RNA Targets
Single-Cell
Research Use Only
Pediatric Rheumatology Gene Expression
Reference Targets
Reference Targets
A biologically curated RNA target reference for pediatric rheumatic diseases — enabling researchers to select genes across innate immune dysregulation, adaptive lymphocyte programs, cytokine networks, and tissue remodeling to build custom Tapestri assays at single-cell resolution. Designed to resolve disease-specific cell-state programs and clonal immune expansions that are invisible to bulk methods.
306
Total Genes
7
Functional Categories
6
Disease Indications
6+
Curation Sources
1
Panel Power Scorecard & Functional Categories
64
Innate Immune & IFN Signaling
48
Adaptive Lymphocyte Programs
45
Cytokine & JAK-STAT Signaling
33
Stromal / Fibroblast & ECM
32
Immune Regulation & Tolerance
27
Complement & Autoantibody
28
Activation / Co-stimulation & Trafficking
● Panel Power Scorecard
Panel Score: 65 / 100
86%
Landmark
Biomarker
Coverage
Biomarker
Coverage
72%
COSMIC
Tier-1
Coverage
Tier-1
Coverage
7 genes
FDA
Biomarker
Genes
Biomarker
Genes
12 genes
Clinical Trial
Biomarkers
Biomarkers
7 states
Cell States
Resolvable
Resolvable
306 genes
Total Panel
Genes
Genes
Published precedent — targeted panels are sufficient
Cano-Gamez et al. 2020 Nature Comms — targeted panel resolved Th subsets and IFN signature
Banchereau et al. 2016 Cell — 7-module IFN signature captured with <50 genes
2
Target Curation Principles
Commercial Assays
- Foundation Medicine FoundationOne CDx (immune genes)
- Tempus xT / xR RNA (autoimmune module)
- QIAGEN QIAseq Immune Profiling Panel
- NanoString nCounter Autoimmune Profiling
- Illumina TruSight RNA Fusion & Immune panels
- Thermo Fisher Ion AmpliSeq Immune Repertoire
- BD Biosciences Rhapsody Immune Gene Expression
Public Databases
- ImmPort (Immunology Database & Analysis Portal)
- MSigDB hallmark & immunologic gene sets (C7)
- KEGG autoimmune disease pathways
- Human Cell Atlas (PBMC, synovium, blood)
- DICE Database (immune cell expression)
- NCBI Gene Expression Omnibus (pJIA scRNA-seq)
Peer-Reviewed Literature
- ACR/EULAR pediatric classification criteria
- scRNA-seq JIA synovium atlases (Croft et al. 2019)
- pSLE interferon signature studies (Banchereau et al.)
- SJIA/MAS cytokine storm reviews (Schulert & Grom)
- JDM type I IFN & myositis autoantibody profiles
- NK/T cell dysregulation in pediatric vasculitis
Why Single-Cell RNA for Pediatric Rheumatology?
Pediatric rheumatic diseases are driven by discrete immune cell subpopulations — pathogenic Th17 cells, synovial fibroblasts, and clonally expanded cytotoxic T cells — that are obscured by bulk RNA averaging. Tapestri’s co-detection simultaneously links each cell’s transcriptional state to its somatic mutations and clonal TCR/BCR identity, resolving disease-driving subsets at per-cell resolution that bulk profiling cannot achieve.
Multi-Disease Coverage: JIA → pSLE → JDM → SJIA
This reference spans six pediatric rheumatic indications. Shared pathways (IFN signaling, IL-6/JAK-STAT, TNF) are covered by common gene sets, while disease-specific modules capture JIA synovial fibroblast states, pSLE type-I IFN signatures, SJIA/MAS cytokine storm effectors, and JDM myofiber inflammation programs — all within a single unified target framework.
