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Propper DJ, Gao F, Saunders MP, Sarker D, Hartley JA, Spanswick VJ, Lowe HL, Hackett LD, Ng TT, Barber PR, Weitsman GE, Pearce S, White L, Lopes A, Forsyth S, Hochhauser D. PANTHER: AZD8931, inhibitor of EGFR, ERBB2 and ERBB3 signalling, combined with FOLFIRI: a Phase I/II study to determine the importance of schedule and activity in colorectal cancer. Br J Cancer 2023; 128:245-254. [PMID: 36352028 PMCID: PMC9902557 DOI: 10.1038/s41416-022-02015-x] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Epidermal growth factor receptor (EGFR) is a therapeutic target to which HER2/HER3 activation may contribute resistance. This Phase I/II study examined the toxicity and efficacy of high-dose pulsed AZD8931, an EGFR/HER2/HER3 inhibitor, combined with chemotherapy, in metastatic colorectal cancer (CRC). METHODS Treatment-naive patients received 4-day pulses of AZD8931 with irinotecan/5-FU (FOLFIRI) in a Phase I/II single-arm trial. Primary endpoint for Phase I was dose limiting toxicity (DLT); for Phase II best overall response. Samples were analysed for pharmacokinetics, EGFR dimers in circulating exosomes and Comet assay quantitating DNA damage. RESULTS Eighteen patients received FOLFIRI and AZD8931. At 160 mg bd, 1 patient experienced G3 DLT; 160 mg bd was used for cohort expansion. No grade 5 adverse events (AE) reported. Seven (39%) and 1 (6%) patients experienced grade 3 and grade 4 AEs, respectively. Of 12 patients receiving 160 mg bd, best overall response rate was 25%, median PFS and OS were 8.7 and 21.2 months, respectively. A reduction in circulating HER2/3 dimer in the two responding patients after 12 weeks treatment was observed. CONCLUSIONS The combination of pulsed high-dose AZD8931 with FOLFIRI has acceptable toxicity. Further studies of TKI sequencing may establish a role for pulsed use of such agents rather than continuous exposure. TRIAL REGISTRATION NUMBER ClinicalTrials.gov number: NCT01862003.
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Affiliation(s)
- David J Propper
- Barts Cancer Institute, Queen Mary, University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Fangfei Gao
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, WC1E 6DD, UK
| | | | - Debashis Sarker
- School of Cancer and Pharmaceutical Sciences, King's College London, London, WC2R 2LS, UK
| | - John A Hartley
- UCL ECMC GCLP Facility, UCL Cancer Institute, Paul O'Gorman Building, University College London, London, WC1E 6DD, UK
| | - Victoria J Spanswick
- UCL ECMC GCLP Facility, UCL Cancer Institute, Paul O'Gorman Building, University College London, London, WC1E 6DD, UK
| | - Helen L Lowe
- UCL ECMC GCLP Facility, UCL Cancer Institute, Paul O'Gorman Building, University College London, London, WC1E 6DD, UK
| | - Louise D Hackett
- UCL ECMC GCLP Facility, UCL Cancer Institute, Paul O'Gorman Building, University College London, London, WC1E 6DD, UK
| | - Tony T Ng
- Barts Cancer Institute, Queen Mary, University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, WC1E 6DD, UK
- Breast Cancer Now Research Unit, Department of Research Oncology, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Paul R Barber
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, WC1E 6DD, UK
| | - Gregory E Weitsman
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King's College London, London, SE1 1UL, UK
| | - Sarah Pearce
- Cancer Research UK & UCL Cancer Trials Centre, University College London, London, W1T 4TJ, UK
| | - Laura White
- Cancer Research UK & UCL Cancer Trials Centre, University College London, London, W1T 4TJ, UK
| | - Andre Lopes
- Cancer Research UK & UCL Cancer Trials Centre, University College London, London, W1T 4TJ, UK
| | - Sharon Forsyth
- Cancer Research UK & UCL Cancer Trials Centre, University College London, London, W1T 4TJ, UK
| | - Daniel Hochhauser
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, WC1E 6DD, UK.
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Barber PR, Weitsman G, Lawler K, Barrett JE, Rowley M, Rodriguez-Justo M, Fisher D, Gao F, Tullis IDC, Deng J, Brown L, Kaplan R, Hochhauser D, Adams R, Maughan TS, Vojnovic B, Coolen ACC, Ng T. HER2-HER3 Heterodimer Quantification by FRET-FLIM and Patient Subclass Analysis of the COIN Colorectal Trial. J Natl Cancer Inst 2020; 112:944-954. [PMID: 31851321 PMCID: PMC7492762 DOI: 10.1093/jnci/djz231] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/27/2019] [Accepted: 12/11/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The phase III MRC COIN trial showed no statistically significant benefit from adding the EGFR-target cetuximab to oxaliplatin-based chemotherapy in first-line treatment of advanced colorectal cancer. This study exploits additional information on HER2-HER3 dimerization to achieve patient stratification and reveal previously hidden subgroups of patients who had differing disease progression and treatment response. METHODS HER2-HER3 dimerization was quantified by fluorescence lifetime imaging microscopy in primary tumor samples from 550 COIN trial patients receiving oxaliplatin and fluoropyrimidine chemotherapy with or without cetuximab. Bayesian latent class analysis and covariate reduction was performed to analyze the effects of HER2-HER3 dimer, RAS mutation, and cetuximab on progression-free survival and overall survival (OS). All statistical tests were two-sided. RESULTS Latent class analysis on a cohort of 398 patients revealed two patient subclasses with differing prognoses (median OS = 1624 days [95% confidence interval [CI] = 1466 to 1816 days] vs 461 days [95% CI = 431 to 504 days]): Class 1 (15.6%) showed a benefit from cetuximab in OS (hazard ratio = 0.43, 95% CI = 0.25 to 0.76, P = .004). Class 2 showed an association of increased HER2-HER3 with better OS (hazard ratio = 0.64, 95% CI = 0.44 to 0.94, P = .02). A class prediction signature was formed and tested on an independent validation cohort (n = 152) validating the prognostic utility of the dimer assay. Similar subclasses were also discovered in full trial dataset (n = 1630) based on 10 baseline clinicopathological and genetic covariates. CONCLUSIONS Our work suggests that the combined use of HER dimer imaging and conventional mutation analyses will be able to identify a small subclass of patients (>10%) who will have better prognosis following chemotherapy. A larger prospective cohort will be required to confirm its utility in predicting the outcome of anti-EGFR treatment.
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Affiliation(s)
- Paul R Barber
- UCL Cancer Institute, Paul O’Gorman Building, University College London, London, UK
| | - Gregory Weitsman
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King’s College London, London, UK
| | - Katherine Lawler
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King’s College London, London, UK
- Institute for Mathematical and Molecular Biomedicine, King’s College London, Guy’s Medical School Campus, London, UK
| | - James E Barrett
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King’s College London, London, UK
| | - Mark Rowley
- Institute for Mathematical and Molecular Biomedicine, King’s College London, Guy’s Medical School Campus, London, UK
- Saddle Point Science Ltd, London, UK
| | | | - David Fisher
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, London, UK
| | - Fangfei Gao
- UCL Cancer Institute, Paul O’Gorman Building, University College London, London, UK
| | - Iain D C Tullis
- Department of Oncology, Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Jinhai Deng
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King’s College London, London, UK
| | - Louise Brown
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, London, UK
| | - Richard Kaplan
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, London, UK
| | - Daniel Hochhauser
- UCL Cancer Institute, Paul O’Gorman Building, University College London, London, UK
| | | | - Timothy S. Maughan
- Department of Oncology, Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Borivoj Vojnovic
- Department of Oncology, Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Anthony C C Coolen
- Institute for Mathematical and Molecular Biomedicine, King’s College London, Guy’s Medical School Campus, London, UK
- Saddle Point Science Ltd, London, UK
| | - Tony Ng
- UCL Cancer Institute, Paul O’Gorman Building, University College London, London, UK
- Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King’s College London, London, UK
- Breast Cancer Now Research Unit, Department of Research Oncology, Guy’s Hospital King’s College London, London, UK
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Boulos JC, Yousof Idres MR, Efferth T. Investigation of cancer drug resistance mechanisms by phosphoproteomics. Pharmacol Res 2020; 160:105091. [PMID: 32712320 DOI: 10.1016/j.phrs.2020.105091] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/20/2020] [Accepted: 07/20/2020] [Indexed: 12/23/2022]
Abstract
Cancer cell mutations can be identified by genomic and transcriptomic techniques. However, they are not sufficient to understand the full complexity of cancer heterogeneity. Analyses of proteins expressed in cancers and their modification profiles show how these mutations could be translated at the functional level. Protein phosphorylation is a major post-translational modification critical for regulating several cellular functions. The covalent addition of phosphate groups to serine, threonine, and tyrosine is catalyzed by protein kinases. Over the past years, kinases were strongly associated with cancer, thus inhibition of protein kinases emanated as novel cancer treatment. However, cancers frequently develop drug resistance. Therefore, a better understanding of drug effects on tumors is urgently needed. In this perspective, phosphoproteomics arose as advanced tool to monitor cancer therapies and to discover novel drugs. This review highlights the role of phosphoproteomics in predicting sensitivity or resistance of cancers towards tyrosine kinase inhibitors and cytotoxic drugs. It also shows the importance of phosphoproteomics in identifying biomarkers that could be applied in clinical diagnostics to predict responses to drugs.
