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Lafront C, Germain L, Audet-Walsh É. Bulk mRNA-seq data from wild-type and prostate cancer-developing mice reveal a reprogramming of the estrogen and androgen responses after carcinogenesis. Data Brief 2024; 57:110870. [PMID: 39290430 PMCID: PMC11405909 DOI: 10.1016/j.dib.2024.110870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/16/2024] [Accepted: 08/19/2024] [Indexed: 09/19/2024] Open
Abstract
Sex hormones are necessary for the development and functions of the normal prostate as well as for the initiation and progression of prostate tumors. Indeed, androgens and estrogens can activate their respective nuclear receptors to modulate the expression of multiple genes and pathways in prostate cells. Nevertheless, the androgen and estrogen responses in the normal prostate, and the transcriptomic changes occurring after carcinogenesis, remain poorly understood. Here, wildtype mice and transgenic mice that spontaneously develop prostate cancer (C57BL/6J PB-Cre4+/-;Pten fl/fl) were castrated to ensure hormone deprivation. After three days, animals received injections of testosterone and/or estradiol. After one day, the prostates were harvested, and RNA was purified for sequencing. Sequencing data were then analyzed to study transcriptional modulations following hormonal exposures in normal and tumoral murine prostates. New analyses can be carried out with specific fold-change thresholds for gene expression, or with different pair-wise combinations between conditions (treatments and/or mouse models). Together, the data generated herein are a useful tool to study hormonal transcriptional responses in prostate and prostate cancer biology.
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Affiliation(s)
- Camille Lafront
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Québec City, Québec, Canada
- Endocrinology - Nephrology Division of Centre de recherche du CHU de Québec - Université Laval, Québec City, Québec, Canada
- Centre de recherche sur le cancer de l'Université Laval, Québec City, Québec, Canada
| | - Lucas Germain
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Québec City, Québec, Canada
- Endocrinology - Nephrology Division of Centre de recherche du CHU de Québec - Université Laval, Québec City, Québec, Canada
- Centre de recherche sur le cancer de l'Université Laval, Québec City, Québec, Canada
| | - Étienne Audet-Walsh
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Québec City, Québec, Canada
- Endocrinology - Nephrology Division of Centre de recherche du CHU de Québec - Université Laval, Québec City, Québec, Canada
- Centre de recherche sur le cancer de l'Université Laval, Québec City, Québec, Canada
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2
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Geng K, Merino LG, Veiga RG, Sommerauer C, Epperlein J, Brinkman EK, Kutter C. Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles. Life Sci Alliance 2024; 7:e202302128. [PMID: 37984988 PMCID: PMC10662290 DOI: 10.26508/lsa.202302128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
The CRISPR-Cas9 system is a powerful tool for studying gene functions and holds potential for disease treatment. However, precise genome editing requires thorough assessments to minimize unintended on- and off-target effects. Here, we report an unexpected 283-kb deletion on Chromosome 10 (10q23.31) in chronic myelogenous leukemia-derived HAP1 cells, which are frequently used in CRISPR screens. The deleted region encodes regulatory genes, including PAPSS2, ATAD1, KLLN, and PTEN We found that this deletion was not a direct consequence of CRISPR-Cas9 off-targeting but rather occurred frequently during the generation of CRISPR-Cas9-modified cells. The deletion was associated with global changes in histone acetylation and gene expression, affecting fundamental cellular processes such as cell cycle and DNA replication. We detected this deletion in cancer patient genomes. As in HAP1 cells, the deletion contributed to similar gene expression patterns among cancer patients despite interindividual differences. Our findings suggest that the unintended deletion of 10q23.31 can confound CRISPR-Cas9 studies and underscore the importance to assess unintended genomic changes in CRISPR-Cas9-modified cells, which could impact cancer research.
