RNA TargetsSolid Tumor · Skin OncologyResearch Use Only
Melanoma Gene Expression
Reference Targets
Reference Targets
A biologically curated RNA target reference for melanoma spanning all histological subtypes — enabling researchers to select genes across MAPK driver oncogenes, phenotypic state switching, IO response biology, and MAPKi resistance mechanisms. Designed to resolve the MITF-high melanocytic vs AXL-high mesenchymal resistance state transition at single-cell resolution.
251
Total Genes
7
Functional Categories
3
Therapy Modalities
6+
Curation Sources
1
Panel Power Scorecard & Functional Categories
● Panel Power Scorecard
Panel Score: 88 / 100
93%
Landmark
Biomarker
Coverage
Biomarker
Coverage
89%
COSMIC
Tier-1
Coverage
Tier-1
Coverage
16 genes
FDA
Biomarker
Genes
Biomarker
Genes
21 genes
Clinical Trial
Biomarkers
Biomarkers
9 states
Cell States
Resolvable
Resolvable
251 genes
Total Panel
Genes
Genes
Published precedent — targeted panels are sufficient
Tirosh et al. 2016 Science — 3,442-cell atlas captured with 600-gene targeted panel
Sade-Feldman et al. 2018 Cell — 20-gene T cell signature sufficient to predict ICI response
63
MAPK Driver Signaling
66
Immune Microenvironment
39
MAPKi Resistance
31
MHC-I & Antigen Presentation
33
Stromal / Angiogenesis
30
Proliferation
38
DNA Damage / UV Signature
2
Target Curation Principles
Commercial Assays
- Foundation Medicine FoundationOne CDx
- Tempus xT RNA (melanoma module)
- QIAGEN QIAseq Melanoma Panel
- Illumina TruSight Oncology 500
- Thermo Fisher Oncomine Comprehensive
- IDT xGen Melanoma Panel
- Castle Biosciences DecisionDx-Melanoma
Public Databases
- TCGA SKCM dataset
- COSMIC melanoma mutation census
- MSigDB hallmark gene sets
- Human Cell Atlas (skin)
- GEO melanoma scRNA-seq atlases (Tirosh 2016, Sade-Feldman 2018)
- cBioPortal TCGA-SKCM cohort
Peer-Reviewed Literature
- Tirosh et al. 2016 Science (melanoma scRNA; phenotype switching)
- Sade-Feldman et al. 2018 Cell (TCF7 ICI response)
- BRIM-3/coBRIM/COLUMBUS MAPKi trials
- KEYNOTE-006 pembrolizumab biomarkers
- Helmink et al. 2020 Nature (TLS = IO response)
- AXL/NRG1/EGFR MAPKi resistance mechanism reviews
Why Single-Cell RNA for Melanoma?
Melanoma phenotype switching — from MITF-high melanocytic to AXL-high mesenchymal resistance state — is the central challenge in MAPKi resistance, but occurs at a subclonal level invisible to bulk RNA. Tapestri simultaneously detects BRAF/NRAS mutation status and MITF/AXL transcriptional state per cell.
IO Response Prediction — The Melanoma Gold Standard
This reference covers all validated IO biomarkers: TCF7+ progenitor-exhausted CD8 T cells, TLS B cell signatures, TREM2+ macrophage resistance program, and MHC-I/B2M antigen presentation status — all resolved simultaneously at single-cell resolution.
