1
|
Ouyang W, Li Q, Niu Q, Qui M, Fu H, Du Y, Mo X. A multiplexed time-resolved fluorescence resonance energy transfer ultrahigh-throughput screening assay for targeting the SMAD4-SMAD3-DNA complex. J Mol Cell Biol 2024; 15:mjad068. [PMID: 37968137 PMCID: PMC11063955 DOI: 10.1093/jmcb/mjad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/07/2023] [Accepted: 11/14/2023] [Indexed: 11/17/2023] Open
Abstract
The transforming growth factor-beta (TGFβ) signaling pathway plays crucial roles in the establishment of an immunosuppressive tumor microenvironment, making anti-TGFβ agents a significant area of interest in cancer immunotherapy. However, the clinical translation of current anti-TGFβ agents that target upstream cytokines and receptors remains challenging. Therefore, the development of small-molecule inhibitors specifically targeting SMAD4, the downstream master regulator of the TGFβ pathway, would offer an alternative approach with significant therapeutic potential for anti-TGFβ signaling. In this study, we present the development of a cell lysate-based multiplexed time-resolved fluorescence resonance energy transfer (TR-FRET) assay in an ultrahigh-throughput screening (uHTS) 1536-well plate format. This assay enables simultaneous monitoring of the protein‒protein interaction between SMAD4 and SMAD3, as well as the protein‒DNA interaction between SMADs and their consensus DNA-binding motif. The multiplexed TR-FRET assay exhibits high sensitivity, allowing the dynamic analysis of the SMAD4-SMAD3-DNA complex at single-amino acid resolution. Moreover, the multiplexed uHTS assay demonstrates robustness for screening small-molecule inhibitors. Through a pilot screening of an FDA-approved bioactive compound library, we identified gambogic acid and gambogenic acid as potential hit compounds. These proof-of-concept findings underscore the utility of our optimized multiplexed TR-FRET platform for large-scale screening to discover small-molecule inhibitors that target the SMAD4-SMAD3-DNA complex as novel anti-TGFβ signaling agents.
Collapse
Affiliation(s)
- Wukun Ouyang
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Qianjin Li
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Qiankun Niu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Min Qui
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Hematology and Medical Oncology and Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xiulei Mo
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
2
|
Ouyang W, Niu Q, Qui M, Fu H, Du Y, Mo X. A multiplexed time-resolved fluorescence resonance energy transfer ultrahigh-throughput screening assay for targeting SMAD4-SMAD3-DNA complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.15.549169. [PMID: 37503208 PMCID: PMC10370110 DOI: 10.1101/2023.07.15.549169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The signaling pathway of transforming growth factor-beta (TGFβ) plays crucial roles in the establishment of an immunosuppressive tumor microenvironment, making anti-TGFβ agents a significant area of interest in cancer immunotherapy. However, the clinical translation of current anti-TGFβ agents that target upstream cytokines and receptors remains challenging. Therefore, the development of small molecule inhibitors specifically targeting SMAD4, the downstream master regulator of TGFβ pathway, would offer an alternative approach with significant therapeutic potential for anti-TGF-β signaling. In this study, we present the development of a cell lysate-based multiplexed time-resolved fluorescence resonance energy transfer (TR-FRET) assay in an ultrahigh-throughput screening (uHTS) 1536-well plate format. This assay enables simultaneous monitoring of the protein-protein interaction (PPI) between SMAD4 and SMAD3, as well as the protein-DNA interaction (PDI) between SMADs and their consensus DNA binding motif. The multiplexed TR-FRET assay exhibits high sensitivity, allowing the dynamic analysis of the SMAD4-SMAD3-DNA complex at single amino acid resolution. Moreover, the multiplexed uHTS assay demonstrates robustness for screening small molecule inhibitors. Through a pilot screening of an FDA-approved and bioactive compound library, we identified gambogic acid and gambogenic acid as potential hit compounds. These proof-of-concept findings underscore the utility of our optimized multiplexed TR-FRET platform for large-scale screening to discover small molecule inhibitors that target the SMAD4-SMAD3-DNA complex as novel anti-TGFβ signaling agents.
Collapse
|
3
|
Szewczyk MM, Owens DDG, Barsyte-Lovejoy D. Measuring Protein-Protein Interactions in Cells using Nanoluciferase Bioluminescence Resonance Energy Transfer (NanoBRET) Assay. Methods Mol Biol 2023; 2706:137-148. [PMID: 37558946 DOI: 10.1007/978-1-0716-3397-7_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Protein-protein interactions (PPIs) are increasingly recognized for their roles in functional cellular networks and their importance in disease-targeting contexts. Assessing PPI in the native cellular environment is challenging and requires specific and quantitative methods. Bioluminescence resonance energy transfer (BRET) is a biophysical process that can be used to quantify PPI. With Nanoluciferase bioluminescent protein as a donor and a fluorescent chloroalkane ligand covalently bound to HaloTag protein as an acceptor, NanoBRET provides a versatile and robust system to quantitatively measure PPI in living cells. BRET efficiency is proportional to the distance between the donor and acceptor, allowing for the measurement of PPI in real time. In this paper, we describe the use of NanoBRET to study specific interactions between proteins of interest in living cells that can be perturbed by using small-molecule antagonists and genetic mutations. Here, we provide a detailed protocol for expressing NanoLuc and HaloTag fusion proteins in cell culture and the necessary optimization of NanoBRET assay conditions. Our example results demonstrate the reliability and sensitivity of NanoBRET for measuring interactions between proteins, protein domains, and short peptides and quantitating the PPI antagonist compound activity in living cells.
