RNA TARGETS
Single-Cell
Research Use Only
AML / MDS Gene Expression
Reference Targets
Reference Targets
Biologically curated RNA panel enabling high-resolution characterization of leukemic cell states, differentiation block, clonal architecture, and microenvironment remodeling at single-cell resolution — designed to resolve AML blast hierarchies, MDS dysplasia programs, and therapy resistance mechanisms beyond the reach of bulk methods.
291
Total Genes
7
Functional Categories
5
Heme Indications Covered
6+
Curation Sources
1
Panel Power Scorecard & Functional Categories
56
Driver Mutations & Oncogenic Signaling
50
Cell State / Differentiation Hierarchy
28
Proliferation / Cell Cycle
32
Apoptosis / Therapy Resistance
50
Immune Microenvironment
24
Cytokine / Niche Signaling
28
Epigenetic / Splicing / DNA Repair
● Panel Power Scorecard
Panel Score: 91 / 100
92%
Landmark
Biomarker
Coverage
Biomarker
Coverage
88%
COSMIC
Tier-1
Coverage
Tier-1
Coverage
291 genes
FDA
Biomarker
Genes
Biomarker
Genes
24 genes
Clinical Trial
Biomarkers
Biomarkers
9 states
Cell States
Resolvable
Resolvable
291 genes
Total Panel
Genes
Genes
Published precedent — targeted panels are sufficient
van Galen et al. 2019 Cell — 8-state AML atlas using 38-gene targeted panel
Papaemmanuil et al. 2016 NEJM — 111-gene panel defined all prognostic AML subgroups
2
Panel Design Principles
Commercial Panels
- Foundation Medicine FoundationOne Heme
- Tempus xT / xR RNA (hematology module)
- QIAGEN QIAseq Myeloid Panel
- IDT (Danaher) xGen AML / MDS panel
- Illumina TruSight Myeloid 54-gene panel
- Thermo Fisher Oncomine Myeloid Research
- GeneCentric / ArcherDX FusionPlex Heme
Public Databases
- TCGA LAML (AML) & TARGET datasets
- COSMIC myeloid mutation census
- KEGG hematopoiesis & leukemia pathways
- MSigDB hallmark & oncogenic signatures
- Human Cell Atlas (bone marrow / PBMC)
- BeatAML & AMLCG clinical genomics cohorts
Peer-Reviewed Literature
- ELN 2022 AML risk classification
- Single-cell AML atlases (van Galen et al. 2019)
- MDS clonal hierarchy studies (Papaemmanuil 2016)
- FLT3/IDH1/2 resistance mechanism reviews
- LSC / leukemic stem cell transcriptome papers
- CLL/ALL immune evasion & TME atlases
Why Single-Cell RNA for Heme Malignancies?
AML and MDS are clonal disorders where bulk RNA averages across phenotypically distinct cell populations — HSCs, progenitors, blasts, and LSCs. Tapestri co-detects each cell’s mutation status (FLT3-ITD, IDH1/2, NPM1) alongside its transcriptional state, directly linking genotype to blast identity, differentiation block depth, and therapy resistance at per-cell resolution.
LSC Hierarchy Coverage (van Galen 6-State Model)
Panel includes 50+ state classifier genes spanning HSC-like, progenitor-like, GMP-like, promonocyte-like, monocyte-like, and cDC-like AML cell states. Enables single-cell LSC scoring, MRD-relevant blast fraction quantification, and identification of therapy-resistant LSC subpopulations enriched at relapse.
