Molecular diagnostics helps to identify distinct subgroups of spinal astrocytomas

Abstract

Primary spinal cord astrocytomas are rare, hence few data exist about the prognostic significance of molecular markers. Here we analyze a panel of molecular alterations in association with the clinical course. Histology and genome sequencing was performed in 26 spinal astrocytomas operated upon between 2000 and 2020. Next-generation DNA/RNA sequencing (NGS) and methylome analysis were performed to determine molecular alterations. Histology and NGS allowed the distinction of 5 tumor subgroups: glioblastoma IDH wildtype (GBM); diffuse midline glioma H3 K27M mutated (DMG-H3); high-grade astrocytoma with piloid features (HAP); diffuse astrocytoma IDH mutated (DA), diffuse leptomeningeal glioneural tumors (DGLN) and pilocytic astrocytoma (PA). Within all tumor entities GBM (median OS: 5.5 months), DMG-H3 (median OS: 13 months) and HAP (median OS: 8 months) showed a fatal prognosis. DMG-H3 tend to emerge in adolescence whereas GBM and HAP develop in the elderly. HAP are characterized by CDKN2A/B deletion and ATRX mutation. 50% of PA tumors carried a mutation in the PIK3CA gene which is seemingly associated with better outcome (median OS: PIK3CA mutated 107.5 vs 45.5 months in wildtype PA). This exploratory molecular profiling of spinal cord astrocytomas allows to identify distinct subgroups by combining molecular markers and histomorphology. DMG-H3 tend to develop in adolescence with a similar dismal prognosis like GBM and HAP in the elderly. We here describe spinal HAP with a distinct molecular profile for the first time.

Keywords: Molecular profile; Next-generation sequencing; Prognostic factor; Spinal astrocytoma.

Fig. 1

Histological features of spinal astrocytomas, hematoxylin and eosin stainings (H&E; left column) and Ki67 immunohistochemistry (right column). PA: pilocytic astrocytoma; GBM: glioblastoma IDH-wild-type; DMG-H3: diffuse midline glioma, H3 K27M mutated; HAP: high-grade astrocytoma with piloid features; Astro, IDH: diffuse astrocytoma IDH 1/2 mutated; DLGNT: diffuse leptomeningeal glioneuronal tumor Scale bar, 100 µm

Fig. 2

Characteristics of spinal astrocytomas. Diagnoses are based on the integration of histological assessment, molecular genetics and, where available, methylation classifier results. The presence of endothelial proliferation and necrosis was assessed by H&E histology, the Ki67 labelling index by immunohistochemistry. LOH 1p/19q, loss of heterozygosity at 1p/19q

