Whole exome sequencing and co-expression analysis identify an SCN1A variant that modifies pathogenicity in a family with genetic epilepsy and febrile seizures plus

Michael F. Hammer; Yanling Pan; Medhane Cumbay; Manuela Pendziwiat; Zaid Afawi; Hadassah Goldberg-Stern; Laurel Johnstone; Ingo Helbig; Theodore R. Cummins

doi:10.1111/epi.17296

Whole exome sequencing and co-expression analysis identify an SCN1A variant that modifies pathogenicity in a family with genetic epilepsy and febrile seizures plus

Michael F. Hammer, Yanling Pan, Medhane Cumbay, Manuela Pendziwiat, Zaid Afawi, Hadassah Goldberg-Stern, Laurel Johnstone, Ingo Helbig, Theodore R. Cummins

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

Abstract

Objective: Family members carrying the same SCN1A variant often exhibit differences in the clinical severity of epilepsy. This variable expressivity suggests that other factors aside from the primary sodium channel variant influence the clinical manifestation. However, identifying such factors has proven challenging in humans. Methods: We perform whole exome sequencing (WES) in a large family in which an SCN1A variant (p.K1372E) is segregating that is associated with a broad spectrum of phenotypes ranging from lack of epilepsy, to febrile seizures and absence seizures, to Dravet syndrome. We assessed the hypothesis that the severity of the SCN1A-related phenotype was affected by alternate alleles at a modifier locus (or loci). Results: One of our top candidates identified by WES was a second variant in the SCN1A gene (p.L375S) that was shared exclusively by unaffected carriers of the K1372E allele. To test the hypothesized that L375S variant nullifies the loss-of-function effect of K1372E, we transiently expressed Nav1.1 carrying the two variants in HEK293T cells and compared their biophysical properties with the wild-type (WT) variant, and then co-expressed WT with K1372E or L375S with K1372E in equal quantity and tested the functional consequence. The data demonstrated that co-expression of the L375S and K1372E alleles reversed the loss-of-function property brought by the K1372E variant, whereas WT-K1372E co-expression remained partial loss-of-function. Significance: These results support the hypothesis that L375S counteracts the loss-of-function effect of K1372E such that individuals carrying both alleles in trans do not present epilepsy-related symptoms. We demonstrate that monogenic epilepsies with wide expressivity can be modified by additional variants in the disease gene, providing a novel framework for the gene-phenotype relationship in genetic epilepsies.

Original language	English
Pages (from-to)	1970-1980
Number of pages	11
Journal	Epilepsia
Volume	63
Issue number	8
DOIs	https://doi.org/10.1111/epi.17296
State	Published - Aug 2022
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2022 International League Against Epilepsy.

Funding

Research reported in this publication was supported by a Dravet Syndrome Foundation grant to MFH. The content is solely the responsibility of the authors and does not necessarily represent the official views of the Dravet Syndrome Foundation. TRC and YP were partially supported by the National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH) award U54NS108874. I.H. was supported by The Hartwell Foundation through an Individual Biomedical Research Award. This work was also supported by the NINDS (K02 NS112600), the Eunice Kennedy Shriver National Institute of Child Health and Human Development through the Intellectual and Developmental Disabilities Research Center (IDDRC) at Children's Hospital of Philadelphia and the University of Pennsylvania (U54 HD086984), and by intramural funds of the Children's Hospital of Philadelphia through the Epilepsy NeuroGenetics Initiative (ENGIN). Research reported in this publication was also supported by the National Center for Advancing Translational Sciences of the NIH under Award Number UL1TR001878. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. This project was also supported in part by the Institute for Translational Medicine and Therapeutics' (ITMAT) Transdisciplinary Program in Translational Medicine and Therapeutics at the Perelman School of Medicine of the University of Pennsylvania. The study also received support through the EuroEPINOMICS-Rare Epilepsy Syndrome (RES) Consortium, and by the German Research Foundation (DFG; HE5415/3-1, HE5415/5-1, HE5415/6-1 to I.H.), including the DFG/FNR INTER Research Unit FOR2715 (He5415/7-1 to I.H.) Research reported in this publication was supported by a Dravet Syndrome Foundation grant to MFH. The content is solely the responsibility of the authors and does not necessarily represent the official views of the Dravet Syndrome Foundation. TRC and YP were partially supported by the National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH) award U54NS108874. I.H. was supported by The Hartwell Foundation through an Individual Biomedical Research Award. This work was also supported by the NINDS (K02 NS112600), the Eunice Kennedy Shriver National Institute of Child Health and Human Development through the Intellectual and Developmental Disabilities Research Center (IDDRC) at Children's Hospital of Philadelphia and the University of Pennsylvania (U54 HD086984), and by intramural funds of the Children's Hospital of Philadelphia through the Epilepsy NeuroGenetics Initiative (ENGIN). Research reported in this publication was also supported by the National Center for Advancing Translational Sciences of the NIH under Award Number UL1TR001878. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. This project was also supported in part by the Institute for Translational Medicine and Therapeutics' (ITMAT) Transdisciplinary Program in Translational Medicine and Therapeutics at the Perelman School of Medicine of the University of Pennsylvania. The study also received support through the EuroEPINOMICS‐Rare Epilepsy Syndrome (RES) Consortium, and by the German Research Foundation (DFG; HE5415/3‐1, HE5415/5‐1, HE5415/6‐1 to I.H.), including the DFG/FNR INTER Research Unit FOR2715 (He5415/7‐1 to I.H.)

