1
|
Hack JB, Horning K, Juroske Short DM, Schreiber JM, Watkins JC, Hammer MF. Distinguishing Loss-of-Function and Gain-of-Function SCN8A Variants Using a Random Forest Classification Model Trained on Clinical Features. Neurol Genet 2023; 9:e200060. [PMID: 37152443 PMCID: PMC10160958 DOI: 10.1212/nxg.0000000000200060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/12/2023] [Indexed: 05/09/2023]
Abstract
Background and Objectives Pathogenic variants at the voltage-gated sodium channel gene, SCN8A, are associated with a wide spectrum of clinical disease outcomes. A critical challenge for neurologists is to determine whether patients carry gain-of-function (GOF) or loss-of-function (LOF) variants to guide treatment decisions, yet in vitro studies to infer channel function are often not feasible in the clinic. In this study, we develop a predictive modeling approach to classify variants based on clinical features present at initial diagnosis. Methods We performed an exhaustive search for individuals deemed to carry SCN8A GOF and LOF variants by means of in vitro studies in heterologous cell systems, or because the variant was classified as truncating, and recorded clinical features. This resulted in a total of 69 LOF variants: 34 missense and 35 truncating variants, including 9 nonsense, 13 frameshift, 6 splice site, 6 indels, and 1 large deletion. We then assembled a truth set of variants with known functional effects, excluding individuals carrying variants at other loci associated with epilepsy. We then trained a predictive model based on random forest using this truth set of 45 LOF variants and 45 GOF variants randomly selected from a set of variants tested by in vitro methods. Results Phenotypic categories assigned to individuals correlated strongly with GOF or LOF variants. All patients with GOF variants experienced early-onset seizures (mean age at onset = 4.5 ± 3.1 months) while only 64.4% patients with LOF variants had seizures, most of which were late-onset absence seizures (mean age at onset = 40.0 ± 38.1 months). With high accuracy (95.4%), our model including 5 key clinical features classified individuals with GOF and LOF variants into 2 distinct cohorts differing in age at seizure onset, development of seizures, seizure type, intellectual disability, and developmental and epileptic encephalopathy. Discussion The results support the hypothesis that patients with SCN8A GOF and LOF variants represent distinct clinical phenotypes. The clinical model developed in this study has great utility because it provides a rapid and highly accurate platform for predicting the functional class of patient variants during SCN8A diagnosis, which can aid in initial treatment decisions and improve prognosis.
Collapse
Affiliation(s)
- Joshua B Hack
- BIO5 Institute (J.B.H., M.F.H.), University of Arizona, Tucson; CombinedBrain (K.H.), Brentwood; DenGen Consulting (D.M.J.S.), Rocky Top, TN; Children's National Medical Center (J.M.S.), Department of Neurology, Washington, DC; Department of Mathematics (J.C.W.), University of Arizona; and Neurology Department (M.F.H.), University of Arizona, Tucson
| | - Kyle Horning
- BIO5 Institute (J.B.H., M.F.H.), University of Arizona, Tucson; CombinedBrain (K.H.), Brentwood; DenGen Consulting (D.M.J.S.), Rocky Top, TN; Children's National Medical Center (J.M.S.), Department of Neurology, Washington, DC; Department of Mathematics (J.C.W.), University of Arizona; and Neurology Department (M.F.H.), University of Arizona, Tucson
| | - Denise M Juroske Short
- BIO5 Institute (J.B.H., M.F.H.), University of Arizona, Tucson; CombinedBrain (K.H.), Brentwood; DenGen Consulting (D.M.J.S.), Rocky Top, TN; Children's National Medical Center (J.M.S.), Department of Neurology, Washington, DC; Department of Mathematics (J.C.W.), University of Arizona; and Neurology Department (M.F.H.), University of Arizona, Tucson
| | - John M Schreiber
- BIO5 Institute (J.B.H., M.F.H.), University of Arizona, Tucson; CombinedBrain (K.H.), Brentwood; DenGen Consulting (D.M.J.S.), Rocky Top, TN; Children's National Medical Center (J.M.S.), Department of Neurology, Washington, DC; Department of Mathematics (J.C.W.), University of Arizona; and Neurology Department (M.F.H.), University of Arizona, Tucson
| | - Joseph C Watkins
- BIO5 Institute (J.B.H., M.F.H.), University of Arizona, Tucson; CombinedBrain (K.H.), Brentwood; DenGen Consulting (D.M.J.S.), Rocky Top, TN; Children's National Medical Center (J.M.S.), Department of Neurology, Washington, DC; Department of Mathematics (J.C.W.), University of Arizona; and Neurology Department (M.F.H.), University of Arizona, Tucson
| | - Michael F Hammer
- BIO5 Institute (J.B.H., M.F.H.), University of Arizona, Tucson; CombinedBrain (K.H.), Brentwood; DenGen Consulting (D.M.J.S.), Rocky Top, TN; Children's National Medical Center (J.M.S.), Department of Neurology, Washington, DC; Department of Mathematics (J.C.W.), University of Arizona; and Neurology Department (M.F.H.), University of Arizona, Tucson
| |
Collapse
|
2
|
Li S, Fernandez JJ, Fabritius AS, Agard DA, Winey M. Electron cryo-tomography structure of axonemal doublet microtubule from Tetrahymena thermophila. Life Sci Alliance 2022; 5:5/3/e202101225. [PMID: 34969817 PMCID: PMC8742875 DOI: 10.26508/lsa.202101225] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 11/24/2022] Open
Abstract
