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Chaudhari S, Acharya LP, Jasti DB, Ware AP, Gorthi SP, Satyamoorthy K. Discovery of a Novel Shared Variant Among RTEL1 Gene and RTEL1-TNFRSF6B lncRNA at Chromosome 20q13.33 in Familial Progressive Myoclonus Epilepsy. Int J Genomics 2024; 2024:7518528. [PMID: 39156922 PMCID: PMC11330336 DOI: 10.1155/2024/7518528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 04/17/2024] [Accepted: 07/20/2024] [Indexed: 08/20/2024] Open
Abstract
Background: Progressive myoclonus epilepsy (PME) is a neurodegenerative disorder marked by recurrent seizures and progressive myoclonus. To date, based on the phenotypes and causal genes, more than 40 subtypes of PMEs have been identified, and more remain to be characterized. Our study is aimed at identifying the aberrant gene(s) possibly associated with PMEs in two siblings born to asymptomatic parents, in the absence of known genetic mutations. Methods: Clinical assessments and molecular analyses, such as the repeat expansion test for CSTB; SCA1, 2, 3, 6, and 7; whole exome sequencing (WES); and mitochondrial genome sequencing coupled with computational analysis, were performed. Results: A family-based segregation analysis of WES data was performed to identify novel genes associated with PMEs. The potassium channel, KCNH8 [c.298T>C; (p.Tyr100His)], a DNA repair gene, regulator of telomere elongation helicase 1 (RTEL1) [c.691G>T; (p.Asp231Tyr)] and long noncoding RNA, RTEL1-TNFRSF6B [chr20:62298898_G>T; NR_037882.1, hg19] were among the candidate genes that were found to be associated with PMEs. These homozygous variations in siblings belong to genes with a loss-of-function intolerant (pLI) score of ≤ 0.86, expected to be detrimental by multiple computational analyses, and were heterozygous in parents. Additionally, computational analysis and the expression of RTEL1 and RTEL1-TNFRSF6B revealed that RTEL1-TNFRSF6B may modulate RTEL1 via hsa-miR-3529-3p. In the patient with the severe phenotype, a further deleterious mutation in SLC22A17 was identified. No de novo variants specific to these probands were identified in the mitochondrial genome. Conclusions: Our study is the first to report variants in KCNH8, RTEL1, and RTEL1-TNFRSF6B among PME cases. These genes when characterized fully may shed light on pathogenicity and have the potential to be used in the diagnosis of PME.
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Affiliation(s)
- Sima Chaudhari
- Department of Cell and Molecular BiologyManipal School of Life SciencesManipal Academy of Higher Education 576104, Manipal, Karnataka, India
| | - Lavanya Prakash Acharya
- Department of Cell and Molecular BiologyManipal School of Life SciencesManipal Academy of Higher Education 576104, Manipal, Karnataka, India
| | - Dushyanth Babu Jasti
- Department of NeurologyKasturba Medical College 576104, Manipal, Karnataka, India
| | - Akshay Pramod Ware
- Department of BioinformaticsManipal School of Life SciencesManipal Academy of Higher Education 576104, Manipal, Karnataka, India
| | - Sankar Prasad Gorthi
- Department of NeurologyKasturba Medical College 576104, Manipal, Karnataka, India
- Department of NeurologyBharati Hospital and Research CenterBharati Vidyapeeth (Deemed to Be University) Medical College and Hospital, Dhankawadi 411043, Pune, Maharashtra, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular BiologyManipal School of Life SciencesManipal Academy of Higher Education 576104, Manipal, Karnataka, India
- SDM College of Medical Sciences and HospitalShri Dharmasthala Manjunatheshwara (SDM) University, Manjushree Nagar, Sattur 580009, Dharwad, Karnataka, India
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Immadisetty K, Fang X, Ramon GS, Hartle CM, McCoy TP, Center RG, Mirshahi T, Delisle BP, Kekenes-Huskey PM. Prediction of Kv11.1 potassium channel PAS-domain variants trafficking via machine learning. J Mol Cell Cardiol 2023; 180:69-83. [PMID: 37187232 DOI: 10.1016/j.yjmcc.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 04/28/2023] [Accepted: 05/09/2023] [Indexed: 05/17/2023]
Abstract
Congenital long QT syndrome (LQTS) is characterized by a prolonged QT-interval on an electrocardiogram (ECG). An abnormal prolongation in the QT-interval increases the risk for fatal arrhythmias. Genetic variants in several different cardiac ion channel genes, including KCNH2, are known to cause LQTS. Here, we evaluated whether structure-based molecular dynamics (MD) simulations and machine learning (ML) could improve the identification of missense variants in LQTS-linked genes. To do this, we investigated KCNH2 missense variants in the Kv11.1 channel protein shown to have wild type (WT) like or class II (trafficking-deficient) phenotypes in vitro. We focused on KCNH2 missense variants that disrupt normal Kv11.1 channel protein trafficking, as it is the most common phenotype for LQTS-associated variants. Specifically, we used computational techniques to correlate structural and dynamic changes in the Kv11.1 channel protein PAS domain (PASD) with Kv11.1 channel protein trafficking phenotypes. These simulations unveiled several molecular features, including the numbers of hydrating waters and hydrogen bonding pairs, as well as folding free energy scores, that are predictive of trafficking. We then used statistical and machine learning (ML) (Decision tree (DT), Random forest (RF), and Support vector machine (SVM)) techniques to classify variants using these simulation-derived features. Together with bioinformatics data, such as sequence conservation and folding energies, we were able to predict with reasonable accuracy (≈75%) which KCNH2 variants do not traffic normally. We conclude that structure-based simulations of KCNH2 variants localized to the Kv11.1 channel PASD led to an improvement in classification accuracy. Therefore, this approach should be considered to complement the classification of variant of unknown significance (VUS) in the Kv11.1 channel PASD.