Collapse
Affiliation(s)
| | - Dominic D G Owens
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
4
|
Besson B, Eun H, Kim S, Windisch MP, Bourhy H, Grailhe R. Optimization of BRET saturation assays for robust and sensitive cytosolic protein-protein interaction studies. Sci Rep 2022; 12:9987. [PMID: 35705637 PMCID: PMC9200754 DOI: 10.1038/s41598-022-12851-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/09/2022] [Indexed: 12/16/2022] Open
Abstract
Bioluminescence resonance energy transfer (BRET) saturation is a method of studying protein–protein interaction (PPI) upon quantification of the dependence of the BRET signal on the acceptor/donor (A:D) expression ratio. In this study, using the very bright Nluc/YFP BRET pair acquired respectively with microplate reader and automated confocal microscopy, we significantly improved BRET saturation assay by extending A:D expression detection range and normalizing A:D expression with a new BRET-free probe. We next found that upon using variable instead of fixed amount of donor molecules co-expressed with increasing acceptor concentrations, BRET saturation assay robustness can be further improved when studying cytosolic protein, although the relative amounts of dimers (BRETmax) and the relative dimer affinity (BRET50) remain similar. Altogether, we show that our method can be applied to many PPI networks, involving the NF-κB pathway, high-affinity nanobody, rabies virus-host interactions, mTOR complex and JAK/STAT signaling. Altogether our approach paves the way for robust PPI validation and characterization in living cells.
Collapse
Affiliation(s)
- Benoit Besson
- Technology Development Platform, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Republic of Korea.,Institut Pasteur, Unité Dynamique des Lyssavirus et Adaptation à l'Hôte, 28 rue du docteur Roux, 75015, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, rue du Docteur Roux, 75015, Paris, France
| | - Hyeju Eun
- Technology Development Platform, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Republic of Korea
| | - Seonhee Kim
- Technology Development Platform, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Republic of Korea
| | - Marc P Windisch
- Applied Molecular Virology, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Republic of Korea
| | - Herve Bourhy
- Institut Pasteur, Unité Dynamique des Lyssavirus et Adaptation à l'Hôte, 28 rue du docteur Roux, 75015, Paris, France
| | - Regis Grailhe
- Technology Development Platform, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, Republic of Korea.
| |
Collapse
|
5
|
Mo X, Niu Q, Ivanov AA, Tsang YH, Tang C, Shu C, Li Q, Qian K, Wahafu A, Doyle SP, Cicka D, Yang X, Fan D, Reyna MA, Cooper LAD, Moreno CS, Zhou W, Owonikoko TK, Lonial S, Khuri FR, Du Y, Ramalingam SS, Mills GB, Fu H. Systematic discovery of mutation-directed neo-protein-protein interactions in cancer. Cell 2022; 185:1974-1985.e12. [PMID: 35512704 DOI: 10.1016/j.cell.2022.04.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 02/27/2022] [Accepted: 04/08/2022] [Indexed: 12/12/2022]
Abstract
Comprehensive sequencing of patient tumors reveals genomic mutations across tumor types that enable tumorigenesis and progression. A subset of oncogenic driver mutations results in neomorphic activity where the mutant protein mediates functions not engaged by the parental molecule. Here, we identify prevalent variant-enabled neomorph-protein-protein interactions (neoPPI) with a quantitative high-throughput differential screening (qHT-dS) platform. The coupling of highly sensitive BRET biosensors with miniaturized coexpression in an ultra-HTS format allows large-scale monitoring of the interactions of wild-type and mutant variant counterparts with a library of cancer-associated proteins in live cells. The screening of 17,792 interactions with 2,172,864 data points revealed a landscape of gain of interactions encompassing both oncogenic and tumor suppressor mutations. For example, the recurrent BRAF V600E lesion mediates KEAP1 neoPPI, rewiring a BRAFV600E/KEAP1 signaling axis and creating collateral vulnerability to NQO1 substrates, offering a combination therapeutic strategy. Thus, cancer genomic alterations can create neo-interactions, informing variant-directed therapeutic approaches for precision medicine.
