Nuclear transcriptome analysis-based verification of sample purity for Purkinje cell nuclei isolated by fluorescence-activated nuclear sorting (FANS).
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE327324 | GEO | 2026/07/30
REPOSITORIES: GEO
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Project description:Spinocerebellar ataxia type 3 (SCA3) is a dominantly inherited neurodegenerative disorder caused by a polyglutamine-encoding CAG repeat expansion in the ATXN3 gene, which encodes a deubiquitinating enzyme, ATXN3, implicated in numerous quality control pathways. Several mechanisms have been proposed to explain the pathogenic role of mutant polyQ-expanded ATXN3 in SCA3 including disease protein aggregation, impairment of ubiquitin-proteasomal degradation and transcriptional dysregulation. A better understanding of the normal functions of this protein may shed light on SCA3 disease pathogenesis. To assess the potential normal role of ATXN3 in regulating transcription, we compared gene expression profiles in wildtype (WT) versus Atxn3 knockout (KO) mouse embryonic fibroblasts (MEFs).
2018-07-13 | GSE117028 | GEO
Project description:Objective Repeat expansion mutations underlie diverse neurogenetic disorders, many involving the peripheral nervous system. Despite peripheral neuropathy being the most common neurological disorder worldwide, its contribution to repeat expansion diseases remains poorly defined, and robust preclinical models are limited. We established a translational framework to study peripheral neuropathy in Spinocerebellar ataxia type 3 (SCA3), a fatal multisystem disorder caused by a pathogenic CAG expansion in ATXN3. Methods SCA3 Knock-In Atxn3Q300/Q6 (KI) and Atxn3-/- Knock-Out (KO) mice underwent sensorimotor nerve conduction and behavioral testing. Peripheral tissues were evaluated for SCA3-related pathology, and transcriptional changes in KI dorsal root ganglia (DRG) were assessed by bulk RNA sequencing. To test therapeutic relevance, we generated a conditional “OFF” SCA3 knock-in (cKI) mouse and crossed it with Avil-Cre to selectively silence mutant ATXN3 in sensory neurons. Peripheral phenotyping was repeated in Avil-Cre; cKI mice. Results KI mice developed progressive sensorimotor deficits, peripheral histopathology, and RNA splicing dysregulation that parallel clinical features of SCA3. In contrast, KO mice showed normal peripheral nerve function, implicating toxic gain-of-function from mutant ATXN3 as the causative driver. Sensory neuron–specific silencing of mutant ATXN3 significantly ameliorated peripheral nerve abnormalities. Interpretation These findings define a pathogenic role for repeat expansion–driven peripheral nerve degeneration in SCA3, identify sensory neurons as key therapeutic targets, and provide a preclinical platform for developing peripheral interventions in SCA3 and related repeat expansion disorders.
2026-05-11 | GSE320015 | GEO
Project description:Objective Repeat expansion mutations underlie diverse neurogenetic disorders, many involving the peripheral nervous system. Despite peripheral neuropathy being the most common neurological disorder worldwide, its contribution to repeat expansion diseases remains poorly defined, and robust preclinical models are limited. We established a translational framework to study peripheral neuropathy in Spinocerebellar ataxia type 3 (SCA3), a fatal multisystem disorder caused by a pathogenic CAG expansion in ATXN3. Methods SCA3 Knock-In Atxn3Q300/Q6 (KI) and Atxn3-/- Knock-Out (KO) mice underwent sensorimotor nerve conduction and behavioral testing. Peripheral tissues were evaluated for SCA3-related pathology, and transcriptional changes in KI dorsal root ganglia (DRG) were assessed by bulk RNA sequencing. To test therapeutic relevance, we generated a conditional “OFF” SCA3 knock-in (cKI) mouse and crossed it with Avil-Cre to selectively silence mutant ATXN3 in sensory neurons. Peripheral phenotyping was repeated in Avil-Cre; cKI mice. Results KI mice developed progressive sensorimotor deficits, peripheral histopathology, and RNA splicing dysregulation that parallel clinical features of SCA3. In contrast, KO mice showed normal peripheral nerve function, implicating toxic gain-of-function from mutant ATXN3 as the causative driver. Sensory neuron–specific silencing of mutant ATXN3 significantly ameliorated peripheral nerve abnormalities. Interpretation These findings define a pathogenic role for repeat expansion–driven peripheral nerve degeneration in SCA3, identify sensory neurons as key therapeutic targets, and provide a preclinical platform for developing peripheral interventions in SCA3 and related repeat expansion disorders.