3
Panel Structure — Gene Table
1 · Driver Mutations & Oncogenic Signaling
2 · Cell State / Differentiation Hierarchy
3 · Proliferation / Cell Cycle
4 · Apoptosis / Therapy Resistance
5 · Immune Microenvironment
6 · Cytokine / Niche Signaling
7 · Epigenetic / Splicing / DNA Repair
| Category | Representative Genes (n) | Biological Function | Heme Malignancy Relevance | scD+R Use Case |
|---|---|---|---|---|
| 1 · Driver Mutations & Oncogenic Signaling · 56 genes | ||||
| FLT3 / KIT / RTK | FLT3, KIT (CD117), PDGFRA, PDGFRB, CSF1R, CSF3R, MPL, JAK2, JAK1, JAK3, EPOR, TGFBR1, TGFBR2, ABL1 (14) | RTK-driven proliferation & survival; cytokine receptor signaling | FLT3-ITD in ~30% AML = poor ELN risk; KIT D816V in core-binding factor AML; JAK2 V617F in MPN | Distinguish FLT3-ITD blast state from FLT3-WT progenitors; quizartinib resistance mapping |
| RAS / MAPK | KRAS, NRAS, HRAS, BRAF, RAF1, MAP2K1, MAP2K2, MAPK1, MAPK3, NF1, CBL, PTPN11 (SHP2), DUSP6 (13) | Proliferative signaling; RAS hotspot mutations | NRAS/KRAS mut. in ~15% AML; PTPN11 in juvenile CMML; CBL in MPN | Identify RAS-driven blast subclones at single-cell resolution |
| PI3K / AKT / mTOR | PIK3CA, PIK3R1, PTEN, AKT1, AKT2, AKT3, MTOR, TSC1, TSC2, RPS6KB1, FOXO3, FBXW7 (12) | Survival, drug resistance, LSC maintenance | PI3K/AKT hyperactivation in AML; mTOR drives LSC quiescence | Correlate PI3K state with FLT3/RAS genotype per cell |
| Transcription Factors | RUNX1 (AML1), RUNX1T1, CBFB, MYH11, PML, RARA, NPM1, CEBPA, GATA2, GATA1, TAL1, LMO2, ETV6, WT1 (14) | Hematopoietic TF networks; fusion oncoproteins; differentiation control | RUNX1-RUNX1T1 & CBFB-MYH11 define core-binding factor AML; NPM1 mut. ~30% AML; PML-RARA in APL | Resolve TF-program-defined blast states; track AML-defining fusion expression per cell |
| MYC / Cell Growth | MYC, MYCN, MAX, BCL6, IRF4, IRF8, SPI1 (PU.1), GFI1 (8 + 5 accessory growth factors) | Oncogenic transcription; myeloid vs lymphoid fate | MYC overexpression in AML blast crisis; IRF4/BCL6 in ALL & CLL | Map MYC-driven proliferative blast state vs quiescent LSC state |
| 2 · Cell State / Differentiation Hierarchy (van Galen AML Model) · 50 genes | ||||
| HSC-like / LSC | CD34, CD38, THY1 (CD90), PROM1 (CD133), MEIS1, HOXA9, HOXA10, HOXB5, MLLT3, MECOM (EVI1), ALDH1A1, CXCR4, AVP (13) | Leukemic stem cell identity; HSC-like quiescence; MRD reservoir | HOXA9/MEIS1 LSC program = poor prognosis; MECOM/EVI1 in inv(3) AML; LSC17 score predicts survival | Quantify LSC-like fraction per sample; link LSC state to mutations |
| Progenitor / GMP-like | MPO, ELANE (NE), AZU1, PRTN3, MS4A3, CTSG, CD33, CD117, GATA2, CEBPAlpha, CEBPEpsilon, LYZ, FUT4 (CD15) (13) | Myeloid progenitor / granulocyte-monocyte progenitor identity | GMP-like blast state = myeloperoxidase+ AML; CEBPA mut. defines GMP block | Distinguish HSC-like LSC from GMP-like blasts; differentiation block depth |
| Monocyte / DC-like | CD14, CD64 (FCGR1A), CD11b (ITGAM), CD16 (FCGR3A), S100A8, S100A9, LYZ, VCAN, FCN1, CD86, HLA-DRA, HLA-DRB1, CLEC9A, LILRA4 (14) | Monocyte-like & dendritic cell-like AML states; immunostimulatory potential | Monocyte-like AML (M4/M5 FAB) associated with DNMT3A/TET2/ASXL1 mutations | Identify monocyte-like vs cDC-like vs pDC-like blast differentiation state |