Collapse
Affiliation(s)
- Xiulei Mo
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Qiankun Niu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrey A Ivanov
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA; Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Yiu Huen Tsang
- Division of Oncologic Science, Oregon Health Sciences University School of Medicine, Portland, OR 97239, USA
| | - Cong Tang
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Urology, The First Affiliated Hospital, Medical School of Xi'An Jiaotong University, Xi'an, Shannxi 710061, PRC
| | - Changfa Shu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Gynecology, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, PRC
| | - Qianjin Li
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kun Qian
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Alafate Wahafu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Neurosurgery, the First Affiliated Hospital of Xi'An Jiaotong University, Xi'an, PRC
| | - Sean P Doyle
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Danielle Cicka
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xuan Yang
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dacheng Fan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Matthew A Reyna
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Lee A D Cooper
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Carlos S Moreno
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA; Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Wei Zhou
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
| | - Taofeek K Owonikoko
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA
| | - Fadlo R Khuri
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA; Department of Internal Medicine, Division of Hematology and Oncology, American University of Beirut, Beirut, 1107-2020, Lebanon
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA; Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | | | - Gordon B Mills
- Division of Oncologic Science, Oregon Health Sciences University School of Medicine, Portland, OR 97239, USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA; Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA; Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA.
| |
Collapse
|
6
|
Tang C, Niu Q, Cicka D, Du Y, Mo X, Fu H. A time-resolved fluorescence resonance energy transfer screening assay for discovery of protein-protein interaction modulators. STAR Protoc 2021; 2:100804. [PMID: 34527960 PMCID: PMC8433285 DOI: 10.1016/j.xpro.2021.100804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Protein-protein interactions (PPIs) have emerged as promising yet challenging therapeutic targets. A robust bioassay is required for rapid PPI modulator discovery. Here, we present a time-resolved Förster's (fluorescence) resonance energy transfer assay protocol for PPI modulator screening in a 1536-well plate format. We use hypomorph SMAD4R361H-SMAD3 PPI as an example to illustrate the application of the protocol for screening of variant-directed PPI inducers. This platform can be readily adapted for the discovery of both small-molecule PPI inducers and inhibitors. For complete details on the use and execution of this protocol, please refer to Tang et al. (2020).
Collapse
Affiliation(s)
- Cong Tang
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- The First Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, Shannxi 710061, P.R. China
| | - Qiankun Niu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Danielle Cicka
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xiulei Mo
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Hematology and Medical Oncology and Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| |
Collapse
|
7
|
Lotz-Havla AS, Woidy M, Guder P, Friedel CC, Klingbeil JM, Bulau AM, Schultze A, Dahmen I, Noll-Puchta H, Kemp S, Erdmann R, Zimmer R, Muntau AC, Gersting SW. iBRET Screen of the ABCD1 Peroxisomal Network and Mutation-Induced Network Perturbations. J Proteome Res 2021; 20:4366-4380. [PMID: 34383492 DOI: 10.1021/acs.jproteome.1c00330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mapping the network of proteins provides a powerful means to investigate the function of disease genes and to unravel the molecular basis of phenotypes. We present an automated informatics-aided and bioluminescence resonance energy transfer-based approach (iBRET) enabling high-confidence detection of protein-protein interactions in living mammalian cells. A screen of the ABCD1 protein, which is affected in X-linked adrenoleukodystrophy (X-ALD), against an organelle library of peroxisomal proteins demonstrated applicability of iBRET for large-scale experiments. We identified novel protein-protein interactions for ABCD1 (with ALDH3A2, DAO, ECI2, FAR1, PEX10, PEX13, PEX5, PXMP2, and PIPOX), mapped its position within the peroxisomal protein-protein interaction network, and determined that pathogenic missense variants in ABCD1 alter the interaction with selected binding partners. These findings provide mechanistic insights into pathophysiology of X-ALD and may foster the identification of new disease modifiers.
Collapse
Affiliation(s)
- Amelie S Lotz-Havla
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
| | - Mathias Woidy
- University Children's Research, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Philipp Guder
- University Children's Research, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Caroline C Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, 80538 Munich, Germany
| | - Julian M Klingbeil
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
| | - Ana-Maria Bulau
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
| | - Anja Schultze
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
| | - Ilona Dahmen
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
| | - Heidi Noll-Puchta
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
| | - Stephan Kemp
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam Gastroenterology & Metabolism, University of Amsterdam, 1105 WX Amsterdam, The Netherlands
| | - Ralf Erdmann
- Systems Biochemistry, Medical Faculty, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Ralf Zimmer
- Institute of Informatics, Ludwig-Maximilians-Universität München, 80538 Munich, Germany
| | - Ania C Muntau
- University Children's Hospital, University Medical Center Hamburg Eppendorf, 20246 Hamburg, Germany
| | - Søren W Gersting
- University Children's Research, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| |
Collapse
|
8
|
Chee SMQ, Wongsantichon J, Yi LS, Sana B, Frosi Y, Robinson RC, Ghadessy FJ. Functional display of bioactive peptides on the vGFP scaffold. Sci Rep 2021; 11:10127. [PMID: 33980885 PMCID: PMC8115314 DOI: 10.1038/s41598-021-89421-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/27/2021] [Indexed: 11/24/2022] Open
Abstract
Grafting bioactive peptides into recipient protein scaffolds can often increase their activities by conferring enhanced stability and cellular longevity. Here, we describe use of vGFP as a novel scaffold to display peptides. vGFP comprises GFP fused to a bound high affinity Enhancer nanobody that potentiates its fluorescence. We show that peptides inserted into the linker region between GFP and the Enhancer are correctly displayed for on-target interaction, both in vitro and in live cells by pull-down, measurement of target inhibition and imaging analyses. This is further confirmed by structural studies highlighting the optimal display of a vGFP-displayed peptide bound to Mdm2, the key negative regulator of p53 that is often overexpressed in cancer. We also demonstrate a potential biosensing application of the vGFP scaffold by showing target-dependent modulation of intrinsic fluorescence. vGFP is relatively thermostable, well-expressed and inherently fluorescent. These properties make it a useful scaffold to add to the existing tool box for displaying peptides that can disrupt clinically relevant protein–protein interactions.