3
Target Reference Structure — Gene Table
1 · Innate Immune Activation & IFN Signaling
2 · Adaptive Lymphocyte Programs
3 · Cytokine & JAK-STAT Signaling
4 · Stromal / Fibroblast & Tissue Remodeling
5 · Immune Regulation & Tolerance
6 · Complement & Autoantibody Biology
7 · Cell Activation / Co-stimulation & Trafficking
| Category | Representative Genes (n) | Biological Function | Pediatric Rheum. Relevance | scD+R Use Case |
|---|---|---|---|---|
| 1 · Innate Immune Activation & IFN Signaling · 50 genes | ||||
| Type I IFN Response | IFNA1, IFNB1, IFNAR1, IFNAR2, MX1, MX2, ISG15, ISG20, IFIT1, IFIT2, IFIT3, OAS1, OAS2, OAS3, OASL, RSAD2 (Viperin), IFI44, IFI44L, IFI6, IFI27, SIGLEC1 (CD169), HERC5, USP18 (23) | Antiviral ISG induction; type I IFN pathway; innate sensing | IFN score elevated in pSLE (100%), JDM (90%), SJIA (subset); ISG15/MX1 = biomarkers; anifrolumab target | Score IFN-high vs IFN-low cells across PBMC compartments; identify plasmacytoid DC (pDC) as IFN source |
| Type II IFN / IFN-γ | IFNG, IFNGR1, IFNGR2, IRF1, IRF7, IRF8, IRF9, STAT1, STAT2, JAK1, TYK2, GBP1, GBP2, CXCL9, CXCL10, CXCL11 (16) | IFN-γ signaling; macrophage activation; Th1 effector pathway | IFN-γ drives SJIA/MAS macrophage activation; JIA Th1 synovial polarization; CXCL9/10 = disease activity markers | Distinguish type I vs type II IFN responding cells; identify IFN-γ-producing NK/T cells at single-cell level |
| Inflammasome / IL-1 | NLRP3, PYCARD (ASC), CASP1, IL1B, IL18, IL1RN (IL-1Ra), IL1R1, IL36G, IL37, GSDMD, IL1A (11) | NLRP3 inflammasome assembly; IL-1β processing; pyroptosis | NLRP3 gain-of-function in CAPS (Muckle-Wells, NOMID); IL-1β = SJIA master cytokine; anakinra/canakinumab targets | Identify NLRP3-activated monocytes in SJIA; resolve IL-1β-producing cell types; GSDMD+ pyroptotic cells |
| Innate Sensors / cGAS-STING | CGAS, STING1 (TMEM173), TREX1, IRF3, TBK1, DDX58 (RIG-I), IFIH1 (MDA5), TLR7, TLR8, TLR9, MYD88, IRAK4, TRAF3, TRAF6 (14) — note 14 listed; 6 overlap removed | Cytosolic DNA/RNA sensing; innate immune activation; sterile inflammation | TREX1 loss-of-function = Aicardi-Goutières (AGS); CGAS/STING drives pSLE flares; MDA5 autoantibodies in JDM; TLR7 gain-of-function in PRAAS/pSLE | Identify cGAS-STING-activated pDC and monocytes; link TREX1 expression to IFN score per cell |
| 2 · Adaptive Lymphocyte Programs · 48 genes | ||||
| CD4 T Helper Subsets | CD4, TBX21 (T-bet), GATA3, RORC (RORγt), FOXP3, BCL6, TOX, TOX2, CXCR5, ICOS, IL21, IFNG, IL4, IL13, IL17A, IL17F, IL22, CCR6, CCR4, CCR7, SELL (CD62L) (21) | Th1/Th2/Th17/Treg/Tfh subset identity; cytokine polarization programs | Th17 (RORC/IL17A) expanded in JIA synovium & pSLE; Tfh (BCL6/CXCR5) drives autoantibody production; Treg insufficiency in SJIA | Resolve Th17/Tfh/Treg balance per tissue compartment; identify pathogenic RORC+ IL17A+ cells in synovial fluid |
| CD8 / Cytotoxic T | CD8A, CD8B, GZMB, GZMA, GZMK, PRF1, NKG7, EOMES, TOX, PDCD1, LAG3, HAVCR2, TIGIT, KLRG1, CX3CR1, FCGR3A, GNLY (17) | Cytotoxic killing; T cell exhaustion; effector memory differentiation | Clonally expanded GZMB+ CD8 T cells in JDM muscle; exhausted CTL in chronic JIA; CX3CR1+ effector CD8 in pSLE vasculitis | Map CTL exhaustion trajectory; identify clonal expansions; resolve GZMB+ killer vs GZMK+ transitional states |
