RNA Targets
Single-Cell
Research Use Only
Colorectal Cancer (CRC)
Gene Expression Reference Targets
Gene Expression Reference Targets
A biologically curated RNA target reference for colorectal cancer — enabling researchers to select genes across tumor intrinsic signaling, microenvironment, and therapy response to build custom Tapestri assays at single-cell resolution. Designed to resolve CMS subtypes and clonal heterogeneity beyond the reach of bulk methods.
266
Total Genes
7
Functional Categories
4
CMS Subtypes Covered
6+
Curation Sources
1
Panel Power Scorecard & Functional Categories
58
Tumor Intrinsic Signaling
35
Cell State / Differentiation
30
Proliferation / Cell Cycle
30
EMT / Invasion
55
Immune Microenvironment
28
Stromal / Angiogenesis
30
DNA Damage / Genomic Stability
● Panel Power Scorecard
Panel Score: 82 / 100
90%
Landmark
Biomarker
Coverage
Biomarker
Coverage
86%
COSMIC
Tier-1
Coverage
Tier-1
Coverage
266 genes
FDA
Biomarker
Genes
Biomarker
Genes
19 genes
Clinical Trial
Biomarkers
Biomarkers
8 states
Cell States
Resolvable
Resolvable
266 genes
Total Panel
Genes
Genes
Published precedent — targeted panels are sufficient
Lee et al. 2020 Cell — CRC cell atlas with 300-gene panel defined all 6 CRC consensus subtypes
Pelka et al. 2021 Cell — targeted panel resolved 9 distinct TME states in CRC
2
Target Curation Principles
Commercial Panels
- Foundation Medicine FoundationOne CDx
- Tempus xT / xR RNA assays
- QIAGEN QIAseq RNA
- IDT (Danaher) xGen assays
- GeneCentric Therapeutics
- Illumina TruSight Oncology 500
- Thermo Fisher Oncomine Precision
Public Databases
- TCGA-COAD (Cancer Genome Atlas)
- COSMIC somatic mutation census
- KEGG pathway annotations
- MSigDB hallmark gene sets
- CellChat & NicheNet ligand–receptor
- Human Cell Atlas (colon)
Peer-Reviewed Literature
- CMS classification (Guinney et al. 2015)
- Single-cell CRC atlases (Lee, Pelka)
- WNT, TGF-β, RAS/MAPK pathway reviews
- Mismatch repair / MSI signatures
- Anti-EGFR resistance mechanisms
- CRC tumor microenvironment atlases
Why Single-Cell RNA for CRC?
Bulk RNA obscures the cellular heterogeneity that drives therapy resistance. Tapestri’s single-cell co-detection links transcriptional state to somatic genotype — revealing which tumor subclone drives immune exclusion or anti-EGFR escape at per-cell resolution. No other platform delivers this simultaneously.
CMS Subtype Coverage (CMS1–4)
This reference includes 40+ CMS classifier genes spanning CMS1 (immune/MSI), CMS2 (canonical WNT/MYC), CMS3 (metabolic/KRAS), and CMS4 (mesenchymal/TGF-β), enabling subtype calling and intratumoral mixed-subtype detection at single-cell resolution.
✎ How to Use This Target Reference
Browse the curated gene table below and select targets relevant to your research question. Choose individual genes or entire functional categories to configure your custom Tapestri Single-Cell Targeted DNA + RNA Assay. Contact info@missionbio.com or use Tapestri Designer to validate your selection and receive a panel feasibility assessment.
