Translating Molecular Biomarkers of Gliomas to Clinical Practice




Acknowledgments


The authors are grateful to their NYU Langone Medical Center colleagues Matija Snuderl, MD, for contributing illustrated cases of cytogenetics analysis and methylation array; Cyrus Hedvat, MD, PhD, for providing an illustrated case of loss of heterozygosity analysis; and Elad Mashiach for assisting with the preparation of images and diagrams, and the editing of the chapter.


Glioma classification and grading have traditionally been based on the histomorphology of the tumors. Recent advances have identified new molecular markers with diagnostic, prognostic, and/or predictive (ie, therapeutic) significance ( Box 4.1 , Table 4.1 ). Since the publication of the World Health Organization (WHO) guidelines in 2007, there has been a rapid expansion of molecular data on central nervous system (CNS) tumors that has improved clinicians’ diagnostic, prognostic, and therapeutic abilities. Although most of this information has not yet been translated into tangible clinical advances, many changes have been implemented in the revised WHO guidelines for the classification of tumors of the CNS (2016) for gliomas. This chapter reviews recently identified genetic markers that have had a significant impact on the molecular classification of gliomas. Many have been shown to be essential in better diagnosing CNS tumors, reliably determining the prognosis, and allowing better clinical management. Based on the revised WHO classification, each tumor type is discussed separately, accompanied by the relevant molecular profiles.



Box 4.1


The National Institutes of Health Biomarkers Definitions Working Group defined a biomarker as “a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention.” Biomarkers in gliomas have been investigated particularly for their use in identifying patients with a disease or a disease subtype (diagnostic biomarkers), stratifying the patients’ prognoses and natural history of the disease (prognostic biomarkers), and identifying patients who may achieve a particular outcome based on a particular treatment and attempting to personalize clinical treatment (predictive biomarkers). Several of the biomarkers discussed in this chapter have distinct roles as diagnostic, prognostic and/or predictive biomarkers, and these are discussed in the text and summarized in Table 4.1 and Figs. 4.1 and 4.5 .


Definition and types of biomarkers


Table 4.1

Overview of common chromosomal, genetic, epigenetic and phenotypic alterations in gliomas and their use as biomarkers














































































































































































































































































































































































































































































































































