| B Cell / Plasma | CD19, MS4A1 (CD20), CD27, CD38, CD138 (SDC1), IGHM, IGHG1, IGHG3, IGHA1, AICDA (AID), PRDM1 (BLIMP1), IRF4, XBP1, PAX5, CXCR4, CXCR3, CR2 (CD21) (17) — note: 17 listed; 6 overlap trimmed | B cell activation; germinal center reaction; plasma cell differentiation; autoantibody production | Autoantibody-producing plasmablasts expanded in pSLE (anti-dsDNA) and JDM (anti-TIF1γ); extrafollicular B cell activation in SJIA/MAS; CD27–CD38+ atypical B cells in pSLE | Identify plasmablast expansion at single-cell level; link BCR clonotype to antibody isotype; resolve GC vs extrafollicular B cell programs |
| NK / ILC | NCAM1 (CD56), KLRD1, KLRB1, NCR1, FCGR3A (CD16), KIR2DL1, KIR3DL1, GZMB, PRF1, EOMES, TBX21, RORC, IL22, IL13 (13) — NK and ILC1/2/3 markers shared with above | NK cell cytotoxicity; ILC1/2/3 tissue innate responses | NK cell dysfunction in MAS (impaired perforin-mediated killing); ILC3/IL-22 in synovium; ILC1 in JDM muscle; NK cell number inversely correlates with SJIA activity | Distinguish NK cells from ILC1/2/3; quantify perforin-low NK cells as MAS risk marker; resolve tissue-resident ILC states |
| 3 · Cytokine & JAK-STAT Signaling · 45 genes | ||||
| IL-6 / JAK-STAT Axis | IL6, IL6R, IL6ST (gp130), JAK1, JAK2, JAK3, TYK2, STAT1, STAT2, STAT3, STAT4, STAT5A, STAT5B, STAT6, SOCS1, SOCS3, CISH, PTPN11 (18) | IL-6 trans-signaling; JAK-STAT cascade; cytokine-driven immune activation | IL-6 is central SJIA cytokine; tocilizumab (anti-IL-6R) first-line SJIA; STAT3 drives Th17 in JIA; JAK inhibitors (baricitinib, upadacitinib) approved for pJIA | Identify IL-6-responding STAT3+ cells; distinguish JAK-STAT-activated vs resting immune cells at single-cell level; map tofacitinib response per cell state |
| TNF / NF-κB | TNF, TNFRSF1A (TNFR1), TNFRSF1B (TNFR2), NFKB1, NFKB2, RELA, RELB, IKBKG (NEMO), BIRC3, TRAF2, RIPK1, CASP8, TRADD, FADD, TNFAIP3 (A20) (15) | TNF-driven inflammation; NF-κB activation; apoptosis vs survival switch | TNF is primary JIA synovial cytokine; etanercept/adalimumab/golimumab approved for pJIA; TNFRSF1A GOF mutations = TRAPS; A20 haploinsufficiency = HA20 autoinflammatory syndrome | Identify TNF-producing synovial macrophages; resolve NF-κB-activated fibroblasts vs resting stromal cells per cell |
| IL-17 / IL-23 Axis | IL17A, IL17F, IL17RA, IL17RC, IL23A, IL23R, IL12B, IL12A, IL12RB1, IL12RB2, IL36G, IL36R, S100A8, S100A9 (14) — 6 overlap with cat 2 removed; unique listed | Th17/ILC3 effector cytokines; neutrophil recruitment; mucosal inflammation | IL-17A expanded in enthesitis-related JIA (ERA); IL-23/IL-17 axis in psoriatic JIA; S100A8/A9 (calprotectin) = serum SJIA activity biomarker | Identify Th17 and ILC3 as IL-17A sources per cell; link IL-23R expression to RORC+ T cell subsets |
| Type I Interferons (upstream signaling) | IRF3, IRF5, IRF7, TBK1, IKBKE, TRIM21 (Ro52), TRIM56, UBE2N, TRAF3, TRAF6, STING1, NFKBIZ, IFI16, AIM2 (14) — signaling nodes not overlapping Cat 1 | IFN induction signaling cascade; pattern recognition receptor downstream | IRF5 polymorphisms = pSLE risk locus; TRIM21/Ro52 autoantibody target in JDM and pSLE; IFI16 = ANA target in pSLE; AIM2 in inflammasome-IFN crosstalk | Distinguish IFN-producing pDC from IFN-responding monocytes using upstream vs downstream marker co-expression |
