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Mukherjee S, Cassini TA, Hu N, Yang T, Li B, Shen W, Moth CW, Rinker DC, Sheehan JH, Cogan JD, Newman JH, Hamid R, Macdonald RL, Roden DM, Meiler J, Kuenze G, Phillips JA, Capra JA. Personalized structural biology reveals the molecular mechanisms underlying heterogeneous epileptic phenotypes caused by de novo KCNC2 variants. HGG Adv 2022; 3:100131. [PMID: 36035247 PMCID: PMC9399384 DOI: 10.1016/j.xhgg.2022.100131] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/11/2022] [Indexed: 11/28/2022] Open
Abstract
Whole-exome sequencing (WES) in the clinic has identified several rare monogenic developmental and epileptic encephalopathies (DEE) caused by ion channel variants. However, WES often fails to provide actionable insight for rare diseases, such as DEEs, due to the challenges of interpreting variants of unknown significance (VUS). Here, we describe a "personalized structural biology" (PSB) approach that leverages recent innovations in the analysis of protein 3D structures to address this challenge. We illustrate this approach in an Undiagnosed Diseases Network (UDN) individual with DEE symptoms and a de novo VUS in KCNC2 (p.V469L), the Kv3.2 voltage-gated potassium channel. A nearby KCNC2 variant (p.V471L) was recently suggested to cause DEE-like phenotypes. Computational structural modeling suggests that both affect protein function. However, despite their proximity, the p.V469L variant is likely to sterically block the channel pore, while the p.V471L variant is likely to stabilize the open state. Biochemical and electrophysiological analyses demonstrate heterogeneous loss-of-function and gain-of-function effects, as well as differential response to 4-aminopyridine treatment. Molecular dynamics simulations illustrate that the pore of the p.V469L variant is more constricted, increasing the energetic barrier for K+ permeation, whereas the p.V471L variant stabilizes the open conformation. Our results implicate variants in KCNC2 as causative for DEE and guide the interpretation of a UDN individual. They further delineate the molecular basis for the heterogeneous clinical phenotypes resulting from two proximal pathogenic variants. This demonstrates how the PSB approach can provide an analytical framework for individualized hypothesis-driven interpretation of protein-coding VUS.
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Affiliation(s)
- Souhrid Mukherjee
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Thomas A. Cassini
- Department of Internal Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20814, USA
| | - Ningning Hu
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Tao Yang
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Bian Li
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Wangzhen Shen
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Christopher W. Moth
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - David C. Rinker
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Jonathan H. Sheehan
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- John T. Milliken Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joy D. Cogan
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Undiagnosed Diseases Network
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Pulmonary Hypertension Center, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- John T. Milliken Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Internal Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20814, USA
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, SAC 04103, Germany
- Department of Chemistry, Leipzig University, Leipzig, SAC 04109, Germany
- Department of Computer Science, Leipzig University, Leipzig, SAC 04109, Germany
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John H. Newman
- Pulmonary Hypertension Center, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rizwan Hamid
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Robert L. Macdonald
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Dan M. Roden
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, SAC 04103, Germany
- Department of Chemistry, Leipzig University, Leipzig, SAC 04109, Germany
- Department of Computer Science, Leipzig University, Leipzig, SAC 04109, Germany
| | - Georg Kuenze
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, SAC 04103, Germany
| | - John A. Phillips
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - John A. Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
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Hanker AB, Brown BP, Meiler J, Marín A, Jayanthan HS, Ye D, Lin CC, Akamatsu H, Lee KM, Chatterjee S, Sudhan DR, Servetto A, Brewer MR, Koch JP, Sheehan JH, He J, Lalani AS, Arteaga CL. Co-occurring gain-of-function mutations in HER2 and HER3 modulate HER2/HER3 activation, oncogenesis, and HER2 inhibitor sensitivity. Cancer Cell 2021; 39:1099-1114.e8. [PMID: 34171264 PMCID: PMC8355076 DOI: 10.1016/j.ccell.2021.06.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/28/2021] [Accepted: 06/02/2021] [Indexed: 12/24/2022]
Abstract
Activating mutations in HER2 (ERBB2) drive the growth of a subset of breast and other cancers and tend to co-occur with HER3 (ERBB3) missense mutations. The HER2 tyrosine kinase inhibitor neratinib has shown clinical activity against HER2-mutant tumors. To characterize the role of HER3 mutations in HER2-mutant tumors, we integrate computational structural modeling with biochemical and cell biological analyses. Computational modeling predicts that the frequent HER3E928G kinase domain mutation enhances the affinity of HER2/HER3 and reduces binding of HER2 to its inhibitor neratinib. Co-expression of mutant HER2/HER3 enhances HER2/HER3 co-immunoprecipitation and ligand-independent activation of HER2/HER3 and PI3K/AKT, resulting in enhanced growth, invasiveness, and resistance to HER2-targeted therapies, which can be reversed by combined treatment with PI3Kα inhibitors. Our results provide a mechanistic rationale for the evolutionary selection of co-occurring HER2/HER3 mutations and the recent clinical observations that HER3 mutations are associated with a poor response to neratinib in HER2-mutant cancers.