Collapse
Affiliation(s)
- Sharon Min Qi Chee
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Jantana Wongsantichon
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Lau Sze Yi
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Barindra Sana
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Yuri Frosi
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand.,Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Farid J Ghadessy
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore.
| |
Collapse
|
9
|
Pipchuk A, Yang X. Using Biosensors to Study Protein-Protein Interaction in the Hippo Pathway. Front Cell Dev Biol 2021; 9:660137. [PMID: 33981705 PMCID: PMC8107278 DOI: 10.3389/fcell.2021.660137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/06/2021] [Indexed: 11/18/2022] Open
Abstract
The Hippo signaling network is dependent on protein–protein interactions (PPIs) as a mechanism of signal transduction to regulate organ size, cellular proliferation and differentiation, tumorigenesis, and other cellular processes. Current efforts aim to resolve the complex regulation of upstream Hippo components or focus on identifying targeted drugs for use in cancer therapy. Despite extensive characterization of the Hippo pathway interactome by affinity purification mass spectrometry (AP-MS) and other methodologies, previous research methods have not been sufficient to achieve these aims. In this review, we describe several recent studies that make use of luciferase-based biosensors as a new approach to study the Hippo Pathway. These biosensors serve as powerful tools with which to study PPIs both in vitro using purified biosensor proteins, and in real time in live cells. Notably, luciferase biosensors have excellent sensitivity and have been used to screen for upstream kinase regulators of the Hippo pathway. Furthermore, the high sensitivity and stability of these biosensors enables their application in high throughput screening for Hippo-targeted chemotherapeutics. Finally, we describe the strengths and weaknesses of this method relative to AP-MS and discuss potential future directions for using biosensors to study Hippo signaling.
Collapse
Affiliation(s)
- Alexander Pipchuk
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Xiaolong Yang
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| |
Collapse
|
10
|
Arcones AC, Vila-Bedmar R, Mirasierra M, Cruces-Sande M, Vallejo M, Jones B, Tomas A, Mayor F, Murga C. GRK2 regulates GLP-1R-mediated early phase insulin secretion in vivo. BMC Biol 2021; 19:40. [PMID: 33658023 PMCID: PMC7931601 DOI: 10.1186/s12915-021-00966-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Insulin secretion from the pancreatic β-cell is finely modulated by different signals to allow an adequate control of glucose homeostasis. Incretin hormones such as glucagon-like peptide-1 (GLP-1) act as key physiological potentiators of insulin release through binding to the G protein-coupled receptor GLP-1R. Another key regulator of insulin signaling is the Ser/Thr kinase G protein-coupled receptor kinase 2 (GRK2). However, whether GRK2 affects insulin secretion or if GRK2 can control incretin actions in vivo remains to be analyzed. RESULTS Using GRK2 hemizygous mice, isolated pancreatic islets, and model β-cell lines, we have uncovered a relevant physiological role for GRK2 as a regulator of incretin-mediated insulin secretion in vivo. Feeding, oral glucose gavage, or administration of GLP-1R agonists in animals with reduced GRK2 levels (GRK2+/- mice) resulted in enhanced early phase insulin release without affecting late phase secretion. In contrast, intraperitoneal glucose-induced insulin release was not affected. This effect was recapitulated in isolated islets and correlated with the increased size or priming efficacy of the readily releasable pool (RRP) of insulin granules that was observed in GRK2+/- mice. Using nanoBRET in β-cell lines, we found that stimulation of GLP-1R promoted GRK2 association to this receptor and that GRK2 protein and kinase activity were required for subsequent β-arrestin recruitment. CONCLUSIONS Overall, our data suggest that GRK2 is an important negative modulator of GLP-1R-mediated insulin secretion and that GRK2-interfering strategies may favor β-cell insulin secretion specifically during the early phase, an effect that may carry interesting therapeutic applications.
