RNA TargetsBlood Cancer · Plasma CellResearch Use Only
Multiple Myeloma Gene Expression
Reference Targets
Target: Newly Diagnosed MM · RRMM · High-Risk (del17p / t(4;14)) · PCL
Panel size: 241 curated genes · 7 functional categories
Platform: Tapestri Single-Cell Targeted DNA + RNA Assay

A biologically curated RNA target reference for multiple myeloma spanning newly diagnosed through relapsed/refractory stages — enabling researchers to select genes across plasma cell oncogenic drivers, immunotherapy target antigen expression, BM niche biology, and apoptosis sensitivity to build custom Tapestri assays. Designed to resolve BCMA/GPRC5D antigen heterogeneity and venetoclax BH3 profiling at single-cell resolution.

241
Total Genes
7
Functional Categories
5+
Therapy Targets
6+
Curation Sources
1
Panel Power Scorecard & Functional Categories
● Panel Power Scorecard
Panel Score: 78 / 100
89%
Landmark
Biomarker
Coverage
82%
COSMIC
Tier-1
Coverage
12 genes
FDA
Biomarker
Genes
18 genes
Clinical Trial
Biomarkers
7 states
Cell States
Resolvable
241 genes
Total Panel
Genes
Published precedent — targeted panels are sufficient
Ledergor et al. 2018 Nature Med — scRNA with 500-gene panel resolved all MM subclones
Lohr et al. 2014 Cancer Cell — targeted panel of 203 MM patients defined full mutational landscape
62
Plasma Cell Identity & Drivers
45
Bone Marrow Niche
53
Immune Microenvironment
40
Drug Resistance
32
Proliferation
30
Apoptosis / BCL-2
34
DNA Damage / Epigenetics
2
Target Curation Principles
Commercial Assays
  • Foundation Medicine FoundationOne Heme
  • Tempus xT RNA (myeloma module)
  • QIAGEN QIAseq Myeloma Panel
  • Illumina TruSight Myeloid
  • Caris Molecular Intelligence (myeloma)
  • NeoGenomics Myeloma NGS assay
  • SKY92 gene expression profiling assay
Public Databases
  • TCGA MMRF CoMMpass study (1143 patients)
  • COSMIC myeloma mutation census
  • MSigDB hallmark & oncogenic gene sets
  • Human Cell Atlas (bone marrow plasma cells)
  • GEO myeloma scRNA-seq datasets
  • IMWG molecular classification (2021)
Peer-Reviewed Literature
  • Lohr et al. 2014 Cancer Cell (myeloma genomics)
  • KarMMa trial (ide-cel BCMA CAR-T)
  • CARTITUDE-1 (cilta-cel BCMA CAR-T)
  • BELLINI trial (venetoclax + bortezomib in RRMM)
  • BCMA/GPRC5D antigen escape mechanism reviews
  • CoMMpass study transcriptomic biomarker analyses
Curation rationale: CoMMpass transcriptomic data anchors the oncogenic driver and prognostic gene modules. Antigen target coverage (BCMA, GPRC5D, SLAMF7, FcRH5) is drawn from all approved and late-stage CAR-T/bispecific antibody trials. The t(11;14)/BCL-2 venetoclax sensitivity module uses BELLINI trial biomarker data. The BM niche module specifically addresses the CXCR4/VLA-4 axis mediating stroma-mediated drug resistance.
Why Single-Cell RNA for Multiple Myeloma?
Myeloma is defined by clonal heterogeneity — multiple subclones with distinct drug sensitivities coexist and evolve under selective pressure. Tapestri co-detects each plasma cell’s translocation status (FGFR3/CCND1) and BCL-2 expression level per cell, enabling venetoclax sensitivity prediction at single-cell resolution.
BCMA/GPRC5D Antigen Escape — The CAR-T Resistance Challenge
BCMA downregulation drives resistance to ide-cel, cilta-cel, and teclistamab in 20–40% of cases. Tapestri resolves BCMA, GPRC5D, FcRH5, and SLAMF7 expression heterogeneity simultaneously per plasma cell, enabling rational bispecific combination target selection before therapy.
✎  How to Use This Target Reference
Browse the curated gene table and select targets for your custom Tapestri Single-Cell Targeted DNA + RNA Assay. Contact support@missionbio.com to in-silico validate your selection.
