BACKGROUND: Diffuse low-grade and intermediate-grade gliomas (which together make up the lower-grade gliomas, World Health Organization grades II and III) have highly variable clinical behavior that is not adequately predicted on the basis of histologic class. Some are indolent; others quickly progress to glioblastoma. The uncertainty is compounded by interobserver variability in histologic diagnosis. Mutations in IDH, TP53, and ATRX and codeletion of chromosome arms 1p and 19q (1p/19q codeletion) have been implicated as clinically relevant markers of lower-grade gliomas. 

METHODS: We performed genomewide analyses of 293 lower-grade gliomas from adults, incorporating exome sequence, DNA copy number, DNA methylation, messenger RNA expression, microRNA expression, and targeted protein expression. These data were integrated and tested for correlation with clinical outcomes. 

RESULTS: Unsupervised clustering of mutations and data from RNA, DNA-copy-number, and DNA-methylation platforms uncovered concordant classification of three robust, nonoverlapping, prognostically significant subtypes of lower-grade glioma that were captured more accurately by IDH, 1p/19q, and TP53 status than by histologic class. Patients who had lower-grade gliomas with an IDH mutation and 1p/19q codeletion had the most favorable clinical outcomes. Their gliomas harbored mutations in CIC, FUBP1, NOTCH1, and the TERT promoter. Nearly all lower-grade gliomas with IDH mutations and no 1p/19q codeletion had mutations in TP53 (94%) and ATRX inactivation (86%). The large majority of lower-grade gliomas without an IDH mutation had genomic aberrations and clinical behavior strikingly similar to those found in primary glioblastoma. 

CONCLUSIONS: The integration of genomewide data from multiple platforms delineated three molecular classes of lower-grade gliomas that were more concordant with IDH, 1p/19q, and TP53 status than with histologic class. Lower-grade gliomas with an IDH mutation either had 1p/19q codeletion or carried a TP53 mutation. Most lower-grade gliomas without an IDH mutation were molecularly and clinically similar to glioblastoma. (Funded by the National Institutes of Health.)

/pdf/comprehensive-integrative-genomic-analysis-of-diffuse-lower-2521cdybt7.pdf

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.

https://www.thelancet.com/pdfs/journals/lancet/PIIS0140-6736(11)61346-9.pdf

Primary brain tumours in adults

Somatic mutations in the IDH1 gene encoding cytosolic NADP+-dependent isocitrate dehydrogenase have been shown in the majority of astrocytomas, oligodendrogliomas and oligoastrocytomas of WHO grades II and III. IDH2 encoding mitochondrial NADP+-dependent isocitrate dehydrogenase is also mutated in these tumors, albeit at much lower frequencies. Preliminary data suggest an importance of IDH1 mutation for prognosis showing that patients with anaplastic astrocytomas, oligodendrogliomas and oligoastrocytomas harboring IDH1 mutations seem to fare much better than patients without this mutation in their tumors. To determine mutation types and their frequencies, we examined 1,010 diffuse gliomas. We detected 716 IDH1 mutations and 31 IDH2 mutations. We found 165 IDH1 (72.7%) and 2 IDH2 mutations (0.9%) in 227 diffuse astrocytomas WHO grade II, 146 IDH1 (64.0%) and 2 IDH2 mutations (0.9%) in 228 anaplastic astrocytomas WHO grade III, 105 IDH1 (82.0%) and 6 IDH2 mutations (4.7%) in 128 oligodendrogliomas WHO grade II, 121 IDH1 (69.5%) and 9 IDH2 mutations (5.2%) in 174 anaplastic oligodendrogliomas WHO grade III, 62 IDH1 (81.6%) and 1 IDH2 mutations (1.3%) in 76 oligoastrocytomas WHO grade II and 117 IDH1 (66.1%) and 11 IDH2 mutations (6.2%) in 177 anaplastic oligoastrocytomas WHO grade III. We report on an inverse association of IDH1 and IDH2 mutations in these gliomas and a non-random distribution of the mutation types within the tumor entities. IDH1 mutations of the R132C type are strongly associated with astrocytoma, while IDH2 mutations predominantly occur in oligodendroglial tumors. In addition, patients with anaplastic glioma harboring IDH1 mutations were on average 6 years younger than those without these alterations.

/pdf/type-and-frequency-of-idh1-and-idh2-mutations-are-related-to-45gk0eyv6d.pdf

Type and frequency of IDH1 and IDH2 mutations are related to astrocytic and oligodendroglial differentiation and age: a study of 1,010 diffuse gliomas.

