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Chaudhri EN, Abbott JM, Islam NN, Weber CA, Coban MA, Bilgili A, Squire JD, Mantia S, Wierenga KJ, Caulfield TR. Statistical Mechanics Metrics in Pairing and Parsing In Silico and Phenotypic Data of a Novel Genetic NFκB1 (c.T638A) Variant. Genes (Basel) 2023; 14:1855. [PMID: 37895204 PMCID: PMC10606260 DOI: 10.3390/genes14101855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
(1) Background: Mutations in NFκB1, a transcriptional regulator of immunomodulating proteins, are a known cause of inborn errors of immunity. Our proband is a 22-year-old male with a diagnosis of common variable immunodeficiency (CVID), cytopenias with massive splenomegaly, and nodular regenerative hyperplasia of the liver. Genetic studies identified a novel, single-point mutation variant in NFκB1, c. T638A p. V213E. (2) Methods: Next-generation panel sequencing of the patient uncovered a novel single-point mutation in the NFκB1 gene that was modeled using the I-TASSER homology-modeling software, and molecular dynamics were assessed using the YASARA2 software (version 20.14.24). (3) Results: This variant replaces valine with glutamic acid at position 213 in the NFκB1 sequence. Molecular modeling and molecular dynamic studies showed altered dynamics in and around the rel homology domain, ankyrin regions, and death domain of the protein. We postulate that these changes alter overall protein function. (4) Conclusions: This case suggests the pathogenicity of a novel variant using protein-modeling techniques and molecular dynamic simulations.
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Affiliation(s)
- Eman N. Chaudhri
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; (E.N.C.); (J.M.A.); (N.N.I.); (C.A.W.); (A.B.)
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Jessica M. Abbott
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; (E.N.C.); (J.M.A.); (N.N.I.); (C.A.W.); (A.B.)
| | - Naeyma N. Islam
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; (E.N.C.); (J.M.A.); (N.N.I.); (C.A.W.); (A.B.)
| | - Caleb A. Weber
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; (E.N.C.); (J.M.A.); (N.N.I.); (C.A.W.); (A.B.)
| | - Mathew A. Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA;
| | - Ahmet Bilgili
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; (E.N.C.); (J.M.A.); (N.N.I.); (C.A.W.); (A.B.)
| | | | - Sarah Mantia
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL 32224, USA (K.J.W.)
| | - Klaas J. Wierenga
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL 32224, USA (K.J.W.)
| | - Thomas R. Caulfield
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA; (E.N.C.); (J.M.A.); (N.N.I.); (C.A.W.); (A.B.)
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Li LX, Jiang LT, Pan YG, Zhang XL, Pan LZ, Nie ZY, Chen YH, Jin LJ. Clinical and Molecular Features of POLG-Related Sensory Ataxic Neuropathy with Dysarthria and Ophthalmoparesis. J Mol Neurosci 2021; 71:2462-2467. [PMID: 33791913 DOI: 10.1007/s12031-021-01831-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 03/15/2021] [Indexed: 10/21/2022]
Abstract
Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis (SANDO) is a rare mitochondrial disorder associated with mutations in the POLG gene, which encodes the DNA polymerase gamma catalytic subunit. A few POLG-related SANDO cases have been reported, but the genotype-phenotype correlation remains unclear. Here, we report a patient with SANDO carrying two novel missense variants (c.2543G>C, p.G848A and c.452 T>C, p.L151P) in POLG. We also reviewed previously reported cases to systematically evaluate the clinical and genetic features of POLG-related SANDO. A total of 35 distinct variants in the coding region of POLG were identified in 63 patients with SANDO. The most frequent variant was the p.A467T variant, followed by the p.W748S variant. The clinical spectrum of SANDO is heterogeneous. No clear correlation has been observed between the mutation types and clinical phenotypes. Our findings expand the mutational spectrum of POLG and contribute to clinical management and genetic counseling for POLG-related SANDO.
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Affiliation(s)
- Li-Xi Li
- Neurotoxin Research Center of Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Neurological Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Li-Ting Jiang
- Neurotoxin Research Center of Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Neurological Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - You-Gui Pan
- Neurotoxin Research Center of Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Neurological Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiao-Long Zhang
- Neurotoxin Research Center of Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Neurological Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Li-Zhen Pan
- Neurotoxin Research Center of Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Neurological Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhi-Yu Nie
- Neurotoxin Research Center of Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Neurological Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yu-Hui Chen
- Neurotoxin Research Center of Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Neurological Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ling-Jing Jin
- Neurotoxin Research Center of Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Neurological Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China.
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Coban MA, Fraga S, Caulfield TR. Structural And Computational Perspectives of Selectively Targeting Mutant Proteins. Curr Drug Discov Technol 2020; 18:365-378. [PMID: 32160847 DOI: 10.2174/1570163817666200311114819] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 11/22/2022]
Abstract
Diseases are often caused by mutant proteins. Many drugs have limited effectiveness and/or toxic side effects because of a failure to selectively target the disease-causing mutant variant, rather than the functional wild type protein. Otherwise, the drugs may even target different proteins with similar structural features. Designing drugs that successfully target mutant proteins selectively represents a major challenge. Decades of cancer research have led to an abundance of potential therapeutic targets, often touted to be "master regulators". For many of these proteins, there are no FDA-approved drugs available; for others, off-target effects result in dose-limiting toxicity. Cancer-related proteins are an excellent medium to carry the story of mutant-specific targeting, as the disease is both initiated and sustained by mutant proteins; furthermore, current chemotherapies generally fail at adequate selective distinction. This review discusses some of the challenges associated with selective targeting from a structural biology perspective, as well as some of the developments in algorithm approach and computational workflow that can be applied to address those issues. One of the most widely researched proteins in cancer biology is p53, a tumor suppressor. Here, p53 is discussed as a specific example of a challenging target, with contemporary drugs and methodologies used as examples of burgeoning successes. The oncogene KRAS, which has been described as "undruggable", is another extensively investigated protein in cancer biology. This review also examines KRAS to exemplify progress made towards selective targeting of diseasecausing mutant proteins. Finally, possible future directions relevant to the topic are discussed.
