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Kpeglo D, Haddrick M, Knowles MA, Evans SD, Peyman SA. Modelling and breaking down the biophysical barriers to drug delivery in pancreatic cancer. Lab Chip 2024; 24:854-868. [PMID: 38240720 DOI: 10.1039/d3lc00660c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
The pancreatic ductal adenocarcinoma (PDAC) stroma and its inherent biophysical barriers to drug delivery are central to therapeutic resistance. This makes PDAC the most prevalent pancreatic cancer with poor prognosis. The chemotherapeutic drug gemcitabine is used against various solid tumours, including pancreatic cancer, but with only a modest effect on patient survival. The growing PDAC tumour mass with high densities of cells and extracellular matrix (ECM) proteins, i.e., collagen, results in high interstitial pressure, leading to vasculature collapse and a dense, hypoxic, mechanically stiff stroma with reduced interstitial flow, critical to drug delivery to cells. Despite this, most drug studies are performed on cellular models that neglect these biophysical barriers to drug delivery. Microfluidic technology offers a promising platform to emulate tumour biophysical characteristics with appropriate flow conditions and transport dynamics. We present a microfluidic PDAC culture model, encompassing the disease's biophysical barriers to therapeutics, to evaluate the use of the angiotensin II receptor blocker losartan, which has been found to have matrix-depleting properties, on improving gemcitabine efficacy. PDAC cells were seeded into our 5-channel microfluidic device for a 21-day culture to mimic the rigid, collagenous PDAC stroma with reduced interstitial flow, which is critical to drug delivery to the cancer cells, and for assessment with gemcitabine and losartan treatment. With losartan, our culture matrix was more porous with less collagen, resulting in increased hydraulic conductivity of the culture interstitial space and improved gemcitabine effect. We demonstrate the importance of modelling tumour biophysical barriers to successfully assess new drugs and delivery methods.
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Affiliation(s)
- Delanyo Kpeglo
- Molecular and Nanoscale Physics Group, School of Physics and Astronomy, University of Leeds, LS2 9 JT, UK.
| | - Malcolm Haddrick
- Medicines Discovery Catapult, Block 35, Mereside Alderley Park, Alderley Edge, SK10 4TG, UK
| | - Margaret A Knowles
- Leeds Institute of Medical Research at St James's (LIMR), School of Medicine, University of Leeds, LS2 9 JT, UK
| | - Stephen D Evans
- Molecular and Nanoscale Physics Group, School of Physics and Astronomy, University of Leeds, LS2 9 JT, UK.
| | - Sally A Peyman
- Molecular and Nanoscale Physics Group, School of Physics and Astronomy, University of Leeds, LS2 9 JT, UK.
- Leeds Institute of Medical Research at St James's (LIMR), School of Medicine, University of Leeds, LS2 9 JT, UK
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2
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Martin HL, Turner AL, Higgins J, Tang AA, Tiede C, Taylor T, Siripanthong S, Adams TL, Manfield IW, Bell SM, Morrison EE, Bond J, Trinh CH, Hurst CD, Knowles MA, Bayliss RW, Tomlinson DC. Affimer-mediated locking of p21-activated kinase 5 in an intermediate activation state results in kinase inhibition. Cell Rep 2023; 42:113184. [PMID: 37776520 DOI: 10.1016/j.celrep.2023.113184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 07/17/2023] [Accepted: 09/13/2023] [Indexed: 10/02/2023] Open
Abstract
Kinases are important therapeutic targets, and their inhibitors are classified according to their mechanism of action, which range from blocking ATP binding to covalent inhibition. Here, a mechanism of inhibition is highlighted by capturing p21-activated kinase 5 (PAK5) in an intermediate state of activation using an Affimer reagent that binds in the P+1 pocket. PAK5 was identified from a non-hypothesis-driven high-content imaging RNAi screen in urothelial cancer cells. Silencing of PAK5 resulted in reduced cell number, G1/S arrest, and enlargement of cells, suggesting it to be important in urothelial cancer cell line survival and proliferation. Affimer reagents were isolated to identify mechanisms of inhibition. The Affimer PAK5-Af17 recapitulated the phenotype seen with siRNA. Co-crystallization revealed that PAK5-Af17 bound in the P+1 pocket of PAK5, locking the kinase into a partial activation state. This mechanism of inhibition indicates that another class of kinase inhibitors is possible.
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Affiliation(s)
- Heather L Martin
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK; Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Amy L Turner
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Julie Higgins
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK
| | - Anna A Tang
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Christian Tiede
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas Taylor
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sitthinon Siripanthong
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas L Adams
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Iain W Manfield
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sandra M Bell
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK; Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Ewan E Morrison
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK; Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Jacquelyn Bond
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK; Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Chi H Trinh
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Carolyn D Hurst
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Margaret A Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Richard W Bayliss
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Darren C Tomlinson
- BioScreening Technology Group, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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3
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Abstract
Bladder cancer is a global health issue with sex differences in incidence and prognosis. Bladder cancer has distinct molecular subtypes with multiple pathogenic pathways depending on whether the disease is non-muscle invasive or muscle invasive. The mutational burden is higher in muscle-invasive than in non-muscle-invasive disease. Commonly mutated genes include TERT, FGFR3, TP53, PIK3CA, STAG2 and genes involved in chromatin modification. Subtyping of both forms of bladder cancer is likely to change considerably with the advent of single-cell analysis methods. Early detection signifies a better disease prognosis; thus, minimally invasive diagnostic options are needed to improve patient outcomes. Urine-based tests are available for disease diagnosis and surveillance, and analysis of blood-based cell-free DNA is a promising tool for the detection of minimal residual disease and metastatic relapse. Transurethral resection is the cornerstone treatment for non-muscle-invasive bladder cancer and intravesical therapy can further improve oncological outcomes. For muscle-invasive bladder cancer, radical cystectomy with neoadjuvant chemotherapy is the standard of care with evidence supporting trimodality therapy. Immune-checkpoint inhibitors have demonstrated benefit in non-muscle-invasive, muscle-invasive and metastatic bladder cancer. Effective management requires a multidisciplinary approach that considers patient characteristics and molecular disease characteristics.
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Affiliation(s)
- Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Donna E Hansel
- Division of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason A Efstathiou
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Margaret A Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Matthew D Galsky
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremy Teoh
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Dan Theodorescu
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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Pettitt GA, Hurst CD, Khan Z, McPherson HR, Dunning MC, Alder O, Platt FM, Black EVI, Burns JE, Knowles MA. Development of resistance to FGFR inhibition in urothelial carcinoma via multiple pathways in vitro. J Pathol 2023; 259:220-232. [PMID: 36385700 PMCID: PMC10107504 DOI: 10.1002/path.6034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/14/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
Alterations of fibroblast growth factor receptors (FGFRs) are common in bladder and other cancers and result in disrupted signalling via several pathways. Therapeutics that target FGFRs have now entered the clinic, but, in common with many cancer therapies, resistance develops in most cases. To model this, we derived resistant sublines of two FGFR-driven bladder cancer cell lines by long-term culture with the FGFR inhibitor PD173074 and explored mechanisms using expression profiling and whole-exome sequencing. We identified several resistance-associated molecular profiles. These included HRAS mutation in one case and reversible mechanisms resembling a drug-tolerant persister phenotype in others. Upregulated IGF1R expression in one resistant derivative was associated with sensitivity to linsitinib and a profile with upregulation of a YAP/TAZ signature to sensitivity to the YAP inhibitor CA3 in another. However, upregulation of other potential therapeutic targets was not indicative of sensitivity. Overall, the heterogeneity in resistance mechanisms and commonality of the persister state present a considerable challenge for personalised therapy. Nevertheless, the reversibility of resistance may indicate a benefit from treatment interruptions or retreatment following disease relapse in some patients. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Geoffrey A Pettitt
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Carolyn D Hurst
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Zubeda Khan
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Helen R McPherson
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Matthew C Dunning
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Olivia Alder
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Fiona M Platt
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Emma VI Black
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Julie E Burns
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
| | - Margaret A Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James'sSt James's University HospitalLeedsUK
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5
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Warrick JI, Knowles MA, Hurst CD, Shuman L, Raman JD, Walter V, Putt J, Dyrskjøt L, Groeneveld C, Castro MAA, Robertson AG, DeGraff DJ. A transcriptional network of cell cycle dysregulation in noninvasive papillary urothelial carcinoma. Sci Rep 2022; 12:16538. [PMID: 36192513 PMCID: PMC9529892 DOI: 10.1038/s41598-022-20927-9] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Human cancers display a restricted set of expression profiles, despite diverse mutational drivers. This has led to the hypothesis that select sets of transcription factors act on similar target genes as an integrated network, buffering a tumor’s transcriptional state. Noninvasive papillary urothelial carcinoma (NIPUC) with higher cell cycle activity has higher risk of recurrence and progression. In this paper, we describe a transcriptional network of cell cycle dysregulation in NIPUC, which was delineated using the ARACNe algorithm applied to expression data from a new cohort (n = 81, RNA sequencing), and two previously published cohorts. The transcriptional network comprised 121 transcription factors, including the pluripotency factors SOX2 and SALL4, the sex hormone binding receptors ESR1 and PGR, and multiple homeobox factors. Of these 121 transcription factors, 65 and 56 were more active in tumors with greater and less cell cycle activity, respectively. When clustered by activity of these transcription factors, tumors divided into High Cell Cycle versus Low Cell Cycle groups. Tumors in the High Cell Cycle group demonstrated greater mutational burden and copy number instability. A putative mutational driver of cell cycle dysregulation, such as homozygous loss of CDKN2A, was found in only 50% of High Cell Cycle NIPUC, suggesting a prominent role of transcription factor activity in driving cell cycle dysregulation. Activity of the 121 transcription factors strongly associated with expression of EZH2 and other members of the PRC2 complex, suggesting regulation by this complex influences expression of the transcription factors in this network. Activity of transcription factors in this network also associated with signatures of pluripotency and epithelial-to-mesenchymal transition (EMT), suggesting they play a role in driving evolution to invasive carcinoma. Consistent with this, these transcription factors differed in activity between NIPUC and invasive urothelial carcinoma.
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Affiliation(s)
- Joshua I Warrick
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA. .,Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
| | - Margaret A Knowles
- Divison of Molecular Medicine, Leeds Institute of Molecular Research at St James's, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Carolyn D Hurst
- Divison of Molecular Medicine, Leeds Institute of Molecular Research at St James's, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Lauren Shuman
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Jay D Raman
- Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Vonn Walter
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Jeffrey Putt
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Clarice Groeneveld
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Équipe Oncologie Moleculaire, Institut Curie, Paris, France
| | - Mauro A A Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, PR, 81520-260, Brazil
| | | | - David J DeGraff
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, 17033, USA. .,Department of Urology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA. .,Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
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6
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Marzouka NAD, Eriksson P, Bernardo C, Hurst CD, Knowles MA, Sjödahl G, Liedberg F, Höglund M. The Lund Molecular Taxonomy Applied to Non-Muscle-Invasive Urothelial Carcinoma. J Mol Diagn 2022; 24:992-1008. [PMID: 35853574 DOI: 10.1016/j.jmoldx.2022.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/29/2022] [Accepted: 05/16/2022] [Indexed: 11/25/2022] Open
Abstract
The precise classification of tumors into relevant molecular subtypes will facilitate both future research and optimal treatment. In the present investigation, the Lund Taxonomy system for molecular classification of urothelial carcinoma was applied to two large and independent cohorts of non-muscle-invasive tumors. Of 752 tumors classified, close to 100% were of the luminal subtypes, 95% urothelial-like (Uro; UroA, UroB, or UroC) and 5% genomically unstable. We show that the obtained subtype structure organizes the tumors into groups with specific and coherent gene mutation, genomic, and clinical profiles. The intrasubtype variability in the largest group of tumors, UroA, is caused by infiltration and proliferation, not considered as cancer cell type-defining properties. Within the UroA subtype, a HOXB/late cell-cycle gene expression polarity is described, strongly associated with FGFR3, STAG2, and TP53 mutations, as well as with chromosome 9 losses. Kaplan-Meier analyses identified the genomically unstable subtype as a progression high-risk group, also valid in the subgroup of T1 tumors. Almost all progression events occurred within 12 months in this subtype. In addition, a general progression gene signature was derived that identifies high- and low-risk tumors. All findings were demonstrated in two independent cohorts. We conclude that the Lund Taxonomy system is applicable to both non-muscle- and muscle-invasive tumors and is a useful biological framework for translational studies.
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Affiliation(s)
- Nour-Al-Dain Marzouka
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Pontus Eriksson
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Carina Bernardo
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Carolyn D Hurst
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, United Kingdom
| | - Margaret A Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, United Kingdom
| | - Gottfrid Sjödahl
- Urology-Urothelial Cancer, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Fredrik Liedberg
- Urology-Urothelial Cancer, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Mattias Höglund
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
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Hurst CD, Cheng G, Platt FM, Alder O, Black EV, Burns JE, Brown J, Jain S, Roulson JA, Knowles MA. Molecular profile of pure squamous cell carcinoma of the bladder identifies major roles for OSMR and YAP signalling. J Pathol Clin Res 2022; 8:279-293. [PMID: 35289095 PMCID: PMC8977277 DOI: 10.1002/cjp2.261] [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] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 11/20/2022]
Abstract
Pure squamous cell carcinoma (SCC) is the most common pure variant form of bladder cancer, found in 2–5% of cases. It often presents late and is unresponsive to cisplatin‐based chemotherapy. The molecular features of these tumours have not been elucidated in detail. We carried out whole‐exome sequencing (WES), copy number, and transcriptome analysis of bladder SCC. Muscle‐invasive bladder cancer (MIBC) samples with no evidence of squamous differentiation (non‐SD) were used for comparison. To assess commonality of features with urothelial carcinoma with SD, we examined data from SD samples in The Cancer Genome Atlas (TCGA) study of MIBC. TP53 was the most commonly mutated gene in SCC (64%) followed by FAT1 (45%). Copy number analysis revealed complex changes in SCC, many differing from those in samples with SD. Gain of 5p and 7p was the most common feature, and focal regions on 5p included OSMR and RICTOR. In addition to 9p deletions, we found some samples with focal gain of 9p24 containing CD274 (PD‐L1). Loss of 4q35 containing FAT1 was found in many samples such that all but one sample analysed by WES had FAT1 mutation or deletion. Expression features included upregulation of oncostatin M receptor (OSMR), metalloproteinases, metallothioneins, keratinisation genes, extracellular matrix components, inflammatory response genes, stem cell markers, and immune response modulators. Exploration of differentially expressed transcription factors identified BNC1 and TFAP2A, a gene repressed by PPARG, as the most upregulated factors. Known urothelial differentiation factors were downregulated along with 72 Kruppel‐associated (KRAB) domain‐containing zinc finger family protein (KZFP) genes. Novel therapies are urgently needed for these tumours. In addition to upregulated expression of EGFR, which has been suggested as a therapeutic target in basal/squamous bladder cancer, we identified expression signatures that indicate upregulated OSMR and YAP/TAZ signalling. Preclinical evaluation of the effects of inhibition of these pathways alone or in combination is merited.