Funders	Funder number
Epilepsy NeuroGenetics Initiative
EuroEPINOMICS-Rare Epilepsy Syndrome
EuroEPINOMICS‐Rare Epilepsy Syndrome
National Institutes of Health
National Institute of Neurological Disorders and Stroke	U54NS108874
National Institute of Child Health and Human Development	U54HD086984
California Department of Fish and Game	HE5415/6‐1, HE5415/5‐1, HE5415/3‐1
National Center for Advancing Translational Sciences	UL1TR001878
Children's Hospital of Philadelphia
Hartwell Foundation	K02 NS112600
University of Pennsylvania	U54 HD086984
Intellectual and Developmental Disabilities Research Center
Department of Forestry and Natural Resources, Purdue University	He5415/7‐1
Perelman School of Medicine, University of Pennsylvania
Institute for Translational Medicine and Therapeutics
Eunice Kennedy Shriver National Institute of Child Health and Human Development
Dravet Syndrome Foundation
Deutsche Forschungsgemeinschaft

Keywords

SCN1A-related epilepsy
biophysical properties
co-expressed variants
modifier gene
whole exome sequencing

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10.1111/epi.17296

Cite this

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title = "Whole exome sequencing and co-expression analysis identify an SCN1A variant that modifies pathogenicity in a family with genetic epilepsy and febrile seizures plus",

abstract = "Objective: Family members carrying the same SCN1A variant often exhibit differences in the clinical severity of epilepsy. This variable expressivity suggests that other factors aside from the primary sodium channel variant influence the clinical manifestation. However, identifying such factors has proven challenging in humans. Methods: We perform whole exome sequencing (WES) in a large family in which an SCN1A variant (p.K1372E) is segregating that is associated with a broad spectrum of phenotypes ranging from lack of epilepsy, to febrile seizures and absence seizures, to Dravet syndrome. We assessed the hypothesis that the severity of the SCN1A-related phenotype was affected by alternate alleles at a modifier locus (or loci). Results: One of our top candidates identified by WES was a second variant in the SCN1A gene (p.L375S) that was shared exclusively by unaffected carriers of the K1372E allele. To test the hypothesized that L375S variant nullifies the loss-of-function effect of K1372E, we transiently expressed Nav1.1 carrying the two variants in HEK293T cells and compared their biophysical properties with the wild-type (WT) variant, and then co-expressed WT with K1372E or L375S with K1372E in equal quantity and tested the functional consequence. The data demonstrated that co-expression of the L375S and K1372E alleles reversed the loss-of-function property brought by the K1372E variant, whereas WT-K1372E co-expression remained partial loss-of-function. Significance: These results support the hypothesis that L375S counteracts the loss-of-function effect of K1372E such that individuals carrying both alleles in trans do not present epilepsy-related symptoms. We demonstrate that monogenic epilepsies with wide expressivity can be modified by additional variants in the disease gene, providing a novel framework for the gene-phenotype relationship in genetic epilepsies.",

keywords = "SCN1A-related epilepsy, biophysical properties, co-expressed variants, modifier gene, whole exome sequencing",

author = "Hammer, {Michael F.} and Yanling Pan and Medhane Cumbay and Manuela Pendziwiat and Zaid Afawi and Hadassah Goldberg-Stern and Laurel Johnstone and Ingo Helbig and Cummins, {Theodore R.}",

note = "Publisher Copyright: {\textcopyright} 2022 International League Against Epilepsy.",

year = "2022",

month = aug,

doi = "10.1111/epi.17296",

language = "אנגלית",

volume = "63",

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T1 - Whole exome sequencing and co-expression analysis identify an SCN1A variant that modifies pathogenicity in a family with genetic epilepsy and febrile seizures plus

AU - Hammer, Michael F.