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Affiliation(s)
- Keyi Geng
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Lara G Merino
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Raül G Veiga
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Christian Sommerauer
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Janine Epperlein
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Eva K Brinkman
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Claudia Kutter
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
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3
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Martinez TC, McNerney ME. Haploinsufficient Transcription Factors in Myeloid Neoplasms. ANNUAL REVIEW OF PATHOLOGY 2024; 19:571-598. [PMID: 37906947 DOI: 10.1146/annurev-pathmechdis-051222-013421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Many transcription factors (TFs) function as tumor suppressor genes with heterozygous phenotypes, yet haploinsufficiency generally has an underappreciated role in neoplasia. This is no less true in myeloid cells, which are normally regulated by a delicately balanced and interconnected transcriptional network. Detailed understanding of TF dose in this circuitry sheds light on the leukemic transcriptome. In this review, we discuss the emerging features of haploinsufficient transcription factors (HITFs). We posit that: (a) monoallelic and biallelic losses can have distinct cellular outcomes; (b) the activity of a TF exists in a greater range than the traditional Mendelian genetic doses; and (c) how a TF is deleted or mutated impacts the cellular phenotype. The net effect of a HITF is a myeloid differentiation block and increased intercellular heterogeneity in the course of myeloid neoplasia.
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Affiliation(s)
- Tanner C Martinez
- Department of Pathology, Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, USA;
- Medical Scientist Training Program, The University of Chicago, Chicago, Illinois, USA
| | - Megan E McNerney
- Department of Pathology, Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, USA;
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4
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Varshavsky A, Lewis K, Chen SJ. Deletions of DNA in cancer and their possible uses for therapy. Bioessays 2023; 45:e2300051. [PMID: 37166062 PMCID: PMC11102808 DOI: 10.1002/bies.202300051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/09/2023] [Accepted: 04/12/2023] [Indexed: 05/12/2023]
Abstract
Despite advances in treatments over the last decades, a uniformly reliable and free of side effects therapy of human cancers remains to be achieved. During chromosome replication, a premature halt of two converging DNA replication forks would cause incomplete replication and a cytotoxic chromosome nondisjunction during mitosis. In contrast to normal cells, most cancer cells bear numerous DNA deletions. A homozygous deletion permanently marks a cell and its descendants. Here, we propose an approach to cancer therapy in which a pair of sequence-specific roadblocks is placed solely at two cancer-confined deletion sites that are located ahead of two converging replication forks. We describe this method, termed "replication blocks specific for deletions" (RBSD), and another deletions-based approach as well. RBSD can be expanded by placing pairs of replication roadblocks on several different chromosomes. The resulting simultaneous nondisjunctions of these chromosomes in cancer cells would further increase the cancer-specific toxicity of RBSD.
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Affiliation(s)
- Alexander Varshavsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Shun-Jia Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
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5
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Vidotto T, Melo CM, Lautert-Dutra W, Chaves LP, Reis RB, Squire JA. Pan-cancer genomic analysis shows hemizygous PTEN loss tumors are associated with immune evasion and poor outcome. Sci Rep 2023; 13:5049. [PMID: 36977733 PMCID: PMC10050165 DOI: 10.1038/s41598-023-31759-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
In tumors, somatic mutations of the PTEN suppressor gene are associated with advanced disease, chemotherapy resistance, and poor survival. PTEN loss of function may occur by inactivating mutation, by deletion, either affecting one copy (hemizygous loss) leading to reduced gene expression or loss of both copies (homozygous) with expression absent. Various murine models have shown that minor reductions in PTEN protein levels strongly influence tumorigenesis. Most PTEN biomarker assays dichotomize PTEN (i.e. presence vs. absence) ignoring the role of one copy loss. We performed a PTEN copy number analysis of 9793 TCGA cases from 30 different tumor types. There were 419 (4.28%) homozygous and 2484 (25.37%) hemizygous PTEN losses. Hemizygous deletions led to reduced PTEN gene expression, accompanied by increased levels of instability and aneuploidy across tumor genomes. Outcome analysis of the pan-cancer cohort showed that losing one copy of PTEN reduced survival to comparable levels as complete loss, and was associated with transcriptomic changes controlling immune response and the tumor microenvironment. Immune cell abundances were significantly altered for PTEN loss, with changes in head and neck, cervix, stomach, prostate, brain, and colon more evident in hemizygous loss tumors. These data suggest that reduced expression of PTEN in tumors with hemizygous loss leads to tumor progression and influences anticancer immune response pathways.
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Affiliation(s)
- T Vidotto
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - C M Melo
- Department of Genetics, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - W Lautert-Dutra
- Department of Genetics, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - L P Chaves
- Department of Genetics, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - R B Reis
- Division of Urology, Department of Surgery and Anatomy, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - J A Squire
- Department of Genetics, Medicine School of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil.
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Canada.