Doublet microtubules (DMTs) provide a scaffold for axoneme assembly in motile cilia. Aside from α/β tubulins, the DMT comprises a large number of non-tubulin proteins in the luminal wall of DMTs, collectively named the microtubule inner proteins (MIPs). We used cryoET to study axoneme DMT isolated from Tetrahymena We present the structures of DMT at nanometer and sub-nanometer resolution. The structures confirm that MIP RIB72A/B binds to the luminal wall of DMT by multiple DM10 domains. We found FAP115, an MIP-containing multiple EF-hand domains, located at the interface of four-tubulin dimers in the lumen of A-tubule. It contacts both lateral and longitudinal tubulin interfaces and playing a critical role in DMT stability. We observed substantial structure heterogeneity in DMT in an FAP115 knockout strain, showing extensive structural defects beyond the FAP115-binding site. The defects propagate along the axoneme. Finally, by comparing DMT structures from Tetrahymena and Chlamydomonas, we have identified a number of conserved MIPs as well as MIPs that are unique to each organism. This conservation and diversity of the DMT structures might be linked to their specific functions. Our work provides structural insights essential for understanding the roles of MIPs during motile cilium assembly and function, as well as their relationships to human ciliopathies.
Collapse
Affiliation(s)
- Sam Li
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Jose-Jesus Fernandez
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Health Research Institute of Asturias (ISPA), Oviedo, Spain
| | - Amy S Fabritius
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA, USA
| | - David A Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Mark Winey
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA, USA
| |
Collapse
|
3
|
Gui M, Farley H, Anujan P, Anderson JR, Maxwell DW, Whitchurch JB, Botsch JJ, Qiu T, Meleppattu S, Singh SK, Zhang Q, Thompson J, Lucas JS, Bingle CD, Norris DP, Roy S, Brown A. De novo identification of mammalian ciliary motility proteins using cryo-EM. Cell 2021; 184:5791-5806.e19. [PMID: 34715025 PMCID: PMC8595878 DOI: 10.1016/j.cell.2021.10.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/12/2021] [Accepted: 10/07/2021] [Indexed: 12/15/2022]
Abstract
Dynein-decorated doublet microtubules (DMTs) are critical components of the oscillatory molecular machine of cilia, the axoneme, and have luminal surfaces patterned periodically by microtubule inner proteins (MIPs). Here we present an atomic model of the 48-nm repeat of a mammalian DMT, derived from a cryoelectron microscopy (cryo-EM) map of the complex isolated from bovine respiratory cilia. The structure uncovers principles of doublet microtubule organization and features specific to vertebrate cilia, including previously unknown MIPs, a luminal bundle of tektin filaments, and a pentameric dynein-docking complex. We identify a mechanism for bridging 48- to 24-nm periodicity across the microtubule wall and show that loss of the proteins involved causes defective ciliary motility and laterality abnormalities in zebrafish and mice. Our structure identifies candidate genes for diagnosis of ciliopathies and provides a framework to understand their functions in driving ciliary motility.
Collapse
Affiliation(s)
- Miao Gui
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Hannah Farley
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Priyanka Anujan
- Institute of Molecular and Cell Biology, Proteos, 138673 Singapore, Singapore; Department of Infection, Immunity & Cardiovascular Disease, The Medical School and The Florey Institute for Host Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, UK
| | - Jacob R Anderson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Dale W Maxwell
- Institute of Molecular and Cell Biology, Proteos, 138673 Singapore, Singapore; School of Biological Sciences, University of Manchester, Manchester M13 9PT, UK
| | | | - J Josephine Botsch
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Tao Qiu
- Institute of Molecular and Cell Biology, Proteos, 138673 Singapore, Singapore
| | - Shimi Meleppattu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Sandeep K Singh
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Qi Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James Thompson
- Biomedical Imaging Unit, Southampton General Hospital, Southampton, UK; Primary Ciliary Dyskinesia Centre, NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Jane S Lucas
- Primary Ciliary Dyskinesia Centre, NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK; University of Southampton Faculty of Medicine, School of Clinical and Experimental Medicine, Southampton, UK
| | - Colin D Bingle
- Department of Infection, Immunity & Cardiovascular Disease, The Medical School and The Florey Institute for Host Pathogen Interactions, University of Sheffield, Sheffield S10 2TN, UK
| | - Dominic P Norris
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK.
| | - Sudipto Roy
- Institute of Molecular and Cell Biology, Proteos, 138673 Singapore, Singapore; Department of Biological Sciences, National University of Singapore, 117543 Singapore, Singapore; Department of Pediatrics, Yong Loo Ling School of Medicine, National University of Singapore, 1E Kent Ridge Road, 119288 Singapore, Singapore.
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|