DNA accessibility profiling at the single nucleus level of post mortem white matter brain tissue of patients with progressive multiple sclerosis and non-neurological disease controls
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE231584 | GEO | 2024/06/21
REPOSITORIES: GEO
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Project description:Multiple sclerosis (MS) is a demyelinating and neurodegenerative disease of the central nervous system (CNS). Repair through remyelination can be extensive, but quantification of remyelination remains challenging. To date, no method for standardized digital quantification of remyelination of MS lesions exists. This methodological study aims to present and validate a novel standardized method for myelin quantification in progressive MS brains to study myelin content more precisely. Fifty-five MS lesions in 32 tissue blocks from 14 progressive MS cases and five tissue blocks from 5 non-neurological controls were sampled. MS lesions were selected by macroscopic investigation of WM by standard histopathological methods. Tissue sections were stained for myelin with luxol fast blue (LFB) and histological assessment of de- or remyelination was performed by light microscopy. The myelin quantity was estimated with a novel myelin quantification method (MQM) in ImageJ. Three independent raters applied the MQM and the inter-rater reliability was calculated. We extended the method to diffusely appearing white matter (DAWM) and encephalitis to test potential wider applicability of the method. Inter-rater agreement was excellent (ICC = 0.96) and there was a high reliability with a lower- and upper limit of agreement up to -5.93% to 18.43% variation in myelin quantity. This study builds on the established concepts of histopathological semi-quantitative assessment of myelin and adds a novel, reliable and accurate quantitative measurement tool for the assessment of myelination in human post-mortem samples.
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Project description:We obtained gene-expression profiles of microdissected renal-tubule cells from patients with proteinuric nephropathies. Based on the renal function during follow-up, the patients were divided in stable (n=14) and progressive (n=7) subjects (table 1). The cells of interest were laser-capture microdissected from frozen sections from archived kidney biopsy material. Initially all samples were processed as technical duplicates (2 x 21 arrays); due to a large number of signal-negative spots several arrays were excluded leaving 36 arrays for analysis. The samples P2, P6, P7, S10, S13 and S14 were analysed as individual arrays, all other samples were analysed after combination of duplicate arrays. Quality control: To test for reproducibility we calculated the intra-array variability of the duplicate arrays. Duplicate arrays were combined before statistical analysis where applicable. Patient and control characteristics can be found in the manuscript and on our website Frozen kidney biopsies were stained for alkaline phospatase, then the tubule cells were lasercapture microdissected using the PixCell II Laser Capture Microdissection System and CapSure; LCM Caps. Set of arrays that are part of repeated experiments Disease State: samples from patients with proteinuric nephropathy (stable or progressive)
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Project description:BackgroundProgressive supranuclear palsy (PSP) is a neuropathologically defined disease presenting with a broad spectrum of clinical phenotypes.ObjectiveTo identify clinical features and investigations that predict or exclude PSP pathology during life, aiming at an optimization of the clinical diagnostic criteria for PSP.MethodsWe performed a systematic review of the literature published since 1996 to identify clinical features and investigations that may predict or exclude PSP pathology. We then extracted standardized data from clinical charts of patients with pathologically diagnosed PSP and relevant disease controls and calculated the sensitivity, specificity, and positive predictive value of key clinical features for PSP in this cohort.ResultsOf 4166 articles identified by the database inquiry, 269 met predefined standards. The literature review identified clinical features predictive of PSP, including features of the following 4 functional domains: ocular motor dysfunction, postural instability, akinesia, and cognitive dysfunction. No biomarker or genetic feature was found reliably validated to predict definite PSP. High-quality original natural history data were available from 206 patients with pathologically diagnosed PSP and from 231 pathologically diagnosed disease controls (54 corticobasal degeneration, 51 multiple system atrophy with predominant parkinsonism, 53 Parkinson's disease, 73 behavioral variant frontotemporal dementia). We identified clinical features that predicted PSP pathology, including phenotypes other than Richardson's syndrome, with varying sensitivity and specificity.ConclusionsOur results highlight the clinical variability of PSP and the high prevalence of phenotypes other than Richardson's syndrome. The features of variant phenotypes with high specificity and sensitivity should serve to optimize clinical diagnosis of PSP. © 2017 International Parkinson and Movement Disorder Society.
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Project description:We obtained gene-expression profiles of microdissected renal-tubule cells from patients with proteinuric nephropathies. Based on the renal function during follow-up, the patients were divided in stable (n=14) and progressive (n=7) subjects (table 1). The cells of interest were laser-capture microdissected from frozen sections from archived kidney biopsy material. Initially all samples were processed as technical duplicates (2 x 21 arrays); due to a large number of signal-negative spots several arrays were excluded leaving 36 arrays for analysis. The samples P2, P6, P7, S10, S13 and S14 were analysed as individual arrays, all other samples were analysed after combination of duplicate arrays. Quality control: To test for reproducibility we calculated the intra-array variability of the duplicate arrays. Duplicate arrays were combined before statistical analysis where applicable. Patient and control characteristics can be found in the manuscript and on our website Frozen kidney biopsies were stained for alkaline phospatase, then the tubule cells were lasercapture microdissected using the PixCell II Laser Capture Microdissection System and CapSure; LCM Caps. Set of arrays that are part of repeated experiments Disease State: samples from patients with proteinuric nephropathy (stable or progressive) Biological Replicate Computed
2008-12-23 | E-GEOD-11513 | biostudies-arrayexpress
Project description:BackgroundThe aim of the study was to characterize molecular diagnoses in patients with childhood-onset progressive neurological disorders of suspected genetic etiology.MethodsWe studied 48 probands (age range from newborn to 17 years old) with progressive neurological disorders of unknown etiology from the largest pediatric neurology clinic in Finland. Phenotypes included encephalopathy (54%), neuromuscular disorders (33%), movement disorders (11%), and one patient (2%) with hemiplegic migraine. All patients underwent whole-exome sequencing and disease-causing genes were analyzed.ResultsWe found 20 (42%) of the patients to have variants in genes previously associated with disease. Of these, 12 were previously reported disease-causing variants, whereas eight patients had a novel variant on a disease-causing gene: ATP7A, CHD2, PURA, PYCR2, SLC1A4, SPAST, TRIT1, and UPF3B. Genetics also enabled us to define atypical clinical presentations of Rett syndrome (MECP2) and Menkes disease (ATP7A). Except for one deletion, all findings were single-nucleotide variants (missense 72%, truncating 22%, splice-site 6%). Nearly half of the variants were de novo.ConclusionsThe most common cause of childhood encephalopathies are de novo variants. Whole-exome sequencing, even singleton, proved to be an efficient tool to gain specific diagnoses and in finding de novo variants in a clinically heterogeneous group of childhood encephalopathies.ImpactWhole-exome sequencing is useful in heterogeneous pediatric neurology cohorts. Our article provides further evidence for and novel variants in several genes. De novo variants are an important cause of childhood encephalopathies.
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Project description:The lungs of mice inoculated with H1N1 were harvested at day 7. The DAPI- lung cells were loaded into a 10x Genomics microfluidics chip and encapsulated with barcoded oligo-dT-containing gel beads using the 10x Genomics Chromium controller using v3 kit according to the manufacturer's instructions.
2022-04-29 | GSE201541 | GEO