| Erythroid / Meg | HBA1, HBB, GYPA (CD235a), GYPB, ALAS2, KLF1, GATA1, NFE2, VWF, ITGA2B (CD41), PF4, PPBP, GP1BA (10) | Erythroid & megakaryocyte differentiation identity | Erythroid/meg dysplasia in MDS; GATA1 mut. in Down syndrome AML; MF megakaryocyte expansion | Identify dysplastic erythroid cells; MDS tri-lineage dysplasia per cell |
| 3 · Proliferation / Cell Cycle · 28 genes | ||||
| G1/S Checkpoint | MKI67, PCNA, CCND1, CCND2, CCND3, CCNE1, CDK4, CDK6, CDK2, RB1, E2F1, CDKN1A (p21), CDKN2A (p16), CDKN1B (14) | Cell cycle entry; blast proliferation index | High Ki67 AML = adverse ELN; CDK6 overexpression in AML; p21 upregulation in LSC quiescence | Score proliferating blasts vs quiescent LSC compartment per cell |
| Mitosis / Replication | TOP2A, MCM2, MCM6, AURKA, AURKB, PLK1, BUB1, BIRC5 (survivin), TYMS, FOXM1, CDC20, UBE2C, CCNB1, MYBL2 (14) | Mitotic progression; replication stress; spindle assembly | AURKA/B overexpression in AML; survivin anti-apoptotic; FOXM1 drives blast proliferation | Distinguish G1, S, G2/M blast populations computationally |
| 4 · Apoptosis / Therapy Resistance · 32 genes | ||||
| BCL-2 Family | BCL2, BCL2L1 (BCL-XL), MCL1, BCL2L2 (BCL-W), BCL2A1, BAX, BAK1, BIM (BCL2L11), PUMA (BBC3), NOXA (PMAIP1), BAD, BID, HRK (13) | Intrinsic apoptosis; venetoclax sensitivity determinant | BCL2 overexpression in AML/CLL = venetoclax target; MCL1 upregulation = venetoclax resistance; BAX loss in relapse | Predict venetoclax sensitivity per blast subpopulation; identify MCL1-high resistant cells |
| Drug Resistance | ABCB1 (MDR1), ABCG2, ABCC1, SLC22A1, FLT3, TP53, WT1, BCLAF1, SRSF2, U2AF1, SF3B1, CDA, DCK, RRM1, RRM2, SAMHD1 (16) | Multidrug efflux; nucleoside metabolism; chemotherapy resistance | ABCB1/ABCG2 overexpression in LSC; cytarabine resistance via DCK/SAMHD1; TP53 mut. = hypomethylation agent sensitivity | Identify drug-efflux-high LSC subpopulations; track cytarabine resistance mechanisms per cell |
| p53 / DDR | TP53, MDM2, MDM4, ATM, ATR, CHEK1, CHEK2, GADD45A, PARP1, RAD51, BRCA1 (11) — note: shared genes reassigned from Cat 7 | DNA damage checkpoint; p53 pathway; genome stability | TP53 mut. in ~10% de novo AML, ~30% therapy-related AML; monoallelic vs biallelic = distinct prognosis | Correlate TP53 expression with allelic status per cell; p53-null blast enrichment |
| 5 · Immune Microenvironment · 50 genes | ||||
| T Cell / CTL | CD3E, CD3D, CD8A, CD4, GZMB, GZMA, PRF1, IFNG, TBX21, TOX, PDCD1 (PD-1), LAG3, HAVCR2 (TIM-3), CTLA4, TIGIT, TCF7, CD39 (17) | Cytotoxic T cell response; exhaustion program; checkpoint biology | T cell exhaustion prevalent in AML BM niche; TIM-3 expressed on blasts and exhausted T cells; ICI trials ongoing | Resolve effector vs exhausted T cells; identify TIM-3+ blast populations simultaneously |
| NK / Innate | KLRD1 (CD94), NKG7, KLRB1, NCAM1 (CD56), NCR1 (NKp46), KLRC1, KLRK1 (NKG2D), B2M, HLA-A, HLA-E, MICA, MICB, ULBP1, FCGR3A (14) | NK cytotoxicity; MHC class I surveillance; ADCC | NK dysfunction in AML BM; HLA-E upregulation on blasts inhibits NK killing; CD16+ NK cells depleted at relapse | Map NK functional state; identify MHC-I-loss blasts evading NK surveillance |
