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Animireddy S, Kavadipula P, Kotapalli V, Gowrishankar S, Rao S, Bashyam MD. Aberrant cytoplasmic localization of ARID1B activates ERK signaling and promotes oncogenesis. J Cell Sci 2021; 134:jcs251637. [PMID: 33443092 DOI: 10.1242/jcs.251637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
The ARID1B (BAF250b) subunit of the human SWI/SNF chromatin remodeling complex is a canonical nuclear tumor suppressor. We employed in silico prediction, intracellular fluorescence and cellular fractionation-based subcellular localization analyses to identify the ARID1B nuclear localization signal (NLS). A cytoplasm-restricted ARID1B-NLS mutant was significantly compromised in its canonical transcription activation and tumor suppressive functions, as expected. Surprisingly however, cytoplasmic localization appeared to induce a gain of oncogenic function for ARID1B, as evidenced from several cell line- and mouse xenograft-based assays. Mechanistically, cytoplasm-localized ARID1B could bind c-RAF (RAF1) and PPP1CA causing stimulation of RAF-ERK signaling and β-catenin (CTNNB1) transcription activity. ARID1B harboring NLS mutations derived from tumor samples also exhibited aberrant cytoplasmic localization and acquired a neo-morphic oncogenic function via activation of RAF-ERK signaling. Furthermore, immunohistochemistry on a tissue microarray revealed significant correlation of ARID1B cytoplasmic localization with increased levels of active forms of ERK1 and ERK2 (also known as MAPK3 and MAPK1) and of β-catenin, as well as with advanced tumor stage and lymph node positivity in human primary pancreatic tumor tissues. ARID1B therefore promotes oncogenesis through cytoplasm-based gain-of-function mechanisms in addition to dysregulation in the nucleus.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Srinivas Animireddy
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal 576104, India
| | - Padmavathi Kavadipula
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | - Viswakalyan Kotapalli
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | | | - Satish Rao
- Krishna Institute of Medical Sciences, Hyderabad 500003, India
| | - Murali Dharan Bashyam
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
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Peier A, Ge L, Boyer N, Frost J, Duggal R, Biswas K, Edmondson S, Hermes JD, Yan L, Zimprich C, Sadruddin A, Kristal Kaan HY, Chandramohan A, Brown CJ, Thean D, Lee XE, Yuen TY, Ferrer-Gago FJ, Johannes CW, Lane DP, Sherborne B, Corona C, Robers MB, Sawyer TK, Partridge AW. NanoClick: A High Throughput, Target-Agnostic Peptide Cell Permeability Assay. ACS Chem Biol 2021; 16:293-309. [PMID: 33539064 DOI: 10.1021/acschembio.0c00804] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Macrocyclic peptides open new opportunities to target intracellular protein-protein interactions (PPIs) that are often considered nondruggable by traditional small molecules. However, engineering sufficient membrane permeability into these molecules is a central challenge for identifying clinical candidates. Currently, there is a lack of high-throughput assays to assess peptide permeability, which limits our capacity to engineer this property into macrocyclic peptides for advancement through drug discovery pipelines. Accordingly, we developed a high throughput and target-agnostic cell permeability assay that measures the relative cumulative cytosolic exposure of a peptide in a concentration-dependent manner. The assay was named NanoClick as it combines in-cell Click chemistry with an intracellular NanoBRET signal. We validated the approach using known cell penetrating peptides and further demonstrated a correlation to cellular activity using a p53/MDM2 model system. With minimal change to the peptide sequence, NanoClick enables the ability to measure uptake of molecules that enter the cell via different mechanisms such as endocytosis, membrane translocation, or passive permeability. Overall, the NanoClick assay can serve as a screening tool to uncover predictive design rules to guide structure-activity-permeability relationships in the optimization of functionally active molecules.
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Affiliation(s)
- Andrea Peier
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Lan Ge
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Nicolas Boyer
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - John Frost
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Ruchia Duggal
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Kaustav Biswas
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Scott Edmondson
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | | | - Lin Yan
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Chad Zimprich
- Promega Corporation, Madison, Wisconsin 53711, United States
| | | | | | | | - Christopher J. Brown
- Agency for Science, Technology and Research (A*STAR) Singapore 138665, Singapore
| | - Dawn Thean
- Agency for Science, Technology and Research (A*STAR) Singapore 138665, Singapore
| | - Xue Er Lee
- Agency for Science, Technology and Research (A*STAR) Singapore 138665, Singapore
| | - Tsz Ying Yuen
- Agency for Science, Technology and Research (A*STAR) Singapore 138665, Singapore
| | | | - Charles W. Johannes
- Agency for Science, Technology and Research (A*STAR) Singapore 138665, Singapore
| | - David P. Lane
- Agency for Science, Technology and Research (A*STAR) Singapore 138665, Singapore
| | - Brad Sherborne
- Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Cesear Corona
- Promega Biosciences Incorporated, San Luis Obispo, California 93401, United States
| | | | - Tomi K. Sawyer
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
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Manzoor O, Soleja N, Mohsin M. Nanoscale gizmos - the novel fluorescent probes for monitoring protein activity. Biochem Eng J 2018; 133:83-95. [PMID: 32518506 PMCID: PMC7270366 DOI: 10.1016/j.bej.2018.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/27/2017] [Accepted: 02/06/2018] [Indexed: 11/15/2022]
Abstract
Genetically-encoded FRET, organic dye, QD based sensors. Real-time monitoring of the respective metabolite level at sub cellular level. Spatio temporal resolution of the fluorophores by low intensity light. Monitoring of various metabolite levels in any cell type prokaryotic and eukaryotic as well. Functional analysis of the role of proteases in several diseases.
