101
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Na Z, Pan S, Uttamchandani M, Yao SQ. Protein-Protein Interaction Inhibitors of BRCA1 Discovered Using Small Molecule Microarrays. Methods Mol Biol 2017; 1518:139-156. [PMID: 27873205 DOI: 10.1007/978-1-4939-6584-7_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microarray screening technology has transformed the life sciences arena over the last decade. The platform is widely used in the area of mapping interaction networks, to molecular fingerprinting and small molecular inhibitor discovery. The technique has significantly impacted both basic and applied research. The microarray platform can likewise enable high-throughput screening and discovery of protein-protein interaction (PPI) inhibitors. Herein we demonstrate the application of microarray-guided PPI inhibitor discovery, using human BRCA1 as an example. Mutations in BRCA1 have been implicated in ~50 % of hereditary breast cancers. By targeting the (BRCT)2 domain, we showed compound 15a and its prodrug 15b inhibited BRCA1 activities in tumor cells. Unlike previously reported peptide-based PPI inhibitors of BRCA1, the compounds identified could be directly administered to tumor cells, thus making them useful in targeting BRCA1/PARP-related pathways involved in DNA damage and repair response, for cancer therapy.
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Affiliation(s)
- Zhenkun Na
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Mahesh Uttamchandani
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.,Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore, Singapore
| | - Shao Q Yao
- Department of Chemistry, Faculty of Science, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.
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102
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Shah NH, Wang Q, Yan Q, Karandur D, Kadlecek TA, Fallahee IR, Russ WP, Ranganathan R, Weiss A, Kuriyan J. An electrostatic selection mechanism controls sequential kinase signaling downstream of the T cell receptor. eLife 2016; 5:e20105. [PMID: 27700984 PMCID: PMC5089863 DOI: 10.7554/elife.20105] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/03/2016] [Indexed: 12/15/2022] Open
Abstract
The sequence of events that initiates T cell signaling is dictated by the specificities and order of activation of the tyrosine kinases that signal downstream of the T cell receptor. Using a platform that combines exhaustive point-mutagenesis of peptide substrates, bacterial surface-display, cell sorting, and deep sequencing, we have defined the specificities of the first two kinases in this pathway, Lck and ZAP-70, for the T cell receptor ζ chain and the scaffold proteins LAT and SLP-76. We find that ZAP-70 selects its substrates by utilizing an electrostatic mechanism that excludes substrates with positively-charged residues and favors LAT and SLP-76 phosphosites that are surrounded by negatively-charged residues. This mechanism prevents ZAP-70 from phosphorylating its own activation loop, thereby enforcing its strict dependence on Lck for activation. The sequence features in ZAP-70, LAT, and SLP-76 that underlie electrostatic selectivity likely contribute to the specific response of T cells to foreign antigens.
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Affiliation(s)
- Neel H Shah
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Qi Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Qingrong Yan
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Deepti Karandur
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Theresa A Kadlecek
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, Department of Medicine, University of California, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, United States
| | - Ian R Fallahee
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - William P Russ
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Rama Ranganathan
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, United States
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Arthur Weiss
- Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, Department of Medicine, University of California, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, United States
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- California Institute for Quantitative Biosciences, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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103
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Bian Y, Li L, Dong M, Liu X, Kaneko T, Cheng K, Liu H, Voss C, Cao X, Wang Y, Litchfield D, Ye M, Li SSC, Zou H. Ultra-deep tyrosine phosphoproteomics enabled by a phosphotyrosine superbinder. Nat Chem Biol 2016; 12:959-966. [DOI: 10.1038/nchembio.2178] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 07/11/2016] [Indexed: 12/26/2022]
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104
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Kennedy SP, Hastings JF, Han JZR, Croucher DR. The Under-Appreciated Promiscuity of the Epidermal Growth Factor Receptor Family. Front Cell Dev Biol 2016; 4:88. [PMID: 27597943 PMCID: PMC4992703 DOI: 10.3389/fcell.2016.00088] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 08/08/2016] [Indexed: 12/26/2022] Open
Abstract
Each member of the epidermal growth factor receptor (EGFR) family plays a key role in normal development, homeostasis, and a variety of pathophysiological conditions, most notably in cancer. According to the prevailing dogma, these four receptor tyrosine kinases (RTKs; EGFR, ERBB2, ERBB3, and ERBB4) function exclusively through the formation of homodimers and heterodimers within the EGFR family. These combinatorial receptor interactions are known to generate increased interactome diversity and therefore influence signaling output, subcellular localization and function of the heterodimer. This molecular plasticity is also thought to play a role in the development of resistance toward targeted cancer therapies aimed at these known oncogenes. Interestingly, many studies now challenge this dogma and suggest that the potential for EGFR family receptors to interact with more distantly related RTKs is much greater than currently appreciated. Here we discuss how the promiscuity of these oncogenic receptors may lead to the formation of many unexpected receptor pairings and the significant implications for the efficiency of many targeted cancer therapies.
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Affiliation(s)
- Sean P Kennedy
- Systems Biology Ireland, University College DublinDublin, Ireland; Kinghorn Cancer Centre, Garvan Institute of Medical ResearchSydney, NSW, Australia
| | - Jordan F Hastings
- Kinghorn Cancer Centre, Garvan Institute of Medical Research Sydney, NSW, Australia
| | - Jeremy Z R Han
- Kinghorn Cancer Centre, Garvan Institute of Medical Research Sydney, NSW, Australia
| | - David R Croucher
- Kinghorn Cancer Centre, Garvan Institute of Medical ResearchSydney, NSW, Australia; School of Medicine, University College DublinDublin, Ireland; St Vincent's Hospital Clinical School, University of New South WalesSydney, NSW, Australia
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105
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Czyzewicz N, Nikonorova N, Meyer MR, Sandal P, Shah S, Vu LD, Gevaert K, Rao AG, De Smet I. The growing story of (ARABIDOPSIS) CRINKLY 4. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4835-4847. [PMID: 27208540 DOI: 10.1093/jxb/erw192] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Receptor kinases play important roles in plant growth and development, but only few of them have been functionally characterized in depth. Over the past decade CRINKLY 4 (CR4)-related research has peaked as a result of a newly discovered role of ARABIDOPSIS CR4 (ACR4) in the root. Here, we comprehensively review the available (A)CR4 literature and describe its role in embryo, seed, shoot, and root development, but we also flag an unexpected role in plant defence. In addition, we discuss ACR4 domains and protein structure, describe known ACR4-interacting proteins and substrates, and elaborate on the transcriptional regulation of ACR4 Finally, we address the missing knowledge in our understanding of ACR4 signalling.
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Affiliation(s)
- Nathan Czyzewicz
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Natalia Nikonorova
- Department of Plant Systems Biology, VIB, B-9052 Ghent University, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Matthew R Meyer
- Roy J. Carver Department of Biochemistry Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Priyanka Sandal
- Roy J. Carver Department of Biochemistry Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Shweta Shah
- Roy J. Carver Department of Biochemistry Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Lam Dai Vu
- Department of Plant Systems Biology, VIB, B-9052 Ghent University, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Medical Biotechnology Center, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Kris Gevaert
- Medical Biotechnology Center, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - A Gururaj Rao
- Roy J. Carver Department of Biochemistry Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Ive De Smet
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK Department of Plant Systems Biology, VIB, B-9052 Ghent University, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Centre for Plant Integrative Biology, University of Nottingham, Loughborough, LE12 5RD, UK
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106
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Croucher DR, Iconomou M, Hastings JF, Kennedy SP, Han JZR, Shearer RF, McKenna J, Wan A, Lau J, Aparicio S, Saunders DN. Bimolecular complementation affinity purification (BiCAP) reveals dimer-specific protein interactions for ERBB2 dimers. Sci Signal 2016; 9:ra69. [PMID: 27405979 DOI: 10.1126/scisignal.aaf0793] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The dynamic assembly of multiprotein complexes is a central mechanism of many cell signaling pathways. This process is key to maintaining the spatiotemporal specificity required for an accurate, yet adaptive, response to rapidly changing cellular conditions. We describe a technique for the specific isolation and downstream proteomic characterization of any two interacting proteins, to the exclusion of their individual moieties and competing binding partners. We termed the approach bimolecular complementation affinity purification (BiCAP) because it combines the use of conformation-specific nanobodies with a protein-fragment complementation assay with affinity purification. Using BiCAP, we characterized the specific interactome of the epidermal growth factor receptor (EGFR) family member ERBB2 when in the form of a homodimer or when in the form of a heterodimer with either EGFR or ERBB3. We identified dimer-specific interaction patterns for key adaptor proteins and identified a number of previously unknown interacting partners. Functional analysis for one of these newly identified partners revealed a noncanonical mechanism of extracellular signal-regulated kinase (ERK) activation that is specific to the ERBB2:ERBB3 heterodimer and acts through the adaptor protein FAM59A in breast cancer cells.
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Affiliation(s)
- David R Croucher
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia. St. Vincent's Hospital Clinical School, University of New South Wales, Sydney, New South Wales 2052, Australia. School of Medicine, University College Dublin, Belfield, Dublin D4, Ireland.
| | - Mary Iconomou
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Jordan F Hastings
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Sean P Kennedy
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia. Systems Biology Ireland, University College Dublin, Belfield, Dublin D4, Ireland
| | - Jeremy Z R Han
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Robert F Shearer
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Jessie McKenna
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia
| | - Adrian Wan
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Joseph Lau
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada. Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Darren N Saunders
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia. School of Medical Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia.
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107
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Song YD, Liu SX, Zhong YQ. Biological agents for treatment of inflammatory bowel disease: Research progress and associated risks. Shijie Huaren Xiaohua Zazhi 2016; 24:2964-2973. [DOI: 10.11569/wcjd.v24.i19.2964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a group of chronic inflammatory gastrointestinal diseases with unknown etiology, which makes it difficult to reach an ideal treatment. Fortunately, with advances in the research of pathogenesis of IBD, several biological agents aiming diverse targets have been developed, bringing good news to patients with IBD. However, these new drugs carry some new risks, which should draw the attention of clinicians. The following review discusses the research progress in biological agents utilized in IBD and the related risks, with an aim to offer a new direction for the clinical treatment of IBD in the future.
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108
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Shinohara H, Inoue K, Yumoto N, Nagashima T, Okada-Hatakeyama M. Stimulus-Dependent Inhibitor of Apoptosis Protein Expression Prolongs the Duration of B Cell Signalling. Sci Rep 2016; 6:27706. [PMID: 27277891 PMCID: PMC4899755 DOI: 10.1038/srep27706] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/24/2016] [Indexed: 01/17/2023] Open
Abstract
Different dynamic behaviours of signalling activity can induce distinct biological responses in a variety of cells. However, the molecular mechanisms that determine the dynamics of kinase activities in immune cells are not well understood. In this study, we showed that the duration of both IκB kinase (IKK) and extracellular signal-regulated kinase (ERK) activities in B cell receptor (BCR)- and CD40-signalling pathways in B cells were regulated by transcriptional feedback loops. We conducted a time-course transcriptome analysis after BCR or CD40 stimulation and identified the following four candidate genes as feedback regulators for IKK and ERK: inhibitor of apoptosis protein (IAP), TNF alpha-induced protein 3, dual-specificity phosphatase 5, and sprouty homolog 2. Quantitative experiments and mathematical modelling suggested that IAP inhibition shortened the duration of IKK and ERK activity following both BCR and CD40 pathway stimulation, indicating a positive role for IAP in B cell signalling. Furthermore, transient kinase activities induced by IAP blockage reduced the levels of delayed expression genes. Together, our findings suggest that IKK and ERK activity durations can be fine-tuned by the coordinated regulation of positive and negative transcriptional feedback and that these network properties determine the biological output of B cells.
