RNA TargetsNeuroimmunologyResearch Use Only
Multiple Sclerosis (MS)
Gene Expression Reference Targets
Gene Expression Reference Targets
A biologically curated RNA target reference for multiple sclerosis spanning T/B cell autoimmune pathways, oligodendrocyte remyelination biology, CNS-resident microglia activation, and therapy target genes (S1P1, CD20, CD52, integrin α4) — enabling researchers to configure custom Tapestri assays for disease mechanism, biomarker, and precision neuroimmunology studies.
230
Total Genes
7
Functional Categories
4
MS Subtypes Covered
6+
Curation Sources
1
Panel Power Scorecard & Functional Categories
● Panel Power Scorecard
Panel Score: 61 / 100
84%
Landmark
Biomarker
Coverage
Biomarker
Coverage
65%
COSMIC
Tier-1
Coverage
Tier-1
Coverage
7 genes
FDA
Biomarker
Genes
Biomarker
Genes
11 genes
Clinical Trial
Biomarkers
Biomarkers
7 states
Cell States
Resolvable
Resolvable
230 genes
Total Panel
Genes
Genes
Published precedent — targeted panels are sufficient
Schirmer et al. 2019 Nature (MS brain single-cell atlas)
Falcão et al. 2018 Nature Neurosci (OPC remyelination fate-mapping)
52
T Cell / Adaptive
38
B Cell / TLS
42
Microglia / CNS
42
OPC / Remyelination
38
Astrocyte / Glia
28
Therapy Targets
20
Cytokines / Biomarkers
2
Background & Curation Principles
Commercial Assays
- NanoString nCounter Neuroinflammation Panel
- HTG EdgeSeq MS Immune Panel
- Qiagen NeuroPathology Panel
- Illumina Neuro Research Panel
Public Databases
- GWAS MS risk loci (International MS Genetics Consortium)
- Human Cell Atlas (CNS / immune)
- GEO MS scRNA datasets
- MSigDB neuroimmune signatures
- Allen Brain Atlas
Peer-Reviewed Literature
- MS single-cell atlas (Schirmer 2019 Nature)
- Oligodendrocyte remyelination atlas (Falcão 2018 Nature Neurosci)
- Microglia homeostatic/activated states (Keren-Shaul 2017 Cell)
- Phase 3 trial biomarkers: CONFIRM/DEFINE (dimethyl fumarate), OPERA (ocrelizumab)
Why Single-Cell RNA for Multiple Sclerosis?
MS lesions are heterogeneous — active demyelinating plaques, chronic active lesions, and remyelinating shadow plaques coexist in the same patient. Bulk RNA of CSF or brain biopsy averages oligodendrocytes, microglia, T cells, and astrocytes into one signal. Tapestri resolves CNS-infiltrating immune cells from CNS-resident cells, and co-detects HLA-DRB1 risk allele expression alongside T cell activation state per cell — a co-detection impossible with any other single-cell platform.
Oligodendrocyte Remyelination — The Unmet Target
Remyelination failure in progressive MS is driven by OPC differentiation block, not OPC depletion. LINGO-1, GPR17, and MYRF control the maturation checkpoint. Panel covers OPC identity (PDGFRA/SOX10/OLIG2), mature oligodendrocyte markers (MBP/PLP1/MOG), and remyelination inhibitors (LINGO1/SEMA3A/PSA-NCAM) — enabling per-cell quantification of the OPC-to-oligodendrocyte differentiation trajectory.