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Affiliation(s)
- Carolyn D Hurst
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Guo Cheng
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Fiona M Platt
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Olivia Alder
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Emma Vi Black
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Julie E Burns
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Joanne Brown
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Sunjay Jain
- Pyrah Department of Urology, St James's University Hospital, Leeds, UK
| | - Jo-An Roulson
- Department of Histopathology, St James's University Hospital, Leeds, UK
| | - Margaret A Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
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8
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Kpeglo D, Hughes MD, Dougan L, Haddrick M, Knowles MA, Evans SD, Peyman SA. Modeling the mechanical stiffness of pancreatic ductal adenocarcinoma. Matrix Biol Plus 2022; 14:100109. [PMID: 35399702 PMCID: PMC8990173 DOI: 10.1016/j.mbplus.2022.100109] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 12/20/2021] [Revised: 02/28/2022] [Accepted: 03/15/2022] [Indexed: 01/18/2023] Open
Abstract
The PDAC stroma stiffness underlines its malignant behavior and drug resistance. 3D in vitro cultures must model the PDAC stroma to effectively drug efficacy. PSCs are responsible for the stroma, and its activity is increased with TGF-β. Develop a 3D culture model of PDAC, which includes PSCs and TGF-β. Assess the mechanical stiffness, stain for collagen, and investigate gemcitabine efficacy.
Despite improvements in the understanding of disease biology, pancreatic ductal adenocarcinoma (PDAC) remains the most malignant cancer of the pancreas. PDAC constitutes ∼95% of all pancreatic cancers, and it is highly resistant to therapeutics. The increased tissue rigidity, which stems from the rich fibrotic stroma in the tumor microenvironment, is central to disease development, physiology, and resistance to drug perfusion. Pancreatic stellate cells (PSCs) are responsible for overproduction of extracellular matrix in the fibrotic stroma, and this is exacerbated by the overexpression of transforming growth factor-β (TGF-β). However, there are few in vitro PDAC models, which include both PSCs and TGF-β or mimic in vivo-like tumor stiffness. In this study, we present a three-dimensional in vitro PDAC model, which includes PSCs and TGF-β, and recapitulates PDAC tissue mechanical stiffness. Using oscillatory shear rheology, we show the mechanical stiffness of the model is within range of the PDAC tissue stiffness by day 21 of culture and highlight that the matrix environment is essential to adequately capture PDAC disease. PDAC is a complex, aggressive disease with poor prognosis, and biophysically relevant in vitro PDAC models, which take into account tissue mechanics, will provide improved tumor models for effective therapeutic assessment.
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Affiliation(s)
- Delanyo Kpeglo
- Molecular and Nanoscale Physics Group, School of Physics and Astronomy, University of Leeds, LS2 9 JT, UK
| | - Matthew D.G. Hughes
- Molecular and Nanoscale Physics Group, School of Physics and Astronomy, University of Leeds, LS2 9 JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK
| | - Lorna Dougan
- Molecular and Nanoscale Physics Group, School of Physics and Astronomy, University of Leeds, LS2 9 JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK
| | - Malcolm Haddrick
- Medicines Discovery Catapult, Block 35, Mereside Alderley Park, Alderley Edge, SK10 4TG, UK
| | - Margaret A. Knowles
- Leeds Institute of Medical Research at St James’s (LIMR), School of Medicine, University of Leeds, LS2 9 JT, UK
| | - Stephen D. Evans
- Molecular and Nanoscale Physics Group, School of Physics and Astronomy, University of Leeds, LS2 9 JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK
| | - Sally A. Peyman
- Molecular and Nanoscale Physics Group, School of Physics and Astronomy, University of Leeds, LS2 9 JT, UK
- Leeds Institute of Medical Research at St James’s (LIMR), School of Medicine, University of Leeds, LS2 9 JT, UK
- Corresponding author at: Molecular and Nanoscale Physics Group, School of Physics and Astronomy, University of Leeds, LS2 9 JT, UK.
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9
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Hurst CD, Cheng G, Platt FM, Castro MA, Marzouka NADS, Eriksson P, Black EV, Alder O, Lawson AR, Lindskrog SV, Burns JE, Jain S, Roulson JA, Brown JC, Koster J, Robertson AG, Martincorena I, Dyrskjøt L, Höglund M, Knowles MA. Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight. Cell Rep Med 2021; 2:100472. [PMID: 35028613 PMCID: PMC8714941 DOI: 10.1016/j.xcrm.2021.100472] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/09/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022]
Abstract
Understanding the molecular determinants that underpin the clinical heterogeneity of non-muscle-invasive bladder cancer (NMIBC) is essential for prognostication and therapy development. Stage T1 disease in particular presents a high risk of progression and requires improved understanding. We present a detailed multi-omics study containing gene expression, copy number, and mutational profiles that show relationships to immune infiltration, disease recurrence, and progression to muscle invasion. We compare expression and genomic subtypes derived from all NMIBCs with those derived from the individual disease stages Ta and T1. We show that sufficient molecular heterogeneity exists within the separate stages to allow subclassification and that this is more clinically meaningful for stage T1 disease than that derived from all NMIBCs. This provides improved biological understanding and identifies subtypes of T1 tumors that may benefit from chemo- or immunotherapy.
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Affiliation(s)
- Carolyn D. Hurst
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James’s, St James’s University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Guo Cheng
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James’s, St James’s University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Fiona M. Platt
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James’s, St James’s University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Mauro A.A. Castro
- Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, Brazil
| | | | - Pontus Eriksson
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Emma V.I. Black
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James’s, St James’s University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Olivia Alder
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James’s, St James’s University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Andrew R.J. Lawson
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Sia V. Lindskrog
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Julie E. Burns
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James’s, St James’s University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Sunjay Jain
- Pyrah Department of Urology, St James’s University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Jo-An Roulson
- Department of Histopathology, St James’s University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Joanne C. Brown
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James’s, St James’s University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Jan Koster
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Cancer Center Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - A. Gordon Robertson
- Canada’s Michael Smith Genome Sciences Center, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Inigo Martincorena
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mattias Höglund
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Margaret A. Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James’s, St James’s University Hospital, Beckett Street, Leeds LS9 7TF, UK
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10
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Turner LD, Trinh CH, Hubball RA, Orritt KM, Lin CC, Burns JE, Knowles MA, Fishwick CWG. From Fragment to Lead: De Novo Design and Development toward a Selective FGFR2 Inhibitor. J Med Chem 2021; 65:1481-1504. [PMID: 34780700 DOI: 10.1021/acs.jmedchem.1c01163] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fibroblast growth factor receptors (FGFRs) are implicated in a range of cancers with several pan-kinase and selective-FGFR inhibitors currently being evaluated in clinical trials. Pan-FGFR inhibitors often cause toxic side effects and few examples of subtype-selective inhibitors exist. Herein, we describe a structure-guided approach toward the development of a selective FGFR2 inhibitor. De novo design was carried out on an existing fragment series to yield compounds predicted to improve potency against the FGFRs. Subsequent iterative rounds of synthesis and biological evaluation led to an inhibitor with nanomolar potency that exhibited moderate selectivity for FGFR2 over FGFR1/3. Subtle changes to the lead inhibitor resulted in a complete loss of selectivity for FGFR2. X-ray crystallographic studies revealed inhibitor-specific morphological differences in the P-loop which were posited to be fundamental to the selectivity of these compounds. Additional docking studies have predicted an FGFR2-selective H-bond which could be utilized to design more selective FGFR2 inhibitors.
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Affiliation(s)
- Lewis D Turner
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, U.K
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, U.K
| | - Ryan A Hubball
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, U.K
| | - Kyle M Orritt
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, U.K
| | - Chi-Chuan Lin
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, U.K
| | - Julie E Burns
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, LS9 7TF, U.K
| | - Margaret A Knowles
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, LS9 7TF, U.K
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11
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Burns JE, Hurst CD, Knowles MA, Phillips RM, Allison SJ. The Warburg effect as a therapeutic target for bladder cancers and intratumoral heterogeneity in associated molecular targets. Cancer Sci 2021; 112:3822-3834. [PMID: 34181805 PMCID: PMC8409428 DOI: 10.1111/cas.15047] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 12/14/2022] Open
Abstract
Bladder cancer is the 10th most common cancer worldwide. For muscle-invasive bladder cancer (MIBC), treatment includes radical cystectomy, radiotherapy, and chemotherapy; however, the outcome is generally poor. For non-muscle-invasive bladder cancer (NMIBC), tumor recurrence is common. There is an urgent need for more effective and less harmful therapeutic approaches. Here, bladder cancer cell metabolic reprogramming to rely on aerobic glycolysis (the Warburg effect) and expression of associated molecular therapeutic targets by bladder cancer cells of different stages and grades, and in freshly resected clinical tissue, is investigated. Importantly, analyses indicate that the Warburg effect is a feature of both NMIBCs and MIBCs. In two in vitro inducible epithelial-mesenchymal transition (EMT) bladder cancer models, EMT stimulation correlated with increased lactate production, the end product of aerobic glycolysis. Protein levels of lactate dehydrogenase A (LDH-A), which promotes pyruvate enzymatic reduction to lactate, were higher in most bladder cancer cell lines (compared with LDH-B, which catalyzes the reverse reaction), but the levels did not closely correlate with aerobic glycolysis rates. Although LDH-A is expressed in normal urothelial cells, LDH-A knockdown by RNAi selectively induced urothelial cancer cell apoptotic death, whereas normal cells were unaffected-identifying LDH-A as a cancer-selective therapeutic target for bladder cancers. LDH-A and other potential therapeutic targets (MCT4 and GLUT1) were expressed in patient clinical specimens; however, positive staining varied in different areas of sections and with distance from a blood vessel. This intratumoral heterogeneity has important therapeutic implications and indicates the possibility of tumor cell metabolic coupling.
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Affiliation(s)
- Julie E. Burns
- Leeds Institute of Medical ResearchSt. James’ University HospitalUniversity of LeedsLeedsUK
| | - Carolyn D. Hurst
- Leeds Institute of Medical ResearchSt. James’ University HospitalUniversity of LeedsLeedsUK
| | - Margaret A. Knowles
- Leeds Institute of Medical ResearchSt. James’ University HospitalUniversity of LeedsLeedsUK
| | | | - Simon J. Allison
- Leeds Institute of Medical ResearchSt. James’ University HospitalUniversity of LeedsLeedsUK
- School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK
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12
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Lindskrog SV, Prip F, Lamy P, Taber A, Groeneveld CS, Birkenkamp-Demtröder K, Jensen JB, Strandgaard T, Nordentoft I, Christensen E, Sokac M, Birkbak NJ, Maretty L, Hermann GG, Petersen AC, Weyerer V, Grimm MO, Horstmann M, Sjödahl G, Höglund M, Steiniche T, Mogensen K, de Reyniès A, Nawroth R, Jordan B, Lin X, Dragicevic D, Ward DG, Goel A, Hurst CD, Raman JD, Warrick JI, Segersten U, Sikic D, van Kessel KEM, Maurer T, Meeks JJ, DeGraff DJ, Bryan RT, Knowles MA, Simic T, Hartmann A, Zwarthoff EC, Malmström PU, Malats N, Real FX, Dyrskjøt L. An integrated multi-omics analysis identifies prognostic molecular subtypes of non-muscle-invasive bladder cancer. Nat Commun 2021; 12:2301. [PMID: 33863885 PMCID: PMC8052448 DOI: 10.1038/s41467-021-22465-w] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
The molecular landscape in non-muscle-invasive bladder cancer (NMIBC) is characterized by large biological heterogeneity with variable clinical outcomes. Here, we perform an integrative multi-omics analysis of patients diagnosed with NMIBC (n = 834). Transcriptomic analysis identifies four classes (1, 2a, 2b and 3) reflecting tumor biology and disease aggressiveness. Both transcriptome-based subtyping and the level of chromosomal instability provide independent prognostic value beyond established prognostic clinicopathological parameters. High chromosomal instability, p53-pathway disruption and APOBEC-related mutations are significantly associated with transcriptomic class 2a and poor outcome. RNA-derived immune cell infiltration is associated with chromosomally unstable tumors and enriched in class 2b. Spatial proteomics analysis confirms the higher infiltration of class 2b tumors and demonstrates an association between higher immune cell infiltration and lower recurrence rates. Finally, the independent prognostic value of the transcriptomic classes is documented in 1228 validation samples using a single sample classification tool. The classifier provides a framework for biomarker discovery and for optimizing treatment and surveillance in next-generation clinical trials.
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Affiliation(s)
- Sia Viborg Lindskrog
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Frederik Prip
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | - Ann Taber
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Clarice S Groeneveld
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France
- Oncologie Moleculaire, UMR144, Institut Curie, Paris, France
| | - Karin Birkenkamp-Demtröder
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jørgen Bjerggaard Jensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Urology, Aarhus University Hospital, Aarhus N, Denmark
| | - Trine Strandgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | - Emil Christensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mateo Sokac
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Nicolai J Birkbak
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Lasse Maretty
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Gregers G Hermann
- Department of Urology, Herlev hospital, Copenhagen University, Copenhagen, Denmark
| | - Astrid C Petersen
- Department of Pathology, Aalborg University Hospital, Aalborg, Denmark
| | - Veronika Weyerer
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | | | - Marcus Horstmann
- Department of Urology, Jena University Hospital, Jena, Germany
- Department of Urology, Malteser Hospital St. Josephshospital, Krefeld Uerdingen, Krefeld, Germany
| | - Gottfrid Sjödahl
- Division of Urological Research, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Mattias Höglund
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Torben Steiniche
- Department of Pathology, Aarhus University Hospital, Aarhus N, Denmark
| | - Karin Mogensen
- Department of Urology, Herlev hospital, Copenhagen University, Copenhagen, Denmark
| | - Aurélien de Reyniès
- Cartes d'Identité des Tumeurs (CIT) Program, Ligue Nationale Contre le Cancer, Paris, France
| | - Roman Nawroth
- Department of Urology, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Brian Jordan
- Departments of Pathology, Urology, Biochemistry and Molecular Genetics, Northwestern University School of Medicine, Chicago, IL, USA
| | - Xiaoqi Lin
- Departments of Pathology, Urology, Biochemistry and Molecular Genetics, Northwestern University School of Medicine, Chicago, IL, USA
| | - Dejan Dragicevic
- Clinic of Urology, Clinical Centre of Serbia, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Douglas G Ward
- Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Anshita Goel
- Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Carolyn D Hurst
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Jay D Raman
- Department of Surgery, Division of Urology, Pennsylvania State University, Hershey, PA, USA
| | - Joshua I Warrick
- Department of Pathology and Laboratory Medicine, Division of Urology, Department of Biochemistry and Molecular Biology, Pennsylvania State University, Hershey, PA, USA
| | - Ulrika Segersten
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Danijel Sikic
- Department of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Kim E M van Kessel
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tobias Maurer
- Department of Urology, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
- Department of Urology and Martini-Clinic, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joshua J Meeks
- Departments of Pathology, Urology, Biochemistry and Molecular Genetics, Northwestern University School of Medicine, Chicago, IL, USA
| | - David J DeGraff
- Department of Pathology and Laboratory Medicine, Division of Urology, Department of Biochemistry and Molecular Biology, Pennsylvania State University, Hershey, PA, USA
| | - Richard T Bryan
- Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Margaret A Knowles
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Tatjana Simic
- Institute of Medical and Clinical Biochemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Ellen C Zwarthoff
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Per-Uno Malmström
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center (CNIO), CIBERONC, Madrid, Spain
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, CIBERONC, Barcelona, Spain
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark.