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Affiliation(s)
- Hisaaki Shinohara
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045, Japan
| | - Kentaro Inoue
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045, Japan
| | - Noriko Yumoto
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045, Japan
| | - Takeshi Nagashima
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045, Japan
| | - Mariko Okada-Hatakeyama
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa 230-0045, Japan
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109
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Terborg RA, Pello J, Mannelli I, Torres JP, Pruneri V. Ultrasensitive interferometric on-chip microscopy of transparent objects. SCIENCE ADVANCES 2016; 2:e1600077. [PMID: 27386571 PMCID: PMC4928994 DOI: 10.1126/sciadv.1600077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 05/19/2016] [Indexed: 05/03/2023]
Abstract
Light microscopes can detect objects through several physical processes, such as scattering, absorption, and reflection. In transparent objects, these mechanisms are often too weak, and interference effects are more suitable to observe the tiny refractive index variations that produce phase shifts. We propose an on-chip microscope design that exploits birefringence in an unconventional geometry. It makes use of two sheared and quasi-overlapped illuminating beams experiencing relative phase shifts when going through the object, and a complementary metal-oxide-semiconductor image sensor array to record the resulting interference pattern. Unlike conventional microscopes, the beams are unfocused, leading to a very large field of view (20 mm(2)) and detection volume (more than 0.5 cm(3)), at the expense of lateral resolution. The high axial sensitivity (<1 nm) achieved using a novel phase-shifting interferometric operation makes the proposed device ideal for examining transparent substrates and reading microarrays of biomarkers. This is demonstrated by detecting nanometer-thick surface modulations on glass and single and double protein layers.
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Affiliation(s)
- Roland A. Terborg
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
| | - Josselin Pello
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
| | - Ilaria Mannelli
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
| | - Juan P. Torres
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
- Department of Signal Theory and Communications, Universitat Politècnica de Catalunya, 08034 Barcelona, Spain
| | - Valerio Pruneri
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, 08860 Castelldefels (Barcelona), Spain
- ICREA-Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08010 Barcelona, Spain
- Corresponding author.
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110
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Naguib A. Following the trail of lipids: Signals initiated by PI3K function at multiple cellular membranes. Sci Signal 2016; 9:re4. [DOI: 10.1126/scisignal.aad7885] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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111
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ERBB3-rs2292239 as primary type 1 diabetes association locus among non-HLA genes in Chinese. Meta Gene 2016; 9:120-3. [PMID: 27331016 PMCID: PMC4908278 DOI: 10.1016/j.mgene.2016.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/18/2016] [Accepted: 05/11/2016] [Indexed: 12/13/2022] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune disease that has strong contribution of genetic factors to its etiology. We aimed to assess the genetic association between non-HLA genes and T1D in a Chinese case-control cohort recruited from multiple centers consisting of 364 patients with T1D and 719 unrelated healthy children. We genotyped 55 single nucleotide polymorphisms (SNP) markers located in 16 non-HLA genes (VTCN1, PTPN22, CTLA4, SUMO4, CD274, IL2RA, INS, DHCR7, ERBB3, VDR, CYP27B1, CD69, CD276, PTPN2, UBASH3A, and IL2RB) using SNaPshot multiple single-base extension methods. After multivariate analysis and correction for multiple comparisons, we identified the SNP rs2292239 in ERBB3 gene were significantly associated with T1D. The frequency of the major G allele was significantly decreased in patients with T1D (68.8% in T1D vs 77.3% in controls, OR 0.65, 95% CI 0.53–0.79, P = 0.02), and the minor allele T was associated with an increased risk of T1D (OR 1.55, 95% CI 1.26–1.90, P = 0.02). Our haplotype analysis confirmed that rs2292239 was the primary T1D association locus in our current investigation. These results indicated that the ERBB3-rs2292239 was the primary T1D association locus among the investigated 55 SNPs in 16 non-HLA genes in Chinese Han population. A large scale case-control genetic association study on type 1 diabetes in Chinese investigating on-HLA genes. rs2292239 in the ERBB3 gene conferred the primary non-HLA association in Chinese type 1 diabetes. Markers in the common candidate genes, such as PTPN22, CTLA4, IL2RA, and INS, were not significantly associated with T1D in our Chinese cohort.
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Key Words
- CI, confidence interval
- DNA, deoxyribonucleic acid
- EGFR, epidermal growth factor receptor
- ERBB3
- GWAS, genome-wide association study
- Genetic association
- HLA, human leukocyte antigen
- HWE, Hardy-Weinberg equilibrium
- OR, odds ratio
- SBE, single-base extension
- SNP, single nucleotide polymorphism
- Single nucleotide polymorphism
- T1D, type 1 diabetes
- Type 1 diabetes
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112
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Heusermann W, Ludin B, Pham NT, Auer M, Weidemann T, Hintersteiner M. A Wide-Field Fluorescence Microscope Extension for Ultrafast Screening of One-Bead One-Compound Libraries Using a Spectral Image Subtraction Approach. ACS COMBINATORIAL SCIENCE 2016; 18:209-19. [PMID: 27057765 DOI: 10.1021/acscombsci.5b00175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The increasing involvement of academic institutions and biotech companies in drug discovery calls for cost-effective methods to identify new bioactive molecules. Affinity-based on-bead screening of combinatorial one-bead one-compound libraries combines a split-mix synthesis design with a simple protein binding assay operating directly at the bead matrix. However, one bottleneck for academic scale on-bead screening is the unavailability of a cheap, automated, and robust screening platform that still provides a quantitative signal related to the amount of target protein binding to individual beads for hit bead ranking. Wide-field fluorescence microscopy has long been considered unsuitable due to significant broad spectrum autofluorescence of the library beads in conjunction with low detection sensitivity. Herein, we demonstrate how such a standard microscope equipped with LED-based excitation and a modern CMOS camera can be successfully used for selecting hit beads. We show that the autofluorescence issue can be overcome by an optical image subtraction approach that yields excellent signal-to-noise ratios for the detection of bead-associated target proteins. A polymer capillary attached to a semiautomated bead-picking device allows the operator to efficiently isolate individual hit beads in less than 20 s. The system can be used for ultrafast screening of >200,000 bead-bound compounds in 1.5 h, thereby making high-throughput screening accessible to a wider group within the scientific community.
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Affiliation(s)
- Wolf Heusermann
- IMCF
Biozentrum, Universität Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Beat Ludin
- Life Imaging Services, Efringerstrasse
79, 4057 Basel, Switzerland
| | - Nhan T Pham
- School
of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, CH Waddington Building, Max Born Crescent, The King's
Buildings, Edinburgh, EH9
3BF, United Kingdom
| | - Manfred Auer
- School
of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, CH Waddington Building, Max Born Crescent, The King's
Buildings, Edinburgh, EH9
3BF, United Kingdom
| | - Thomas Weidemann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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113
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Buntru A, Trepte P, Klockmeier K, Schnoegl S, Wanker EE. Current Approaches Toward Quantitative Mapping of the Interactome. Front Genet 2016; 7:74. [PMID: 27200083 PMCID: PMC4854875 DOI: 10.3389/fgene.2016.00074] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/18/2016] [Indexed: 01/01/2023] Open
Abstract
Protein–protein interactions (PPIs) play a key role in many, if not all, cellular processes. Disease is often caused by perturbation of PPIs, as recently indicated by studies of missense mutations. To understand the associations of proteins and to unravel the global picture of PPIs in the cell, different experimental detection techniques for PPIs have been established. Genetic and biochemical methods such as the yeast two-hybrid system or affinity purification-based approaches are well suited to high-throughput, proteome-wide screening and are mainly used to obtain qualitative results. However, they have been criticized for not reflecting the cellular situation or the dynamic nature of PPIs. In this review, we provide an overview of various genetic methods that go beyond qualitative detection and allow quantitative measuring of PPIs in mammalian cells, such as dual luminescence-based co-immunoprecipitation, Förster resonance energy transfer or luminescence-based mammalian interactome mapping with bait control. We discuss the strengths and weaknesses of different techniques and their potential applications in biomedical research.
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Affiliation(s)
| | - Philipp Trepte
- Max Delbrueck Center for Molecular Medicine Berlin, Germany
| | | | | | - Erich E Wanker
- Max Delbrueck Center for Molecular Medicine Berlin, Germany
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114
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Shin M, Yang EG, Song HK, Jeon H. Insulin activates EGFR by stimulating its interaction with IGF-1R in low-EGFR-expressing TNBC cells. BMB Rep 2016; 48:342-7. [PMID: 25341922 PMCID: PMC4578621 DOI: 10.5483/bmbrep.2015.48.6.157] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Indexed: 01/11/2023] Open
Abstract
The expression of epidermal growth factor receptor (EGFR) is an important diagnostic marker for triple-negative breast cancer (TNBC) cells, which lack three hormonal receptors: estrogen and progesterone receptors as well as epidermal growth factor receptor 2. EGFR transactivation can cause drug resistance in many cancers including TNBC, but the mechanism underlying this phenomenon is poorly defined. Here, we demonstrate that insulin treatment induces EGFR activation by stimulating the interaction of EGFR with insulin-like growth factor receptor 1 (IGF-1R) in the MDA-MB-436 TNBC cell line. These cells express low levels of EGFR, while exhibiting high levels of IGF-1R expression and phosphorylation. Low-EGFRexpressing MDA-MB-436 cells show high sensitivity to insulinstimulated cell growth. Therefore, unexpectedly, insulin stimulation induced EGFR transactivation by regulating its interaction with IGF-1R in low-EGFR-expressing TNBC cells.
