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Stefanski KM, Li GC, Marinko JT, Carter BD, Samuels DC, Sanders CR. Reply to Record et al. "The role of PMP22 T118M in Charcot-Marie-Tooth disease remains unsolved". J Biol Chem 2023; 299:105181. [PMID: 37716137 PMCID: PMC10509702 DOI: 10.1016/j.jbc.2023.105181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2023] [Indexed: 09/18/2023] Open
Affiliation(s)
- Katherine M Stefanski
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Geoffrey C Li
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Justin T Marinko
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Bruce D Carter
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - David C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
| | - Charles R Sanders
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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Stefanski KM, Bauer J, Kenworthy AK, Sanders CR. High-throughput screening to identify modulators of membrane protein raft affinity in giant plasma membrane vesicles. Biophys J 2023; 122:449a. [PMID: 36784305 DOI: 10.1016/j.bpj.2022.11.2422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
| | - Joshua Bauer
- Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Anne K Kenworthy
- University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Charles R Sanders
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
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Stefanski KM, Li GC, Marinko JT, Carter BD, Samuels DC, Sanders CR. How T118M peripheral myelin protein 22 predisposes humans to Charcot-Marie-Tooth disease. J Biol Chem 2023; 299:102839. [PMID: 36581210 PMCID: PMC9860121 DOI: 10.1016/j.jbc.2022.102839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/27/2022] Open
Abstract
Data from gnomAD indicate that a missense mutation encoding the T118M variation in human peripheral myelin protein 22 (PMP22) is found in roughly one of every 75 genomes of western European lineage (1:120 in the overall human population). It is unusual among PMP22 variants that cause Charcot-Marie-Tooth (CMT) disease in that it is not 100% penetrant. Here, we conducted cellular and biophysical studies to determine why T118M PMP22 predisposes humans to CMT, but with only incomplete penetrance. We found that T118M PMP22 is prone to mistraffic but differs even from the WT protein in that increased expression levels do not result in a reduction in trafficking efficiency. Moreover, the T118M mutant exhibits a reduced tendency to form large intracellular aggregates relative to other disease mutants and even WT PMP22. NMR spectroscopy revealed that the structure and dynamics of T118M PMP22 resembled those of WT. These results show that the main consequence of T118M PMP22 in WT/T118M heterozygous individuals is a reduction in surface-trafficked PMP22, unaccompanied by formation of toxic intracellular aggregates. This explains the incomplete disease penetrance and the mild neuropathy observed for WT/T118M CMT cases. We also analyzed BioVU, a biobank linked to deidentified electronic medical records, and found a statistically robust association of the T118M mutation with the occurrence of long and/or repeated episodes of carpal tunnel syndrome. Collectively, our results illuminate the cellular effects of the T118M PMP22 variation leading to CMT disease and indicate a second disorder for which it is a risk factor.
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Affiliation(s)
- Katherine M Stefanski
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Geoffrey C Li
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Justin T Marinko
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Bruce D Carter
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - David C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
| | - Charles R Sanders
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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Fricke N, Raghunathan K, Tiwari A, Stefanski KM, Balakrishnan M, Waterson AG, Capone R, Huang H, Sanders CR, Bauer JA, Kenworthy AK. High-Content Imaging Platform to Discover Chemical Modulators of Plasma Membrane Rafts. ACS Cent Sci 2022; 8:370-378. [PMID: 35355811 PMCID: PMC8961798 DOI: 10.1021/acscentsci.1c01058] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 05/05/2023]
Abstract
Plasma membrane organization profoundly impacts cellular functionality. A well-known mechanism underlying this organization is through nanoscopic clustering of distinct lipids and proteins in membrane rafts. Despite their physiological importance, rafts remain a difficult-to-study aspect of membrane organization, in part because of the paucity of chemical tools to experimentally modulate their properties. Methods to selectively target rafts for therapeutic purposes are also currently lacking. To tackle these problems, we developed a high-throughput screen and an accompanying image analysis pipeline to identify small molecules that enhance or inhibit raft formation. Cell-derived giant plasma membrane vesicles were used as the experimental platform. A proof-of-principle screen using a bioactive lipid library demonstrates that this method is robust and capable of validating established raft modulators including C6- and C8-ceramide, miltefosine, and epigallocatechin gallate as well as identifying new ones. The platform we describe here represents a powerful tool to discover new chemical approaches to manipulate rafts and their components.