Purpose: Anaplastic oligodendroglioma are chemotherapy-sensitive tumors. We now present the long-term follow-up findings of a randomized phase III study on the addition of six cycles of procarbazine, lomustine, and vincristine (PCV) chemotherapy to radiotherapy (RT). Patients and Methods: Adult patients with newly diagnosed anaplastic oligodendroglial tumors were randomly assigned to either 59.4 Gy of RT or the same RT followed by six cycles of adjuvant PCV. An exploratory analysis of the correlation between 1p/19q status and survival was part of the study. Retrospectively, the methylation status of the methyl-guanine methyl transferase gene promoter and the mutational status of the isocitrate dehydrogenase (IDH) gene were determined. The primary end points were overall survival (OS) and progression-free survival based on intent-to-treat analysis. Results: A total of 368 patients were enrolled. With a median follow-up of 140 months, OS in the RT/PCV arm was significantly longer (42.3 v 30.6 months in the RT arm, hazard ratio [HR], 0.75; 95% CI, 0.60 to 0.95). In the 80 patients with a 1p/19q codeletion, OS was increased, with a trend toward more benefit from adjuvant PCV (OS not reached in the RT/PCV group v 112 months in the RT group; HR, 0.56; 95% CI, 0.31 to 1.03). IDH mutational status was also of prognostic significance. Conclusion: The addition of six cycles of PCV after 59.4 Gy of RT increases both OS and PFS in anaplastic oligodendroglial tumors. 1p/19q-codeleted tumors derive more benefit from adjuvant PCV compared with non-1p/19q-deleted tumors.

https://ascopubs.org/doi/pdf/10.1200/JCO.2012.43.2229

Adjuvant Procarbazine, Lomustine, and Vincristine Chemotherapy in Newly Diagnosed Anaplastic Oligodendroglioma: Long-Term Follow-Up of EORTC Brain Tumor Group Study 26951

In modern clinical neuro-oncology, histopathological diagnosis affects therapeutic decisions and prognostic estimation more than any other variable. Among high-grade gliomas, histologically classic glioblastomas and anaplastic oligodendrogliomas follow markedly different clinical courses. Unfortunately, many malignant gliomas are diagnostically challenging; these nonclassic lesions are difficult to classify by histological features, generating considerable interobserver variability and limited diagnostic reproducibility. The resulting tentative pathological diagnoses create significant clinical confusion. We investigated whether gene expression profiling, coupled with class prediction methodology, could be used to classify high-grade gliomas in a manner more objective, explicit, and consistent than standard pathology. Microarray analysis was used to determine the expression of ∼12,000 genes in a set of 50 gliomas, 28 glioblastomas and 22 anaplastic oligodendrogliomas. Supervised learning approaches were used to build a two-class prediction model based on a subset of 14 glioblastomas and 7 anaplastic oligodendrogliomas with classic histology. A 20-feature k -nearest neighbor model correctly classified 18 of the 21 classic cases in leave-one-out cross-validation when compared with pathological diagnoses. This model was then used to predict the classification of clinically common, histologically nonclassic samples. When tumors were classified according to pathology, the survival of patients with nonclassic glioblastoma and nonclassic anaplastic oligodendroglioma was not significantly different ( P = 0.19). However, class distinctions according to the model were significantly associated with survival outcome ( P = 0.05). This class prediction model was capable of classifying high-grade, nonclassic glial tumors objectively and reproducibly. Moreover, the model provided a more accurate predictor of prognosis in these nonclassic lesions than did pathological classification. These data suggest that class prediction models, based on defined molecular profiles, classify diagnostically challenging malignant gliomas in a manner that better correlates with clinical outcome than does standard pathology.

https://cancerres.aacrjournals.org/content/canres/63/7/1602.full.pdf

Gene expression-based classification of malignant gliomas correlates better with survival than histological classification.

BACKGROUND

Accurate histologic diagnosis of gliomas is fundamental to proper patient management and to the interpretation of basic and clinical investigations. Diagnostic accuracy and reproducibility are compromised by the subjective histologic criteria currently used to classify and grade gliomas.



METHODS

The histologic features of 4 sets of gliomas (a total of 244 cases) were reviewed independently by 4 neuropathologists to determine interobserver diagnostic concordance rates. Cases wherein diagnostic disagreements arose were reviewed jointly to identify and refine the histologic criteria that were adversely affecting diagnostic reproducibility. Using the criteria developed in the study, a set of 315 gliomas with known survival data was evaluated in order to validate the usefulness of the criteria.