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Affiliation(s)
- Miyoung Shin
- Division of Life Sciences, Korea University, Seoul 136-701; Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Korea
| | - Eun Gyeong Yang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Korea
| | - Hyun Kyu Song
- Division of Life Sciences, Korea University, Seoul 136-701, Korea
| | - Hyesung Jeon
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 136-791, Korea; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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115
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Jadwin JA, Oh D, Curran TG, Ogiue-Ikeda M, Jia L, White FM, Machida K, Yu J, Mayer BJ. Time-resolved multimodal analysis of Src Homology 2 (SH2) domain binding in signaling by receptor tyrosine kinases. eLife 2016; 5:e11835. [PMID: 27071344 PMCID: PMC4841779 DOI: 10.7554/elife.11835] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 03/14/2016] [Indexed: 12/20/2022] Open
Abstract
While the affinities and specificities of SH2 domain-phosphotyrosine interactions have been well characterized, spatio-temporal changes in phosphosite availability in response to signals, and their impact on recruitment of SH2-containing proteins in vivo, are not well understood. To address this issue, we used three complementary experimental approaches to monitor phosphorylation and SH2 binding in human A431 cells stimulated with epidermal growth factor (EGF): 1) phospho-specific mass spectrometry; 2) far-Western blotting; and 3) live cell single-molecule imaging of SH2 membrane recruitment. Far-Western and MS analyses identified both well-established and previously undocumented EGF-dependent tyrosine phosphorylation and binding events, as well as dynamic changes in binding patterns over time. In comparing SH2 binding site phosphorylation with SH2 domain membrane recruitment in living cells, we found in vivo binding to be much slower. Delayed SH2 domain recruitment correlated with clustering of SH2 domain binding sites on the membrane, consistent with membrane retention via SH2 rebinding. DOI:http://dx.doi.org/10.7554/eLife.11835.001 Individual cells in a multicellular organism must receive signals from the environment and from other cells, and adjust their behavior accordingly. Such signals may cause a cell to grow and multiply, move, or even die. Often these signals are received by receptor proteins, which span the cell membrane and thus provide a way for signals from outside the cell to cause changes inside the cell. The tyrosine kinases are one such group of membrane receptors. When a signal binds to a tyrosine kinase, the receptor is activated and it can add chemical tags called phosphates to the part of itself, or a neighboring protein, that is inside the cell. These phosphates provide binding sites for other types of proteins, many of which contain a section called a SH2 domain. This transmits the signal and leads to further changes in the cell. However, there are over a hundred different SH2 domain-containing proteins in human cells and we do not have a clear picture of what exactly happens when receptor tyrosine kinases are activated. Jadwin, Oh et al. have now looked at how the number of SH2 domain binding sites changes over time after a signal is received. The experiments used three different experimental approaches to study a tyrosine kinase called the Epidermal Growth Factor (EGF) receptor, which is often over-active in human cancers. Jadwin, Oh et al. found that the timing of the changes in the number of SH2 domain binding sites on EGF varied widely. The different methods provided different perspectives on exactly when the changes happen, for example, directly observing the binding of SH2 domains to the membrane of living cells under the microscope showed that binding was much slower than expected from other methods that used purified proteins in solutions. This might be due to the receptors taking a relatively long time to form clusters at the membrane after they receive a signal. Further experiments suggested that what happens when EGF is activated may depend not only on the number of SH2 domain binding sites made, but also the timing and the physical arrangement of those sites. A long-term goal for further studies is to understand how various types of signals can lead to different outcomes in the cell. DOI:http://dx.doi.org/10.7554/eLife.11835.002
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Affiliation(s)
- Joshua A Jadwin
- Raymond and Beverly Sackler Laboratory of Molecular Medicine, Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, United States
| | - Dongmyung Oh
- Richard D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, United States
| | - Timothy G Curran
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Mari Ogiue-Ikeda
- Raymond and Beverly Sackler Laboratory of Molecular Medicine, Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, United States
| | - Lin Jia
- Raymond and Beverly Sackler Laboratory of Molecular Medicine, Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, United States
| | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Kazuya Machida
- Raymond and Beverly Sackler Laboratory of Molecular Medicine, Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, United States
| | - Ji Yu
- Richard D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, United States
| | - Bruce J Mayer
- Raymond and Beverly Sackler Laboratory of Molecular Medicine, Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, United States.,Richard D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, United States
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116
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Wu Z, Song N, Menz R, Pingali B, Yang YW, Zheng Y. Nanoparticles functionalized with supramolecular host-guest systems for nanomedicine and healthcare. Nanomedicine (Lond) 2016; 10:1493-514. [PMID: 25996121 DOI: 10.2217/nnm.15.1] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Synthetic macrocyclic host compounds can interact with suitable guest molecules via noncovalent interactions to form functional supramolecular systems. With the synergistic integration of the response of molecules and the unique properties at the nanoscale, nanoparticles functionalized with the host-guest supramolecular systems have shown great potentials for a broad range of applications in the fields of nanoscience and nanotechnology. In this review article, we focus on the applications of the nanoparticles functionalized with supramolecular host-guest systems in nanomedicine and healthcare, including therapeutic delivery, imaging, sensing and removal of harmful substances. A large number of examples are included to elucidate the working mechanisms, advantages, limitations and future developments of the nanoparticle-supramolecule systems in these applications.
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Affiliation(s)
| | - Nan Song
- 2State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
| | | | | | - Ying-Wei Yang
- 2State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry (NMAC), Jilin University, 2699 Qianjin Street, Changchun 130012, P. R. China
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117
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Huang Y, Bharill S, Karandur D, Peterson SM, Marita M, Shi X, Kaliszewski MJ, Smith AW, Isacoff EY, Kuriyan J. Molecular basis for multimerization in the activation of the epidermal growth factor receptor. eLife 2016; 5. [PMID: 27017828 PMCID: PMC4902571 DOI: 10.7554/elife.14107] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/27/2016] [Indexed: 12/18/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) is activated by dimerization, but activation also generates higher-order multimers, whose nature and function are poorly understood. We have characterized ligand-induced dimerization and multimerization of EGFR using single-molecule analysis, and show that multimerization can be blocked by mutations in a specific region of Domain IV of the extracellular module. These mutations reduce autophosphorylation of the C-terminal tail of EGFR and attenuate phosphorylation of phosphatidyl inositol 3-kinase, which is recruited by EGFR. The catalytic activity of EGFR is switched on through allosteric activation of one kinase domain by another, and we show that if this is restricted to dimers, then sites in the tail that are proximal to the kinase domain are phosphorylated in only one subunit. We propose a structural model for EGFR multimerization through self-association of ligand-bound dimers, in which the majority of kinase domains are activated cooperatively, thereby boosting tail phosphorylation. DOI:http://dx.doi.org/10.7554/eLife.14107.001
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Affiliation(s)
- Yongjian Huang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Shashank Bharill
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Deepti Karandur
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Sean M Peterson
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Morgan Marita
- Department of Chemistry, University of Akron, Akron, United States
| | - Xiaojun Shi
- Department of Chemistry, University of Akron, Akron, United States
| | | | - Adam W Smith
- Department of Chemistry, University of Akron, Akron, United States
| | - Ehud Y Isacoff
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, United States
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Chemistry, University of California, Berkeley, Berkeley, United States
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118
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Campbell J, Ryan CJ, Brough R, Bajrami I, Pemberton HN, Chong IY, Costa-Cabral S, Frankum J, Gulati A, Holme H, Miller R, Postel-Vinay S, Rafiq R, Wei W, Williamson CT, Quigley DA, Tym J, Al-Lazikani B, Fenton T, Natrajan R, Strauss SJ, Ashworth A, Lord CJ. Large-Scale Profiling of Kinase Dependencies in Cancer Cell Lines. Cell Rep 2016; 14:2490-501. [PMID: 26947069 PMCID: PMC4802229 DOI: 10.1016/j.celrep.2016.02.023] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/07/2015] [Accepted: 02/01/2016] [Indexed: 12/27/2022] Open
Abstract
One approach to identifying cancer-specific vulnerabilities and therapeutic targets is to profile genetic dependencies in cancer cell lines. Here, we describe data from a series of siRNA screens that identify the kinase genetic dependencies in 117 cancer cell lines from ten cancer types. By integrating the siRNA screen data with molecular profiling data, including exome sequencing data, we show how vulnerabilities/genetic dependencies that are associated with mutations in specific cancer driver genes can be identified. By integrating additional data sets into this analysis, including protein-protein interaction data, we also demonstrate that the genetic dependencies associated with many cancer driver genes form dense connections on functional interaction networks. We demonstrate the utility of this resource by using it to predict the drug sensitivity of genetically or histologically defined subsets of tumor cell lines, including an increased sensitivity of osteosarcoma cell lines to FGFR inhibitors and SMAD4 mutant tumor cells to mitotic inhibitors.
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MESH Headings
- Cell Line, Tumor
- Gene Expression Profiling
- Humans
- Mutation
- Neoplasms/enzymology
- Neoplasms/genetics
- Neoplasms/pathology
- Protein Kinases/chemistry
- Protein Kinases/genetics
- Protein Kinases/metabolism
- RNA Interference
- RNA, Small Interfering/metabolism
- Receptor, ErbB-2/antagonists & inhibitors
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Receptor, Fibroblast Growth Factor, Type 1/antagonists & inhibitors
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
- Smad4 Protein/antagonists & inhibitors
- Smad4 Protein/genetics
- Smad4 Protein/metabolism
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Affiliation(s)
- James Campbell
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Colm J Ryan
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Rachel Brough
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Ilirjana Bajrami
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Helen N Pemberton
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Irene Y Chong
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; Royal Marsden Hospital, London SW3 6JJ, UK
| | - Sara Costa-Cabral
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Jessica Frankum
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Aditi Gulati
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Harriet Holme
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Rowan Miller
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Sophie Postel-Vinay
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | - Rumana Rafiq
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Wenbin Wei
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - Chris T Williamson
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
| | - David A Quigley
- UCSF Helen Diller Family Comprehensive Cancer Centre, San Francisco, CA 94158, USA
| | - Joe Tym
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, Sutton SM2 5NG, UK
| | - Bissan Al-Lazikani
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, Sutton SM2 5NG, UK
| | - Timothy Fenton
- UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Rachael Natrajan
- Functional Genomics Laboratory, The Breast Cancer Now Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Sandra J Strauss
- UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Alan Ashworth
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK.
| | - Christopher J Lord
- The Breast Cancer Now Research Centre and CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK.
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119
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El-Sayed NS, Shirazi AN, El-Meligy MG, El-Ziaty AK, Nagieb ZA, Parang K, Tiwari RK. Design, synthesis, and evaluation of chitosan conjugated GGRGDSK peptides as a cancer cell-targeting molecular transporter. Int J Biol Macromol 2016; 87:611-22. [PMID: 26976071 DOI: 10.1016/j.ijbiomac.2016.03.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/01/2016] [Accepted: 03/09/2016] [Indexed: 12/26/2022]
Abstract
Targeting cancer cells using integrin receptor is one of the promising targeting strategies in drug delivery. In this study, we conjugated an integrin-binding ligand (GGRGDSK) peptide to chitosan oligosaccharide (COS) using sulfo-SMCC as a bifunctional linker to afford COS-SMCC-GGRGDSK. The conjugated polymer was characterized by FT-IR, (1)H NMR, (13)C NMR, and SEM. COS-SMCC-GGRGDSK did not show cytotoxicity up to a concentration of 1mg/mL in the human leukemia cell line (CCRF-CEM). The conjugate was evaluated for its ability to enhance the cellular uptake of a cell-impermeable cargo (e.g., F'-G(pY)EEI phosphopeptide) in CCRF-CEM, and human ovarian carcinoma (SK-OV-3) cancer cell lines. Additionally, RGD modified and unmodified COS polymers were used to prepare nanoparticles by ionic gelation and showed particle size ranging from 187 to 338nm, and zeta potential of 12.2-18.3mV using dynamic light scattering. The efficiency of COS-NPs and COS-SMCC-RGDSK NPs was assayed for translocation of two synthetic cytotoxic agents ((2-(2-aminoethylamino)-4-(4-chlorophenyl)-6-(1H-indol-3-yl) nicotinonitrile (ACIN), and 2-(2-aminoethylamino)-6-(1H-indol-3-yl)-4-(4-methoxyphenyl)-nicotinonitrile (AMIN)) into CCRF-CEM and human prostate (DU-145) cancer cell lines. The results showed a dramatic reduction in the cell viability on their treatment with RGD targeted COS NPs in comparison to paclitaxel (PTX), free drug, and drug-loaded COS NPs.
