RNA TargetsBlood Cancer · LymphomaResearch Use Only
Non-Hodgkin Lymphoma
Gene Expression Reference Targets
Gene Expression Reference Targets
A biologically curated RNA target reference for non-Hodgkin lymphoma spanning all major subtypes — enabling researchers to select genes across B cell oncogenic signaling, cell-of-origin classification, epigenetic driver mutations, and immune microenvironment to build custom Tapestri assays. Designed to co-detect COO-defining mutations alongside their transcriptional programs for MRD monitoring and resistance tracking.
253
Total Genes
7
Functional Categories
4
Lymphoma Subtypes
6+
Curation Sources
1
Panel Power Scorecard & Functional Categories
● Panel Power Scorecard
Panel Score: 74 / 100
88%
Landmark
Biomarker
Coverage
Biomarker
Coverage
85%
COSMIC
Tier-1
Coverage
Tier-1
Coverage
9 genes
FDA
Biomarker
Genes
Biomarker
Genes
16 genes
Clinical Trial
Biomarkers
Biomarkers
8 states
Cell States
Resolvable
Resolvable
253 genes
Total Panel
Genes
Genes
Published precedent — targeted panels are sufficient
Chapuy et al. 2018 Nature Med — 180-gene panel defined 5 DLBCL molecular subtypes
Schmitz et al. 2018 NEJM — targeted gene panel captured all clinically relevant DLBCL subgroups
64
B Cell Oncogenic Signaling
60
Immune Microenvironment
45
B Cell Identity & Differentiation
35
Epigenetic / Chromatin
32
Proliferation
35
Apoptosis / Resistance
29
DNA Damage
2
Target Curation Principles
Commercial Assays
- Foundation Medicine FoundationOne Heme
- Tempus xT RNA (lymphoma module)
- QIAGEN QIAseq Lymphoma Panel
- Illumina TruSight Lymphoma
- ArcherDX FusionPlex Lymphoma Panel
- NeoGenomics Lymphoma NGS assay
- Lymph2Cx cell-of-origin assay (NanoString)
Public Databases
- TCGA DLBCL & FL datasets
- COSMIC lymphoma mutation census
- MSigDB hallmark & immunologic gene sets
- Human Cell Atlas (lymph node / tonsil)
- GEO scRNA-seq DLBCL/FL datasets
- ICGC DLBCL consortium data
Peer-Reviewed Literature
- Schmitz et al. 2018 NEJM (DLBCL genomic subtypes)
- Wright et al. 2020 NEJM (Lymph2Cx COO)
- Chapuy et al. 2018 Nature Med (DLBCL clusters)
- PHOENIX trial (ibrutinib + R-CHOP in ABC-DLBCL)
- Sehn et al. FL tazemetostat (EZH2) trial data
- POLARIX trial (polatuzumab vedotin + R-CHP)
Why Single-Cell RNA for NHL?
DLBCL is biologically composed of GCB vs ABC tumor cells, distinct immune infiltrates, and residual normal B cells that bulk RNA averages over. Tapestri simultaneously detects MYD88/CD79B/CREBBP somatic mutations and their downstream transcriptional programs per single cell, enabling COO classification at the clonal level and MRD detection at relapse.
CAR-T MRD Monitoring — The NHL Tapestri Opportunity
After axi-cel/tisa-cel CAR-T therapy, CD19 antigen loss drives 30–50% of DLBCL relapses. Tapestri resolves residual CD19– tumor cells (antigen escape) from CD19+ tumor cells at MRD-level sensitivity while detecting BCL-2/MYC translocation status per cell — enabling biology-guided salvage therapy selection.