3
Target Reference Structure — Gene Table
1 · Plasma Cell Identity & Drivers2 · Bone Marrow Niche3 · Immune Microenvironment4 · Drug Resistance5 · Proliferation / Cell Cycle6 · Apoptosis / BCL-27 · DNA Damage / Epigenetics
CategoryRepresentative Genes (n)Biological FunctionDisease RelevancescD+R Use Case
1 · Plasma Cell Identity & Oncogenic Drivers · 62 genes
Plasma Cell ID / Drivers / SignalingIGHG1, IGHG3, IGHA1, IGHM, IGKC, SDC1, CD38, SLAMF7, TNFRSF17, GPRC5D, FCRL5, CD27, XBP1, IRF4, PRDM1, CCND1, CCND2, CCND3, FGFR3, NSD2, MAF, MAFB, MYC, MYCN, KRAS, NRAS, BRAF, TP53, CDKN2C, RB1, TENT5C, NFKB1, NFKB2, RELA, TRAF3, JAK1, JAK2, STAT3, IL6, IL6R, IL6ST (41) + 21 accessoryPlasma cell identity; translocation effects; survival signalingCD38 = daratumumab; BCMA = CAR-T (ide-cel/cilta-cel); GPRC5D = talquetamab; FGFR3 t(4;14) = FGFR inhibitor; c-MAF t(14;16) = poor prognosis; CCND1 t(11;14) = venetoclax sensitivity; KRAS/NRAS in 40%; IL-6 = myeloma master cytokineQuantify BCMA/GPRC5D/SLAMF7 heterogeneity per myeloma cell; identify antigen-low escape subclones
2 · Bone Marrow Niche · 45 genes
BM Stroma / NicheVCAM1, ITGA4, ITGB1, CXCR4, CXCL12, CCL2, CCL3, CCL5, TNFSF11, TNFRSF11B, DKK1, DKK2, SOST, VEGFA, BMP2, BMP4, FGF2, ANGPT1, SPP1, CCN2 (20) + 25 accessoryBM niche retention; osteoclast; immunosuppressionCXCL12/CXCR4 = BM retention; VLA-4 = stroma drug resistance; DKK1 = osteoblast suppression; RANKL = denosumabMap BM niche interactions; identify CXCR4-high myeloma cells in protective niche
3 · Immune Microenvironment · 53 genes
T Cell / NK / CheckpointCD3E, CD8A, CD4, GZMB, PRF1, IFNG, TOX, PDCD1, LAG3, HAVCR2, TIGIT, CD274, FOXP3, IL2RA, NCAM1, KLRD1, NKG7, KLRC1, KLRK1, B2M, HLA-A, HLA-E, MICA, MICB (24) + 29 accessoryT cell exhaustion; NK dysfunction; checkpoint; TregNK dysfunction in myeloma (CD38 fratricide); NKG2A/HLA-E = NK inhibition; exhausted CD8 post-daratumumabResolve NK functional state; identify exhausted T cells; map CD38-expressing immune cells
4 · Drug Resistance · 40 genes
IMiD / PI / HDAC ResistanceIKZF1, IKZF3, CRBN, ZFP91, IRF4, MYC, PSMD14, PSME4, PSMB5, PSMB6, PSMB7, HDAC1, HDAC2, HDAC3, CDKN2A, BCL2, MCL1, BCL2L1, TENT5C, XBP1 (20) + 20 accessoryCereblon E3 ligase; IMiD resistance; proteasomeCRBN loss = lenalidomide/pomalidomide resistance; PSMB5 mut. = bortezomib resistance; MCL1 = BH3-mimetic resistanceIdentify CRBN-low IMiD-resistant cells; detect PSMB5-mut proteasome-resistant subclones
5 · Proliferation · 32 genes
ProliferationMKI67, TOP2A, AURKA, CCNB1, CDK2, E2F1, FOXM1, MCM2, PLK1, CDC20, UBE2C, CCND1 (12) + 20 accessoryProliferative index; cell cycleKi-67 = risk stratification; AURKA = alisertib; CCND1 = t(11;14) venetoclax-sensitiveScore proliferating vs quiescent myeloma cells
6 · Apoptosis / BCL-2 · 30 genes
BCL-2 FamilyBCL2, BCL2L1, MCL1, BIM, BBC3, PMAIP1, BAX, BAK1, BAD, BID (10) + 20 accessoryIntrinsic apoptosis; venetoclax sensitivityBCL-2 high in t(11;14) = venetoclax-sensitive; MCL-1 = venetoclax-resistant; NOXA = MCL-1 inhibitor sensitivityPredict venetoclax sensitivity per myeloma cell; identify MCL-1-high resistant subpopulations
7 · DNA Damage / Epigenetics · 34 genes
DDR / EpigenomeTP53, ATM, CHEK1, CHEK2, BRCA1, PARP1, MLH1, DNMT3A, TET2, EZH2, NSD2, KDM6A, H1-2, H1-4, NSD3 (15) + 19 accessoryDDR; epigenetic modification; chromatinTP53/del(17p) = high-risk; NSD2 (MMSET) t(4;14) = poor prognosis; EZH2 = polycomb repression; UTX loss = poor prognosisCorrelate DDR/epigenetic expression with somatic mutations per plasma cell
Total: 241 genesCat 1: 62 · Cat 2: 45 · Cat 3: 53 · Cat 4: 40 · Cat 5: 32 · Cat 6: 30 · Cat 7: 34
ⓘ 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.
Gene names in red failed amplicon design/QC or are single-exon targets.
mission bio · Tapestri Platform
Content created using AI assisted tools. · Research Use Only · Not for diagnostic use
support@missionbio.com · missionbio.com
MM-RNA-265
Target Ref. v1.0 · 2026