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Affiliation(s)
- Naglaa S El-Sayed
- Cellulose and Paper Department, National Research Center, Dokki 12622, Cairo, Egypt; Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618, United States
| | - Amir N Shirazi
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618, United States
| | - Magda G El-Meligy
- Cellulose and Paper Department, National Research Center, Dokki 12622, Cairo, Egypt
| | - Ahmed K El-Ziaty
- Chemistry Department, Faculty of Science, Ain Shams University, Abbassia, Cairo 11566, Egypt
| | - Zenat A Nagieb
- Cellulose and Paper Department, National Research Center, Dokki 12622, Cairo, Egypt
| | - Keykavous Parang
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618, United States
| | - Rakesh K Tiwari
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618, United States.
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120
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Detection and quantification of protein-protein interactions by far-western blotting. Methods Mol Biol 2016; 1312:379-98. [PMID: 26044019 DOI: 10.1007/978-1-4939-2694-7_38] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Far-western blotting is a convenient method to characterize protein-protein interactions, in which protein samples of interest are immobilized on a membrane and then probed with a non-antibody protein. In contrast to western blotting, which uses specific antibodies to detect target proteins, far-western blotting detects proteins on the basis of the presence or absence of binding sites for the protein probe. When specific modular protein binding domains are used as probes, this approach allows characterization of protein-protein interactions involved in biological processes such as signal transduction, including interactions regulated by posttranslational modification. We here describe a rapid and simple protocol for far-western blotting, in which GST-tagged Src homology 2 (SH2) domains are used to probe cellular proteins in a phosphorylation-dependent manner. We also present a batch quantification method that allows for the direct comparison of probe binding patterns.
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121
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Juric D, Dienstmann R, Cervantes A, Hidalgo M, Messersmith W, Blumenschein GR, Tabernero J, Roda D, Calles A, Jimeno A, Wang X, Bohórquez SS, Leddy C, Littman C, Kapp AV, Shames DS, Penuel E, Amler LC, Pirzkall A, Baselga J. Safety and Pharmacokinetics/Pharmacodynamics of the First-in-Class Dual Action HER3/EGFR Antibody MEHD7945A in Locally Advanced or Metastatic Epithelial Tumors. Clin Cancer Res 2016; 21:2462-70. [PMID: 26034219 DOI: 10.1158/1078-0432.ccr-14-2412] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The novel dual-action humanized IgG1 antibody MEHD7945A targeting HER3 and EGFR inhibits ligand-dependent HER dimer signaling. This phase I study evaluated the safety, pharmacokinetics, pharmacodynamics, and antitumor activity of MEHD7945A. EXPERIMENTAL DESIGN Patients with locally advanced or metastatic epithelial tumors received escalating doses of MEHD7945A (1-30 mg/kg) every 2 weeks (q2w) until disease progression or intolerable toxicity. An expansion cohort was enrolled at the recommended phase II dose (14 mg/kg, q2w). Plasma samples, tumor biopsies, FDG-PET were obtained for assessment of pharmacokinetics, and pharmacodynamic modulation downstream of EGFR and HER3. RESULTS No dose-limiting toxicities or MEHD7945A-related grade ≥ 4 adverse events (AE) were reported in dose-escalation (n = 30) or expansion (n = 36) cohorts. Related grade 3 AEs were limited to diarrhea and nausea in the same patient (30 mg/kg). Related AEs in ≥20% of patients ≤24 hours after the first infusion included grade 1/2 headache, fever, and chills, which were managed with premedication and/or symptomatic treatment. Pharmacodynamic data indicated target inhibition in 25% of evaluable patients. Best response by RECIST included 2 confirmed partial responses in squamous cell carcinomas of head and neck (SCCHN) patients with high tumor tissue levels of the HER3 ligand heregulin; 14 patients had stable disease ≥8 weeks, including SCCHN (n = 3), colorectal cancer (n = 6), and non-small cell lung cancer (n = 3). CONCLUSIONS MEHD7945A was well-tolerated as single agent with evidence of tumor pharmacodynamic modulation and antitumor activity in SCCHN. Phase II studies were initiated with flat (nonweight-based) dosing at 1,100 mg q2w in SCCHN and colorectal cancer.
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MESH Headings
- Adult
- Aged
- Antibodies, Monoclonal/administration & dosage
- Antibodies, Monoclonal, Humanized/administration & dosage
- Antibodies, Monoclonal, Humanized/adverse effects
- Antibodies, Monoclonal, Humanized/pharmacokinetics
- Antineoplastic Combined Chemotherapy Protocols
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/immunology
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/immunology
- Carcinoma, Squamous Cell/pathology
- Cetuximab/administration & dosage
- Dose-Response Relationship, Drug
- Drug-Related Side Effects and Adverse Reactions/classification
- Drug-Related Side Effects and Adverse Reactions/pathology
- ErbB Receptors/antagonists & inhibitors
- ErbB Receptors/immunology
- Erlotinib Hydrochloride/administration & dosage
- Female
- Head and Neck Neoplasms/drug therapy
- Head and Neck Neoplasms/immunology
- Head and Neck Neoplasms/pathology
- Humans
- Immunoglobulin G/administration & dosage
- Immunoglobulin G/adverse effects
- Immunoglobulin G/immunology
- Male
- Middle Aged
- Panitumumab
- Receptor, ErbB-3/antagonists & inhibitors
- Receptor, ErbB-3/immunology
- Squamous Cell Carcinoma of Head and Neck
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Affiliation(s)
- Dejan Juric
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Rodrigo Dienstmann
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Andres Cervantes
- Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | | | | | | | - Josep Tabernero
- Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Desamparados Roda
- Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | | | | | | | | | | | | | - Amy V Kapp
- Genentech, Inc., South San Francisco, California
| | | | | | | | | | - José Baselga
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.
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122
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Sinzinger MD, Chung YD, Adjobo-Hermans MJW, Brock R. A microarray-based approach to evaluate the functional significance of protein-binding motifs. Anal Bioanal Chem 2016; 408:3177-84. [PMID: 26892640 PMCID: PMC4830892 DOI: 10.1007/s00216-016-9382-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 01/14/2016] [Accepted: 02/01/2016] [Indexed: 11/25/2022]
Abstract
Intracellular proteins comprise numerous peptide motifs that interact with protein-binding domains. However, using sequence information alone, the identification of functionally relevant interaction motifs remains a challenge. Here, we present a microarray-based approach for the evaluation of peptides as protein-binding motifs. To this end, peptides corresponding to protein interaction motifs were spotted as a microarray. First, peptides were titrated with a pan-specific binder and the apparent Kd value of this binder for each peptide was determined. For phosphotyrosine-containing peptides, an anti-phosphotyrosine antibody was employed. Then, in the presence of the pan-specific binder, arrays were competitively titrated with cell lysate and competition constants were determined. Using the Cheng-Prusoff equation, binding constants for the pan-specific binder and inhibition constants for the lysates were converted into affinity constants for the lysate. We experimentally validate this method using a phosphotyrosine-binding SH2 domain as a further reference. Furthermore, strong binders correlated with binding motifs engaging in numerous interactions as predicted by Scansite. This method provides a highly parallel and robust approach to identify peptides corresponding to interaction motifs with strong binding capacity for proteins in the cell lysate. Using an antibody as a pan-specific binder the capacity of interaction motifs to bind to proteins from cell lysates can be probed. Competition of the antibody is observed for only those peptides to which a lysate protein binds ![]()
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Affiliation(s)
- Michael D Sinzinger
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Yi-Da Chung
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Merel J W Adjobo-Hermans
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Roland Brock
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands.
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123
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PP2A-3 interacts with ACR4 and regulates formative cell division in the Arabidopsis root. Proc Natl Acad Sci U S A 2016; 113:1447-52. [PMID: 26792519 DOI: 10.1073/pnas.1525122113] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In plants, the generation of new cell types and tissues depends on coordinated and oriented formative cell divisions. The plasma membrane-localized receptor kinase ARABIDOPSIS CRINKLY 4 (ACR4) is part of a mechanism controlling formative cell divisions in the Arabidopsis root. Despite its important role in plant development, very little is known about the molecular mechanism with which ACR4 is affiliated and its network of interactions. Here, we used various complementary proteomic approaches to identify ACR4-interacting protein candidates that are likely regulators of formative cell divisions and that could pave the way to unraveling the molecular basis behind ACR4-mediated signaling. We identified PROTEIN PHOSPHATASE 2A-3 (PP2A-3), a catalytic subunit of PP2A holoenzymes, as a previously unidentified regulator of formative cell divisions and as one of the first described substrates of ACR4. Our in vitro data argue for the existence of a tight posttranslational regulation in the associated biochemical network through reciprocal regulation between ACR4 and PP2A-3 at the phosphorylation level.
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124
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Abstract
On a past volume of this monograph we have reviewed general aspects of the varied technologies available to generate peptide arrays. Hallmarks in the development of the technology and a main sketch of preparative steps and applications in binding assays were used to walk the reader through details of peptide arrays. In this occasion, we resume from that work and bring in some considerations on quantitative evaluation of measurements as well as on selected reports applying the technology.
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Affiliation(s)
| | - Rudolf Volkmer
- Institute of Medical Immunology, Charité-Universitätsmedizin zu Berlin, Hessische Str. 3-4, Berlin, 10115, Germany
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125
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Abstract
Selective targeting of protein-protein interactions in the cell is of great interest in biological research. Computational structure-based design of peptides to bind protein interaction interfaces could provide a potential means of generating such reagents. However, to avoid perturbing off-target interactions, methods that explicitly account for interaction specificity are needed. Further, as peptides often retain considerable flexibility upon association, their binding reaction is computationally demanding to model-a stark limitation for structure-based design. Here we present a protocol for designing peptides that selectively target a given peptide-binding domain, relative to a pre-specified set of possibly related domains. We recently used the method to design peptides that discriminate with high selectivity between two closely related PDZ domains. The framework accounts for the flexibility of the peptide in the binding site, but is efficient enough to quickly analyze trade-offs between affinity and selectivity, enabling the identification of optimal peptides.
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Affiliation(s)
- Fan Zheng
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Gevorg Grigoryan
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA.
- Department of Computer Science, Dartmouth College, Hanover, NH, 03755, USA.
