ATRX mRNA expression combined with IDH1/2 mutational status and Ki-67 expression refines the molecular classification of astrocytic tumors: evidence from the whole transcriptome sequencing of 169 samples samples

Abstract

Astrocytic tumors are the most common primary brain tumors in adults. ATRX mutations have been identified in gliomas and are correlated with its loss of expression, which causes alternative lengthening of telomeres (ALT) leading to genomic instability. In this study, we aimed to explore the role of ATRX mRNA expression alteration in the progression and subclassification of astrocytic tumors and examine its impact on clinical outcome. We investigated ATRX mRNA expression and its association with IDH1 and IDH2 mutations in 169 adult astrocytic tumors using whole transcriptome sequencing. In our cohort, low ATRX mRNA expression was detected in 68% of astrocytomas, 50% of anaplastic astrocytomas and 41.6% of glioblastomas. Low ATRX expression closely overlapped with mutations in IDH1/2 (P<0.0001) in astrocytic tumors across WHO grades II-IV. Significant association between low ATRX expression and longer overall survival was identified in our cohort (P<0.01). ATRX combined with IDH1/2 and Ki-67 was used to re-classify patients with astrocytic tumors: group A1 containing IDH1/2 mutations and low ATRX expression predicted a better prognostic outcome, whereas group A3 carrying wild-type IDH1/2 and high Ki-67 expression had the shortest overall survival; IDH-mutant tumors with low ATRX expression and IDH-wild-type tumors with high Ki-67 expression were grouped into group A2. In summary, our results showed that ATRX in cooperation with IDH1/2 and Ki-67 defines three subgroups of astrocytic tumors regardless of the conventional WHO grades consensus. The molecular stratification in astrocytic tumors may aid in treatment strategy selection, therapeutic trial design, and clinical prognosis evaluation.

Figure 1. Overview of histology, molecular aberrations and molecular classification in the cohort (n=139)

Each column represents a patient. “Molecular Classification” is defined as A1 (IDH-mut astrocytic tumors with ATRX-low; n=44), A2 (IDH-mut tumors with ATRX-high and IDH-WT with low Ki-67 expression; n=61), A3 (IDH-WT tumors with high Ki-67 expression; n=34).

Figure 2. Correlation of ATRX mRNA expression and Ki-67 protein expression with histology and IDH1/2 mutational status

a. ATRX mRNA expression (RPKM) was different in grade II-IV astrocytic tumors (P<0.05) and decreased in As than in pGBMs and sGBM (P<0.05, P<0.05, respectively). b. ATRX mRNA expression (RPKM) in tumors with IDH mutations was decreased compared with IDH-wild-type tumors (P<0.01). c. Ki-67 protein expression significantly differed in the three grades of astrocytic tumors (P<0.0001) and the expression levels in GBMs was significantly higher than that in astrocytomas and anaplastic astrocytomas (P<0.0001 and P<0.01, respectively). *P < 0.05, **P < 0.01, ****P < 0.0001.

Figure 3. Kaplan-Meier estimates of survival for astrocytic tumor patients

a. Among patients with astrocytic tumors of all grades, there was no significant difference in survival between anaplastic astrocytomas and GBMs when patients were only stratified by the histopathological diagnosis of their tumors. b, c, d. ATRX, IDH1/2 status and Ki-67 are biomarkers associated with survival of patients in astrocytic tumors. e. Among all patients with astrocytic tumors (n=139, except non-classifiable), there was a significant difference in overall survival between the new three subgroups, and the A1 group and A2 group survived significantly longer (median OS, 1208 and 689 days, respectively) than the A3 group (309 days; P<0.0001).

Figure 4. Model for classification of astrocytic tumors based on molecular markers

IDH-mut tumors with ATRX-low was defined as A1 (median OS=4 years), IDH-WT tumors with high Ki-67 expression as A3 (median OS=1 years), and IDH-mut tumors with ATRX-high and IDH-WT with low Ki-67 expression were termed as A2 (median OS=2 years). MS: median OS.