Single-Cell & Spatial Multi-Omics in Multiple Sclerosis: Oligodendrocyte Remyelination Failure, MIMS Microglia & EBV Immunogenomics
Analyzing post-mortem MS white/gray matter snRNA-seq, MERFISH lesion rim gradients, and CSF single-cell BCR/TCR repertoires.
Why do some Multiple Sclerosis plaques remyelinate into shadow plaques while others evolve into chronically inflamed, iron-rimmed lesions that drive relentless axonal degeneration? High-resolution single-nucleus RNA sequencing (snRNA-seq), spatial transcriptomics (MERFISH / Visium), and paired CSF single-cell V(D)J receptor profiling have transformed our understanding of MS cellular niches. This guide covers best practices for analyzing glial state transitions, C1q-mediated microglial-astrocytic signaling, and Epstein-Barr Virus (EBV) molecular mimicry in open MS multi-omics datasets.
1. Dissecting the Chronic Active Lesion Rim: MIMS-Iron, MIMS-Foamy & Reactive Astrocytes
- Always include lesion stage (NAWM, Chronic Active Rim, Core, Shadow Plaque) and brain region (white matter vs. cortical gray matter) in pseudobulk differential expression models.
- Score MIMS-iron (FTH1, FTL, C1QA, FCGR2A, HLA-DRA) versus MIMS-foamy (LPL, APOE, CD68, PPARG) gene modules using scanpy.tl.score_genes.
- In spatial transcriptomics (MERFISH / Visium), compute continuous signed distance from the demyelinated lesion border rather than relying solely on discrete cluster labels.
2. Oligodendrocyte Lineage Heterogeneity, Remyelination Block & EBV B-Cell Repertoires
Python Example: Computing Spatial Gene Expression Gradients Across the MS Chronic Active Lesion Rim (Scanpy / NumPy)
Standard Python template ready for integration into local Jupyter notebooks or automated pipelines.
import anndata as ad
import numpy as np
import pandas as pd
from scipy.spatial import cKDTree
def compute_lesion_rim_spatial_gradient(adata: ad.AnnData, rim_annotation: str = "Chronic_Active_Rim"):
"""
Calculate each cell's Euclidean distance (in micrometers) to the nearest MS chronic active
lesion rim coordinate and summarize MIMS-iron / OPC gene module expression across spatial zones.
"""
coords = adata.obsm["spatial"] # (N_cells, 2) spatial coordinates in micrometers
is_rim = (adata.obs["lesion_zone"] == rim_annotation).values
# Build KD-Tree on lesion rim coordinates for fast nearest-neighbor distance lookup
rim_tree = cKDTree(coords[is_rim])
distances_um, _ = rim_tree.query(coords, k=1)
adata.obs["dist_to_rim_um"] = distances_um
# Bin cells into concentric 100-um spatial rings from the paramagnetic rim
adata.obs["spatial_ring"] = pd.cut(
adata.obs["dist_to_rim_um"],
bins=[-1, 50, 150, 300, 600, np.inf],
labels=["0-50um (Rim Core)", "50-150um (Inner Periplaque)", "150-300um", "300-600um", ">600um (NAWM)"]
)
return adata.obs.groupby("spatial_ring", observed=True)["dist_to_rim_um"].count()Research Governance & Reproducibility Checklist
- Separate subpial cortical gray matter lesions from periventricular white matter lesions before comparing glial transcriptomes.
- Control for donor age, sex, Post-Mortem Interval (PMI), and cause of death in multi-donor post-mortem MS atlases.
- When analyzing CSF scBCR-seq/scTCR-seq, filter for productive paired heavy+light (IGH+IGK/IGL) chains before clonotype clustering.
Key Biomarkers & Standards Referenced in This Guide
High-throughput transcriptomic profiling at individual cell or nucleus resolution, enabling identification of disease-associated microglia (DAM), astrocytes, and vulnerable neuronal subtypes.
Subcellular-resolution spatial transcriptomics imaging hundreds to thousands of RNA species in intact brain tissue sections while preserving cytoarchitecture.
Standard Python/HDF5 container for single-cell and spatial omics, storing expression matrices (X) alongside cell annotations (obs), gene metadata (var), and embeddings (obsm).
Chronic white matter MS lesions bordered by a dense rim of iron-laden, proinflammatory activated microglia/macrophages, visible on T2* phase MRI, SWI, and QSM.
Latent B-cell-tropic herpesvirus established as the leading causal environmental trigger of Multiple Sclerosis (~32-fold risk increase), driving CNS autoimmunity via EBNA1 molecular mimicry.
Oral small-molecule therapeutics crossing the blood-brain barrier to simultaneously inhibit B-cell receptor signaling and FcγR-mediated proinflammatory microglial activation in Multiple Sclerosis.
Intermediate filament protein of astrocytes released into CSF and blood during reactive astrogliosis; tracks smoldering PIRA progression in MS and amyloid-induced astrocytic reactivity in Alzheimer's.
Axonal cytoskeletal protein released into CSF and blood upon neuroaxonal injury; a cross-disease biomarker of neurodegeneration rate in ALS, MS, AD, and FTD.
Live Open Datasets & Papers Matching This Guide
BICCN Whole Human Brain Single-Cell Transcriptomic Cell Type Atlas
Cell atlas spanning >3 million single nuclei across 100+ human brain regions, mapping distinct vulnerable neuronal and glial sublineages.
Spatial Transcriptomics of Chronic Active Multiple Sclerosis Lesions Reveals Iron-Laden MIMS Microglia Driving OPC Differentiation Arrest
Subcellular MERFISH and single-nucleus RNA sequencing across human post-mortem white matter lesions map complement C1q signaling and interferon-responsive oligodendrocyte states at paramagnetic lesion rims.
Dandiset 000108: Single-Cell Patch-seq Electrophysiology and Morphometry of Human Neocortical Neurons
Over 1,200 human surgical neocortical pyramidal neurons and interneurons characterized with patch-clamp electrophysiology, morphological reconstruction, and scRNA-seq.
Peripheral Immune Alterations and T Cell Clonal Dynamics Across the Parkinson's Disease Spectrum
The role of peripheral immunity in Parkinsons disease (PD) remains incompletely understood. Here, we performed paired single-cell RNA sequencing (scRNA-seq) and T-cell receptor (TCR) profiling of 630k peripheral blood mononuclear cells (PBMCs) from 168 donors spanning idiopathic and genetic PD, prod...
Allen Brain Atlas: Aging Dementia TBI - non-ISH data
Neuropathologic, molecular and transcriptomic study of aging, dementia, and Traumatic Brain Injury (TBI) of brains from control and TBI cases in a unique aged population-based cohort from the Adult Changes in Thought (ACT) study. Non-ISH data.... Freely accessible open data product maintained by the Allen Institute for Brain Science.
Allen Brain Atlas: Non-Human Primate Macrodissection Microarray
Genome-wide microarray data profiling gene expression in gross brain structures using rhesus macaque-specific DNA microarrays.... Freely accessible open data product maintained by the Allen Institute for Brain Science.