RNA TARGETSHEMATOLOGIC ONCOLOGYRESEARCH USE ONLY
B-Cell Lymphoma
Gene Expression Reference Targets
Gene Expression Reference Targets
A biologically curated RNA target reference spanning all major mature B-cell lymphoma subtypes — DLBCL, FL, MCL, MZL, and Burkitt — enabling researchers to configure custom Tapestri assays that simultaneously resolve cell-of-origin identity, oncogenic signaling, immune microenvironment composition, and therapy resistance mechanisms at single-cell resolution. Designed for subtype classification, MRD monitoring, resistance tracking after R-CHOP, CAR-T, and venetoclax, and translocation co-detection.
189
Total Genes
7
Functional Categories
5
B-Cell Subtypes
6+
Curation Sources
1
Panel Power Scorecard & Functional Categories
● Panel Power Scorecard
Panel Score: 82 / 100
91%
Landmark
Biomarker
Coverage
Biomarker
Coverage
88%
COSMIC
Tier-1
Coverage
Tier-1
Coverage
14 genes
FDA
Biomarker
Genes
Biomarker
Genes
22 genes
Clinical Trial
Biomarkers
Biomarkers
10 states
Cell States
Resolvable
Resolvable
189 genes
Total Panel
Genes
Genes
Published precedent — targeted panels are sufficient for B-cell lymphoma subtyping
Schmitz et al. 2018 NEJM — targeted gene expression panel identified all clinically relevant DLBCL genomic subtypes (C1–C5)
Chapuy et al. 2018 Nature Medicine — 180-gene panel resolved 5 DLBCL molecular clusters with distinct biology and outcomes
Scott et al. 2015 JCO — Lymph2Cx 20-gene assay is the clinical standard for COO classification in DLBCL
64
COO / Oncogenic Signaling
56
Immune Microenvironment
54
B-Cell Identity & Subtype
38
Epigenetic / Chromatin
35
Proliferation / Cell Cycle
35
Apoptosis / Therapy Resistance
28
DNA Damage / Translocation
2
Background & Curation Principles
Commercial Assays
- Foundation Medicine FoundationOne Heme
- Lymph2Cx NanoString COO assay (Scott 2015)
- Tempus xT RNA Heme / Lymphoma module
- QIAGEN QIAseq Targeted RNA Lymphoma Panel
- Illumina TruSight Lymphoma / Oncology panels
- ArcherDX FusionPlex Heme + Lymphoma
Public Databases
- TCGA DLBCL, FL, and MCL multi-omic datasets
- COSMIC lymphoma tier-1 mutation census
- MSigDB hallmark, oncogenic, and immunologic sets
- Human Cell Atlas lymph node / tonsil scRNA-seq
- GEO DLBCL / FL / MCL single-cell RNA datasets
- ICGC Malignant Lymphoma consortium data
Peer-Reviewed Literature
- Schmitz et al. 2018 NEJM (DLBCL C1–C5 subtypes)
- Chapuy et al. 2018 Nature Med (DLBCL clusters)
- Wright et al. 2020 NEJM (Lymph2Cx COO)
- Bea et al. 2013 PNAS (MCL SOX11 / IGHV)
- Pastore et al. 2015 JCO (m7-FLIPI in FL)
- POLARIX, PHOENIX, CORAL trial biomarker data
Why Single-Cell RNA for B-Cell Lymphoma?
DLBCL, FL, and MCL are biologically heterogeneous: GCB vs ABC tumor cells, distinct immune infiltrates, and residual normal B cells are averaged over by bulk RNA. Tapestri simultaneously detects MYD88/CD79B/CREBBP somatic mutations and their downstream transcriptional programs per single cell — enabling true COO classification at the clonal level, identification of antigen-escape variants post-CAR-T, and MRD detection at relapse.