Collapse
Affiliation(s)
- Alba C Arcones
- Departamento de Biología Molecular and Centro de Biología Molecular Severo Ochoa (CBMSO) UAM-CSIC; Instituto de Investigación Sanitaria Hospital Universitario La Princesa; CIBER de Enfermedades Cardiovasculares (CIBERCV), UNIVERSIDAD AUTONOMA DE MADRID and Instituto de Salud Carlos III, Madrid, Spain
| | - Rocío Vila-Bedmar
- Departamento de Ciencias Básicas de la Salud, Facultad de Ciencias de la Salud, Universidad Rey Juan Carlos (URJC), Madrid, Spain
| | - Mercedes Mirasierra
- Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM); Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (Ciberdem), Madrid, Spain
| | - Marta Cruces-Sande
- Departamento de Biología Molecular and Centro de Biología Molecular Severo Ochoa (CBMSO) UAM-CSIC; Instituto de Investigación Sanitaria Hospital Universitario La Princesa; CIBER de Enfermedades Cardiovasculares (CIBERCV), UNIVERSIDAD AUTONOMA DE MADRID and Instituto de Salud Carlos III, Madrid, Spain
| | - Mario Vallejo
- Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM); Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (Ciberdem), Madrid, Spain
| | - Ben Jones
- Section of Investigative Medicine, Imperial College London, London, W12 0NN, UK
| | - Alejandra Tomas
- Section of Cell Biology and Functional Genomics, Imperial College London, London, W12 0NN, UK
| | - Federico Mayor
- Departamento de Biología Molecular and Centro de Biología Molecular Severo Ochoa (CBMSO) UAM-CSIC; Instituto de Investigación Sanitaria Hospital Universitario La Princesa; CIBER de Enfermedades Cardiovasculares (CIBERCV), UNIVERSIDAD AUTONOMA DE MADRID and Instituto de Salud Carlos III, Madrid, Spain.
| | - Cristina Murga
- Departamento de Biología Molecular and Centro de Biología Molecular Severo Ochoa (CBMSO) UAM-CSIC; Instituto de Investigación Sanitaria Hospital Universitario La Princesa; CIBER de Enfermedades Cardiovasculares (CIBERCV), UNIVERSIDAD AUTONOMA DE MADRID and Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
11
|
Syed AJ, Anderson JC. Applications of bioluminescence in biotechnology and beyond. Chem Soc Rev 2021; 50:5668-5705. [DOI: 10.1039/d0cs01492c] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bioluminescent probes have hugely benefited from the input of synthetic chemistry and protein engineering. Here we review the latest applications of these probes in biotechnology and beyond, with an eye on current limitations and future directions.
Collapse
Affiliation(s)
- Aisha J. Syed
- Department of Chemistry
- University College London
- London
- UK
| | | |
Collapse
|
12
|
Krasitskaya VV, Bashmakova EE, Frank LA. Coelenterazine-Dependent Luciferases as a Powerful Analytical Tool for Research and Biomedical Applications. Int J Mol Sci 2020; 21:E7465. [PMID: 33050422 PMCID: PMC7590018 DOI: 10.3390/ijms21207465] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 12/19/2022] Open
Abstract
: The functioning of bioluminescent systems in most of the known marine organisms is based on the oxidation reaction of the same substrate-coelenterazine (CTZ), catalyzed by luciferase. Despite the diversity in structures and the functioning mechanisms, these enzymes can be united into a common group called CTZ-dependent luciferases. Among these, there are two sharply different types of the system organization-Ca2+-regulated photoproteins and luciferases themselves that function in accordance with the classical enzyme-substrate kinetics. Along with deep and comprehensive fundamental research on these systems, approaches and methods of their practical use as highly sensitive reporters in analytics have been developed. The research aiming at the creation of artificial luciferases and synthetic CTZ analogues with new unique properties has led to the development of new experimental analytical methods based on them. The commercial availability of many ready-to-use assay systems based on CTZ-dependent luciferases is also important when choosing them by first-time-users. The development of analytical methods based on these bioluminescent systems is currently booming. The bioluminescent systems under consideration were successfully applied in various biological research areas, which confirms them to be a powerful analytical tool. In this review, we consider the main directions, results, and achievements in research involving these luciferases.
Collapse
Affiliation(s)
- Vasilisa V. Krasitskaya
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (E.E.B.)
| | - Eugenia E. Bashmakova
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (E.E.B.)
| | - Ludmila A. Frank
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (E.E.B.)
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
| |
Collapse
|
13
|
Disruption of a key ligand-H-bond network drives dissociative properties in vamorolone for Duchenne muscular dystrophy treatment. Proc Natl Acad Sci U S A 2020; 117:24285-24293. [PMID: 32917814 DOI: 10.1073/pnas.2006890117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Duchenne muscular dystrophy is a genetic disorder that shows chronic and progressive damage to skeletal and cardiac muscle leading to premature death. Antiinflammatory corticosteroids targeting the glucocorticoid receptor (GR) are the current standard of care but drive adverse side effects such as deleterious bone loss. Through subtle modification to a steroidal backbone, a recently developed drug, vamorolone, appears to preserve beneficial efficacy but with significantly reduced side effects. We use combined structural, biophysical, and biochemical approaches to show that loss of a receptor-ligand hydrogen bond drives these remarkable therapeutic effects. Moreover, vamorolone uniformly weakens coactivator associations but not corepressor associations, implicating partial agonism as the main driver of its dissociative properties. Additionally, we identify a critical and evolutionarily conserved intramolecular network connecting the ligand to the coregulator binding surface. Interruption of this allosteric network by vamorolone selectively reduces GR-driven transactivation while leaving transrepression intact. Our results establish a mechanistic understanding of how vamorolone reduces side effects, guiding the future design of partial agonists as selective GR modulators with an improved therapeutic index.
