Reclassification of TCGA Diffuse Glioma Profiles Linked to Transcriptomic, Epigenetic, Genomic and Clinical Data, According to the 2021 WHO CNS Tumor Classification

Abstract

In 2021, the fifth edition of the WHO classification of tumors of the central nervous system (WHO CNS5) was published. Molecular features of tumors were directly incorporated into the diagnostic decision tree, thus affecting both the typing and staging of the tumor. It has changed the traditional approach, based solely on histopathological classification. The Cancer Genome Atlas project (TCGA) is one of the main sources of molecular information about gliomas, including clinically annotated transcriptomic and genomic profiles. Although TCGA itself has played a pivotal role in developing the WHO CNS5 classification, its proprietary databases still retain outdated diagnoses which frequently appear incorrect and misleading according to the WHO CNS5 standards. We aimed to define the up-to-date annotations for gliomas from TCGA's database that other scientists can use in their research. Based on WHO CNS5 guidelines, we developed an algorithm for the reclassification of TCGA glioma samples by molecular features. We updated tumor type and diagnosis for 828 out of a total of 1122 TCGA glioma cases, after which available transcriptomic and methylation data showed clustering features more consistent with the updated grouping. We also observed better stratification by overall survival for the updated diagnoses, yet WHO grade 3 IDH-mutant oligodendrogliomas and astrocytomas are still indistinguishable. We also detected altered performance in the previous diagnostic transcriptomic molecular biomarkers (expression of SPRY1, CRNDE and FREM2 genes and FREM2 molecular pathway) and prognostic gene signature (FN1, ITGA5, OSMR, and NGFR) after reclassification. Thus, we conclude that further efforts are needed to reconsider glioma molecular biomarkers.

Keywords: TCGA; The Cancer Genome Atlas; WHO CNS5; adult-type diffuse gliomas; cancer biomarkers; classification of CNS tumors; epigenetic profiles; genomics; glioblastoma; transcriptomics.

Figure 1

Algorithm of the classification of diffuse gliomas according to the 5th edition of the WHO Classification of tumors of the CNS (WHO CNS5). MVP—microvascular proliferation. * ATRX mutation in an IDH-mutant diffuse glioma is sufficient for the diagnosis of IDH-mutant astrocytoma, obviating the need for 1p/19q testing in order to exclude oligodendroglioma. ** For IDH-wildtype gliomas without molecular features of a glioblastoma or when they are unknown it is worth performing a differential diagnosis from pediatric-type diffuse gliomas, especially in the case of young adults.

Figure 2

The algorithm of the reclassification of gliomas from The Cancer Genome Atlas (TCGA) databases based on molecular alterations according to WHO CNS5 guidelines. HD—homozygous deletion; wt—wildtype; mut—mutation; amp—amplification. * We combined “NOS” (Not Otherwise Specified) and “NEC” (Not Elsewhere Classified) into «NA» category.

Figure 3

Distribution of TCGA glioma cases according to the WHO CNS5 criteria. Only cases with known histology reviewed (n = 1047).

Figure 4

Hierarchical unsupervised clustering dendrogram of RNA sequencing profiles for glioma samples (combined TCGA-LGG and TCGA-GBM databases). Color markers indicate tumor labels according to TCGA clinical annotation, or according to the WHO CNS5 criteria. Clinical cases with two or more transcriptome profiles are highlighted (samples that fall into different clusters are additionally highlighted in bold). tC1–5—transcriptome clusters 1–5. NA—diagnosis is not available due to insufficient data about molecular features of a tumor.

Figure 5

Hierarchical unsupervised clustering dendrogram of DNA methylation profiles for glioma samples (combined TCGA-LGG and TCGA-GBM databases). Color markers indicate tumor labels according to TCGA clinical annotation, or according to the WHO CNS5 criteria. Clinical cases with two or more DNA methylation profiles are highlighted (samples that fall into different clusters are additionally highlighted in bold). mC1–7—DNA methylation clusters 1–7. NA—diagnosis is not available due to insufficient data about molecular features of a tumor.

Figure 6

Heatmap of 50-gene signatures for three glioblastoma subtypes [28]. Transcriptomic profiles for glioblastoma samples were taken from combined TCGA-LGG and TCGA-GBM databases. Color markers indicate tumor labels according to TCGA clinical annotation, or according to the WHO CNS5 criteria. Clinical cases with two or more transcriptome profiles are highlighted (samples that fall into different clusters are additionally highlighted in bold). MES—Mesenchymal subtype; PN—Proneural subtype; CL—Classical subtype; NA—diagnosis is not available due to insufficient data about molecular features of a tumor.

Figure 7

Kaplan–Meier analysis of 1043 TCGA patients with gliomas. Patient groups are shown according to the basic TCGA (a) and the WHO CNS5 (b) classifications. A_II-III—astrocytoma, grade II–III; GBM_IV—glioblastoma, grade IV; OA_II-III—oligoastrocytoma, grade II–III; O_II-III—oligodendroglioma, grade II–III; GBM_4—glioblastoma, IDH-wildtype, grade 4; O_2-3—oligodendroglioma, IDH-mutant, and 1p/19q-codeleted, grade 2–3; A_2-4—astrocytoma, IDH-mutant, grade 2–4.

Figure 8

Forest plot of univariate hazard ratio of overall survival for adult patients with diffuse gliomas. Patient groups are shown according to the basic TCGA (a) and the WHO CNS5 (b) classifications.

Figure 9

Pairwise comparisons for overall survival for patients with diffuse gliomas according to the basic TCGA and the WHO CNS5 classifications. CI—confidence interval; HR—hazard ratio. GBM_IV—glioblastoma, grade IV; OA_II-III—oligoastrocytoma, grade II–III; O_II-III—oligodendroglioma, grade II–III; A_II-III—astrocytoma, grades II–III; GBM_4—glioblastoma, IDH-wildtype, grade 4; O_2-3—oligodendroglioma, IDH-mutant, and 1p/19q-codeleted, grade 2–3; A_2-4—astrocytoma, IDH-mutant, grade 2–4. * p ≤ 0.05; ** p ≤ 0.01; *** p ≤ 0.001.

Figure 10

Performance of CRNDE, SPRY1, and FREM2 expression and FREM2 pathway activation levels for discrimination of glioma types. GBM_IV—glioblastoma, grade IV (n = 169); OA_II-III—oligoastrocytoma, grade II–III (n = 115); O_II-III—oligodendroglioma, grade II–III (n = 181); A_II-III—astrocytoma, grade II–III (n = 169); GBM_4—glioblastoma, IDH-wildtype, grade 4 (n = 220); O_2-3—oligodendroglioma, IDH-mutant, and 1p/19q-codeleted, grade 2–3 (n = 150); A_2-3—astrocytoma, IDH-mutant, grade 2–3 (n = 206); A_4—astrocytoma, IDH-mutant, grade 4 (n = 24). * p ≤ 0.05; ** p ≤ 0.01; *** p ≤ 0.001.

Figure 11

Performance of the 4-gene signature [35] to predict the survival of patients with glioblastoma according to the basic TCGA (left panel) and the WHO CNS5 (right panel) classifications.