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6
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Lacombe L, Hovington H, Brisson H, Mehdi S, Beillevaire D, Émond JP, Wagner A, Villeneuve L, Simonyan D, Ouellet V, Barrès V, Latour M, Aprikian A, Bergeron A, Castonguay V, Couture F, Chevalier S, Brimo F, Fazli L, Fleshner N, Gleave M, Karakiewicz PI, Lattouf JB, Trudel D, van der Kwast T, Mes-Masson AM, Pouliot F, Fradet Y, Audet-Walsh E, Saad F, Guillemette C, Lévesque E. UGT2B28 accelerates prostate cancer progression through stabilization of the endocytic adaptor protein HIP1 regulating AR and EGFR pathways. Cancer Lett 2023; 553:215994. [PMID: 36343786 DOI: 10.1016/j.canlet.2022.215994] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/28/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
The androgen inactivating UGT2B28 pathway emerges as a predictor of progression in prostate cancer (PCa). However, the clinical significance of UGT2B28 tumoral expression and its contribution to PCa progression remain unclear. Using the Canadian Prostate Cancer Biomarker Network biobank (CPCBN; n = 1512), we analyzed UGT2B28 tumor expression in relation to clinical outcomes in men with localized PCa. UGT2B28 was overexpressed in tumors compared to paired normal adjacent prostatic tissue and was associated with inferior outcomes. Functional analyses indicated that UGT2B28 promoted cell proliferation, and its expression was regulated by the androgen receptor (AR)/ARv7. Mechanistically, UGT2B28 was shown to be a protein partner of the endocytic adaptor protein huntingtin-interacting protein 1 (HIP1), increasing its stability and priming AR/epidermal growth factor receptor (EGFR) pathways, leading to ERK1/2 activation triggering cell proliferation and epithelial-to-mesenchymal transition (EMT). HIP1 knockdown in UGT2B28 positive cells, and dual pharmacological targeting of AR and EGFR pathways, abolished cell proliferative advantages conferred by UGT2B28. In conclusion, UGT2B28 is a prognosticator of progression in localized PCa, regulates both AR and EGFR oncogenic signaling pathways via HIP1, and therefore can be therapeutically targeted by using combination of existing AR/EGFR inhibitors.
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Affiliation(s)
- Louis Lacombe
- Centre de recherche du Centre Hospitalier Universitaire de Québec - Université Laval (CRCHUQc-UL), Centre de recherche sur le cancer (CRC) de l'Université Laval, Faculty of Medicine, Université Laval, Québec, Québec, Canada.
| | - Hélène Hovington
- Centre de recherche du Centre Hospitalier Universitaire de Québec - Université Laval (CRCHUQc-UL), Centre de recherche sur le cancer (CRC) de l'Université Laval, Faculty of Medicine, Université Laval, Québec, Québec, Canada
| | - Hervé Brisson
- Centre de recherche du Centre Hospitalier Universitaire de Québec - Université Laval (CRCHUQc-UL), Centre de recherche sur le cancer (CRC) de l'Université Laval, Faculty of Medicine, Université Laval, Québec, Québec, Canada
| | - Sadia Mehdi
- Centre de recherche du Centre Hospitalier Universitaire de Québec - Université Laval (CRCHUQc-UL), Centre de recherche sur le cancer (CRC) de l'Université Laval, Faculty of Medicine, Université Laval, Québec, Québec, Canada
| | - Déborah Beillevaire
- Centre de recherche du Centre Hospitalier Universitaire de Québec - Université Laval (CRCHUQc-UL), Centre de recherche sur le cancer (CRC) de l'Université Laval, Faculty of Medicine, Université Laval, Québec, Québec, Canada
| | - Jean-Philippe Émond
- Pharmacogenomics Laboratory, CRCHUQc-UL, Centre de recherche sur le cancer (CRC) de l'Université Laval and Faculty of Pharmacy, Université Laval, Québec, Québec, Canada
| | - Antoine Wagner
- Pharmacogenomics Laboratory, CRCHUQc-UL, Centre de recherche sur le cancer (CRC) de l'Université Laval and Faculty of Pharmacy, Université Laval, Québec, Québec, Canada
| | - Lyne Villeneuve
- Pharmacogenomics Laboratory, CRCHUQc-UL, Centre de recherche sur le cancer (CRC) de l'Université Laval and Faculty of Pharmacy, Université Laval, Québec, Québec, Canada
| | - David Simonyan
- Clinical and Evaluative Research Platform, CRCHUQc-UL, Québec, Québec, Canada
| | - Véronique Ouellet
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montréal, Québec, Canada
| | - Véronique Barrès
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montréal, Québec, Canada
| | - Mathieu Latour
