay and has recently been accepted as a validated method for measuring the cell viability of 3D in vitro models. Here, we describe how to form 3D prostate tumor spheroids using the polyHEMA technique, apply drug treatments and WST-8 assay to these spheroids, and calculate their cell viability. The advantages of our protocol are the formation of spheroids without adding extracellular matrix components, and the elimination of the critique handling process needed for transferring spheroids. Although this protocol exemplifies the determination of percentage cell viability in PC-3 prostate tumor spheroids, it can be adapted and optimized for other prostate cell lines and other types of cancers.
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Affiliation(s)
- Ezgi Oner
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Izmir Katip Celebi University, Balatcik, Izmir, Turkey
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland
- Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
| | - Steven G Gray
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland
- Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
| | - Stephen P Finn
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland.
- Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland.
- Department of Histopathology and Morbid Anatomy, Sir Patrick Dun Translational Research Lab, St. James's Hospital, Dublin, Ireland.
- Department of Histopathology, Labmed Directorate, St. James's Hospital, Dublin, Ireland.
- Cancer Molecular Diagnostics, Labmed Directorate, St. James's Hospital, Dublin, Ireland.
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14
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Bubendorf L, Zoche M, Dafni U, Rüschoff JH, Prince SS, Marti N, Stavrou A, Kammler R, Finn SP, Moch H, Peters S, Stahel RA. Prognostic impact of tumour mutational burden in resected stage I and II lung adenocarcinomas from a European Thoracic Oncology Platform Lungscape cohort. Lung Cancer 2022; 174:27-35. [PMID: 36283211 DOI: 10.1016/j.lungcan.2022.09.014] [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: 07/25/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND The primary objective of this study is to evaluate tumor mutational burden (TMB), its associations with selected clinicopathological and molecular characteristics as well as its clinical significance, in a retrospective cohort of surgically resected stage I-II lung adenocarcinomas, subset of the ETOP Lungscape cohort. METHODS TMB was evaluated on tumor DNA extracted from resected primary lung adenocarcinomas, based on FoundationOne®CDx (F1CDx) genomic profiling, centrally performed at the University Hospital Zurich. The F1CDx test sequences the complete exons of 324 cancer-related genes and detects substitutions, insertions and deletions (indels), copy number alterations and gene rearrangements. In addition, the genomic biomarkers TMB and microsatellite instability (MSI) are analyzed. RESULTS In the Lungscape cohort, TMB was assessed in 78 surgically resected lung adenocarcinomas from two Swiss centers (62 % males, 55 %/45 % stage I/II). Median TMB was 7.6 Muts/Mb, with TMB high (≥10 Muts/Mb) in 40 % of cases (95 %CI:29 %-52 %). The most frequently mutated genes were TP53/KRAS/EGFR/MLL2 detected in 58 %/38 %/33 %/30 % of samples, respectively. TMB was significantly higher among males (TMB high: 50 % vs 23 % in females, p = 0.032), as well as among current/former smokers (TMB high: 44 % vs 8 % in never smokers, p = 0.023). Furthermore, TMB was significantly higher in TP53 mutated than in non-mutated patients (TMB high: 60 % vs 12 %, p < 0.001), while it was higher in EGFR non-mutated patients compared to EGFR mutated (TMB high: 48 % vs 23 %, p = 0.049). At a median follow-up time of 56.1 months (IQR:38.8-72.0), none of the three outcome variables (OS, RFS, TTR) differed significantly by TMB status (all p-values > 5 %). This was also true when adjusting for clinicopathological characteristics. CONCLUSIONS While presence of TP53 mutations and absence of EGFR mutations are associated with high TMB, increased TMB had no significant prognostic impact in patients with resected stage I/II lung adenocarcinoma beyond T and N classification, in both unadjusted and adjusted analyses.
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Affiliation(s)
- Lukas Bubendorf
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Martin Zoche
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Urania Dafni
- ETOP IBCSG Partners Foundation Statistical Center, Frontier Science Foundation-Hellas & National and Kapodistrian University of Athens, Athens, Greece
| | - Jan Hendrik Rüschoff
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Spasenija Savic Prince
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Nesa Marti
- Translational Research Coordination, ETOP IBCSG Partners Foundation, Coordinating Center Bern, Switzerland
| | - Androniki Stavrou
- ETOP IBCSG Partners Foundation Statistical Center, Frontier Science Foundation-Hellas, Athens, Greece
| | - Roswitha Kammler
- Translational Research Coordination, ETOP IBCSG Partners Foundation, Coordinating Center Bern, Switzerland
| | - Stephen P Finn
- Cancer Molecular Diagnostics and Histopathology, St. James's Hospital and Trinity College Dublin, Ireland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Solange Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Rolf A Stahel
- ETOP IBCSG Partners Foundation, Coordinating Center, Bern, Switzerland.
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15
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Barr MP, Baird AM, Halliday S, Martin P, Allott EH, Phelan J, Korpanty G, Coate L, O’Brien C, Gray SG, Sui JSY, Hayes B, Cuffe S, Finn SP. Liquid Biopsy: A Multi-Parametric Analysis of Mutation Status, Circulating Tumor Cells and Inflammatory Markers in EGFR-Mutated NSCLC. Diagnostics (Basel) 2022; 12:diagnostics12102360. [PMID: 36292049 PMCID: PMC9600124 DOI: 10.3390/diagnostics12102360] [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: 08/11/2022] [Revised: 09/07/2022] [Accepted: 09/17/2022] [Indexed: 11/22/2022] Open
Abstract
The liquid biopsy has the potential to improve patient care in the diagnostic and therapeutic setting in non-small cell lung cancer (NSCLC). Consented patients with epidermal growth factor receptor (EGFR) positive disease (n = 21) were stratified into two cohorts: those currently receiving EGFR tyrosine kinase inhibitor (TKI) therapy (n = 9) and newly diagnosed EGFR TKI treatment-naïve patients (n = 12). Plasma genotyping of cell-free DNA was carried out using the FDA-approved cobas® EGFR mutation test v2 and compared to next generation sequencing (NGS) cfDNA panels. Circulating tumor cell (CTC) numbers were correlated with treatment response and EGFR exon 20 p.T790M. The prognostic significance of the neutrophil to lymphocyte ratio (NLR) and lactate dehydrogenase (LDH) was also investigated. Patients in cohort 1 with an EGFR exon 20 p.T790M mutation progressed more rapidly than those with an EGFR sensitizing mutation, while patients in cohort 2 had a significantly longer progression-free survival (p = 0.04). EGFR exon 20 p.T790M was detected by liquid biopsy prior to disease progression indicated by computed tomography (CT) imaging. The cobas® EGFR mutation test detected a significantly greater number of exon 20 p.T790M mutations (p = 0.05). High NLR and derived neutrophil to lymphocyte ratio (dNLR) were associated with shorter time to progression and worse survival outcomes (p < 0.05). High LDH levels were significantly associated with shorter time to disease progression (p = 0.03). These data support the use of liquid biopsy for monitoring EGFR mutations and inflammatory markers as prognostic indicators in NSCLC.
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Affiliation(s)
- Martin P. Barr
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Correspondence: ; Tel.: +353-1-8963620
| | - Anne-Marie Baird
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Sophia Halliday
- Patrick G. Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK
| | - Petra Martin
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
- Department of Medical Oncology, Midlands Regional Hospital, R35 NY51 Tullamore, Ireland
| | - Emma H. Allott
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Patrick G. Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK
| | - James Phelan
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Greg Korpanty
- Department of Medical Oncology, University Hospital Limerick, V94 F858 Limerick, Ireland
| | - Linda Coate
- Department of Medical Oncology, University Hospital Limerick, V94 F858 Limerick, Ireland
| | - Cathal O’Brien
- Cancer Molecular Diagnostics Laboratory, St James’s Hospital, D08 W9RT Dublin, Ireland
| | - Steven G. Gray
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Jane S. Y. Sui
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
| | - Brian Hayes
- Department of Histopathology, Cork University Hospital, T12 XF62 Cork, Ireland
- Department of Pathology, University College Cork, T12 DC4A Cork, Ireland
| | - Sinead Cuffe
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
- Department of Medical Oncology, St James’s Hospital, D08 NHY1 Dublin, Ireland
| | - Stephen P. Finn
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
- Department of Histopathology, St James’s Hospital, D08 RX0X Dublin, Ireland
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Keogh A, Ryan L, Nur MM, Baird AM, Nicholson S, Cuffe S, Fitzmaurice GJ, Ryan R, Young VK, Finn SP, Gray SG. USO1 expression is dysregulated in non-small cell lung cancer. Transl Lung Cancer Res 2022; 11:1877-1895. [PMID: 36248341 PMCID: PMC9554690 DOI: 10.21037/tlcr-22-230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/18/2022] [Indexed: 11/26/2022]
Abstract
Background USO1 vesicle transport factor (USO1) is a vesicular transport factor crucial for endoplasmic reticulum (ER) to Golgi transport and is required for transcytotic fusion and subsequent binding of the vesicles to the target membrane. USO1 has been studied in multiple cancers revealing high levels of expression and exerting its oncogenic role by increasing cell proliferation and evasion of apoptosis. Furthermore, multiple studies have implicated dysregulation of the Erk signalling pathway in the involvement of USO1 in multiple cancers. Overall survival (OS) in non-small cell lung cancer (NSCLC) remains low despite recent advances in treatments which are mainly due to the late stage of diagnosis and a significant cohort of patients lacking an available targeted therapy. The aim of this study was to investigate USO1 expression in NSCLC. Methods An in-house NSCLC tissue microarray (TMA) comprising (n=204 patients) was stained for USO1. Scoring intensity (H score) was used to interrogate for correlations between USO1 expression and established prognostic factors, and OS. Further evaluation of the expression of USO1 in NSCLC was done using multiple online datasets including Lung Cancer Explorer (LCE), UALCAN, GEPIA, KM plotter, TIMER2 and MuTarget. Results USO1, when highly expressed in lung adenocarcinomas (LUADs) leads to a significantly increased OS (P=0.028). There was no significant correlation between age, smoking status, lymph node status, tumour subgroup and stage. USO1 was significantly higher in patients with tumour size <5 cm compared to those ≥5 cm (P=0.016). Overexpression in LUAD occurred at an early stage being significantly upregulated in Stage 1 and N0 tumours. USO1’s first neighbours, also involved in ER-Golgi transport have altered expression in LUAD and significantly impact overall survival. Overexpression occurred independently of commonly mutated genes in NSCLC and had no correlation with changes in the TME. Conclusions This study highlights the importance of USO1 and ER-Golgi vesicular transport system in LUAD. USO1 overexpression occurs as an early event in LUAD and independently of commonly mutated genes in NSCLC and therefore may represent an attractive diagnostic biomarker as well as a potential target for treatment.
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Affiliation(s)
- Anna Keogh
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James’s Hospital, Dublin, Ireland
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Lisa Ryan
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, Dublin, Ireland
| | - Mutaz M. Nur
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James’s Hospital, Dublin, Ireland
- Division of Pathology, Department of Medicine, University Hospital Waterford, Waterford, Ireland
| | - Anne-Marie Baird
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James’s Hospital, Dublin, Ireland
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Siobhan Nicholson
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, Dublin, Ireland
| | - Sinéad Cuffe
- HOPE Directorate, St James’s Hospital, Dublin, Ireland
| | - Gerard J. Fitzmaurice
- Surgery, Anaesthesia and Critical Care Directorate, St James’s Hospital, Dublin, Ireland
| | - Ronan Ryan
- Surgery, Anaesthesia and Critical Care Directorate, St James’s Hospital, Dublin, Ireland
| | - Vincent K. Young
- Surgery, Anaesthesia and Critical Care Directorate, St James’s Hospital, Dublin, Ireland
| | - Stephen P. Finn
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James’s Hospital, Dublin, Ireland
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
- Cancer Molecular Diagnostics, Labmed Directorate, St. James’s Hospital, Dublin, Ireland
- Department of Histopathology and Morbid Anatomy, Trinity College Dublin, Dublin, Ireland
| | - Steven G. Gray
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James’s Hospital, Dublin, Ireland
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
- Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
- School of Biological Sciences, Technological University Dublin, Dublin, Ireland
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17
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Sui JSY, Martin P, Keogh A, Murchan P, Ryan L, Nicholson S, Cuffe S, Broin PÓ, Finn SP, Fitzmaurice GJ, Ryan R, Young V, Gray SG. Altered expression of ACOX2 in non-small cell lung cancer. BMC Pulm Med 2022; 22:321. [PMID: 35999530 PMCID: PMC9396774 DOI: 10.1186/s12890-022-02115-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 03/25/2022] [Accepted: 08/16/2022] [Indexed: 12/24/2022] Open
Abstract
Peroxisomes are organelles that play essential roles in many metabolic processes, but also play roles in innate immunity, signal transduction, aging and cancer. One of the main functions of peroxisomes is the processing of very-long chain fatty acids into metabolites that can be directed to the mitochondria. One key family of enzymes in this process are the peroxisomal acyl-CoA oxidases (ACOX1, ACOX2 and ACOX3), the expression of which has been shown to be dysregulated in some cancers. Very little is however known about the expression of this family of oxidases in non-small cell lung cancer (NSCLC). ACOX2 has however been suggested to be elevated at the mRNA level in over 10% of NSCLC, and in the present study using both standard and bioinformatics approaches we show that expression of ACOX2 is significantly altered in NSCLC. ACOX2 mRNA expression is linked to a number of mutated genes, and associations between ACOX2 expression and tumour mutational burden and immune cell infiltration were explored. Links between ACOX2 expression and candidate therapies for oncogenic driver mutations such as KRAS were also identified. Furthermore, levels of acyl-CoA oxidases and other associated peroxisomal genes were explored to identify further links between the peroxisomal pathway and NSCLC. The results of this biomarker driven study suggest that ACOX2 may have potential clinical utility in the diagnosis, prognosis and stratification of patients into various therapeutically targetable options.