2026-05-11 | GSE329323 | GEO
Project description:The neurodegenerative disease spinocerebellar ataxia type 3 (SCA3; also called Machado-Joseph disease, MJD) is a trinucleotide repeat disorder caused by expansion of CAG repeats which encoding an abnormal long polyglutamine (polyQ) tract in ataxin-3 of the ATXN3 gene. Even now the pathogenic mechanism has remained elusive and no cure method is currently available. In this study, we first applied CRISPR/Cas9-mediated approach using homologous recombination to achieve one-step genetic correction in SCA3-specific induced pluripotent stem cells (iPSCs) by adjusting pathological 80 CAG repeats to normal 13 CAG repeats, without detectable off-target based on whole exon sequencing or polyacrylamide gel electrophoresis (PAGE). The correction normalized SCA3 pathogenic signal pathways (like transcription, apoptosis, and ubiquitin-dependent protein catabolic process) and reversed disease-associated phenotypes. Our strategy provides deep insights into pathogenic mechanism of SCA3 disease and suggests potential therapeutic applications of trinucleotide repeat disorders.
2020-01-17 | GSE93713 | GEO
Project description:Spinocerebellar ataxia type 3 (SCA3) is the most common dominantly inherited ataxia. Currently, no preventative or disease-modifying treatments exist for this progressive neurodegenerative disorder, although efforts using gene silencing approaches are under clinical trial investigation. The disease is caused by a CAG repeat expansion in the mutant gene, ATXN3, producing an enlarged polyglutamine tract in the mutant protein. Similar to other paradigmatic neurodegenerative diseases, studies evaluating the pathogenic mechanism focus primarily on neuronal implications. Consequently, therapeutic interventions often overlook non-neuronal contributions to disease. Our lab recently reported that oligodendrocytes display some of the earliest and most progressive dysfunction in SCA3 mice. Evidence of disease-associated oligodendrocyte signatures has also been reported in other neurodegenerative diseases, including Alzheimer's disease, Amyotrophic Lateral Sclerosis, Parkinson's disease, and Huntington's disease. Here, we assess the effects of anti-ATXN3 antisense oligonucleotide (ASO) treatment on oligodendrocyte dysfunction in premanifest and symptomatic SCA3 mice. We report a severe, but modifiable, deficit in oligodendrocyte maturation caused by the toxic gain-of-function of mutant ATXN3 early in SCA3 disease that is transcriptionally, biochemically, and functionally rescued with anti-ATXN3 ASO. Our results highlight the promising use of an ASO therapy across neurodegenerative diseases that requires glial targeting in addition to affected neuronal populations.
2024-03-19 | GSE261670 | GEO
Project description:Spinocerebellar ataxia type 3 (SCA3) is a neurodegenerative disease caused by polyglutamine repeat expansion in the ATXN3 gene. Despite the ubiquitous expression of ATXN3 throughout the body, SCA3 pathology is pronounced in select, vulnerable regions within the central nervous system (CNS). Notably, imaging studies of SCA3 patients have revealed spinal cord atrophy prior to ataxia symptom onset and progressing with disease severity. However, the molecular mechanisms underlying SCA3 pathology in the spinal cord remain largely unexplored. Here, we present, for the first time, a comprehensive analysis of the spinal cord transcriptome using SCA3 tissue from humans and mouse models. Our data demonstrates both early and progressive transcriptional dysregulation in the spinal cord, impacting key biological processes such as lipid metabolism, inflammation, cellular structure, and nucleic acid processing. Transcriptomic profiling of Atxn3 knockout mice revealed only weak transcriptional changes in the spinal cord, with minimal overlap compared to the robust alterations observed in SCA3 knock-in mice, indicating that the molecular signature of the disease in the spinal cord is likely not driven by ATXN3 loss of function. In addition, we identified aberrant RNA splicing, particularly affecting genes involved in cytoskeletal organization. Collectively, our findings indicate that SCA3-associated transcriptional dysregulation in the spinal cord contributes to canonical pathological mechanisms of SCA3 both early and progressively. These results underscore the central role of the spinal cord in SCA3 pathogenesis and advocate for its inclusion as a key therapeutic target.