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
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13
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Abstract
The identification of mutations in FGFR3 in bladder tumors in 1999 led to major interest in this receptor and during the subsequent 20 years much has been learnt about the mutational profiles found in bladder cancer, the phenotypes associated with these and the potential of this mutated protein as a target for therapy. Based on mutational and expression data, it is estimated that >80% of non-muscle-invasive bladder cancers (NMIBC) and ∼40% of muscle-invasive bladder cancers (MIBC) have upregulated FGFR3 signalling, and these frequencies are likely to be even higher if alternative splicing of the receptor, expression of ligands and changes in regulatory mechanisms are taken into account. Major efforts by the pharmaceutical industry have led to development of a range of agents targeting FGFR3 and other FGF receptors. Several of these have entered clinical trials, and some have presented very encouraging early results in advanced bladder cancer. Recent reviews have summarised the drugs and related clinical trials in this area. This review will summarise what is known about the effects of FGFR3 and its mutant forms in normal urothelium and bladder tumors, will suggest when and how this protein contributes to urothelial cancer pathogenesis and will highlight areas that may benefit from further study.
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Affiliation(s)
- Margaret A. Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James’s, St James’s University Hospital, Leeds LS9 7TF, UK
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14
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Pritchard JJG, Hamilton G, Hurst CD, Fraser S, Orange C, Knowles MA, Jones RJ, Leung HY, Iwata T. Monitoring of urothelial cancer disease status after treatment by digital droplet PCR liquid biopsy assays. Urol Oncol 2020; 38:737.e1-737.e10. [PMID: 32532529 DOI: 10.1016/j.urolonc.2020.05.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 12/04/2019] [Revised: 04/12/2020] [Accepted: 05/10/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Real-time monitoring of disease status would be beneficial for timely decision making in the treatment of urothelial cancer (UC), and may accelerate the evaluation of clinical trials. Use of cell free tumor DNA (cftDNA) as a biomarker in liquid biopsy is minimally invasive and its successful use has been reported in various cancer types, including UC. The objective of this study was to evaluate the use of digital droplet PCR (ddPCR)-based assays to monitor UC after treatment. METHOD AND MATERIALS Blood, urine and matching formalin fixed, paraffin embedded diagnostic specimens were collected from 20 patients diagnosed with stage T1 (n = 2) and T2/T3 (n = 18) disease. SNaPshot assays, Sanger sequencing and whole exome sequencing were used to identify tumor-specific mutations, and somatic mutation status was confirmed using patient-matched DNAs extracted from buffy coats and peripheral blood mononucleocytes. The ddPCR assays of the tumor-specific mutations were used to detect the fractional abundance of cftDNA in plasma and urine. RESULTS SNaPshot and Sanger sequencing identified point mutations in 70% of the patients that were assayable by ddPCR. Cases of remission and relapse monitored by assays for PIK3CA E542K and TP53 Y163C mutations in plasma and urine concurred with clinical observations up to 48 months from the start of chemotherapy. A new ddPCR assay for the telomerase reverse transcriptase (TERT) promoter (-124) mutation was developed. The TERT assay was able to detect mutations in cases below the limit of detection by SNaPshot. Whole exome sequencing identified a novel mutation, CNTNAP4 G727*. A ddPCR assay designed to detect this mutation was able to distinguish mutant from wild-type alleles. CONCLUSIONS The study demonstrated that ddPCR assays could be used to detect cftDNA in liquid biopsy monitoring of the post-therapy disease status in patients with UC. Overall, 70% of the patients in our study harbored mutations that were assayable by ddPCR.
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Affiliation(s)
- John J G Pritchard
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Graham Hamilton
- Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom
| | - Carolyn D Hurst
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Sioban Fraser
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Clare Orange
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Margaret A Knowles
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, United Kingdom
| | - Robert J Jones
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom; Cancer Research UK Beatson Institute, Glasgow, United Kingdom; Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Hing Y Leung
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom; Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Tomoko Iwata
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom.
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15
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Clausen TM, Kumar G, Ibsen EK, Ørum-Madsen MS, Hurtado-Coll A, Gustavsson T, Agerbæk MØ, Gatto F, Todenhöfer T, Basso U, Knowles MA, Sanchez-Carbayo M, Salanti A, Black PC, Daugaard M. A simple method for detecting oncofetal chondroitin sulfate glycosaminoglycans in bladder cancer urine. Cell Death Discov 2020; 6:65. [PMID: 32793395 PMCID: PMC7385127 DOI: 10.1038/s41420-020-00304-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 06/09/2020] [Revised: 06/29/2020] [Accepted: 07/13/2020] [Indexed: 11/10/2022] Open
Abstract
Proteoglycans in bladder tumors are modified with a distinct oncofetal chondroitin sulfate (ofCS) glycosaminoglycan that is normally restricted to placental trophoblast cells. This ofCS-modification can be detected in bladder tumors by the malarial VAR2CSA protein, which in malaria pathogenesis mediates adherence of parasite-infected erythrocytes within the placenta. In bladder cancer, proteoglycans are constantly shed into the urine, and therefore have the potential to be used for detection of disease. In this study we investigated whether recombinant VAR2CSA (rVAR2) protein could be used to detect ofCS-modified proteoglycans (ofCSPGs) in the urine of bladder cancer patients as an indication of disease presence. We show that ofCSPGs in bladder cancer urine can be immobilized on cationic nitrocellulose membranes and subsequently probed for ofCS content by rVAR2 protein in a custom-made dot-blot assay. Patients with high-grade bladder tumors displayed a marked increase in urinary ofCSPGs as compared to healthy individuals. Urine ofCSPGs decreased significantly after complete tumor resection compared to matched urine collected preoperatively from patients with bladder cancer. Moreover, ofCSPGs in urine correlated with tumor size of bladder cancer patients. These findings demonstrate that rVAR2 can be utilized in a simple biochemical assay to detect cancer-specific ofCS-modifications in the urine of bladder cancer patients, which may be further developed as a noninvasive approach to detect and monitor the disease.
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Affiliation(s)
- Thomas Mandel Clausen
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC Canada
- Vancouver Prostate Centre, Vancouver, BC Canada
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, Copenhagen, Denmark
| | - Gunjan Kumar
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC Canada
- Vancouver Prostate Centre, Vancouver, BC Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC Canada
| | - Emilie K. Ibsen
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, Copenhagen, Denmark
| | - Maj S. Ørum-Madsen
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC Canada
- Vancouver Prostate Centre, Vancouver, BC Canada
| | - Antonio Hurtado-Coll
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC Canada
- Vancouver Prostate Centre, Vancouver, BC Canada
| | - Tobias Gustavsson
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mette Ø. Agerbæk
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, Copenhagen, Denmark
- VarCT Diagnostics ApS, Copenhagen, Denmark
| | - Francesco Gatto
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Present Address: Elypta AB, Stockholm, Sweden
| | - Tilman Todenhöfer
- Department of Urology, University Hospital Tübingen, Eberhard-Karls University Tübingen, Tübingen, Germany
- Studienpraxis Urologie, Clinical Trial Unit, Steinengrabenstr. 17, Nürtingen, Germany
| | - Umberto Basso
- Medical Oncology Unit 1, Istituto Oncologico Veneto IOV – IRCCS, Padova, Italy
| | - Margaret A. Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James’s, St James’s University Hospital, Beckett Street, Leeds, UK
| | | | - Ali Salanti
- Centre for Medical Parasitology at Department for Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen and Department of Infectious Disease, Copenhagen University Hospital, Copenhagen, Denmark
| | - Peter C. Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC Canada
- Vancouver Prostate Centre, Vancouver, BC Canada
| | - Mads Daugaard
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC Canada
- Vancouver Prostate Centre, Vancouver, BC Canada
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16
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Mostafid AH, Porta N, Cresswell J, Griffiths TR, Kelly JD, Penegar SR, Davenport K, McGrath JS, Campain N, Cooke P, Masood S, Knowles MA, Feber A, Knight A, Catto JW, Lewis R, Hall E. CALIBER: a phase II randomized feasibility trial of chemoablation with mitomycin-C vs surgical management in low-risk non-muscle-invasive bladder cancer. BJU Int 2020; 125:817-826. [PMID: 32124514 PMCID: PMC7318672 DOI: 10.1111/bju.15038] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To evaluate the activity of intravesical mitomycin-C (MMC) to ablate recurrent low-risk non-muscle-invasive bladder cancer (NMIBC) and assess whether it may enable patients to avoid surgical intervention for treatment of recurrence. PATIENTS AND METHODS CALIBER is a phase II feasibility study. Participants were randomized (2:1) to treatment with four once-weekly MMC 40-mg intravesical instillations (chemoablation arm) or to surgical management. The surgical group was included to assess the feasibility of randomization. The primary endpoint was complete response to intravesical MMC in the chemoablation arm at 3 months, reported with exact 95% confidence intervals (CIs). Secondary endpoints included time to subsequent recurrence, summarized by Kaplan-Meier methods. RESULTS Between February 2015 and August 2017, 82 patients with visual diagnosis of recurrent low-risk NMIBC were enrolled from 24 UK hospitals (chemoablation, n = 54; surgical management, n =28). The median follow-up was 24 months. Complete response at 3 months was 37.0% (20/54; 95% CI 24.3-51.3) with chemoablation and 80.8% (21/26; 95% CI 60.6-93.4) with surgical management. Amongst patients with complete response at 3 months, a similar proportion was recurrence-free by 12 months in both groups (84%). Amongst those with residual disease at 3 months, the 12-month recurrence-free proportion was lower in the surgical management group (40.0%) than in the chemoablation group (84%). Recruitment stopped early as chemoablation did not meet the prespecified threshold of 45% complete responses at 3 months. CONCLUSION Intravesical chemoablation in low-risk NMIBC is feasible and safe, but did not demonstrate sufficient response in the present trial. After chemoablation there may be a reduction in recurrence rate, even in non-responders, that is greater than with surgery alone. Further research is required to investigate the role and optimal schedule of neoadjuvant intravesical chemotherapy prior to surgery for NMIBC.
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Affiliation(s)
| | | | | | | | | | | | - Kim Davenport
- Gloucestershire Hospitals NHS Foundation TrustCheltenhamUK
| | | | | | - Peter Cooke
- Royal Wolverhampton Hospitals NHS TrustWolverhamptonUK
| | | | | | | | | | | | | | - Emma Hall
- Institute of Cancer ResearchLondonUK
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17
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di Martino E, Alder O, Hurst CD, Knowles MA. ETV5 links the FGFR3 and Hippo signalling pathways in bladder cancer. Sci Rep 2019; 9:5740. [PMID: 30952872 PMCID: PMC6450944 DOI: 10.1038/s41598-018-36456-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 12/02/2016] [Accepted: 11/14/2018] [Indexed: 12/29/2022] Open
Abstract
Activating mutations of fibroblast growth factor receptor 3 (FGFR3) are common in urothelial carcinoma of the bladder (UC). Silencing or inhibition of mutant FGFR3 in bladder cancer cell lines is associated with decreased malignant potential, confirming its important driver role in UC. However, understanding of how FGFR3 activation drives urothelial malignant transformation remains limited. We have previously shown that mutant FGFR3 alters the cell-cell and cell-matrix adhesion properties of urothelial cells, resulting in loss of contact-inhibition of proliferation. In this study, we investigate a transcription factor of the ETS-family, ETV5, as a putative effector of FGFR3 signalling in bladder cancer. We show that FGFR3 signalling induces a MAPK/ERK-mediated increase in ETV5 levels, and that this results in increased level of TAZ, a co-transcriptional regulator downstream of the Hippo signalling pathway involved in cell-contact inhibition. We also demonstrate that ETV5 is a key downstream mediator of the oncogenic effects of mutant FGFR3, as its knockdown in FGFR3-mutant bladder cancer cell lines is associated with reduced proliferation and anchorage-independent growth. Overall this study advances our understanding of the molecular alterations occurring during urothelial malignant transformation and indicates TAZ as a possible therapeutic target in FGFR3-dependent bladder tumours.
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Affiliation(s)
- Erica di Martino
- University of Leeds, Leeds Institute of Medical Research at St James's, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - Olivia Alder
- University of Leeds, Leeds Institute of Medical Research at St James's, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - Carolyn D Hurst
- University of Leeds, Leeds Institute of Medical Research at St James's, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - Margaret A Knowles
- University of Leeds, Leeds Institute of Medical Research at St James's, St. James's University Hospital, Leeds, LS9 7TF, UK.
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18
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Abstract
Non-muscle-invasive bladder cancer (NMIBC) includes stage Ta and stage T1 tumors and carcinoma in situ (CIS). Grading of Ta tumors subdivides these lesions into papillary urothelial neoplasms of low malignant potential and low- and high-grade noninvasive papillary urothelial carcinoma. CIS is by definition high-grade and the majority of stage T1 tumors are of high-grade. This pathologic heterogeneity is associated with divergent clinical outcome, with significantly worse prognosis for patients with T1 tumors or CIS. A wealth of molecular information has accumulated on NMIBC including mutational data that ranges from the whole chromosome level to next generation sequence data at nucleotide level. This has not only identified key genes that are mutated in NMIBC, but also provides insight into the processes that shape their mutational landscape. Although molecular analyses cannot yet provide definitive personal prognostic information, many differences between these entities promise improved disease management in the future. Most information is available for Ta and T1 samples and this is the focus of this review.
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Affiliation(s)
- Carolyn D Hurst
- Section of Molecular Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, United Kingdom
| | - Margaret A Knowles
- Section of Molecular Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, United Kingdom.