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Trinh AL, Ber S, Howitt A, Valls PO, Fries MW, Venkitaraman AR, Esposito A. Fast single-cell biochemistry: theory, open source microscopy and applications. Methods Appl Fluoresc 2019; 7:044001. [PMID: 31422954 PMCID: PMC7000240 DOI: 10.1088/2050-6120/ab3bd2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fluorescence lifetime sensing enables researchers to probe the physicochemical environment of a fluorophore providing a window through which we can observe the complex molecular make-up of the cell. Fluorescence lifetime imaging microscopy (FLIM) quantifies and maps cell biochemistry, a complex ensemble of dynamic processes. Unfortunately, typical high-resolution FLIM systems exhibit rather limited acquisition speeds, often insufficient to capture the time evolution of biochemical processes in living cells. Here, we describe the theoretical background that justifies the developments of high-speed single photon counting systems. We show that systems with low dead-times not only result in faster acquisition throughputs but also improved dynamic range and spatial resolution. We also share the implementation of hardware and software as an open platform, show applications of fast FLIM biochemical imaging on living cells and discuss strategies to balance precision and accuracy in FLIM. The recent innovations and commercialisation of fast time-domain FLIM systems are likely to popularise FLIM within the biomedical community, to impact biomedical research positively and to foster the adoption of other FLIM techniques as well. While supporting and indeed pursuing these developments, with this work we also aim to warn the community about the possible shortcomings of fast single photon counting techniques and to highlight strategies to acquire data of high quality.
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Long Y, Stahl Y, Weidtkamp-Peters S, Smet W, Du Y, Gadella TWJ, Goedhart J, Scheres B, Blilou I. Optimizing FRET-FLIM Labeling Conditions to Detect Nuclear Protein Interactions at Native Expression Levels in Living Arabidopsis Roots. Front Plant Sci 2018; 9:639. [PMID: 29868092 PMCID: PMC5962846 DOI: 10.3389/fpls.2018.00639] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/25/2018] [Indexed: 05/21/2023]
Abstract
Protein complex formation has been extensively studied using Förster resonance energy transfer (FRET) measured by Fluorescence Lifetime Imaging Microscopy (FLIM). However, implementing this technology to detect protein interactions in living multicellular organism at single-cell resolution and under native condition is still difficult to achieve. Here we describe the optimization of the labeling conditions to detect FRET-FLIM in living plants. This study exemplifies optimization procedure involving the identification of the optimal position for the labels either at the N or C terminal region and the selection of the bright and suitable, fluorescent proteins as donor and acceptor labels for the FRET study. With an effective optimization strategy, we were able to detect the interaction between the stem cell regulators SHORT-ROOT and SCARECROW at endogenous expression levels in the root pole of living Arabidopsis embryos and developing lateral roots by FRET-FLIM. Using this approach we show that the spatial profile of interaction between two transcription factors can be highly modulated in reoccurring and structurally resembling organs, thus providing new information on the dynamic redistribution of nuclear protein complex configurations in different developmental stages. In principle, our optimization procedure for transcription factor complexes is applicable to any biological system.
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Affiliation(s)
- Yuchen Long
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany
| | | | - Wouter Smet
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Yujuan Du
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Theodorus W. J. Gadella
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Joachim Goedhart
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Ben Scheres
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Ikram Blilou
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
- Plant Cell and Developmental Biology, King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering (BESE), Thuwal, Saudi Arabia
- *Correspondence: Ikram Blilou
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7
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Abstract
Multiplexed immunofluorescence imaging of formalin-fixed, paraffin-embedded tissues is a powerful tool for investigating proteomic profiles and diagnosing disease. However, conventional immunofluorescence with organic dyes is limited in the number of colors that can be simultaneously visualized, is made less sensitive by tissue autofluorescence background, and is usually incompatible with commonly used hematoxylin and eosin staining. Herein, we demonstrate the comparative advantages of using time-gated luminescence microscopy in combination with an emissive Tb(III) complex, Lumi4-Tb, for tissue imaging in terms of sensitivity, multiplexing potential, and compatibility with common immunohistochemistry protocols. We show that time-gated detection of millisecond-scale Tb(III) emission increases signal-to-noise ratio relative to conventional steady-state detection of organic dye fluorescence and permits visualization of low-abundance tissue markers such as Bcl-6 or MSH-6. In addition, temporal separation of long- and short-lifetime (∼nanosecond) signals adds a second dimension for multiplexing and also permits detection of intermolecular Tb(III)-to-dye Förster resonance energy transfer. Furthermore, we demonstrate that the Lumi4-Tb complex is compatible with tyramide signal amplification and, unlike conventional organic dyes, can be reliably used on tissue stained with hematoxylin and eosin. Our results indicate that time-gated luminescence microscopy using Tb(III) labels can provide a sensitive and robust method to perform multiplexed immunofluorescence on archived or clinical tissue specimens.
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Affiliation(s)
- Ting Chen
- Department of Chemistry, University of Illinois at Chicago , 845 West Taylor Street, Chicago, Illinois 60607, United States
| | - Rui Hong
- Ventana Medical Systems , 1910 E Innovation Park Drive, Tucson, Arizona 85755, United States
| | - Darren Magda
- Lumiphore, Inc. , 600 Bancroft Way, Suite B, Berkeley, California 94710, United States
| | - Christopher Bieniarz
- Ventana Medical Systems , 1910 E Innovation Park Drive, Tucson, Arizona 85755, United States
| | - Larry Morrison
- Ventana Medical Systems , 1910 E Innovation Park Drive, Tucson, Arizona 85755, United States
| | - Lawrence W Miller
- Department of Chemistry, University of Illinois at Chicago , 845 West Taylor Street, Chicago, Illinois 60607, United States
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8
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Lönn P, Landegren U. Close Encounters - Probing Proximal Proteins in Live or Fixed Cells. Trends Biochem Sci 2017; 42:504-15. [PMID: 28566215 DOI: 10.1016/j.tibs.2017.05.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/25/2017] [Accepted: 05/03/2017] [Indexed: 12/30/2022]
Abstract
The well-oiled machinery of the cellular proteome operates via variable expression, modifications, and interactions of proteins, relaying genomic and transcriptomic information to coordinate cellular functions. In recent years, a number of techniques have emerged that serve to identify sets of proteins acting in close proximity in the course of orchestrating cellular activities. These proximity-dependent assays, including BiFC, BioID, APEX, FRET, and isPLA, have opened up new avenues to examine protein interactions in live or fixed cells. We review herein the current status of proximity-dependent in situ techniques. We compare the advantages and limitations of the methods, underlining recent progress and the growing importance of these techniques in basic research, and we discuss their potential as tools for drug development and diagnostics.
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Mumtaz MW, Hamid AA, Akhtar MT, Anwar F, Rashid U, AL-Zuaidy MH. An overview of recent developments in metabolomics and proteomics – phytotherapic research perspectives. Frontiers in Life Science 2017. [DOI: 10.1080/21553769.2017.1279573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Muhammad Waseem Mumtaz
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Chemistry, Faculty of Science, University of Gujrat, Gujrat, Pakistan
| | - Azizah Abdul Hamid
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Malaysia
| | - Muhammad Tayyab Akhtar
- Institute of Bioscience, Laboratory of Natural Products, Universiti Putra Malaysia, Serdang, Malaysia
| | - Farooq Anwar
- Department of Chemistry, University of Sargodha, Sargodha, Pakistan
| | - Umer Rashid
- Institute of Advanced Technology, Universiti Putra Malaysia, Serdang, Malaysia
| | - Mizher Hezam AL-Zuaidy
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Malaysia
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Bosch-Vilaró A, Jacobs B, Pomella V, Asbagh LA, Kirkland R, Michel J, Singh S, Liu X, Kim P, Weitsman G, Barber PR, Vojnovic B, Ng T, Tejpar S. Feedback activation of HER3 attenuates response to EGFR inhibitors in colon cancer cells. Oncotarget 2017; 8:4277-4288. [PMID: 28032592 PMCID: PMC5354831 DOI: 10.18632/oncotarget.13834] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 09/14/2016] [Accepted: 11/30/2016] [Indexed: 02/07/2023] Open
Abstract
The EGFR inhibitor cetuximab is approved for the treatment of colorectal cancer. However, both innate and acquired resistance mechanisms, including compensatory feedback loops, limit its efficacy. Nevertheless, the emergence of these feedback loops has remained largely unexplored to date. Here, we showed feedback upregulation of HER3 and induction of HER3 phosphorylation after cetuximab treatment in colon cancer cells. We also showed that this upregulation occurs, at least partly, through AKT inhibition. Together with this, we observed increased HER2:HER3 dimerization upon cetuximab treatment. Interestingly, lapatinib, a dual EGFR and HER2 tyrosine kinase inhibitor, blocked the increase of cetuximab-induced HER3 phosphorylation. Additionally, we showed that upon HER3 knockdown, cetuximab combined with lapatinib was able to decrease cell viability compared to HER3 expressing cells. These results suggest the existence of a cetuximab-induced feedback HER3 activation that could potentially result in reduced cetuximab efficacy in colorectal cancer patients. Taken together, we provide evidence of the limited effectiveness of cetuximab monotherapy compared to rational combinations.