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Affiliation(s)
- Mathew A Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, 32224, United States
| | - Sarah Fraga
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, United States
| | - Thomas R Caulfield
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, 32224, United States
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Apolipoprotein E and Alzheimer disease: pathobiology and targeting strategies. Nat Rev Neurol 2019; 15:501-518. [PMID: 31367008 DOI: 10.1038/s41582-019-0228-7] [Citation(s) in RCA: 697] [Impact Index Per Article: 139.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2019] [Indexed: 02/06/2023]
Abstract
Polymorphism in the apolipoprotein E (APOE) gene is a major genetic risk determinant of late-onset Alzheimer disease (AD), with the APOE*ε4 allele conferring an increased risk and the APOE*ε2 allele conferring a decreased risk relative to the common APOE*ε3 allele. Strong evidence from clinical and basic research suggests that a major pathway by which APOE4 increases the risk of AD is by driving earlier and more abundant amyloid pathology in the brains of APOE*ε4 carriers. The number of amyloid-β (Aβ)-dependent and Aβ-independent pathways that are known to be differentially modulated by APOE isoforms is increasing. For example, evidence is accumulating that APOE influences tau pathology, tau-mediated neurodegeneration and microglial responses to AD-related pathologies. In addition, APOE4 is either pathogenic or shows reduced efficiency in multiple brain homeostatic pathways, including lipid transport, synaptic integrity and plasticity, glucose metabolism and cerebrovascular function. Here, we review the recent progress in clinical and basic research into the role of APOE in AD pathogenesis. We also discuss how APOE can be targeted for AD therapy using a precision medicine approach.
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Hines SL, Mohammad AN, Jackson J, Macklin S, Caulfield TR. Integrative data fusion for comprehensive assessment of a novel CHEK2 variant using combined genomics, imaging, and functional-structural assessments via protein informatics. Mol Omics 2019; 15:59-66. [PMID: 30633282 DOI: 10.1039/c8mo00137e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The CHEK2 gene and its encoded protein Chk2 have a well-known role in cancers, especially those related to breast cancer mediated through the BRCA1 gene. Additionally Chk2 has a crucial role in DNA repair, apoptosis and the cell cycle, which is why classification of variants of uncertain significance (VUS) is an area highly sought for a better elucidation of the "genomic effect" that results. Because it can often take years before enough clinical data is accumulated, and the costly and expensive functional analysis for individual variants presents a significant hurdle, it is important to identify other tools to help aid in clarifying the impact of specific variants on a protein's function and eventually the patient's health outcome. Here we describe a newly identified CHEK2 variant and analyze with an integrated approach combining genomics (whole exome analysis), clinical study, radiographic imaging, and protein informatics to identify and predict the functional impact of the VUS on the protein's behavior and predicted impact on the related pathways. The observed and analyzed defects in the protein were consistent with the expected clinical effect. Here, we support the use of personalized protein modeling and informatics and further our goal of developing a large-scale protein deposition archive for all protein-level VUS.
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Affiliation(s)
- Stephanie L Hines
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL 32224, USA
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Hines SL, Richter JE, Mohammad AN, Mahim J, Atwal PS, Caulfield TR. Protein informatics combined with multiple data sources enriches the clinical characterization of novel TRPV4 variant causing an intermediate skeletal dysplasia. Mol Genet Genomic Med 2019; 7:e566. [PMID: 30693671 PMCID: PMC6418443 DOI: 10.1002/mgg3.566] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 11/02/2018] [Accepted: 12/02/2018] [Indexed: 01/19/2023] Open
Abstract
Background Transient receptor potential cation channel subfamily V member 4 (TRPV4) is an ion channel permeable to Ca2+ that is sensitive to physical, hormonal, and chemical stimuli. This protein is expressed in many cell types, including osteoclasts, chondrocytes, and sensory neurons. As such, pathogenic variants of this gene are associated with skeletal dysplasias and neuromuscular disorders. Pathogenesis of these phenotypes is not yet completely understood, but it is known that genotype–phenotype correlations for TRPV4 pathogenic variants often are not present. Methods Newly characterized, suspected pathogenic variant in TRPV4 was analyzed using protein informatics and personalized protein‐level molecular studies, genomic exome analysis, and clinical study. Results This statement is demonstrated in the family of our proband, a 47‐year‐old female having the novel c.2401A>G (p.K801E) variant of TRPV4. We discuss the common symptoms between the proband, her father, and her daughter, and compare her phenotype to known TRPV4‐associated skeletal dysplasias. Conclusions Protein informatics and molecular modeling are used to confirm the pathogenicity of the unique TRPV4 variant found in this family. Multiple data were combined in a comprehensive manner to give complete overall perspective on the patient disease and prognosis.
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Affiliation(s)
- Stephanie L Hines
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida.,Department of General Internal Medicine, Mayo Clinic, Jacksonville, Florida.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, Florida
| | - John E Richter
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida
| | - Ahmed N Mohammad
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida
| | - Jain Mahim
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, Maryland
| | | | - Thomas R Caulfield
- Center for Individualized Medicine, Mayo Clinic, Jacksonville, Florida.,Department of Neuroscience, Mayo Clinic, Jacksonville, Florida.,Mayo Graduate School, Neurobiology of Disease, Mayo Clinic, Jacksonville, Florida
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