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19
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Foth M, Ismail NFB, Kung JSC, Tomlinson D, Knowles MA, Eriksson P, Sjödahl G, Salmond JM, Sansom OJ, Iwata T. FGFR3 mutation increases bladder tumourigenesis by suppressing acute inflammation. J Pathol 2018; 246:331-343. [PMID: 30043421 PMCID: PMC6334176 DOI: 10.1002/path.5143] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/20/2018] [Accepted: 07/18/2018] [Indexed: 12/15/2022]
Abstract
Recent studies of muscle-invasive bladder cancer show that FGFR3 mutations are generally found in a luminal papillary tumour subtype that is characterised by better survival than other molecular subtypes. To better understand the role of FGFR3 in invasive bladder cancer, we examined the process of tumour development induced by the tobacco carcinogen OH-BBN in genetically engineered models that express mutationally activated FGFR3 S249C or FGFR3 K644E in the urothelium. Both occurrence and progression of OH-BBN-driven tumours were increased in the presence of an S249C mutation compared to wild-type control mice. Interestingly, at an early tumour initiation stage, the acute inflammatory response in OH-BBN-treated bladders was suppressed in the presence of an S249C mutation. However, at later stages of tumour progression, increased inflammation was observed in S249C tumours, long after the carcinogen administration had ceased. Early-phase neutrophil depletion using an anti-Ly6G monoclonal antibody resulted in an increased neutrophil-to-lymphocyte ratio at later stages of pathogenesis, indicative of enhanced tumour pathogenesis, which supports the hypothesis that suppression of acute inflammation could play a causative role. Statistical analyses of correlation showed that while initial bladder phenotypes in morphology and inflammation were FGFR3-dependent, increased levels of inflammation were associated with tumour progression at the later stage. This study provides a novel insight into the tumour-promoting effect of FGFR3 mutations via regulation of inflammation at the pre-tumour stage in the bladder. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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MESH Headings
- Animals
- Butylhydroxybutylnitrosamine
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cholecystitis, Acute/chemically induced
- Cholecystitis, Acute/genetics
- Cholecystitis, Acute/immunology
- Cholecystitis, Acute/metabolism
- Disease Models, Animal
- Disease Progression
- Female
- Genetic Predisposition to Disease
- Lymphocytes/immunology
- Lymphocytes/metabolism
- Lymphocytes/pathology
- Male
- Mice, Inbred C57BL
- Mice, Transgenic
- Mutation
- Neutrophil Infiltration
- Neutrophils/immunology
- Neutrophils/metabolism
- Neutrophils/pathology
- Phenotype
- Receptor, Fibroblast Growth Factor, Type 3/genetics
- Receptor, Fibroblast Growth Factor, Type 3/metabolism
- Time Factors
- Tumor Microenvironment
- Urinary Bladder/immunology
- Urinary Bladder/metabolism
- Urinary Bladder/pathology
- Urinary Bladder Neoplasms/chemically induced
- Urinary Bladder Neoplasms/genetics
- Urinary Bladder Neoplasms/immunology
- Urinary Bladder Neoplasms/metabolism
- Urothelium/immunology
- Urothelium/metabolism
- Urothelium/pathology
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Affiliation(s)
- Mona Foth
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
- Cancer Research UK Beatson InstituteGlasgowUK
| | - Nur Faezah Binti Ismail
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Jeng Sum Charmaine Kung
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Darren Tomlinson
- Leeds Institute of Cancer and PathologySt James's University HospitalLeedsUK
| | - Margaret A Knowles
- Leeds Institute of Cancer and PathologySt James's University HospitalLeedsUK
| | - Pontus Eriksson
- Division of Oncology and Pathology, Department of Clinical SciencesLund UniversityLundSweden
| | - Gottfrid Sjödahl
- Division of Urological Research, Department of Translational MedicineLund University, Skåne University HospitalMalmöSweden
| | | | - Owen J Sansom
- Cancer Research UK Beatson InstituteGlasgowUK
- Institute of Cancer Sciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowUK
| | - Tomoko Iwata
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
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20
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Mellor P, Marshall JDS, Ruan X, Whitecross DE, Ross RL, Knowles MA, Moore SA, Anderson DH. Patient-derived mutations within the N-terminal domains of p85α impact PTEN or Rab5 binding and regulation. Sci Rep 2018; 8:7108. [PMID: 29740032 PMCID: PMC5940657 DOI: 10.1038/s41598-018-25487-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 01/18/2018] [Accepted: 04/20/2018] [Indexed: 12/11/2022] Open
Abstract
The p85α protein regulates flux through the PI3K/PTEN signaling pathway, and also controls receptor trafficking via regulation of Rab-family GTPases. In this report, we determined the impact of several cancer patient-derived p85α mutations located within the N-terminal domains of p85α previously shown to bind PTEN and Rab5, and regulate their respective functions. One p85α mutation, L30F, significantly reduced the steady state binding to PTEN, yet enhanced the stimulation of PTEN lipid phosphatase activity. Three other p85α mutations (E137K, K288Q, E297K) also altered the regulation of PTEN catalytic activity. In contrast, many p85α mutations reduced the binding to Rab5 (L30F, I69L, I82F, I177N, E217K), and several impacted the GAP activity of p85α towards Rab5 (E137K, I177N, E217K, E297K). We determined the crystal structure of several of these p85α BH domain mutants (E137K, E217K, R262T E297K) for bovine p85α BH and found that the mutations did not alter the overall domain structure. Thus, several p85α mutations found in human cancers may deregulate PTEN and/or Rab5 regulated pathways to contribute to oncogenesis. We also engineered several experimental mutations within the p85α BH domain and identified L191 and V263 as important for both binding and regulation of Rab5 activity.
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Affiliation(s)
- Paul Mellor
- Cancer Research Group, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Jeremy D S Marshall
- Cancer Research Group, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada.,Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Xuan Ruan
- Cancer Research Group, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Dielle E Whitecross
- Cancer Research Group, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Rebecca L Ross
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, United Kingdom
| | - Margaret A Knowles
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, United Kingdom
| | - Stanley A Moore
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Deborah H Anderson
- Cancer Research Group, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada. .,Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada. .,Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada.
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21
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Baldia PH, Maurer A, Heide T, Rose M, Stoehr R, Hartmann A, Williams SV, Knowles MA, Knuechel R, Gaisa NT. Fibroblast growth factor receptor (FGFR) alterations in squamous differentiated bladder cancer: a putative therapeutic target for a small subgroup. Oncotarget 2018; 7:71429-71439. [PMID: 27669755 PMCID: PMC5342089 DOI: 10.18632/oncotarget.12198] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 07/16/2016] [Accepted: 09/16/2016] [Indexed: 11/25/2022] Open
Abstract
Although drugable fibroblast growth factor receptor (FGFR) alterations in squamous cell carcinomas (SCC) of various entities are well known, little is known about FGFR modifications in squamous differentiated bladder cancer. Therefore, our study evaluated FGFR1-3 alterations as a putative therapeutic target in this subgroup. We analyzed 73 squamous differentiated bladder cancers (n = 10 pT2, n = 55 pT3, n = 8 pT4) for FGFR1-3 protein expression, FGFR1-3 copy number variations, FGFR3 chromosomal rearrangements (fluorescence in situ hybridization (FISH)) and FGFR3 mutations (SNapShot analysis). Only single cases displayed enhanced protein expression, most frequently FGFR3 overexpression (9.4% (6/64)). FISH showed no amplifications of FGFR1, 2 or 3. Break apart events were only slightly above the cut off in 12.1% (8/66) of cases and no FGFR3-TACC3 rearrangements could be proven by qPCR. FGFR3 mutations (p.S249C) were found in 8.5% (6/71) of tumors and were significantly associated with FGFR3 protein overexpression (p < 0.001), and unfavourable clinical outcome (p = 0.001). Our findings are consistent with the results of the TCGA data set for the “squamous-like” subtype of bladder cancer (n = 85), which revealed reduced overall expression of FGFR1 and FGFR2 in tumors compared to normal tissue, while expression of FGFR3 remained high. In the TCGA “squamous-like” subtype FGFR3 mutations were found in 4.9% and correlated with high FGFR3 RNA expression. Mutations of FGFR1 and FGFR2 were less frequent (2.4% and 1.2%). Hence, our comprehensive study provides novel insights into a subgroup of squamous differentiated bladder tumors that hold clues for novel therapeutic regimens and may benefit from FGFR3-targeted therapies.
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Affiliation(s)
| | - Angela Maurer
- Institute of Pathology, RWTH Aachen University, Aachen, Germany
| | - Timon Heide
- Institute of Pathology, RWTH Aachen University, Aachen, Germany
| | - Michael Rose
- Institute of Pathology, RWTH Aachen University, Aachen, Germany
| | - Robert Stoehr
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University, Erlangen-Nuremberg, Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University, Erlangen-Nuremberg, Erlangen, Germany
| | - Sarah V Williams
- Section of Molecular Oncology, Leeds Institute of Cancer and Pathology, University of Leeds, St. James's University Hospital, United Kingdom
| | - Margaret A Knowles
- Section of Molecular Oncology, Leeds Institute of Cancer and Pathology, University of Leeds, St. James's University Hospital, United Kingdom
| | - Ruth Knuechel
- Institute of Pathology, RWTH Aachen University, Aachen, Germany
| | - Nadine T Gaisa
- Institute of Pathology, RWTH Aachen University, Aachen, Germany
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22
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Affiliation(s)
- Carolyn D Hurst
- Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, University of Leeds, Leeds LS9 7TF, UK
| | - Margaret A Knowles
- Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, University of Leeds, Leeds LS9 7TF, UK
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23
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Turner LD, Summers AJ, Johnson LO, Knowles MA, Fishwick CWG. Identification of an Indazole-Based Pharmacophore for the Inhibition of FGFR Kinases Using Fragment-Led de Novo Design. ACS Med Chem Lett 2017; 8:1264-1268. [PMID: 29259745 DOI: 10.1021/acsmedchemlett.7b00349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/10/2017] [Indexed: 12/21/2022] Open
Abstract
Structure-based drug design (SBDD) has become a powerful tool utilized by medicinal chemists to rationally guide the drug discovery process. Herein, we describe the use of SPROUT, a de novo-based program, to identify an indazole-based pharmacophore for the inhibition of fibroblast growth factor receptor (FGFR) kinases, which are validated targets for cancer therapy. Hit identification using SPROUT yielded 6-phenylindole as a small fragment predicted to bind to FGFR1. With the aid of docking models, several modifications to the indole were made to optimize the fragment to an indazole-containing pharmacophore, leading to a library of compounds containing 23 derivatives. Biological evaluation revealed that these indazole-containing fragments inhibited FGFR1-3 in the range of 0.8-90 μM with excellent ligand efficiencies of 0.30-0.48. Some compounds exhibited moderate selectivity toward individual FGFRs, indicating that further optimization using SBDD may lead to potent and selective inhibitors of the FGFR family.
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Affiliation(s)
- Lewis D. Turner
- School
of Chemistry and †Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS2 9JT, U.K
| | - Abbey J. Summers
- School
of Chemistry and †Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS2 9JT, U.K
| | - Laura O. Johnson
- School
of Chemistry and †Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS2 9JT, U.K
| | | | - Colin W. G. Fishwick
- School
of Chemistry and †Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS2 9JT, U.K
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24
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Lombardi B, Ashford P, Moya-Garcia AA, Rust A, Crawford M, Williams SV, Knowles MA, Katan M, Orengo C, Godovac-Zimmermann J. Unique signalling connectivity of FGFR3-TACC3 oncoprotein revealed by quantitative phosphoproteomics and differential network analysis. Oncotarget 2017; 8:102898-102911. [PMID: 29262532 PMCID: PMC5732698 DOI: 10.18632/oncotarget.22048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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: 08/15/2017] [Accepted: 10/03/2017] [Indexed: 12/14/2022] Open
Abstract
The FGFR3-TACC3 fusion is an oncogenic driver in diverse malignancies, including bladder cancer, characterized by upregulated tyrosine kinase activity. To gain insights into distinct properties of FGFR3-TACC3 down-stream signalling, we utilised telomerase-immortalised normal human urothelial cell lines expressing either the fusion or wild-type FGFR3 (isoform IIIb) for subsequent quantitative proteomics and network analysis. Cellular lysates were chemically labelled with isobaric tandem mass tag reagents and, after phosphopeptide enrichment, liquid chromatography-high mass accuracy tandem mass spectrometry (LC-MS/MS) was used for peptide identification and quantification. Comparison of data from the two cell lines under non-stimulated and FGF1 stimulated conditions and of data representing physiological stimulation of FGFR3 identified about 200 regulated phosphosites. The identified phosphoproteins and quantified phosphosites were further analysed in the context of functional biological networks by inferring kinase-substrate interactions, mapping these to a comprehensive human signalling interaction network, filtering based on tissue-expression profiles and applying disease module detection and pathway enrichment methods. Analysis of our phosphoproteomics data using these bioinformatics methods combined into a new protocol-Disease Relevant Analysis of Genes On Networks (DRAGON)-allowed us to tease apart pathways differentially involved in FGFR3-TACC3 signalling in comparison to wild-type FGFR3 and to investigate their local phospho-signalling context. We highlight 9 pathways significantly regulated only in the cell line expressing FGFR3-TACC3 fusion and 5 pathways regulated only by stimulation of the wild-type FGFR3. Pathways differentially linked to FGFR3-TACC3 fusion include those related to chaperone activation and stress response and to regulation of TP53 expression and degradation that could contribute to development and maintenance of the cancer phenotype.
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Affiliation(s)
- Benedetta Lombardi
- Proteomics and Molecular Cell Dynamics, Center for Nephrology, School of Life and Medical Sciences, University College London, London NW3 2PF, United Kingdom
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Paul Ashford
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Aurelio A. Moya-Garcia
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Aleksander Rust
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Mark Crawford
- Proteomics and Molecular Cell Dynamics, Center for Nephrology, School of Life and Medical Sciences, University College London, London NW3 2PF, United Kingdom
| | - Sarah V. Williams
- Section of Molecular Oncology, Leeds Institute of Molecular Medicine, St James’s University Hospital, Leeds LS9 7TF, United Kingdom
| | - Margaret A. Knowles
- Section of Molecular Oncology, Leeds Institute of Molecular Medicine, St James’s University Hospital, Leeds LS9 7TF, United Kingdom
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Christine Orengo
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Jasminka Godovac-Zimmermann
- Proteomics and Molecular Cell Dynamics, Center for Nephrology, School of Life and Medical Sciences, University College London, London NW3 2PF, United Kingdom
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25
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Hurst CD, Alder O, Platt FM, Droop A, Stead LF, Burns JE, Burghel GJ, Jain S, Klimczak LJ, Lindsay H, Roulson JA, Taylor CF, Thygesen H, Cameron AJ, Ridley AJ, Mott HR, Gordenin DA, Knowles MA. Genomic Subtypes of Non-invasive Bladder Cancer with Distinct Metabolic Profile and Female Gender Bias in KDM6A Mutation Frequency. Cancer Cell 2017; 32:701-715.e7. [PMID: 29136510 PMCID: PMC5774674 DOI: 10.1016/j.ccell.2017.08.005] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 05/13/2017] [Accepted: 08/09/2017] [Indexed: 01/01/2023]
Abstract
Bladder cancer incurs a higher lifetime treatment cost than other cancers due to frequent recurrence of non-invasive disease. Improved prognostic biomarkers and localized therapy are needed for this large patient group. We defined two major genomic subtypes of primary stage Ta tumors. One of these was characterized by loss of 9q including TSC1, increased KI67 labeling index, upregulated glycolysis, DNA repair, mTORC1 signaling, features of the unfolded protein response, and altered cholesterol homeostasis. Comparison with muscle-invasive bladder cancer mutation profiles revealed lower overall mutation rates and more frequent mutations in RHOB and chromatin modifier genes. More mutations in the histone lysine demethylase KDM6A were present in non-invasive tumors from females than males.