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Affiliation(s)
- Albert Bosch-Vilaró
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Bart Jacobs
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Valentina Pomella
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Layka Abbasi Asbagh
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | | | - Joe Michel
- Prometheus Laboratories, San Diego, CA, USA
| | | | - Xinjun Liu
- Prometheus Laboratories, San Diego, CA, USA
| | | | - Gregory Weitsman
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, King's College London, Guy's Medical School Campus, London, UK
| | - Paul R. Barber
- Department of Oncology, Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Borivoj Vojnovic
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, King's College London, Guy's Medical School Campus, London, UK
- Department of Oncology, Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Tony Ng
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, King's College London, Guy's Medical School Campus, London, UK
- Breast Cancer Now Research Unit, King's College London, London, UK
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, UK
| | - Sabine Tejpar
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
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Abstract
Phosphate addition is a posttranslational modification of proteins, and this modification can affect the activity and other properties of intracellular proteins. Different animal species can be used to generate phosphosite-specific antibodies as either polyclonals or monoclonals, and each approach offers its own benefits and disadvantages. The validation of phosphosite-specific antibodies requires multiple techniques and tactics to demonstrate their specificity. These antibodies can be used in arrays, flow cytometry, and imaging platforms. The specificity of phosphosite-specific antibodies is vital for their use in proteomics and profiling of disease.
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Affiliation(s)
- Kathy Brumbaugh
- Bio-Techne, Inc., 614 McKinley Place NE, Minneapolis, MN, 55413, USA.
| | - Wen-Chie Liao
- Bio-Techne, Inc., 614 McKinley Place NE, Minneapolis, MN, 55413, USA
| | - J P Houchins
- Bio-Techne, Inc., 614 McKinley Place NE, Minneapolis, MN, 55413, USA
| | - Jeff Cooper
- Bio-Techne, Inc., 614 McKinley Place NE, Minneapolis, MN, 55413, USA
| | - Steve Stoesz
- Bio-Techne, Inc., 614 McKinley Place NE, Minneapolis, MN, 55413, USA
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Weitsman G, Barber PR, Nguyen LK, Lawler K, Patel G, Woodman N, Kelleher MT, Pinder SE, Rowley M, Ellis PA, Purushotham AD, Coolen AC, Kholodenko BN, Vojnovic B, Gillett C, Ng T. HER2-HER3 dimer quantification by FLIM-FRET predicts breast cancer metastatic relapse independently of HER2 IHC status. Oncotarget 2016; 7:51012-51026. [PMID: 27618787 PMCID: PMC5239455 DOI: 10.18632/oncotarget.9963] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 04/07/2016] [Accepted: 05/23/2016] [Indexed: 01/08/2023] Open
Abstract
Overexpression of HER2 is an important prognostic marker, and the only predictive biomarker of response to HER2-targeted therapies in invasive breast cancer. HER2-HER3 dimer has been shown to drive proliferation and tumor progression, and targeting of this dimer with pertuzumab alongside chemotherapy and trastuzumab, has shown significant clinical utility. The purpose of this study was to accurately quantify HER2-HER3 dimerisation in formalin fixed paraffin embedded (FFPE) breast cancer tissue as a novel prognostic biomarker.FFPE tissues were obtained from patients included in the METABRIC (Molecular Taxonomy of Breast Cancer International Consortium) study. HER2-HER3 dimerisation was quantified using an improved fluorescence lifetime imaging microscopy (FLIM) histology-based analysis. Analysis of 131 tissue microarray cores demonstrated that the extent of HER2-HER3 dimer formation as measured by Förster Resonance Energy Transfer (FRET) determined through FLIM predicts the likelihood of metastatic relapse up to 10 years after surgery (hazard ratio 3.91 (1.61-9.5), p = 0.003) independently of HER2 expression, in a multivariate model. Interestingly there was no correlation between the level of HER2 protein expressed and HER2-HER3 heterodimer formation. We used a mathematical model that takes into account the complex interactions in a network of all four HER proteins to explain this counterintuitive finding.Future utility of this technique may highlight a group of patients who do not overexpress HER2 protein but are nevertheless dependent on the HER2-HER3 heterodimer as driver of proliferation. This assay could, if validated in a group of patients treated with, for instance pertuzumab, be used as a predictive biomarker to predict for response to such targeted therapies.
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Affiliation(s)
- Gregory Weitsman
- Richard Dimbleby Department of Cancer Research, Randall Division and Division of Cancer Studies, King's College London, Guy's Medical School Campus, London, UK
| | - Paul R. Barber
- Department of Oncology, Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
- Institute for Mathematical and Molecular Biomedicine, King's College London, Guy's Medical School Campus, London, UK
| | - Lan K. Nguyen
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences and Biomedical Discovery Institute, Monash University, Melbourne, Australia
| | - Katherine Lawler
- Institute for Mathematical and Molecular Biomedicine, King's College London, Guy's Medical School Campus, London, UK
| | - Gargi Patel
- Richard Dimbleby Department of Cancer Research, Randall Division and Division of Cancer Studies, King's College London, Guy's Medical School Campus, London, UK
- Sussex Cancer Centre, Brighton and Sussex University Hospitals, Royal Sussex County Hospital, Brighton, UK
| | - Natalie Woodman
- Research Oncology, Division of Cancer Studies, King's College London, Guy's Hospital, Great Maze Pond, London, UK
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy's Hospital King's College London School of Medicine, London, UK
| | - Muireann T. Kelleher
- Department of Medical Oncology, St George's Hospital NHS Foundation Trust, London, UK
| | - Sarah E. Pinder
- Research Oncology, Division of Cancer Studies, King's College London, Guy's Hospital, Great Maze Pond, London, UK
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy's Hospital King's College London School of Medicine, London, UK
| | - Mark Rowley
- Institute for Mathematical and Molecular Biomedicine, King's College London, Guy's Medical School Campus, London, UK
| | - Paul A. Ellis
- Research Oncology, Division of Cancer Studies, King's College London, Guy's Hospital, Great Maze Pond, London, UK
| | - Anand D. Purushotham
- Research Oncology, Division of Cancer Studies, King's College London, Guy's Hospital, Great Maze Pond, London, UK
| | - Anthonius C. Coolen
- Institute for Mathematical and Molecular Biomedicine, King's College London, Guy's Medical School Campus, London, UK
| | - Boris N. Kholodenko
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland
| | - Borivoj Vojnovic
- Richard Dimbleby Department of Cancer Research, Randall Division and Division of Cancer Studies, King's College London, Guy's Medical School Campus, London, UK
- Department of Oncology, Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Cheryl Gillett
- Research Oncology, Division of Cancer Studies, King's College London, Guy's Hospital, Great Maze Pond, London, UK
| | - Tony Ng
- Richard Dimbleby Department of Cancer Research, Randall Division and Division of Cancer Studies, King's College London, Guy's Medical School Campus, London, UK
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy's Hospital King's College London School of Medicine, London, UK
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, UK
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13
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Abstract
The clinical success of trastuzumab in breast cancer taught us that appropriate tumor evaluation is mandatory for the correct identification of patients eligible for targeted therapies. Although HER2 protein expression by immunohistochemistry (IHC) and gene amplification by fluorescence in situ hybridization (FISH) assays are routinely used to select patients to receive trastuzumab, both assays only partially predict response to the drug. In the case of epidermal growth factor receptor (EGFR), the link between the presence of the receptor or its amplification and response to anti-EGFR therapies could not be demonstrated. Even less is known for HER3 and HER4, mainly due to lack of robust and validated assays detecting these proteins. It is becoming evident that, besides FISH and IHC, we need better assays to quantify HER receptors and categorize the patients for individualized treatments. Here, we present the current available methodologies to measure HER family receptors and discuss the clinical implications of target quantification.
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Affiliation(s)
- Paolo Nuciforo
- Molecular Oncology Laboratory, Vall d'Hebron Institute of Oncology, Passeig Vall d'Hebron 119-129, Barcelona, 08035, Spain.
- Universitat Autònoma de Barcelona, Barcelona, 08035, Spain.
| | - Nina Radosevic-Robin
- ERTICa Research Group, University of Auvergne EA4677, 63000, Clermont-Ferrand, France.
- Biopathology, Jean Perrin Comprehensive Cancer Center, 58 rue Montalembert, 63011, Clermont-Ferrand, France.
| | - Tony Ng
- Richard Dimbleby Department of Cancer Research, Randall Division of Cell and Molecular Biophysics and Division of Cancer Studies, King's College London, London, SE1 1UL, UK.
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, WC1E 6DD, UK.
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy's Hospital King's College London School of Medicine, London, SE1 9RT, UK.
| | - Maurizio Scaltriti
- Human Oncology and Pathogenesis Program (HOPP), Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 20, New York, NY, 10065, USA.
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14
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Abstract
Optical imaging assays, especially fluorescence molecular assays, are minimally invasive if not completely noninvasive, and thus an ideal technique to be applied to live specimens. These fluorescence imaging assays are a powerful tool in biomedical sciences as they allow the study of a wide range of molecular and physiological events occurring in biological systems. Furthermore, optical imaging assays bridge the gap between the in vitro cell-based analysis of subcellular processes and in vivo study of disease mechanisms in small animal models. In particular, the application of Förster resonance energy transfer (FRET) and fluorescence lifetime imaging (FLIM), well-known techniques widely used in microscopy, to the optical imaging assay toolbox, will have a significant impact in the molecular study of protein-protein interactions during cancer progression. This review article describes the application of FLIM-FRET to the field of optical imaging and addresses their various applications, both current and potential, to anti-cancer drug delivery and cancer research.