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Affiliation(s)
- Nico Fricke
- Department
of Molecular Physiology and Biophysics, Vanderbilt School of Medicine, Nashville, Tennessee 37232, United States
| | - Krishnan Raghunathan
- Department
of Molecular Physiology and Biophysics, Vanderbilt School of Medicine, Nashville, Tennessee 37232, United States
| | - Ajit Tiwari
- Department
of Molecular Physiology and Biophysics, Vanderbilt School of Medicine, Nashville, Tennessee 37232, United States
| | - Katherine M. Stefanski
- Department
of Biochemistry, Vanderbilt School of Medicine, Nashville, Tennessee 37240, United States
| | - Muthuraj Balakrishnan
- Center
for Membrane and Cell Physiology and Department of Molecular Physiology
and Biological Physics, University of Virginia
School of Medicine, Charlottesville, Virginia 22903, United States
| | - Alex G. Waterson
- Department
of Pharmacology, Vanderbilt School of Medicine, Nashville, Tennessee 37232, United States
| | - Ricardo Capone
- Department
of Molecular Physiology and Biophysics, Vanderbilt School of Medicine, Nashville, Tennessee 37232, United States
| | - Hui Huang
- Department
of Biochemistry, Vanderbilt School of Medicine, Nashville, Tennessee 37240, United States
| | - Charles R. Sanders
- Department
of Biochemistry, Vanderbilt School of Medicine, Nashville, Tennessee 37240, United States
| | - Joshua A. Bauer
- Department
of Biochemistry, Vanderbilt School of Medicine, Nashville, Tennessee 37240, United States
- Vanderbilt
Institute of Chemical Biology, High-Throughput Screening Facility, Vanderbilt School of Medicine, Nashville, Tennessee 37232, United States
| | - Anne K. Kenworthy
- Department
of Molecular Physiology and Biophysics, Vanderbilt School of Medicine, Nashville, Tennessee 37232, United States
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Stefanski KM, Russeull CM, Westerfield JM, Lamichhane R, Barrera FN. PIP2 Promotes Conformation-Specific Dimerization of the EPHA2 Transmembrane Domain through Juxtamembrane Interactions. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Stefanski KM, Russell CM, Westerfield JM, Lamichhane R, Barrera FN. PIP 2 promotes conformation-specific dimerization of the EphA2 membrane region. J Biol Chem 2021; 296:100149. [PMID: 33277361 PMCID: PMC7900517 DOI: 10.1074/jbc.ra120.016423] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/18/2020] [Accepted: 12/04/2020] [Indexed: 12/27/2022] Open
Abstract
The impact of the EphA2 receptor on cancer malignancy hinges on the two different ways it can be activated. EphA2 induces antioncogenic signaling after ligand binding, but ligand-independent activation of EphA2 is pro-oncogenic. It is believed that the transmembrane (TM) domain of EphA2 adopts two alternate conformations in the ligand-dependent and the ligand-independent states. However, it is poorly understood how the difference in TM helical crossing angles found in the two conformations impacts the activity and regulation of EphA2. We devised a method that uses hydrophobic matching to stabilize two conformations of a peptide comprising the EphA2 TM domain and a portion of the intracellular juxtamembrane (JM) segment. The two conformations exhibit different TM crossing angles, resembling the ligand-dependent and ligand-independent states. We developed a single-molecule technique using styrene maleic acid lipid particles to measure dimerization in membranes. We observed that the signaling lipid PIP2 promotes TM dimerization, but only in the small crossing angle state, which we propose corresponds to the ligand-independent conformation. In this state the two TMs are almost parallel, and the positively charged JM segments are expected to be close to each other, causing electrostatic repulsion. The mechanism PIP2 uses to promote dimerization might involve alleviating this repulsion due to its high density of negative charges. Our data reveal a conformational coupling between the TM and JM regions and suggest that PIP2 might directly exert a regulatory effect on EphA2 activation in cells that is specific to the ligand-independent conformation of the receptor.
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Affiliation(s)
- Katherine M Stefanski
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, USA
| | - Charles M Russell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Rajan Lamichhane
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA.
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA.