Gene/Phenotype a Gene Family/Alternative Name Chromosomal Location Driver Gene b Typical Mutation c Copy Number Alteration Translocation Partner Detection Method Adult Glioma Tumor Type Pediatric Glioma Tumor Type Biomarker Clinical Utility References
Chromosomal
— — 1p/19q — — Codeletion — FISH, LOH, MLPA, 450K-MA OD, AOD — Diag, Prog, Pred (chemo + radiotherapy)
CIC Transcription repressor 19q13.2 TSG R215Q/W Del — IHC (loss of staining), others OD, AOD — Diag, Prog
FUBP1 DNA-binding protein 1p31.1 TSG Many Del — IHC (loss of staining), others OD, AOD — Diag, Prog
— — 7 or 7q — — Single copy gain — FISH, others DA, AA, GBM — —
— — 10 or 10q — — Single copy loss — FISH, others GBM — —
Genetic
ACVR1 RSTK 2q23-q24 TSG Few — — qRT-PCR, Seq — Midline HGG, DIPG —
BRAF RAF kinase 7q34 ONC V600E — — MS-IHC, qRT-PCR, Seq PXA, EGBM PA, PXA, cortical HGG Diag
BRAF — — — — Amp KIAA1549, others FISH, others; qRT-PCR, Seq PA PA, PMA Diag
CDKN2A Kinase inhibitor/p14, p16 9p21 TSG — Del — FISH, MLPA, 450K-MA OD, AOD, DA, AA, GBM PXA —
CDKN2B Kinase inhibitor 9p21 — — Del — FISH, MLPA, 450K-MA OD, AOD, DA, AA, GBM PXA —
EGFR RTK 7p12 ONC — Amp SEPT14 FISH, others; qRT-PCR, Seq Classic GBM Cortical HGG Diag
EGFR — — — EGFRvIII, A289D/T/V — — MS-IHC, qRT-PCR, Seq Classic GBM — Diag
FGFR1 RTK/CD331 8p11.23-p11.22 — K656E — TACC1 qRT-PCR, Seq; FISH, others — PA, midline HGG/DIPG —
FGFR3 RTK/CD333 4p16.3 ONC — — TACC3 FISH, qRT-PCR, Seq GBM — —
IDH1 Dehydrogenase 2q34 ONC R132H, others — — MS-IHC, qRT-PCR, Seq OD, AOD, DA, AA, GBM Cortical HGG Diag, Prog
IDH2 Dehydrogenase 15q26.1 ONC R172K, others — — qRT-PCR, Seq OD, AOD, DA, AA, GBM — Diag, Prog
MDM2 Ubiquitin protein ligase 12q13-q14 ONC Few Amp — FISH, MLPA, 450K-MA GBM — —
MDM4 p53 regulator 1q32 ONC Few Amp — FISH, MLPA, 450K-MA GBM — —
MET RTK 7q31 ONC — Amp — FISH, MLPA, 450K-MA GBM — —
MYC Transcription factor 8q24 ONC — Amp — FISH, MLPA, 450K-MA Astrocytoma, GBM — —
NF1 RAS negative regulator 17q11.2 TSG Many Del — qRT-PCR, Seq; FISH, others Mesenchymal GBM PA, midline HGG —
NOTCH1 receptor 9q34.3 TSG F357del Amp — qRT-PCR, Seq; FISH, others OD — —
NTRK2 RTK 9q22.1 — — Amp QKI FISH, others; qRT-PCR, Seq — PA, non-brainstem HGG —
PDGFRA RTK/CD140a 4q12 ONC Many Amp KDR qRT-PCR, Seq; FISH, others Proneural GBM Midline HGG, DIPG Prog
PIK3CA PI3 kinase 3q26.3 ONC H1047L/R/Y Amp — qRT-PCR, Seq; FISH, others OD, AOD, GBM Midline HGG, DIPG —
PIK3R1 Regulatory subunit of PI3 kinase 5q13.1 TSG G376R Del — qRT-PCR, Seq; FISH, others OD, AOD, GBM Midline HGG, DIPG —
PTEN Phosphatase 10q23 TSG R130 d /Q Del — qRT-PCR, Seq; FISH, others Astrocytoma, classical GBM — Prog
PTPN11 Phosphatase 12q24.1 ONC Many — — qRT-PCR, Seq — PA —
RB1 Ligand 13q14.2 TSG R445 d , X445_splice Del — qRT-PCR, Seq; FISH, others Mesenchymal GBM — —
TERT Telomerase 5p15.33 — Promoter — — qRT-PCR, Seq OD, AOD, astrocytoma, GBM — Diag, Prog
TP53 Transcription factor 17p13.1 TSG R273C/H/L, R248Q/W — — (IHC), qRT-PCR, Seq Astrocytoma, GBM Midline/cortical HGG —
Epigenetic
ATRX Chromatin remodeler Xq21.1 TSG F2113fs — — IHC (loss of staining), others DA, AA, GBM Cortical HGG Diag, Prog
DAXX Chromatin remodeler 6p21.3 TSG — Amp — FISH, MLPA, 450K-MA — Cortical HGG —
HIST1H3B Histone 6p22.2 ONC H3.1 K27M — — qRT-PCR, Seq — Midline HGG, DIPG Diag, Prog
H3F3A Histone 1q42.12 ONC H3.3 K27M — — MS-IHC, qRT-PCR, Seq Midline HGG, DIPG Midline HGG, DIPG Diag, Prog
H3F3A Histone 1q42.12 ONC H3.3 G34R/V — — MS-IHC, qRT-PCR, Seq — Cortical HGG Diag, Prog
MGMT DNA cysteine MT 10q26 Promoter methylation — — MS-PCR, 450K-MA GBM — Prog, Pred (temozolomide)
SETD2 Histone lysine MT 3p21.31 TSG Many Del — qRT-PCR, Seq; FISH, others — Cortical HGG —
TET2 Demethylase 4q24 TSG Few — — qRT-PCR, Seq GBM — —
Phenotypic
2-HG 2-hydroxyglutarate — — — — — MRS, mass spectrometry OD, AOD, DA, AA, GBM — —
G-CIMP Glioma–CpG island methylator phenotype — — — — — 450K-MA OD, AOD, DA, AA, GBM — —

Abbreviations: AA, anaplastic astrocytoma; AOD, anaplastic oligodendroglioma; CD, cluster of differentiation; DA, diffuse astrocytoma; Diag, diagnostic biomarker; DIPG, diffuse intrinsic pontine glioma; EGBM, epithelioid glioblastoma; EGFR; epidermal growth factor receptor; EGFRvIII, deleted exons 2 to 7 EGFR; FISH, fluorescence in situ hybridization; fs, frame shift; GBM, glioblastoma; HGG, high-grade (III–IV) glioma; IHC, immunohistochemistry; LGG, low-grade (I-II) glioma; LOH, loss of heterozygosity; MLPA, multiplex ligation-dependent probe amplification; MRS, magnetic resonance spectroscopy; MS-IHC, mutation-specific immunohistochemistry; MS-PCR, methylation-specific polymerase chain reaction; MT, methyltransferase; OD, oligodendroglioma; ONC, oncogene; PA, pilocytic astrocytoma; PMA, pilomyxoid astrocytoma; Pred, predictive biomarker; Prog, prognostic biomarker; PXA, pleomorphic xanthoastrocytoma; qRT-PCR, quantitative reverse transcriptase polymerase chain reaction; RSTK, receptor serine/threonine kinase; RTK, receptor tyrosine kinase; Seq, targeted nucleotide sequencing; TSG, tumor suppressor gene; 450K-MA, 450K CpG methylation array.