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126
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Stites EC, Aziz M, Creamer MS, Von Hoff DD, Posner RG, Hlavacek WS. Use of mechanistic models to integrate and analyze multiple proteomic datasets. Biophys J 2016; 108:1819-1829. [PMID: 25863072 DOI: 10.1016/j.bpj.2015.02.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 02/18/2015] [Accepted: 02/24/2015] [Indexed: 11/30/2022] Open
Abstract
Proteins in cell signaling networks tend to interact promiscuously through low-affinity interactions. Consequently, evaluating the physiological importance of mapped interactions can be difficult. Attempts to do so have tended to focus on single, measurable physicochemical factors, such as affinity or abundance. For example, interaction importance has been assessed on the basis of the relative affinities of binding partners for a protein of interest, such as a receptor. However, multiple factors can be expected to simultaneously influence the recruitment of proteins to a receptor (and the potential of these proteins to contribute to receptor signaling), including affinity, abundance, and competition, which is a network property. Here, we demonstrate that measurements of protein copy numbers and binding affinities can be integrated within the framework of a mechanistic, computational model that accounts for mass action and competition. We use cell line-specific models to rank the relative importance of protein-protein interactions in the epidermal growth factor receptor (EGFR) signaling network for 11 different cell lines. Each model accounts for experimentally characterized interactions of six autophosphorylation sites in EGFR with proteins containing a Src homology 2 and/or phosphotyrosine-binding domain. We measure importance as the predicted maximal extent of recruitment of a protein to EGFR following ligand-stimulated activation of EGFR signaling. We find that interactions ranked highly by this metric include experimentally detected interactions. Proteins with high importance rank in multiple cell lines include proteins with recognized, well-characterized roles in EGFR signaling, such as GRB2 and SHC1, as well as a protein with a less well-defined role, YES1. Our results reveal potential cell line-specific differences in recruitment.
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Affiliation(s)
- Edward C Stites
- Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, Arizona; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri.
| | - Meraj Aziz
- Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Matthew S Creamer
- Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, Arizona; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut
| | - Daniel D Von Hoff
- Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Richard G Posner
- Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, Arizona; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona.
| | - William S Hlavacek
- Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, Arizona; Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico.
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127
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Davey NE, Cyert MS, Moses AM. Short linear motifs - ex nihilo evolution of protein regulation. Cell Commun Signal 2015; 13:43. [PMID: 26589632 PMCID: PMC4654906 DOI: 10.1186/s12964-015-0120-z] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 11/13/2015] [Indexed: 12/12/2022] Open
Abstract
Short sequence motifs are ubiquitous across the three major types of biomolecules: hundreds of classes and thousands of instances of DNA regulatory elements, RNA motifs and protein short linear motifs (SLiMs) have been characterised. The increase in complexity of transcriptional, post-transcriptional and post-translational regulation in higher Eukaryotes has coincided with a significant expansion of motif use. But how did the eukaryotic cell acquire such a vast repertoire of motifs? In this review, we curate the available literature on protein motif evolution and discuss the evidence that suggests SLiMs can be acquired by mutations, insertions and deletions in disordered regions. We propose a mechanism of ex nihilo SLiM evolution – the evolution of a novel SLiM from “nothing” – adding a functional module to a previously non-functional region of protein sequence. In our model, hundreds of motif-binding domains in higher eukaryotic proteins connect simple motif specificities with useful functions to create a large functional motif space. Accessible peptides that match the specificity of these motif-binding domains are continuously created and destroyed by mutations in rapidly evolving disordered regions, creating a dynamic supply of new interactions that may have advantageous phenotypic novelty. This provides a reservoir of diversity to modify existing interaction networks. Evolutionary pressures will act on these motifs to retain beneficial instances. However, most will be lost on an evolutionary timescale as negative selection and genetic drift act on deleterious and neutral motifs respectively. In light of the parallels between the presented model and the evolution of motifs in the regulatory segments of genes and (pre-)mRNAs, we suggest our understanding of regulatory networks would benefit from the creation of a shared model describing the evolution of transcriptional, post-transcriptional and post-translational regulation.
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Affiliation(s)
- Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland.
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
| | - Alan M Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada. .,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada.
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128
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A supergene determines highly divergent male reproductive morphs in the ruff. Nat Genet 2015; 48:79-83. [PMID: 26569125 PMCID: PMC5218575 DOI: 10.1038/ng.3443] [Citation(s) in RCA: 291] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/16/2015] [Indexed: 12/13/2022]
Abstract
Three strikingly different alternative male mating morphs (aggressive “Independents”, semi-cooperative “Satellites” and female mimic “Faeders”) coexist as a balanced polymorphism in the ruff, Philomachus pugnax, a lek-breeding wading bird1,2,3. Major differences in body size, ornamentation, and aggressive and mating behaviour are inherited as an autosomal polymorphism4,5. We show that development into Satellites and Faeders is determined by a supergene6,7,8 consisting of divergent alternative, dominant, non-recombining haplotypes of an inversion on chromosome 11, which contains 125 predicted genes. Independents are homozygous for the ancestral sequence. One breakpoint of the inversion disrupts the essential Centromere protein N (CENP-N) gene, and pedigree analysis confirms lethality of inversion homozygotes. We describe novel behavioural, testes size, and steroid metabolic differences among morphs, and identify polymorphic genes within the inversion that are likely to contribute to the differences among morphs in reproductive traits.
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129
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Mo D, Gu B, Gong X, Wu L, Wang H, Jiang Y, Zhang B, Zhang M, Zhang Y, Xu J, Pan S. miR-1290 is a potential prognostic biomarker in non-small cell lung cancer. J Thorac Dis 2015; 7:1570-9. [PMID: 26543604 DOI: 10.3978/j.issn.2072-1439.2015.09.38] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
BACKGROUND miR-1290 is a newly discovered microRNA (miRNA), and its role in non-small cell lung cancer (NSCLC) remains unknown. This study aimed to evaluate the expression levels of miR-1290 in NSCLC tissues and serum, and explore its associations with clinicopathological characteristics and prognosis of NSCLC patients. METHODS A total of 33 pairs of tissues and 73 serum samples were obtained from NSCLC patients and expression levels of miR-1290 were detected by specific TaqMan qRT-PCR. The relationship between miR-1290 expression levels in NSCLC tissues and serum and clinicopathological characteristics was estimated respectively. The correlation between serum miR-1290 expression levels and overall survival of NSCLC patients was performed by Kaplan-Meier analysis and Cox proportional hazards model. RESULTS We determined that miR-1290 expression levels were increased significantly in NSCLC tissues compared with non-tumor adjacent normal tissues, and higher miR-1290 expression levels were positively correlated with high tumor stage (P=0.004) and positive lymph node metastasis (P=0.013). Compared with benign lung disease and healthy controls, serum levels of NSCLC patients exhibited higher expression of miR-1290. Furthermore, the up-regulation of serum miR-1290 more frequently occurred in NSCLC patients with high TNM stage, positive lymph node metastasis (P=0.022 and P=0.024, respectively). Kaplan-Meier analysis demonstrated that high serum miR-1290 expression levels predicted poor survival (P=0.022). Cox proportional hazards risk analysis indicated that miR-1290 was an independent prognostic factor for NSCLC. CONCLUSIONS Our study suggests that miR-1290 is overexpressed in NSCLC, and serum miR-1290 may be used as a potential prognostic biomarker for NSCLC.
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Affiliation(s)
- Dongping Mo
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Bing Gu
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Xue Gong
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Lei Wu
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Hong Wang
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Ye Jiang
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Bingfeng Zhang
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Meijuan Zhang
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Yan Zhang
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Jian Xu
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
| | - Shiyang Pan
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical Department of Laboratory Medicine, Nanjing 210029, China
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130
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Landry BD, Clarke DC, Lee MJ. Studying Cellular Signal Transduction with OMIC Technologies. J Mol Biol 2015; 427:3416-40. [PMID: 26244521 PMCID: PMC4818567 DOI: 10.1016/j.jmb.2015.07.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 07/25/2015] [Accepted: 07/27/2015] [Indexed: 11/24/2022]
Abstract
In the gulf between genotype and phenotype exists proteins and, in particular, protein signal transduction systems. These systems use a relatively limited parts list to respond to a much longer list of extracellular, environmental, and/or mechanical cues with rapidity and specificity. Most signaling networks function in a highly non-linear and often contextual manner. Furthermore, these processes occur dynamically across space and time. Because of these complexities, systems and "OMIC" approaches are essential for the study of signal transduction. One challenge in using OMIC-scale approaches to study signaling is that the "signal" can take different forms in different situations. Signals are encoded in diverse ways such as protein-protein interactions, enzyme activities, localizations, or post-translational modifications to proteins. Furthermore, in some cases, signals may be encoded only in the dynamics, duration, or rates of change of these features. Accordingly, systems-level analyses of signaling may need to integrate multiple experimental and/or computational approaches. As the field has progressed, the non-triviality of integrating experimental and computational analyses has become apparent. Successful use of OMIC methods to study signaling will require the "right" experiments and the "right" modeling approaches, and it is critical to consider both in the design phase of the project. In this review, we discuss common OMIC and modeling approaches for studying signaling, emphasizing the philosophical and practical considerations for effectively merging these two types of approaches to maximize the probability of obtaining reliable and novel insights into signaling biology.
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Affiliation(s)
- Benjamin D Landry
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - David C Clarke
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6 Canada
| | - Michael J Lee
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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131
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Systems biology approach reveals possible evolutionarily conserved moonlighting functions for enolase. Comput Biol Chem 2015; 58:1-8. [DOI: 10.1016/j.compbiolchem.2015.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 04/13/2015] [Accepted: 04/19/2015] [Indexed: 01/07/2023]
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132
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Abstract
The Abelson (ABL) tyrosine kinases were identified as drivers of leukemia in mice and humans. Emerging data has shown a role for the ABL family kinases, ABL1 and ABL2, in the progression of several solid tumors. This review will focus on recent reports of the involvement of the ABL kinases in tumor progression using mouse models as well as recent data generated from genomic and proteomic studies linking enhanced expression and hyper-activation of the ABL kinases to some human cancers. Preclinical studies on small molecule inhibitors of the ABL kinases suggest that their use may have beneficial effects for the treatment of selected solid tumors.
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Affiliation(s)
- Jun Wang
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 27710 USA
| | - Ann Marie Pendergast
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, NC 27710 USA
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133
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The discovery of modular binding domains: building blocks of cell signalling. Nat Rev Mol Cell Biol 2015; 16:691-8. [PMID: 26420231 DOI: 10.1038/nrm4068] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cell signalling - the ability of a cell to process information from the environment and change its behaviour in response - is a central property of life. Signalling depends on proteins that are assembled from a toolkit of modular domains, each of which confers a specific activity or function. The discovery of modular protein- and lipid-binding domains was a crucial turning point in understanding the logic and evolution of signalling mechanisms.