Collapse
|
14
|
Rusnak L, Tang C, Qi Q, Mo X, Fu H. Large tumor suppressor 2, LATS2, activates JNK in a kinase-independent mechanism through ASK1. J Mol Cell Biol 2019; 10:549-558. [PMID: 30496488 DOI: 10.1093/jmcb/mjy061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/15/2018] [Indexed: 12/25/2022] Open
Abstract
Apoptosis signal-regulating kinase 1 (ASK1) is an important mediator of the cell stress response pathways. Because of its central role in regulating cell death, the activity of ASK1 is tightly regulated by protein-protein interactions and post-translational modifications. Deregulation of ASK1 activity has been linked to human diseases, such as neurological disorders and cancer. Here we describe the identification and characterization of large tumor suppressor 2 (LATS2) as a novel binding partner for ASK1. LATS2 is a core kinase in the Hippo signaling pathway and is commonly downregulated in cancer. We found that LATS2 interacts with ASK1 and increases ASK1-mediated signaling to promote apoptosis and activate the JNK mitogen-activated protein kinase (MAPK). This change in MAPK signaling is dependent on the catalytic activity of ASK1 but does not require LATS2 kinase activity. This work identifies a novel role for LATS2 as a positive regulator of the ASK1-MKK-JNK signaling pathway and establishes a kinase-independent function of LATS2 that may be part of the intricate regulatory system for cellular response to diverse stress signals.
Collapse
Affiliation(s)
- Lauren Rusnak
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA, USA.,Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA, USA
| | - Cong Tang
- Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA, USA.,The First Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, China
| | - Qi Qi
- Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA, USA
| | - Xiulei Mo
- Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA, USA
| | - Haian Fu
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA, USA.,Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA, USA.,Winship Cancer Institute, Emory University, Atlanta, GA, USA.,Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
| |
Collapse
|
15
|
Ni D, Lu S, Zhang J. Emerging roles of allosteric modulators in the regulation of protein-protein interactions (PPIs): A new paradigm for PPI drug discovery. Med Res Rev 2019; 39:2314-2342. [PMID: 30957264 DOI: 10.1002/med.21585] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 03/12/2019] [Accepted: 03/24/2019] [Indexed: 12/26/2022]
Abstract
Protein-protein interactions (PPIs) are closely implicated in various types of cellular activities and are thus pivotal to health and disease states. Given their fundamental roles in a wide range of biological processes, the modulation of PPIs has enormous potential in drug discovery. However, owing to the general properties of large, flat, and featureless interfaces of PPIs, previous attempts have demonstrated that the generation of therapeutic agents targeting PPI interfaces is challenging, rendering them almost "undruggable" for decades. To date, rapid progress in chemical and structural biology techniques has promoted the exploitation of allostery as a novel approach in drug discovery. By attaching to allosteric sites that are topologically and spatially distinct from PPI interfaces, allosteric modulators can achieve improved physiochemical properties. Thus, allosteric modulators may represent an alternative strategy to target intractable PPIs and have attracted intense pharmaceutical interest. In this review, we first briefly introduce the characteristics of PPIs and then present different approaches for investigating PPIs, as well as the latest methods for modulating PPIs. Importantly, we comprehensively review the recent progress in the development of allosteric modulators to inhibit or stabilize PPIs. Finally, we conclude with future perspectives on the discovery of allosteric PPI modulators, especially the application of computational methods to aid in allosteric PPI drug discovery.
Collapse
Affiliation(s)
- Duan Ni
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Shaoyong Lu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Center for Single-Cell Omics, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| |
Collapse
|
16
|
Dale NC, Johnstone EKM, White CW, Pfleger KDG. NanoBRET: The Bright Future of Proximity-Based Assays. Front Bioeng Biotechnol 2019; 7:56. [PMID: 30972335 PMCID: PMC6443706 DOI: 10.3389/fbioe.2019.00056] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/04/2019] [Indexed: 12/17/2022] Open
Abstract
Bioluminescence resonance energy transfer (BRET) is a biophysical technique used to monitor proximity within live cells. BRET exploits the naturally occurring phenomenon of dipole-dipole energy transfer from a donor enzyme (luciferase) to an acceptor fluorophore following enzyme-mediated oxidation of a substrate. This results in production of a quantifiable signal that denotes proximity between proteins and/or molecules tagged with complementary luciferase and fluorophore partners. BRET assays have been used to observe an array of biological functions including ligand binding, intracellular signaling, receptor-receptor proximity, and receptor trafficking, however, BRET assays can theoretically be used to monitor the proximity of any protein or molecule for which appropriate fusion constructs and/or fluorophore conjugates can be produced. Over the years, new luciferases and approaches have been developed that have increased the potential applications for BRET assays. In particular, the development of the small, bright and stable Nanoluciferase (NanoLuc; Nluc) and its use in NanoBRET has vastly broadened the potential applications of BRET assays. These advances have exciting potential to produce new experimental methods to monitor protein-protein interactions (PPIs), protein-ligand interactions, and/or molecular proximity. In addition to NanoBRET, Nluc has also been exploited to produce NanoBiT technology, which further broadens the scope of BRET to monitor biological function when NanoBiT is combined with an acceptor. BRET has proved to be a powerful tool for monitoring proximity and interaction, and these recent advances further strengthen its utility for a range of applications.