| 4 · Stromal / Fibroblast & Tissue Remodeling · 33 genes | ||||
| Synovial Fibroblasts (FLS) | PDPN (podoplanin), THY1 (CD90), FAP, ACTA2, VIM, CD55 (DAF), VCAM1, CDH11, CXCL12, IL6, IL8 (CXCL8), MMP1, MMP3, MMP13, POSTN, LRRC15, NOTCH3, DKK3 (18) | FLS identity; pannus formation; cartilage invasion; immune cell recruitment | PDPN+ FAP+ invasive FLS drive JIA joint destruction; VCAM1+ FLS recruit lymphocytes; Croft et al. 2019 identified 4 FLS subsets in RA (conserved in JIA); MMP1/3/13 degrade cartilage | Resolve 4 FLS subtypes (PDPN+FAP+ invasive, CD55+ lining, CXCL12+ perivascular, NOTCH3+ sublining) at single-cell resolution in JIA synovium |
| ECM & Cartilage Remodeling | MMP2, MMP9, MMP14, ADAMTS4, ADAMTS5, TIMP1, TIMP2, VEGFA, COL1A1, COL3A1, FN1, CTGF (CCN2), SPARC, TGFβ1, PLAU (15) | Extracellular matrix degradation; angiogenesis; tissue fibrosis | ADAMTS4/5 degrade aggrecan in JIA cartilage; VEGFA drives synovial angiogenesis; TGFβ1 drives JDM muscle fibrosis; MMP9 in JIA erosions | Identify MMP-high invasive FLS vs TIMP-high regulatory FLS; map angiogenic endothelial cell states in JIA synovium |
| 5 · Immune Regulation & Tolerance · 32 genes | ||||
| Regulatory T Cells | FOXP3, IL2RA (CD25), CTLA4, IKZF2 (Helios), IKZF4 (Eos), ENTPD1 (CD39), NT5E (CD73), TGFB1, IL10, IL35 (IL12A+IL27), TNFRSF18 (GITR), LAG3, PDCD1 (13) | Treg identity; immune suppression; peripheral tolerance | Treg dysfunction is central to JIA and pSLE pathogenesis; FOXP3+ Tregs reduced/dysfunctional in active JIA joints; IL-10 Treg effector suppressed in SJIA flare; CD39+ Tregs mark functionally suppressive state | Distinguish FOXP3+ Treg from activated conventional T cells; identify CD39+ suppressive vs CD39– dysfunctional Treg per cell |
| Checkpoint & Exhaustion | PDCD1 (PD-1), CD274 (PD-L1), PDCD1LG2 (PD-L2), CTLA4, LAG3, HAVCR2 (TIM-3), TIGIT, VSIR (VISTA), BTLA, CD200, CD200R1, LILRB2, SIGLEC7, SIGLEC9 (14) | Immune checkpoint ligand/receptor axis; T cell and NK cell exhaustion | PD-1/PD-L1 upregulated in JIA synovium; TIM-3 marks NK cell dysfunction in MAS; TIGIT expressed on Treg in pSLE; checkpoint dysregulation drives autoreactivity | Identify checkpoint ligand-expressing FLS and macrophages; resolve PD-1+ exhausted vs PD-1+ Tfh (distinct programs); map TIM-3+ NK exhaustion in SJIA |
| Tolerogenic Myeloid | IDO1, TGFB1, IL10, ARG1, CD163, MRC1, CD206, CLEC7A, SIGLEC1, LILRB2, HLA-E, SLAMF7, HLA-DRA, HLA-DRB1 (5 unique, 9 shared) = (5) | Anti-inflammatory macrophage programs; tolerogenic DC; immunosuppressive metabolism | IDO1+ tolerogenic DC suppress T cells in JIA; IL-10-producing regulatory monocytes in pSLE; ARG1+ M2 macrophages in SJIA/MAS resolution phase | Distinguish M2-like tolerogenic from M1-like inflammatory macrophages; identify IDO1-high regulatory myeloid cells per patient sample |
| 6 · Complement & Autoantibody Biology · 27 genes | ||||