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134
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Minus MB, Liu W, Vohidov F, Kasembeli MM, Long X, Krueger MJ, Stevens A, Kolosov MI, Tweardy DJ, Sison EAR, Redell MS, Ball ZT. Rhodium(II) Proximity-Labeling Identifies a Novel Target Site on STAT3 for Inhibitors with Potent Anti-Leukemia Activity. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506889] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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135
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Minus MB, Liu W, Vohidov F, Kasembeli MM, Long X, Krueger MJ, Stevens A, Kolosov MI, Tweardy DJ, Sison EAR, Redell MS, Ball ZT. Rhodium(II) Proximity-Labeling Identifies a Novel Target Site on STAT3 for Inhibitors with Potent Anti-Leukemia Activity. Angew Chem Int Ed Engl 2015; 54:13085-9. [PMID: 26480340 DOI: 10.1002/anie.201506889] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Indexed: 12/31/2022]
Abstract
Nearly 40 % of children with acute myeloid leukemia (AML) suffer relapse arising from chemoresistance, often involving upregulation of the oncoprotein STAT3 (signal transducer and activator of transcription 3). Herein, rhodium(II)-catalyzed, proximity-driven modification identifies the STAT3 coiled-coil domain (CCD) as a novel ligand-binding site, and we describe a new naphthalene sulfonamide inhibitor that targets the CCD, blocks STAT3 function, and halts its disease-promoting effects in vitro, in tumor growth models, and in a leukemia mouse model, validating this new therapeutic target for resistant AML.
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Affiliation(s)
- Matthew B Minus
- Department of Chemistry, Rice University, Houston, TX 77005 (USA)
| | - Wei Liu
- Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX 77030 (USA)
| | - Farrukh Vohidov
- Department of Chemistry, Rice University, Houston, TX 77005 (USA)
| | - Moses M Kasembeli
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030 (USA)
| | - Xin Long
- Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX 77030 (USA)
| | - Michael J Krueger
- Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX 77030 (USA)
| | - Alexandra Stevens
- Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX 77030 (USA)
| | - Mikhail I Kolosov
- Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX 77030 (USA)
| | - David J Tweardy
- The University of Texas MD Anderson Cancer Center, Houston, TX 77030 (USA).
| | - Edward Allan R Sison
- Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX 77030 (USA)
| | - Michele S Redell
- Baylor College of Medicine, Texas Children's Cancer Center, Houston, TX 77030 (USA).
| | - Zachary T Ball
- Department of Chemistry, Rice University, Houston, TX 77005 (USA).
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136
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Blikstad C, Ivarsson Y. High-throughput methods for identification of protein-protein interactions involving short linear motifs. Cell Commun Signal 2015; 13:38. [PMID: 26297553 PMCID: PMC4546347 DOI: 10.1186/s12964-015-0116-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/11/2015] [Indexed: 02/07/2023] Open
Abstract
Interactions between modular domains and short linear motifs (3–10 amino acids peptide stretches) are crucial for cell signaling. The motifs typically reside in the disordered regions of the proteome and the interactions are often transient, allowing for rapid changes in response to changing stimuli. The properties that make domain-motif interactions suitable for cell signaling also make them difficult to capture experimentally and they are therefore largely underrepresented in the known protein-protein interaction networks. Most of the knowledge on domain-motif interactions is derived from low-throughput studies, although there exist dedicated high-throughput methods for the identification of domain-motif interactions. The methods include arrays of peptides or proteins, display of peptides on phage or yeast, and yeast-two-hybrid experiments. We here provide a survey of scalable methods for domain-motif interaction profiling. These methods have frequently been applied to a limited number of ubiquitous domain families. It is now time to apply them to a broader set of peptide binding proteins, to provide a comprehensive picture of the linear motifs in the human proteome and to link them to their potential binding partners. Despite the plethora of methods, it is still a challenge for most approaches to identify interactions that rely on post-translational modification or context dependent or conditional interactions, suggesting directions for further method development.
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Affiliation(s)
- Cecilia Blikstad
- Department of Chemistry - BMC, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Husargatan 3, 751 23, Uppsala, Sweden.
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Lindsey ML, Mayr M, Gomes AV, Delles C, Arrell DK, Murphy AM, Lange RA, Costello CE, Jin YF, Laskowitz DT, Sam F, Terzic A, Van Eyk J, Srinivas PR. Transformative Impact of Proteomics on Cardiovascular Health and Disease: A Scientific Statement From the American Heart Association. Circulation 2015. [PMID: 26195497 DOI: 10.1161/cir.0000000000000226] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The year 2014 marked the 20th anniversary of the coining of the term proteomics. The purpose of this scientific statement is to summarize advances over this period that have catalyzed our capacity to address the experimental, translational, and clinical implications of proteomics as applied to cardiovascular health and disease and to evaluate the current status of the field. Key successes that have energized the field are delineated; opportunities for proteomics to drive basic science research, facilitate clinical translation, and establish diagnostic and therapeutic healthcare algorithms are discussed; and challenges that remain to be solved before proteomic technologies can be readily translated from scientific discoveries to meaningful advances in cardiovascular care are addressed. Proteomics is the result of disruptive technologies, namely, mass spectrometry and database searching, which drove protein analysis from 1 protein at a time to protein mixture analyses that enable large-scale analysis of proteins and facilitate paradigm shifts in biological concepts that address important clinical questions. Over the past 20 years, the field of proteomics has matured, yet it is still developing rapidly. The scope of this statement will extend beyond the reaches of a typical review article and offer guidance on the use of next-generation proteomics for future scientific discovery in the basic research laboratory and clinical settings.
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138
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Liu H, Li L, Voss C, Wang F, Liu J, Li SSC. A Comprehensive Immunoreceptor Phosphotyrosine-based Signaling Network Revealed by Reciprocal Protein-Peptide Array Screening. Mol Cell Proteomics 2015; 14:1846-58. [PMID: 25907764 PMCID: PMC4587333 DOI: 10.1074/mcp.m115.047951] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 04/22/2015] [Indexed: 01/18/2023] Open
Abstract
Cells of the immune system communicate with their environment through immunoreceptors. These receptors often harbor intracellular tyrosine residues, which, when phosphorylated upon receptor activation, serve as docking sites to recruit downstream signaling proteins containing the Src Homology 2 (SH2) domain. A systematic investigation of interactions between the SH2 domain and the immunoreceptor tyrosine-based regulatory motifs (ITRM), including inhibitory (ITIM), activating (ITAM), or switching (ITSM) motifs, is critical for understanding cellular signal transduction and immune function. Using the B cell inhibitory receptor CD22 as an example, we developed an approach that combines reciprocal or bidirectional phosphopeptide and SH2 domain array screens with in-solution binding assays to identify a comprehensive SH2-CD22 interaction network. Extending this approach to 194 human ITRM sequences and 78 SH2 domains led to the identification of a high-confidence immunoreceptor interactome containing 1137 binary interactions. Besides recapitulating many previously reported interactions, our study uncovered numerous novel interactions. The resulting ITRM-SH2 interactome not only helped to fill many gaps in the immune signaling network, it also allowed us to associate different SH2 domains to distinct immune functions. Detailed analysis of the NK cell ITRM-mediated interactions led to the identification of a network nucleated by the Vav3 and Fyn SH2 domains. We showed further that these SH2 domains have distinct functions in cytotoxicity. The bidirectional protein-peptide array approach described herein may be applied to the numerous other peptide-binding modules to identify potential protein-protein interactions in a systematic and reliable manner.
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Affiliation(s)
- Huadong Liu
- From the ‡Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1
| | - Lei Li
- From the ‡Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1
| | - Courtney Voss
- From the ‡Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1
| | - Feng Wang
- §Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Juewen Liu
- §Department of Chemistry, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Shawn Shun-Cheng Li
- From the ‡Department of Biochemistry and the Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1;
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139
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Thompson CM, Bloom LR, Ogiue-Ikeda M, Machida K. SH2-PLA: a sensitive in-solution approach for quantification of modular domain binding by proximity ligation and real-time PCR. BMC Biotechnol 2015; 15:60. [PMID: 26112401 PMCID: PMC4482279 DOI: 10.1186/s12896-015-0169-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 05/17/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is a great interest in studying phosphotyrosine dependent protein-protein interactions in tyrosine kinase pathways that play a critical role in many aspects of cellular function. We previously established SH2 profiling, a phosphoproteomic approach based on membrane binding assays that utilizes purified Src Homology 2 (SH2) domains as a molecular tool to profile the global tyrosine phosphorylation state of cells. However, in order to use this method to investigate SH2 binding sites on a specific target in cell lysate, additional procedures such as pull-down or immunoprecipitation which consume large amounts of sample are required. RESULTS We have developed PLA-SH2, an alternative in-solution modular domain binding assay that takes advantage of Proximity Ligation Assay and real-time PCR. The SH2-PLA assay utilizes oligonucleotide-conjugated anti-GST and anti-EGFR antibodies recognizing a GST-SH2 probe and cellular EGFR, respectively. If the GST-SH2 and EGFR are in close proximity as a result of SH2-phosphotyrosine interactions, the two oligonucleotides are brought within a suitable distance for ligation to occur, allowing for efficient complex amplification via real-time PCR. The assay detected signal across at least 3 orders of magnitude of lysate input with a linear range spanning 1-2 orders and a low femtomole limit of detection for EGFR phosphotyrosine. SH2 binding kinetics determined by PLA-SH2 showed good agreement with established far-Western analyses for A431 and Cos1 cells stimulated with EGF at various times and doses. Further, we showed that PLA-SH2 can survey lung cancer tissues using 1 μl lysate without requiring phospho-enrichment. CONCLUSIONS We showed for the first time that interactions between SH2 domain probes and EGFR in cell lysate can be determined in a microliter-scale assay using SH2-PLA. The obvious benefit of this method is that the low sample requirement allows detection of SH2 binding in samples which are difficult to analyze using traditional protein interaction assays. This feature along with short assay runtime makes this method a useful platform for the development of high throughput assays to determine modular domain-ligand interactions which could have wide-ranging applications in both basic and translational cancer research.
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Affiliation(s)
- Christopher M Thompson
- Raymond and Beverly Sackler Laboratory of Genetics and Molecular Medicine, Genetics and Genome Sciences, University of Connecticut School of Medicine, 400 Farmington Avenue, 06030, Farmington, CT, USA.
| | - Lee R Bloom
- Raymond and Beverly Sackler Laboratory of Genetics and Molecular Medicine, Genetics and Genome Sciences, University of Connecticut School of Medicine, 400 Farmington Avenue, 06030, Farmington, CT, USA.
| | - Mari Ogiue-Ikeda
- Raymond and Beverly Sackler Laboratory of Genetics and Molecular Medicine, Genetics and Genome Sciences, University of Connecticut School of Medicine, 400 Farmington Avenue, 06030, Farmington, CT, USA.
| | - Kazuya Machida
- Raymond and Beverly Sackler Laboratory of Genetics and Molecular Medicine, Genetics and Genome Sciences, University of Connecticut School of Medicine, 400 Farmington Avenue, 06030, Farmington, CT, USA.