Nanobiotechnology has emerged inherently as an interdisciplinary field, with collaborations from researchers belonging to diverse backgrounds like molecular biology, materials science and organic chemistry. Till the current times, researchers have been able to design numerous types of nanoscale fluorescent tool kits for monitoring protein–protein interactions through real time cellular imagery in a fluorescence microscope. It is apparent that supplementing any protein of interest with a fluorescence habit traces its function and regulation within a cell. Our review therefore highlights the application of several fluorescent probes such as molecular organic dyes, quantum dots (QD) and fluorescent proteins (FPs) to determine activity state, expression and localization of proteins in live and fixed cells. The focus is on Fluorescence Resonance Energy Transfer (FRET) based nanosensors that have been developed by researchers to visualize and monitor protein dynamics and quantify metabolites of diverse nature. FRET based toolkits permit the resolution of ambiguities that arise due to the rotation of sensor molecules and flexibility of the probe. Achievements of live cell imaging and efficient spatiotemporal resolution however have been possible only with the advent of fluorescence microscopic technology, equipped with precisely sensitive automated softwares.
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Savaryn JP, Skinner OS, Fornelli L, Fellers RT, Compton PD, Terhune SS, Abecassis MM, Kelleher NL. Targeted analysis of recombinant NF kappa B (RelA/p65) by denaturing and native top down mass spectrometry. J Proteomics 2016; 134:76-84. [PMID: 25952688 PMCID: PMC4633404 DOI: 10.1016/j.jprot.2015.04.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/06/2015] [Accepted: 04/24/2015] [Indexed: 02/03/2023]
Abstract
Measuring post-translational modifications on transcription factors by targeted mass spectrometry is hampered by low protein abundance and inefficient isolation. Here, we utilized HaloTag technology to overcome these limitations and evaluate various top down mass spectrometry approaches for measuring NF-κB p65 proteoforms isolated from human cells. We show isotopic resolution of N-terminally acetylated p65 and determined it is the most abundant proteoform expressed following transfection in 293T cells. We also show MS(1) evidence for monophosphorylation of p65 under similar culture conditions and describe a high propensity for p65 proteoforms to fragment internally during beam-style MS(2) fragmentation; up to 71% of the fragment ions could be matched as internals in some fragmentation spectra. Finally, we used native spray mass spectrometry to measure proteins copurifying with p65 and present evidence for the native detection of p65, 71kDa heat shock protein, and p65 homodimer. Collectively, our work demonstrates the efficient isolation and top down mass spectrometry analysis of p65 from human cells, and we discuss the perturbations of overexpressing tagged proteins to study their biochemistry. This article is part of a Special Issue entitled: Protein Species. BIOLOGICAL SIGNIFICANCE Characterizing transcription factor proteoforms in human cells is of high value to the field of molecular biology; many agree that post-translational modifications and combinations thereof play a critical role in modulating transcription factor activity. Thus, measuring these modifications promises increased understanding of molecular mechanisms governing the regulation of complex gene expression outcomes. To date, comprehensive characterization of transcription factor proteoforms within human cells has eluded measurement, owing primarily-with regard to top down mass spectrometry-to large protein size and low relative abundance. Here, we utilized HaloTag technology and recombinant protein expression to overcome these limitations and show top down mass spectrometry characterization of proteoforms of the 60kDa NF-kB protein, p65. By optimizing the analytical procedure (i.e. purification, MS(1), and MS(2)), our results make important progress toward the ultimate goal of targeted transcription factor characterization from endogenous loci.
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Affiliation(s)
- John Paul Savaryn
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA; Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Owen S Skinner
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Luca Fornelli
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Ryan T Fellers
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Philip D Compton
- Department of Chemistry, Northwestern University, Evanston, IL, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Scott S Terhune
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Mike M Abecassis
- Comprehensive Transplant Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, USA; Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.
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Abstract
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Exploration of protein function and
interaction is critical for
discovering links among genomics, proteomics, and disease state; yet,
the immense complexity of proteomics found in biological systems currently
limits our investigational capacity. Although affinity and autofluorescent
tags are widely employed for protein analysis, these methods have
been met with limited success because they lack specificity and require
multiple fusion tags and genetic constructs. As an alternative approach,
the innovative HaloTag protein fusion platform allows protein function
and interaction to be comprehensively analyzed using a single genetic
construct with multiple capabilities. This is accomplished using a
simplified process, in which a variable HaloTag ligand binds rapidly
to the HaloTag protein (usually linked to the protein of interest)
with high affinity and specificity. In this review, we examine all
current applications of the HaloTag technology platform for biomedical
applications, such as the study of protein isolation and purification,
protein function, protein–protein and protein–DNA interactions,
biological assays, in vitro cellular imaging, and in vivo molecular imaging. In addition, novel uses of the
HaloTag platform are briefly discussed along with potential future
applications.
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Affiliation(s)
- Christopher G England
- †Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Haiming Luo
- ‡Department of Radiology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Weibo Cai
- †Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,‡Department of Radiology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,§University of Wisconsin Carbone Cancer Center, Madison, Wisconsin 53705, United States
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