CAR-T & Novel Therapy Resistance — The Tapestri Opportunity
CD19 antigen loss drives 30–50% of DLBCL relapses after axi-cel / tisa-cel. Tapestri resolves CD19– antigen-escape clones from CD19+ residual tumor while co-detecting BCL-2/MYC translocation status and MYD88/BTK mutation per cell. For MCL, CCND1 and SOX11 expression can be tracked alongside TP53/ATM mutation to stratify aggressive vs indolent disease at single-cell resolution.
3
Target Reference Structure — Gene Table
1 · COO / Oncogenic Signaling2 · Immune Microenvironment3 · B-Cell Identity & Subtype4 · Epigenetic / Chromatin5 · Proliferation / Cell Cycle6 · Apoptosis / Therapy Resistance7 · DNA Damage / Translocation
| Category | Representative Genes (n) | Biological Function | Disease Relevance | scRNA Use Case |
|---|---|---|---|---|
| 1 · COO / Oncogenic Signaling · 64 genes | ||||
| BCR / NF-κB / MYC | CD79A, CD79B, SYK, BTK, BLNK, PLCG2, PIK3CD, AKT1, MTOR, NFKB1, NFKB2, RELA, RELB, IKBKG, CARD11, BCL10, MALT1, MYD88, IRAK4, TRAF6, MYC, MAX, FOXP1, IRF4, SPIB, XBP1, PIM1, PIM2, LMO2, BCL6, CCND1, CDK4, CDK6, RB1, PIK3CA, PTEN, CDKN2A, TP53, REL, TRAF1 (40) + 22 accessory | BCR signaling; NF-κB activation; MYC amplification; COO transcription factors | MYD88 L265P = ABC-DLBCL → ibrutinib / zanubrutinib; CD79B mut = ABC; BTK = acalabrutinib; CCND1 overexpression = MCL hallmark; MYC transloc = double-hit DLBCL | Co-detect MYD88 / CD79B genotype + NF-κB transcriptional output per cell; resolve ABC vs GCB transcriptional state |
| 2 · Immune Microenvironment · 56 genes | ||||
| T Cell / NK / TAM / TLS | CD3E, CD8A, CD4, GZMB, PRF1, IFNG, TOX, PDCD1, LAG3, HAVCR2, TIGIT, VSIR, CD274, FOXP3, IL2RA, TCF7, CXCL9, CXCL10, CXCL13, CCL5, NCAM1, NKG7, CD68, CD163, TREM2, SPP1, ARG1, IDO1, B2M, HLA-A, MS4A1, TNFRSF18, CXCR3 (33) + 22 accessory | CTL effector; checkpoint exhaustion; regulatory T cells; TAM polarisation; NK cells; tertiary lymphoid structure (TLS) | CD8 T cell infiltration = favorable DLBCL / FL prognosis; PD-L1 (CD274) = pembrolizumab; TREM2+ TAMs = lenalidomide resistance; TLS density predicts IO response; B2M loss = immunotherapy escape | Resolve TIL exhaustion states (TOX-high vs TCF7-high); classify TAM subtypes; quantify TLS; detect antigen-loss escape |
| 3 · B-Cell Identity & Subtype · 54 genes | ||||
| COO / Surface / Subtype | BCL6, AICDA, CD27, CD38, SDC1, PRDM1, PAX5, MS4A1, CD22, CD19, CR2, IGHM, IGHG1, IGHG3, IGHA1, CXCR4, CXCR5, CCR7, MME, SOX11, CCND1, IGHD, MYC, TCF3, ID3, TCF4, MZB1, JCHAIN, CD72, SELL, BACH2, BLK, CD74, CD83, TCL1A, TNFRSF17 (36) + 12 accessory | GC B-cell identity; plasma cell differentiation; memory B cell; MCL (SOX11/CCND1); Burkitt (TCF3/ID3 axis); MZL surface markers | BCL6+AID+ = GCB-DLBCL / FL; BLIMP1 (PRDM1) = plasmablastic; SOX11 = MCL aggressive vs indolent; TCF3/ID3 mut = Burkitt; CD20 = rituximab; CD19 = tafasitamab / CAR-T; CD22 = polatuzumab | Resolve GCB vs ABC vs plasma cell vs mantle cell vs marginal zone states at single-cell resolution |