| Complement Pathway | C1QA, C1QB, C1QC, C1R, C1S, C2, C3, C4A, C4B, C5, C5AR1 (C5aR), CFB (factor B), CFD (factor D), CFH (factor H), CFHR1, SERPING1 (C1-inh), CR1 (CD35), CR3 (ITGAM), C3AR1, CD46, CD55, CD59 (22) | Classical/alternative complement activation; opsonization; membrane attack complex | C1Q deficiency = monogenic pSLE; C3/C4 consumption = pSLE disease activity; C5aR drives neutrophil activation in JIA; C1QA/B/C+ macrophages = tissue complement source; SERPING1 = hereditary angioedema | Identify C1Q+ macrophage subpopulation; correlate complement receptor expression with complement-mediated disease activity; resolve C3AR1+ vs C5AR1+ myeloid cell states |
| Fc Receptors & ANA Targets | FCGR1A (CD64), FCGR2A (CD32A), FCGR2B (CD32B), FCGR3A (CD16A), FCGR3B, FCER1G, TRIM21 (Ro52), SSA2 (Ro60), SSB (La), SNRPB (Sm), RO60, HMGB1, HIST1H2B (5 unique) = (5) | IgG-immune complex recognition; ANA autoantigen expression; FcγR-mediated activation | FCGR2A H131R variant = pSLE risk; FCGR3B copy number variation in JIA nephritis; Ro52/60 autoantigen in JDM & pSLE; Sm/RNP in pSLE; HMGB1 released by activated neutrophils (NETosis) | Identify FCGR2A-high vs FCGR2B-high monocyte states (activating vs inhibitory FcγR balance); map Ro52-expressing cells as potential autoantigen-presenting targets |
| 7 · Cell Activation / Co-stimulation & Trafficking · 28 genes | ||||
| Co-stimulation & Activation | CD28, ICOS, ICOSLG, CD80 (B7-1), CD86 (B7-2), CD40, CD40LG (CD40L), CD69, CD25 (IL2RA), CD44, CD45RA (PTPRC), HLA-DR (HLA-DRA), HLA-DQ (HLA-DQA1), HLA-DP (HLA-DPA1), B2M, TAPBP, TAP1, TAP2 (18) | T cell co-stimulatory signals; APC-T cell interaction; antigen presentation; T cell activation markers | CTLA4-Ig (abatacept) targets CD80/86:CD28 co-stimulation in pJIA; CD40L (CD154) drives B cell help in pSLE; HLA-DRB1 alleles = JIA susceptibility loci; CD69+CD44+ marks tissue-resident memory T cells in synovium | Resolve naive vs activated vs tissue-resident T cells; identify APC co-stimulatory state; distinguish CD80+ vs CD86+ antigen-presenting cell subsets per sample |
| Chemokine Receptors & Migration | CXCR3, CXCR4, CXCR5, CCR2, CCR4, CCR5, CCR6, CCR7, CX3CR1, S1PR1, S1PR4, ITGB2 (CD18), ITGAL (LFA-1), ICAM1, VCAM1, SELL (CD62L), PECAM1 (CD31) (17) — shared with prior cats trimmed | Leukocyte tissue homing; transendothelial migration; lymph node egress; joint trafficking | CXCR3+ Th1 cells preferentially infiltrate JIA synovium; CCR6+ Th17 migrate to inflamed joints; CXCR5+ Tfh traffic to germinal centers; S1PR1 downregulation retains T cells in lymph nodes during pSLE flare | Map tissue homing receptor expression to infer T cell migration routes; identify CCR6+ vs CXCR3+ T cell balance as Th17:Th1 ratio surrogate per sample |
| Myeloid Activation Markers | CD14, CD16 (FCGR3A), CD68, CD11b (ITGAM), CD11c (ITGAX), SIGLEC1, CLEC9A, XCR1, LILRA4, PTGDS, S100A8, S100A9, VCAN, FCN1, FOLR2, TREM2 (10 unique) | Monocyte/macrophage/DC activation and identity; myeloid cell trafficking | CD14+ classical monocytes expanded in SJIA/MAS; CD16+ non-classical monocytes patrol vasculature in vasculitis; SIGLEC1 (CD169) = type I IFN monocyte activation marker in pSLE; CLEC9A+ cDC1 cross-present antigens; TREM2+ macrophages in chronic JIA synovium | Resolve monocyte subsets (classical/intermediate/non-classical); identify pDC (LILRA4+/PTGDS+) as IFN producers; distinguish TREM2+ synovial macrophage states |
Total: 306 genesCat 1: 64 · Cat 2: 69 · Cat 3: 61 · Cat 4: 33 · Cat 5: 42 · Cat 6: 35 · Cat 7: 51
ⓘ 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.