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Affiliation(s)
- Carolyn D. Hurst
- Section of Molecular Oncology, Leeds Institute of Cancer and Pathology, St James’s University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Olivia Alder
- Section of Molecular Oncology, Leeds Institute of Cancer and Pathology, St James’s University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Fiona M. Platt
- Section of Molecular Oncology, Leeds Institute of Cancer and Pathology, St James’s University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Alastair Droop
- Cancer Research UK Leeds Centre, Leeds Institute of Cancer and Pathology, St. James’s University Hospital, Leeds LS9 7TF, UK
| | - Lucy F. Stead
- Section of Oncology and Clinical Research, Leeds Institute of Cancer and Pathology, St James’s University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Julie E. Burns
- Section of Molecular Oncology, Leeds Institute of Cancer and Pathology, St James’s University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - George J. Burghel
- DNA Laboratory, Genetics Service, Ashley Wing, St James University Hospital, Leeds, LS9 7TF, UK
| | - Sunjay Jain
- Pyrah Department of Urology, St James’s University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Helen Lindsay
- DNA Laboratory, Genetics Service, Ashley Wing, St James University Hospital, Leeds, LS9 7TF, UK
| | - Jo-An Roulson
- Department of Histopathology, St James’s University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Claire F. Taylor
- Cancer Research UK Leeds Centre, Leeds Institute of Cancer and Pathology, St. James’s University Hospital, Leeds LS9 7TF, UK
| | - Helene Thygesen
- Cancer Research UK Leeds Centre, Leeds Institute of Cancer and Pathology, St. James’s University Hospital, Leeds LS9 7TF, UK
| | - Angus J. Cameron
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Anne J. Ridley
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
- Randall Division of Cell and Molecular Biophysics, New Hunt’s House, King’s College London, Guy’s Campus, London SE1 1UL, UK
| | - Helen R. Mott
- Department of Biochemistry, 80, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Margaret A. Knowles
- Section of Molecular Oncology, Leeds Institute of Cancer and Pathology, St James’s University Hospital, Beckett Street, Leeds, LS9 7TF, UK
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26
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Pettitt GA, McPherson HR, Hurst CD, Burns JE, Alder OA, Dunning MC, Knowles MA. Abstract 3145: Mechanisms of resistance to FGFR-targeted therapy in bladder cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3145] [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: 11/16/2022]
Abstract
Abstract
Fibroblast growth factor receptor 3 (FGFR3) overexpression, point mutations or gene fusions are found in ~80% of non muscle-invasive and ~15% of muscle-invasive bladder cancer. FGFR inhibitors have entered clinical trials in advanced bladder cancer however, as with other targeted therapies, intrinsic and acquired resistance are expected to limit treatment efficacy. We have used an in vitro model to explore possible mechanisms of resistance.
The urothelial cancer cell line RT112 expresses an FGFR3-TACC3 fusion protein and is sensitive to FGFR inhibition. Isogenic resistant cell lines, termed R1, R2 and R3, were derived by long-term culture of RT112 in the presence of the FGFR inhibitor PD173074. Compared to parental RT112, R1 and R2 show reduced proliferation and have a more mesenchymal morphology, decreased expression of FGFR3 and increased expression of N-cadherin. R3 has a faster growth rate, more epithelial morphology and lower N-cadherin expression than R1 and R2.
The changes in morphology and gene expression between parental and resistant derivatives R1 and R2 were reversed when the resistant cells were cultured without PD173074 for 4 passages. Despite this, the cells retained their resistance when re-exposed to PD173074.
Exome sequencing, RNA microarray analysis and phospho-receptor tyrosine kinase array data on the parental cells and resistant derivatives and will be presented. Our data suggests that diverse mechanisms of resistance occur following prolonged FGFR inhibition.
Citation Format: Geoffrey A. Pettitt, Helen R. McPherson, Carolyn D. Hurst, Julie E. Burns, Olivia A. Alder, Matthew C. Dunning, Margaret A. Knowles. Mechanisms of resistance to FGFR-targeted therapy in bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3145. doi:10.1158/1538-7445.AM2017-3145
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Ross RL, McPherson HR, Kettlewell L, Shnyder SD, Hurst CD, Alder O, Knowles MA. PIK3CA dependence and sensitivity to therapeutic targeting in urothelial carcinoma. BMC Cancer 2016; 16:553. [PMID: 27465249 PMCID: PMC4964013 DOI: 10.1186/s12885-016-2570-0] [Citation(s) in RCA: 24] [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: 05/09/2016] [Accepted: 07/15/2016] [Indexed: 12/21/2022] Open
Abstract
Background Many urothelial carcinomas (UC) contain activating PIK3CA mutations. In telomerase-immortalized normal urothelial cells (TERT-NHUC), ectopic expression of mutant PIK3CA induces PI3K pathway activation, cell proliferation and cell migration. However, it is not clear whether advanced UC tumors are PIK3CA-dependent and whether PI3K pathway inhibition is a good therapeutic option in such cases. Methods We used retrovirus-mediated delivery of shRNA to knock down mutant PIK3CA in UC cell lines and assessed effects on pathway activation, cell proliferation, migration and tumorigenicity. The effect of the class I PI3K inhibitor GDC-0941 was assessed in a panel of UC cell lines with a range of known molecular alterations in the PI3K pathway. Results Specific knockdown of PIK3CA inhibited proliferation, migration, anchorage-independent growth and in vivo tumor growth of cells with PIK3CA mutations. Sensitivity to GDC-0941 was dependent on hotspot PIK3CA mutation status. Cells with rare PIK3CA mutations and co-occurring TSC1 or PTEN mutations were less sensitive. Furthermore, downstream PI3K pathway alterations in TSC1 or PTEN or co-occurring AKT1 and RAS gene mutations were associated with GDC-0941 resistance. Conclusions Mutant PIK3CA is a potent oncogenic driver in many UC cell lines and may represent a valuable therapeutic target in advanced bladder cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2570-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- R L Ross
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - H R McPherson
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - L Kettlewell
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - S D Shnyder
- Institute of Cancer Therapeutics, University of Bradford, Richmond Road, Bradford, BD7 1DP, UK
| | - C D Hurst
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - O Alder
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - M A Knowles
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK.
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Hurst CD, Alder O, Platt FM, Droop A, Stead LF, Burns JE, Burghel GJ, Jain S, Klimczak LJ, Lindsay H, Roulson JA, Taylor CF, Thygesen H, Cameron AJ, Ridley AJ, Mott HR, Gordenin DA, Knowles MA. Abstract LB-323: The genomic landscape of non-muscle-invasive bladder cancer: implications for molecular classification and treatment. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-lb-323] [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: 11/16/2022]
Abstract
Abstract
Non-muscle-invasive bladder cancers (NMIBC) and muscle-invasive bladder cancers (MIBC) show distinct molecular and clinical features and are considered to follow different pathogenesis pathways. MIBC commonly metastasise (>50%) and have poor prognosis whereas NMIBC, particularly low-stage low-grade tumors, rarely progress to invade muscle (<5%). Patients diagnosed with NMIBC frequently suffer disease recurrence, demanding long-term disease monitoring and repeated resection of recurrences. Large MIBC cohorts have been extensively interrogated on a genome-wide scale but relatively few NMIBC have been studied at this level. To address this we determined the mutational landscape of 82 non-muscle-invasive tumors (stage Ta grade 2) using whole-exome and targeted deep sequencing. Whole-exome sequencing identified an average of 124±79 synonymous and non-synonymous somatic mutations (single nucleotide substitutions and indels) per sample, giving mean and median somatic mutation rates of 2.41 and 1.64 per megabase, respectively. Overall, 47% of nucleotide substitutions were C>T transitions, followed by C>G transversions (24.8%). Similar to MIBC, APOBEC mutagenesis was the strongest source of mutation in NMIBC with 75% of samples showing up to 5-fold enrichment of the APOBEC mutation signature. Significantly mutated genes included genes implicated in epigenetic regulation and several genes that have not previously been reported as significantly mutated in bladder cancer. Comparison of mutation frequencies in NMIBC with those found in MIBC revealed both known differences (absence of TP53 mutations and high frequency of FGFR3, PIK3CA and STAG2 mutations in NMIBC) and novel findings including a higher frequency of mutations in chromatin-state regulators in NMIBC. Notably CDKN1A, RB1, ERCC2, ERBB3 and FBXW7, which are mutated in >10% of MIBC were not significantly mutated in TaG2 tumors, further delineating the distinct pathogenesis pathways of NMIBC and MIBC. Whole-genome expression array profiling and immunohistochemistry using a panel of markers were carried out to further examine the molecular features of NMIBC samples and define potentially clinically relevant subtypes. These data provide a detailed view of the genomic landscape of NMIBC that highlights chromatin modification as a key area for consideration in the development of potential future therapeutic approaches to the treatment of patients with non-muscle-invasive disease.
Citation Format: Carolyn D. Hurst, Olivia Alder, Fiona M. Platt, Alastair Droop, Lucy F. Stead, Julie E. Burns, George J. Burghel, Sunjay Jain, Leszek J. Klimczak, Helen Lindsay, Jo-An Roulson, Claire F. Taylor, Helene Thygesen, Angus J. Cameron, Anne J. Ridley, Helene R. Mott, Dmitry A. Gordenin, Margaret A. Knowles. The genomic landscape of non-muscle-invasive bladder cancer: implications for molecular classification and treatment. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-323.
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Affiliation(s)
| | | | | | | | | | | | | | - Sunjay Jain
- 2St. James's University Hospital, Leeds, United Kingdom
| | | | - Helen Lindsay
- 2St. James's University Hospital, Leeds, United Kingdom
| | - Jo-An Roulson
- 2St. James's University Hospital, Leeds, United Kingdom
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Abstract
Bladder tumors show diverse molecular features and clinical outcome. Muscle-invasive bladder cancer has poor prognosis and novel approaches to systemic therapy are urgently required. Non-muscle-invasive bladder cancer has good prognosis, but high recurrence rate and the requirement for life-long disease monitoring places a major burden on patients and healthcare providers. Studies of tumor tissues from both disease groups have identified frequent alterations of FGFRs, including mutations of FGFR3 and dysregulated expression of FGFR1 and FGFR3 that suggest that these may be valid therapeutic targets. We summarize current understanding of the molecular alterations affecting these receptors in bladder tumors, preclinical studies validating them as therapeutic targets, available FGFR-targeted agents and results from early clinical trials in bladder cancer patients.
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Affiliation(s)
- Erica di Martino
- Section of Molecular Oncology, Leeds Institute of Cancer & Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Darren C Tomlinson
- Astbury Centre for Structural & Molecular Biology, School of Molecular & Cellular Biology, Astbury Building, University of Leeds, Leeds, LS2 9JT, UK
| | - Sarah V Williams
- Section of Molecular Oncology, Leeds Institute of Cancer & Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Margaret A Knowles
- Section of Molecular Oncology, Leeds Institute of Cancer & Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
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30
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Patani H, Bunney TD, Thiyagarajan N, Norman RA, Ogg D, Breed J, Ashford P, Potterton A, Edwards M, Williams SV, Thomson GS, Pang CS, Knowles MA, Breeze AL, Orengo C, Phillips C, Katan M. Landscape of activating cancer mutations in FGFR kinases and their differential responses to inhibitors in clinical use. Oncotarget 2016; 7:24252-68. [PMID: 26992226 PMCID: PMC5029699 DOI: 10.18632/oncotarget.8132] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/28/2016] [Indexed: 01/09/2023] Open
Abstract
Frequent genetic alterations discovered in FGFRs and evidence implicating some as drivers in diverse tumors has been accompanied by rapid progress in targeting FGFRs for anticancer treatments. Wider assessment of the impact of genetic changes on the activation state and drug responses is needed to better link the genomic data and treatment options. We here apply a direct comparative and comprehensive analysis of FGFR3 kinase domain variants representing the diversity of point-mutations reported in this domain. We reinforce the importance of N540K and K650E and establish that not all highly activating mutations (for example R669G) occur at high-frequency and conversely, that some "hotspots" may not be linked to activation. Further structural characterization consolidates a mechanistic view of FGFR kinase activation and extends insights into drug binding. Importantly, using several inhibitors of particular clinical interest (AZD4547, BGJ-398, TKI258, JNJ42756493 and AP24534), we find that some activating mutations (including different replacements of the same residue) result in distinct changes in their efficacy. Considering that there is no approved inhibitor for anticancer treatments based on FGFR-targeting, this information will be immediately translatable to ongoing clinical trials.
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Affiliation(s)
- Harshnira Patani
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Tom D. Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Nethaji Thiyagarajan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Richard A. Norman
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | - Derek Ogg
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | - Jason Breed
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | - Paul Ashford
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Andrew Potterton
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Mina Edwards
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Sarah V. Williams
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, St James's University Hospital, Leeds LS9 7TF, UK
| | - Gary S. Thomson
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Camilla S.M. Pang
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Margaret A. Knowles
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, St James's University Hospital, Leeds LS9 7TF, UK
| | - Alexander L. Breeze
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Christine Orengo
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
| | - Chris Phillips
- Discovery Sciences, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St, London WC1E 6BT, UK
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Pouessel D, Neuzillet Y, Mertens LS, van der Heijden MS, de Jong J, Sanders J, Peters D, Leroy K, Manceau A, Maille P, Soyeux P, Moktefi A, Semprez F, Vordos D, de la Taille A, Hurst CD, Tomlinson DC, Harnden P, Bostrom PJ, Mirtti T, Horenblas S, Loriot Y, Houédé N, Chevreau C, Beuzeboc P, Shariat SF, Sagalowsky AI, Ashfaq R, Burger M, Jewett MAS, Zlotta AR, Broeks A, Bapat B, Knowles MA, Lotan Y, van der Kwast TH, Culine S, Allory Y, van Rhijn BWG. Tumor heterogeneity of fibroblast growth factor receptor 3 (FGFR3) mutations in invasive bladder cancer: implications for perioperative anti-FGFR3 treatment. Ann Oncol 2016; 27:1311-6. [PMID: 27091807 DOI: 10.1093/annonc/mdw170] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [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: 02/04/2016] [Accepted: 04/06/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Fibroblast growth factor receptor 3 (FGFR3) is an actionable target in bladder cancer. Preclinical studies show that anti-FGFR3 treatment slows down tumor growth, suggesting that this tyrosine kinase receptor is a candidate for personalized bladder cancer treatment, particularly in patients with mutated FGFR3. We addressed tumor heterogeneity in a large multicenter, multi-laboratory study, as this may have significant impact on therapeutic response. PATIENTS AND METHODS We evaluated possible FGFR3 heterogeneity by the PCR-SNaPshot method in the superficial and deep compartments of tumors obtained by transurethral resection (TUR, n = 61) and in radical cystectomy (RC, n = 614) specimens and corresponding cancer-positive lymph nodes (LN+, n = 201). RESULTS We found FGFR3 mutations in 13/34 (38%) T1 and 8/27 (30%) ≥T2-TUR samples, with 100% concordance between superficial and deeper parts in T1-TUR samples. Of eight FGFR3 mutant ≥T2-TUR samples, only 4 (50%) displayed the mutation in the deeper part. We found 67/614 (11%) FGFR3 mutations in RC specimens. FGFR3 mutation was associated with pN0 (P < 0.001) at RC. In 10/201 (5%) LN+, an FGFR3 mutation was found, all concordant with the corresponding RC specimen. In the remaining 191 cases, RC and LN+ were both wild type. CONCLUSIONS FGFR3 mutation status seems promising to guide decision-making on adjuvant anti-FGFR3 therapy as it appeared homogeneous in RC and LN+. Based on the results of TUR, the deep part of the tumor needs to be assessed if neoadjuvant anti-FGFR3 treatment is considered. We conclude that studies on the heterogeneity of actionable molecular targets should precede clinical trials with these drugs in the perioperative setting.