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Stefanski KM, Westerfield JM, Barrera FN. Transmembrane and Juxtamembrane Interactions of EphA2 with Lipid Membranes in the Active and Inactive States. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Alves DS, Westerfield JM, Shi X, Nguyen VP, Stefanski KM, Smith AW, Barrera FN. A Conditional Transmembrane Peptide Inhibits Cell Migration by Activation of the EphA2 Receptor Tyrosine Kinase. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Alves DS, Westerfield JM, Shi X, Nguyen VP, Stefanski KM, Booth KR, Kim S, Morrell-Falvey J, Wang BC, Abel SM, Smith AW, Barrera FN. A novel pH-dependent membrane peptide that binds to EphA2 and inhibits cell migration. eLife 2018; 7:36645. [PMID: 30222105 PMCID: PMC6192698 DOI: 10.7554/elife.36645] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/16/2018] [Indexed: 12/19/2022] Open
Abstract
Misregulation of the signaling axis formed by the receptor tyrosine kinase (RTK) EphA2 and its ligand, ephrinA1, causes aberrant cell-cell contacts that contribute to metastasis. Solid tumors are characterized by an acidic extracellular medium. We intend to take advantage of this tumor feature to design new molecules that specifically target tumors. We created a novel pH-dependent transmembrane peptide, TYPE7, by altering the sequence of the transmembrane domain of EphA2. TYPE7 is highly soluble and interacts with the surface of lipid membranes at neutral pH, while acidity triggers transmembrane insertion. TYPE7 binds to endogenous EphA2 and reduces Akt phosphorylation and cell migration as effectively as ephrinA1. Interestingly, we found large differences in juxtamembrane tyrosine phosphorylation and the extent of EphA2 clustering when comparing TYPE7 with activation by ephrinA1. This work shows that it is possible to design new pH-triggered membrane peptides to activate RTK and gain insights on its activation mechanism.
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Affiliation(s)
- Daiane S Alves
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
| | - Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
| | - Xiaojun Shi
- Department of Chemistry, University of Akron, Akron, United States.,Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States.,Pharmacology, Case Western Reserve University, Cleveland, United States.,Rammelkamp Center for Research, MetroHealth Medical Center, Cleveland, United States
| | - Vanessa P Nguyen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
| | - Katherine M Stefanski
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, United States
| | - Kristen R Booth
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
| | - Soyeon Kim
- Department of Chemistry, University of Akron, Akron, United States
| | - Jennifer Morrell-Falvey
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, United States
| | - Bing-Cheng Wang
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States.,Pharmacology, Case Western Reserve University, Cleveland, United States.,Rammelkamp Center for Research, MetroHealth Medical Center, Cleveland, United States
| | - Steven M Abel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, United States.,National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, United States
| | - Adam W Smith
- Department of Chemistry, University of Akron, Akron, United States
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
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Westerfield JM, Alves DS, Shi X, Nguyen VP, Pullen RH, Stefanski KM, Booth K, Morrell-Falvey J, Wang BC, Abel SM, Smith AW, Barrera FN. A Novel Membrane Peptide that Inhibits Cell Migration by Activation of the Receptor Tyrosine Kinase EphA2. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Stefanski KM, Gardner GE, Seipelt-Thiemann RL. Development of a Lac Operon Concept Inventory (LOCI). CBE Life Sci Educ 2016; 15:15/2/ar24. [PMID: 27252300 PMCID: PMC4909346 DOI: 10.1187/cbe.15-07-0162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 02/12/2016] [Accepted: 02/23/2016] [Indexed: 05/24/2023]
Abstract
Concept inventories (CIs) are valuable tools for educators that assess student achievement and identify misconceptions held by students. Results of student responses can be used to adjust or develop new instructional methods for a given topic. The regulation of gene expression in both prokaryotes and eukaryotes is an important concept in genetics and one that is particularly challenging for undergraduate students. As part of a larger study examining instructional methods related to gene regulation, the authors developed a 12-item CI assessing student knowledge of the lac operon. Using an established protocol, the authors wrote open-ended questions and conducted in-class testing with undergraduate microbiology and genetics students to discover common errors made by students about the lac operon and to determine aspects of item validity. Using these results, we constructed a 12-item multiple-choice lac operon CI called the Lac Operon Concept Inventory (LOCI), The LOCI was reviewed by two experts in the field for content validity. The LOCI underwent item analysis and was assessed for reliability with a sample of undergraduate genetics students (n = 115). The data obtained were found to be valid and reliable (coefficient alpha = 0.994) with adequate discriminatory power and item difficulty.
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Affiliation(s)
| | - Grant E Gardner
- Biology Department, Middle Tennessee State University, Murfreesboro, TN 37132 Math and Science Education Program, Middle Tennessee State University, Murfreesboro, TN 37132
| | - Rebecca L Seipelt-Thiemann
- Biology Department, Middle Tennessee State University, Murfreesboro, TN 37132 Math and Science Education Program, Middle Tennessee State University, Murfreesboro, TN 37132 Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN 37132
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