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montréal, Québec, Canada
| | - Armen Aprikian
- Research Institute of the McGill University Health Centre and Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Alain Bergeron
- Centre de recherche du Centre Hospitalier Universitaire de Québec - Université Laval (CRCHUQc-UL), Centre de recherche sur le cancer (CRC) de l'Université Laval, Faculty of Medicine, Université Laval, Québec, Québec, Canada
| | - Vincent Castonguay
- Centre de recherche du Centre Hospitalier Universitaire de Québec - Université Laval (CRCHUQc-UL), Centre de recherche sur le cancer (CRC) de l'Université Laval, Faculty of Medicine, Université Laval, Québec, Québec, Canada
| | - Félix Couture
- Centre de recherche du Centre Hospitalier Universitaire de Québec - Université Laval (CRCHUQc-UL), Centre de recherche sur le cancer (CRC) de l'Université Laval, Faculty of Medicine, Université Laval, Québec, Québec, Canada
| | - Simone Chevalier
- Research Institute of the McGill University Health Centre and Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Fadi Brimo
- Research Institute of the McGill University Health Centre and Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Ladan Fazli
- Vancouver Prostate Cancer Centre, Vancouver, British Columbia, Canada
| | | | - Martin Gleave
- Vancouver Prostate Cancer Centre, Vancouver, British Columbia, Canada
| | - Pierre I Karakiewicz
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montréal, Québec, Canada
| | - Jean-Baptiste Lattouf
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montréal, Québec, Canada
| | - Dominique Trudel
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montréal, Québec, Canada
| | | | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montréal, Québec, Canada
| | - Frédéric Pouliot
- Centre de recherche du Centre Hospitalier Universitaire de Québec - Université Laval (CRCHUQc-UL), Centre de recherche sur le cancer (CRC) de l'Université Laval, Faculty of Medicine, Université Laval, Québec, Québec, Canada
| | - Yves Fradet
- Centre de recherche du Centre Hospitalier Universitaire de Québec - Université Laval (CRCHUQc-UL), Centre de recherche sur le cancer (CRC) de l'Université Laval, Faculty of Medicine, Université Laval, Québec, Québec, Canada
| | - Etienne Audet-Walsh
- Centre de recherche du Centre Hospitalier Universitaire de Québec - Université Laval (CRCHUQc-UL), Centre de recherche sur le cancer (CRC) de l'Université Laval, Faculty of Medicine, Université Laval, Québec, Québec, Canada
| | - Fred Saad
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montréal, Québec, Canada
| | - Chantal Guillemette
- Pharmacogenomics Laboratory, CRCHUQc-UL, Centre de recherche sur le cancer (CRC) de l'Université Laval and Faculty of Pharmacy, Université Laval, Québec, Québec, Canada.
| | - Eric Lévesque
- Centre de recherche du Centre Hospitalier Universitaire de Québec - Université Laval (CRCHUQc-UL), Centre de recherche sur le cancer (CRC) de l'Université Laval, Faculty of Medicine, Université Laval, Québec, Québec, Canada.
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7
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Dai X, Thompson EW, Ostrikov K(K. Receptor-Mediated Redox Imbalance: An Emerging Clinical Avenue against Aggressive Cancers. Biomolecules 2022; 12:biom12121880. [PMID: 36551308 PMCID: PMC9775490 DOI: 10.3390/biom12121880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer cells are more vulnerable to abnormal redox fluctuations due to their imbalanced antioxidant system, where cell surface receptors sense stress and trigger intracellular signal relay. As canonical targets of many targeted therapies, cell receptors sensitize the cells to specific drugs. On the other hand, cell target mutations are commonly associated with drug resistance. Thus, exploring effective therapeutics targeting diverse cell receptors may open new clinical avenues against aggressive cancers. This paper uses focused case studies to reveal the intrinsic relationship between the cell receptors of different categories and the primary cancer hallmarks that are associated with the responses to external or internal redox perturbations. Cold atmospheric plasma (CAP) is examined as a promising redox modulation medium and highly selective anti-cancer therapeutic modality featuring dynamically varying receptor targets and minimized drug resistance against aggressive cancers.