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Affiliation(s)
- Shilpi Rajoria
- Albany Medical College, The Center for Cardiovascular Sciences, Albany, NY, 12208
| | - Lingling Zhao
- Rensselaer Polytechnic Institute, Biomedical imaging Center and Department of Biomedical Engineering, Troy, NY 12180
| | - Xavier Intes
- Rensselaer Polytechnic Institute, Biomedical imaging Center and Department of Biomedical Engineering, Troy, NY 12180
| | - Margarida Barroso
- Albany Medical College, The Center for Cardiovascular Sciences, Albany, NY, 12208
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15
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Weitsman G, Lawler K, Kelleher MT, Barrett JE, Barber PR, Shamil E, Festy F, Patel G, Fruhwirth GO, Huang L, Tullis ID, Woodman N, Ofo E, Ameer-Beg SM, Irshad S, Condeelis J, Gillett CE, Ellis PA, Vojnovic B, Coolen AC, Ng T. Imaging tumour heterogeneity of the consequences of a PKCα-substrate interaction in breast cancer patients. Biochem Soc Trans 2014; 42:1498-505. [PMID: 25399560 PMCID: PMC4259014 DOI: 10.1042/bst20140165] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Breast cancer heterogeneity demands that prognostic models must be biologically driven and recent clinical evidence indicates that future prognostic signatures need evaluation in the context of early compared with late metastatic risk prediction. In pre-clinical studies, we and others have shown that various protein-protein interactions, pertaining to the actin microfilament-associated proteins, ezrin and cofilin, mediate breast cancer cell migration, a prerequisite for cancer metastasis. Moreover, as a direct substrate for protein kinase Cα, ezrin has been shown to be a determinant of cancer metastasis for a variety of tumour types, besides breast cancer; and has been described as a pivotal regulator of metastasis by linking the plasma membrane to the actin cytoskeleton. In the present article, we demonstrate that our tissue imaging-derived parameters that pertain to or are a consequence of the PKC-ezrin interaction can be used for breast cancer prognostication, with inter-cohort reproducibility. The application of fluorescence lifetime imaging microscopy (FLIM) in formalin-fixed paraffin-embedded patient samples to probe protein proximity within the typically <10 nm range to address the oncological challenge of tumour heterogeneity, is discussed.
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Affiliation(s)
- Gregory Weitsman
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London SE1 1UL, U.K
| | - Katherine Lawler
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London SE1 1UL, U.K
- Department of Mathematics, King’s College London, Strand Campus, London WC2R 2LS, U.K
| | - Muireann T. Kelleher
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London SE1 1UL, U.K
- Department of Medical Oncology, St George’s NHS Trust, London SW17 0QT, U.K
| | - James E. Barrett
- Department of Mathematics, King’s College London, Strand Campus, London WC2R 2LS, U.K
| | - Paul R. Barber
- Gray Institute for Radiation Oncology & Biology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Eamon Shamil
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London SE1 1UL, U.K
| | - Frederic Festy
- Biomaterials, Biomimetics and Biophotonics Division, King’s College London Dental Institute, London SE1 9RT, U.K
| | - Gargi Patel
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London SE1 1UL, U.K
- Department of Medical Oncology, Guy’s and St. Thomas Foundation Trust, London SE1 9RT, U.K
| | - Gilbert O. Fruhwirth
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London SE1 1UL, U.K
- Division of Imaging Science and Biomedical Engineering, King’s College London, London SE1 7EH, U.K
| | - Lufei Huang
- Gray Institute for Radiation Oncology & Biology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Iain D.C. Tullis
- Gray Institute for Radiation Oncology & Biology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Natalie Woodman
- Guy’s & St. Thomas’ Breast Tissue & Data Bank, King’s College London, Guy’s Hospital, London SE1 9RT, U.K
| | - Enyinnaya Ofo
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London SE1 1UL, U.K
| | - Simon M. Ameer-Beg
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London SE1 1UL, U.K
| | - Sheeba Irshad
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy’s Hospital King’s College London School of Medicine, London, SE1 9RT, U.K
| | - John Condeelis
- Tumor Microenvironment and Metastasis Program, Albert Einstein Cancer Center, New York, NY 10461, U.S.A
| | - Cheryl E. Gillett
- Guy’s & St. Thomas’ Breast Tissue & Data Bank, King’s College London, Guy’s Hospital, London SE1 9RT, U.K
| | - Paul A. Ellis
- Department of Medical Oncology, Guy’s and St. Thomas Foundation Trust, London SE1 9RT, U.K
| | - Borivoj Vojnovic
- Gray Institute for Radiation Oncology & Biology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Randall Division of Cell & Molecular Biophysics, King’s College London, London, U.K
| | - Anthony C.C. Coolen
- Department of Mathematics, King’s College London, Strand Campus, London WC2R 2LS, U.K
| | - Tony Ng
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, Kings College London, Guy’s Medical School Campus, London SE1 1UL, U.K
- Breakthrough Breast Cancer Research Unit, Department of Research Oncology, Guy’s Hospital King’s College London School of Medicine, London, SE1 9RT, U.K
- UCL Cancer Institute, Paul O’Gorman Building, University College London, London WC1E 6DD, U.K
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16
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Zhu Z, Liu Z, Liu J, Bi M, Yang T, Wang J. Proteomic profiling of human placenta-derived mesenchymal stem cells upon transforming LIM mineralization protein-1 stimulation. Cytotechnology 2014; 67:285-97. [PMID: 24468833 DOI: 10.1007/s10616-013-9684-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 12/23/2013] [Indexed: 02/07/2023] Open
Abstract
Human placenta-derived mesenchymal stem cells (hPDMSCs) can differentiate into different types of cells and thus have tremendous potential for cell therapy and tissue engineering. LIM mineralization protein-1 (LMP-1) plays an important role in osteoblast differentiation, maturation and bone formation. To determine a global effect of LMP-1 on hPDMSCs, we designed a study using a proteomic approach combined with adenovirus-mediated gene transfer of LMP-1 to identify LMP-1-induced changes in hPDMSCs on proteome level. We have generated proteome maps of undifferentiated hPDMSCs and LMP-1 induced hPDMSCs. Two dimensional gel electrophoresis revealed 22 spots with at least 2.0-fold changes in expression and 15 differently expressed proteins were successfully identified by MALDI-TOF-MS. The proteins regulated by LMP-1 included cytoskeletal proteins, cadmium-binding proteins, and metabolic proteins, etc. The expression of some identified proteins was confirmed by further Western blot analyses. Our results will play an important role in better elucidating the underlying molecular mechanism in LMP-1 included hPDMSCs differentiation into osteoblasts.
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Affiliation(s)
- Zhen Zhu
- Stomatology Hospital, Jilin University, Changchun, 130021, People's Republic of China
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17
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Nobis M, Carragher NO, McGhee EJ, Morton JP, Sansom OJ, Anderson KI, Timpson P. Advanced intravital subcellular imaging reveals vital three-dimensional signalling events driving cancer cell behaviour and drug responses in live tissue. FEBS J 2013; 280:5177-97. [PMID: 23678945 DOI: 10.1111/febs.12348] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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: 04/11/2013] [Revised: 05/13/2013] [Accepted: 05/14/2013] [Indexed: 12/18/2022]
Abstract
The integration of signal transduction pathways plays a fundamental role in governing disease initiation, progression and outcome. It is therefore necessary to understand disease at the signalling level to enable effective treatment and to intervene in its progression. The recent extension of in vitro subcellular image-based analysis to live in vivo modelling of disease is providing a more complete picture of real-time, dynamic signalling processes or drug responses in live tissue. Intravital imaging offers alternative strategies for studying disease and embraces the biological complexities that govern disease progression. In the present review, we highlight how three-dimensional or live intravital imaging has uncovered novel insights into biological mechanisms or modes of drug action. Furthermore, we offer a prospective view of how imaging applications may be integrated further with the aim of understanding disease in a more physiological and functional manner within the framework of the drug discovery process.
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Affiliation(s)
- Max Nobis
- The Beatson Institute for Cancer Research, Glasgow, UK
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18
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BARBER PR, TULLIS IDC, PIERCE GP, NEWMAN RG, PRENTICE J, ROWLEY MI, MATTHEWS DR, AMEER-BEG SM, VOJNOVIC B. The Gray Institute 'open' high-content, fluorescence lifetime microscopes. J Microsc 2013; 251:154-67. [PMID: 23772985 PMCID: PMC3910159 DOI: 10.1111/jmi.12057] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [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: 12/11/2012] [Accepted: 05/09/2013] [Indexed: 01/07/2023]
Abstract
We describe a microscopy design methodology and details of microscopes built to this 'open' design approach. These demonstrate the first implementation of time-domain fluorescence microscopy in a flexible automated platform with the ability to ease the transition of this and other advanced microscopy techniques from development to use in routine biology applications. This approach allows easy expansion and modification of the platform capabilities, as it moves away from the use of a commercial, monolithic, microscope body to small, commercial off-the-shelf and custom made modular components. Drawings and diagrams of our microscopes have been made available under an open license for noncommercial use at http://users.ox.ac.uk/~atdgroup. Several automated high-content fluorescence microscope implementations have been constructed with this design framework and optimized for specific applications with multiwell plates and tissue microarrays. In particular, three platforms incorporate time-domain FLIM via time-correlated single photon counting in an automated fashion. We also present data from experiments performed on these platforms highlighting their automated wide-field and laser scanning capabilities designed for high-content microscopy. Devices using these designs also form radiation-beam 'end-stations' at Oxford and Surrey Universities, showing the versatility and extendibility of this approach.
