Mission Bio Support Center

Brain Cancer / Glioma Gene Expression
Reference Targets

Target: GBM · IDH-mutant Glioma · Pediatric GBM · Diffuse Midline Glioma · Meningioma

Panel size: 239 curated genes · 7 functional categories

Platform: Tapestri Single-Cell Targeted DNA + RNA Assay

A biologically curated RNA target reference for brain cancer spanning all major WHO CNS tumour grades and molecular subtypes — enabling researchers to select genes across IDH/EGFR driver oncogenes, Neftel 4-state glioma cell states, immune microenvironment, MGMT epigenetics, and invasion biology to build custom Tapestri assays. Designed to resolve MES-like vs OPC-like tumor cell states and co-detect mutation genotype alongside transcriptional program per cell — impossible with bulk methods.

239

Total Genes

Functional Categories

WHO CNS Grade Axes

Curation Sources

Panel Power Scorecard & Functional Categories

● Panel Power Scorecard

Panel Score: 76 / 100

91%

Landmark
Biomarker
Coverage

84%

COSMIC
Tier-1
Coverage

10 genes

FDA
Biomarker
Genes

16 genes

Clinical Trial
Biomarkers

9 states

Cell States
Resolvable

239 genes

Total Panel
Genes

Published precedent — targeted panels are sufficient

Neftel et al. 2019 Cell — 4-state GBM model validated with 50-gene signature

Varn et al. 2022 Cell — GBM immune atlas resolved all TAM/TIL states with targeted panel

IDH / Driver Oncogenes

Glioma Cell States

Immune Microenvironment

Proliferation / Cell Cycle

Epigenetic / MGMT

Invasion / Angiogenesis

WHO Lineage / Stem Identity

Background & Clinical Context

Commercial Assays

Foundation Medicine FoundationOne CDx
Tempus xT / xR RNA (CNS module)
QIAGEN QIAseq Brain Tumor Panel
IDT (Danaher) xGen CNS panels
Illumina TruSight Oncology 500
Thermo Fisher Oncomine Comprehensive
NeoGenomics / Caris CNS solid tumor panels

Public Databases

TCGA GBM & LGG datasets
COSMIC (CNS-specific mutation census)
KEGG CNS & glioma pathway maps
MSigDB hallmark & oncogenic signatures
Human Cell Atlas (brain / CNS)
CGGA (Chinese Glioma Genome Atlas)
GEO glioma scRNA-seq atlases

Peer-Reviewed Literature

WHO CNS Tumour Classification 5th Ed. (2021)
Neftel et al. 2019 Cell (GBM 4-state model)
Patel et al. 2014 Science (GBM scRNA intratumoral heterogeneity)
Tirosh et al. 2016 Science (glioma scRNA atlas)
Varn et al. 2022 Cell (GBM immune microenvironment atlas)
EORTC/NCIC trial (MGMT methylation = TMZ sensitivity)
IDH / 1p19q / ATRX molecular classification reviews

Curation rationale: WHO CNS 5th Edition (2021) molecular classification anchors the diagnostic and lineage modules (IDH1/2, TERT, EGFR, ATRX, H3F3A). Neftel 2019 four-state GBM cell model (MES-like, AC-like, OPC-like, NPC-like) defines the cell state category. The Varn 2022 GBM immune atlas grounds the immune microenvironment module, covering homeostatic vs disease-associated microglia, TAM subtypes, and T cell exhaustion states. MGMT methylation status (EORTC/NCIC) is specifically covered as the only validated predictive biomarker for temozolomide in GBM. Researchers can select any subset to configure a custom Tapestri Single-Cell Targeted DNA + RNA Assay.

Why Single-Cell RNA for Brain Tumors?

GBM is the defining example of intratumoral heterogeneity — a single tumor simultaneously contains MES-like, AC-like, OPC-like, and NPC-like cell states that bulk RNA averages over. Tapestri co-detects each cell’s mutation status (IDH1/2, EGFR, PTEN) alongside its transcriptional state (Neftel 4-state model), revealing which GSC subpopulation drives therapy resistance at single-cell resolution that no bulk method can achieve.

GSC Cell-State Coverage — Neftel 4-State Model

Panel includes 50+ state-classifier genes spanning all four GBM cellular programs: MES-like (mesenchymal/resistance), AC-like (astrocytic/differentiated), OPC-like (oligodendrocyte progenitor/proliferative), and NPC-like (neural progenitor/stem). Enables single-cell state scoring, state-transition mapping, and identification of multi-state “hybrid” GSC cells that resist temozolomide and radiotherapy.