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Affiliation(s)
- Xiaofeng Dai
- Wuxi School of Medicine, Jiangnan University, Wuxi 214122, China
- Correspondence:
| | - Erik W. Thompson
- School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD 4059, Australia
- Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Kostya (Ken) Ostrikov
- School of Chemistry, Physics and Center for Biomedical Technologies, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia
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8
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Winter JM, Fresenius HL, Cunningham CN, Wei P, Keys HR, Berg J, Bott A, Yadav T, Ryan J, Sirohi D, Tripp SR, Barta P, Agarwal N, Letai A, Sabatini DM, Wohlever ML, Rutter J. Collateral deletion of the mitochondrial AAA+ ATPase ATAD1 sensitizes cancer cells to proteasome dysfunction. eLife 2022; 11:82860. [PMID: 36409067 DOI: 10.7554/elife.82860] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/20/2022] [Indexed: 11/23/2022] Open
Abstract
The tumor suppressor gene PTEN is the second most commonly deleted gene in cancer. Such deletions often include portions of the chromosome 10q23 locus beyond the bounds of PTEN itself, which frequently disrupts adjacent genes. Coincidental loss of PTEN-adjacent genes might impose vulnerabilities that could either affect patient outcome basally or be exploited therapeutically. Here, we describe how the loss of ATAD1, which is adjacent to and frequently co-deleted with PTEN, predisposes cancer cells to apoptosis triggered by proteasome dysfunction and correlates with improved survival in cancer patients. ATAD1 directly and specifically extracts the pro-apoptotic protein BIM from mitochondria to inactivate it. Cultured cells and mouse xenografts lacking ATAD1 are hypersensitive to clinically used proteasome inhibitors, which activate BIM and trigger apoptosis. This work furthers our understanding of mitochondrial protein homeostasis and could lead to new therapeutic options for the hundreds of thousands of cancer patients who have tumors with chromosome 10q23 deletion.
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Affiliation(s)
- Jacob M Winter
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - Heidi L Fresenius
- Department of Chemistry & Biochemistry, University of Toledo, Toledo, United States
| | - Corey N Cunningham
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - Peng Wei
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - Heather R Keys
- Whitehead Institute for Biomedical Research, Cambridge, United States
| | - Jordan Berg
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - Alex Bott
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - Tarun Yadav
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - Jeremy Ryan
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Deepika Sirohi
- University of Utah and ARUP Laboratories, Salt Lake City, United States
| | - Sheryl R Tripp
- University of Utah and ARUP Laboratories, Salt Lake City, United States
| | - Paige Barta
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - Neeraj Agarwal
- Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Anthony Letai
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - David M Sabatini
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Matthew L Wohlever
- Department of Chemistry & Biochemistry, University of Toledo, Toledo, United States
| | - Jared Rutter
- Department of Biochemistry, University of Utah, Salt Lake City, United States.,Huntsman Cancer Institute, University of Utah, Salt Lake City, United States.,Howard Hughes Medical Institute, Salt Lake City, United States
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9
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Progressing Vulvar Melanoma Caused by Instability in cKIT Juxtamembrane Domain: A Case Report and Review of Literature. Curr Oncol 2022; 29:3130-3137. [PMID: 35621644 PMCID: PMC9139488 DOI: 10.3390/curroncol29050254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 01/15/2023] Open
Abstract
In order to identify the molecular pathways governing melanoma and track its progression, the next-generation sequencing (NGS) approach and targeted sequencing of cancer genes were employed. The primary tumor, as well as metastatic tissue, of an 84-year-old patient diagnosed with vulvar melanoma (VM), were investigated. The primary tumor specimen showed multiple somatic mutations in TP53 gene, suggesting its major contribution to melanoma origin. The metastatic sample showed additional alterations, including other melanoma-related genes. Clinical relevancy is postulated to juxtamembrane region instability of KIT gene (c-KIT). We did not identify BRAF or NRAS alterations, which are typical for the most common melanoma pathway–MAPK cascade. However, it should be noted that this is the first report evidencing PDGFRA in melanoma, although its role in triggering VM needs to be further elucidated.