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Affiliation(s)
- Jane S Y Sui
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, D08RX0X, Ireland.,Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Petra Martin
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, D08RX0X, Ireland.,Midland Regional Hospital Tullamore, Tullamore, Ireland
| | - Anna Keogh
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, D08RX0X, Ireland
| | - Pierre Murchan
- Department of Histopathology and Morbid Anatomy, Trinity College Dublin, Dublin, Ireland.,School of Mathematics, Statistics, and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
| | - Lisa Ryan
- Department of Histopathology, Labmed Directorate, St. James's Hospital, Dublin, Ireland
| | - Siobhan Nicholson
- Department of Histopathology, Labmed Directorate, St. James's Hospital, Dublin, Ireland
| | - Sinead Cuffe
- HOPE Directorate, St James's Hospital, Dublin, Ireland
| | - Pilib Ó Broin
- School of Mathematics, Statistics, and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
| | - Stephen P Finn
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, D08RX0X, Ireland.,Department of Histopathology and Morbid Anatomy, Trinity College Dublin, Dublin, Ireland.,Department of Histopathology, Labmed Directorate, St. James's Hospital, Dublin, Ireland.,Cancer Molecular Diagnostics, Labmed Directorate, St. James's Hospital, Dublin, Ireland
| | - Gerard J Fitzmaurice
- Surgery, Anaesthesia and Critical Care Directorate, St James's Hospital, Dublin, Ireland
| | - Ronan Ryan
- Surgery, Anaesthesia and Critical Care Directorate, St James's Hospital, Dublin, Ireland
| | - Vincent Young
- Surgery, Anaesthesia and Critical Care Directorate, St James's Hospital, Dublin, Ireland
| | - Steven G Gray
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, D08RX0X, Ireland. .,Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland. .,School of Biological Sciences, Technological University Dublin, Dublin, Ireland.
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18
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Collins DC, Poretti D, Murphy V, Ganter M, Girotti R, Healey Bird B, Galibert MD, Dienstmann R, McDermott RS, McVeigh TP, Finn SP. Developing the educational molecular tumor board in Ireland: Pilot to national initiative. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.e13533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e13533 Background: The accelerated use of next generation sequencing (NGS) in oncology requires the integration of cancer genomics and precision oncology education to facilitate appropriate clinical decisions. The Molecular Tumour Board (MTB) in Ireland was established in November 2020 as a cross-institutional, educational and multi-disciplinary pilot and expanded nationally under Cancer Trials Ireland as a resource for clinicians and other oncology groups. Methods: The Irish MTB program was co-designed with Roche and local Health Care Providers (HCPs) over the pillars of co-creation, co-benefitting and co-education. Individual anonymized patient cases are discussed at each monthly meeting, supported by four multidisciplinary experts that discuss genomic findings, characterized mutations and their actionability, in addition to available therapies. The standardized end-to-end process to ensure preparation and proper handling of sensitive data is managed by an independent partner. A survey questionnaire was regularly administered to the MTB attendees to evaluate progress since the MTB initiation. Results: From November 2020 until December 2021, the program has grown to a monthly meeting where 30 patient cases have been discussed and 157 cumulative participants have been part of the sessions from 16 institutions. Survey findings revealed all of participants admitted that MTBs they attended met, exceeded, or significantly exceeded their expectations and 90% of presenters confirmed that experts communicated effectively. The majority of participants (87%) considered the discussions on clinical implications of targeted therapies or immunotherapies associated with genomic alterations as the most valuable component, 80% of presenters confirmed that the MTB discussions helped them to confirm, modify or change the treatment plan for at least one of their patients, and 65% of participants were very satisfied with the insights shared around molecular profiling and biological pathways. The pilot MTB has now been incorporated by the national trials group, Cancer Trials Ireland. Conclusions: The development of a national MTB in Ireland utilized pharmaceutical sponsorship and support to gather impetus for an independent national MTB managed by Cancer Trials Ireland. It offers a national forum for the discussion of cancers with specific molecular alterations in addition to complex clinical cases. Furthermore, it has created academic opportunities for the clinical application of precision medicine. Future directions will include leveraging the MTB infrastructure for research and the creation of a national Molecular Cancer Registry. Continued integration of experts will be key to secure the continuation of the national Irish MTB and to ultimately improving precision oncology delivery in patient care and trial enrolment through meaningful insights based on the collected data.
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Affiliation(s)
| | | | | | | | | | - Brian Healey Bird
- Bon Secours Hospital Cork, Cancer Trials Ireland, and University College Cork, Cork, Ireland
| | - Marie-Dominique Galibert
- Hospital University of Rennes, Department of Molecular Genetics and Genomics, IGRD-CNRS, Rennes, France
| | | | | | - Terri Patricia McVeigh
- The Royal Marsden NHS Foundation Trust and The Institute of Cancer Research, London, United Kingdom
| | - Stephen P. Finn
- St. James's Hospital and Trinity College Dublin, Cancer Molecular Diagnostics, Dublin, Ireland
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19
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Stopsack KH, Tyekucheva S, Wang M, Gerke TA, Vaselkiv JB, Penney KL, Kantoff PW, Finn SP, Fiorentino M, Loda M, Lotan TL, Parmigiani G, Mucci LA. Extent, impact, and mitigation of batch effects in tumor biomarker studies using tissue microarrays. eLife 2021; 10:71265. [PMID: 34939926 PMCID: PMC8849344 DOI: 10.7554/elife.71265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/22/2021] [Indexed: 12/05/2022] Open
Abstract
Tissue microarrays (TMAs) have been used in thousands of cancer biomarker studies. To what extent batch effects, measurement error in biomarker levels between slides, affects TMA-based studies has not been assessed systematically. We evaluated 20 protein biomarkers on 14 TMAs with prospectively collected tumor tissue from 1448 primary prostate cancers. In half of the biomarkers, more than 10% of biomarker variance was attributable to between-TMA differences (range, 1–48%). We implemented different methods to mitigate batch effects (R package batchtma), tested in plasmode simulation. Biomarker levels were more similar between mitigation approaches compared to uncorrected values. For some biomarkers, associations with clinical features changed substantially after addressing batch effects. Batch effects and resulting bias are not an error of an individual study but an inherent feature of TMA-based protein biomarker studies. They always need to be considered during study design and addressed analytically in studies using more than one TMA. To understand cancer, researchers need to know which molecules tumor cells use. These so-called ‘biomarkers’ tag cancer cells as being different from healthy cells, and can be used to predict how aggressive a tumor may be, or how well it might respond to treatment. A popular technique for assessing biomarkers across multiple tumors is to use tissue microarrays. This involves taking samples from different tumors and embedding them in a block of wax, which is then cut into micro-thin slices and stained with reagents that can detect specific biomarkers, such as proteins. Each block contains hundreds of samples, which all experience the same conditions. So, any patterns detected in the staining are likely to represent real variations in the biomarkers present. Many cancer studies, however, often compare samples from multiple tissue microarrays, which may increase the risk of technical artifacts: for example, staining may look stronger in one batch of tissue samples than another, even though the amount of biomarker present in these different arrays is roughly the same. These ‘batch effects’ could potentially bias the results of the experiment and lead to the identification of misleading patterns. To evaluate how batch effects impact tissue microarray studies, Stopsack et al. examined 14 wax blocks which contained tumor samples from 1,448 men with prostate cancer. This revealed that for some biomarkers, but not others, there were noticeable differences between tissue microarrays that were clearly the result of batch effects. Stopsack et al. then tested six different ways of fixing these discrepancies using statistical methods. All six approaches were successful, even if the arrays included tumors with different characteristics, such as tumors that had been diagnosed more or less recently. This work highlights the importance of considering batch effects when using tissue microarrays to study cancer. Stopsack et al. have used their statistical approaches to develop freely available software which can reduce the biases that sometimes arise from these technical artifacts. This could help researchers avoid misleading patterns in their data and make it easier to detect real variations in the biomarkers present between tumor samples.
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Affiliation(s)
- Konrad H Stopsack
- Department of Epidemiology, Harvard T.H. Chan School of Public Health
| | | | - Molin Wang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health
| | - Travis A Gerke
- Department of Cancer Epidemiology, Moffitt Cancer Center
| | - J Bailey Vaselkiv
- Department of Epidemiology, Harvard T.H. Chan School of Public Health
| | | | | | | | | | - Massimo Loda
- Department of Pathology, Weill Cornell Medical Center
| | | | | | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health
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20
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McDermott RS, Greene J, McCaffrey J, Parker I, Helanova S, Baird AM, Teiserskiene A, Lim M, Matthews H, Deignan O, Feeney J, Thirion PG, Finn SP, Kelly PJ. Radium-223 in combination with enzalutamide in metastatic castration-resistant prostate cancer: a multi-centre, phase II open-label study. Ther Adv Med Oncol 2021; 13:17588359211042691. [PMID: 34512801 PMCID: PMC8427915 DOI: 10.1177/17588359211042691] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 04/29/2021] [Accepted: 08/11/2021] [Indexed: 01/19/2023] Open
Abstract
Background: Radium-223 and enzalutamide are approved agents for patients with metastatic castration-resistant prostate cancer (mCRPC). Combining radium-223 and enzalutamide to improve outcomes is of clinical interest due to their differing modes of action and non-overlapping toxicity profiles. Methods: This phase II study enrolled patients with mCRPC and bone metastases. Patients received six cycles of radium-223 in combination with enzalutamide, followed by enzalutamide alone. The primary endpoint was safety for the combination; secondary endpoints included radiographic/clinical progression-free survival (PFS), PSA PFS, overall survival (OS), change in alkaline phosphatase, patient-reported pain outcomes and skeletal related events. Results: Forty-five patients received the combination treatment: 42 patients (93.3%) received all six cycles. Fourteen patients (31.1%) developed grade 3 or 4 toxicities, most commonly fatigue and neutropaenia. Fractures during the combination period occurred in four patients (8.9%). A further 13 patients (28.9%) developed fractures after completing combination treatment, giving a total of 17 patients (37.8%) who developed a fracture at any time on study. The median time to fracture was greater than 17.2 months [95% confidence interval (CI), 17.2–not estimable]. The median time to PSA progression was 18.1 months (95% CI, 12.68–22.60) and the median time to radiological/clinical progression was 28.0 months (95% CI, 22.54–not reached). At the primary analysis, 19 (42.2%) out of 45 patients had died with a median OS not reached (mean 34.8 months, standard error 1.4). Conclusion: In men with progressive mCRPC and bone metastases, the combination of radium-223 and enzalutamide was tolerable with the majority of patients completing the combination treatment. Bone fractures during the combination period were uncommon; however, we did identify a higher incidence of fractures occurring in patients after completing combination treatment. Bone health agents should be administered and bone health should be closely monitored following treatment with radium-223 and enzalutamide.
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Affiliation(s)
| | - John Greene
- Cancer Trials Ireland, Innovation House, Glasnevin, Dublin 8, IrelandTallaght University Hospital, Dublin, Ireland Trinity College Dublin, Ireland
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21
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Silva R, Moran B, Baird AM, O'Rourke CJ, Finn SP, McDermott R, Watson W, Gallagher WM, Brennan DJ, Perry AS. Longitudinal analysis of individual cfDNA methylome patterns in metastatic prostate cancer. Clin Epigenetics 2021; 13:168. [PMID: 34454584 PMCID: PMC8403420 DOI: 10.1186/s13148-021-01155-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/16/2021] [Accepted: 08/17/2021] [Indexed: 01/27/2023] Open
Abstract
Background Disease progression and therapeutic resistance are hallmarks of advanced stage prostate cancer (PCa), which remains a major cause of cancer-related mortality around the world. Longitudinal studies, coupled with the use of liquid biopsies, offer a potentially new and minimally invasive platform to study the dynamics of tumour progression. Our aim was to investigate the dynamics of personal DNA methylomic profiles of metastatic PCa (mPCa) patients, during disease progression and therapy administration. Results Forty-eight plasma samples from 9 mPCa patients were collected, longitudinally, over 13–21 months. After circulating cell-free DNA (cfDNA) isolation, DNA methylation was profiled using the Infinium MethylationEPIC BeadChip. The top 5% most variable probes across time, within each individual, were utilised to study dynamic methylation patterns during disease progression and therapeutic response. Statistical testing was carried out to identify differentially methylated genes (DMGs) in cfDNA, which were subsequently validated in two independent mPCa (cfDNA and FFPE tissue) cohorts. Individual cfDNA global methylation patterns were temporally stable throughout the disease course. However, a proportion of CpG sites presented a dynamic temporal pattern that was consistent with clinical events, including different therapies, and were prominently associated with genes linked to immune response pathways. Additionally, study of the tumour fraction of cfDNA identified > 2000 DMGs with dynamic methylation patterns. Conclusions Longitudinal assessment of cfDNA methylation in mPCa patients unveiled dynamic patterns associated with disease progression and therapy administration, thus highlighting the potential of using liquid biopsies to study PCa evolution at a methylomic level. ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01155-w.
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Affiliation(s)
- Romina Silva
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,School of Medicine, University College Dublin, Dublin, Ireland.,School of Biology and Environmental Science, Science West, O'Brien Science Centre, University College Dublin, Dublin, Ireland
| | - Bruce Moran
- Department of Pathology, St. Vincent's University Hospital, Dublin, Ireland
| | - Anne-Marie Baird
- Department of Clinical Medicine, Trinity College, Dublin, Ireland
| | - Colm J O'Rourke
- Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stephen P Finn
- Department of Clinical Medicine, Trinity College, Dublin, Ireland.,Department of Histopathology, St James's Hospital, Dublin, Ireland
| | - Ray McDermott
- Cancer Trials Ireland, Dublin, Ireland.,Department of Medical Oncology, St. Vincent's University Hospital, Dublin, Ireland
| | - William Watson
- School of Medicine, University College Dublin, Dublin, Ireland
| | - William M Gallagher
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Donal J Brennan
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,School of Medicine, University College Dublin, Dublin, Ireland
| | - Antoinette S Perry
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland. .,School of Biology and Environmental Science, Science West, O'Brien Science Centre, University College Dublin, Dublin, Ireland.
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22
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Murchan P, Ó’Brien C, O’Connell S, McNevin CS, Baird AM, Sheils O, Ó Broin P, Finn SP. Deep Learning of Histopathological Features for the Prediction of Tumour Molecular Genetics. Diagnostics (Basel) 2021; 11:1406. [PMID: 34441338 PMCID: PMC8393642 DOI: 10.3390/diagnostics11081406] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
Advanced diagnostics are enabling cancer treatments to become increasingly tailored to the individual through developments in immunotherapies and targeted therapies. However, long turnaround times and high costs of molecular testing hinder the widespread implementation of targeted cancer treatments. Meanwhile, gold-standard histopathological assessment carried out by a trained pathologist is widely regarded as routine and mandatory in most cancers. Recently, methods have been developed to mine hidden information from histopathological slides using deep learning applied to scanned and digitized slides; deep learning comprises a collection of computational methods which learn patterns in data in order to make predictions. Such methods have been reported to be successful in a variety of cancers for predicting the presence of biomarkers such as driver mutations, tumour mutational burden, and microsatellite instability. This information could prove valuable to pathologists and oncologists in clinical decision making for cancer treatment and triage for in-depth sequencing. In addition to identifying molecular features, deep learning has been applied to predict prognosis and treatment response in certain cancers. Despite reported successes, many challenges remain before the clinical implementation of such diagnostic strategies in the clinical setting is possible. This review aims to outline recent developments in the field of deep learning for predicting molecular genetics from histopathological slides, as well as to highlight limitations and pitfalls of working with histopathology slides in deep learning.