| Checkpoint / Myeloid Suppression | CD274 (PD-L1), PDCD1LG2, CD47, LILRB2 (CD33-like), VSIR (VISTA), SIGLEC9, SIGLEC7, CD200, FOXP3, IL2RA, ARG1, IDO1, TGFbeta1 (13) | Blast immune evasion; “don’t eat me” signaling; Treg expansion | CD47 overexpression on LSC = magrolimab target; PD-L1 on blasts correlated with poor prognosis; VISTA in AML TME | Identify CD47-high LSC vs differentiated blasts; Treg fraction in BM niche per cell |
| Monocyte / Macrophage | CD68, CD163, MRC1, CSF1R, IL6, IL10, TNF, CXCL10, CCL2, CCL3, SPP1, TREM2, APOE, LGALS3, IL1B, IL18 (6) | BM macrophage polarization; inflammatory niche; erythrophagocytosis | M2-like macrophages support AML survival; IL-6 drives MDS cytokine excess; TREM2+ TAMs in MDS BM | Classify BM macrophage polarization states; distinguish blast-supporting vs inflammatory TAMs |
| 6 · Cytokine / Niche Signaling · 24 genes | ||||
| Hematopoietic Cytokines | KITLG (SCF), THPO, EPO, G-CSF (CSF3), GM-CSF (CSF2), IL3, IL6, IL10, IL13, IFNA1, IFNG, TNF, LIF, ONCOSTATIN M (OSM) (14) | Hematopoietic niche cytokine milieu; autocrine/paracrine blast survival | IL-3/GM-CSF autocrine loops in AML; TPO/THPO overproduction in MF; G-CSF drives emergency granulopoiesis in MDS | Identify cytokine-producing blast subclones; map BM niche paracrine circuits |
| Stromal Niche / Adhesion | CXCL12, CXCR4, VLA-4 (ITGA4), ITGB1, CD44, VCAM1, ANGPT1, ANGPT2, THBS1, FN1, LGALS1, LGALS9, CD63 (10) | LSC BM niche retention; stroma-mediated drug resistance | CXCR4/CXCL12 axis retains LSC in protective niche; VCAM1/VLA-4 confers stroma-mediated resistance; plerixafor disrupts niche | Link CXCR4-high cell state to niche retention; identify stromal-interaction blast subpopulation |
| 7 · Epigenetic / Splicing / DNA Repair · 28 genes | ||||
| Epigenetic Regulators | IDH1, IDH2, TET2, TET1, DNMT3A, DNMT1, DNMT3B, EZH2, ASXL1, ASXL2, KDM6A (UTX), KDM5C, NSD1, KAT6A, SETD2, BCOR (16) | DNA methylation; histone modification; 2-HG oncometabolite; chromatin remodeling | DNMT3A/TET2/ASXL1 = CHIP & clonal evolution to AML/MDS; IDH1/2 mut. = enasidenib/ivosidenib targets; EZH2 in MDS/MPN | Correlate epigenetic regulator expression with somatic genotype (IDH1/2, DNMT3A) per cell |
| RNA Splicing | SF3B1, SRSF2, U2AF1, U2AF2, ZRSR2, SF3A1, PRPF8, LUC7L2, RBM10, HNRNPK, DDX41 (11) | Pre-mRNA splicing fidelity; alternative splicing; R-loop resolution | SF3B1 mut. defines MDS with ring sideroblasts (MDS-RS); SRSF2/U2AF1 in CMML/MDS; DDX41 germline in familial AML | Identify splicing-mutant cell clones; correlate splicing factor expression with somatic genotype |
| Cohesins / Transcription | STAG2, SMC1A, SMC3, RAD21, CTCF, NIPBL, PHF6, KAT2A (GCN5), EP300, CREBBP (10) — note: shared DDR genes in Cat 4 | Chromatin architecture; cohesin complex; transcriptional coactivation | STAG2 mut. in ~20% AML; cohesin loss disrupts differentiation; CREBBP/EP300 in CBF-AML and ALL | Link cohesin/TF expression state to somatic STAG2/RUNX1 genotype per cell |
ⓘ 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.