AU - Pan, Yanling

AU - Cumbay, Medhane

AU - Pendziwiat, Manuela

AU - Afawi, Zaid

AU - Goldberg-Stern, Hadassah

AU - Johnstone, Laurel

AU - Helbig, Ingo

AU - Cummins, Theodore R.

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N2 - Objective: Family members carrying the same SCN1A variant often exhibit differences in the clinical severity of epilepsy. This variable expressivity suggests that other factors aside from the primary sodium channel variant influence the clinical manifestation. However, identifying such factors has proven challenging in humans. Methods: We perform whole exome sequencing (WES) in a large family in which an SCN1A variant (p.K1372E) is segregating that is associated with a broad spectrum of phenotypes ranging from lack of epilepsy, to febrile seizures and absence seizures, to Dravet syndrome. We assessed the hypothesis that the severity of the SCN1A-related phenotype was affected by alternate alleles at a modifier locus (or loci). Results: One of our top candidates identified by WES was a second variant in the SCN1A gene (p.L375S) that was shared exclusively by unaffected carriers of the K1372E allele. To test the hypothesized that L375S variant nullifies the loss-of-function effect of K1372E, we transiently expressed Nav1.1 carrying the two variants in HEK293T cells and compared their biophysical properties with the wild-type (WT) variant, and then co-expressed WT with K1372E or L375S with K1372E in equal quantity and tested the functional consequence. The data demonstrated that co-expression of the L375S and K1372E alleles reversed the loss-of-function property brought by the K1372E variant, whereas WT-K1372E co-expression remained partial loss-of-function. Significance: These results support the hypothesis that L375S counteracts the loss-of-function effect of K1372E such that individuals carrying both alleles in trans do not present epilepsy-related symptoms. We demonstrate that monogenic epilepsies with wide expressivity can be modified by additional variants in the disease gene, providing a novel framework for the gene-phenotype relationship in genetic epilepsies.

AB - Objective: Family members carrying the same SCN1A variant often exhibit differences in the clinical severity of epilepsy. This variable expressivity suggests that other factors aside from the primary sodium channel variant influence the clinical manifestation. However, identifying such factors has proven challenging in humans. Methods: We perform whole exome sequencing (WES) in a large family in which an SCN1A variant (p.K1372E) is segregating that is associated with a broad spectrum of phenotypes ranging from lack of epilepsy, to febrile seizures and absence seizures, to Dravet syndrome. We assessed the hypothesis that the severity of the SCN1A-related phenotype was affected by alternate alleles at a modifier locus (or loci). Results: One of our top candidates identified by WES was a second variant in the SCN1A gene (p.L375S) that was shared exclusively by unaffected carriers of the K1372E allele. To test the hypothesized that L375S variant nullifies the loss-of-function effect of K1372E, we transiently expressed Nav1.1 carrying the two variants in HEK293T cells and compared their biophysical properties with the wild-type (WT) variant, and then co-expressed WT with K1372E or L375S with K1372E in equal quantity and tested the functional consequence. The data demonstrated that co-expression of the L375S and K1372E alleles reversed the loss-of-function property brought by the K1372E variant, whereas WT-K1372E co-expression remained partial loss-of-function. Significance: These results support the hypothesis that L375S counteracts the loss-of-function effect of K1372E such that individuals carrying both alleles in trans do not present epilepsy-related symptoms. We demonstrate that monogenic epilepsies with wide expressivity can be modified by additional variants in the disease gene, providing a novel framework for the gene-phenotype relationship in genetic epilepsies.

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Whole exome sequencing and co-expression analysis identify an SCN1A variant that modifies pathogenicity in a family with genetic epilepsy and febrile seizures plus

Abstract

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Funding

Keywords

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