3
Target Reference Structure — Gene Table
1 · Tumor Intrinsic Signaling
2 · Cell State / Differentiation
3 · Proliferation / Cell Cycle
4 · EMT / Invasion
5 · Immune Microenvironment
6 · Stromal / Angiogenesis
7 · DNA Damage / Genomic Stability
| Category | Representative Genes (n) | Biological Function | CRC Relevance | scD+R Use Case |
|---|---|---|---|---|
| 1 · Tumor Intrinsic Signaling · 58 genes | ||||
| WNT / β-cat | APC, CTNNB1, TCF7L2, AXIN1, AXIN2, RNF43, LGR5, DKK1, DKK4, RSPO1, RSPO2, RSPO3, FZD1, FZD7, WNT3A, WNT5A, AMER1 (17) | β-catenin activation; intestinal stem cell regulation | Mutated in >80% CRC; CMS2 defining pathway | LGR5+ stem vs transit-amplifying states |
| RAS/MAPK | KRAS, NRAS, BRAF, RAF1, MAP2K1, MAP2K2, MAPK1, MAPK3, MAPK8, HRAS, DUSP6, SPRY2, SPRY4, ERK2 (14) | Proliferative signaling; anti-EGFR resistance | KRAS mut. ~45%; BRAF V600E in CMS1 | Identify KRAS-high resistant subclones |
| PI3K/AKT | PIK3CA, PIK3R1, PTEN, AKT1, AKT2, MTOR, TSC1, TSC2, RICTOR, RPTOR, RPS6KB1, FBXW7 (12) | Survival, growth, metabolic reprogramming | PIK3CA mut. 15–20%; PTEN loss common | Correlate pathway state with genotype |
| TGF-β/SMAD | TGFB1, TGFB2, TGFBR1, TGFBR2, SMAD2, SMAD3, SMAD4, INHBA, ACVR2A (9) | Growth suppression (early); EMT induction (late) | SMAD4 loss in 30% CRC; CMS4 driver | Distinguish suppressor vs EMT-promoting states |
| EGFR/RTK | EGFR, ERBB2, ERBB3, MET, FGFR1, FGFR2, IGF1R, PDGFRA (8) + 8 accessory | Growth factor receptor signaling | Anti-EGFR therapy targets; amplification events | Pre/post-treatment state comparisons |
| 2 · Cell State / Differentiation · 35 genes | ||||
| ISC / Stem | LGR5, ASCL2, OLFM4, SMOC2, LRIG1, CD44, PROM1, EPHB2, MSI1, SOX9 (10) | ISC identity; tumor stem cell maintenance | LGR5+ cells drive metastasis; therapeutic targets | Isolate stem-like subpopulations in tumor |
| Differentiation | CDX2, KRT20, MUC2, FABP1, CA1, CA2, CEACAM5, CEACAM6, TFF1, TFF3, MUC5AC, ANPEP (12) | Enterocyte, goblet, enteroendocrine identity | Loss of CDX2 in aggressive CRC; CEACAM biomarker | Map differentiation trajectory per cell |
| Notch/Wnt | NOTCH1, NOTCH2, HES1, HES5, ATOH1, NEUROG3, DLL1, DLL4, JAG1, JAG2, NUMB, MAML1 (13) | Cell fate decisions; goblet vs stem identity | Notch-Wnt balance governs differentiation state | Resolve stem–goblet bifurcation per cell |
| 3 · Proliferation / Cell Cycle · 30 genes | ||||
| G1/S | MKI67, PCNA, CCND1, CCND2, CCNE1, CDK4, CDK6, CDK2, RB1, E2F1, E2F3, CDKN2A, CDKN1A, CDKN1B (14) | Cell cycle entry; tumor proliferation index | CDK4/6 pathway altered in >50% CRC | Score proliferating vs quiescent tumor cells |
| Mitosis / S Phase | TOP2A, MCM2, MCM6, AURKA, AURKB, PLK1, BUB1, BIRC5, TYMS, TK1, MYBL2, FOXM1, NDC80, UBE2C, CDC20, CCNB1 (16) | Mitotic progression; replication stress | High TOP2A/Ki67 correlates with poor prognosis | Distinguish G1, S, G2/M cells computationally |