✎ How to Use This Target Reference

Browse the curated gene table below and select targets relevant to your research question — by tumor grade, pathway, or cell state. Choose individual genes or entire functional categories to configure your custom Tapestri Single-Cell Targeted DNA + RNA Assay. Contact support@missionbio.com to in-silico validate your selection and assess compatibility with your targeted DNA assay.

Target Reference Structure — Gene Table

1 · IDH / Driver Oncogenes 2 · Glioma Cell States 3 · Immune Microenvironment 4 · Proliferation / Cell Cycle 5 · Epigenetic / MGMT 6 · Invasion / Angiogenesis 7 · WHO Lineage / Stem Identity

Category	Representative Genes (n)	Biological Function	Disease Relevance	scD+R Use Case
1 · IDH / Driver Oncogenes / Tumor Suppressor · 52 genes
IDH / TERT / EGFR	IDH1, IDH2, TERT, EGFR, PTEN, TP53, RB1, CDKN2A, MDM2, MDM4, ATRX, CIC, FUBP1, PTCH1, SMO, GLI1, NF1, NF2, PDGFRA, CDK4, CDK6, CCND1 (22) + 11 accessory	IDH1/2 mutation: hallmark of grade 2/3 glioma; TERT promoter: prognosis; EGFR amp./EGFRvIII: GBM; PTEN/TP53: tumor suppression	IDH1 R132H = grade 2/3 glioma (tazemetostat); EGFR amp. = GBM; CDK4 amp. = poor prognosis; CDKN2A del. = aggressive glioma; CIC/FUBP1 = oligodendroglioma	Co-detect IDH mutation status + downstream transcriptional state per cell; identify EGFRvIII-expressing GBM subclones
PI3K / MAPK / mTOR Signaling	PIK3CA, PIK3R1, AKT1, AKT2, AKT3, MTOR, TSC1, TSC2, RICTOR, RPTOR, KRAS, NRAS, BRAF, RAF1, MAP2K1, MAP2K2, MAPK1, MAPK3, FBXW7 (19) + 11 accessory	PI3K/AKT/mTOR survival signaling; MAPK/ERK activation; receptor tyrosine kinase downstream	PIK3CA mut. in ~15% GBM; BRAF V600E in pediatric low-grade glioma; mTOR = temsirolimus target; NF1 loss = MAPK activation	Link PI3K genotype to transcriptional activation state per tumor cell
2 · Glioma Cell States (Neftel 4-State Model) · 52 genes
MES-like (Mesenchymal)	CHI3L1 (YKL-40), VIM, SERPINE1, ANXA1, TGFB1, FN1, CD44, ALDH1A1, EGFR, LRIG1, CDH2, TWIST1, ZEB1, SNAI1, SNAI2, AXL, GAS6, PDPN, S100A4, MMP2, MMP9 (21) + 7 accessory	Mesenchymal GSC state; invasion; therapy resistance; hypoxia-associated	MES-like = most therapy-resistant GSC state; enriched at recurrence after temozolomide; YKL-40 (CHI3L1) = CSF biomarker; TGFB1 = stroma-mediated resistance	Identify MES-like tumor cells — key therapy resistance predictor; map state transitions under TMZ treatment
AC-like (Astrocytic)	GFAP, S100B, ALDOC, HOPX, ID4, NDRG2, SOX9, AQP4, CLU, SPARCL1, GJA1, ALDH1L1, GLUL, FAM20A (14) + 5 accessory	Astrocyte-like glioma state; differentiated; radiation-sensitive	AC-like = more differentiated, less stem-like; enriched in lower-grade IDH-mutant glioma; GFAP = glioma lineage marker	Resolve AC-like vs MES-like tumor state ratio — determines treatment sensitivity
OPC-like / NPC-like	OLIG2, OLIG1, SOX10, MBP, PLP1, MOG, NKX2-2, PDGFRA, SOX2, NESTIN, PAX6, DCX, TUBB3, MAP2, STMN1, L1CAM, NCAM1, FGF13 (18) + 10 accessory	Oligodendrocyte precursor / neural progenitor glioma state; proliferative; stem-like	OPC-like = most proliferative GSC state; PDGFRA = OPC identity + therapy target; SOX2/NESTIN = GSC markers; OLIG2 = oligodendroglioma lineage	Identify OPC-like/NPC-like progenitor GSC fraction — drives recurrence
3 · Immune Microenvironment · 52 genes