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Affiliation(s)
- Pierre Murchan
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland; (P.M.); (C.Ó.); (C.S.M.)
| | - Cathal Ó’Brien
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland; (P.M.); (C.Ó.); (C.S.M.)
- Department of Histopathology, St James’s Hospital, P.O. Box 580, James’s Street, D08 X4RX Dublin, Ireland
| | - Shane O’Connell
- School of Mathematics, Statistics, and Applied Mathematics, National University of Ireland Galway, H91 TK33 Galway, Ireland; (S.O.); (P.Ó.B.)
| | - Ciara S. McNevin
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland; (P.M.); (C.Ó.); (C.S.M.)
- Department of Medical Oncology, St James’s Hospital, D08 NHY1 Dublin, Ireland
| | - Anne-Marie Baird
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D02 A440 Dublin, Ireland; (A.-M.B.); (O.S.)
| | - Orla Sheils
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D02 A440 Dublin, Ireland; (A.-M.B.); (O.S.)
| | - Pilib Ó Broin
- School of Mathematics, Statistics, and Applied Mathematics, National University of Ireland Galway, H91 TK33 Galway, Ireland; (S.O.); (P.Ó.B.)
| | - Stephen P. Finn
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland; (P.M.); (C.Ó.); (C.S.M.)
- Department of Histopathology, St James’s Hospital, P.O. Box 580, James’s Street, D08 X4RX Dublin, Ireland
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23
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Doherty T, McKeever S, Al-Attar N, Murphy T, Aura C, Rahman A, O'Neill A, Finn SP, Kay E, Gallagher WM, Watson RWG, Gowen A, Jackman P. Feature fusion of Raman chemical imaging and digital histopathology using machine learning for prostate cancer detection. Analyst 2021; 146:4195-4211. [PMID: 34060548 DOI: 10.1039/d1an00075f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The diagnosis of prostate cancer is challenging due to the heterogeneity of its presentations, leading to the over diagnosis and treatment of non-clinically important disease. Accurate diagnosis can directly benefit a patient's quality of life and prognosis. Towards addressing this issue, we present a learning model for the automatic identification of prostate cancer. While many prostate cancer studies have adopted Raman spectroscopy approaches, none have utilised the combination of Raman Chemical Imaging (RCI) and other imaging modalities. This study uses multimodal images formed from stained Digital Histopathology (DP) and unstained RCI. The approach was developed and tested on a set of 178 clinical samples from 32 patients, containing a range of non-cancerous, Gleason grade 3 (G3) and grade 4 (G4) tissue microarray samples. For each histological sample, there is a pathologist labelled DP-RCI image pair. The hypothesis tested was whether multimodal image models can outperform single modality baseline models in terms of diagnostic accuracy. Binary non-cancer/cancer models and the more challenging G3/G4 differentiation were investigated. Regarding G3/G4 classification, the multimodal approach achieved a sensitivity of 73.8% and specificity of 88.1% while the baseline DP model showed a sensitivity and specificity of 54.1% and 84.7% respectively. The multimodal approach demonstrated a statistically significant 12.7% AUC advantage over the baseline with a value of 85.8% compared to 73.1%, also outperforming models based solely on RCI and mean and median Raman spectra. Feature fusion of DP and RCI does not improve the more trivial task of tumour identification but does deliver an observed advantage in G3/G4 discrimination. Building on these promising findings, future work could include the acquisition of larger datasets for enhanced model generalization.
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Affiliation(s)
- Trevor Doherty
- Technological University Dublin, School of Computer Science, City Campus, Grangegorman Lower, Dublin 7, Ireland.
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24
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MacDonagh L, Gallagher MF, Ffrench B, Gasch C, Gray SG, Reidy M, Nicholson S, Leonard N, Ryan R, Young V, O'Leary JJ, Cuffe S, Finn SP, O'Byrne KJ, Barr MP. MicroRNA expression profiling and biomarker validation in treatment-naïve and drug resistant non-small cell lung cancer. Transl Lung Cancer Res 2021; 10:1773-1791. [PMID: 34012792 PMCID: PMC8107736 DOI: 10.21037/tlcr-20-959] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Background In the absence of targetable mutations or immune checkpoints, cisplatin-doublet chemotherapy remains the standard of care in non-small cell lung cancer (NSCLC). Drug resistance has however become a significant clinical challenge. Exploring a role for small non-coding microRNAs (miRNA) as biomarker candidates in cisplatin resistant (CisR) lung cancer is lacking and warrants further investigation. Methods miRNA expression profiling was assessed in a panel of cisplatin sensitive and resistant NSCLC cell lines and validated by qPCR. Modulation of altered miRNAs was studied using antagomiRs and pre-miRs while functional assays were used to assess cisplatin response. The translational relevance of these miRNAs as potential biomarkers was assessed in serum and matched normal and tumour lung tissues from chemo-naïve NSCLC patients, in addition to xenograft formalin-fixed paraffin-embedded (FFPE) tumours derived from cisplatin sensitive and resistant cell lines. Results Differential expression of a 5-miR signature (miR-30a-3p, miR-30b-5p, miR-30c-5p, miR-34a-5p, miR-4286) demonstrated their ability to distinguish between normal and tumour lung tissue and between NSCLC histologies. In squamous cell carcinoma (SqCC), tissue miRNA expression was associated with poor survival. miR-4286 showed promise as a blood-based diagnostic biomarker that could distinguish between adenocarcinoma and SqCC histologies. In a xenograft model of cisplatin resistance, using 7-9 week old female NOD/SCID mice (NOD.CB17-Prkdcscid/NCrCrl), a 5-miRNA panel showed altered expression between sensitive and resistant tumours. Conclusions This study identified a panel of miRNAs which may have diagnostic and prognostic potential as novel biomarkers in lung cancer and furthermore, may have a predictive role in monitoring the emergence of resistance to cisplatin.
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Affiliation(s)
- Lauren MacDonagh
- Thoracic Oncology Research Group, School of Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St. James's Hospital and Trinity College Dublin, Dublin, Ireland
| | - Michael F Gallagher
- Histopathology Department, Sir Patrick Dun Laboratories, Central Pathology Laboratory, St. James's Hospital & Pathology Research Laboratory, Coombe Women and Infant's University Hospital, Dublin, Ireland
| | - Brendan Ffrench
- Histopathology Department, Sir Patrick Dun Laboratories, Central Pathology Laboratory, St. James's Hospital & Pathology Research Laboratory, Coombe Women and Infant's University Hospital, Dublin, Ireland
| | - Claudia Gasch
- Histopathology Department, Sir Patrick Dun Laboratories, Central Pathology Laboratory, St. James's Hospital & Pathology Research Laboratory, Coombe Women and Infant's University Hospital, Dublin, Ireland
| | - Steven G Gray
- Thoracic Oncology Research Group, School of Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St. James's Hospital and Trinity College Dublin, Dublin, Ireland
| | - Marie Reidy
- Department of Histopathology, St. James's Hospital, Dublin, Ireland
| | | | - Niamh Leonard
- Department of Histopathology, St. James's Hospital, Dublin, Ireland
| | - Ronan Ryan
- Department of Cardiothoracic Surgery, St. James's Hospital, Dublin, Ireland
| | - Vincent Young
- Department of Cardiothoracic Surgery, St. James's Hospital, Dublin, Ireland
| | - John J O'Leary
- Histopathology Department, Sir Patrick Dun Laboratories, Central Pathology Laboratory, St. James's Hospital & Pathology Research Laboratory, Coombe Women and Infant's University Hospital, Dublin, Ireland
| | - Sinead Cuffe
- Thoracic Oncology Research Group, School of Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St. James's Hospital and Trinity College Dublin, Dublin, Ireland.,Department of Medical Oncology, St James's Hospital, Dublin, Ireland
| | - Stephen P Finn
- Thoracic Oncology Research Group, School of Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St. James's Hospital and Trinity College Dublin, Dublin, Ireland.,Department of Histopathology, St. James's Hospital, Dublin, Ireland
| | - Kenneth J O'Byrne
- Cancer & Ageing Research Program, Queensland University of Technology, Brisbane, Australia
| | - Martin P Barr
- Thoracic Oncology Research Group, School of Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St. James's Hospital and Trinity College Dublin, Dublin, Ireland
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25
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MacDonagh L, Santiago RM, Gray SG, Breen E, Cuffe S, Finn SP, O'Byrne KJ, Barr MP. Exploitation of the vitamin A/retinoic acid axis depletes ALDH1-positive cancer stem cells and re-sensitises resistant non-small cell lung cancer cells to cisplatin. Transl Oncol 2021; 14:101025. [PMID: 33550205 PMCID: PMC7868629 DOI: 10.1016/j.tranon.2021.101025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 07/22/2020] [Revised: 01/17/2021] [Accepted: 01/18/2021] [Indexed: 12/23/2022] Open
Abstract
Despite advances in personalised medicine and the emerging role of immune checkpoints in directing treatment decisions in subsets of lung cancer patients, non-small cell lung cancer (NSCLC) remains the most common cause of cancer-related deaths worldwide. The development of drug resistance plays a key role in the relapse of lung cancer patients in the clinical setting, mainly due to the unlimited renewal capacity of residual cancer stem cells (CSCs) within the tumour cell population during chemotherapy. In this study, we investigated the function of the CSC marker, aldehyde dehydrogenase (ALDH1) in retinoic acid cell signalling using an in vitro model of cisplatin resistant NSCLC. The addition of key components in retinoic acid cell signalling, all-trans retinoic acid (ATRA) and retinol to cisplatin chemotherapy, significantly reduced ALDH1-positive cell subsets in cisplatin resistant NSCLC cells relative to their sensitive counterparts resulting in the re-sensitisation of chemo-resistant cells to the cytotoxic effects of cisplatin. Furthermore, combination of ATRA or retinol with cisplatin significantly inhibited cell proliferation, colony formation and increased cisplatin-induced apoptosis. This increase in apoptosis may, at least in part, be due to differential gene expression of the retinoic acid (RARα/β) and retinoid X (RXRα) nuclear receptors in cisplatin-resistant lung cancer cells. These data support the concept of exploiting the retinoic acid signalling cascade as a novel strategy in targeting subsets of CSCs in cisplatin resistant lung tumours.
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Affiliation(s)
- Lauren MacDonagh
- Thoracic Oncology Research Group, School of Clinical Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St James's Hospital & Trinity College Dublin, Ireland.
| | - Rhyla Mae Santiago
- Thoracic Oncology Research Group, School of Clinical Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St James's Hospital & Trinity College Dublin, Ireland.
| | - Steven G Gray
- Thoracic Oncology Research Group, School of Clinical Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St James's Hospital & Trinity College Dublin, Ireland.
| | - Eamon Breen
- Flow Cytometry Facility, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, Trinity College Dublin, Ireland.
| | - Sinead Cuffe
- Thoracic Oncology Research Group, School of Clinical Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St James's Hospital & Trinity College Dublin, Ireland; Medical Oncology Department, St James's Hospital, Dublin, Ireland.
| | - Stephen P Finn
- Thoracic Oncology Research Group, School of Clinical Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St James's Hospital & Trinity College Dublin, Ireland; Histopathology Department, St James's Hospital & Trinity College Dublin, Ireland.
| | - Kenneth J O'Byrne
- Cancer & Ageing Research Program, Queensland University of Technology, Brisbane, Australia.
| | - Martin P Barr
- Thoracic Oncology Research Group, School of Clinical Medicine, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St James's Hospital & Trinity College Dublin, Ireland.
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26
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Oner E, Kotmakci M, Baird AM, Gray SG, Debelec Butuner B, Bozkurt E, Kantarci AG, Finn SP. Development of EphA2 siRNA-loaded lipid nanoparticles and combination with a small-molecule histone demethylase inhibitor in prostate cancer cells and tumor spheroids. J Nanobiotechnology 2021; 19:71. [PMID: 33685469 PMCID: PMC7938557 DOI: 10.1186/s12951-021-00781-z] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/22/2021] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND siRNAs hold a great potential for cancer therapy, however, poor stability in body fluids and low cellular uptake limit their use in the clinic. To enhance the bioavailability of siRNAs in tumors, novel, safe, and effective carriers are needed. RESULTS Here, we developed cationic solid lipid nanoparticles (cSLNs) to carry siRNAs targeting EphA2 receptor tyrosine kinase (siEphA2), which is overexpressed in many solid tumors including prostate cancer. Using DDAB cationic lipid instead of DOTMA reduced nanoparticle size and enhanced both cellular uptake and gene silencing in prostate cancer cells. DDAB-cSLN showed better cellular uptake efficiency with similar silencing compared to commercial transfection reagent (Dharmafect 2). After verifying the efficacy of siEphA2-loaded nanoparticles, we further evaluated a potential combination with a histone lysine demethylase inhibitor, JIB-04. Silencing EphA2 by siEphA2-loaded DDAB-cSLN did not affect the viability (2D or 3D culture), migration, nor clonogenicity of PC-3 cells alone. However, upon co-administration with JIB-04, there was a decrease in cellular responses. Furthermore, JIB-04 decreased EphA2 expression, and thus, silencing by siEphA2-loaded nanoparticles was further increased with co-treatment. CONCLUSIONS We have successfully developed a novel siRNA-loaded lipid nanoparticle for targeting EphA2. Moreover, preliminary results of the effects of JIB-04, alone and in combination with siEphA2, on prostate cancer cells and prostate cancer tumor spheroids were presented for the first time. Our delivery system provides high transfection efficiency and shows great promise for targeting other genes and cancer types in further in vitro and in vivo studies.
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Affiliation(s)
- Ezgi Oner
- Department of Histopathology and Morbid Anatomy, Sir Patrick Dun Translational Research Lab, St. James's Hospital, Dublin, Ireland.,Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir, Turkey.,Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Izmir Katip Celebi University, Balatcik, Izmir, Turkey
| | - Mustafa Kotmakci
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir, Turkey
| | - Anne-Marie Baird
- Department of Histopathology and Morbid Anatomy, Sir Patrick Dun Translational Research Lab, St. James's Hospital, Dublin, Ireland.,Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland.,Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
| | - Steven G Gray
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland.,Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
| | - Bilge Debelec Butuner
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir, Turkey
| | - Emir Bozkurt
- Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, Balcova, Izmir, Turkey
| | - Ayse Gulten Kantarci
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir, Turkey
| | - Stephen P Finn
- Department of Histopathology and Morbid Anatomy, Sir Patrick Dun Translational Research Lab, St. James's Hospital, Dublin, Ireland. .,Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland. .,Department of Histopathology, Labmed Directorate, St. James's Hospital, Dublin, Ireland. .,Cancer Molecular Diagnostics, Labmed Directorate, St. James's Hospital, Dublin, Ireland.