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Affiliation(s)
- D Pouessel
- Inserm U955, Hôpital Henri Mondor, APHP, Team 7 Translational Research of Genito-Urinary Oncogenesis, Créteil Department of Medical Oncology, Hôpital Saint-Louis, AP-HP, Paris, France
| | | | | | | | | | - J Sanders
- Pathology Molecular Pathology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - D Peters
- Molecular Pathology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | | | | | | | - P Soyeux
- Inserm U955, Hôpital Henri Mondor, APHP, Team 7 Translational Research of Genito-Urinary Oncogenesis, Créteil
| | | | - F Semprez
- Inserm U955, Hôpital Henri Mondor, APHP, Team 7 Translational Research of Genito-Urinary Oncogenesis, Créteil
| | - D Vordos
- Urology, Hôpital Henri Mondor, APHP, Créteil, France
| | - A de la Taille
- Inserm U955, Hôpital Henri Mondor, APHP, Team 7 Translational Research of Genito-Urinary Oncogenesis, Créteil Urology, Hôpital Henri Mondor, APHP, Créteil, France
| | - C D Hurst
- Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK
| | - D C Tomlinson
- Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK
| | - P Harnden
- Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK
| | - P J Bostrom
- Departments of Urology Department of Surgical Oncology (Urology), University Health Network, Princess Margaret Cancer Centre, University of Toronto, Toronto
| | - T Mirtti
- Pathology, University of Turku, Turku, Finland
| | | | - Y Loriot
- Department of Cancer Medicine and INSERM U981, Gustave Roussy, Cancer Campus, Grand Paris, Villejuif
| | - N Houédé
- Department of Oncological Medicine, Institut Bergonié, Bordeaux
| | - C Chevreau
- Department of Oncological Medicine, Institut Claudius Régaud, Toulouse
| | - P Beuzeboc
- Department of Oncological Medicine, Institut Curie, Paris, France
| | - S F Shariat
- Departments of Urology Department of Urology, Medical University of Vienna, Vienna General Hospital, Vienna, Austria
| | | | - R Ashfaq
- Pathology, University of Texas, Southwestern Medical Center, Dallas, USA
| | - M Burger
- Department of Urology, Caritas St Josef Medical Centre, University of Regensburg, Regensburg, Germany
| | - M A S Jewett
- Department of Surgical Oncology (Urology), University Health Network, Princess Margaret Cancer Centre, University of Toronto, Toronto
| | - A R Zlotta
- Department of Surgical Oncology (Urology), University Health Network, Princess Margaret Cancer Centre, University of Toronto, Toronto Departments of Surgery (Urology)
| | - A Broeks
- Molecular Pathology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - B Bapat
- Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto
| | - M A Knowles
- Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK
| | | | - T H van der Kwast
- Department of Pathology, University Health Network, Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - S Culine
- Department of Medical Oncology, Hôpital Saint-Louis, AP-HP, Paris, France Department of Medical Oncology, Paris 7 University, Paris
| | - Y Allory
- Inserm U955, Hôpital Henri Mondor, APHP, Team 7 Translational Research of Genito-Urinary Oncogenesis, Créteil Departments of Pathology Department of Pathology, Université Paris Est, UPEC, Créteil, France
| | - B W G van Rhijn
- Departments of Surgical Oncology (Urology) Department of Urology, Caritas St Josef Medical Centre, University of Regensburg, Regensburg, Germany Department of Surgical Oncology (Urology), University Health Network, Princess Margaret Cancer Centre, University of Toronto, Toronto Departments of Surgery (Urology) Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto
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De Faveri LE, Hurst CD, Roulson JA, Wood H, Sanchez-Carbayo M, Knowles MA, Chapman EJ. Polycomb Repressor Complex 1 Member, BMI1 Contributes to Urothelial Tumorigenesis through p16-Independent Mechanisms. Transl Oncol 2015; 8:387-399. [PMID: 26500029 PMCID: PMC4631094 DOI: 10.1016/j.tranon.2015.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/28/2015] [Accepted: 08/10/2015] [Indexed: 01/29/2023] Open
Abstract
Urothelial carcinoma (UC) causes significant morbidity and remains the most expensive cancer to treat because of the need for repeated resections and lifelong monitoring for patients with non-muscle-invasive bladder cancer (NMIBC). Novel therapeutics and stratification approaches are needed to improve the outlook for both NMIBC and muscle-invasive bladder cancer. We investigated the expression and effects of B Lymphoma Mo-MLV Insertion Region 1 (BMI1) in UC. BMI1 was found to be overexpressed in most UC cell lines and primary tumors by quantitative real-time polymerase chain reaction and immunohistochemistry. In contrast to some previous reports, no association with tumor stage or grade was observed in two independent tumor panels. Furthermore, upregulation of BMI1 was detected in premalignant bladder lesions, suggesting a role early in tumorigenesis. BMI1 is not located within a common region of genomic amplification in UC. The CDKN2A locus (which encodes the p16 tumor suppressor gene) is a transcriptional target of BMI1 in some cellular contexts. In UC cell lines and primary tissues, no correlation between BMI1 and p16 expression was observed. Retroviral-mediated overexpression of BMI1 immortalized normal human urothelial cells (NHUC) in vitro and was associated with induction of telomerase activity, bypass of senescence, and repression of differentiation. The effects of BMI1 on gene expression were identified by expression microarray analysis of NHUC-BMI1. Metacore analysis of the gene expression profile implicated downstream effects of BMI1 on α4/β1 integrin-mediated adhesion, cytoskeleton remodeling, and CREB1-mediated transcription.
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Affiliation(s)
- Lia E De Faveri
- Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, Leeds, LS97TF, UK
| | - Carolyn D Hurst
- Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, Leeds, LS97TF, UK
| | - Jo-An Roulson
- Department of Pathology and Tumor Biology, St James's University Hospital, Beckett Street, Leeds, LS97TF, UK
| | - Henry Wood
- Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, Leeds, LS97TF, UK
| | - Marta Sanchez-Carbayo
- Bladder Cancer Group, Lascaray Research Center, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - Margaret A Knowles
- Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, Leeds, LS97TF, UK
| | - Emma J Chapman
- Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, Leeds, LS97TF, UK.
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Ambrose SR, Gordon NS, Goldsmith JC, Wei W, Zeegers MP, James ND, Knowles MA, Bryan RT, Ward DG. Use of Aleuria alantia Lectin Affinity Chromatography to Enrich Candidate Biomarkers from the Urine of Patients with Bladder Cancer. Proteomes 2015; 3:266-282. [PMID: 28248271 PMCID: PMC5217382 DOI: 10.3390/proteomes3030266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/25/2015] [Accepted: 08/27/2015] [Indexed: 12/22/2022] Open
Abstract
Developing a urine test to detect bladder tumours with high sensitivity and specificity is a key goal in bladder cancer research. We hypothesised that bladder cancer-specific glycoproteins might fulfill this role. Lectin-ELISAs were used to study the binding of 25 lectins to 10 bladder cell lines and serum and urine from bladder cancer patients and non-cancer controls. Selected lectins were then used to enrich glycoproteins from the urine of bladder cancer patients and control subjects for analysis by shotgun proteomics. None of the lectins showed a strong preference for bladder cancer cell lines over normal urothlelial cell lines or for urinary glycans from bladder cancer patients over those from non-cancer controls. However, several lectins showed a strong preference for bladder cell line glycans over serum glycans and are potentially useful for enriching glycoproteins originating from the urothelium in urine. Aleuria alantia lectin affinity chromatography and shotgun proteomics identified mucin-1 and golgi apparatus protein 1 as proteins warranting further investigation as urinary biomarkers for low-grade bladder cancer. Glycosylation changes in bladder cancer are not reliably detected by measuring lectin binding to unfractionated proteomes, but it is possible that more specific reagents and/or a focus on individual proteins may produce clinically useful biomarkers.
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Affiliation(s)
- Sarah R Ambrose
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Naheema S Gordon
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - James C Goldsmith
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Wenbin Wei
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Maurice P Zeegers
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK.
- Department of Complex Genetics, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre, Maastricht 6200 MD, The Netherlands.
| | - Nicholas D James
- Clinical Trials Unit, University of Warwick, Coventry CV4 7AL, UK.
| | - Margaret A Knowles
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's' University Hospital, Beckett Street, Leeds LS9 7TF, UK.
| | - Richard T Bryan
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Douglas G Ward
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK.
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Stoehr R, Taubert H, Zinnall U, Giedl J, Gaisa NT, Burger M, Ruemmele P, Hurst CD, Knowles MA, Wullich B, Hartmann A. Frequency of TERT Promoter Mutations in Prostate Cancer. Pathobiology 2015; 82:53-7. [PMID: 25997473 DOI: 10.1159/000381903] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/25/2015] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Recently, recurrent mutations within the core promoter of the human telomerase reverse transcriptase (TERT) gene generating consensus binding sites for ETS transcription factor family members were described in melanomas and other malignancies (e.g. bladder cancer, hepatocellular carcinoma). These mutations were discussed as early drivers for malignant transformation. In prostate cancer (PrCa) TERT expression has been associated with a poor prognosis and higher risk for disease recurrence. The underlying mechanisms for high TERT expression in PrCa have still not been clarified. To date, data on TERT promoter mutation analysis in PrCa are sparse. Therefore, we performed sequence analysis of the core promoter region of the TERT gene in an unselected cohort of prostate tumors. METHODS Sections from 167 formalin-fixed, paraffin-embedded and cryopreserved prostate tumors were microdissected and used for DNA isolation. The mutation hotspot region within the TERT core promoter (-260 to +60) was analyzed by direct Sanger sequencing or SNaPshot analysis. RESULTS All cases were analyzed successfully. Mutations within the core promoter of the TERT gene were not detected in any of the cases with all tumors exhibiting a wild-type sequence. CONCLUSION TERT core promoter mutations reported from several other malignancies were not detected in our unselected cohort of PrCa. These data indicate that alterations within the core promoter of the TERT gene do not play an important role in prostate carcinogenesis.
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Affiliation(s)
- Robert Stoehr
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
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Bryan RT, Regan HL, Pirrie SJ, Devall AJ, Cheng KK, Zeegers MP, James ND, Knowles MA, Ward DG. Protein shedding in urothelial bladder cancer: prognostic implications of soluble urinary EGFR and EpCAM. Br J Cancer 2015; 112:1052-8. [PMID: 25719831 PMCID: PMC4366887 DOI: 10.1038/bjc.2015.21] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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: 10/03/2014] [Revised: 01/05/2015] [Accepted: 01/12/2015] [Indexed: 12/30/2022] Open
Abstract
Background: Better biomarkers must be found to develop clinically useful urine tests for bladder cancer. Proteomics can be used to identify the proteins released by cancer cell lines and generate candidate markers for developing such tests. Methods: We used shotgun proteomics to identify proteins released into culture media by eight bladder cancer cell lines. These data were compared with protein expression data from the Human Protein Atlas. Epidermal growth factor receptor (EGFR) was identified as a candidate biomarker and measured by ELISA in urine from 60 noncancer control subjects and from 436 patients with bladder cancer and long-term clinical follow-up. Results: Bladder cancer cell lines shed soluble EGFR ectodomain. Soluble EGFR is also detectable in urine and is highly elevated in some patients with high-grade bladder cancer. Urinary EGFR is an independent indicator of poor bladder cancer-specific survival with a hazard ratio of 2.89 (95% CI 1.81–4.62, P<0.001). In multivariable models including both urinary EGFR and EpCAM, both biomarkers are predictive of bladder cancer-specific survival and have prognostic value over and above that provided by standard clinical observations. Conclusions: Measuring urinary EGFR and EpCAM may represent a simple and useful approach for fast-tracking the investigation and treatment of patients with the most aggressive bladder cancers.
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Affiliation(s)
- R T Bryan
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - H L Regan
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - S J Pirrie
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - A J Devall
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - K K Cheng
- School of Population and Health Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - M P Zeegers
- 1] School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK [2] Department of Complex Genetics, NUTRIM School for Nutrition, Toxicology and Metabolism, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - N D James
- Clinical Trials Unit, University of Warwick, Coventry CV4 7AL, UK
| | - M A Knowles
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - D G Ward
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
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Bunney TD, Wan S, Thiyagarajan N, Sutto L, Williams SV, Ashford P, Koss H, Knowles MA, Gervasio FL, Coveney PV, Katan M. The Effect of Mutations on Drug Sensitivity and Kinase Activity of Fibroblast Growth Factor Receptors: A Combined Experimental and Theoretical Study. EBioMedicine 2015; 2:194-204. [PMID: 26097890 PMCID: PMC4471147 DOI: 10.1016/j.ebiom.2015.02.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [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: 12/09/2014] [Revised: 02/11/2015] [Accepted: 02/13/2015] [Indexed: 12/13/2022] Open
Abstract
Fibroblast growth factor receptors (FGFRs) are recognized therapeutic targets in cancer. We here describe insights underpinning the impact of mutations on FGFR1 and FGFR3 kinase activity and drug efficacy, using a combination of computational calculations and experimental approaches including cellular studies, X-ray crystallography and biophysical and biochemical measurements. Our findings reveal that some of the tested compounds, in particular TKI258, could provide therapeutic opportunity not only for patients with primary alterations in FGFR but also for acquired resistance due to the gatekeeper mutation. The accuracy of the computational methodologies applied here shows a potential for their wider application in studies of drug binding and in assessments of functional and mechanistic impacts of mutations, thus assisting efforts in precision medicine.
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Affiliation(s)
- Tom D. Bunney
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St., London WC1E 6BT, UK
| | - Shunzhou Wan
- Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon St., London WC1H 0AJ, UK
| | - Nethaji Thiyagarajan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St., London WC1E 6BT, UK
| | - Ludovico Sutto
- Institute of Structural and Molecular Biology, Department of Chemistry, University College London, Gower St., London WC1E 6BT, UK
| | - Sarah V. Williams
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Paul Ashford
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St., London WC1E 6BT, UK
| | - Hans Koss
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St., London WC1E 6BT, UK
- Division of Molecular Structure, MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, UK
| | - Margaret A. Knowles
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - Francesco L. Gervasio
- Institute of Structural and Molecular Biology, Department of Chemistry, University College London, Gower St., London WC1E 6BT, UK
| | - Peter V. Coveney
- Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon St., London WC1H 0AJ, UK
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower St., London WC1E 6BT, UK
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37
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Abstract
Urothelial carcinoma of the bladder comprises two long-recognized disease entities with distinct molecular features and clinical outcome. Low-grade non-muscle-invasive tumours recur frequently but rarely progress to muscle invasion, whereas muscle-invasive tumours are usually diagnosed de novo and frequently metastasize. Recent genome-wide expression and sequencing studies identify genes and pathways that are key drivers of urothelial cancer and reveal a more complex picture with multiple molecular subclasses that traverse conventional grade and stage groupings. This improved understanding of molecular features, disease pathogenesis and heterogeneity provides new opportunities for prognostic application, disease monitoring and personalized therapy.