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Affiliation(s)
- PR BARBER
- Gray Institute for Radiation Oncology & Biology, Dept. Of Oncology, University of OxfordOxford, U.K.
- Institute for Mathematical and Molecular Biomedicine, King's College LondonLondon, U.K.
- Randall Division of Cell and Molecular Biophysics, New Hunts House, King's College LondonLondon, U.K.
| | - IDC TULLIS
- Gray Institute for Radiation Oncology & Biology, Dept. Of Oncology, University of OxfordOxford, U.K.
| | - GP PIERCE
- Gray Institute for Radiation Oncology & Biology, Dept. Of Oncology, University of OxfordOxford, U.K.
| | - RG NEWMAN
- Gray Institute for Radiation Oncology & Biology, Dept. Of Oncology, University of OxfordOxford, U.K.
| | - J PRENTICE
- Gray Institute for Radiation Oncology & Biology, Dept. Of Oncology, University of OxfordOxford, U.K.
| | - MI ROWLEY
- Randall Division of Cell and Molecular Biophysics, New Hunts House, King's College LondonLondon, U.K.
| | - DR MATTHEWS
- Richard Dimbleby Department of Cancer Research, New Hunts House, King's College LondonLondon, U.K.
- Randall Division of Cell and Molecular Biophysics, New Hunts House, King's College LondonLondon, U.K.
- Now at The University of Queensland, Brisbane St LuciaAustralia
| | - SM AMEER-BEG
- Richard Dimbleby Department of Cancer Research, New Hunts House, King's College LondonLondon, U.K.
- Randall Division of Cell and Molecular Biophysics, New Hunts House, King's College LondonLondon, U.K.
| | - B VOJNOVIC
- Gray Institute for Radiation Oncology & Biology, Dept. Of Oncology, University of OxfordOxford, U.K.
- Randall Division of Cell and Molecular Biophysics, New Hunts House, King's College LondonLondon, U.K.
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19
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Villar EL, Cho WC. Proteomics and Cancer Research. In: Wang X, editor. Bioinformatics of Human Proteomics. Dordrecht: Springer Netherlands; 2013. pp. 75-101. [DOI: 10.1007/978-94-007-5811-7_4] [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: 01/01/2023]
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20
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Boja ES, Rodriguez H. Mass spectrometry-based targeted quantitative proteomics: achieving sensitive and reproducible detection of proteins. Proteomics 2012; 12:1093-110. [PMID: 22577011 DOI: 10.1002/pmic.201100387] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Traditional shotgun proteomics used to detect a mixture of hundreds to thousands of proteins through mass spectrometric analysis, has been the standard approach in research to profile protein content in a biological sample which could lead to the discovery of new (and all) protein candidates with diagnostic, prognostic, and therapeutic values. In practice, this approach requires significant resources and time, and does not necessarily represent the goal of the researcher who would rather study a subset of such discovered proteins (including their variations or posttranslational modifications) under different biological conditions. In this context, targeted proteomics is playing an increasingly important role in the accurate measurement of protein targets in biological samples in the hope of elucidating the molecular mechanism of cellular function via the understanding of intricate protein networks and pathways. One such (targeted) approach, selected reaction monitoring (or multiple reaction monitoring) mass spectrometry (MRM-MS), offers the capability of measuring multiple proteins with higher sensitivity and throughput than shotgun proteomics. Developing and validating MRM-MS-based assays, however, is an extensive and iterative process, requiring a coordinated and collaborative effort by the scientific community through the sharing of publicly accessible data and datasets, bioinformatic tools, standard operating procedures, and well characterized reagents.
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Affiliation(s)
- Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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21
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Jayo A, Parsons M. Imaging of cell adhesion events in 3D matrix environments. Eur J Cell Biol 2012; 91:824-33. [PMID: 22705211 DOI: 10.1016/j.ejcb.2012.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 05/08/2012] [Accepted: 05/08/2012] [Indexed: 01/28/2023] Open
Abstract
Cell adhesion plays an essential role in development and homeostasis, but is also a key regulator of many diseases such as cancer and immune dysfunction. Numerous studies over the past three decades have revealed a wealth of information detailing signalling molecules required for cell adhesion to two-dimensional surfaces. However, in vivo many cells are completely surrounded by matrix and this will very likely influence the size, composition and dynamics of adhesive structures. The study of adhesion in cells within three-dimensional environments is still in its infancy, thus the role and regulation of adhesions in these complex environments remains unclear. The recent development of new experimental models coupled with significant advances in cell imaging approaches have provided platforms for researchers to begin to dissect adhesion signalling in cells in 3D matrices. Here we summarise the recent insights in cell adhesion formation and regulation in 3D model systems and the imaging approaches used to analyse these events.
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Affiliation(s)
- Asier Jayo
- Randall Division of Cell and Molecular Biophysics, King's College London, Guys Campus, UK
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22
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López E, Madero L, López-Pascual J, Latterich M. Clinical proteomics and OMICS clues useful in translational medicine research. Proteome Sci 2012; 10:35. [PMID: 22642823 PMCID: PMC3536680 DOI: 10.1186/1477-5956-10-35] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 05/04/2012] [Indexed: 12/21/2022] Open
Abstract
Since the advent of the new proteomics era more than a decade ago, large-scale studies of protein profiling have been used to identify distinctive molecular signatures in a wide array of biological systems, spanning areas of basic biological research, clinical diagnostics, and biomarker discovery directed toward therapeutic applications. Recent advances in protein separation and identification techniques have significantly improved proteomic approaches, leading to enhancement of the depth and breadth of proteome coverage. Proteomic signatures, specific for multiple diseases, including cancer and pre-invasive lesions, are emerging. This article combines, in a simple manner, relevant proteomic and OMICS clues used in the discovery and development of diagnostic and prognostic biomarkers that are applicable to all clinical fields, thus helping to improve applications of clinical proteomic strategies for translational medicine research.
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Affiliation(s)
- Elena López
- Centro de Investigación i + 12, Hospital 12 de Octubre, Av, De Córdoba s/n, 28040, Madrid, Spain.
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23
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López E, Muñoz SR, Pascual JL, Madero L. Relevant phosphoproteomic and mass spectrometry: approaches useful in clinical research. Clin Transl Med 2012; 1:2. [PMID: 23369602 PMCID: PMC3552569 DOI: 10.1186/2001-1326-1-2] [Citation(s) in RCA: 12] [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: 02/23/2012] [Accepted: 03/29/2012] [Indexed: 01/03/2023] Open
Abstract
Background "It's not what we do, it's the way that we do it". Never has this maxim been truer in proteomics than now. Mass Spectrometry-based proteomics/phosphoproteomics tools are critical to understand the structure and dynamics (spatial and temporal) of signalling that engages and migrates through the entire proteome. Approaches such as affinity purification followed by Mass Spectrometry (MS) have been used to elucidate relevant biological questions disease vs. health. Thousands of proteins interact via physical and chemical association. Moreover, certain proteins can covalently modify other proteins post-translationally. These post-translational modifications (PTMs) ultimately give rise to the emergent functions of cells in sequence, space and time. Findings Understanding the functions of phosphorylated proteins thus requires one to study proteomes as linked-systems rather than collections of individual protein molecules. Indeed, the interacting proteome or protein-network knowledge has recently received much attention, as network-systems (signalling pathways) are effective snapshots in time, of the proteome as a whole. MS approaches are clearly essential, in spite of the difficulties of some low abundance proteins for future clinical advances. Conclusion Clinical proteomics-MS has come a long way in the past decade in terms of technology/platform development, protein chemistry, and together with bioinformatics and other OMICS tools to identify molecular signatures of diseases based on protein pathways and signalling cascades. Hence, there is great promise for disease diagnosis, prognosis, and prediction of therapeutic outcome on an individualized basis. However, and as a general rule, without correct study design, strategy and implementation of robust analytical methodologies, the efforts, efficiency and expectations to make biomarkers (especially phosphorylated kinases) a useful reality in the near future, can easily be hampered.
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Affiliation(s)
- Elena López
- Hospital Universitario Infantil Niño Jesús, Av, Menéndez Pelayo 65, 28009 Madrid, Spain.
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24
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Abstract
Advances in fluorescence microscopy have enabled the study of membrane diffusion, cell adhesion and signal transduction at the molecular level in living cells grown in culture. By contrast, imaging in living organisms has primarily been restricted to the localization and dynamics of cells in tissues. Now, imaging of molecular dynamics is on the cusp of progressing from cell culture to living tissue. This transition has been driven by the understanding that the microenvironment critically determines many developmental and pathological processes. Here, we review recent progress in fluorescent protein imaging in vivo by drawing primarily on cancer-related studies in mice. We emphasize the need for techniques that can be easily combined with genetic models and complement fluorescent protein imaging by providing contextual information about the cellular environment. In this Commentary we will consider differences between in vitro and in vivo experimental design and argue for an approach to in vivo imaging that is built upon the use of intermediate systems, such as 3-D and explant culture models, which offer flexibility and control that is not always available in vivo. Collectively, these methods present a paradigm shift towards the molecular-level investigation of disease and therapy in animal models of disease.