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27
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Feng X, Zhou CK, Clish CB, Wilson KM, Pernar CH, Dickerman BA, Loda M, Finn SP, Penney KL, Schmidt DR, Heiden MGV, Giovannucci EL, Ebot EM, Mucci LA. Association of Prediagnostic Blood Metabolomics with Prostate Cancer Defined by ERG or PTEN Molecular Subtypes. Cancer Epidemiol Biomarkers Prev 2021; 30:1000-1008. [PMID: 33627383 DOI: 10.1158/1055-9965.epi-20-1363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/24/2020] [Accepted: 02/19/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The TMPRSS2:ERG gene fusion and PTEN loss are two of the most common somatic molecular alterations in prostate cancer. Here, we investigated the association of prediagnostic-circulating metabolomics and prostate cancer defined by ERG or PTEN status to improve understanding of these etiologically distinct molecular prostate cancer subtypes. METHODS The study was performed among 277 prostate cancer cases with ERG status, 211 with PTEN status, and 294 controls nested in the Health Professionals Follow-up Study (HPFS) and the Physicians' Health Study (PHS). We profiled 223 polar and non-polar metabolites using LC-MS in prediagnostic plasma specimens. We applied enrichment analysis and multinomial logistic regression models to identify biological metabolite classes and individual metabolites associated with prostate cancer defined by ERG or PTEN status. RESULTS Compared with noncancer controls, sphingomyelin (P: 0.01), ceramide (P: 0.04), and phosphatidylethanolamine (P: 0.03) circulating levels were enriched among ERG-positive prostate cancer cases. Sphingomyelins (P: 0.02), ceramides (P: 0.005), and amino acids (P: 0.02) were enriched among tumors exhibiting PTEN-loss; unsaturated diacylglycerols (P: 0.003) were enriched among PTEN-intact cases; and unsaturated triacylglycerols were enriched among both PTEN-loss (P: 0.001) and PTEN-intact (P: 0.0001) cases. Although several individual metabolites identified in the above categories were nominally associated with ERG or PTEN-defined prostate cancer, none remained significant after accounting for multiple testing. CONCLUSIONS The molecular process of prostate carcinogenesis may be distinct for men with different metabolomic profiles. IMPACT These novel findings provide insights into the metabolic environment for the development of prostate cancer.
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Affiliation(s)
- Xiaoshuang Feng
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.
| | - Cindy Ke Zhou
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | | | - Kathryn M Wilson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Claire H Pernar
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Barbra A Dickerman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Massimo Loda
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Stephen P Finn
- Department of Histopathology Research, Trinity College, Dublin, Ireland
| | - Kathryn L Penney
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Daniel R Schmidt
- David H. Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Matthew G Vander Heiden
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,David H. Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Ericka M Ebot
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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28
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Finn SP, Addeo A, Dafni U, Thunnissen E, Bubendorf L, Madsen LB, Biernat W, Verbeken E, Hernandez-Losa J, Marchetti A, Cheney R, Warth A, Speel EJM, Quinn AM, Monkhorst K, Jantus-Lewintre E, Tischler V, Marti N, Dimopoulou G, Molina-Vila MA, Kammler R, Kerr KM, Peters S, Stahel RA. Prognostic Impact of KRAS G12C Mutation in Patients With NSCLC: Results From the European Thoracic Oncology Platform Lungscape Project. J Thorac Oncol 2021; 16:990-1002. [PMID: 33647504 DOI: 10.1016/j.jtho.2021.02.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [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: 07/28/2020] [Revised: 02/01/2021] [Accepted: 02/10/2021] [Indexed: 01/18/2023]
Abstract
INTRODUCTION KRAS mutations, the most frequent gain-of-function alterations in NSCLC, are currently emerging as potential predictive therapeutic targets. The role of KRAS-G12C (Kr_G12C) is of special interest after the recent discovery and preclinical analyses of two different Kr_G12C covalent inhibitors (AMG-510, MRTX849). METHODS KRAS mutations were evaluated in formalin-fixed, paraffin-embedded tissue sections by a microfluidic-based multiplex polymerase chain reaction platform as a component of the previously published European Thoracic Oncology Platform Lungscape 003 Multiplex Mutation study, of clinically annotated, resected, stage I to III NSCLC. In this study, -Kr_G12C mutation prevalence and its association with clinicopathologic characteristics, molecular profiles, and postoperative patient outcome (overall survival, relapse-free survival, time-to-relapse) were explored. RESULTS KRAS gene was tested in 2055 Lungscape cases (adenocarcinomas: 1014 [49%]) with I or II or III stage respective distribution of 53% or 24% or 22% and median follow-up of 57 months. KRAS mutation prevalence in the adenocarcinoma cohort was 38.0% (95% confidence interval (CI): 35.0% to 41.0%), with Kr_G12C mutation representing 17.0% (95% CI: 14.7% to 19.4%). In the "histologic-subtype" cohort, Kr_G12C prevalence was 10.5% (95% CI: 9.2% to 11.9%). When adjusting for clinicopathologic characteristics, a significant negative prognostic effect of Kr_G12C presence versus other KRAS mutations or nonexistence of KRAS mutation was identified in the adenocarcinoma cohort alone and in the "histologic-subtype" cohort. For overall survival in adenocarcinomas, hazard ratio (HR)G12C versus other KRAS is equal to 1.39 (95% CI: 1.03 to 1.89, p = 0.031) and HRG12C versus no KRAS is equal to 1.32 (95% CI: 1.03 to 1.69, p = 0.028) (both also significant in the "histologic-subtype" cohort). For time-to-relapse, HRG12C versus other KRAS is equal to 1.41 (95% CI: 1.03 to 1.92, p = 0.030). In addition, among all patients, for relapse-free survival, HRG12C versus no KRAS is equal to 1.27 (95% CI: 1.04 to 1.54, p = 0.017). CONCLUSIONS In this large, clinically annotated stage I to III NSCLC cohort, the specific Kr_G12C mutation is significantly associated with poorer prognosis (adjusting for clinicopathologic characteristics) among adenocarcinomas and in unselected NSCLCs.
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Affiliation(s)
- Stephen P Finn
- Cancer Molecular Diagnostics Laboratory, Institute of Molecular Medicine, St. James Hospital, Dublin, Ireland.
| | - Alfredo Addeo
- Department of Oncology, University Hospital Geneva, Geneva, Switzerland
| | - Urania Dafni
- ETOP Statistics Center, Frontier Science Foundation-Hellas, Athens, Greece; Department of Nursing, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Erik Thunnissen
- Department of Pathology, Free University Medical Center, Amsterdam, the Netherlands
| | - Lukas Bubendorf
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Line Bille Madsen
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Wojciech Biernat
- Department of Pathology, Medical University of Gdansk, Gdansk, Poland
| | - Eric Verbeken
- Department of Pathology, University Hospital KU Leuven, Leuven, Belgium
| | | | - Antonio Marchetti
- Department of Pathology, Ospedale Clinicizzato Chieti, Chieti, Italy
| | - Richard Cheney
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Arne Warth
- Department of Pathology, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Ernst-Jan M Speel
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Anne Marie Quinn
- Department of Histopathology, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Kim Monkhorst
- Division of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Eloisa Jantus-Lewintre
- Department of Biotechnology, Universitat Politècnica de València, Valencia, Spain; Mixed Unit TRIAL (General University Hospital Valencia Research Foundation and Píncipe Felipe Research Center), Valencia, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Valencia, Spain
| | - Verena Tischler
- Division of Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Nesa Marti
- European Thoracic Oncology Platform, Bern, Switzerland
| | - Georgia Dimopoulou
- ETOP Statistics Center, Frontier Science Foundation-Hellas, Athens, Greece
| | | | | | - Keith M Kerr
- Department of Pathology, Aberdeen Royal Infirmary, Aberdeen, United Kingdom
| | - Solange Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Rolf A Stahel
- European Thoracic Oncology Platform, Bern, Switzerland
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29
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Greene J, Baird AM, Lim M, Flynn J, McNevin C, Brady L, Sheils O, Gray SG, McDermott R, Finn SP. Differential CircRNA Expression Signatures May Serve as Potential Novel Biomarkers in Prostate Cancer. Front Cell Dev Biol 2021; 9:605686. [PMID: 33718350 PMCID: PMC7946979 DOI: 10.3389/fcell.2021.605686] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 09/12/2020] [Accepted: 02/05/2021] [Indexed: 12/17/2022] Open
Abstract
Circular RNAs (circRNAs), a recently discovered non-coding RNA, have a number of functions including the regulation of miRNA expression. They have been detected in a number of malignancies including prostate cancer (PCa). The differential expression pattern of circRNAs associated with PCa and androgen receptor (AR) status was investigated in this study. circRNA profiling was performed using a high throughout microarray assay on a panel of prostate cell lines, which consisted of normal, benign, and malignant cells (n = 9). circRNAs were more commonly significantly up-regulated (p < 0.05) than downregulated in malignant cell lines (n = 3,409) vs. benign cell lines (n = 2,949). In a grouped analysis based on AR status, there were 2,127 down-regulated circRNAs in androgen independent cell lines compared to 2,236 in androgen dependent cell lines, thus identifying a potential circRNA signature reflective of androgen dependency. Through a bioinformatics approach, the parental genes associated with the top 10 differentially expressed circRNAs were identified such as hsa_circ_0064644, whose predicted parental gene target is RBMS3, and hsa_circ_0060539, whose predicted gene target is SDC4. Furthermore, we identified three circRNAs associated with the parental gene Caprin1 (hsa_circ_0021652, hsa_circ_0000288, and hsa_circ_0021647). Other studies have shown the importance of Caprin1 in PCa cell survival and drug resistance. Given the modified circRNA expression signatures identified here, these hypothesis generating results suggest that circRNAs may serve as potential putative diagnostic and predictive markers in PCa. However, further validation studies are required to assess the true potential of these markers in the clinical setting.
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Affiliation(s)
- John Greene
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College, Dublin, Ireland.,Department of Medical Oncology, Tallaght University Hospital, Dublin, Ireland
| | - Anne-Marie Baird
- School of Medicine, Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland
| | - Marvin Lim
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College, Dublin, Ireland.,Department of Medical Oncology, Tallaght University Hospital, Dublin, Ireland
| | - Joshua Flynn
- School of Medicine, Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland
| | - Ciara McNevin
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College, Dublin, Ireland.,Department of Medical Oncology, Tallaght University Hospital, Dublin, Ireland
| | - Lauren Brady
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College, Dublin, Ireland
| | - Orla Sheils
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College, Dublin, Ireland.,School of Medicine, Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland
| | - Steven G Gray
- School of Medicine, Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland.,Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland
| | - Raymond McDermott
- Department of Medical Oncology, Tallaght University Hospital, Dublin, Ireland.,Department of Medical Oncology, St. Vincent's University Hospital, Dublin, Ireland
| | - Stephen P Finn
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College, Dublin, Ireland.,Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland.,Department of Histopathology, St. James's Hospital, Dublin, Ireland
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30
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McNevin CS, Baird AM, McDermott R, Finn SP. Diagnostic Strategies for Treatment Selection in Advanced Prostate Cancer. Diagnostics (Basel) 2021; 11:345. [PMID: 33669657 PMCID: PMC7922176 DOI: 10.3390/diagnostics11020345] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 12/31/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/22/2022] Open
Abstract
Prostate Cancer (PCa) is a leading cause of morbidity and mortality among men worldwide. For most men with PCa, their disease will follow an indolent course. However, advanced PCa is associated with poor outcomes. There has been an advent of new therapeutic options with proven efficacy for advanced PCa in the last decade which has improved survival outcomes for men with this disease. Despite this, advanced PCa continues to be associated with a high rate of death. There is a lack of strong evidence guiding the timing and sequence of these novel treatment strategies. This paper focuses on a review of the strategies for diagnostic and the current evidence available for treatment selection in advanced PCa.
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Affiliation(s)
- Ciara S. McNevin
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland;
- Department of Medical Oncology, St. James Hospital, D08 NHY1 Dublin, Ireland
| | - Anne-Marie Baird
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D02 A440 Dublin, Ireland;
| | - Ray McDermott
- Department of Medical Oncology, Tallaght University Hospital, D24 NR0A Dublin, Ireland;
- Department of Medical Oncology, St. Vincent’s University Hospital, D04 YN26 Dublin, Ireland
| | - Stephen P. Finn
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland;
- Department of Histopathology, St. James’s Hospital, P.O. Box 580, James’s Street, D08 X4RX Dublin, Ireland
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31
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Radonic T, Geurts-Giele WRR, Samsom KG, Roemen GMJM, von der Thüsen JH, Thunnissen E, Meijssen IC, Sleddens HFBM, Dinjens WNM, Boelens MC, Weijers K, Speel EJM, Finn SP, O'Brien C, van Wezel T, Cohen D, Monkhorst K, Roepman P, Dubbink HJ. RET Fluorescence In Situ Hybridization Analysis Is a Sensitive but Highly Unspecific Screening Method for RET Fusions in Lung Cancer. J Thorac Oncol 2021; 16:798-806. [PMID: 33588111 DOI: 10.1016/j.jtho.2021.01.1619] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 09/12/2020] [Revised: 01/09/2021] [Accepted: 01/19/2021] [Indexed: 12/31/2022]
Abstract
INTRODUCTION RET gene fusions are established oncogenic drivers in 1% of NSCLC. Accurate detection of advanced patients with RET fusions is essential to ensure optimal therapy choice. We investigated the performance of fluorescence in situ hybridization (FISH) as a diagnostic test for detecting functional RET fusions. METHODS Between January 2016 and November 2019, a total of 4873 patients with NSCLC were routinely screened for RET fusions using either FISH (n = 2858) or targeted RNA next-generation sequencing (NGS) (n = 2015). If sufficient material was available, positive cases were analyzed by both methods (n = 39) and multiple FISH assays (n = 17). In an independent cohort of 520 patients with NSCLC, whole-genome sequencing data were investigated for disruptive structural variations and functional fusions in the RET and compared with ALK and ROS1 loci. RESULTS FISH analysis revealed RET rearrangement in 48 of 2858 cases; of 30 rearranged cases double tested with NGS, only nine had a functional RET fusion. RNA NGS yielded RET fusions in 14 of 2015 cases; all nine cases double tested by FISH had RET locus rearrangement. Of these 18 verified RET fusion cases, 16 had a split signal and two a complex rearrangement by FISH. By whole-genome sequencing, the prevalence of functional fusions compared with all disruptive events was lower in the RET (4 of 9, 44%) than the ALK (27 of 34, 79%) and ROS1 (9 of 12, 75%) loci. CONCLUSIONS FISH is a sensitive but unspecific technique for RET screening, always requiring a confirmation using an orthogonal technique, owing to frequently occurring RET rearrangements not resulting in functional fusions in NSCLC.
