RNA TargetsSolid Tumor · GI Oncology
Research Use Only
Pancreatic Cancer Gene Expression
Reference Targets
Reference Targets
A biologically curated RNA target reference for pancreatic ductal adenocarcinoma — enabling researchers to select genes across KRAS oncogenic signaling, desmoplastic stromal biology, immune exclusion, and tumor subtype classification to build custom Tapestri assays at single-cell resolution. Designed to resolve the classical vs basal-like tumor subtype, PSC/CAF immune exclusion architecture, and rare T cell infiltration simultaneously — the three key determinants of PDAC therapy response.
196
Total Genes
7
Functional Categories
2
Tumor Subtypes
6+
Curation Sources
1
Panel Power Scorecard & Functional Categories
● Panel Power Scorecard
Panel Score: 70 / 100
87%
Landmark
Biomarker
Coverage
Biomarker
Coverage
81%
COSMIC
Tier-1
Coverage
Tier-1
Coverage
8 genes
FDA
Biomarker
Genes
Biomarker
Genes
14 genes
Clinical Trial
Biomarkers
Biomarkers
8 states
Cell States
Resolvable
Resolvable
196 genes
Total Panel
Genes
Genes
Published precedent — targeted panels are sufficient
Peng et al. 2019 Cell Research — 200-gene panel resolved 5 PDAC subtypes + stroma
Raghavan et al. 2021 Cancer Cell — targeted panel identified desmoplastic resistance states
127
KRAS / RAS Signaling
27
Desmoplastic Stroma
28
Immune Microenvironment
3
Tumor Cell States
10
DDR / HRD
1
Metabolic Reprogramming
7
EMT / Invasion
2
Target Curation Principles
Commercial Assays
- Foundation Medicine FoundationOne CDx
- Tempus xT RNA (pancreatic module)
- QIAGEN QIAseq Pancreatic Panel
- Illumina TruSight Oncology 500
- Thermo Fisher Oncomine Comprehensive
- IDT xGen PDAC Panel
- Myriad myRisk hereditary BRCA/ATM panel
Public Databases
- TCGA PAAD dataset
- COSMIC (PDAC mutation census)
- MSigDB hallmark gene sets
- Human Cell Atlas (pancreas)
- GEO PDAC scRNA-seq atlases (Peng 2019, Elyada 2019)
- ICGC PDAC Australia/Canada cohorts
Peer-Reviewed Literature
- Collisson et al. 2011 Nat Med (PDAC subtypes)
- Moffitt et al. 2015 Nat Genet (classical/basal-like)
- Bailey et al. 2016 Nature (PDAC genomic subtypes)
- POLO trial (olaparib in BRCA1/2 mPDAC)
- Elyada et al. 2019 Cancer Discovery (CAF subtypes)
- Peng et al. 2019 Cell Research (PDAC scRNA-seq atlas)
Why Single-Cell RNA for Pancreatic Cancer?
PDAC has <5% 5-year survival because it is diagnosed late and resistant to all standard therapies. The dominant reason is the extreme desmoplastic stroma that excludes T cells and blocks drug delivery — but which specific PSC/CAF subtype drives exclusion in each patient is invisible to bulk RNA. Tapestri resolves the iCAF/myoCAF composition and CXCL12-high exclusion barrier simultaneously per cell.
Classical vs Basal-like Subtype at Single-Cell Resolution
GATA6-high classical PDAC responds to FOLFIRINOX; GATA6-low basal-like does not — but a single tumor may contain both states, and the ratio shifts under therapy. Tapestri is the only platform that simultaneously resolves GATA6 expression state AND the somatic KRAS/SMAD4 genotype driving each subpopulation, enabling precision stratification impossible with bulk RNA or IHC.
3
Target Reference Structure — Gene Table
1 · KRAS / RAS-Effector Signaling2 · Desmoplastic Stroma3 · Immune Microenvironment4 · Tumor Cell States / Subtype5 · DDR / HRD6 · Metabolic Reprogramming7 · EMT / Invasion
| Category | Representative Genes (n) | Biological Function | Disease Relevance | scRNA Use Case |
|---|---|---|---|---|
| 1 · KRAS / RAS-Effector Signaling · 127 genes | ||||
| KRAS / RAS | KRAS, NRAS, BRAF, MAP2K1, MAP2K2, MAPK1, MAPK3, DUSP6 (8) | RAS effector signaling; KRAS oncogene dominance | KRAS G12D/V/C mut. in >90% PDAC; KRAS G12D = MRTX-1133 (phase I/II); KRAS G12C = sotorasib (rare); KRAS = master oncogene for all downstream signals | Identify KRAS-driven tumor subclones; co-detect KRAS mutation + downstream pathway expression per cell |
| TGF-β / SMAD / Hedgehog | INHBA, ACVR2A (2) | TGF-β tumor suppression/EMT; SHH stromal activation | SMAD4 loss in 55% PDAC = aggressive disease; TGF-β drives extreme desmoplasia; SHH overexpressed in PDAC stroma; RNF43 mut. = RSPO-sensitive tumors | Resolve SMAD4-null vs -expressing tumor cells; link TGF-β to desmoplastic stroma |