Fig. 3

t-SNE clustering of analyzed cases against the DKFZ reference dataset [9]. Reference cases are colored according to the respective methylation classes. A: pilocytic astrocytoma; GBM: glioblastoma IDH-wild-type; DMG-H3: diffuse midline glioma, H3 K27M mutated; HAP: high-grade astrocytoma with piloid features; Astro, IDH: diffuse astrocytoma IDH 1/2 mutated; DLGNT: diffuse leptomeningeal glioneuronal tumor. Abbreviations of reference classes: A, IDH: astrocytoma, IDH mutant; A, IDH HG: astrocytoma, IDH mutant, high-grade; ANA, PA: high-grade astrocytoma with piloid features; ATRT, MYC: atypical teratoid/rhabdoid tumor, MYC-associated; ATRT, SHH: atypical teratoid/rhabdoid tumor, sonic hedgehog/Notch-associated; ATRT, TYR: atypical teratoid/rhabdoid tumor, tyrosinase-associated; CHGL: chordoid glioma; CHORDM: chordoma; CN: central neurocytoma; CNS, NB FOXR2: CNS neurolastoma, FOXR2-activated; CONTR, ADENOPIT: control tissue, adenohypophysis; CONTR, CEBM: control tissue, cerebellar hemisphere; CONTR, HEMI: control tissue, cerebral hemispheric cortex; CONTR, HYPTHAL: control tissue, hypothalamus; CONTR, INFLAM: control tissue, inflammatory tumor microenvironment; CONTR, PINEAL: control tissue, pineal gland; CONTR, PONS: control tissue, pons; CONTR, REACT: control tissue, reactive tumor microenvironment; CONTR, WM: control tissue, white matter; CPH, ADM: adamantinomatous craniopharyngeoma; CPH, PAP: papillary craniopharyngeoma; DLGNT: diffuse leptomeningeal glioneuronal tumor; DMG, K27: diffuse midline glioma, H3 K27M mutant; EFT, CIC: CNS Ewing Sarcoma Family Tumor with CIC alteration; ENB, A: esthesioneuroblastoma, subclass A; ENB, B: esthesioneuroblastoma, subclass B; EPN, MPE: myxopapillary ependymoma; EPN, PF A: ependymoma, posterior fossa A; EPN, PF B: ependymoma, posterior fossa B; EPN, RELA: ependymoma, RELA fusion positive; EPN, SPINE: ependymoma, spinal; EPN, YAP: ependymoma, YAP fusion positive; ETMR: embryonal tumor with multilayered rosettes; EWS: Ewing sarcoma; GBM, G34: glioblastoma, IDH wildt-type, H3-3 G34 mutant; GBM, MES: glioblastoma, IDH wild-type, mesenchymal; GBM, MID: glioblastoma, IDH wild-type, midline; GBM, MYCN: glioblastoma, IDH wild-type, MYCN-associated; GBM, RTK I: glioblastoma, IDH wild-type, receptor tyrosine kinase I; GBM, RTK II: glioblastoma, IDH wild-type, receptor tyrosine kinase II; GBM, RTK III: glioblastoma, IDH wild-type, receptor tyrosine kinase III; HGNET, BCOR: CNS high grade neuroepithelial tumor with BCOR alteration; HGNET, MN1: CNS high grade neuroepithelial tumor with MN1 alteration; HMB: hemangioblastoma; IHG: infantile hemispheric glioma; LGG, DNT: low-grade glioma, dysembryoplastic neuroepithelial tumor; LGG, GG: low-grade glioma, ganglioglioma; LGG, MYB: low-grade glioma, MYB/MYBL1 altered; LGG, PA MID: low-grade glioma, midline pilocytic astrocytoma; LGG, PA PF: low-grade glioma, posterior fossa pilocytic astrocytoma; LGG, PA/GG ST: low-grade glioma, hemispheric pilocytic astrocytoma and ganglioglioma; LGG, RGNT: low-grade glioma, rosette-forming glioneuronal tumor; LGG, SEGA: low-grade glioma, subependymal giant-cell astrocytoma; LIPN: cerebellar liponeurocytoma; LYMPHO: lymphoma; MB, G3: medulloblastoma, group 3; MB, G4: medulloblastoma, group 4; MB, SHH CHL ADL: medulloblastoma, sonic hedgehog activated A (children/adult); MB, SHH INF: medulloblastoma, sonic hedgehog activated B (infant); MB, WNT: medulloblastoma, WNT activated; MELAN: malignant melanoma; MELCYT: melanocytoma; MNG: meningioma; O, IDH: oligodendroglioma, IDH-mutant; PGG, nC: paraganglioma, spinal non-CIMP; PIN, T PB A: pineoblastoma group A / intracranial retinoblastoma; PIN, T PB B: pineoblastoma group B; PIN, T PPT: pineal parenchymal tumor; PITAD, ACTH: pituitary adenoma, ACTH; PITAD, FSH LH: pituitary adenoma, FSH/LH; PITAD, PRL: pituitary adenoma, prolactin; PITAD, STH DNS A: pituitary adenoma, STH densely granulated, group A; PITAD, STH DNS B: pituitary adenoma, STH densely granulated, group B; PITAD, STH SPA: pituitary adenoma, STH sparsely granulated; PITAD, TSH: pituitary adenoma, TSH; PITUI: pituicytoma / granular cell tumor / spindle cell oncocytoma; PLASMA: plasmacytoma; PLEX, AD: plexus tumor, subclass adult; PLEX, PED A: plexus tumor, subclass pediatric A; PLEX, PED B: plexus tumor, subclass pediatric B; PTPR, A: papillary tumor of the pineal region, group A; PTPR, B: papillary tumor of the pineal region, group B; PXA: pleomorphic xanthoastrocytoma; RETB: retinoblastoma; SCHW: schwannoma; SCHW, MEL: melanotic schwannoma; SFT, HMPC: solitary fibrous tumor / hemangiopericytoma; SUBEPN, PF: subependymoma, posterior fossa; SUBEPN, SPINE: subependymoma, spinal; SUBEPN, ST: subependymoma, supratentorial;

Fig. 4

Kaplan–Meier analysis of overall survival stratified by subgroup (GBM, DMG-H3, HAP, DA, DLGNT and PA)