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Affiliation(s)
- Margaret A Knowles
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Carolyn D Hurst
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
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38
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Rafnar T, Sulem P, Thorleifsson G, Vermeulen SH, Helgason H, Saemundsdottir J, Gudjonsson SA, Sigurdsson A, Stacey SN, Gudmundsson J, Johannsdottir H, Alexiusdottir K, Petursdottir V, Nikulasson S, Geirsson G, Jonsson T, Aben KKH, Grotenhuis AJ, Verhaegh GW, Dudek AM, Witjes JA, van der Heijden AG, Vrieling A, Galesloot TE, De Juan A, Panadero A, Rivera F, Hurst C, Bishop DT, Sak SC, Choudhury A, Teo MTW, Arici C, Carta A, Toninelli E, de Verdier P, Rudnai P, Gurzau E, Koppova K, van der Keur KA, Lurkin I, Goossens M, Kellen E, Guarrera S, Russo A, Critelli R, Sacerdote C, Vineis P, Krucker C, Zeegers MP, Gerullis H, Ovsiannikov D, Volkert F, Hengstler JG, Selinski S, Magnusson OT, Masson G, Kong A, Gudbjartsson D, Lindblom A, Zwarthoff E, Porru S, Golka K, Buntinx F, Matullo G, Kumar R, Mayordomo JI, Steineck DG, Kiltie AE, Jonsson E, Radvanyi F, Knowles MA, Thorsteinsdottir U, Kiemeney LA, Stefansson K. Genome-wide association study yields variants at 20p12.2 that associate with urinary bladder cancer. Hum Mol Genet 2014; 23:5545-57. [PMID: 24861552 DOI: 10.1093/hmg/ddu264] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [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] [Indexed: 01/04/2023] Open
Abstract
Genome-wide association studies (GWAS) of urinary bladder cancer (UBC) have yielded common variants at 12 loci that associate with risk of the disease. We report here the results of a GWAS of UBC including 1670 UBC cases and 90 180 controls, followed by replication analysis in additional 5266 UBC cases and 10 456 controls. We tested a dataset containing 34.2 million variants, generated by imputation based on whole-genome sequencing of 2230 Icelanders. Several correlated variants at 20p12, represented by rs62185668, show genome-wide significant association with UBC after combining discovery and replication results (OR = 1.19, P = 1.5 × 10(-11) for rs62185668-A, minor allele frequency = 23.6%). The variants are located in a non-coding region approximately 300 kb upstream from the JAG1 gene, an important component of the Notch signaling pathways that may be oncogenic or tumor suppressive in several forms of cancer. Our results add to the growing number of UBC risk variants discovered through GWAS.
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Affiliation(s)
| | | | | | | | - Hannes Helgason
- deCODE Genetics/AMGEN, Reykjavik 101, Iceland School of Engineering and Natural Sciences and
| | | | | | | | | | | | | | | | | | | | | | - Thorvaldur Jonsson
- Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland Department of Surgery, Landspitali-University Hospital, Reykjavik 101, Iceland
| | - Katja K H Aben
- Department for Health Evidence Comprehensive Cancer Center The Netherlands, Utrecht, The Netherlands
| | | | - Gerald W Verhaegh
- Department of Urology, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands
| | - Aleksandra M Dudek
- Department of Urology, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands
| | - J Alfred Witjes
- Department of Urology, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands
| | | | | | | | - Ana De Juan
- Division of Medical Oncolology, Marques de Valdecilla University Hospital, Santander 39008, Spain
| | - Angeles Panadero
- Division of Medical Oncolology, Ciudad de Coria Hospital, Coria 10800, Spain
| | - Fernando Rivera
- Division of Medical Oncolology, Marques de Valdecilla University Hospital, Santander 39008, Spain
| | - Carolyn Hurst
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds LS9 7TF, UK
| | - D Timothy Bishop
- Section of Epidemiology & Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS2 9JT, UK
| | - Sei C Sak
- Mid Yorkshire NHS Trust, Pinderfields Hospital, Wakefield WF1 4DG, UK
| | | | - Mark T W Teo
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Cecilia Arici
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health University of Brescia, Brescia 1-25125, Italy
| | - Angela Carta
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health University of Brescia, Brescia 1-25125, Italy
| | - Elena Toninelli
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health University of Brescia, Brescia 1-25125, Italy
| | - Petra de Verdier
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm S171 76, Sweden
| | - Peter Rudnai
- Department of Environmental Epidemiology, National Institute of Environmental Health, Budapest H-1450, Hungary
| | - Eugene Gurzau
- Health Department, Environmental Health Center, Babes Bolyai University, Cluj-Napoca 3400, Romania
| | - Kvetoslava Koppova
- Department of Environmental Health, Regional Authority of Public Health, Banska Bystrica 975 56, Slovakia
| | | | - Irene Lurkin
- Department of Pathology, Erasmus MC, Rotterdam 3000 CA, The Netherlands
| | - Mieke Goossens
- Department of General Practice, Catholic University of Leuven, Leuven 3000, Belgium
| | - Eliane Kellen
- Leuven University Centre for Cancer Prevention (LUCK), Leuven 3000, Belgium
| | | | - Alessia Russo
- Human Genetics Foundation, HuGeF, Torino I-10126, Italy Department of Medical Sciences and
| | - Rossana Critelli
- Human Genetics Foundation, HuGeF, Torino I-10126, Italy Department of Medical Sciences and
| | - Carlotta Sacerdote
- Human Genetics Foundation, HuGeF, Torino I-10126, Italy Unit of Cancer Epidemiology, University of Torino, Torino 10126, Italy Centre for Cancer Epidemiology and Prevention (CPO Piemonte), Torino 10126, Italy
| | - Paolo Vineis
- Human Genetics Foundation, HuGeF, Torino I-10126, Italy Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Clémentine Krucker
- CNRS, UMR 144, Oncologie Moléculaire, Institut Curie, Paris 75248 Cedex 05, France Institut Curie, Centre de Recherche, Paris 75248 Cedex 05, France
| | - Maurice P Zeegers
- Department of Epidemiology & Complex Genetics NUTRIM/Faculty of Health, Medicine and Life Sciences Maastricht University, Maastricht 6200 MD, The Netherlands
| | - Holger Gerullis
- Department of Urology, Lukasklinik Neuss, Preussenstr. 64, Neuss 41464, Germany
| | - Daniel Ovsiannikov
- Department of Urology, St.-Josefs-Hospital Dortmund-Hörde, Dortmund 44263, Germany
| | - Frank Volkert
- Department of Urology, Evangelisches Krankenhaus Paul Gerhardt Foundation, Lutherstadt Wittenberg 06886, Germany
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Dortmund 44139, Germany
| | - Silvia Selinski
- Leibniz Research Centre for Working Environment and Human Factors, Dortmund 44139, Germany
| | | | | | - Augustine Kong
- deCODE Genetics/AMGEN, Reykjavik 101, Iceland School of Engineering and Natural Sciences and
| | - Daniel Gudbjartsson
- deCODE Genetics/AMGEN, Reykjavik 101, Iceland School of Engineering and Natural Sciences and
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm S171 76, Sweden
| | - Ellen Zwarthoff
- Department of Pathology, Erasmus MC, Rotterdam 3000 CA, The Netherlands
| | - Stefano Porru
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health University of Brescia, Brescia 1-25125, Italy
| | - Klaus Golka
- Leibniz Research Centre for Working Environment and Human Factors, Dortmund 44139, Germany
| | - Frank Buntinx
- Department of General Practice, Catholic University of Leuven, Leuven 3000, Belgium Research School Care & Department of General Practice, Maastricht University, Maastricht 6200 MD, The Netherlands
| | - Giuseppe Matullo
- Human Genetics Foundation, HuGeF, Torino I-10126, Italy Department of Medical Sciences and
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg D-69120, Germany
| | - José I Mayordomo
- Division of Medical Oncology, University of Zaragoza, Zaragoza 50009, Spain
| | - D Gunnar Steineck
- Department of Oncology and Pathology, Karolinska Hospital, Stockholm S171 76, Sweden Department of Oncology, Sahlgrenska University Hospital, Goteborg S-413 45, Sweden
| | - Anne E Kiltie
- Gray Institute for Radiation Oncology and Biology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | | | - François Radvanyi
- CNRS, UMR 144, Oncologie Moléculaire, Institut Curie, Paris 75248 Cedex 05, France Institut Curie, Centre de Recherche, Paris 75248 Cedex 05, France
| | - Margaret A Knowles
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Unnur Thorsteinsdottir
- deCODE Genetics/AMGEN, Reykjavik 101, Iceland Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Lambertus A Kiemeney
- Department for Health Evidence Department of Urology, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands
| | - Kari Stefansson
- deCODE Genetics/AMGEN, Reykjavik 101, Iceland Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
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Hurst CD, Platt FM, Knowles MA. Abstract 2240: TERT promoter mutations are highly prevalent in bladder cancer and represent a potential new urinary biomarker. Mol Cell Biol 2014. [DOI: 10.1158/1538-7445.am2014-2240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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40
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di Martino E, Kelly G, Roulson JA, Knowles MA. Alteration of cell-cell and cell-matrix adhesion in urothelial cells: an oncogenic mechanism for mutant FGFR3. Mol Cancer Res 2014; 13:138-48. [PMID: 25223521 DOI: 10.1158/1541-7786.mcr-14-0022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED Activating mutations of FGFR3 are a common and early event in bladder cancer. Ectopic expression of mutant FGFR3 in normal urothelial cells has both pro-proliferative and antiapoptotic effects at confluence, suggesting that mutant cells are insensitive to cell-cell contact inhibition. Herein, detailed analysis revealed that these cells have reduced cell-cell adhesion, with large intercellular spaces observable at confluence, and diminished cell-substrate adhesion to collagen IV, collagen I, and fibronectin. These phenotypic alterations are accompanied by changes in the expression of genes involved in cell adhesion and extracellular matrix remodeling. Silencing of endogenous mutant FGFR3 in bladder cancer cells induced converse changes in transcript levels of CDH16, PLAU, MMP10, EPCAM, TNC, and HAS3, confirming them as downstream gene targets of mutant FGFR3. Overexpression of EPCAM, HAS3, and MMP10 transcripts was found in a large fraction of primary bladder tumors analyzed, supporting their key role in bladder tumorigenesis in vivo. However, no correlation was found between their protein and/or mRNA expression and FGFR3 mutation status in tumor specimens, indicating that these genes may be targeted by several converging oncogenic pathways. Overall, these results indicate that mutant FGFR3 favors the development and progression of premalignant bladder lesions by altering key genes regulating the cell-cell and cell-matrix adhesive properties of urothelial cells. IMPLICATIONS The ability of mutant FGFR3 to drive transcriptional expression profiles involved in tumor cell adhesion suggests a mechanism for expansion of premalignant urothelial lesions.
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Affiliation(s)
- Erica di Martino
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds, United Kingdom
| | - Gavin Kelly
- Bioinformatics and Biostatistics Service, Cancer Research UK, London Research Institute, Lincoln's Inn Fields Laboratories, London, United Kingdom
| | - Jo-An Roulson
- Section of Pathology and Tumour Biology, Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds, United Kingdom
| | - Margaret A Knowles
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds, United Kingdom.
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Goebell PJ, Kamat AM, Sylvester RJ, Black P, Droller M, Godoy G, Hudson MA, Junker K, Kassouf W, Knowles MA, Schulz WA, Seiler R, Schmitz-Dräger BJ. Assessing the quality of studies on the diagnostic accuracy of tumor markers. Urol Oncol 2014; 32:1051-60. [PMID: 25159014 DOI: 10.1016/j.urolonc.2013.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/03/2013] [Accepted: 10/05/2013] [Indexed: 01/11/2023]
Abstract
OBJECTIVES With rapidly increasing numbers of publications, assessments of study quality, reporting quality, and classification of studies according to their level of evidence or developmental stage have become key issues in weighing the relevance of new information reported. Diagnostic marker studies are often criticized for yielding highly discrepant and even controversial results. Much of this discrepancy has been attributed to differences in study quality. So far, numerous tools for measuring study quality have been developed, but few of them have been used for systematic reviews and meta-analysis. This is owing to the fact that most tools are complicated and time consuming, suffer from poor reproducibility, and do not permit quantitative scoring. METHODS The International Bladder Cancer Network (IBCN) has adopted this problem and has systematically identified the more commonly used tools developed since 2000. RESULTS In this review, those tools addressing study quality (Quality Assessment of Studies of Diagnostic Accuracy and Newcastle-Ottawa Scale), reporting quality (Standards for Reporting of Diagnostic Accuracy), and developmental stage (IBCN phases) of studies on diagnostic markers in bladder cancer are introduced and critically analyzed. Based upon this, the IBCN has launched an initiative to assess and validate existing tools with emphasis on diagnostic bladder cancer studies. CONCLUSIONS The development of simple and reproducible tools for quality assessment of diagnostic marker studies permitting quantitative scoring is suggested.
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Affiliation(s)
- Peter J Goebell
- Urologische Klinik, Friedrich-Alexander-Universität, Erlangen, Germany
| | - Ashish M Kamat
- Department of Urology, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Peter Black
- Department of Urology, Division of Surgery, University of British Columbia, Vancouver, Canada
| | | | - Guilherme Godoy
- Scott Department of Urology, Baylor College of Medicine, Houston, TX
| | - M'Liss A Hudson
- Ochsner Clinic Foundation, Tom and Gayle Benson Cancer Center, New Orleans, LA
| | - Kerstin Junker
- Urologische Klinik und Poliklinik, Universität des Saarlandes, Saarland, Germany
| | - Wassim Kassouf
- Department of Surgery (Urology), McGill University, Montreal, Quebec, Canada
| | - Margaret A Knowles
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK
| | - Wolfgang A Schulz
- Urologische Klinik und Poliklinik, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Roland Seiler
- Department of Urology, University of Berne, Berne, Switzerland
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Acquaviva J, He S, Zhang C, Jimenez JP, Nagai M, Sang J, Sequeira M, Smith DL, Ogawa LS, Inoue T, Tatsuta N, Knowles MA, Bates RC, Proia DA. FGFR3 translocations in bladder cancer: differential sensitivity to HSP90 inhibition based on drug metabolism. Mol Cancer Res 2014; 12:1042-54. [PMID: 24784839 DOI: 10.1158/1541-7786.mcr-14-0004] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED Activating mutations and/or overexpression of FGFR3 are common in bladder cancer, making FGFR3 an attractive therapeutic target in this disease. In addition, FGFR3 gene rearrangements have recently been described that define a unique subset of bladder tumors. Here, a selective HSP90 inhibitor, ganetespib, induced loss of FGFR3-TACC3 fusion protein expression and depletion of multiple oncogenic signaling proteins in RT112 bladder cells, resulting in potent cytotoxicity comparable with the pan-FGFR tyrosine kinase inhibitor BGJ398. However, in contrast to BGJ398, ganetespib exerted pleiotropic effects on additional mitogenic and survival pathways and could overcome the FGFR inhibitor-resistant phenotype of FGFR3 mutant-expressing 97-7 and MHG-U3 cells. Combinatorial benefit was observed when ganetespib was used with BGJ398 both in vitro and in vivo. Interestingly, two additional FGFR3 fusion-positive lines (RT4 and SW480) retained sensitivity to HSP90 inhibitor treatment by the ansamycins 17-AAG and 17-DMAG yet displayed intrinsic resistance to ganetespib or AUY922, both second-generation resorcinol-based compounds. Both cell lines, compared with RT112, expressed considerably higher levels of endogenous UGT1A enzyme; this phenotype resulted in a rapid glucuronidation-dependent metabolism and subsequent efflux of ganetespib from SW780 cells, thus providing a mechanism to account for the lack of bioactivity. IMPLICATIONS Pharmacologic blockade of the molecular chaperone HSP90 represents a promising approach for treating bladder tumors driven by oncogenic gene rearrangements of FGFR3. Furthermore, UDP-glucuronosyltransferase enzyme expression may serve as a predictive factor for clinical response to resorcinol-based HSP90 inhibitors.