| 4 · Epigenetic / Chromatin · 38 genes | ||||
| EZH2 / CREBBP / KMT2D | EZH2, SUZ12, EED, CREBBP, EP300, KMT2D, KMT2C, KDM6A, ARID1A, SMARCB1, DNMT3A, TET2, TET1, ASXL1, ID3, BCL7A, HIST1H1C, HIST1H1E, HDAC1, HDAC2, KDM5C, SETD2, BCOR, ARID2, PHF6 (25) + 13 accessory | PRC2 complex; histone acetyltransferase; chromatin remodeling; DNA methylation | EZH2 Y641 = GCB-DLBCL / FL → tazemetostat; CREBBP / EP300 mut >40% FL; KMT2D = most frequently mutated in FL; DNMT3A / TET2 = clonal haematopoiesis overlap; SETD2 = MCL aggressive | Correlate EZH2 / CREBBP expression with somatic genotype per subclone; identify epigenetic reprogramming driving relapse |
| 5 · Proliferation / Cell Cycle · 35 genes | ||||
| Proliferation | MKI67, TOP2A, CCNB1, CCNE1, CDK2, CDK1, E2F1, E2F2, FOXM1, MCM2, MCM6, PLK1, AURKA, AURKB, BUB1, BUB1B, CDC20, UBE2C, PCNA, RRM2, TYMS (21) + 14 accessory | S-phase entry; mitotic progression; DNA synthesis; spindle assembly checkpoint | MKI67 (Ki-67) = DLBCL / FL prognosis; TOP2A = doxorubicin (R-CHOP) sensitivity; CCND1 co-expression with SOX11 = MCL proliferative variant; high proliferation = Burkitt signature | Score proliferating vs quiescent lymphoma cells; identify cycling tumor cells vs bystander B cells; track treatment-induced senescence |
| 6 · Apoptosis / Therapy Resistance · 35 genes | ||||
| BCL-2 / Venetoclax / MDR | BCL2, BCL2L1, MCL1, BCL2L2, BAX, BAK1, BCL2L11, BBC3, PMAIP1, BIRC5, XIAP, BIRC3, TP53, MDM2, CDKN2A, ABCB1, ABCG2, XPO1, NF2, FAS, CASP3, CASP8, CASP9, CFLAR (24) + 10 accessory | Intrinsic apoptosis; BCL-2 family balance; multidrug resistance; p53 pathway | BCL-2 translocation t(14;18) = GCB-DLBCL / FL → venetoclax; MCL1 high = venetoclax resistance; XPO1 E571K = selinexor (MCL / DLBCL); ABCB1 (MDR1) = R-CHOP resistance; TP53 mut = poor prognosis across all subtypes | Identify BCL-2-high venetoclax-sensitive clones; track MCL1-high resistant subclones; correlate TP53 genotype with p53 pathway suppression |
| 7 · DNA Damage / Translocation Biology · 28 genes | ||||
| DDR / AID / SHM | TP53, ATM, CHEK2, BRCA1, BRCA2, MLH1, MSH2, MSH6, PMS2, POLE, AICDA, RAG1, RAG2, APEX1, PARP1, FANCD2, MRE11, NBN, DNTT (19) + 9 accessory | DDR; AID-mediated somatic hypermutation and class-switch recombination; translocation surveillance | TP53 mut = poor prognosis DLBCL / MCL; ATM biallelic del = MCL hallmark; AID (AICDA) drives SHM and BCL2 / MYC translocations; dMMR (MLH1 / MSH2) = pembrolizumab; POLE = ultra-hypermutated lymphoma | Correlate DDR expression with somatic genotype per B-cell subclone; detect AID-driven instability in individual tumor cells |
Total: 189 genesCat 1: 64 · Cat 2: 56 · Cat 3: 54 · Cat 4: 38 · Cat 5: 35 · Cat 6: 35 · Cat 7: 28
ⓘ 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.