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10
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Goetze S, Schüffler P, Athanasiou A, Koetemann A, Poyet C, Fankhauser CD, Wild PJ, Schiess R, Wollscheid B. Use of MS-GUIDE for identification of protein biomarkers for risk stratification of patients with prostate cancer. Clin Proteomics 2022; 19:9. [PMID: 35477343 PMCID: PMC9044739 DOI: 10.1186/s12014-022-09349-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 04/05/2022] [Indexed: 11/25/2022] Open
Abstract
Background Non-invasive liquid biopsies could complement current pathological nomograms for risk stratification of prostate cancer patients. Development and testing of potential liquid biopsy markers is time, resource, and cost-intensive. For most protein targets, no antibodies or ELISAs for efficient clinical cohort pre-evaluation are currently available. We reasoned that mass spectrometry-based prescreening would enable the cost-effective and rational preselection of candidates for subsequent clinical-grade ELISA development. Methods Using Mass Spectrometry-GUided Immunoassay DEvelopment (MS-GUIDE), we screened 48 literature-derived biomarker candidates for their potential utility in risk stratification scoring of prostate cancer patients. Parallel reaction monitoring was used to evaluate these 48 potential protein markers in a highly multiplexed fashion in a medium-sized patient cohort of 78 patients with ground-truth prostatectomy and clinical follow-up information. Clinical-grade ELISAs were then developed for two of these candidate proteins and used for significance testing in a larger, independent patient cohort of 263 patients. Results Machine learning-based analysis of the parallel reaction monitoring data of the liquid biopsies prequalified fibronectin and vitronectin as candidate biomarkers. We evaluated their predictive value for prostate cancer biochemical recurrence scoring in an independent validation cohort of 263 prostate cancer patients using clinical-grade ELISAs. The results of our prostate cancer risk stratification test were statistically significantly 10% better than results of the current gold standards PSA alone, PSA plus prostatectomy biopsy Gleason score, or the National Comprehensive Cancer Network score in prediction of recurrence. Conclusion Using MS-GUIDE we identified fibronectin and vitronectin as candidate biomarkers for prostate cancer risk stratification. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-022-09349-x.
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Affiliation(s)
- Sandra Goetze
- Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology, ETH Zurich, 8093, Zurich, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland.,ETH PHRT Swiss Multi-Omics Center (SMOC), 8093, Zurich, Switzerland
| | - Peter Schüffler
- Institute of General and Surgical Pathology, Technical University of Munich, 81675, Munich, Germany
| | | | - Anika Koetemann
- Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology, ETH Zurich, 8093, Zurich, Switzerland
| | - Cedric Poyet
- Clinic of Urology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | | | - Peter J Wild
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland. .,Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, 60590, Frankfurt, Germany. .,Frankfurt Institute for Advanced Studies (FIAS), 60438, Frankfurt, Germany. .,WILDLAB, University Hospital Frankfurt MVZ GmbH, 60590, Frankfurt, Germany.
| | | | - Bernd Wollscheid
- Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology, ETH Zurich, 8093, Zurich, Switzerland. .,Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland. .,ETH PHRT Swiss Multi-Omics Center (SMOC), 8093, Zurich, Switzerland.
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11
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Shui L, Ren H, Yang X, Li J, Chen Z, Yi C, Zhu H, Shui P. The Era of Radiogenomics in Precision Medicine: An Emerging Approach to Support Diagnosis, Treatment Decisions, and Prognostication in Oncology. Front Oncol 2021; 10:570465. [PMID: 33575207 PMCID: PMC7870863 DOI: 10.3389/fonc.2020.570465] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 12/08/2020] [Indexed: 02/05/2023] Open
Abstract
With the rapid development of new technologies, including artificial intelligence and genome sequencing, radiogenomics has emerged as a state-of-the-art science in the field of individualized medicine. Radiogenomics combines a large volume of quantitative data extracted from medical images with individual genomic phenotypes and constructs a prediction model through deep learning to stratify patients, guide therapeutic strategies, and evaluate clinical outcomes. Recent studies of various types of tumors demonstrate the predictive value of radiogenomics. And some of the issues in the radiogenomic analysis and the solutions from prior works are presented. Although the workflow criteria and international agreed guidelines for statistical methods need to be confirmed, radiogenomics represents a repeatable and cost-effective approach for the detection of continuous changes and is a promising surrogate for invasive interventions. Therefore, radiogenomics could facilitate computer-aided diagnosis, treatment, and prediction of the prognosis in patients with tumors in the routine clinical setting. Here, we summarize the integrated process of radiogenomics and introduce the crucial strategies and statistical algorithms involved in current studies.