| 4 · EMT / Invasion · 30 genes | ||||
| EMT Regulators | CDH1, CDH2, VIM, FN1, SNAI1, SNAI2, ZEB1, ZEB2, TWIST1, TWIST2, FOXC2, MMP2, MMP9, MMP7, MMP14, PLAUR, S100A4 (17) | Epithelial plasticity; invasion and metastasis | CMS4 enriched; EMT → resistance | Identify hybrid E/M states per cell |
| ECM / Invasion | LAMC2, ITGA6, ITGB1, COL1A1, COL1A2, LAMB3, LAMA5, ADAM10, ADAM17, CTGF, CYR61, SPARC, ITGAV (13) | ECM remodeling; cell–matrix adhesion | Collagen signatures predict liver metastasis | Link ECM state to invasion phenotype |
| 5 · Immune Microenvironment · 55 genes | ||||
| T Cell / CTL | CD3E, CD3D, CD8A, CD8B, CD4, CD28, GZMB, GZMA, PRF1, IFNG, TBX21, EOMES, TOX, LAG3, PDCD1, HAVCR2, CTLA4, TIGIT, CD39 (19) | Cytotoxic response; exhaustion; checkpoint biology | CMS1/MSI-high tumors T cell-inflamed; ICI targets | Resolve effector, memory, exhausted T cell states |
| Myeloid / TAM | CD68, CD163, MRC1, CSF1R, IL6, IL10, TNF, CXCL10, CXCL9, CXCL8, CCL2, CCL5, ARG1, NOS2, TGFB1, SPP1, MARCO (17) | TAM polarization; cytokine milieu | M2 macrophages → poor prognosis | Classify M1/M2/SPP1+ TAM states per cell |
| Checkpoint / Treg | CD274 (PD-L1), PDCD1LG2, FOXP3, IL2RA, NCAM1, KLRD1, NKG7, KLRB1, CD19, MS4A1, CD79A, HHLA2, VSIR, NECTIN2, IDO1, B2M, HLA-A, HLA-E, ENTPD1 (19) | Checkpoint ligands; immunosuppression; antigen presentation | PD-L1 ICI eligibility; emerging targets | Identify checkpoint ligand-expressing tumor cells |
| 6 · Stromal / Angiogenesis · 28 genes | ||||
| CAF Subtypes | ACTA2, FAP, PDGFRA, PDGFRB, S100A4, POSTN, LRRC15, MYH11, CXCL12, IL6, CXCL14, LUM, DCN, COL6A1 (14) | CAF identity; stroma remodeling | CAF subtypes modulate drug delivery & immunosuppression | Classify myoCAF vs iCAF vs apCAF states |
| Angiogenesis | VEGFA, VEGFB, VEGFC, KDR, FLT1, ANGPT1, ANGPT2, TEK, NRP1, PECAM1, CD34, ENG, THY1, NOTCH4 (14) | Neovascularization; anti-angiogenic therapy targets | Bevacizumab target; VEGF prognostic marker | Resolve tip vs stalk endothelial cell states |
| 7 · DNA Damage / Genomic Stability · 30 genes | ||||
| MMR / MSI | MLH1, MSH2, MSH6, PMS2, EPCAM, MLH3, MSH3, POLE, POLD1 (9) | Mismatch repair; replication fidelity | dMMR/MSI-H in 15% CRC; ICI eligibility | Identify MMR-deficient tumor cell fraction |
| DDR / p53 | TP53, ATM, ATR, CHEK1, CHEK2, BRCA1, BRCA2, RAD51, PALB2, PARP1, CDKN2A, MDM2, MDM4, GADD45A (14) | DNA damage response; apoptosis; genome integrity | TP53 mutated in 60% CRC; HRD therapeutic opportunity | Correlate DDR expression with somatic genotype |
| Apoptosis / Stress | BCL2, BCL2L1, MCL1, BAX, BCL2L11, BBC3, BAD, PMAIP1, CASP3, CASP7, HSPA5, DDIT3 (12) — shared genes from Cat 1 reassigned here | Intrinsic apoptosis; ER stress; drug sensitivity | BCL2 family governs chemotherapy response | Stratify apoptosis-prone vs resistant subpopulations |
ⓘ 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.