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Affiliation(s)
- Teodora Radonic
- Department of Pathology, Cancer Center Amsterdam, Vrije University, Amsterdam University Medical Center, Amsterdam, The Netherlands.
| | - W R R Geurts-Giele
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Kris G Samsom
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Guido M J M Roemen
- Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jan H von der Thüsen
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Erik Thunnissen
- Department of Pathology, Cancer Center Amsterdam, Vrije University, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Isabelle C Meijssen
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Hein F B M Sleddens
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Mirjam C Boelens
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Karin Weijers
- Department of Pathology, Cancer Center Amsterdam, Vrije University, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Ernst Jan M Speel
- Department of Pathology, Maastricht University Medical Center, Maastricht, The Netherlands; School for Oncology and Developmental Biology (GROW), Maastricht, The Netherlands
| | - Stephen P Finn
- Department of Histopathology, St. James's Hospital and Trinity College Dublin, Dublin, Ireland; Cancer Molecular Diagnostics, St. James's Hospital and Trinity College Dublin, Dublin, Ireland; Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's Hospital and Trinity College Dublin, Dublin, Ireland
| | - Cathal O'Brien
- Department of Histopathology, St. James's Hospital and Trinity College Dublin, Dublin, Ireland; Cancer Molecular Diagnostics, St. James's Hospital and Trinity College Dublin, Dublin, Ireland; Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's Hospital and Trinity College Dublin, Dublin, Ireland
| | - Tom van Wezel
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Danielle Cohen
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Kim Monkhorst
- Department of Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - H J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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32
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Pernar CH, Parmigiani G, Giovannucci EL, Rimm EB, Tyekucheva S, Loda M, Finn SP, Heiden MGV, Fiorentino M, Ebot EM, Mucci LA. Gene Expression Pathways in Prostate Tissue Associated with Vigorous Physical Activity in Prostate Cancer. Cancer Epidemiol Biomarkers Prev 2021; 30:751-756. [PMID: 33500320 DOI: 10.1158/1055-9965.epi-20-1461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/10/2020] [Accepted: 01/08/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Men engaged in high physical activity have lower risks of advanced and fatal prostate cancer. Mechanisms underlying this association are not well understood but may include systemic and tumor-specific effects. We investigated potential mechanisms linking physical activity and gene expression in prostate tissue from men with prostate cancer. METHODS We included a subset of 118 men in the Health Professionals Follow-up Study diagnosed with prostate cancer between 1986 and 2005 with whole-transcriptome gene expression profiling on tumor and adjacent normal prostate tissue and physical activity data. Long-term vigorous physical activity was self-reported as the average time spent engaged in various forms of recreational physical activity at baseline and biennially until prostate cancer diagnosis. Gene set enrichment analysis was performed among KEGG and Hallmark gene sets to identify pathways with differential expression based on vigorous physical activity. RESULTS In adjacent normal tissue, we identified 25 KEGG gene sets enriched (downregulated) in the highest compared with lowest quintile of vigorous physical activity at an FDR <0.10, including a number of cancer- and immune-related pathways. Although no gene sets reached statistical significance in tumor tissue, top gene sets differentially expressed included TGF beta, apoptosis, and p53 signaling pathways. CONCLUSIONS These findings suggest that physical activity may influence the tumor microenvironment. Future studies are needed to confirm these findings and further investigate potential mechanisms linking physical activity to lethal prostate cancer. IMPACT Identification of gene expression alterations in the prostate associated with physical activity can improve our understanding of prostate cancer etiology.
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Affiliation(s)
- Claire H Pernar
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.
| | - Giovanni Parmigiani
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Eric B Rimm
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Svitlana Tyekucheva
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York Presbyterian Hospital, New York, New York
| | - Stephen P Finn
- Department of Histopathology, Trinity College, Dublin, Ireland.,Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew G Vander Heiden
- Koch Institute for Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michelangelo Fiorentino
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Pathology Unit, Addarii Institute, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Ericka M Ebot
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts.,Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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33
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Bracken-Clarke D, Kapoor D, Baird AM, Buchanan PJ, Gately K, Cuffe S, Finn SP. Vaping and lung cancer - A review of current data and recommendations. Lung Cancer 2021; 153:11-20. [PMID: 33429159 DOI: 10.1016/j.lungcan.2020.12.030] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [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: 09/08/2020] [Revised: 12/15/2020] [Accepted: 12/19/2020] [Indexed: 10/22/2022]
Abstract
OBJECTIVES Lung cancer is the most common cause of cancer mortality worldwide and, while tobacco smoke remains the primary cause, there is increasing concern that vaping and E-cigarette use may also increase lung cancer risk. This review concentrates on the current data, scholarship and active foci of research regarding potential cancer risk and oncogenic mechanisms of vaping and lung cancer. MATERIALS AND METHODS We performed a literature review of current and historical publications on lung cancer oncogenesis, vaping device/e-liquid contents and daughter products, molecular oncogenic mechanisms and the fundamental, potentially oncogenic, effects of electronic cigarette smoke/e-liquid products. RESULTS E-cigarette devices and vaping fluids demonstrably contain a series of both definite and probable oncogens including nicotine derivatives (e.g. nitrosnornicotine, nitrosamine ketone), polycyclic aromatic hydrocarbons, heavy metals (including organometal compounds) and aldehydes/other complex organic compounds. These arise both as constituents of the e-liquid (with many aldehydes and other complex organics used as flavourings) and as a result of pyrolysis/complex organic reactions in the electronic cigarette device (including unequivocal carcinogens such as formaldehyde - formed from pyrolysis of glycerol). Various studies demonstrate in vitro transforming and cytotoxic activity of these derivatives. E-cigarette device use has been significantly increasing - particularly amongst the younger cohort and non-smokers; thus, this is an area of significant concern for the future. CONCLUSION Although research remains somewhat equivocal, there is clear reason for concern regarding the potential oncogenicity of E-Cigarettes/E-Liquids with a strong basic and molecular science basis. Given lag times (extrapolating from tobacco smoke data) of perhaps 20 years, this may have significant future public health implications. Thus, the authors feel further study in this field is strongly warranted and consideration should be made for tighter control and regulation of these products.
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Affiliation(s)
| | - Dhruv Kapoor
- Department of Medical Oncology, St James' Hospital, Dublin, Ireland
| | - Anne Marie Baird
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, Ireland
| | - Paul James Buchanan
- DCU Cancer Research, Faculty of Science and Health, Dublin City University, Dublin, Ireland; National Institute of Cellular Biotechnology, Dublin City University, Dublin, Ireland
| | - Kathy Gately
- Department of Clinical Medicine, Trinity College School of Medicine and St James's Hospital, Dublin, Ireland
| | - Sinead Cuffe
- Department of Medical Oncology, St James' Hospital, Dublin, Ireland
| | - Stephen P Finn
- Department of Pathology, St James' Hospital and Trinity College School of Medicine, Dublin, Ireland
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34
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Baird AM, Finn SP, Gray SG, Sheils O. Epigenetic Modifier UHRF1 May Be a Potential Target in Malignant Pleural Mesothelioma. J Thorac Oncol 2021; 16:14-16. [PMID: 33384056 DOI: 10.1016/j.jtho.2020.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Anne-Marie Baird
- School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Dublin, Ireland.
| | - Stephen P Finn
- School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Dublin, Ireland; Department of Histopathology. St. James's Hospital, Dublin, Ireland
| | - Steven G Gray
- School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Dublin, Ireland; LabMed Directorate, St. James's Hospital, Dublin, Ireland
| | - Orla Sheils
- School of Medicine, Trinity College Dublin, Dublin, Ireland; Trinity St. James's Cancer Institute, Dublin, Ireland
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35
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Abstract
The receptor tyrosine kinase (RTK) c-MET plays important roles in cancer, yet despite being frequently overexpressed, clinical responses to targeting this receptor have been limited in the clinical setting. A singular significant challenge has been the accurate identification of biomarkers for the selection of responsive patients. However, recently mutations which result in the loss of exon 14 (called METex14 skipping) have emerged as novel biomarkers in non-small cell lung carcinomas (NSCLC) to predict for responsiveness to targeted therapy with c-MET inhibitors. Currently, the diverse genomic alterations responsible for METex14 skipping pose a challenge for routine clinical diagnostic testing. Next generation sequencing (NGS) is the current gold standard for identifying the diverse mutations associated with METex14, but the cost for such a procedure remains to some degree prohibitive as often NGS is requested on a case-by-case basis, and many hospitals may not even have the capacity or resources to conduct NGS.However, PCR-based approaches to detect METex14 have been developed which can be conducted in most routine hospital laboratories and may therefore allow a cost-effective approach to pre-screen patients that may respond to c-MET inhibitors prior to conducting NGS, or until all patients will have NGS conducted as routine practise. In this chapter, we describe one such PCR-based approach for screening samples for the detection of METex14 in NSCLC.
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Affiliation(s)
- Jane S Y Sui
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland
- Department of Medical Oncology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Stephen P Finn
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland
- Department of Histopathology, Cancer Molecular Diagnostics, Labmed Directorate, St. James's Hospital, Dublin, Ireland
- Department of Histopathology and Morbid Anatomy, Trinity College Dublin, Dublin, Ireland
| | - Steven G Gray
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland.
- Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland.
- School of Biological Sciences, Dublin Institute of Technology, Dublin, Ireland.
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36
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O'Gorman P, Naimimohasses S, Monaghan A, Kennedy M, Melo AM, Ní Fhloinn D, Doherty DG, Beddy P, Finn SP, Moore JB, Gormley J, Norris S. Improvement in histological endpoints of MAFLD following a 12-week aerobic exercise intervention. Aliment Pharmacol Ther 2020; 52:1387-1398. [PMID: 32717123 DOI: 10.1111/apt.15989] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/03/2020] [Accepted: 07/01/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Lifestyle interventions are the primary treatment for metabolic (dysfunction) associated fatty liver disease (MAFLD). However, the histological and cardiometabolic effects of aerobic exercise in MAFLD remain unclear. AIMS To assess the effects of a 12-week aerobic exercise intervention on histological and cardiometabolic endpoints in MAFLD. METHODS Patients with biopsy-confirmed MAFLD participated in a 12-week aerobic exercise intervention. Liver histology, cardiorespiratory fitness (estimated V̇O2max ), physical activity, anthropometry and biochemical markers were assessed at baseline, intervention completion, and 12 and 52 weeks after intervention completion. RESULTS Twenty-four patients completed the exercise intervention (exercise group n = 16, control group n = 8). In the exercise group, 12 weeks of aerobic exercise reduced fibrosis and hepatocyte ballooning by one stage in 58% (P = 0.034) and 67% (P = 0.020) of patients, with no changes in steatosis (P = 1.000), lobular inflammation (P = 0.739) or NAFLD activity score (P = 0.172). Estimated V̇O2max increased by 17% compared to the control group (P = 0.027) but this level of improvement was not maintained at 12 or 52 weeks after the intervention. Patients with fibrosis and ballooning improvement increased estimated V̇O2max by 25% (P = 0.020) and 26% (P = 0.010), respectively. Anthropometric reductions including body mass (P = 0.038), waist circumference (P = 0.015) and fat mass (P = 0.007) were also observed, but no patient achieved 7%-10% weight loss. CONCLUSION This study highlights the potential benefits of a 12-week aerobic exercise intervention in improving histological endpoints of MAFLD. The development of strategies to ensure continued engagement in aerobic exercise in MAFLD are needed.
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Affiliation(s)
- Philip O'Gorman
- Discipline of Physiotherapy, Trinity College Dublin, Dublin, Ireland
| | - Sara Naimimohasses
- Department of Hepatology, St James's Hospital, Dublin, Ireland.,Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
| | - Ann Monaghan
- Discipline of Physiotherapy, Trinity College Dublin, Dublin, Ireland
| | - Megan Kennedy
- Discipline of Physiotherapy, Trinity College Dublin, Dublin, Ireland
| | - Ashanty M Melo
- Department of Immunology, Trinity College Dublin, Dublin, Ireland
| | - Deirdre Ní Fhloinn
- Department of Hepatology, St James's Hospital, Dublin, Ireland.,Department of Nutritional Sciences, University of Surrey, Surrey, UK
| | - Derek G Doherty
- Department of Immunology, Trinity College Dublin, Dublin, Ireland
| | - Peter Beddy
- Department of Radiology, St James's Hospital, Dublin, Ireland
| | - Stephen P Finn
- Department of Histopathology, St James's Hospital and Trinity College Dublin, Dublin, Ireland
| | | | - John Gormley
- Discipline of Physiotherapy, Trinity College Dublin, Dublin, Ireland
| | - Suzanne Norris
- Department of Hepatology, St James's Hospital, Dublin, Ireland.,Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
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37
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O'Gorman P, Naimimohasses S, Monaghan A, Kennedy M, Finn SP, Moore JB, Gormley J, Norris S. Letter: proving the benefit of exercise intervention in metabolic associated fatty liver disease-authors' reply. Aliment Pharmacol Ther 2020; 52:1426-1427. [PMID: 33105979 DOI: 10.1111/apt.16070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Affiliation(s)
- Philip O'Gorman
- Discipline of Physiotherapy, Trinity College Dublin, Dublin, Ireland
| | - Sara Naimimohasses
- Department of Hepatology, St James's Hospital, Dublin, Ireland.,Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
| | - Ann Monaghan
- Discipline of Physiotherapy, Trinity College Dublin, Dublin, Ireland
| | - Megan Kennedy
- Discipline of Physiotherapy, Trinity College Dublin, Dublin, Ireland
| | - Stephen P Finn
- Department of Histopathology, St James's Hospital and Trinity College Dublin, Dublin, Ireland
| | | | - John Gormley
- Discipline of Physiotherapy, Trinity College Dublin, Dublin, Ireland
| | - Suzanne Norris
- Department of Hepatology, St James's Hospital, Dublin, Ireland.,Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland
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38
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Hashim D, Gonzalez-Feliciano AG, Ahearn TU, Pettersson A, Barber L, Pernar CH, Ebot EM, Isikbay M, Finn SP, Giovannucci EL, Lis RT, Loda M, Parmigiani G, Lotan T, Kantoff PW, Mucci LA, Graff RE. Family history of prostate cancer and the incidence of ERG- and phosphatase and tensin homolog-defined prostate cancer. Int J Cancer 2020; 146:2694-2702. [PMID: 31318977 DOI: 10.1002/ijc.32577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 01/27/2019] [Revised: 06/18/2019] [Accepted: 06/28/2019] [Indexed: 01/08/2023]
Abstract
Family history is among the strongest known risk factors for prostate cancer (PCa). Emerging data suggest molecular subtypes of PCa, including two somatic genetic aberrations: fusions of androgen-regulated promoters with ERG and, separately, phosphatase and tensin homolog (PTEN) loss. We examined associations between family history and incidence of these subtypes in 44,126 men from the prospective Health Professionals Follow-up Study. ERG and PTEN status were assessed by immunohistochemistry. Multivariable competing risks models were used to estimate hazard ratios (HR) and 95% confidence intervals (CI) for associations between self-reported family history of PCa and molecular subtypes of disease. Thirteen percent of men had a positive family history of PCa at baseline. During a median follow-up of 18.5 years, 5,511 PCa cases were diagnosed. Among them, 888 were assayed for ERG status (47% ERG-positive) and 715 were assayed for PTEN loss (14% PTEN null). Family history was more strongly associated with risk of ERG-negative (HR: 2.15; 95% CI: 1.71-2.70) than ERG-positive (HR: 1.49; 95% CI: 1.13-1.95) disease (pheterogeneity : 0.04). The strongest difference was among men with an affected father (HRERG-negative : 2.09; 95% CI: 1.64-2.66; HRERG-positive : 1.30; 95% CI: 0.96-1.76; pheterogeneity : 0.01). Family history of PCa was positively associated with both PTEN null (HR: 2.10; 95% CI: 1.26-3.49) and PTEN intact (HR: 1.72; 95% CI: 1.39-2.13) PCa (pheterogeneity : 0.47). Our results indicate that PCa family history may be positively associated with PCa in all ERG and PTEN subtypes, suggesting a role of genetic susceptibility in their development. It is possible that ERG-negative disease could be especially associated with positive family history.
