Biology subjects

Hammer, M. F.

Publications and source records attributed to Hammer, M. F..

4 recordsLinked to original sources

bioRxiv2026

A De Novo, Intragenic Modifier in Cis Rescues Scn8a-N1768D Epilepsy and Defines a Therapeutic Window Bounded by Gain- and Loss-of-Function

Gain-of-function variants in SCN8A, encoding NaV1.6, cause developmental and epileptic encephalopathy with early-onset, drug-resistant seizures. SCN8A is a Goldilocks gene: both excess and deficit of NaV1.6 are deleterious, so therapies that lower NaV1.6 must operate within a narrow window. Here we characterize a congenic C3H/HeJ.C57BL/6J colony carrying Scn8a-N1768D and identify a tightly linked, cis-acting modifier (L) that converts a severe phenotype into graded outcomes. Among N1768D homozygotes on a 98.4% C3H/HeJ.C57BL/6J background, three phenotypes segregate: short-lived (SL) mice with early lethal tonic-clonic seizures (TCS), long-lived (LL) mice with delayed onset and reduced seizure burden, and hindlimb-paralysis (HP) mice with early death. Heterozygotes separate into D/+ SL mice, which develop spontaneous TCS and die of epilepsy, and D/+ LL mice, which lack spontaneous TCS and epilepsy-related death. Genetic analysis places a second locus (L) tightly linked to Scn8a and co-segregating with phenotype. Hippocampal RNA-seq shows dose-dependent Scn8a mRNA reduction: none in SL (D+/D+), 30% in LL (DL/D+), and 70% in HP (DL/DL). Long-read trio DNA sequencing identifies a de novo 2-bp frameshift in coding exon 15 of Scn8a, in cis with N1768D, that introduces a premature stop codon ~26 kb upstream of the exon--exon junction, predicted to trigger nonsense-mediated decay. Allele-specific read counting confirms selective, cis-acting loss of DL transcripts with preserved D+ output. Thus, a de novo, intragenic frameshift variant titrates NaV1.6 through a Goldilocks window in which intermediate reduction rescues Gain-of-function epilepsy, whereas insufficient or excessive reduction remains lethal, validating Scn8a-lowering and its therapeutic dose window.

genetics↗

bioRxiv2026

Cis-Attenuation of Pathogenic Scn8a Variant Causing Childhood Epilepsy Reveals Opposing Transcriptional Programs Driving NaV1.6 Gain and Loss of Function Phenotypes

Pathogenic variants in SCN8A, encoding the voltage-gated sodium channel NaV1.6, cause disease through opposing gain-of-function (GoF) and loss-of-function (LoF) mechanisms, yet the downstream cellular programs that distinguish these directions have not been resolved within a single genetic system. We used an isogenic Scn8a allelic series in which a cis-acting modifier produces a stepwise reduction of NaV1.6 on the N1768D background, isolating GoF, rescued, and LoF states on a shared background, and profiled the hippocampal transcriptome with pathway-level inference. The gain- and loss-of-function extremes engaged mechanistically opposite programs: an active fibro-inflammatory injury cascade in the seizing brain versus suppression of neuronal-signaling and growth programs, including cAMP Response Element-Binding signaling (CREB) in neurons, in the LoF state. The injury core was conserved across genetic backgrounds, appeared only after seizures rather than tracking channel dose, and was durably suppressed in the rescued genotype without erosion after seizure onset. Genetic rescue and the repurposed angiotensin-receptor blocker candesartan converged on the same injury program through distinct routes, and the same program was engaged in an -synuclein model of Parkinson's disease and in human epileptic tissue. These findings show that the two clinical directions of SCN8A disease have distinct tissue-level correlates and call for opposite therapeutic logic, channel or injury-cascade suppression for GoF and restoration of channel output for LoF, and identify a conserved, seizure-driven injury core as a tractable cross-disease target.

genetics↗

bioRxiv2025

A splice-switching antisense oligonucleotide approach for pediatric genetic epilepsies

Summary ParagraphVariants in ion channel genes are common causes of pediatric epilepsy, often leading to intractable seizures, developmental delay and other comorbidities, which increases risk of death. Pathogenic variants in the SCN8A gene, which encodes a voltage-gated sodium channel critical for action potential generation in the brain, account for [~]1% of genetic epilepsies. The voltage sensor in SCN8A domain 1 is encoded by one of two developmentally-regulated mutually exclusive alternative exons, 5N and 5A. We observe that variants in these exons are more likely to cause infantile spasms, a severe seizure type, than variants elsewhere in SCN8A, and that some pathogenic variants affect exon 5 splicing, impacting patient phenotype. Molecular and evolutionary analyses implicate the exon sequences of these and other voltage-gated ion channel alternative exons in splicing regulation. We identified antisense oligonucleotides (ASOs) that shift splicing of SCN8A exon 5N to 5A or vice versa. These ASOs normalize neuronal activity in patient-derived iPSC neurons, and reduce seizures and motor impairment and extend lifespan in a new exon 5N mutant mouse model. Our results demonstrate that splice-switching ASOs can effectively reduce the expression of pathogenic isoforms and rescue both seizure and non-seizure phenotypes. Similar approaches should be applicable to pediatric genetic epilepsies caused by mutations in other ion channel alternative exons.

neuroscience↗

bioRxiv2018

Substructured population growth in the Ashkenazi Jews inferred with Approximate Bayesian Computation

The Ashkenazi Jews (AJ) are a population isolate that have resided in Central Europe since at least the 10th century and share ancestry with both European and Middle Eastern populations. Between the 11th and 16th centuries, AJ expanded eastward leading to two culturally distinct communities, one in central Europe and one in eastern Europe. Our aim was to determine if there are genetically distinct AJ subpopulations that reflect the cultural groups, and if so, what demographic events contributed to the population differentiation. We used Approximate Bayesian Computation (ABC) to choose among models of AJ history and infer demographic parameter values, including divergence times, effective population size, and gene flow. For the ABC analysis we used allele frequency spectrum and identical by descent based statistics to capture information on a wide timescale. We also mitigated the effects of ascertainment bias when performing ABC on SNP array data by jointly modeling and inferring the SNP discovery. We found that the most likely model was population differentiation between the Eastern and Western AJ ~400 years ago. The differentiation between the Eastern and Western AJ could be attributed to more extreme population growth in the Eastern AJ (0.25 per generation) than the Western AJ (0.069 per generation).

genomics↗