3
Target Reference Structure — Gene Table
1 · MAPK Driver Signaling2 · Immune Microenvironment3 · MAPKi Resistance4 · MHC-I & Antigen Presentation5 · Stromal / Angiogenesis6 · Proliferation / Cell Cycle7 · DNA Damage / UV Signature
| Category | Representative Genes (n) | Biological Function | Disease Relevance | scD+R Use Case |
|---|---|---|---|---|
| 1 · MAPK Driver Signaling · 63 genes | ||||
| BRAF/NRAS/MEK + Phenotype | BRAF, NRAS, MAP2K1, MAP2K2, MAPK3, MAPK1, KRAS, NF1, KIT, PDGFRA, MET, AXL, FGFR1, EGFR, PIK3CA, PTEN, AKT1, MTOR, CTNNB1, APC, MYC, CCND1, CDK4, CDK6, RB1, TP53, CDKN2A, MDM2, SOX10, SOX9, MITF, PAX3, ZEB1, ZEB2, SNAI1, TWIST1, NGFR, CDKN1A, RXRG (39) + 24 accessory | MAPK oncogene; phenotype switching; PI3K/WNT | BRAF V600E in 50% = vemurafenib/dabrafenib; NRAS mut. 15%; NF1 loss = MEKi; MITF = melanocytic state; low-MITF/high-AXL = invasive resistance state; WNT/β-catenin = immune desert | Identify BRAF-mut vs NRAS-mut subclones; resolve MITF-high vs MITF-low cell states |
| 2 · Immune Microenvironment · 66 genes | ||||
| T Cell / ICI / Myeloid / TLS | CD3E, CD8A, CD4, GZMB, PRF1, IFNG, TBX21, TOX, PDCD1, LAG3, HAVCR2, TIGIT, CD274, CTLA4, TCF7, CXCR5, ICOS, FOXP3, IL2RA, ENTPD1, CXCL13, B2M, CD68, CD163, TREM2, SPP1, CXCL9, CXCL10, ARG1, IDO1, MS4A1, CD19, NCAM1, NKG7, LILRA4 (35) + 31 accessory | CTL exhaustion; checkpoint; TAM; TLS B cells | Pembrolizumab/nivolumab; ipilimumab; TCF7+ progenitor = ICI response; TLS = nivolumab predictor; TREM2+ = IO resistance; IDO1 = immune evasion | Identify TCF7+ progenitor-exhausted T cells; resolve TAM subtypes; identify TLS |
| 3 · MAPKi Resistance · 39 genes | ||||
| Resistance / Bypass | EGFR, FGFR1, NRG1, AXL, PDGFRB, MET, MAP3K8, DUSP4, DUSP6, SPRY2, CCND1, CDK4, RB1, CDKN2A, MITF, SOX10, YAP1, WWTR1 (18) + 21 accessory | Bypass signaling; feedback; phenotype switching | Acquired MAPKi resistance via ERK reactivation or RTK bypass; AXL = stem-like resistance; YAP1 = transcriptional resistance | Identify MAPKi-resistant subclones before progression |
| 4 · MHC-I / Antigen Presentation · 31 genes | ||||
| MHC-I / Neoantigen | HLA-A, HLA-B, HLA-C, B2M, TAP1, TAP2, TAPBP, PSMB8, PSMB9, NLRC5, IRF1, STAT1, JAK1, JAK2, TYRP1, DCT, TYR, MLANA, PMEL (19) + 12 accessory | MHC-I antigen presentation; tumor antigens | B2M/HLA-A loss = ICI resistance; JAK1/2 = acquired resistance; MLANA/GP100/TYRP1 = TAA targets | Map MHC-I-loss subpopulations; resolve antigen-expressing tumor cells |
| 5 · Stromal / Angiogenesis · 33 genes | ||||
| Stroma / Vasculature | ACTA2, FAP, VEGFA, KDR, ANGPT1, PECAM1, CXCL12, COL1A1, FN1, MMP2, MMP9, POSTN, LRRC15, TGFB1 (14) + 19 accessory | CAF; vasculature; ECM | Desmoplastic stroma in metastatic melanoma; VEGF; LRRC15+ apCAF | Map stromal exclusion barrier; identify LRRC15+ apCAF |
| 6 · Proliferation · 30 genes | ||||
| Proliferation | MKI67, TOP2A, CCNB1, AURKA, CDK2, E2F1, FOXM1, MCM2, PLK1, CDC20 (10) + 20 accessory | Proliferation index | Ki-67 = prognosis; CDK4 amp. = palbociclib; AURKA = alisertib | Score proliferating vs invasive vs quiescent cells |
| 7 · DNA Damage / UV Signature · 38 genes | ||||
| UV DDR / TMB | TP53, ATM, PARP1, BRCA1, BRCA2, ERCC2, ERCC3, XPC, MLH1, MSH2, POLE, CDKN2A, MDM2, CHEK1, CHEK2, GADD45A (16) + 22 accessory | UV DNA damage; DDR; TMB | UV signature SBS7a/7b = high TMB; CDKN2A most frequent somatic loss; dMMR = pembrolizumab; TMB ≥10 = ICI eligibility | Correlate UV-DDR expression with TMB |
Total: 251 genesCat 1: 63 · Cat 2: 66 · Cat 3: 39 · Cat 4: 31 · Cat 5: 33 · Cat 6: 30 · Cat 7: 38
ⓘ 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.