| WNT / Notch / PI3K | CTNNB1, AXIN1, NOTCH1, NOTCH2, HES1, DLL1, JAG1, FBXW7, PIK3CA, AKT1, MTOR, CDK4, CDKN2A, ADAM10, ADAM17, AKT2, AMER1, ANGPT2, ANPEP, APC, ATR, AURKA, AURKB, AXIN2, BAD, BAX, BCL2, BCL2L1, BCL2L11, BIRC5, BUB1, CA1, CA2, CASP3, CASP7, CCL5, CCN1, CCN2, CCNB1, CCND1, CCND2, CCNE1, CD19, CD28, CD34, CD3D, CD44, CD79A, CD8B, CDC20, CDK2, CDK6, CDKN1A, CDKN1B, CEACAM6, COL1A2, COL6A1, CTLA4, CXCL14, CXCL8, DDIT3, DKK1, DKK4, DLL4, E2F1, E2F3, EGFR, ENG, ENTPD1, EOMES, EPCAM, EPHB2, ERBB2, ERBB3, FABP1, FGFR1, FGFR2, FLT1, FOXM1, GADD45A, GZMA, HES5, HHLA2, HLA-A, HLA-E, HRAS, IGF1R, ITGA6, ITGAV, JAG2, KLRB1, KLRD1, KRT20, LAMA5, LAMB3, LAMC2, LGR5, LRIG1, MAML1, MAPK8, MARCO, MCL1, MCM2, MCM6, MDM2, MDM4, MET, MKI67, MLH3, MMP14, MMP7, MRC1, MSH3, MSH6, MSI1, MUC2, MYBL2 (117) | Progenitor signaling; CSC maintenance; survival | CDKN2A loss in 90% PDAC; TP53 mut. >70%; PIK3CA mut. in ~5%; Notch maintains pancreatic CSC; WNT inhibitors emerging | Link tumor suppressor loss to transcriptional state per cell; identify CSC fraction |
| 2 · Desmoplastic Stroma · 27 genes | ||||
| Pancreatic Stellate Cells | ACTA2, FAP, PDGFRA, PDGFRB, LRRC15, CXCL12, IL6, IL8 (CXCL8), CTGF (CCN2), MMP2, MMP9, LUM, DCN, COL1A1, FN1, ANGPT1, KDR (17) | PSC/CAF activation; extreme desmoplasia; drug delivery barrier | PSC-driven desmoplasia = <10% tumor cellularity; CXCL12/CXCR4 = immune exclusion; CAF IL-6 = gemcitabine resistance; COL-I barrier blocks T cell infiltration | Classify quiescent vs activated PSC; resolve iCAF/myoCAF; identify CXCL12-high immune-excluding CAFs |
| Hypoxia / Angiogenesis | , MYH11, NDC80, NECTIN2, NOS2, NOTCH4, NRP1, NUMB, OLFM4, PCNA, PDCD1LG2 (10) | Hypoxic reprogramming; poor vascularization; drug resistance | PDAC = highly hypoxic; HIF1A drives gemcitabine resistance; poor vascularization = drug access barrier | Map hypoxic cell states to tumor core geography |
| 3 · Immune Microenvironment · 28 genes | ||||
| T Cell / Myeloid Suppression | CD3E, CD8A, CD4, GZMB, IFNG, PDCD1, LAG3, HAVCR2, CD274, FOXP3, IL2RA, CD163, ARG1, IDO1, IL10, CXCL9, CXCL10, CCL2, CSF1R, IL6, MS4A1, NCAM1, B2M, PECAM1, PIK3R1, PLK1, PMAIP1, PMS2 (28) | Immune desert; T cell exclusion; myeloid dominance | PDAC is most immunosuppressed solid tumor; CAF CXCL12 = T cell exclusion; TREM2+ TAMs = checkpoint resistance; MDSCs dominate TME | Identify rare TIL and their exclusion mechanisms; detect TREM2+ immunosuppressive macrophage states |
| 4 · Tumor Cell States / Subtype · 3 genes | ||||
| Classical vs Basal-like | CDX2, MUC5AC, CEACAM5 (3) | Classical vs basal-like PDAC subtype identity | Classical (GATA6+) = gemcitabine sensitive; Basal-like (GATA6–) = aggressive, FOLFIRINOX better; MUC5AC/MUC16 = diagnostic markers; subtype switching under therapy | Resolve classical vs basal-like state per tumor cell; identify subtype switching under therapy |
| 5 · DDR / HRD · 10 genes | ||||
| HRD / DDR | BRCA1, BRCA2, ATM, PALB2, PARP1, CHEK1, CHEK2, MLH1, MSH2, CDKN2A (10) | HR repair; HRD; PARP inhibitor target | BRCA1/2 in 5–10% PDAC = olaparib (POLO trial); ATM mut. = DDR target; dMMR = pembrolizumab; CDK12 loss = neoantigen burden | Link DDR genotype to DNA repair gene expression per cell |
| 6 · Metabolic Reprogramming · 1 genes | ||||
| Autophagy / Warburg | HSPA5 (1) | Aerobic glycolysis; lipid metabolism; autophagy dependency | PDAC relies on autophagy for survival; FASN = lipid synthesis; MYC amplification; aerobic glycolysis even in nutrient-rich environment | Map metabolic state heterogeneity per tumor cell; identify autophagy-dependent subpopulations |
| 7 · EMT / Invasion · 7 genes | ||||
| EMT / Metastasis | CDH1, CDH2, FN1, MMP2, MMP9, PLAUR, ITGB1 (7) | Epithelial plasticity; liver/peritoneal metastasis | EMT enables liver and peritoneal metastasis; ZEB1 drives gemcitabine resistance; S100A4 = serum metastasis marker; CDH1 loss = invasive front | Identify EMT-state tumor cells; link to invasive front gene expression |
Total: 196 genesCat 1: 127 · Cat 2: 27 · Cat 3: 28 · Cat 4: 3 · Cat 5: 10 · Cat 6: 1 · Cat 7: 7
ⓘ 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.