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Affiliation(s)
- Jaime Acquaviva
- Authors' Affiliations: Synta Pharmaceuticals Corp., Lexington, Massachusetts; and
| | - Suqin He
- Authors' Affiliations: Synta Pharmaceuticals Corp., Lexington, Massachusetts; and
| | - Chaohua Zhang
- Authors' Affiliations: Synta Pharmaceuticals Corp., Lexington, Massachusetts; and
| | - John-Paul Jimenez
- Authors' Affiliations: Synta Pharmaceuticals Corp., Lexington, Massachusetts; and
| | - Masazumi Nagai
- Authors' Affiliations: Synta Pharmaceuticals Corp., Lexington, Massachusetts; and
| | - Jim Sang
- Authors' Affiliations: Synta Pharmaceuticals Corp., Lexington, Massachusetts; and
| | - Manuel Sequeira
- Authors' Affiliations: Synta Pharmaceuticals Corp., Lexington, Massachusetts; and
| | - Donald L Smith
- Authors' Affiliations: Synta Pharmaceuticals Corp., Lexington, Massachusetts; and
| | - Luisa Shin Ogawa
- Authors' Affiliations: Synta Pharmaceuticals Corp., Lexington, Massachusetts; and
| | - Takayo Inoue
- Authors' Affiliations: Synta Pharmaceuticals Corp., Lexington, Massachusetts; and
| | - Noriaki Tatsuta
- Authors' Affiliations: Synta Pharmaceuticals Corp., Lexington, Massachusetts; and
| | - Margaret A Knowles
- Leeds Institute of Molecular Medicine, St. James's University Hospital, Leeds, United Kingdom
| | - Richard C Bates
- Authors' Affiliations: Synta Pharmaceuticals Corp., Lexington, Massachusetts; and
| | - David A Proia
- Authors' Affiliations: Synta Pharmaceuticals Corp., Lexington, Massachusetts; and
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Teo MTW, Dyrskjøt L, Nsengimana J, Buchwald C, Snowden H, Morgan J, Jensen JB, Knowles MA, Taylor G, Barrett JH, Borre M, Ørntoft TF, Bishop DT, Kiltie AE. Next-generation sequencing identifies germline MRE11A variants as markers of radiotherapy outcomes in muscle-invasive bladder cancer. Ann Oncol 2014; 25:877-883. [PMID: 24623370 PMCID: PMC3969555 DOI: 10.1093/annonc/mdu014] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/17/2013] [Accepted: 12/31/2013] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Muscle-invasive bladder cancer (MIBC) can be cured by radical radiotherapy (RT). We previously found tumour MRE11 expression to be predictive of survival following RT in MIBC, and this was independently validated in a separate institute. Here, we investigated germline MRE11A variants as possible predictors of RT outcomes in MIBC, using next-generation sequencing (NGS). PATIENTS AND METHODS The MRE11A gene was amplified in germline DNA from 186 prospectively recruited MIBC patients treated with RT and sequenced using bar-coded multiplexed NGS. Germline variants were analysed for associations with cancer-specific survival (CSS). For validation as a prognostic or predictive marker, rs1805363 was then genotyped in a cystectomy-treated MIBC cohort of 256 individuals. MRE11A mRNA isoform expression was measured in bladder cancer cell lines and primary tumour samples. RESULTS Carriage of at least one of six (five novel) rare variants was associated with the worse RT outcome (hazard ratio [HR] 4.04, 95% confidence interval [95% CI] 1.42-11.51, P = 0.009). The single-nucleotide polymorphism (SNP), rs1805363 (minor allele frequency 11%), was also associated with worse CSS (per-allele HR 2.10, 95% CI 1.34-3.28, Ptrend = 0.001) following RT in MIBC, with a gene-dosage effect observed, but no effect seen on CSS in the cystectomy cohort (Ptrend = 0.89). Furthermore, rs1805363 influenced relative MRE11A isoform expression, with increased isoform 2 expression with carriage of the rs1805363 minor A allele. CONCLUSIONS Germline MRE11A SNP rs1805363 was predictive of RT, but not of cystectomy outcome in MIBC. If successfully validated in an independent RT-treated cohort, this SNP could be a useful clinical tool for selecting patients for bladder-conserving treatment.
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Affiliation(s)
- M T W Teo
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - L Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - J Nsengimana
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - C Buchwald
- Department of Oncology, Gray Institute for Radiation Oncology and Biology, University of Oxford, Oxford
| | - H Snowden
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - J Morgan
- Genomics Facility, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - J B Jensen
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - M A Knowles
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - G Taylor
- Genomics Facility, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - J H Barrett
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - M Borre
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - T F Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - D T Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - A E Kiltie
- Department of Oncology, Gray Institute for Radiation Oncology and Biology, University of Oxford, Oxford.
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Turo R, Platt FM, Hurst CD, Harnden P, Cross WR, Knowles MA. MP28-02 MOLECULAR GENETIC ANALYSIS OF MULTIFOCAL BLADDER TUMOURS. J Urol 2014. [DOI: 10.1016/j.juro.2014.02.651] [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] [Indexed: 10/25/2022]
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Abstract
Therapeutic decisions for muscle-invasive bladder cancer (MIBC) are largely based on histopathologic characteristics. In this issue of Cancer Cell, Choi and colleagues report three molecular subtypes of MIBC with the potential to guide prognosis, patient stratification, and treatment.
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Affiliation(s)
- Carolyn D Hurst
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Margaret A Knowles
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK.
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Stadler LKJ, Tomlinson DC, Lee T, Knowles MA, Ko Ferrigno P. The use of a neutral peptide aptamer scaffold to anchor BH3 peptides constitutes a viable approach to studying their function. Cell Death Dis 2014; 5:e1037. [PMID: 24481451 PMCID: PMC4040713 DOI: 10.1038/cddis.2013.564] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [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: 07/25/2013] [Revised: 11/26/2013] [Accepted: 11/27/2013] [Indexed: 11/11/2022]
Abstract
The B-cell CLL/lymphoma-2 (Bcl-2) family of proteins are important regulators of the intrinsic pathway of apoptosis, and their interactions, driven by Bcl-2 homology (BH) domains, are of great interest in cancer research. Particularly, the BH3 domain is of clinical relevance, as it promotes apoptosis through activation of Bcl-2-associated x protein (Bax) and Bcl-2 antagonist killer (Bak), as well as by antagonising the anti-apoptotic Bcl-2 family members. Although investigated extensively in vitro, the study of the BH3 domain alone inside cells is more problematic because of diminished secondary structure of the unconstrained peptide and a lack of stability. In this study, we report the successful use of a novel peptide aptamer scaffold – Stefin A quadruple mutant – to anchor and present the BH3 domains from Bcl-2-interacting mediator of cell death (Bim), p53 upregulated modulator of apoptosis (Puma), Bcl-2-associated death promoter (Bad) and Noxa, and demonstrate its usefulness in the study of the BH3 domains in vivo. When expressed intracellularly, anchored BH3 peptides exhibit much the same binding specificities previously established in vitro, however, we find that, at endogenous expression levels, Bcl-2 does not bind to any of the anchored BH3 domains tested. Nonetheless, when expressed inside cells the anchored PUMA and Bim BH3 α-helices powerfully induce cell death in the absence of efficient targeting to the mitochondrial membrane, whereas the Noxa helix requires a membrane insertion domain in order to kill Mcl-1-dependent myeloma cells. Finally, the binding of the Bim BH3 peptide to Bax was the only interaction with a pro-apoptotic effector protein observed in this study.
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Affiliation(s)
- L K J Stadler
- 1] Section of Experimental Therapeutics, Leeds LS9 7TF, UK [2] Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - D C Tomlinson
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - T Lee
- Section of Experimental Therapeutics, Leeds LS9 7TF, UK
| | - M A Knowles
- Section of Experimental Oncology, Leeds Institute of Molecular Medicine, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK
| | - P Ko Ferrigno
- Section of Experimental Therapeutics, Leeds LS9 7TF, UK
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Taylor CF, Platt FM, Hurst CD, Thygesen HH, Knowles MA. Frequent inactivating mutations of STAG2 in bladder cancer are associated with low tumour grade and stage and inversely related to chromosomal copy number changes. Hum Mol Genet 2013; 23:1964-74. [PMID: 24270882 PMCID: PMC3959811 DOI: 10.1093/hmg/ddt589] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Inactivating mutations of STAG2 have been reported at low frequency in several cancers. In glioblastoma, the function of STAG2 has been related to maintenance of euploidy via its role in the cohesin complex. In a screen of a large series of bladder tumours and cell lines, we found inactivating mutations (nonsense, frameshift and splicing) in 67 of 307 tumours (21.8%) and 6 of 47 cell lines. Thirteen missense mutations of unknown significance were also identified. Inactivating mutation was associated with low tumour stage (P = 0.001) and low grade (P = 0.0002). There was also a relationship with female patient gender (P = 0.042). Examination of copy number profiles revealed an inverse relationship of mutation with both fraction of genome altered and whole chromosome copy number changes. Immunohistochemistry showed that in the majority of cases with inactivating mutations, STAG2 protein expression was absent. Strikingly, we identified a relatively large subset of tumours (12%) with areas of both positive and negative immunoreactivity, in only four of which a potentially function-altering mutation was detected. Regions of differential expression were contiguous and showed similar morphological phenotype in all cases. Microdissected positive and negative areas from one tumour showed an inactivating mutation to be present only in the negative area, suggesting intra-tumoral sub-clonal genomic evolution. Our findings indicate that loss of STAG2 function plays a more important role in non-invasive than that in muscle-invasive bladder cancer and suggest that cohesin complex-independent functions are likely to be important in these cases.
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Acquaviva JL, Zhang C, He S, Jimenez JP, Nagai M, Sang J, Sequeira M, Smith DL, Knowles MA, Proia DA. Abstract C130: The Hsp90 inhibitor ganetespib promotes the degradation of FGFR3 in bladder cancer models and induces regression in tumors harboring oncogenic FGFR3 fusions. Mol Cancer Ther 2013. [DOI: 10.1158/1535-7163.targ-13-c130] [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: 11/16/2022]
Abstract
Abstract
Background: Fibroblast growth factor receptor 3 (FGFR3) is activated by point mutation, chromosomal rearrangement, and/or receptor overexpression in a high percentage of bladder cancers, making FGFR3 an attractive therapeutic target for bladder cancer. Heat shock protein 90 (Hsp90) is a molecular chaperone required for the stability of FGFR3 and hundreds of other kinases and oncoproteins (termed “client proteins”), many of which are known to support tumorigenesis. Ganetespib is a selective inhibitor of Hsp90 currently being evaluated in several clinical trials, including a pivotal Phase 3 study. Here, we investigated the preclinical activity of ganetespib in bladder cancer models expressing FGFR3, as monotherapy or in combination with an FGFR inhibitor.
Results: Ganetespib displayed strong anticancer activity across a panel of 20 bladder cancer cell lines with diverse genetic backgrounds (mean EC50 = 38 nM), including those overexpressing wt FGFR3 or FGFR3 fusions. Notably, ganetespib was 10 times more potent than the selective FGFR3 inhibitor BGJ398 in bladder cancer cells with activating mutations in FGFR3. At the molecular level, ganetespib induced the rapid destabilization of full-length FGFR3 and the FGFR3-TACC3 fusion protein within 4 hours suggesting that FGFR3 is a highly sensitive Hsp90 client. Consequently, MAPK and AKT/mTOR signaling were suppressed, resulting in apoptosis evident by decreased levels of P-BAD and an increase in BIM, cleaved Caspase-3, and PARP expression. In vivo, ganetespib treatment led to tumor regression in RT112 xenografts coordinate with the deactivation of FGFR3-TACC3, as well as numerous other client proteins and their downstream effectors, as determined by phosphoprotein array. Combining ganetespib with BGJ398 increased tumor regression 3-fold compared to monotherapy.
Conclusions: The Hsp90 inhibitor ganetespib elicits the rapid degradation of FGFR3 mutants and fusion proteins in bladder cancer cells resulting in tumor regression in animal models, which could be further enhanced by combination with an FGFR inhibitor. These results may provide a framework for the future treatment of FGFR3-dependent bladder cancer.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C130.
Citation Format: Jaime L. Acquaviva, Chaohua Zhang, Suqin He, John-Paul Jimenez, Masa Nagai, Jim Sang, Manuel Sequeira, Donald L. Smith, Margaret A. Knowles, David A. Proia. The Hsp90 inhibitor ganetespib promotes the degradation of FGFR3 in bladder cancer models and induces regression in tumors harboring oncogenic FGFR3 fusions. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C130.
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Affiliation(s)
| | | | - Suqin He
- 1Synta Pharmaceuticals Corp., Lexington, MA
| | | | - Masa Nagai
- 1Synta Pharmaceuticals Corp., Lexington, MA
| | - Jim Sang
- 1Synta Pharmaceuticals Corp., Lexington, MA
| | | | | | - Margaret A. Knowles
- 2Leeds Institute of Molecular Medicine, St James's University Hospital, Leeds, United Kingdom
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Hurst CD, Platt FM, Knowles MA. Comprehensive mutation analysis of the TERT promoter in bladder cancer and detection of mutations in voided urine. Eur Urol 2013; 65:367-9. [PMID: 24035680 DOI: 10.1016/j.eururo.2013.08.057] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/21/2013] [Indexed: 01/19/2023]
Affiliation(s)
- Carolyn D Hurst
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK
| | - Fiona M Platt
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK
| | - Margaret A Knowles
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK.
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Herrera-Abreu MT, Pearson A, Campbell J, Shnyder SD, Knowles MA, Ashworth A, Turner NC. Parallel RNA interference screens identify EGFR activation as an escape mechanism in FGFR3-mutant cancer. Cancer Discov 2013; 3:1058-71. [PMID: 23744832 PMCID: PMC3770512 DOI: 10.1158/2159-8290.cd-12-0569] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [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] [Indexed: 11/16/2022]
Abstract
UNLABELLED Activation of fibroblast growth factor receptors (FGFR) is a common oncogenic event. Little is known about the determinants of sensitivity to FGFR inhibition and how these may vary between different oncogenic FGFRs. Using parallel RNA interference (RNAi) genetic screens, we show that the EGF receptor (EGFR) limits sensitivity to FGFR inhibition in FGFR3-mutant and -translocated cell lines, but not in other FGFR-driven cell lines. We also identify two distinct mechanisms through which EGFR limits sensitivity. In partially FGFR3-dependent lines, inhibition of FGFR3 results in transient downregulation of mitogen-activated protein kinase signaling that is rescued by rapid upregulation of EGFR signaling. In cell lines that are intrinsically resistant to FGFR inhibition, EGFR dominates signaling via repression of FGFR3, with EGFR inhibition rescued by delayed upregulation of FGFR3 expression. Importantly, combinations of FGFR and EGFR inhibitors overcome these resistance mechanisms in vitro and in vivo. Our results illustrate the power of parallel RNAi screens in identifying common resistance mechanisms to targeted therapies. SIGNIFICANCE Our data identify a novel therapeutic approach to the treatment of FGFR3-mutant cancer, emphasizing the potential of combination approaches targeting both FGFR3 and EGFR. Our data extend the role of EGFR in mediating resistance to inhibitors targeting a mutant oncogene, showing that EGFR signaling can repress mutant FGFR3 to induce intrinsic resistance to FGFR targeting.
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Affiliation(s)
- Maria Teresa Herrera-Abreu
- 1The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research; 2Breast Unit, Royal Marsden Hospital, London; 3Institute of Cancer Therapeutics, University of Bradford, Bradford; and 4Section of Experimental Oncology, Leeds Institute of Molecular Medicine, St James's University Hospital, Leeds, United Kingdom
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