Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA173693 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Vanishing white matter (VWM) is a leukodystrophy that primarily manifests in young children. In this disease, the brain white matter is differentially affected in a predictable pattern with telencephalic brain areas being more severely affected, while others remain allegedly completely spared. Using high-resolution mass spectrometry-based proteomics, we investigated the proteome patterns of the severely affected white matter in the frontal lobe and normal appearing pons in VWM and control cases to identify molecular bases underlying regional vulnerability. By comparing VWM patients to controls, we identified disease-specific proteome patterns. We showed substantial pathogenic changes in both the frontal white matter and pons at the protein level. Side-by-side comparison of brain region-specific proteome patterns further revealed regional differences. We found that different cell types are affected in the VWM frontal white matter than in the pons. Gene ontology and pathway analyses identified involvement of region distinct biological processes, of which pathways implicated in cellular respiratory metabolism were overarching features. In the VWM frontal white matter, proteome changes were associated with decrease in glycolysis/gluconeogenesis and metabolism of various amino acids. By contrast, in the VWM pons white matter, we found a decrease in oxidative phosphorylation. Taken together, our data show that brain regions are affected in parallel in VWM, but to different degrees. We found region-specific involvement of different cell types and discovered that cellular respiratory metabolism is differently affected across white matter regions in VWM. These region-specific changes help explain regional vulnerability to pathology in VWM.
2023-06-28 | PXD040861 | Pride
Project description:Amyotrophic lateral sclerosis (ALS) and parkinsonism-dementia complex (PDC) (ALS/PDC) is a unique endemic neurodegenerative disease, with high-incidence foci in the Kii Peninsula, Japan. Although ALS/PDC presents with multiple proteinopathies, the genetic and environmental factors that influence disease onset remain unknown. We performed transcriptome analyses of patients’ brains, which may provide new insights into the pathomechanisms underlying Kii ALS/PDC. We prepared frozen brains from 3 healthy controls (frontal lobe and temporal lobe), 3 patients with Alzheimer’s disease (AD) (frontal lobe and temporal lobe) as tauopathy-disease controls, and 21 patients with Kii ALS/PDC (frontal lobe and/or temporal lobe). We acquired microarray data from the cerebral gray and white matter tissues of Kii ALS/PDC patients. Microarray data revealed that the expression levels of genes associated with neurons, heat shock proteins (Hsps), DNA binding/damage, and senescence were significantly changed in Kii ALS/PDC brains compared with those in control brains. The RNA expression pattern observed for Kii ALS type brains was similar to that for Kii PDC type brains and unlike those of control and AD brains. Additionally, pathway and network analyses indicated that the molecular pathogenic mechanism underlying Kii ALS/PDC may be associated with the oxidative phosphorylation of mitochondria, ribosomes, and the synaptic vesicle cycle; in particular, upstream regulators of these mechanisms may be found in synapses and during synaptic trafficking. Therefore, we propose the novel disease concept of “synaptopathy” for Kii ALS/PDC. Furthermore, phenotypic differences between Kii ALS type and Kii PDC type were observed, based on the human leukocyte antigen (HLA) haplotype. We performed exhaustive transcriptome analyses of Kii ALS/PDC brains, for the first time, and revealed new insights indicating that Kii ALS/PDC may be a synaptopathy. Determining the relationship between synaptic dysfunction and the pathogenesis of ALS/PDC may provide a new step toward understanding this mysterious disease.
2019-10-26 | GSE139384 | GEO
Project description:We compared the gene expression in post-mortem brain specimen dissected from 2 CADASIL patients with samples from 5 non-affected controls in order to discover genes differentially expressed that could be involved in the development of neuronal damage in SVD. Samples form frontal cortex and white matter and occipital cortex and white matter were used.
2015-03-12 | E-MTAB-3395 | biostudies-arrayexpress
Project description:The transcriptome of normal-appearing white matter for relapse-remitting multiple sclerosis (MS), primary progressive MS and secondary progressive MS was determined using total RNA-sequencing. We then performed a differential gene analysis comparing the normal-appearing white matter for each clinical subtype of MS with non-MS control tissue
2022-10-04 | GSE214334 | GEO
Project description:Using the Illumina 450K array and a stringent statistical analysis with age and gender correction, we report genome-wide differences in DNA methylation between pathology-free regions derived from human multiple sclerosis–affected and control brains. Differences were subtle, but widespread and reproducible in an independent validation cohort. The transcriptional consequences of differential DNA methylation were further defined by genome-wide RNA-sequencing analysis and validated in two independent cohorts. Genes regulating oligodendrocyte survival, such as BCL2L2 and NDRG1, were hypermethylated and expressed at lower levels in multiple sclerosis–affected brains than in controls, while genes related to proteolytic processing (for example, LGMN, CTSZ) were hypomethylated and expressed at higher levels. These results were not due to differences in cellular composition between multiple sclerosis and controls. Thus, epigenomic changes in genes affecting oligodendrocyte susceptibility to damage are detected in pathology-free areas of multiple sclerosis–affected brains.
2013-11-24 | GSE40360 | GEO
Project description:Genome-wide DNA methylation level was studied to determine whether multiple sclerosis patients (cases) has methylation differences comparing to normal controls in PBLs. We used Illumina HumanMethylation450 BeadChip array to determine the genome-wide DNA methylation difference in peripheral blood from multiple sclerosis patients (cases) and normal controls
2018-04-20 | GSE106648 | GEO
Project description:RNA-seq of peripheral blood from healthy controls and established relapsing-remitting multiple sclerosis patients
2025-01-24 | E-GEOD-66573 | ExpressionAtlas
Project description:Finding the differences in gene expression in three regions of the brain, basal ganglia, white matter, and frontal cortex, in normal, HIV infected, HIV infected with neurocognitive impairment, and HIV infected with both neurocognitive impairment and encephalitis patients.
2012-08-01 | GSE35864 | GEO
Project description:Label-free global proteomic analysis of progressive multiple sclerosis (P-MS) and control (ODC) brain tissue (cortex/CTX, normal appearing white matter/NAWM, white matter lesions/WML), primary human neural cell types (neurons, microglia, astrocytes, oligodendrocyte progenitor cells), and CNS tissue (brain, spinal cord) from mouse models of MS (EAE and cuprizone).
2025-01-07 | MSV000096790 | MassIVE
Project description:Methylation state of human post-mortem brain tissue from the frontal lobe of patients with Frontotemporal Dementia caused by mutations in GRN, MAPT and C9orf72 and healthy controls
2023-02-01 | E-MTAB-12674 | biostudies-arrayexpress