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140
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Álvarez-Silva MC, Yepes S, Torres MM, Barrios AFG. Proteins interaction network and modeling of IGVH mutational status in chronic lymphocytic leukemia. Theor Biol Med Model 2015; 12:12. [PMID: 26088082 PMCID: PMC4479082 DOI: 10.1186/s12976-015-0008-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/08/2015] [Indexed: 12/30/2022] Open
Abstract
Background Chronic lymphocytic leukemia (CLL) is an incurable malignancy of mature B-lymphocytes, characterized as being a heterogeneous disease with variable clinical manifestation and survival. Mutational statuses of rearranged immunoglobulin heavy chain variable (IGVH) genes has been consider one of the most important prognostic factors in CLL, but despite of its proven value to predict the course of the disease, the regulatory programs and biological mechanisms responsible for the differences in clinical behavior are poorly understood. Methods In this study, (i) we performed differential gene expression analysis between the IGVH statuses using multiple and independent CLL cohorts in microarrays platforms, based on this information, (ii) we constructed a simplified protein-protein interaction (PPI) network and (iii) investigated its structure and critical genes. This provided the basis to (iv) develop a Boolean model, (v) infer biological regulatory mechanism and (vi) performed perturbation simulations in order to analyze the network in dynamic state. Results The result of topological analysis and the Boolean model showed that the transcriptional relationships of IGVH mutational status were determined by specific regulatory proteins (PTEN, FOS, EGR1, TNF, TGFBR3, IFGR2 and LPL). The dynamics of the network was controlled by attractors whose genes were involved in multiple and diverse signaling pathways, which may suggest a variety of mechanisms related with progression occurring over time in the disease. The overexpression of FOS and TNF fixed the fate of the system as they can activate important genes implicated in the regulation of process of adhesion, apoptosis, immune response, cell proliferation and other signaling pathways related with cancer. Conclusion The differences in prognosis prediction of the IGVH mutational status are related with several regulatory hubs that determine the dynamic of the system. Electronic supplementary material The online version of this article (doi:10.1186/s12976-015-0008-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- María Camila Álvarez-Silva
- Grupo de Diseño de Productos y Procesos (GDPP), Departamento de Ingeniería Química, Universidad de los Andes, Bogotá, DC, Colombia.
| | - Sally Yepes
- Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de los Andes, Bogotá, DC, Colombia.
| | - Maria Mercedes Torres
- Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de los Andes, Bogotá, DC, Colombia.
| | - Andrés Fernando González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Departamento de Ingeniería Química, Universidad de los Andes, Bogotá, DC, Colombia.
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141
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Association analysis revealed one susceptibility locus for vitiligo with immune-related diseases in the Chinese Han population. Immunogenetics 2015; 67:347-54. [PMID: 25952005 DOI: 10.1007/s00251-015-0843-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/29/2015] [Indexed: 01/10/2023]
Abstract
Generalized vitiligo is an autoimmune disease characterized by melanocyte loss, which results in patchy depigmentation of skin and hair, and is associated with an elevated risk of other immune-related diseases. However, there is no reported study on the associations between immune susceptibility polymorphisms and the risk of vitiligo with immune-related diseases. The aim of this study was to evaluate the potential influence of 10 single-nucleotide polymorphisms (SNPs) at 18q21.31 (rs10503019), 4p16.1 (rs11940117), 3q28 (rs1464510), 14q12 (rs2273844), 12q13.2 (rs2456973), 16q12.2 (rs3213758), 10q25.3 (rs4353229), 3q13.33 (rs59374417), and 10p15.1 (rs706779 and rs7090530) on vitiligo with immune-related diseases in the Chinese Han population. All SNPs were genotyped in 552 patients with vitiligo-associated immune-related diseases and 1656 controls using the Sequenom MassArray system. Data were analyzed with PLINK 1.07 software. The C allele of rs2456973 at 12q13.2 was observed to be significantly associated with vitiligo-associated immune-related diseases (autoimmune diseases and allergic diseases) (P = 0.0028, odds ratio (OR) = 1.27). In subphenotype analysis, the rs2456973 C allele was also significantly associated with early-onset vitiligo by comparing with controls (P = 0.0001) and in the case-only analysis (P = 0.0114). We confirmed that 12q13.2 was an important candidate locus for vitiligo with immune-related diseases (autoimmune diseases and allergic diseases) and affected disease phenotypes with early onset.
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142
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Groll N, Emele F, Poetz O, Rothbauer U. Towards multiplexed protein-protein interaction analysis using protein tag-specific nanobodies. J Proteomics 2015; 127:289-99. [PMID: 25937269 DOI: 10.1016/j.jprot.2015.04.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 03/27/2015] [Accepted: 04/14/2015] [Indexed: 01/28/2023]
Abstract
UNLABELLED Dynamic protein-protein interactions (PPIs) are an integral part of cellular processes. The discovery of modulators that disrupt or stabilize such interactions is highly important to understand PPIs and address correlating diseases. Bead-based protein assays analyzing PPIs between bait- and prey-proteins exemplify emerging methodologies. To date, most studies employ purified bait-proteins from bacteria. Such proteins are of limited use as they do not undergo eukaryotic folding and lack posttranslational modifications. Here, we present a novel method to generate bead-based protein arrays combining μ-scale purification of bait-proteins combined with site-directed immobilization. First, we express individual bait-proteins as GST- or GFP-fusion constructs in bacterial and mammalian cells. Next, we purify and immobilize these bait-proteins from crude lysates using high affinity tag-specific nanobodies coupled to color-coded beads. Finally, we combined those bait-coupled beads in a protein-array for miniaturized multiplexed GST- and GFP pulldown studies. In a proof-of-principle we study dynamic changes of the endogenous prey-protein β-catenin following proteasomal inhibition or signaling pathway perturbation. Our strategy enables a fast isolation of highly pure and stable bait-proteins derived from small-scale expression cultures. We propose that this approach enables the generation of bead-based protein arrays comprising hundreds of bait-proteins from different expression systems to study complex PPIs. BIOLOGICAL SIGNIFICANCE Protein arrays and multiplexed sandwich immunoassays, are widely applied to study protein-protein interaction or to investigate the signaling status of stimulated cells. This study describes for the first time the application of tag-specific nanobodies for site directed immobilization of bait-proteins from different expression systems to generate bead based protein arrays. The analysis of the Wnt-pathway activation by multiplexed μ-scale pulldowns demonstrated the advantages of eukaryotic expression systems regarding the stability and binding properties of individual bait proteins. This article is part of a Special Issue entitled: HUPO 2014.
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Affiliation(s)
- Nicola Groll
- Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Felix Emele
- Pharmaceutical Biotechnology, Eberhard Karls University, Tuebingen, Germany
| | - Oliver Poetz
- Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany.
| | - Ulrich Rothbauer
- Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany; Pharmaceutical Biotechnology, Eberhard Karls University, Tuebingen, Germany.
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143
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Chylek LA, Wilson BS, Hlavacek WS. Modeling biomolecular site dynamics in immunoreceptor signaling systems. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 844:245-62. [PMID: 25480645 DOI: 10.1007/978-1-4939-2095-2_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The immune system plays a central role in human health. The activities of immune cells, whether defending an organism from disease or triggering a pathological condition such as autoimmunity, are driven by the molecular machinery of cellular signaling systems. Decades of experimentation have elucidated many of the biomolecules and interactions involved in immune signaling and regulation, and recently developed technologies have led to new types of quantitative, systems-level data. To integrate such information and develop nontrivial insights into the immune system, computational modeling is needed, and it is essential for modeling methods to keep pace with experimental advances. In this chapter, we focus on the dynamic, site-specific, and context-dependent nature of interactions in immunoreceptor signaling (i.e., the biomolecular site dynamics of immunoreceptor signaling), the challenges associated with capturing these details in computational models, and how these challenges have been met through use of rule-based modeling approaches.
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Affiliation(s)
- Lily A Chylek
- Department of Chemistry and Chemical Biology, Cornell University, 14853, Ithaca, NY, USA,
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144
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Combinatorial proteomic analysis of intercellular signaling applied to the CD28 T-cell costimulatory receptor. Proc Natl Acad Sci U S A 2015; 112:E1594-603. [PMID: 25829543 DOI: 10.1073/pnas.1503286112] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Systematic characterization of intercellular signaling approximating the physiological conditions of stimulation that involve direct cell-cell contact is challenging. We describe a proteomic strategy to analyze physiological signaling mediated by the T-cell costimulatory receptor CD28. We identified signaling pathways activated by CD28 during direct cell-cell contact by global analysis of protein phosphorylation. To define immediate CD28 targets, we used phosphorylated forms of the CD28 cytoplasmic region to obtain the CD28 interactome. The interaction profiles of selected CD28-interacting proteins were further characterized in vivo for amplifying the CD28 interactome. The combination of the global phosphorylation and interactome analyses revealed broad regulation of CD28 and its interactome by phosphorylation. Among the cellular phosphoproteins influenced by CD28 signaling, CapZ-interacting protein (CapZIP), a regulator of the actin cytoskeleton, was implicated by functional studies. The combinatorial approach applied herein is widely applicable for characterizing signaling networks associated with membrane receptors with short cytoplasmic tails.
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145
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Wang GP, Han XF. CD9 modulates proliferation of human glioblastoma cells via epidermal growth factor receptor signaling. Mol Med Rep 2015; 12:1381-6. [PMID: 25760022 DOI: 10.3892/mmr.2015.3466] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 01/02/2015] [Indexed: 12/14/2022] Open
Abstract
The tetraspanin CD9 has previously been shown to be involved in various cellular activities, including proliferation and migration. In addition, CD9 has been shown to be associated with epidermal growth factor receptor (EGFR). A common characteristic of glioblastoma multiforme histology is EGFR amplification, which affects signal transduction processes. The anti-proliferative effects of CD9 have been linked to EGFR signaling pathways, including phosphorylation of phosphoinositide-3-kinase (PI3K)/Akt and activation of mitogen-activated protein kinase (MAPK)/extracellular signal-regulated protein kinase (Erk). The present study demonstrated that CD9 decreased the phosphorylation of EGFR at specific sites. In addition, CD9 attenuated EGFR signaling of PI3K/Akt and MAPK/Erk, which was associated with cell growth and proliferation. Conversely, small hairpin RNA-mediated knockdown of CD9 expression enhanced the activation of EGFR signal transduction pathways, including PI3K/Akt and MAPK/Erk. These results suggested that the mechanism underlying CD9-induced suppression of cell proliferation may involve the inhibition of phosphorylation of EGFR and the activity of PI3K/Akt and MAPK/Erk signaling pathways.