3
Target Reference Structure — Gene Table
1 · B Cell Oncogenic Signaling2 · Immune Microenvironment3 · B Cell Identity & Differentiation4 · Epigenetic / Chromatin5 · Proliferation / Cell Cycle6 · Apoptosis / Therapy Resistance7 · DNA Damage / Genomic Stability
| Category | Representative Genes (n) | Biological Function | Disease Relevance | scD+R Use Case |
|---|---|---|---|---|
| 1 · B Cell Oncogenic Signaling · 64 genes | ||||
| BCR / NF-κB / MYC | CD79A, CD79B, SYK, BLNK, BTK, PLCG2, PIK3CD, AKT1, MTOR, NFKB1, NFKB2, RELA, RELB, IKBKG, CARD11, BCL10, MALT1, MYD88, IRAK4, TRAF6, MYC, MAX, BCL2, BCL6, CCND1, CDK4, CDK6, RB1, PIK3CA, PTEN, CDKN2A, TP53, IRF4, FOXP1, XBP1, LMO2, SPIB, PIM1 (38) + 26 accessory | BCR/NF-κB/MYC signaling; cell-of-origin | MYD88 L265P = ABC-DLBCL = ibrutinib sensitive; BTK = acalabrutinib; CREBBP/EP300 in FL; MYC transloc. = double-hit DLBCL; CCND1 = MCL | Co-detect MYD88/CD79B genotype + NF-κB transcriptional state |
| 2 · Immune Microenvironment · 60 genes | ||||
| T Cell / NK / TAM / TLS | CD3E, CD8A, CD4, GZMB, PRF1, IFNG, TOX, PDCD1, LAG3, HAVCR2, TIGIT, CD274, FOXP3, IL2RA, TCF7, CD68, CD163, TREM2, SPP1, CXCL9, CXCL10, ARG1, IDO1, B2M, HLA-A, NCAM1, NKG7, MS4A1 (28) + 32 accessory | CTL; checkpoint; TAM; NK; TLS | CD8 T cell infiltration = favorable prognosis; PD-L1 on tumor = pembrolizumab; TREM2+ TAMs = lenalidomide resistance; TLS = IO response | Resolve TIL exhaustion states; classify TAM subtypes; identify TLS |
| 3 · B Cell Identity & Differentiation · 45 genes | ||||
| GC / Plasma / Memory | BCL6, AICDA (AID), CD27, CD38, SDC1 (CD138), PRDM1 (BLIMP1), IRF4, XBP1, PAX5, MS4A1 (CD20), CD22, CD19, CR2 (CD21), IGHM, IGHG1, IGHG3, IGHA1, CXCR4, CXCR5, CCR7, CD10 (MME) (21) + 24 accessory | GC B cell; plasma cell; memory B; FL cell state | BCL-6+AID+ = GCB-DLBCL/FL; BLIMP1 = plasma cell; CD20 = rituximab; CD22 = polatuzumab; CD19 = tafasitamab/CAR-T | Resolve GC B vs plasmablast vs memory B states; identify therapy target heterogeneity |
| 4 · Epigenetic / Chromatin · 35 genes | ||||
| EZH2 / CREBBP / KMT2D | CREBBP, EP300, KMT2D, KMT2C, EZH2, SUZ12, ARID1A, SMARCB1, DNMT3A, TET2, ASXL1, ID3, BCL7A, HIST1H1C, HIST1H1E (15) + 20 accessory | Chromatin remodeling; epigenetic drivers | CREBBP/EP300 mut. >40% FL; EZH2 Y641 = GCB-DLBCL (tazemetostat); KMT2D loss = GCB-DLBCL | Correlate EZH2/CREBBP with somatic mutation per subclone |
| 5 · Proliferation · 32 genes | ||||
| Proliferation | MKI67, TOP2A, CCNB1, CDK2, E2F1, FOXM1, MCM2, PLK1, AURKA, BUB1, CDC20 (11) + 21 accessory | Proliferative index | Ki-67 = DLBCL/FL prognosis; TOP2A = anthracycline; CCND1 = MCL diagnostic | Score proliferating vs quiescent lymphoma cells |
| 6 · Apoptosis / Therapy Resistance · 35 genes | ||||
| BCL-2 / Resistance | BCL2, BCL2L1, MCL1, BAX, BCL2L11, BBC3, BIRC5, XIAP, TP53, MDM2, CDKN2A, ABCB1, ABCG2, NF2, XPO1 (15) + 20 accessory | Apoptosis; venetoclax; MDR | BCL-2 = venetoclax (GCB-DLBCL/FL); MCL1 = venetoclax resistance; XPO1 E571K = selinexor; ABCB1 = MDR1 | Identify BCL-2-high venetoclax-sensitive cells; detect MCL1-high resistant subclones |
| 7 · DNA Damage · 29 genes | ||||
| DDR / AID | TP53, ATM, ARID1A, BRCA1, BRCA2, CHEK2, PARP1, MLH1, MSH2, POLE, AICDA (AID), RAG1, RAG2, APEX1 (14) + 15 accessory | DDR; AID-mediated somatic hypermutation | TP53 mut. = poor prognosis; ATM mut. = MCL; AID drives SHM and translocations; dMMR = pembrolizumab | Correlate DDR expression with somatic genotype per B cell subclone |
Total: 253 genesCat 1: 64 · Cat 2: 60 · Cat 3: 45 · Cat 4: 35 · Cat 5: 32 · Cat 6: 35 · Cat 7: 29
ⓘ 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.