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Affiliation(s)
- Paul Timpson
- The Beatson Institute for Cancer Research, Garscube Estate, Glasgow G611BD, UK
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25
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Carlin LM, Evans R, Milewicz H, Fernandes L, Matthews DR, Perani M, Levitt J, Keppler MD, Monypenny J, Coolen T, Barber PR, Vojnovic B, Suhling K, Fraternali F, Ameer-Beg S, Parker PJ, Thomas NSB, Ng T. A targeted siRNA screen identifies regulators of Cdc42 activity at the natural killer cell immunological synapse. Sci Signal 2011; 4:ra81. [PMID: 22126964 DOI: 10.1126/scisignal.2001729] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Natural killer (NK) cells kill tumor cells and virally infected cells, and an effective NK cell response requires processes, such as motility, recognition, and directional secretion, that rely on cytoskeletal rearrangement. The Rho guanosine triphosphatase (GTPase) Cdc42 coordinates cytoskeletal reorganization downstream of many receptors. The Rho-related GTPase from plants 1 (ROP1) exhibits oscillatory activation behavior at the apical plasma membrane of growing pollen tubes; however, a similar oscillation in Rho GTPase activity has so far not been demonstrated in mammalian cells. We hypothesized that oscillations in Cdc42 activity might occur within NK cells as they interact with target cells. Through fluorescence lifetime imaging of a Cdc42 biosensor, we observed that in live NK cells forming immunological synapses with target cells, Cdc42 activity oscillated after exhibiting an initial increase. We used protein-protein interaction networks and structural databases to identify candidate proteins that controlled Cdc42 activity, leading to the design of a targeted short interfering RNA screen. The guanine nucleotide exchange factors RhoGEF6 and RhoGEF7 were necessary for Cdc42 activation within the NK cell immunological synapse. In addition, the kinase Akt and the p85α subunit of phosphoinositide 3-kinase (PI3K) were required for Cdc42 activation, the periodicity of the oscillation in Cdc42 activity, and the subsequent polarization of cytotoxic vesicles toward target cells. Given that PI3Ks are targets of tumor therapies, our findings suggest the need to monitor innate immune function during the course of targeted therapy against these enzymes.
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Affiliation(s)
- Leo M Carlin
- Richard Dimbleby Department of Cancer Research, King's College London, London SE1 1UL, UK
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26
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Zhang X, Yuan Z, Shen B, Zhu M, Liu C, Xu W. Discovery of serum protein biomarkers in rheumatoid arthritis using MALDI-TOF-MS combined with magnetic beads. Clin Exp Med 2012; 12:145-51. [PMID: 21922190 DOI: 10.1007/s10238-011-0154-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 08/09/2011] [Indexed: 12/30/2022]
Abstract
The aim of this study was to discover potential biomarkers for rheumatoid arthritis (RA) using Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry combined with magnetic beads. Proteomic fingerprint technology combining magnetic beads with MALDI-TOF-MS was used to profile and compare the proteomes in serum samples from 60 patients with RA, 35 patients with osteoarthritis and 36 healthy controls. The proteomic pattern associated with RA was identified by Biomarker Patterns Software. Model of biomarkers was constructed and evaluated through the Biomarker Patterns Software. A total of 33 discriminative peaks were identified to be related with RA, in which the 5 peaks with the mass-charge ratio (m/z) peaks at 15,715.5, 7,771.4, 8,959.4, 8,469.8 and 8,710.8 Da were used to construct a model for the diagnosis of RA by pattern recognition software. The blind testing data indicated a sensitivity of 86.7% and a specificity of 90.0% in RA diagnosis. These results demonstrated that potential protein biomarkers for RA could be discovered in serum by MALDI-TOF-MS combined with WCX magnetic beads. The diagnosis mode tree based on the five candidate biomarkers could provide a powerful and reliable diagnostic method for RA with high sensitivity and specificity.
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Leung RWK, Yeh SCA, Fang Q. Effects of incomplete decay in fluorescence lifetime estimation. Biomed Opt Express 2011; 2:2517-31. [PMID: 21991544 PMCID: PMC3184861 DOI: 10.1364/boe.2.002517] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 07/21/2011] [Accepted: 07/31/2011] [Indexed: 05/06/2023]
Abstract
Fluorescence lifetime imaging has emerged as an important microscopy technique, where high repetition rate lasers are the primary light sources. As fluorescence lifetime becomes comparable to intervals between consecutive excitation pulses, incomplete fluorescence decay from previous pulses can superimpose onto the subsequent decay measurements. Using a mathematical model, the incomplete decay effect has been shown to lead to overestimation of the amplitude average lifetime except in mono-exponential decays. An inverse model is then developed to correct the error from this effect and the theoretical simulations are tested by experimental results.
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Affiliation(s)
- Regina Won Kay Leung
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Institute of Biomaterials & Biomedical Engineering, University of Toronto,164 College Street, Toronto, Ontario M5S 3G9, Canada
- Contributed equally
| | - Shu-Chi Allison Yeh
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Contributed equally
| | - Qiyin Fang
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
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Abstract
Better biomarkers are urgently needed to cancer detection, diagnosis, and prognosis. While the genomics community is making significant advances in understanding the molecular basis of disease, proteomics will delineate the functional units of a cell, proteins and their intricate interaction network and signaling pathways for the underlying disease. Great progress has been made to characterize thousands of proteins qualitatively and quantitatively in complex biological systems by utilizing multi-dimensional sample fractionation strategies, mass spectrometry and protein microarrays. Comparative/quantitative analysis of high-quality clinical biospecimen (e.g., tissue and biofluids) of human cancer proteome landscape has the potential to reveal protein/peptide biomarkers responsible for this disease by means of their altered levels of expression, post-translational modifications as well as different forms of protein variants. Despite technological advances in proteomics, major hurdles still exist in every step of the biomarker development pipeline. The National Cancer Institute's Clinical Proteomic Technologies for Cancer initiative (NCI-CPTC) has taken a critical step to close the gap between biomarker discovery and qualification by introducing a pre-clinical "verification" stage in the pipeline, partnering with clinical laboratory organizations to develop and implement common standards, and developing regulatory science documents with the US Food and Drug Administration to educate the proteomics community on analytical evaluation requirements for multiplex assays in order to ensure the safety and effectiveness of these tests for their intended use.
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Affiliation(s)
- Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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McGhee EJ, Morton JP, Von Kriegsheim A, Schwarz JP, Karim SA, Carragher NO, Sansom OJ, Anderson KI, Timpson P. FLIM-FRET imaging in vivo reveals 3D-environment spatially regulates RhoGTPase activity during cancer cell invasion. Small GTPases 2011; 2:239-244. [PMID: 22145098 PMCID: PMC3225915 DOI: 10.4161/sgtp.2.4.17275] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 07/13/2011] [Indexed: 11/19/2022] Open
Abstract
Many conceptual advances in biology have been achieved by experimental studies using planar two-dimensional cell culture systems. Recent adaptations of molecular techniques to three-dimensional model systems are bridging the gap in our understanding of biological events in vitro and in vivo in the study of disease progression. Recently, in vitro studies using Förster resonance energy transfer (FRET) have shown that the prototypical RhoGTPases Cdc42, Rac and RhoA are temporally and spatially synchronized during cell migration, with initial RhoA activity inducing protrusion prior to activation of Rac. This simultaneous FRET approach illustrates the tight control and dynamic regulation of RhoGTPase activity necessary for coordinated cell migration in vitro. Here, we discuss our recent work using FLIM-FRET analysis in a three-dimensional setting to reveal another layer of regulation in which RhoA activity is governed by the extracellular microenvironment. We demonstrate that RhoA is spatially regulated into discrete fractions of activity at the leading edge and rear of cells during invasion in vivo or within three-dimensional matrices. Significantly, this spatial regulation of RhoA was absent in two-dimensional in vitro settings. This distinct sub-cellular regulation of RhoA at the poles of invading cells in three-dimensions sets a precedent that other RhoGTPases or signaling proteins may also be differentially regulated in a con-text-dependent manner during key biological processes such as invasion.