3
Target Reference Structure — Gene Table
1 · T Cell / Autoimmune Pathways2 · B Cell / Plasma Cell3 · Microglia / CNS Innate4 · Oligodendrocyte / Remyelination5 · Astrocyte / Neuroinflammation6 · Therapy Targets7 · Cytokines / Complement
| Category | Representative Genes (n) | Biological Function | Disease Relevance | scD+R Use Case |
|---|---|---|---|---|
| 1 · T Cell / Adaptive Autoimmune Pathways · 52 genes | ||||
| Immune | CD3E, CD4, CD8A, FOXP3, IL2RA, RORC, TBX21, GATA3, CCR6, CXCR3, CXCR4, CCR7, SELL, ICOS, CD28, CD80, CD86, IL17A, IL17F, IFNG, TNF, IL21, IL10, STAT3, JAK1, JAK2 (26) + 26 accessory | Th1/Th17/Treg polarization; CNS trafficking; JAK-STAT signaling | IL17A/RORC = Th17 pathology (spinal cord lesions); FOXP3 = Treg deficiency; JAK1 = baricitinib target; CXCR3 = CNS infiltration | Resolve Th1 vs Th17 vs Treg proportions; map JAK-STAT activation per T cell subset |
| 2 · B Cell / Plasma Cell / Tertiary Lymphoid Structures · 38 genes | ||||
| Signaling | MS4A1, CD19, CD38, CD27, CXCR5, CXCL13, AICDA, PRDM1, IRF4, XBP1, IGHG1, IGHM, IGHD, PDCD1, CD274, BCL6, PAX5 (17) + 21 accessory | Meningeal B cell aggregates; intrathecal Ig synthesis; anti-CD20 target | MS4A1/CD19 = ocrelizumab target; CXCL13 = TLS marker in progressive MS; AICDA = active affinity maturation; intrathecal IgG = diagnostic | Map meningeal TLS B cell aggregates; identify plasmablast vs memory B cell subsets in CSF |
| 3 · Microglia / CNS Innate Immunity · 42 genes | ||||
| DDR | TREM2, P2RY12, TMEM119, CX3CR1, SALL1, HEXB, C1QA, C1QB, CSF1R, CD68, SPP1, CCL2, TNF, IL1B, IL6, NLRP3, IRF8, PYCARD, CGAS, STING1 (20) + 22 accessory | Homeostatic vs disease-associated microglia; neuroinflammation; inflammasome | P2RY12/TMEM119 = homeostatic microglia; TREM2+SPP1+ = chronic active lesion (CAL) microglia; NLRP3 = inflammasome target; STING = innate immune activation | Resolve homeostatic vs DAM microglia states; identify CAL-associated myeloid phenotypes |
| 4 · Oligodendrocyte / Remyelination Biology · 42 genes | ||||
| Lineage | OLIG2, OLIG1, SOX10, NKX2-2, PDGFRA, MBP, PLP1, MOG, MAG, CNP, MYRF, LINGO1, GPR17, SEMA3A, CSPG4, FYN, NOTCH1, ASCL1, SOX2 (19) + 23 accessory | OPC identity; mature oligodendrocyte; remyelination inhibitors/promoters | PDGFRA/OLIG2 = OPC; MBP/PLP1 = mature oligodendrocyte; LINGO1 = remyelination inhibitor (anti-LINGO-1 trial); GPR17 = differentiation checkpoint | Track OPC differentiation trajectory; identify remyelination failure at single-cell resolution |
| 5 · Astrocyte / Neuroinflammation / Glia Scar · 38 genes | ||||
| Stromal | GFAP, S100B, ALDH1L1, VIM, NESTIN, AQP4, ALDOC, LCN2, CXCL10, C3, COMPLEMENT1, SERPINA3, GJA1, SLC1A2, GLUL, STAT3, NFKB1, NRF2, HMOX1 (19) + 19 accessory | Reactive astrocyte states (A1/A2); glia scar formation; glutamate homeostasis | GFAP = astrocyte activation; LCN2 = A1 neurotoxic astrocyte; AQP4 = NMO autoantibody target (aquaporin-4); C3 = complement-dependent A1 induction | Classify A1 vs A2 astrocyte activation states; identify NMO-specific AQP4+ subpopulations |
| 6 · Therapy Target Genes · 28 genes | ||||
| Driver | S1PR1, S1PR3, S1PR4, S1PR5, ITGA4, ITGB1, VCAM1, CD52, FCGR3A, FCGR2B, MS4A1, CD38, IL2RA, IL7R, CLEC16A, HLA-DRB1, HLA-DQB1, CD58, CD226, CLEC16A (20) + 8 accessory | Approved and investigational MS therapy targets | S1PR1 = fingolimod/siponimod/ozanimod; ITGA4 = natalizumab; CD52 = alemtuzumab; CD20 = ocrelizumab/ofatumumab; IL2RA = daclizumab | Map therapy target expression per immune cell subset; identify subpopulations that escape targeted therapy |
| 7 · Cytokines / Complement / Biomarkers · 20 genes | ||||
| Metabolism | NEFL, NEFM, NEFH, VGF, CHI3L1, CXCL13, CCL19, CXCL9, IL6, IL10, IFNB1, IFNA1, GM-CSF (CSF2), LIF, BMP4, IGF1, BDNF, NRG1, S100A4 (19) + 1 accessory | CSF biomarkers; neurofilament light (NfL); neuroprotection | NEFL = neuroaxonal damage (NfL biomarker); CXCL13 = B cell follicle / TLS; CHI3L1 = astrocyte activation biomarker; LIF = neuroprotective | Identify CSF biomarker-expressing cell types; map cytokine networks driving lesion formation |
Total: 230 genesCat 1: 52 · Cat 2: 38 · Cat 3: 42 · Cat 4: 42 · Cat 5: 38 · Cat 6: 28 · Cat 7: 24
ⓘ Select genes appear in more than one functional category reflecting their multi-role biology. The total above counts unique genes; per-category counts include all category-relevant entries.