2025-10-29 | GSE309548 | GEO
Project description:Spinocerebellar ataxia type 3 (SCA3) is a neurodegenerative disease caused by polyglutamine repeat expansion in the ATXN3 gene. Despite the ubiquitous expression of ATXN3 throughout the body, SCA3 pathology is pronounced in select, vulnerable regions within the central nervous system (CNS). Notably, imaging studies of SCA3 patients have revealed spinal cord atrophy prior to ataxia symptom onset and progressing with disease severity. However, the molecular mechanisms underlying SCA3 pathology in the spinal cord remain largely unexplored. Here, we present, for the first time, a comprehensive analysis of the spinal cord transcriptome using SCA3 tissue from humans and mouse models. Our data demonstrates both early and progressive transcriptional dysregulation in the spinal cord, impacting key biological processes such as lipid metabolism, inflammation, cellular structure, and nucleic acid processing. Transcriptomic profiling of Atxn3 knockout mice revealed only weak transcriptional changes in the spinal cord, with minimal overlap compared to the robust alterations observed in SCA3 knock-in mice, indicating that the molecular signature of the disease in the spinal cord is likely not driven by ATXN3 loss of function. In addition, we identified aberrant RNA splicing, particularly affecting genes involved in cytoskeletal organization. Collectively, our findings indicate that SCA3-associated transcriptional dysregulation in the spinal cord contributes to canonical pathological mechanisms of SCA3 both early and progressively. These results underscore the central role of the spinal cord in SCA3 pathogenesis and advocate for its inclusion as a key therapeutic target.
2025-10-29 | GSE309549 | GEO
Project description:Spinocerebellar ataxia type 3 (SCA3) is a neurodegenerative disease caused by polyglutamine repeat expansion in the ATXN3 gene. Despite the ubiquitous expression of ATXN3 throughout the body, SCA3 pathology is pronounced in select, vulnerable regions within the central nervous system (CNS). Notably, imaging studies of SCA3 patients have revealed spinal cord atrophy prior to ataxia symptom onset and progressing with disease severity. However, the molecular mechanisms underlying SCA3 pathology in the spinal cord remain largely unexplored. Here, we present, for the first time, a comprehensive analysis of the spinal cord transcriptome using SCA3 tissue from humans and mouse models. Our data demonstrates both early and progressive transcriptional dysregulation in the spinal cord, impacting key biological processes such as lipid metabolism, inflammation, cellular structure, and nucleic acid processing. Transcriptomic profiling of Atxn3 knockout mice revealed only weak transcriptional changes in the spinal cord, with minimal overlap compared to the robust alterations observed in SCA3 knock-in mice, indicating that the molecular signature of the disease in the spinal cord is likely not driven by ATXN3 loss of function. In addition, we identified aberrant RNA splicing, particularly affecting genes involved in cytoskeletal organization. Collectively, our findings indicate that SCA3-associated transcriptional dysregulation in the spinal cord contributes to canonical pathological mechanisms of SCA3 both early and progressively. These results underscore the central role of the spinal cord in SCA3 pathogenesis and advocate for its inclusion as a key therapeutic target.
2025-10-29 | GSE309535 | GEO
Project description:Fluorescence-Activated Nuclei Sorting (FANS)-assisted Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) This work sought to identify endothelial-specific enhancer elements by applying ATAC-Seq to nuclei isolated from Tg(fli1a:egfp) transgenic zebrafish embryos.
2017-06-08 | GSE97255 | GEO
Project description:Spinocerebellar ataxia type 3 (SCA3) is the most common dominantly inherited ataxia caused by a toxic gain-of-function CAG expansion in ATXN3. Currently, no effective preventive or disease-modifying treatments exist for this uniformly fatal disorder. This progressive, multisystem disorder is typified by neuronal degeneration and demyelination of critical parts of the central nervous system. Additionally, more than half of individuals with SCA3 also exhibit peripheral neuropathy symptoms like reduced limb sensation or burning pains, significantly impacting quality of life and contributing to mobility impairments. However, exploration into cell types and disease mechanisms underlying the SCA3 peripheral nervous system abnormalities remains limited by lack of comprehensive SCA3 animal model characterizations. This study employs the transgenic full-length human mutant ATXN3 YACQ84 (Q84/Q84) mouse to assess progression of sensorimotor behaviors, nerve conduction abnormalities, and ultrastructural features of neuropathy. Nerve conduction studies in Q84/Q84 mice show prominent sensorimotor nerve conduction velocity reductions in the sciatic and sural nerves and blunted signal amplitudes in the sural nerve, suggestive of axon loss and demyelination. Behaviorally, Q84/Q84 mice display abnormal responses to thermal and mechanical stimuli. Histological analysis of Q84/Q84 peripheral nerves reveals combined neuronal and glial pathology, characterized by loss of both large myelinated and small unmyelinated fibers, alongside demyelination pathologies. Bulk analyses of Q84/Q84 dorsal root ganglia and sciatic nerves revealed sensory neuropathy-related transcriptional and splicing dysregulation spanning diverse somatosensory pathways. Our results characterize significant peripheral neuropathy in a representative SCA3 mouse model, providing a strong foundation for future mechanistic and therapeutic studies of peripheral neuropathy in SCA3.
2026-05-11 | GSE320100 | GEO