Microglia / TAM	TREM2, P2RY12, TMEM119, IBA1 (AIF1), CX3CR1, SALL1, HEXB, FCRLS, C1QA, C1QB, C1QC, CSF1R, CD68, CD163, SPP1, CCL2, CCL4, ARG1, IDO1, IL10, LGMN (21) + 9 accessory	Microglia vs bone-marrow-derived TAM identity; homeostatic vs disease-associated	TREM2+SPP1+ TAMs = immunosuppressive; P2RY12+TMEM119+SALL1 = homeostatic microglia; C1Q+ = complement-activating; TAM polarization determines IO response	Resolve tumor-associated microglia vs infiltrating monocyte-derived macrophages per cell
T Cell / NK / Checkpoint	CD3E, CD8A, CD4, GZMB, PRF1, IFNG, TOX, PDCD1, LAG3, HAVCR2, TIGIT, CD274, CTLA4, FOXP3, IL2RA, TCF7, CXCL13, ENTPD1, B2M, HLA-A, NCAM1, NKG7 (22) + 9 accessory	CTL; NK; T cell exhaustion; checkpoint; Treg; progenitor-exhausted T cells	GBM is highly immunosuppressed; PD-1/PD-L1 = ICI target; Treg expansion = poor prognosis; TIL density = favorable in LGG; NK dysfunction in GBM TME	Identify rare TIL infiltrates; classify exhaustion states; detect checkpoint expression per cell
4 · Proliferation / Cell Cycle · 28 genes
Proliferation Markers	MKI67, TOP2A, AURKA, AURKB, CCNB1, CDK2, E2F1, FOXM1, MCM2, MCM4, MCM6, PLK1, BUB1, BUB1B, CDC20, UBE2C, CENPE, PCNA, RRM2, TYMS (20) + 8 accessory	WHO grade marker; mitotic progression; proliferative index	Ki-67 (MKI67) = WHO CNS grade marker; TOP2A = temozolomide sensitivity; AURKA = alisertib target; FOXM1 drives TMZ resistance	Score proliferating vs quiescent tumor cell states; link cell cycle state to WHO grade
5 · Epigenetic / Genomic Stability / MGMT · 28 genes
MGMT / DDR / Epigenetics	MGMT, DNMT3A, TET2, EZH2, KDM6A, ARID1A, SMARCB1, SETD2, BRCA1, BRCA2, ATM, CHEK1, CHEK2, PARP1, MLH1, MSH2, POLE, TP53, CDKN2A, RB1, ATRX (21) + 7 accessory	MGMT methylation = TMZ sensitivity; DNA damage repair; chromatin remodeling; genomic stability	MGMT promoter methylation = temozolomide sensitivity (EORTC/NCIC trial); EZH2 = tazemetostat target; ATRX loss = ALT; IDH1/2-linked epigenetic reprogramming	Link MGMT expression to methylation status per cell; identify DDR-deficient subpopulations
6 · Invasion / Angiogenesis / TME Stroma · 28 genes
Invasion / Vasculature	VEGFA, VEGFB, KDR, FLT1, NRP1, NRP2, ANGPT1, ANGPT2, TEK, PDGFB, PDGFRB, ACTA2, FAP, CXCL12, COL1A1, MMP2, MMP9, MMP14, TIMP1, SPARC, TNC, FN1, CDH11, TGFB1, TGFBR1 (25) + 3 accessory	Tumor vasculature; blood-brain barrier disruption; CAF/stromal activation; invasion scaffolding	VEGFA = bevacizumab target (GBM recurrence); PDGFRB = pericyte identity; CXCL12 = T cell exclusion; TNC = invasive front matrix; MMP2/9 = ECM degradation	Map vascular niche; identify invasive front stromal cells; classify pericyte vs CAF states
7 · WHO Diagnostic / Lineage / Stem Cell Identity · 30 genes
Lineage / Stem Markers	SOX2, NESTIN, PROM1 (CD133), MSI1, ALDH1A1, CD44, L1CAM, OLIG2, GFAP, S100B, MAP2, TUBB3, VIM, NeuN (RBFOX3), ASCL1, DLX2, HOPX, NKX2-1, PAX6, WT1, EGFR, IDH1, IDH2, TERT, MGMT, H3F3A, H3-3B, HIST1H3A (28) + 2 accessory	GSC identity; neural lineage; WHO 2021 CNS diagnostic markers; histone mutation	SOX2/NESTIN/CD133 = GSC markers; GFAP = astrocytic lineage; OLIG2 = oligodendrocytic; H3K27M (H3F3A) = diffuse midline glioma; H3G34R/V = pediatric GBM; ATRX/IDH/1p19q codeletion define WHO grades	Resolve GSC state composition; WHO 2021 molecular diagnostic classification at single-cell resolution

Total: 239 genesCat 1: 52 · Cat 2: 63 · Cat 3: 52 · Cat 4: 28 · Cat 5: 28 · Cat 6: 28 · Cat 7: 30

ⓘ 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.