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Affiliation(s)
- Gong-Ping Wang
- First Department of Neurosurgery, Xianyang Hospital of Yanan University, Central Hospital of 20th Bureau of China Railway Group, Xianyang, Shaanxi 712000, P.R. China
| | - Xiao-Fang Han
- Department of Medical Teaching, Xianyang Hospital of Yanan University, Central Hospital of 20th Bureau of China Railway Group, Xianyang, Shaanxi 712000, P.R. China
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146
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Stern HM, Gardner H, Burzykowski T, Elatre W, O'Brien C, Lackner MR, Pestano GA, Santiago A, Villalobos I, Eiermann W, Pienkowski T, Martin M, Robert N, Crown J, Nuciforo P, Bee V, Mackey J, Slamon DJ, Press MF. PTEN Loss Is Associated with Worse Outcome in HER2-Amplified Breast Cancer Patients but Is Not Associated with Trastuzumab Resistance. Clin Cancer Res 2015; 21:2065-74. [PMID: 25649019 DOI: 10.1158/1078-0432.ccr-14-2993] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/31/2014] [Indexed: 01/03/2023]
Abstract
PURPOSE To investigate the clinical relevance of PTEN in HER2-amplified and HER2-nonamplified disease. EXPERIMENTAL DESIGN We assessed PTEN status in two large adjuvant breast cancer trials (BCIRG-006 and BCIRG-005) using a PTEN immunohistochemical (IHC) assay that was previously validated in a panel of 33 breast cancer cell lines and prostate cancer tissues with known PTEN gene deletion. RESULTS In the HER2-positive patient population, absence of tumor cell PTEN staining occurred at a rate of 5.4% and was independent of ER/PR status. In contrast, 15.9% of HER2-negative patients exhibited absence of PTEN staining with the highest frequency seen in triple-negative breast cancer (TNBC) subgroup versus ER/PR-positive patients (35.1% vs. 10.9%). Complete absence of PTEN staining in tumor cells was associated with poor clinical outcome in HER2-positive disease. Those patients whose cancers demonstrated absent PTEN staining had a significant decrease in disease-free survival (DFS) and overall survival (OS) compared with patients with tumors exhibiting any PTEN staining patterns (low, moderate, or high). Trastuzumab appeared to provide clinical benefit even for patients lacking PTEN staining. In the HER2-negative population, there were no statistically significant differences in clinical outcome based on PTEN status. CONCLUSIONS This study is the largest to date examining PTEN status in breast cancer and the data suggest that the rate and significance of PTEN status differ between HER2-positive and HER2-negative disease. Furthermore, the data clearly suggest that HER2-positive patients with PTEN loss still benefit from trastuzumab.
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Affiliation(s)
- Howard M Stern
- Genentech Research and Early Development, South San Francisco, California
| | | | | | - Wafaa Elatre
- USC/Norris Comprehensive Cancer Center, Los Angeles, California
| | - Carol O'Brien
- Genentech Research and Early Development, South San Francisco, California
| | - Mark R Lackner
- Genentech Research and Early Development, South San Francisco, California
| | | | - Angela Santiago
- USC/Norris Comprehensive Cancer Center, Los Angeles, California
| | | | | | | | | | - Nicholas Robert
- Virginia Cancer Specialists/U.S. Oncology Research Network, Fairfax, Virginia
| | - John Crown
- Irish Cooperative Oncology Research Group, St. Vincent's University Hospital, Dublin, Ireland
| | | | - Valerie Bee
- Cancer International Research Group/Translational Research in Oncology, Paris, France
| | - John Mackey
- Department of Oncology, University of Alberta, Edmonton, Canada
| | - Dennis J Slamon
- Department of Medicine, Geffen School of Medicine at UCLA, Los Angeles, California.
| | - Michael F Press
- USC/Norris Comprehensive Cancer Center, Los Angeles, California.
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147
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Beclin 1 regulates growth factor receptor signaling in breast cancer. Oncogene 2015; 34:5352-62. [PMID: 25639875 PMCID: PMC4522409 DOI: 10.1038/onc.2014.454] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/05/2014] [Accepted: 12/08/2014] [Indexed: 01/09/2023]
Abstract
Beclin 1 is a haploinsufficient tumor suppressor that is decreased in many human tumors. The function of beclin 1 in cancer has been attributed primarily to its role in the degradative process of macroautophagy. However, beclin 1 is a core component of the vacuolar protein sorting 34 (Vps34)/class III phosphatidylinositoI-3 kinase (PI3KC3) and Vps15/p150 complex that regulates multiple membrane-trafficking events. In the current study, we describe an alternative mechanism of action for beclin 1 in breast cancer involving its control of growth factor receptor signaling. We identify a specific stage of early endosome maturation that is regulated by beclin 1, the transition of APPL1-containing phosphatidyIinositol 3-phosphate-negative (PI3P(-)) endosomes to PI3P(+) endosomes. Beclin 1 regulates PI3P production in response to growth factor stimulation to control the residency time of growth factor receptors in the PI3P(-)/APPL(+)-signaling-competent compartment. As a result, suppression of BECN1 sustains growth factor-stimulated AKT and ERK activation resulting in increased breast carcinoma cell invasion. In human breast tumors, beclin 1 expression is inversely correlated with AKT and ERK phosphorylation. Our data identify a novel role for beclin 1 in regulating growth factor signaling and reveal a mechanism by which loss of beclin 1 expression would enhance breast cancer progression.
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148
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Ji J, Yuan Z, Zhang X, Li F, Xu J, Liu Y, Li H, Wang J, Xue F. Detection for pathway effect contributing to disease in systems epidemiology with a case-control design. BMJ Open 2015; 5:e006721. [PMID: 25596199 PMCID: PMC4298111 DOI: 10.1136/bmjopen-2014-006721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVES Identification of pathway effects responsible for specific diseases has been one of the essential tasks in systems epidemiology. Despite some advance in procedures for distinguishing specific pathway (or network) topology between different disease status, statistical inference at a population level remains unsolved and further development is still needed. To identify the specific pathways contributing to diseases, we attempt to develop powerful statistics which can capture the complex relationship among risk factors. SETTING AND PARTICIPANTS Acute myeloid leukaemia (AML) data obtained from 133 adults (98 patients and 35 controls; 47% female). RESULTS Simulation studies indicated that the proposed Pathway Effect Measures (PEM) were stable; bootstrap-based methods outperformed the others, with bias-corrected bootstrap CI method having the highest power. Application to real data of AML successfully identified the specific pathway (Treg→TGFβ→Th17) effect contributing to AML with p values less than 0.05 under various methods and the bias-corrected bootstrap CI (-0.214 to -0.020). It demonstrated that Th17-Treg correlation balance was impaired in patients with AML, suggesting that Th17-Treg imbalance potentially plays a role in the pathogenesis of AML. CONCLUSIONS The proposed bootstrap-based PEM are valid and powerful for detecting the specific pathway effect contributing to disease, thus potentially providing new insight into the underlying mechanisms and ways to study the disease effects of specific pathways more comprehensively.
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Affiliation(s)
- Jiadong Ji
- Department of Epidemiology and Biostatistics, School of Public Health, Shandong University, Jinan, China
| | - Zhongshang Yuan
- Department of Epidemiology and Biostatistics, School of Public Health, Shandong University, Jinan, China
| | - Xiaoshuai Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Shandong University, Jinan, China
| | - Fangyu Li
- Department of Neurology, Capital Medical University, Xuanwu Hospital, Beijing, China
| | - Jing Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Shandong University, Jinan, China
| | - Ying Liu
- Department of Public Health and Clinical Medicine, Umea University, Umea, Sweden
| | - Hongkai Li
- Department of Epidemiology and Biostatistics, School of Public Health, Shandong University, Jinan, China
| | - Jia Wang
- School of Mathematics, Shandong University, Jinan, China
| | - Fuzhong Xue
- Department of Epidemiology and Biostatistics, School of Public Health, Shandong University, Jinan, China
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149
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Curran TG, Zhang Y, Ma DJ, Sarkaria JN, White FM. MARQUIS: a multiplex method for absolute quantification of peptides and posttranslational modifications. Nat Commun 2015; 6:5924. [PMID: 25581283 PMCID: PMC4293043 DOI: 10.1038/ncomms6924] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 11/21/2014] [Indexed: 01/08/2023] Open
Abstract
Absolute quantification of protein expression and post-translational modifications by mass spectrometry has been challenging due to a variety of factors, including the potentially large dynamic range of phosphorylation response. To address these issues, we have developed MARQUIS — Multiplex Absolute Regressed Quantification with Internal Standards — a novel mass spectrometry-based approach using a combination of isobaric tags and heavy-labeled standard peptides to construct internal standard curves for peptides derived from key nodes in signal transduction networks. We applied MARQUIS to quantify phosphorylation dynamics within the EGFR network at multiple time points following stimulation with several ligands, enabling a quantitative comparison of EGFR phosphorylation sites and demonstrating that receptor phosphorylation is qualitatively similar but quantitatively distinct for each EGFR ligand tested. MARQUIS was also applied to quantify the effect of EGFR kinase inhibition on glioblastoma patient derived xenografts. MARQUIS is a versatile method, broadly applicable and extendable to multiple mass spectrometric platforms.
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Affiliation(s)
- Timothy G Curran
- 1] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Yi Zhang
- Thermo-Fisher Scientific, San Jose, California 95134, USA
| | - Daniel J Ma
- Department of Radiation Oncology, Mayo Clinic, 200 First Street South West, Rochester, Minnesota 55905, USA
| | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, 200 First Street South West, Rochester, Minnesota 55905, USA
| | - Forest M White
- 1] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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150
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Sathyamurthy A, Yin DM, Barik A, Shen C, Bean JC, Figueiredo D, She JX, Xiong WC, Mei L. ERBB3-mediated regulation of Bergmann glia proliferation in cerebellar lamination. Development 2015; 142:522-32. [PMID: 25564653 DOI: 10.1242/dev.115931] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cortical lamination is crucial for the assembly of cerebellar circuitry. In this process, granule neurons (GNs) migrate along Bergmann glia (BG), which are specialized astroglial cells, from the external granule layer to the internal granule layer. However, the molecular mechanisms underlying BG development are not well understood. Here, we show that GFAP::Cre;Erbb3(F/F) mice, which lack Erbb3 in both radial glia and neurons, exhibit impairments in balance and motor coordination. Cerebellar lamination is aberrant, with misplaced Purkinje neurons and GN clusters. These phenotypes were not observed in Math1::CreER(T2);Erbb3(F/F) mice, where the Erbb3 gene was deleted in GNs, suggesting involvement of non-neuronal Erbb3 in cerebellar lamination. Mechanistic studies indicate that ERBB3 is crucial for the proliferation of BG, which are required for GN migration. These observations identify a crucial role for ERBB3 in cerebellar lamination and reveal a novel mechanism that regulates BG development.
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Affiliation(s)
- Anupama Sathyamurthy
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Dong-Min Yin
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Arnab Barik
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Chengyong Shen
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA Charlie Norwood VA Medical Center, Augusta, GA 30904, USA
| | - Jonathan C Bean
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Dwight Figueiredo
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA Charlie Norwood VA Medical Center, Augusta, GA 30904, USA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Wen-Cheng Xiong
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA Charlie Norwood VA Medical Center, Augusta, GA 30904, USA Department of Neurology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
| | - Lin Mei
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA Charlie Norwood VA Medical Center, Augusta, GA 30904, USA Department of Neurology, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912, USA
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