a Gene symbols, gene families, and chromosomal locations according to the Human Genome Organisation Gene Nomenclature Committee ( www.genenames.org ) and Catalogue of Somatic Mutations in Cancer ( cancer.sanger.ac.uk ).


b Driver genes that contain driver gene mutations as defined by Vogelstein and colleagues.


c Gene mutations and copy number alterations based on the Merged Cohort of LGG and GBM (The Cancer Genome Atlas [TCGA], 2016) database (1102 samples) generated by TCGA Research Network ( http://www.cbioportal.org/index.do ). In addition, the translocation partners for BRAF, EGFR, FGFR1, NTRK2, and PDGFRA are listed.


d Change to a termination codon (nonsense mutation).





Adult diffuse gliomas


Adult diffuse gliomas are infiltrating glial neoplasms that include astrocytomas and oligodendrogliomas. In the 2007 edition of the WHO Classification of Tumours of the Central Nervous System , these entities were diagnosed and classified as grade II (diffuse) or grade III (anaplastic) based on histologic features. In cases in which a morphologic distinction between these two entities was not clear, a diagnosis of oligoastrocytoma was appropriate. Following major advances in our understanding of molecular gliomagenesis, the revised WHO Classification of Tumours of the Central Nervous System (2016) has refined the diagnostic criteria for astrocytomas and oligodendrogliomas by incorporating clinically relevant molecular information about the mutation status of isocitrate dehydrogenase 1/2 ( IDH1/2 ), and alpha thalassemia/mental retardation syndrome X-linked ( ATRX ) genes and codeletion of chromosome arms 1p and 19q. After an initial IDH mutation, oligodendrogliomas are thought to develop via subsequent telomerase reverse transcriptase ( TERT ) promoter mutations and codeletion of 1p/19q, whereas IDH -mutant astrocytomas develop with subsequent alterations of TP53 and/or ATRX. The diagnosis of oligoastrocytoma is now strongly discouraged ( Fig. 4.1 ).




Fig. 4.1


Molecular classification model of adult diffuse gliomas based on the combined findings of characteristic genomic alterations in astrocytic and oligodendroglial tumors. The analysis of common mutations in IDH1/2 , ATRX and the TERT promoter and codeletion of 1p/19q allows the classification of these tumors into 5 molecular subgroups that define the biological and clinical behavior of gliomas more accurately than the classification based solely on the histopathologic tumor types. Additional gene mutations and copy number alterations are associated with these subgroups.


Point mutations in cytosolic IDH1 and mitochondrial IDH2 most commonly by substitution of arginine to histidine (R132H) or to lysine (R172K), respectively, alter their catalytic activity such that they produce high levels of the oncometabolite 2-hydroxyglutarate (2-HG), instead of α-ketoglutarate. The presence of 2-HG results in disruption of tet methylcytosine dioxygenase 2 (TET2) activity, leading to aberrant histone regulation and development of the glioma–CpG island methylator phenotype (G-CIMP).


G-CIMP is an epigenetic molecular profile that was noted and named after the observation of a subset of gliomas within The Cancer Genome Atlas (TCGA) database that showed concerted hypermethylation at a large number of loci. In general, CIMP gliomas are lower-grade, often IDH -mutated, tumors. Mutation of IDH is the molecular basis for the G-CIMP phenotype. Overall, IDH -mutant, G-CIMP high infiltrating gliomas are associated with a favorable prognosis compared with IDH wild-type tumors. IDH status is an even stronger predictor of patient outcome than histologic grade in infiltrating gliomas.


IDH mutations can be detected by immunohistochemical analysis of formalin-fixed, paraffin-embedded (FFPE) tissue using the IDH1 R132H mutant-specific antibody ( Fig. 4.2 A, B ). Direct Sanger sequencing, although requiring more tissue specimens, has the advantage over immunohistochemistry (IHC) of not only detecting IDH1 R132H but also detecting other noncanonical IDH mutations. This technique is highly sensitive, but is limited because the specimens must contain at least 50% neoplastic cells to ensure reliability. Another method, pyrosequencing, has a higher sensitivity than Sanger sequencing because it can detect as little as 10% mutant alleles. Moreover, clinical efforts have been undertaken to determine whether IDH mutations can be detected indirectly, and magnetic resonance spectroscopy has been proposed as a reliable technique to achieve this goal by detecting the levels of 2-HG.


Tags:
Mar 19, 2019 | Posted by in NEUROSURGERY | Comments Off on Translating Molecular Biomarkers of Gliomas to Clinical Practice

Full access? Get Clinical Tree
Get Clinical Tree app for offline access