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Affiliation(s)
| | - Xuan Fang
- Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
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de Souza JV, Reznikov S, Zhu R, Bronowska AK. Druggability assessment of mammalian Per-Arnt-Sim [PAS] domains using computational approaches. MEDCHEMCOMM 2019; 10:1126-1137. [PMID: 31391885 PMCID: PMC6640724 DOI: 10.1039/c9md00148d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 05/01/2019] [Indexed: 01/10/2023]
Abstract
Per-Arnt-Sim (PAS) domains are key regions that occur in different regulatory proteins from all kingdoms of life. PAS domains show a remarkably conserved structural scaffold, despite a highly variable primary sequence. In this study we have attempted to address some of the gaps in knowledge regarding the druggability of PAS-A domains, differences in structure and dynamics within the PAS domain family and how this affects the druggability potential, as well as give insight into the druggability of steroid receptor coactivators and putative binding modes of the NCOA1. Investigations were performed through a range of computational methods including molecular docking studies, atomistic molecular dynamics simulations, and hotspot mapping. Atomistic molecular dynamics simulations show that the function of the AhR PAS-B domain is regulated by the dynamics of the highly conserved tyrosine Y322 residue, which acts as a "gatekeeper" controlling the access to the binding cavity and finely tuning the binding affinity. Furthermore, the transition between the partially unfolded and helical conformation of the loop1 segment within PAS-B domains was shown to be essential for the generation of "druggable" sites, especially for the NCOA1 PAS-B domain. Finally, our simulations indicated the undruggability of PAS-A domains, caused by the inherent characteristics of their putative binding sites. In conclusion, this work emphasises the role of intrinsic dynamics in tuning the druggability of PAS-B domains and shows that PAS-B domains of steroid receptor coactivators, such as NCOA1, can be targeted by small molecule ligands, which highlights the potential of developing new therapeutics designed to target these coactivators using structure-based approaches.
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Affiliation(s)
- João V de Souza
- School of Natural and Environmental Sciences , Newcastle University , NE1 7RU Newcastle , UK .
| | - Sylvia Reznikov
- School of Natural and Environmental Sciences , Newcastle University , NE1 7RU Newcastle , UK .
| | - Ruidi Zhu
- School of Natural and Environmental Sciences , Newcastle University , NE1 7RU Newcastle , UK .
| | - Agnieszka K Bronowska
- School of Natural and Environmental Sciences , Newcastle University , NE1 7RU Newcastle , UK .
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Zangari A, Micheli D, Galeazzi R, Tozzi A. Node of Ranvier as an Array of Bio-Nanoantennas for Infrared Communication in Nerve Tissue. Sci Rep 2018; 8:539. [PMID: 29323217 PMCID: PMC5764955 DOI: 10.1038/s41598-017-18866-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/18/2017] [Indexed: 01/21/2023] Open
Abstract
Electromagnetic radiation, in the visible and infrared spectrum, is increasingly being investigated for its possible role in the most evolved brain capabilities. Beside experimental evidence of electromagnetic cellular interactions, the possibility of light propagation in the axon has been recently demonstrated using computational modelling, although an explanation of its source is still not completely understood. We studied electromagnetic radiation onset and propagation at optical frequencies in myelinated axons, under the assumption that ion channel currents in the node of Ranvier behave like an array of nanoantennas emitting in the wavelength range from 300 to 2500 nm. Our results suggest that the wavelengths below 1600 nm are most likely to propagate throughout myelinated segments. Therefore, a broad wavelength window exists where both generation and propagation could happen, which in turn raises the possibility that such a radiation may play some role in neurotransmission.
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Affiliation(s)
- Andrea Zangari
- Azienda Ospedaliera San Camillo Forlanini, Pediatric Surgery and Urology Unit, Circonvallazione Gianicolense 87-00152, Roma, Italy
| | - Davide Micheli
- TIM S.P.A., Wireless Access Engineering Department, Viale Parco de' Medici, 61 - 00148, Roma, Italy.
| | - Roberta Galeazzi
- Dipartimento di Scienze della Vita e dell'Ambiente, università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Antonio Tozzi
- UOC Fisica Sanitaria, Azienda USL Toscana Sud Est, via Senese 161, 58100, Grosseto, Italy
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Eag1 Voltage-Dependent Potassium Channels: Structure, Electrophysiological Characteristics, and Function in Cancer. J Membr Biol 2017; 250:123-132. [DOI: 10.1007/s00232-016-9944-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 12/19/2016] [Indexed: 01/07/2023]
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