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Affiliation(s)
- Lin Shui
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Haoyu Ren
- Department of General, Visceral and Transplantation Surgery, University Hospital, LMU Munich, Munich, Germany
| | - Xi Yang
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jian Li
- Department of Pharmacy, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Ziwei Chen
- Department of Nephrology, Chengdu Integrated TCM and Western Medicine Hospital, Chengdu, China
| | - Cheng Yi
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hong Zhu
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Pixian Shui
- School of Pharmacy, Southwest Medical University, Luzhou, China
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12
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Information Theory: New Look at Oncogenic Signaling Pathways. Trends Cell Biol 2019; 29:862-875. [DOI: 10.1016/j.tcb.2019.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 12/23/2022]
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13
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Doi T, Fujiwara Y, Matsubara N, Tomomatsu J, Iwasa S, Tanaka A, Endo-Tsukude C, Nakagawa S, Takahashi S. Phase I study of ipatasertib as a single agent and in combination with abiraterone plus prednisolone in Japanese patients with advanced solid tumors. Cancer Chemother Pharmacol 2019; 84:393-404. [PMID: 31227862 PMCID: PMC6647215 DOI: 10.1007/s00280-019-03882-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/31/2019] [Indexed: 11/26/2022]
Abstract
PURPOSE Ipatasertib is a selective inhibitor of Akt, a frequently activated protein kinase in human cancers. The current study assessed the safety, tolerability, and pharmacokinetics of ipatasertib in Japanese patients with solid tumors. METHODS This was a phase I, open-label, 3 + 3 dose-escalation study conducted in two stages. In stage I, Japanese patients with solid tumors were administered ipatasertib 200, 400, or 600 mg/day for 21 days of a 28-day cycle. In stage II, Japanese patients with castration-resistant prostate cancer were administered ipatasertib 200 or 400 mg/day in combination with abiraterone and prednisolone in 28-day cycles. Dose-limiting toxicity (DLT) was assessed at each dose before enrolling patients at a higher dose; DLT was used to determine the maximum tolerated dose (MTD) and maximum administered dose (MAD). Pharmacokinetic parameters were assessed after a single dose and at steady state. RESULTS Fifteen patients were enrolled in Stage I and six in Stage II. The ipatasertib MTD was 600 mg as monotherapy and MAD was 400 mg in combination with abiraterone and prednisolone. Ipatasertib plasma exposure was dose proportional across the dose range, and was not markedly affected by concurrent administration of abiraterone plus prednisolone. Stable disease (SD) was observed in eight patients treated with ipatasertib monotherapy (53.3%); four patients had SD and one had complete response with ipatasertib plus abiraterone and prednisolone. CONCLUSIONS Ipatasertib, at the monotherapy MTD of 600 mg/day and MAD of 400 mg/day in combination with abiraterone and prednisolone, was safe and tolerable in Japanese patients with solid tumors.
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Affiliation(s)
- Toshihiko Doi
- Department of Experimental Therapeutics, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa-shi, Chiba-ken, 277-8577, Japan.
| | - Yutaka Fujiwara
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
| | - Nobuaki Matsubara
- Department of Breast and Medical Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Junichi Tomomatsu
- Department of Medical Oncology, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Satoru Iwasa
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
| | - Akari Tanaka
- Clinical Science and Strategy Department, Chugai Pharmaceutical Co., Ltd, Tokyo, Japan
| | | | - Shintaro Nakagawa
- Clinical Information and Intelligence Department, Chugai Pharmaceutical Co., Ltd., Tokyo, Japan
| | - Shunji Takahashi
- Department of Medical Oncology, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
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14
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Gonthier K, Poluri RTK, Audet-Walsh É. Functional genomic studies reveal the androgen receptor as a master regulator of cellular energy metabolism in prostate cancer. J Steroid Biochem Mol Biol 2019; 191:105367. [PMID: 31051242 DOI: 10.1016/j.jsbmb.2019.04.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 12/19/2022]
Abstract
Sex-steroid hormones have been investigated for decades for their oncogenic properties in hormone-dependent cancers. The increasing body of knowledge on the biological actions of androgens in prostate cancer has led to the development of several targeted therapies that still represent the standard of care for cancer patients to this day. In the prostate, androgens promote cellular differentiation and proper tissue development. These hormones also promote the aberrant proliferation and survival of prostate cancer cells. Over the past few years, sequencing technologies for functional genomic analyses have rapidly expanded, revealing novel functions of sex-steroid hormone receptors other than their classic roles. In this article, we will focus on transcriptomic- and genomic-based evidence that demonstrates the importance of the androgen receptor signaling in the regulation of prostate cancer cell metabolism. This is significant because the reprogramming of cell metabolism is a hallmark of cancer. In fact, it is clear now that the androgen receptor contributes to the reprogramming of specific cellular metabolic pathways that promote tumor growth and disease progression, including aerobic glycolysis, mitochondrial respiration, fatty acid ß-oxidation, and de novo lipid synthesis. Overall, beyond regulating development, differentiation, and proliferation, the androgen receptor is also a master regulator of cellular energy metabolism.