Collapse
Affiliation(s)
- Natasha C Dale
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia.,Australian Research Council Centre for Personalised Therapeutics TechnologiesAustralia
| | - Elizabeth K M Johnstone
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia.,Australian Research Council Centre for Personalised Therapeutics TechnologiesAustralia
| | - Carl W White
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia.,Australian Research Council Centre for Personalised Therapeutics TechnologiesAustralia
| | - Kevin D G Pfleger
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia.,Australian Research Council Centre for Personalised Therapeutics TechnologiesAustralia.,Dimerix Limited, Nedlands, WA, Australia
| |
Collapse
|
17
|
Grzeskowiak CL, Kundu ST, Mo X, Ivanov AA, Zagorodna O, Lu H, Chapple RH, Tsang YH, Moreno D, Mosqueda M, Eterovic K, Fradette JJ, Ahmad S, Chen F, Chong Z, Chen K, Creighton CJ, Fu H, Mills GB, Gibbons DL, Scott KL. In vivo screening identifies GATAD2B as a metastasis driver in KRAS-driven lung cancer. Nat Commun 2018; 9:2732. [PMID: 30013058 PMCID: PMC6048166 DOI: 10.1038/s41467-018-04572-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 05/02/2018] [Indexed: 12/26/2022] Open
Abstract
Genetic aberrations driving pro-oncogenic and pro-metastatic activity remain an elusive target in the quest of precision oncology. To identify such drivers, we use an animal model of KRAS-mutant lung adenocarcinoma to perform an in vivo functional screen of 217 genetic aberrations selected from lung cancer genomics datasets. We identify 28 genes whose expression promoted tumor metastasis to the lung in mice. We employ two tools for examining the KRAS-dependence of genes identified from our screen: 1) a human lung cell model containing a regulatable mutant KRAS allele and 2) a lentiviral system permitting co-expression of DNA-barcoded cDNAs with Cre recombinase to activate a mutant KRAS allele in the lungs of mice. Mechanistic evaluation of one gene, GATAD2B, illuminates its role as a dual activity gene, promoting both pro-tumorigenic and pro-metastatic activities in KRAS-mutant lung cancer through interaction with c-MYC and hyperactivation of the c-MYC pathway.
Collapse
Affiliation(s)
- Caitlin L Grzeskowiak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Samrat T Kundu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiulei Mo
- Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Andrei A Ivanov
- Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Oksana Zagorodna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hengyu Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard H Chapple
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yiu Huen Tsang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Daniela Moreno
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maribel Mosqueda
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Karina Eterovic
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jared J Fradette
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sumreen Ahmad
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Fengju Chen
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zechen Chong
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Chad J Creighton
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Haian Fu
- Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, 77030, USA.
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| |
Collapse
|
18
|
Kaskova ZM, Tsarkova AS, Yampolsky IV. 1001 lights: luciferins, luciferases, their mechanisms of action and applications in chemical analysis, biology and medicine. Chem Soc Rev 2018; 45:6048-6077. [PMID: 27711774 DOI: 10.1039/c6cs00296j] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bioluminescence (BL) is a spectacular phenomenon involving light emission by live organisms. It is caused by the oxidation of a small organic molecule, luciferin, with molecular oxygen, which is catalysed by the enzyme luciferase. In nature, there are approximately 30 different BL systems, of which only 9 have been studied to various degrees in terms of their reaction mechanisms. A vast range of in vitro and in vivo analytical techniques have been developed based on BL, including tests for different analytes, immunoassays, gene expression assays, drug screening, bioimaging of live organisms, cancer studies, the investigation of infectious diseases and environmental monitoring. This review aims to cover the major existing applications for bioluminescence in the context of the diversity of luciferases and their substrates, luciferins. Particularly, the properties and applications of d-luciferin, coelenterazine, bacterial, Cypridina and dinoflagellate luciferins and their analogues along with their corresponding luciferases are described. Finally, four other rarely studied bioluminescent systems (those of limpet Latia, earthworms Diplocardia and Fridericia and higher fungi), which are promising for future use, are also discussed.