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Affiliation(s)
- Ewan J McGhee
- The Beatson Institute for Cancer Research; Glasgow; Edinburgh, UK
| | | | | | | | - Saadia A Karim
- The Beatson Institute for Cancer Research; Glasgow; Edinburgh, UK
| | - Neil O Carragher
- Edinburgh Cancer Research Centre; Institute of Genetics and Molecular Medicine; University of Edinburgh; Edinburgh, UK
| | - Owen J Sansom
- The Beatson Institute for Cancer Research; Glasgow; Edinburgh, UK
| | - Kurt I Anderson
- The Beatson Institute for Cancer Research; Glasgow; Edinburgh, UK
| | - Paul Timpson
- The Beatson Institute for Cancer Research; Glasgow; Edinburgh, UK
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Presson AP, Yoon NK, Bagryanova L, Mah V, Alavi M, Maresh EL, Rajasekaran AK, Goodglick L, Chia D, Horvath S. Protein expression based multimarker analysis of breast cancer samples. BMC Cancer 2011; 11:230. [PMID: 21651811 PMCID: PMC3142534 DOI: 10.1186/1471-2407-11-230] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [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: 10/13/2010] [Accepted: 06/08/2011] [Indexed: 12/11/2022] Open
Abstract
Background Tissue microarray (TMA) data are commonly used to validate the prognostic accuracy of tumor markers. For example, breast cancer TMA data have led to the identification of several promising prognostic markers of survival time. Several studies have shown that TMA data can also be used to cluster patients into clinically distinct groups. Here we use breast cancer TMA data to cluster patients into distinct prognostic groups. Methods We apply weighted correlation network analysis (WGCNA) to TMA data consisting of 26 putative tumor biomarkers measured on 82 breast cancer patients. Based on this analysis we identify three groups of patients with low (5.4%), moderate (22%) and high (50%) mortality rates, respectively. We then develop a simple threshold rule using a subset of three markers (p53, Na-KATPase-β1, and TGF β receptor II) that can approximately define these mortality groups. We compare the results of this correlation network analysis with results from a standard Cox regression analysis. Results We find that the rule-based grouping variable (referred to as WGCNA*) is an independent predictor of survival time. While WGCNA* is based on protein measurements (TMA data), it validated in two independent Affymetrix microarray gene expression data (which measure mRNA abundance). We find that the WGCNA patient groups differed by 35% from mortality groups defined by a more conventional stepwise Cox regression analysis approach. Conclusions We show that correlation network methods, which are primarily used to analyze the relationships between gene products, are also useful for analyzing the relationships between patients and for defining distinct patient groups based on TMA data. We identify a rule based on three tumor markers for predicting breast cancer survival outcomes.
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Patel GS, Kiuchi T, Lawler K, Ofo E, Fruhwirth GO, Kelleher M, Shamil E, Zhang R, Selvin PR, Santis G, Spicer J, Woodman N, Gillett CE, Barber PR, Vojnovic B, Kéri G, Schaeffter T, Goh V, O'Doherty MJ, Ellis PA, Ng T. The challenges of integrating molecular imaging into the optimization of cancer therapy. Integr Biol (Camb) 2011; 3:603-31. [PMID: 21541433 DOI: 10.1039/c0ib00131g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We review novel, in vivo and tissue-based imaging technologies that monitor and optimize cancer therapeutics. Recent advances in cancer treatment centre around the development of targeted therapies and personalisation of treatment regimes to individual tumour characteristics. However, clinical outcomes have not improved as expected. Further development of the use of molecular imaging to predict or assess treatment response must address spatial heterogeneity of cancer within the body. A combination of different imaging modalities should be used to relate the effect of the drug to dosing regimen or effective drug concentration at the local site of action. Molecular imaging provides a functional and dynamic read-out of cancer therapeutics, from nanometre to whole body scale. At the whole body scale, an increase in the sensitivity and specificity of the imaging probe is required to localise (micro)metastatic foci and/or residual disease that are currently below the limit of detection. The use of image-guided endoscopic biopsy can produce tumour cells or tissues for nanoscopic analysis in a relatively patient-compliant manner, thereby linking clinical imaging to a more precise assessment of molecular mechanisms. This multimodality imaging approach (in combination with genetics/genomic information) could be used to bridge the gap between our knowledge of mechanisms underlying the processes of metastasis, tumour dormancy and routine clinical practice. Treatment regimes could therefore be individually tailored both at diagnosis and throughout treatment, through monitoring of drug pharmacodynamics providing an early read-out of response or resistance.
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Affiliation(s)
- G S Patel
- Richard Dimbleby Department of Cancer Research, Randall Division & Division of Cancer Studies, King's College London, Guy's Medical School Campus, London, SE1 1UL, UK.
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Abstract
Proteomics technologies have revolutionized cell biology and biochemistry by providing powerful new tools to characterize complex proteomes, multiprotein complexes and post-translational modifications. Although proteomics technologies could address important problems in clinical and translational cancer research, attempts to use proteomics approaches to discover cancer biomarkers in biofluids and tissues have been largely unsuccessful and have given rise to considerable skepticism. The National Cancer Institute has taken a leading role in facilitating the translation of proteomics from research to clinical application, through its Clinical Proteomic Technologies for Cancer. This article highlights the building of a more reliable and efficient protein biomarker development pipeline that incorporates three steps: discovery, verification and qualification. In addition, we discuss the merits of multiple reaction monitoring mass spectrometry, a multiplex targeted proteomics platform, which has emerged as a potentially promising, high-throughput protein biomarker measurements technology for preclinical 'verification'.
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Affiliation(s)
- Emily Boja
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiative, National Cancer Institute, NIH, 31 Center Drive, MS 2590, Bethesda, MD 20892, USA
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Isherwood B, Timpson P, McGhee EJ, Anderson KI, Canel M, Serrels A, Brunton VG, Carragher NO. Live cell in vitro and in vivo imaging applications: accelerating drug discovery. Pharmaceutics 2011; 3:141-70. [PMID: 24310493 DOI: 10.3390/pharmaceutics3020141] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 03/21/2011] [Accepted: 03/31/2011] [Indexed: 12/20/2022] Open
Abstract
Dynamic regulation of specific molecular processes and cellular phenotypes in live cell systems reveal unique insights into cell fate and drug pharmacology that are not gained from traditional fixed endpoint assays. Recent advances in microscopic imaging platform technology combined with the development of novel optical biosensors and sophisticated image analysis solutions have increased the scope of live cell imaging applications in drug discovery. We highlight recent literature examples where live cell imaging has uncovered novel insight into biological mechanism or drug mode-of-action. We survey distinct types of optical biosensors and associated analytical methods for monitoring molecular dynamics, in vitro and in vivo. We describe the recent expansion of live cell imaging into automated target validation and drug screening activities through the development of dedicated brightfield and fluorescence kinetic imaging platforms. We provide specific examples of how temporal profiling of phenotypic response signatures using such kinetic imaging platforms can increase the value of in vitro high-content screening. Finally, we offer a prospective view of how further application and development of live cell imaging technology and reagents can accelerate preclinical lead optimization cycles and enhance the in vitro to in vivo translation of drug candidates.
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34
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Fruhwirth GO, Fernandes LP, Weitsman G, Patel G, Kelleher M, Lawler K, Brock A, Poland SP, Matthews DR, Kéri G, Barber PR, Vojnovic B, Ameer‐Beg SM, Coolen ACC, Fraternali F, Ng T. How Förster Resonance Energy Transfer Imaging Improves the Understanding of Protein Interaction Networks in Cancer Biology. Chemphyschem 2011; 12:442-61. [DOI: 10.1002/cphc.201000866] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 01/07/2011] [Indexed: 01/22/2023]
Affiliation(s)
- Gilbert O. Fruhwirth
- Richard Dimbleby Department of Cancer Research, Division of Cancer Studies, King's College London, Guy's Medical School Campus, NHH, SE1 1UL (UK), Fax: (+44) (0) 20 7848 6220, Fax: (+44) (0) 20 7848 8056
- Comprehensive Cancer Imaging Centre, New Hunt's House, Guy's Medical School Campus, NHH, SE1 1UL (UK)
| | - Luis P. Fernandes
- Randall Division of Cell & Molecular Biophysics, King's College London, Guy's Medical School Campus, NHH, SE1 1UL (UK)
| | - Gregory Weitsman
- Richard Dimbleby Department of Cancer Research, Division of Cancer Studies, King's College London, Guy's Medical School Campus, NHH, SE1 1UL (UK), Fax: (+44) (0) 20 7848 6220, Fax: (+44) (0) 20 7848 8056
| | - Gargi Patel
- Richard Dimbleby Department of Cancer Research, Division of Cancer Studies, King's College London, Guy's Medical School Campus, NHH, SE1 1UL (UK), Fax: (+44) (0) 20 7848 6220, Fax: (+44) (0) 20 7848 8056
| | - Muireann Kelleher
- Richard Dimbleby Department of Cancer Research, Division of Cancer Studies, King's College London, Guy's Medical School Campus, NHH, SE1 1UL (UK), Fax: (+44) (0) 20 7848 6220, Fax: (+44) (0) 20 7848 8056
| | - Katherine Lawler
- Comprehensive Cancer Imaging Centre, New Hunt's House, Guy's Medical School Campus, NHH, SE1 1UL (UK)
| | - Adrian Brock
- Richard Dimbleby Department of Cancer Research, Division of Cancer Studies, King's College London, Guy's Medical School Campus, NHH, SE1 1UL (UK), Fax: (+44) (0) 20 7848 6220, Fax: (+44) (0) 20 7848 8056
| | - Simon P. Poland
- Comprehensive Cancer Imaging Centre, New Hunt's House, Guy's Medical School Campus, NHH, SE1 1UL (UK)
| | - Daniel R. Matthews
- Richard Dimbleby Department of Cancer Research, Division of Cancer Studies, King's College London, Guy's Medical School Campus, NHH, SE1 1UL (UK), Fax: (+44) (0) 20 7848 6220, Fax: (+44) (0) 20 7848 8056
| | - György Kéri
- Vichem Chemie Research Ltd. Herman Ottó utca 15, Budapest, Hungary and Pathobiochemistry Research Group of Hungarian Academy of Science, Semmelweis University, Budapest, 1444 Bp 8. POB 260 (Hungary)
| | - Paul R. Barber
- Gray Institute for Radiation Oncology & Biology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ (UK)
| | - Borivoj Vojnovic
- Randall Division of Cell & Molecular Biophysics, King's College London, Guy's Medical School Campus, NHH, SE1 1UL (UK)
- Gray Institute for Radiation Oncology & Biology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ (UK)
| | - Simon M. Ameer‐Beg
- Richard Dimbleby Department of Cancer Research, Division of Cancer Studies, King's College London, Guy's Medical School Campus, NHH, SE1 1UL (UK), Fax: (+44) (0) 20 7848 6220, Fax: (+44) (0) 20 7848 8056
- Randall Division of Cell & Molecular Biophysics, King's College London, Guy's Medical School Campus, NHH, SE1 1UL (UK)
| | - Anthony C. C. Coolen
- Randall Division of Cell & Molecular Biophysics, King's College London, Guy's Medical School Campus, NHH, SE1 1UL (UK)
- Department of Mathematics, King's College London, Strand Campus, London, WC2R 2LS (UK)
| | - Franca Fraternali
- Randall Division of Cell & Molecular Biophysics, King's College London, Guy's Medical School Campus, NHH, SE1 1UL (UK)
| | - Tony Ng
- Richard Dimbleby Department of Cancer Research, Division of Cancer Studies, King's College London, Guy's Medical School Campus, NHH, SE1 1UL (UK), Fax: (+44) (0) 20 7848 6220, Fax: (+44) (0) 20 7848 8056
- Randall Division of Cell & Molecular Biophysics, King's College London, Guy's Medical School Campus, NHH, SE1 1UL (UK)
- Comprehensive Cancer Imaging Centre, New Hunt's House, Guy's Medical School Campus, NHH, SE1 1UL (UK)
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Brumbaugh K, Johnson W, Liao WC, Lin MS, Houchins JP, Cooper J, Stoesz S, Campos-Gonzalez R. Overview of the generation, validation, and application of phosphosite-specific antibodies. Methods Mol Biol 2011; 717:3-43. [PMID: 21370022 DOI: 10.1007/978-1-61779-024-9_1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein phosphorylation is a universal key posttranslational modification that affects the activity and other properties of intracellular proteins. Phosphosite-specific antibodies can be produced as polyclonals or monoclonals in different animal species, and each approach offers its own benefits and disadvantages. The validation of phosphosite-specific antibodies requires multiple techniques and tactics to demonstrate their specificity. These antibodies can be used in arrays, flow cytometry, and imaging platforms. The specificity of phosphosite-specific antibodies is key for their use in proteomics and profiling of disease.