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Affiliation(s)
- Kevin Gonthier
- Department of Molecular Medicine, Axe Endocrinologie - Néphrologie du Centre de recherche du CHU de Québec, Canada; Centre de recherche sur le cancer - Université Laval, Canada
| | - Raghavendra Tejo Karthik Poluri
- Department of Molecular Medicine, Axe Endocrinologie - Néphrologie du Centre de recherche du CHU de Québec, Canada; Centre de recherche sur le cancer - Université Laval, Canada
| | - Étienne Audet-Walsh
- Department of Molecular Medicine, Axe Endocrinologie - Néphrologie du Centre de recherche du CHU de Québec, Canada; Centre de recherche sur le cancer - Université Laval, Canada.
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15
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Dysregulated Transcriptional Control in Prostate Cancer. Int J Mol Sci 2019; 20:ijms20122883. [PMID: 31200487 PMCID: PMC6627928 DOI: 10.3390/ijms20122883] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 12/24/2022] Open
Abstract
Recent advances in whole-genome and transcriptome sequencing of prostate cancer at different stages indicate that a large number of mutations found in tumors are present in non-protein coding regions of the genome and lead to dysregulated gene expression. Single nucleotide variations and small mutations affecting the recruitment of transcription factor complexes to DNA regulatory elements are observed in an increasing number of cases. Genomic rearrangements may position coding regions under the novel control of regulatory elements, as exemplified by the TMPRSS2-ERG fusion and the amplified enhancer identified upstream of the androgen receptor (AR) gene. Super-enhancers are increasingly found to play important roles in aberrant oncogenic transcription. Several players involved in these processes are currently being evaluated as drug targets and may represent new vulnerabilities that can be exploited for prostate cancer treatment. They include factors involved in enhancer and super-enhancer function such as bromodomain proteins and cyclin-dependent kinases. In addition, non-coding RNAs with an important gene regulatory role are being explored. The rapid progress made in understanding the influence of the non-coding part of the genome and of transcription dysregulation in prostate cancer could pave the way for the identification of novel treatment paradigms for the benefit of patients.
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Álvarez-Garcia V, Tawil Y, Wise HM, Leslie NR. Mechanisms of PTEN loss in cancer: It's all about diversity. Semin Cancer Biol 2019; 59:66-79. [PMID: 30738865 DOI: 10.1016/j.semcancer.2019.02.001] [Citation(s) in RCA: 210] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/22/2019] [Accepted: 02/05/2019] [Indexed: 01/04/2023]
Abstract
PTEN is a phosphatase which metabolises PIP3, the lipid product of PI 3-Kinase, directly opposing the activation of the oncogenic PI3K/AKT/mTOR signalling network. Accordingly, loss of function of the PTEN tumour suppressor is one of the most common events observed in many types of cancer. Although the mechanisms by which PTEN function is disrupted are diverse, the most frequently observed events are deletion of a single gene copy of PTEN and gene silencing, usually observed in tumours with little or no PTEN protein detectable by immunohistochemistry. Accordingly, with the exceptions of glioblastoma and endometrial cancer, mutations of the PTEN coding sequence are uncommon (<10%) in most types of cancer. Here we review the data relating to PTEN loss in seven common tumour types and discuss mechanisms of PTEN regulation, some of which appear to contribute to reduced PTEN protein levels in cancers.
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Affiliation(s)
- Virginia Álvarez-Garcia
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Yasmine Tawil
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Helen M Wise
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, EH14 4AS, UK
| | - Nicholas R Leslie
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, EH14 4AS, UK.
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