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MESH Headings
- Aminopyridines/administration & dosage
- Animals
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Cell Line, Tumor
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Female
- Gain of Function Mutation
- Humans
- Mice, Nude
- Molecular Docking Simulation
- Molecular Dynamics Simulation
- Morpholines/administration & dosage
- Phosphatidylinositol 3-Kinases/metabolism
- Phosphoinositide-3 Kinase Inhibitors/administration & dosage
- Protein Multimerization
- Quinolines/administration & dosage
- Quinolines/chemistry
- Quinolines/metabolism
- Quinolines/pharmacology
- Receptor, ErbB-2/antagonists & inhibitors
- Receptor, ErbB-2/chemistry
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Receptor, ErbB-3/chemistry
- Receptor, ErbB-3/genetics
- Receptor, ErbB-3/metabolism
- Trastuzumab/pharmacology
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
- Ariella B Hanker
- UTSW Simmons Comprehensive Cancer Center, Dallas, 5323 Harry Hines Boulevard, TX 75390, USA; Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Benjamin P Brown
- Chemical and Physical Biology Program, Center for Structural Biology, and Medical Scientist Training Program, Vanderbilt University, Nashville, TN 37240, USA
| | - Jens Meiler
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA; Institute for Drug Discovery, Leipzig University Medical School, Leipzig, SAC 04103, Germany
| | - Arnaldo Marín
- UTSW Simmons Comprehensive Cancer Center, Dallas, 5323 Harry Hines Boulevard, TX 75390, USA; Doctoral Program in Medical Sciences, Faculty of Medicine, University of Chile, Santiago 8380453, Chile
| | - Harikrishna S Jayanthan
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Dan Ye
- UTSW Simmons Comprehensive Cancer Center, Dallas, 5323 Harry Hines Boulevard, TX 75390, USA
| | - Chang-Ching Lin
- UTSW Simmons Comprehensive Cancer Center, Dallas, 5323 Harry Hines Boulevard, TX 75390, USA
| | - Hiroaki Akamatsu
- UTSW Simmons Comprehensive Cancer Center, Dallas, 5323 Harry Hines Boulevard, TX 75390, USA
| | - Kyung-Min Lee
- UTSW Simmons Comprehensive Cancer Center, Dallas, 5323 Harry Hines Boulevard, TX 75390, USA; Department of Life Sciences, College of Natural Science, Hanyang University, Seoul 04736, Republic of Korea
| | - Sumanta Chatterjee
- UTSW Simmons Comprehensive Cancer Center, Dallas, 5323 Harry Hines Boulevard, TX 75390, USA
| | - Dhivya R Sudhan
- UTSW Simmons Comprehensive Cancer Center, Dallas, 5323 Harry Hines Boulevard, TX 75390, USA
| | - Alberto Servetto
- UTSW Simmons Comprehensive Cancer Center, Dallas, 5323 Harry Hines Boulevard, TX 75390, USA
| | - Monica Red Brewer
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - James P Koch
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jonathan H Sheehan
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jie He
- Foundation Medicine, Cambridge, MA 02141, USA
| | | | - Carlos L Arteaga
- UTSW Simmons Comprehensive Cancer Center, Dallas, 5323 Harry Hines Boulevard, TX 75390, USA; Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
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