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Affiliation(s)
- Dana Hashim
- Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY
| | | | - Thomas U Ahearn
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA.,Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Andreas Pettersson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA.,Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Lauren Barber
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Claire H Pernar
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Ericka M Ebot
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Masis Isikbay
- Department of Surgery, University of California, San Francisco, San Francisco, CA
| | - Stephen P Finn
- Department of Histopathology, St. James's Hospital and Trinity College Dublin Medical School, Dublin, Ireland
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA.,Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Rosina T Lis
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Massimo Loda
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Giovanni Parmigiani
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Tamara Lotan
- Department of Pathology, Johns Hopkins Bayview Medical Center, Baltimore, MD
| | - Philip W Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA.,Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Rebecca E Graff
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA
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39
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Thunnissen E, Kerr KM, Dafni U, Bubendorf L, Finn SP, Soltermann A, Biernat W, Cheney R, Verbeken E, Warth A, Marchetti A, Speel EJM, Pokharel S, Quinn AM, Monkhorst K, Navarro A, Madsen LB, Tsourti Z, Geiger T, Kammler R, Peters S, Stahel RA. Programmed death-ligand 1 expression influenced by tissue sample size. Scoring based on tissue microarrays' and cross-validation with resections, in patients with, stage I-III, non-small cell lung carcinoma of the European Thoracic Oncology Platform Lungscape cohort. Mod Pathol 2020; 33:792-801. [PMID: 31740722 DOI: 10.1038/s41379-019-0383-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 11/08/2022]
Abstract
PD-L1, as assessed by immunohistochemistry, is a predictive biomarker for immuno-oncology treatment in lung cancer. Different scoring methods have been used to assess its status, resulting in a wide range of positivity rates. We use the European Thoracic Oncology Platform Lungscape non-small cell lung carcinoma cohort to explore this issue. PD-L1 expression was assessed via immunohistochemistry on tissue microarrays (up to four cores per case), using the DAKO 28-8 immunohistochemistry assay, following a two-round external quality assessment procedure. All samples were analyzed under the same protocol. Cross-validation of scoring between tissue microarray and whole sections was performed in 10% randomly selected samples. Cutoff points considered: ≥1, 50 (primarily), and 25%. At the two external quality assessment rounds, tissue microarray scoring agreement rates between pathologists were: 73% and 81%. There were 2008 cases with valid immunohistochemistry tissue microarray results (50% all cores evaluable). Concordant cases at 1, 25, and 50% were: 85, 91, and 93%. Tissue microarray core results were identical for 70% of cases. Sensitivity of the tissue microarray method for 1, 25, and 50% was: 80, 78, and 79% (specificity: 90, 95, 98%). Complete agreement between tissue microarrays and whole sections was achieved for 60% of the cases. Highest sensitivity rates for 1% and 50% cutoffs were detected for higher number of cores. Underestimation of PD-L1 expression on small samples is more common than overestimation. We demonstrated that classification of PD-L1 on small biopsy samples does not represent the overall expression of PD-L1 in all non-small cell cancer carcinoma cases, although the majority of cases are 'correctly' classified. In future studies, sampling more and larger biopsies, recording the biopsy size and tumor load may permit further refinement, increasing predictive accuracy.
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Affiliation(s)
- Erik Thunnissen
- Department of Pathology, Amsterdam University Medical Center, location VU University Medical Center, Amsterdam, Netherlands.
| | - Keith M Kerr
- Department of Pathology, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Urania Dafni
- Froniter Science Foundation-Hellas & National and Kapodistrian University of Athens, Athens, Greece
| | - Lukas Bubendorf
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Stephen P Finn
- Department of Histopathology, St James's Hospital and Trinity College, Dublin, Ireland
| | - Alex Soltermann
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Richard Cheney
- Department of Pathology, State University of New York at Buffalo, Buffalo, NY, USA
| | - Erik Verbeken
- Department of Pathology, University Hospital KU Leuven, Leuven, Belgium
| | - Arne Warth
- Department of Pathology, Universitätsklinikum Heidelberg, Heidelberg, Germany
- Institute of Pathology, Cytopathology, and Molecular Pathology MVZ UEGP Giessen, Wetzlar, Limburg, Germany
| | - Antonio Marchetti
- Center of Predicitve Predictive Molecular Medicine, CeSI, University of Chieti-Pescara, Chieti, Italy
| | - Ernst-Jan M Speel
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Saraswati Pokharel
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Anne Marie Quinn
- Wythenshawe Hospital, Department of Histopathology, Manchester University NHS Foundation Trust, Manchester, UK
| | - Kim Monkhorst
- Division of Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Atilio Navarro
- Department of Pathology, Consorcio Hospital General Universitario de Valencia, Valencia, Spain
| | - Line Bille Madsen
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Zoi Tsourti
- Frontier Science Foundation-Hellas & University of Athens, Athens, Greece
| | - Thomas Geiger
- Translational Research Coordination, European Thoracic Oncology Platform Coordinating Office, Bern, Switzerland
| | - Roswitha Kammler
- Translational Research Coordination, European Thoracic Oncology Platform Coordinating Office, Bern, Switzerland
| | - Solange Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Rolf A Stahel
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
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Allott EH, Ebot EM, Stopsack KH, Gonzalez-Feliciano AG, Markt SC, Wilson KM, Ahearn TU, Gerke TA, Downer MK, Rider JR, Freedland SJ, Lotan TL, Kantoff PW, Platz EA, Loda M, Stampfer MJ, Giovannucci E, Sweeney CJ, Finn SP, Mucci LA. Statin Use Is Associated with Lower Risk of PTEN-Null and Lethal Prostate Cancer. Clin Cancer Res 2020; 26:1086-1093. [PMID: 31754047 PMCID: PMC7056554 DOI: 10.1158/1078-0432.ccr-19-2853] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 08/29/2019] [Revised: 10/22/2019] [Accepted: 11/15/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Statins are associated with lower risk of aggressive prostate cancer, but lethal prostate cancer is understudied and contributing mechanisms are unclear. We prospectively examined statins and lethal prostate cancer risk in the Health Professionals Follow-up Study (HPFS), tested associations with molecular subtypes, and integrated gene expression profiling to identify putative mechanisms. EXPERIMENTAL DESIGN Our study included 44,126 men cancer-free in 1990, followed for prostate cancer incidence through 2014, with statin use recorded on biennial questionnaires. We used multivariable Cox regression to examine associations between statins and prostate cancer risk overall, by measures of clinically significant disease, and by ERG and PTEN status. In an exploratory analysis, age-adjusted gene set enrichment analysis identified statin-associated pathways enriched in tumor and adjacent normal prostate tissue. RESULTS During 24 years of follow-up, 6,305 prostate cancers were diagnosed and 801 (13%) were lethal (metastatic at diagnosis or metastatic/fatal during follow-up). Relative to never/past use, current statin use was inversely associated with risk of lethal prostate cancer [HR, 0.76; 95% confidence interval (CI), 0.60-0.96] but not overall disease. We found a strong inverse association for risk of PTEN-null cancers (HR, 0.40; 95% CI, 0.19-0.87) but not PTEN-intact cancers (HR, 1.18; 95% CI, 0.95-1.48; P heterogeneity = 0.01). Associations did not differ by ERG. Inflammation and immune pathways were enriched in normal prostate tissue of statin ever (n = 10) versus never users (n = 103). CONCLUSIONS Molecular tumor classification identified PTEN and inflammation/immune activation as potential mechanisms linking statins with lower lethal prostate cancer risk. These findings support a potential causal association and could inform selection of relevant biomarkers for statin clinical trials.
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Affiliation(s)
- Emma H Allott
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom.
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Ericka M Ebot
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Konrad H Stopsack
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Sarah C Markt
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Kathryn M Wilson
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Thomas U Ahearn
- National Cancer Institute, Division of Cancer Epidemiology and Genetics, Epidemiology and Biostatistics Program, Rockville, Maryland
| | - Travis A Gerke
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Mary K Downer
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Jennifer R Rider
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts
| | - Stephen J Freedland
- Cedars-Sinai Medical Center, Los Angeles, California
- Durham Veterans Affairs Medical Center, Durham, North Carolina
| | - Tamara L Lotan
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Philip W Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Meir J Stampfer
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Edward Giovannucci
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Christopher J Sweeney
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Stephen P Finn
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts.
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Ceraolo C, Gerke TA, Zareba P, Pettersson A, Stopsack KH, Chowdhury D, Ebot EM, Flavin R, Finn SP, Kantoff PW, Stampfer MJ, Loda M, Fiorentino M, Mucci LA. Tumor protein expression of BRCA1 and development of lethal prostate cancer. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.6_suppl.65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
65 Background: DNA repair genes including BRCA1 are commonly altered in metastatic prostate tumors. However, mutations and copy number aberrations in these genes are rare in primary tumors. Instead, preliminary studies suggest that higher tumor expression of the BRCA1 protein may be associated with worse prognosis. Methods: We undertook a prospective study of tumor BRCA1 protein expression and lethal prostate cancer among men with clinically localized prostate cancer in the Health Professionals Follow-up Study. We performed immunohistochemical staining for BRCA1 on tumor tissue microarrays using a validated antibody and scored expression as positive or negative. We also assessed tumor proliferation by immunostaining for Ki67, angiogenesis by immunostaining for CD34, and apoptosis using a TUNEL assay. Proportional hazards regression was used to evaluate the association between BRCA1 protein expression and development of lethal prostate cancer (metastasis or cancer-specific death). Results: Ten percent of tumors (60 of 589) stained positive for the BRCA1 protein. BRCA1-positive tumors were characterized by higher Gleason scores, a higher proliferative index, and a higher apoptotic index. During a median follow-up of 14.3 years, 18 men (34%) in the BRCA1-positive group and 74 men (14%) in the BRCA1-negative group developed lethal prostate cancer. There was a strong positive association between BRCA1 protein expression and lethal prostate cancer in both unadjusted analyses (HR 2.71, 95% CI 1.73–4.26) and after adjusting for clinical factors (HR 2.00, 95% CI 1.26–3.18). The positive association with BRCA1 protein expression was also independent of proliferation index. Conclusions: Primary prostate tumors expressing the BRCA1 protein have a highly proliferative phenotype and are more likely to progress to lethal disease, independent of its higher proliferative index. Assessing tumor protein expression of BRCA1 may help elucidate the Janus-faced role of DNA repair pathways in prostate cancer progression.[Table: see text]
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Affiliation(s)
- Carl Ceraolo
- Harvard University T H Chan School of Public Health, Cambridge, MA
| | | | - Piotr Zareba
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Stephen P. Finn
- St. James's Hospital and Trinity College Dublin, Cancer Molecular Diagnostics, Dublin, Ireland
| | - Philip W. Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Meir J. Stampfer
- Harvard T.H. Chan School of Public Health, Harvard Medical School, Brigham and Women's Hospital, Boston, MA
| | - Massimo Loda
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA
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Silva R, Moran B, Russell NM, Fahey C, Vlajnic T, Manecksha RP, Finn SP, Brennan DJ, Gallagher WM, Perry AS. Evaluating liquid biopsies for methylomic profiling of prostate cancer. Epigenetics 2020; 15:715-727. [PMID: 32000564 PMCID: PMC7574384 DOI: 10.1080/15592294.2020.1712876] [Citation(s) in RCA: 12] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background: Liquid biopsies offer significant potential for informing on cancer progression and therapeutic resistance via minimally invasive serial monitoring of genetic alterations. Although the cancer epigenome is a central driving force in most neoplasia, the accuracy of monitoring the tumor methylome using liquid biopsies remains relatively unknown. Objectives: to investigate how well two types of liquid biopsy (urine and blood) capture the prostate cancer methylome, and may thus serve as a non-invasive surrogate for studying the tumor epigenome. Methods: A cohort of four metastatic treatment naïve prostate cancer (PCa) patients was selected. Matched biopsy cores (tumor and histologically matched-normal), post-DRE, pre-biopsy urine, and peripheral blood plasma were available for each subject. DNA methylation was profiled utilizing the Infinium® MethylationEPIC BeadChip (Illumina) and analysed using the RnBeads software. Significantly (FDR adjusted P < 0.05) differentially methylated probes (DMPs) between tumor and MN were identified and examined in the liquids (done at a grouped and individual subject level). Results: DNA methylation analysis of urine and blood in men with metastatic PCa showed highly correlated patterns between the different liquid types (ρ = 0.93, P < 0.0001), with large contributions from non-tumor sources. DNA methylation profiles of liquids were more similar between subjects, than intra-individual liquid-tumor correlations. Overall, both urine and plasma are viable surrogates for tumor tissue biopsies, capturing up to 39.40% and 64.14% of tumor-specific methylation alterations, respectively. Conclusion: We conclude that both urine and blood plasma are easily accessible and sensitive biofluids for the study of PCa epigenomic alterations.