Collapse
Affiliation(s)
- Zinaida M Kaskova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia. and Pirogov Russian National Research Medical University, Ostrovitianova 1, Moscow 117997, Russia
| | - Aleksandra S Tsarkova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia. and Pirogov Russian National Research Medical University, Ostrovitianova 1, Moscow 117997, Russia
| | - Ilia V Yampolsky
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia. and Pirogov Russian National Research Medical University, Ostrovitianova 1, Moscow 117997, Russia
| |
Collapse
|
19
|
Liu X, Huang S, Liu C, Liu X, Shen Y, Cui Z. PPP1CC is associated with astrocyte and microglia proliferation after traumatic spinal cord injury in rats. Pathol Res Pract 2017; 213:1355-1364. [DOI: 10.1016/j.prp.2017.09.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 09/15/2017] [Accepted: 09/16/2017] [Indexed: 10/18/2022]
|
20
|
Mo X, Qi Q, Ivanov AA, Niu Q, Luo Y, Havel J, Goetze R, Bell S, Moreno CS, Cooper LAD, Johns MA, Khuri FR, Du Y, Fu H. AKT1, LKB1, and YAP1 Revealed as MYC Interactors with NanoLuc-Based Protein-Fragment Complementation Assay. Mol Pharmacol 2017; 91:339-347. [PMID: 28087810 DOI: 10.1124/mol.116.107623] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/09/2017] [Indexed: 01/07/2023] Open
Abstract
The c-Myc (MYC) transcription factor is a major cancer driver and a well-validated therapeutic target. However, directly targeting MYC has been challenging. Thus, identifying proteins that interact with and regulate MYC may provide alternative strategies to inhibit its oncogenic activity. In this study, we report the development of a NanoLuc-based protein-fragment complementation assay (NanoPCA) and mapping of the MYC protein interaction hub in live mammalian cells. The NanoPCA system was configured to enable detection of protein-protein interactions (PPI) at the endogenous level, as shown with PRAS40 dimerization, and detection of weak interactions, such as PINCH1-NCK2. Importantly, NanoPCA allows the study of PPI dynamics with reversible interactions. To demonstrate its utility for large-scale PPI detection in mammalian intracellular environment, we have used NanoPCA to examine MYC interaction with 83 cancer-associated proteins in live cancer cell lines. Our new MYC PPI data confirmed known MYC-interacting proteins, such as MAX, GSK3A, and SMARCA4, and revealed a panel of novel MYC interaction partners, such as RAC-α serine/threonine-protein kinase (AKT)1, liver kinase B (LKB)1, and Yes-associated protein (YAP)1. The MYC interactions with AKT1, LKB1, and YAP1 were confirmed by coimmunoprecipitation of endogenous proteins. Importantly, AKT1, LKB1, and YAP1 were able to activate MYC in a transcriptional reporter assay. Thus, these vital growth control proteins may represent promising MYC regulators, suggesting new mechanisms that couple energetic and metabolic pathways and developmental signaling to MYC-regulated cellular programs.
Collapse
Affiliation(s)
- Xiulei Mo
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Qi Qi
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Andrei A Ivanov
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Qiankun Niu
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Yin Luo
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Jonathan Havel
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Russell Goetze
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Sydney Bell
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Carlos S Moreno
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Lee A D Cooper
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Margaret A Johns
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Fadlo R Khuri
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Yuhong Du
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| | - Haian Fu
- Department of Pharmacology and Emory Chemical Biology Discovery Center (X.M., Q.Q., A.A.I., Q.N., Y.L., J.H., R.G., S.B., M.A.J., Y.D., H.F.) and Department of Biomedical Informatics (L.A.D.C.), Emory University School of Medicine, Atlanta, Georgia; Departments of Hematology and Medical Oncology (F.R.K., H.F.) and Pathology and Laboratory Medicine (C.S.M.) and Winship Cancer Institute, Emory University, Atlanta, Georgia; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China (Y.L.); and Department of Biomedical Engineering, Emory University School of Medicine/Georgia Institute of Technology, Atlanta, Georgia (L.A.D.C.)
| |
Collapse
|
21
|
Novel bioluminescent binding assays for interaction studies of protein/peptide hormones with their receptors. Amino Acids 2016; 48:1151-60. [DOI: 10.1007/s00726-016-2220-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/16/2016] [Indexed: 10/22/2022]
|
22
|
Mo XL, Fu H. BRET: NanoLuc-Based Bioluminescence Resonance Energy Transfer Platform to Monitor Protein-Protein Interactions in Live Cells. Methods Mol Biol 2016; 1439:263-271. [PMID: 27317001 DOI: 10.1007/978-1-4939-3673-1_17] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bioluminescence resonance energy transfer (BRET) is a prominent biophysical technology for monitoring molecular interactions, and has been widely used to study protein-protein interactions (PPI) in live cells. This technology requires proteins of interest to be associated with an energy donor (i.e., luciferase) and an acceptor (e.g., fluorescent protein) molecule. Upon interaction of the proteins of interest, the donor and acceptor will be brought into close proximity and energy transfer of chemical reaction-induced luminescence to its corresponding acceptor will result in an increased emission at an acceptor-defined wavelength, generating the BRET signal. We leverage the advantages of the superior optical properties of the NanoLuc(®) luciferase (NLuc) as a BRET donor coupled with Venus, a yellow fluorescent protein, as acceptor. We term this NLuc-based BRET platform "BRET(n)". BRET(n) has been demonstrated to have significantly improved assay performance, compared to previous BRET technologies, in terms of sensitivity and scalability. This chapter describes a step-by-step practical protocol for developing a BRET(n) assay in a multi-well plate format to detect PPIs in live mammalian cells.
Collapse
Affiliation(s)
- Xiu-Lei Mo
- Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Haian Fu
- Department of Pharmacology and Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Hematology and Medical Oncology and Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA
| |
Collapse
|