Foundry120 atlas

Altered oligodendrocyte heterogeneity in Multiple sclerosis.

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Dataset overview

Participants 9
Samples 20
Reuse readiness 6.0/10 evidence-backed score

Altered human oligodendrocyte heterogeneity in multiple sclerosis.

Abstract

Oligodendrocyte pathology is increasingly implicated in neurodegenerative diseases as oligodendrocytes both myelinate and provide metabolic support to axons. In multiple sclerosis (MS), demyelination in the central nervous system thus leads to neurodegeneration, but the severity of MS between patients is very variable. Disability does not correlate well with the extent of demyelination<sup>1</sup>, which suggests that other factors contribute to this variability. One such factor may be oligodendrocyte heterogeneity. Not all oligodendrocytes are the same-those from the mouse spinal cord inherently produce longer myelin sheaths than those from the cortex<sup>2</sup>, and single-cell analysis of the mouse central nervous system identified further differences<sup>3,4</sup>. However, the extent of human oligodendrocyte heterogeneity and its possible contribution to MS pathology remain unknown. Here we performed single-nucleus RNA sequencing from white matter areas of post-mortem human brain from patients with MS and from unaffected controls. We identified subclusters of oligodendroglia in control human white matter, some with similarities to mouse, and defined new markers for these cell states. Notably, some subclusters were underrepresented in MS tissue, whereas others were more prevalent. These differences in mature oligodendrocyte subclusters may indicate different functional states of oligodendrocytes in MS lesions. We found similar changes in normal-appearing white matter, showing that MS is a more diffuse disease than its focal demyelination suggests. Our findings of an altered oligodendroglial heterogeneity in MS may be important for understanding disease progression and developing therapeutic approaches.

Study facts

Organism
Homo sapiens
Platform
Illumina HiSeq 2500
Age group
adult
Disease groups
—
Anatomical sites
white matter brain tissue

Data availability

  • Raw counts
  • Processed matrix

File types TXT

Files and samples

Strengths & limitations for reuse

Strengths

  • Raw counts are advertised
  • Processed matrices are advertised
  • Cell metadata are advertised
  • Participant counts are documented
Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

FieldValueEvidence
assay.assay_type single-nucleus RNA sequencing
single nuclei RNA-sequencing (snRNA-seq)

Section series_summary, offset —

assay.library_chemistry 10x Genomics Single Cell 3' v2
10x Genomics Single Cell 3' v2

Section extract_protocol, offset —

assay.platform Illumina HiSeq 2500
Illumina HiSeq 2500

Section instrument_model, offset —

assay.reference_genome GRCh38
genome build: GRCh38

Section data_processing, offset —

assay.sequencing_type snrna_seq
single nuclei RNA-sequencing (snRNA-seq)

Section series_summary, offset —

Cohort

FieldValueEvidence
cohort.age_group adult
Adult

Section meshHeadingList, offset —

cohort.non_ibd_controls 5
We isolated single nuclei from white matter post-mortem tissue from 5 non-neurological control samples (Ctrl)

Section series_overall_design, offset —

cohort.study_design cross_sectional inferred
post-mortem tissue from 4 progressive Multiple sclerosis (MS) patients

Section series_overall_design, offset —

cohort.total_participants 9 inferred
We isolated single nuclei from white matter post-mortem tissue from 5 non-neurological control samples (Ctrl) and post-mortem tissue from 4 progressive Multiple sclerosis (MS) patients.

Section series_overall_design, offset —

Data_Assets

FieldValueEvidence
data_assets.cell_metadata True
GSE118257_MSCtr_snRNA_FinalAnnotationTable.txt.gz

Section dataset-authority, offset —

data_assets.open_access True
Public on Jan 23 2019

Section series_status, offset —

data_assets.processed_matrix True
GSE118257_MSCtr_snRNA_ExpressionMatrix_R.txt.gz

Section dataset-authority, offset —

data_assets.raw_counts True
Processed data includes raw UMI counts matrix

Section data_processing, offset —

Processing

FieldValueEvidence
processing.cell_type_annotation_method CellRanger processing with assigned celltype clusters and annotation tables
Processed data includes raw UMI counts matrix with the assigned celltype clusters

Section data_processing, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['white matter brain tissue']
White Matter brain tissue

Section characteristics.tissue, offset —

specimens.number_of_samples 20
20

Section sample_count, offset —