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Rodriguez H, Rivers R, Kinsinger C, Mesri M, Hiltke T, Rahbar A, Boja E. Reconstructing the pipeline by introducing multiplexed multiple reaction monitoring mass spectrometry for cancer biomarker verification: an NCI-CPTC initiative perspective. Proteomics Clin Appl 2010; 4:904-14. [PMID: 21137031 DOI: 10.1002/prca.201000057] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 09/13/2010] [Accepted: 09/15/2010] [Indexed: 01/10/2023]
Abstract
Proteomics holds great promise in personalized medicine for cancer in the post-genomic era. In the past decade, clinical proteomics has significantly evolved in terms of technology development, optimization and standardization, as well as in advanced bioinformatics data integration and analysis. Great strides have been made for characterizing a large number of proteins qualitatively and quantitatively in a proteome, including the use of sample fractionation, protein microarrays and MS. It is believed that differential proteomic analysis of high-quality clinical biospecimen (tissue and biofluids) can potentially reveal protein/peptide biomarkers responsible for cancer by means of their altered levels of expression and/or PTMs. Multiple reaction monitoring, a multiplexed platform using stable isotope dilution-MS with sensitivity and reproducibility approaching that of traditional ELISAs commonly used in the clinical setting, has emerged as a potentially promising technique for next-generation high-throughput protein biomarker measurements for diagnostics and therapeutics.
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Affiliation(s)
- Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiative, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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37
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Wessels JT, Yamauchi K, Hoffman RM, Wouters FS. Advances in cellular, subcellular, and nanoscale imaging in vitro and in vivo. Cytometry A 2010; 77:667-76. [PMID: 20564541 DOI: 10.1002/cyto.a.20931] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
This review focuses on technical advances in fluorescence microscopy techniques including laser scanning techniques, fluorescence-resonance energy transfer (FRET) microscopy, fluorescence lifetime imaging (FLIM), stimulated emission depletion (STED)-based super-resolution microscopy, scanning confocal endomicroscopes, thin-sheet laser imaging microscopy (TSLIM), and tomographic techniques such as early photon tomography (EPT) as well as on clinical laser-based endoscopic and microscopic techniques. We will also discuss the new developments in the field of fluorescent dyes and fluorescent genetic reporters that enable new possibilities in high-resolution and molecular imaging both in in vitro and in vivo. Small animal and tissue imaging benefit from the development of new fluorescent proteins, dyes, and sensing constructs that operate in the far red and near-infrared spectrum.
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Affiliation(s)
- Johannes T Wessels
- Department of Nephrology and Rheumatology, Molecular and Optical Live Cell Imaging, Center for Internal Medicine, University Medicine Goettingen, Göttingen, Germany.
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Fan X, Li X, Lv S, Wang Y, Zhao Y, Luo G. Comparative proteomics research on rat MSCs differentiation induced by Shuanglong Formula. J Ethnopharmacol 2010; 131:575-580. [PMID: 20659544 DOI: 10.1016/j.jep.2010.07.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 06/28/2010] [Accepted: 07/18/2010] [Indexed: 05/29/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Shuanglong Formula (SLF) is a classic formula for treating heart disease in traditional Chinese medicine (TCM). And it has been reported that the combinational treatment of SLF with autologous mesenchymal stem cells (MSCs) transplantation could be of benefit to people with acute myocardial infarction. However, their underlying mechanisms are not clear. AIM OF THE STUDY The effects of whole formula and its herbal main ingredients on rat MSCs differentiation towards cardiomyocytes were investigated and the distinct protein expression profile in MSC-derived cardiomyocytes studied. MATERIALS AND METHODS The protein expression profiles of rat MSCs and cardiomyocyte-like cells were determined with two-dimensional gel electrophoresis (2-DE). RESULTS Our data demonstrated that SLF can induce MSCs into cardiomyocyte-like cells and around 36 proteins mainly involved in cytoskeleton, cell tissue energy metabolism and signal transduction have been shown to be regulated distinctly by SLF treatment. CONCLUSIONS Data presented in this study suggest that large rearrangement of the proteome occur during the differentiation process of the MSCs to terminally differentiated cardiomyocyte-like cells and offer the possibility for further characterization of specific targets driving the stem cell differentiation.
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Affiliation(s)
- Xuemei Fan
- School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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Fredolini C, Liotta LA, Petricoin EF. Application of proteomic technologies for prostate cancer detection, prognosis, and tailored therapy. Crit Rev Clin Lab Sci 2010; 47:125-38. [PMID: 20858067 DOI: 10.3109/10408363.2010.503558] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Prostate cancer affects 3 in 10 men over the age of 50 years, and, unfortunately, the clinical course of the disease is poorly predicted. At present, there is no means that can distinguish indolent from aggressive/metastatic tumors. Thus, a personalized clinical approach could be helpful in diagnosing clinically relevant disease and guiding appropriate patient therapy. Individualized medicine requires a deep knowledge of the molecular mechanisms underpinning prostate cancer carcinogenesis. Proteomics may be the most powerful way to uncover biomarkers of detection, prognosis, and prediction, as proteins do the work of the cell and represent the majority of the diagnostic markers and drug targets today. Proteomic technologies are rapidly advancing beyond the two-dimensional gel separation techniques of the past to new types of mass spectrometry and protein microarray analyses. Biological fluids and tissue-cell proteomes from men with prostate cancer are being explored to identify diagnostic and prognostic biomarkers and therapeutic targets using these new proteomic approaches. Traditional and novel proteomic technology and their application to prostate cancer studies in translational research will be presented and discussed in this review. Proteomics coupled with powerful nanotechnology-based biomarker discovery approaches may provide a new and exciting opportunity for body fluid-borne biomarker discovery and characterization. While innovative mass spectrometry technology and nanotrap could be applied to improve the discovery and measurement of biomarkers for the early detection of prostate cancer, the use of tissue proteomic tools such as the reverse-phase protein microarray may provide new approaches for personalization of therapies tailored to each tumor's unique pathway activation network.
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40
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Abstract
The article by Roesch-Ely and colleagues in a recent issue of The Journal of Pathology describes the use of proteomic techniques to examine mucosal biopsies in patients with head and neck squamous cell cancer (HNSCC) and in corresponding control samples. The authors were able to determine the anatomical site of origin of the biopsies based on modelling of multiplex protein datasets, and to use the information to analyse field cancerization as a means of predicting tumour recurrence. Although the study included only a relatively small number of cases, and will require future validation in a larger patient cohort, the results point to the potential of proteomics to increase our understanding of cancer biology, and in this instance to offer clinical value.
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Affiliation(s)
- David Arnott
- Protein Chemistry Department, Genentech, Inc, South San Francisco, CA 94080, USA.
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