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Affiliation(s)
- Romina Silva
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin, Ireland.,School of Medicine, University College Dublin , Dublin, Ireland
| | - Bruce Moran
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin, Ireland.,Ireland East Hospital Group (IEHG), St. Vincent's University Hospital , Dublin, Ireland
| | - Niamh M Russell
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin, Ireland.,School of Biomolecular and Biomedical Science, University College Dublin , Dublin, Ireland
| | - Ciara Fahey
- Prostate Molecular Oncology, Trinity Translational Medicine Institute, Trinity College Dublin , Dublin, Ireland
| | - Tatjana Vlajnic
- Department of Histopathology, St James's Hospital , Dublin, Ireland.,Institute of Pathology, University Hospital Basel , Basel, Switzerland
| | - Rustom P Manecksha
- Department of Urology, St. James's Hospital and Trinity College Dublin , Dublin, Ireland
| | - Stephen P Finn
- Department of Histopathology, St James's Hospital , Dublin, Ireland
| | - Donal J Brennan
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin, Ireland.,School of Medicine, University College Dublin , Dublin, Ireland
| | - William M Gallagher
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin, Ireland.,School of Biomolecular and Biomedical Science, University College Dublin , Dublin, Ireland
| | - Antoinette S Perry
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin , Dublin, Ireland.,Prostate Molecular Oncology, Trinity Translational Medicine Institute, Trinity College Dublin , Dublin, Ireland.,School of Biology and Environmental Science, University College Dublin , Dublin, Ireland
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Sheill G, Brady L, Guinan EM, Hussey JM, Hayes B, Baird AM, Stanfill B, Casey O, Murphy V, Rudman SM, Peat N, Sheils O, Cahill F, Van Hemelrijck M, McCaffrey J, O'Donnell DM, Mucci L, Grogan W, McDermott R, Finn SP. A randomized trial of exercise on quality of life in men with metastatic prostate cancer: The ExPeCT Trial. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.31_suppl.97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
97 Background: All patients living with cancer, including those with metastatic cancer, are encouraged to be physically active. This paper examines the feasibility of an aerobic exercise intervention for men with metastatic prostate cancer. Methods: ExPeCT (Exercise, Prostate Cancer and Circulating Tumour Cells), was a multi-centre randomised control trial for men living with metastatic prostate cancer. Participants were randomized to either control or exercise arms. Participants in the exercise arm completed six- months of prescribed aerobic exercise. Quality of life assessments were completed at baseline, at 3 months and at 6 months using a standardised questionnaire derived from the Harvard Health Professionals Follow-up study. Physical activity was measured using a self-administered physical activity questionnaire. Exercise adherence data was collected via Polar heart rate monitors, worn by the patient for every exercise session undertaken. Results: A total of 61 patients were included (69.4±7.3 yr, Body Mass Index 29.2±5.8 kg/m2). The median time since diagnosis was 34 months (IQR 7-54). A total of 35 (55%) of participants had >1 region affected by metastatic disease. A total of 54 (81%) of participants completed the 3 month assessment and 52 (78%) of the participants completed the 6 month assessment. Adherence to the supervised sessions was 83% (329 out of 396 sessions attended). Participants were adherent to both the intensity (82%) and duration (83%) of the prescribed exercise programme during class sessions. No adverse events were reported by participants enrolled in this study. There was no significant difference in physical activity levels, sedentary time or quality of life between either group at baseline, 3 months or 6 months. Systolic blood pressure was significantly lower in the exercise group when compared to the control group at 3 months (p=.008) and 6 months (p=.011). Conclusions: The exercise intervention was tolerated well by a group of patients with a high burden of metastatic prostate cancer however did not lead to change in physical activity levels or quality of life. This trial provides proof of principle evidence for future exercise studies involving this patient group. Clinical trial information: NCT02453139.
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Affiliation(s)
| | - Lauren Brady
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | | | | | - Brian Hayes
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Department of Histopathology, Cork University Hospital, Wilton, Cork, Ireland
| | | | | | | | | | | | - Nicola Peat
- Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Orla Sheils
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Fidelma Cahill
- King’s College London, Division of Cancer Studies, Cancer Epidemiology Group, London, United Kingdom
| | - Mieke Van Hemelrijck
- King’s College London, Division of Cancer Studies, Cancer Epidemiology Group, London, United Kingdom
| | - John McCaffrey
- Mater Misericordiae University Hospital, Dublin, Ireland
| | | | | | - William Grogan
- Department of Medical Oncology, Beaumont Hospital, Dublin, Ireland
| | - Ray McDermott
- Department of Oncology, Tallaght University Hospital, Dublin, Ireland
| | - Stephen P. Finn
- St. James's Hospital and Trinity College Dublin, Cancer Molecular Diagnostics, Dublin, Ireland
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Greene J, Baird AM, Casey O, Brady L, Blackshields G, Lim M, O'Brien O, Gray SG, McDermott R, Finn SP. Circular RNAs are differentially expressed in prostate cancer and are potentially associated with resistance to enzalutamide. Sci Rep 2019; 9:10739. [PMID: 31341219 PMCID: PMC6656767 DOI: 10.1038/s41598-019-47189-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [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] [Received: 09/03/2018] [Accepted: 07/04/2019] [Indexed: 12/19/2022] Open
Abstract
Most forms of castration-resistant prostate cancer (CRPC) are dependent on the androgen receptor (AR) for survival. While, enzalutamide provides a substantial survival benefit, it is not curative and many patients develop resistance to therapy. Although not yet fully understood, resistance can develop through a number of mechanisms, such as AR copy number gain, the generation of splice variants such as AR-V7 and mutations within the ligand binding domain (LBD) of the AR. circular RNAs (circRNAs) are a novel type of non-coding RNA, which can regulate the function of miRNA, and may play a key role in the development of drug resistance. circRNAs are highly resistant to degradation, are detectable in plasma and, therefore may serve a role as clinical biomarkers. In this study, AR-V7 expression was assessed in an isogenic model of enzalutamide resistance. The model consisted of age matched control cells and two sub-line clones displaying varied resistance to enzalutamide. circRNA profiling was performed on the panel using a high throughout microarray assay. Bioinformatic analysis identified a number of differentially expressed circRNAs and predicted five miRNA binding sites for each circRNA. miRNAs were stratified based on known associations with prostate cancer, and targets were validated using qPCR. Overall, circRNAs were more often down regulated in resistant cell lines compared with control (588 vs. 278). Of particular interest was hsa_circ_0004870, which was down-regulated in enzalutamide resistant cells (p ≤ 0.05, vs. sensitive cells), decreased in cells that highly express AR (p ≤ 0.01, vs. AR negative), and decreased in malignant cells (p ≤ 0.01, vs. benign). The associated parental gene was identified as RBM39, a member of the U2AF65 family of proteins. Both genes were down-regulated in resistant cells (p < 0.05, vs. sensitive cells). This is one of the first studies to profile and demonstrate discrete circRNA expression patterns in an enzalutamide resistant cell line model of prostate cancer. Our data suggests that hsa_circ_0004870, through RBM39, may play a critical role in the development of enzalutamide resistance in CRPC.
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Affiliation(s)
- John Greene
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College Dublin, Dublin 8, Ireland. .,Department of Medical Oncology, Tallaght Hospital, Dublin 24, Ireland.
| | - Anne-Marie Baird
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College Dublin, Dublin 8, Ireland.,Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's Hospital, Dublin 8, Ireland.,Department of Clinical Medicine, Trinity College Dublin, Dublin 2, Ireland.,Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Orla Casey
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Lauren Brady
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Gordon Blackshields
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College Dublin, Dublin 8, Ireland
| | - Marvin Lim
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College Dublin, Dublin 8, Ireland.,Department of Medical Oncology, Tallaght Hospital, Dublin 24, Ireland
| | | | - Steven G Gray
- Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's Hospital, Dublin 8, Ireland.,Department of Clinical Medicine, Trinity College Dublin, Dublin 2, Ireland.,Labmed Directorate, St. James's Hospital, Dublin 8, Ireland.,HOPE Directorate, St. James's Hospital, Dublin 8, Ireland
| | - Raymond McDermott
- Department of Medical Oncology, Tallaght Hospital, Dublin 24, Ireland.,Department of Histopathology, St. James's Hospital, Dublin 8, Ireland.,Department of Medical Oncology, St. Vincent's Hospital, Dublin 4, Ireland
| | - Stephen P Finn
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College Dublin, Dublin 8, Ireland.,Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's Hospital, Dublin 8, Ireland.,Department of Clinical Medicine, Trinity College Dublin, Dublin 2, Ireland.,Department of Histopathology, St. James's Hospital, Dublin 8, Ireland
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Kerr KM, Thunnissen E, Dafni U, Finn SP, Bubendorf L, Soltermann A, Verbeken E, Biernat W, Warth A, Marchetti A, Speel EJM, Pokharel S, Quinn AM, Monkhorst K, Navarro A, Madsen LB, Radonic T, Wilson J, De Luca G, Gray SG, Cheney R, Savic S, Martorell M, Muley T, Baas P, Meldgaard P, Blackhall F, Dingemans AM, Dziadziuszko R, Vansteenkiste J, Weder W, Polydoropoulou V, Geiger T, Kammler R, Peters S, Stahel R. A retrospective cohort study of PD-L1 prevalence, molecular associations and clinical outcomes in patients with NSCLC: Results from the European Thoracic Oncology Platform (ETOP) Lungscape Project. Lung Cancer 2019; 131:95-103. [PMID: 31027705 DOI: 10.1016/j.lungcan.2019.03.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [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: 07/16/2018] [Revised: 01/10/2019] [Accepted: 03/14/2019] [Indexed: 01/10/2023]
Abstract
INTRODUCTION The PD-L1 biomarker is an important factor in selecting patients with non-small cell lung cancer for immunotherapy. While several reports suggest that PD-L1 positivity is linked to a poor prognosis, others suggest that PD-L1 positive status portends a good prognosis. METHODS PD-L1 positivity prevalence, assessed via immunohistochemistry (IHC) on tissue microarrays (TMAs), and its association with clinicopathological characteristics, molecular profiles and patient outcome- Relapse-free Survival (RFS), Time-to-Relapse (TTR) and Overall Survival (OS)- is explored in the ETOP Lungscape cohort of stage I-III non-small cell lung cancer (NSCLC). Tumors are considered positive if they have ≥1/5/25/50% neoplastic cell membrane staining. RESULTS PD-L1 expression was assessed in 2182 NSCLC cases (2008 evaluable, median follow-up 4.8 years, 54.6% still alive), from 15 ETOP centers. Adenocarcinomas represent 50.9% of the cohort (squamous cell: 42.4%). Former smokers are 53.7% (current: 31.6%, never: 10.5%). PD-L1 positivity prevalence is present in more than one third of the Lungscape cohort (1%/5% cut-offs). It doesn't differ between adenocarcinomas and squamous cell histologies, but is more frequently detected in higher stages, never smokers, larger tumors (1/5/25% cut-offs). With ≥1% cut-off it is significantly associated with IHC MET overexpression, expression of PTEN, EGFR and KRAS mutation (only for adenocarcinoma). Results for 5%, 25% and 50% cut-offs were similar, with MET being significantly associated with PD-L1 positivity both for AC (p < 0.001, 5%/25%/50% cut-offs) and SCC (p < 0.001, 5% & 50% cut-offs and p = 0.0017 for 25%). When adjusting for clinicopathological characteristics, a significant prognostic effect was identified in adenocarcinomas (adjusted p-values: 0.024/0.064/0.063 for RFS/TTR/OS 1% cut-off, analogous for 5%/25%, but not for 50%). Similar results obtained for the model including all histologies, but no effect was found for the squamous cell carcinomas. CONCLUSION PD-L1 positivity, when adjusted for clinicopathological characteristics, is associated with a better prognosis for non-metastatic adenocarcinoma patients.
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Affiliation(s)
- Keith M Kerr
- Department of Pathology, Aberdeen Royal Infirmary, Aberdeen, United Kingdom.