RESULTS

There was significant improvement in diagnostic concordance with each session (P = 0.02). For the first session, the concordance rates were as follows: all 4 reviewers, 52%; any 3 reviewers, 60%; 2 reviewers, 70%. For the fourth session, the respective rates were 69%, 75%, and 80%. Although features important in grading, particularly microvascular proliferation, were sometimes problematic, most disagreements related to the classification of tumors. Much of the improvement related to the refinement of criteria distinguishing diffuse astrocytomas from oligodendrogliomas/oligoastrocytomas and pilocytic astrocytomas. It was concluded that the presence of any typical oligodendroglioma was sufficient to remove a tumor from the astrocytoma category.



CONCLUSIONS

The authors' data indicate that oligodendroglial tumors comprise up to 25% of gliomas, a significantly higher proportion than was previously recognized. The data also suggest that the wide range of survival times reported for patients with anaplastic astrocytoma may reflect "contamination" resulting from misdiagnosis, particularly of oligodendroglial tumors and pilocytic astrocytomas. Cancer 1997; 79:1381-93. © 1997 American Cancer Society.

Improving diagnostic accuracy and interobserver concordance in the classification and grading of primary gliomas

BACKGROUND Regional heterogeneity causes significant errors in the histologic classification and grading of gliomas, but little is known about its implications for other modalities. Attempts to predict glioma behavior using flow cytometry (FCM) have yielded contradictory results, possibly due to regional heterogeneity in DNA content, a recognized phenomenon that has not been evaluated systematically. METHODS The authors used FCM to analyze the DNA content of 353 regions from 18 resected human gliomas. Five to 60 regions were sampled from each tumor, and the topographic relationships of ploidy, proliferative activity (S-phase fraction [SPF]), and histologic features were established. RESULTS Most tumors demonstrated heterogeneity among regions in the number and relative sizes of aneuploid populations and/or proliferative activity. The degree of heterogeneity increased with tumor grade. Heterogeneity in histologic features, ploidy, and proliferative activity appeared to vary independently, except for a significant association between the presence of mitotic figures and the SPF of individual regions (P < 0.0001). The clustering of regions with similar percentages of aneuploid cells supported the concept of local clonal expansion. CONCLUSIONS Gliomas express significant regional heterogeneity in ploidy and proliferative activity and this will have an adverse effect on the usefulness of their analysis. However, the independent variation of ploidy, proliferative activity, and histologic features suggests that the use of multiple analyses may allow more accurate prediction of glioma patient survival. Regional heterogeneity appears be a fundamental property of malignant gliomas; systematic studies to determine its effects on the diagnostic usefulness of other new methods used to evaluate gliomas are indicated.

https://acsjournals.onlinelibrary.wiley.com/doi/pdf/10.1002/1097-0142%2819931115%2972%3A10%3C3052%3A%3AAID-CNCR2820721030%3E3.0.CO%3B2-7

Regional heterogeneity in the DNA content of human gliomas

BACKGROUND

The histologic differentiation of mitotic figures is a cornerstone of several highly predictive grading systems for gliomas. In some systems, the presence of even a single mitotic figure is sufficient to classify an astrocytoma as high grade. However, the extent of microscopic examination necessary to exclude the presence of significant mitotic activity has not been determined.



METHODS

Hematoxylin and eosin-stained slides from 410 astrocytomas and 107 oligodendrogliomas/oligoastrocytomas were reviewed until the first mitosis was identified or 100 400x fields had been reviewed without identification of a mitosis. The number of the field in which the first mitosis was found was correlated with diagnosis, grade, and survival.



RESULTS

A review of 50 400x fields was necessary to achieve a >90% sensitivity in identifying a mitosis in a Grade 3 astrocytoma specimen, compared with 20 400x fields in anaplastic (Grade 3 and 4) oligodendroglioma specimens. For Grade 3 astrocytomas, there was a significant independent correlation between survival and the field in which the first mitosis was found (P = 0.02). For the oligodendroglial tumors, there was a strong correlation between the number of fields counted until the first mitosis was found and grade (P < 0.0001).



CONCLUSIONS

The evaluation of mitotic activity offers more prognostic information than can be obtained by the simple approach of noting only their presence or absence. Data were acquired regarding the diligence of the microscopic examination necessary to evaluate the presence or absence of mitotic activity. A 1 cm x 0.1 cm needle biopsy contains adequate tissue to evaluate mitotic activity for the purpose of histologic grading; however, this adequacy is dependent on the sample's being representative and composed entirely of cellular tumor. Cancer 1998;82:1550-5. © 1998 American Cancer Society.

Stephen W. Coons

Papers

Improving diagnostic accuracy and interobserver concordance in the classification and grading of primary gliomas

Regional heterogeneity in the DNA content of human gliomas

Mitosis identification in diffuse gliomas : Implications for tumor grading