| | - Erik Thunnissen
- Department of Pathology, VU University Medical Center, Amsterdam, Netherlands
| | - Urania Dafni
- Froniter Science Foundation-Hellas & University of Athens, Athens, Greece
| | - Stephen P Finn
- Department of Histopathology, St James's Hospital and Trinity College, Dublin, Ireland
| | - Lukas Bubendorf
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Alex Soltermann
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Eric Verbeken
- Department of Pathology, University Hospital KU Leuven, Leuven, Belgium
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Arne Warth
- Department of Pathology, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Antonio Marchetti
- Center of Predicitve Predictive Molecular Medicine, CeSI, University of Chieti-Pescara, Chieti, Italy
| | - Ernst-Jan M Speel
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Sarawati Pokharel
- Department of Pathology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Anne Marie Quinn
- Wythenshawe Hospital, Department of Histopathology, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Kim Monkhorst
- Division of Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Atilio Navarro
- Department of Pathology, Consorcio Hospital General Universitario de Valencia, Valencia, Spain
| | - Line Bille Madsen
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Teodora Radonic
- Department of Pathology, VU University Medical Center, Amsterdam, Netherlands
| | - Joan Wilson
- Department of Pathology, Aberdeen Royal Infirmary, Aberdeen, United Kingdom
| | - Graziano De Luca
- Center of Predicitve Predictive Molecular Medicine, CeSI, University of Chieti-Pescara, Chieti, Italy
| | - Steven G Gray
- Department of Clinical Medicine, St James's Hospital and Trinity College Dublin, Dublin, Ireland
| | - Richard Cheney
- Department of Pathology, State University of New York at Buffalo, Buffalo, NY, USA
| | - Spasenija Savic
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Miguel Martorell
- Department of Pathology, Consorcio Hospital General Universitario de Valencia, Valencia, Spain
| | - Thomas Muley
- Translational Research Unit, Thoraxklinik, University Hospital of Heidelberg, and Translational Lung Research Center (TLRC) Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
| | - Paul Baas
- Department of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Peter Meldgaard
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Fiona Blackhall
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Anne-Marie Dingemans
- Department of Pulmonology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Rafal Dziadziuszko
- Department of Oncology and Radiotherapy, Medical University of Gdansk, Gdansk, Poland
| | - Johan Vansteenkiste
- Department of Respiratory Oncology, University Hospital KU Leuven, Leuven, Belgium
| | - Walter Weder
- Department of Thoracic Surgery, University Hospital Zurich, Zurich, Switzerland
| | | | - Thomas Geiger
- Translational Research Coordination, ETOP Coordinating Office, Bern, Switzerland
| | - Roswitha Kammler
- Translational Research Coordination, ETOP Coordinating Office, Bern, Switzerland
| | - Solange Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Rolf Stahel
- Clinic of Oncology, University Hospital Zurich, Zurich, Switzerland
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Greene JP, Lim MCJ, Baird AM, Deignan O, McCaffrey J, Prior LM, Parker I, Bowes A, Teiserskiene A, Feeney J, Thirion PG, Finn SP, Kelly PJ, McDermott R. An updated analysis evaluating skeletal related events (SREs) in CTRIAL-IE 13-21: Phase II trial of radium-223 (R223) in combination with enzalutamide (ENZA) for patients (pts) with metastatic castration-resistant prostate cancer (mCRPC). J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.7_suppl.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
215 Background: This phase II single arm study, previously reported on the safety and tolerability of the combination of R223 and ENZA in pts with mCRPC. R223 in combination with ENZA was well tolerated with acceptable safety and toxicity profiles. Methods: This study enrolled pts with mCRPC to bone with or without visceral/lymph node involvement progressing on ADT. Pts received 6 cycles of R223 (55 kBq/kg IV Q4W) in combination with ENZA (160mg/day), followed by ENZA alone. Bone health agents were initiated as per treating clinician choice. SREs were defined as: a pathologic fracture, spinal cord compression (SCC), necessity for external beam radiation (EBRT) or surgery to bone. SREs during the combination period and after completion of R223 are reported here. An unplanned retrospective analysis of all scans performed on each patient for any fracture was performed and is included. Results: From July 2015 to July 2017, 45 pts were enrolled. 42 pts (93.3%) received all 6 cycles of combination therapy. 16 pts (35.5%) remain on ENZA alone. In total, 6 pts (13.3%) had SREs. 4 developed pathological fractures (femur = 1, vertebrae = 3) while 3 had EBRT for pain. Of these 6 pts, 2 developed SCC requiring EBRT. The average time from starting R223 to SRE was 615 days. 2/6 pts were not receiving bone protection. One pt who developed a pathological fracture has subsequently died related to progressive disease (time to death = 292 days). In the retrospective analysis, 4 pts (8.8%) developed fractures which were associated with a history of trauma (radius = 1, tibia = 1 ribs = 2). 11 pts (24.4%) developed asymptomatic insufficiency fractures (ankle = 1, femur = 1, sacrum = 2, vertebrae = 4, ribs = 4). The average time to insufficiency fracture was 354 days. No interventions were required. The majority of pts (75.5%) on the study were receiving bone health agents. Conclusions: SREs were in keeping with previously published data. In an unplanned retrospective analysis, there was a higher incidence of asymptomatic insufficiency fractures in this cohort of patients, however no interventions were required. Clinical trial information: NCT02225704.
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Affiliation(s)
| | | | | | | | - John McCaffrey
- Mater Misericordiae University Hospital, Dublin, Ireland
| | | | - Imelda Parker
- Mater Misericordiae University Hospital, Dublin, Ireland
| | | | | | - John Feeney
- Adelaide and Meath Hospital, Dublin, Ireland
| | | | - Stephen P. Finn
- St. James's Hospital and Trinity College Dublin, Cancer Molecular Diagnostics, Dublin, Ireland
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Brady L, Hayes B, Sheill G, Baird AM, Guinan EM, Stanfill B, Vlajnic T, Casey O, Greene JP, Allott E, Hussey JM, Cahill F, Van Hemelrijck M, Peat N, Rudman SM, Mucci L, Sheils O, John O, McDermott R, Finn SP. The effect of a structured exercise intervention on CTCs and platelet cloaking in patients with metastatic prostate cancer. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.7_suppl.243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
243 Background: Physical activity has been described as an effective adjunct for improving quality of life in patients with metastatic prostate cancer (PrCa). Circulating tumor cells (CTCs) are a morphologically distinct set of cancer cells, involved in disease progression. Platelet cloaking, the surrounding and subsequent attachment of platelets to CTCs, has been proposed as effective in aiding extravasation, thus enhancing metastatic spread. The ExPeCT (Exercise, Prostate Cancer and Circulating Tumor Cells) trial aimed to examine the impact of a structured exercise intervention on the mechanisms of metastasis, including CTC cloaking, in patients with metastatic PrCa. Methods: ExPeCT was a multi-center, randomized trial for patients with metastatic PrCa (n=61). Participants were randomized to either control or exercise arms. Participants in the exercise arm (n=29) completed six months of prescribed aerobic exercise. Whole blood was collected for all participants at baseline (T0), three months (T3) and six months (T6), and analyzed for the presence of CTCs, CTC clusters and platelet cloaking. Results: No significant difference in CTC number between the exercise and control arms was observed (p=0.2630), however significant alterations in CTC number were observed within group over time (p<0.001). Platelet cloaking was modelled as a binary response (presence/absence). A trend towards higher levels of platelet cloaking in the control group was observed (p=0.1005). Further, all findings were compared to a range of clinical variables. CTC clusters were positively correlated with PSA levels (p=0.0393) and a positive correlation between CTC number and white blood cell count (p<0.001) was determined. Conclusions: No significant relationship between CTCs and physical activity was observed, however the exercise program was well tolerated by ExPeCT participants. This study has, for the first time, shown platelet cloaking of CTCs in metastatic PrCa, in addition to a significant positive correlation between CTCs and white blood cells. These findings provide critical insight into immune crosstalk and the metastatic cascade in metastatic PrCa. Clinical trial information: NCT02453139.
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Affiliation(s)
- Lauren Brady
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Brian Hayes
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin,Department of Histopathology, Cork University Hospital, Wilton, Cork, Cork, Ireland
| | | | | | | | | | - Tatjana Vlajnic
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | | | | | - Emma Allott
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, 8 Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Northern Ireland, Belfast, United Kingdom
| | | | - Fidelma Cahill
- King’s College London, Division of Cancer Studies, Cancer Epidemiology Group, London, United Kingdom
| | - Mieke Van Hemelrijck
- King’s College London, Division of Cancer Studies, Cancer Epidemiology Group, London, United Kingdom
| | - Nicola Peat
- Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | | | | | - Orla Sheils
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - O'Leary John
- Department of Histopathology, St James's Hospital, Dublin, Ireland
| | | | - Stephen P. Finn
- St. James's Hospital and Trinity College Dublin, Cancer Molecular Diagnostics, Dublin, Ireland
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O'Brien O, Wright MC, O'Brien C, Geoghegan O, Leonard N, Nicholson S, Cuffe S, Fabre A, Jochum W, Joerger M, Gray SG, Finn SP. Cost-Efficient and Easy to Perform PCR-Based Assay to Identify Met Exon 14 Skipping in Formalin-Fixed Paraffin-Embedded (FFPE) Non-Small Cell Lung Cancer (NSCLC) Samples. Diagnostics (Basel) 2019; 9:diagnostics9010013. [PMID: 30669306 PMCID: PMC6468531 DOI: 10.3390/diagnostics9010013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 11/23/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 01/03/2023] Open
Abstract
MET is a receptor tyrosine kinase (RTK) that plays important roles in carcinogenesis. Despite being frequently overexpressed in cancer, clinical responses to targeting this receptor have been limited. Recently novel splicing mutations involving the loss of exon 14 (called METex14 skipping) have emerged as potential biomarkers to predict for responsiveness to targeted therapies with Met inhibitors in non-small cell lung cancer (NSCLC). Currently, the diverse genomic alterations responsible for METex14 skipping pose a challenge for routine clinical diagnostic testing. In this report, we examine three different methodologies to detect METex14 and assess their potential utility for use as a diagnostic assay for both the identification of METex14 and intra-tumoural distribution in NSCLC.
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Affiliation(s)
- Odharnaith O'Brien
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, D08 W9RT Dublin, Ireland.
- Department of Histopathology, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
| | - Mark C Wright
- Department of Histopathology, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
| | - Cathal O'Brien
- Cancer Molecular Diagnostics, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
| | - Orla Geoghegan
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, D08 W9RT Dublin, Ireland.
| | - Niamh Leonard
- Department of Histopathology, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
| | - Siobhan Nicholson
- Department of Histopathology, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
| | - Sinéad Cuffe
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, D08 W9RT Dublin, Ireland.
- HOPE Directorate, St. James's Hospital, D08 RT2X Dublin, Ireland.
| | - Aurelie Fabre
- Department of Pathology, St. Vincent's University Hospital, University College Dublin School of Medicine, D04 T6F4 Dublin, Ireland.
| | - Wolfram Jochum
- Department of Pathology, Cantonal Hospital, 9007 St. Gallen, Switzerland.
| | - Markus Joerger
- Department of Medical Oncology & Hematology, Cantonal Hospital, 9007 St. Gallen, Switzerland.
| | - Steven G Gray
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, D08 W9RT Dublin, Ireland.
- Department of Clinical Medicine, Trinity College Dublin, D02 PN40 Dublin, Ireland.
- School of Biological Sciences, Dublin Institute of Technology, D08 NF82 Dublin, Ireland.
| | - Stephen P Finn
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, D08 W9RT Dublin, Ireland.
- Department of Histopathology, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
- Cancer Molecular Diagnostics, Labmed Directorate, St. James's Hospital, D08 RX0X Dublin, Ireland.
- Department of Histopathology and Morbid Anatomy, Trinity College Dublin, D08 X4RX Dublin, Ireland.
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Rulle U, Tsourti Z, Casanova R, Deml KF, Verbeken E, Thunnissen E, Warth A, Cheney R, Sejda A, Speel EJ, Madsen LB, Nonaka D, Navarro A, Sansano I, Marchetti A, Finn SP, Monkhorst K, Kerr KM, Haberecker M, Wu C, Zygoura P, Kammler R, Geiger T, Gendreau S, Schulze K, Vrugt B, Wild P, Moch H, Weder W, Ciftlik AT, Dafni U, Peters S, Bubendorf L, Stahel RA, Soltermann A. Computer-Based Intensity Measurement Assists Pathologists in Scoring Phosphatase and Tensin Homolog Immunohistochemistry — Clinical Associations in NSCLC Patients of the European Thoracic Oncology Platform Lungscape Cohort. J Thorac Oncol 2018; 13:1851-1863. [DOI: 10.1016/j.jtho.2018.08.2034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 07/16/2018] [Accepted: 08/02/2018] [Indexed: 12/31/2022]
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50
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Pernar CH, Ebot EM, Pettersson A, Graff RE, Giunchi F, Ahearn TU, Gonzalez-Feliciano AG, Markt SC, Wilson KM, Stopsack KH, Gazeeva E, Lis RT, Parmigiani G, Rimm EB, Finn SP, Giovannucci EL, Fiorentino M, Mucci LA. A Prospective Study of the Association between Physical Activity and Risk of Prostate Cancer Defined by Clinical Features and TMPRSS2:ERG. Eur Urol 2018; 76:33-40. [PMID: 30301696 DOI: 10.1016/j.eururo.2018.09.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 05/21/2018] [Accepted: 09/21/2018] [Indexed: 01/07/2023]
Abstract
BACKGROUND Growing evidence shows that clinical and molecular subtypes of prostate cancer (PCa) have specific risk factors. Observational studies suggest that physical activity may lower the risk of aggressive PCa. To our knowledge, the association between physical activity and PCa defined by TMPRSS2:ERG has not been evaluated. OBJECTIVE To prospectively examine the association between physical activity and risk of PCa defined by clinical features and TMPRSS2:ERG. DESIGN, SETTING, AND PARTICIPANTS We studied 49160 men aged 40-75 yr in the Health Professionals Follow-up Study from 1986 to 2012. Data was collected at baseline and every 2 yr with >90% follow-up. Total and vigorous physical activity were measured in metabolic equivalent of task (MET)-h/wk. OUTCOME MEASURES AND STATISTICAL ANALYSIS Advanced PCa was defined as stage T3b, T4, N1, or M1 at diagnosis and lethal PCa as distant metastases or death due to disease over follow-up. Presence of TMPRSS2:ERG was estimated by immunohistochemistry of ERG protein expression. Cox proportional hazards models were used to obtain multivariable hazard ratios (HRs) and 95% confidence intervals (CIs) for incidence of subtype-specific PCa. RESULTS AND LIMITATIONS During 26 yr of follow-up, 6411 developed PCa overall and 888 developed lethal disease. There were no significant associations between total physical activity and risk of PCa in the overall cohort. In multivariable-adjusted models, men in the highest quintile of vigorous activity had a significant 30% lower risk of advanced PCa (HR: 0.70, 95% CI: 0.53-0.92) and 25% lower risk of lethal PCa (HR: 0.75, 95% CI: 0.59-0.94) than men in the lowest quintile of vigorous activity. The association was independent of screening history. Vigorous activity was not associated with total PCa in the overall cohort but was inversely associated among highly screened men (top vs bottom quintile, HR: 0.83, 95% CI: 0.70-0.97). Of all cases, 945 were assayed for ERG (48% ERG-positive). Men with higher vigorous activity had a lower risk of ERG-positive PCa (top vs bottom quintile, HR: 0.71, 95% CI: 0.52-0.97). There was no significant association with the risk of ERG-negative disease (p heterogeneity=0.09). CONCLUSIONS Our study confirms that vigorous physical activity is associated with lower risk of advanced and lethal PCa and provides novel evidence for a lower risk of TMPRSS2:ERG-positive disease. PATIENT SUMMARY The identification of modifiable lifestyle factors for prevention of clinically important prostate cancer (PCa) is needed. In this report, we compared risk of PCa in men with different levels of physical activity. Men with higher vigorous activity had a lower risk of developing advanced and lethal PCa and PCa with the common TMPRSS2:ERG gene fusion.
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Affiliation(s)
- Claire H Pernar
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Ericka M Ebot
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andreas Pettersson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Rebecca E Graff
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Francesca Giunchi
- Pathology Unit, Addarii Institute, S. Orsola-Malpighi Hospital, Bologna, Italy
| | - Thomas U Ahearn
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Sarah C Markt
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Kathryn M Wilson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Konrad H Stopsack
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizaveta Gazeeva
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rosina T Lis
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Giovanni Parmigiani
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Eric B Rimm
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stephen P Finn
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Histopathology, Trinity College, Dublin, Ireland
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Michelangelo Fiorentino
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Pathology Unit, Addarii Institute, S. Orsola-Malpighi Hospital, Bologna, Italy; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lorelei A Mucci
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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