Prognostic and Predictive Markers in Glioma and Other Neuroepithelial Tumors

Multi-Omics Analysis Reveals Novel Subtypes and Driver Genes in Glioblastoma

Glioblastoma is the most lethal malignant primary brain tumor; nevertheless, there remains a lack of accurate prognostic markers and drug targets. In this study, we analyzed 117 primary glioblastoma patients’ data that contained SNP, DNA copy, DNA methylation, mRNA expression, and clinical information. After the quality of control examination, we conducted the single nucleotide polymorphism (SNP) analysis, copy number variation (CNV) analysis, and infiltrated immune cells estimate. And moreover, by using the cluster of cluster analysis (CoCA) methods, we finally divided these GBM patients into two novel subtypes, HX-1 (Cluster 1) and HX-2 (Cluster 2), which could be co-characterized by 3 methylation variable positions [cg16957313(DUSP1), cg17783509(PHOX2B), cg23432345(HOXA7)] and 15 (PCDH1, CYP27B1, LPIN3, GPR32, BCL6, OR4Q3, MAGI3, SKIV2L, PCSK5, AKAP12, UBE3B, MAP4, TP53BP1, F5, RHOBTB1) gene mutations pattern. Compared to HX-1 subtype, the HX-2 subtype was identified with higher gene co-occurring events, tumor mutation burden (TBM), and poor median overall survival [231.5 days (HX-2) vs. 445 days (HX-1), P-value = 0.00053]. We believe that HX-1 and HX-2 subtypes may make sense as the potential prognostic biomarkers for patients with glioblastoma.

Identification of a multidimensional transcriptome signature for survival prediction of postoperative glioblastoma multiforme patients

Background

Glioblastoma multiform (GBM) is a devastating brain tumor with maximum surgical resection, radiotherapy plus concomitant and adjuvant temozolomide (TMZ) as the standard treatment. Diverse clinicopathological and molecular features are major obstacles to accurate predict survival and evaluate the efficacy of chemotherapy or radiotherapy. Reliable prognostic biomarkers are urgently needed for postoperative GBM patients.

Methods

The protein coding genes (PCGs) and long non-coding RNA (lncRNA) gene expression profiles of 233 GBM postoperative patients were obtained from The Cancer Genome Atlas (TCGA), TANRIC and Gene Expression Omnibus (GEO) database. We randomly divided the TCGA set into a training (n = 76) and a test set (n = 77) and used GSE7696 (n = 80) as an independent validation set. Survival analysis and the random survival forest algorithm were performed to screen survival associated signature.

Results

Six PCGs (EIF2AK3, EPRS, GALE, GUCY2C, MTHFD2, RNF212) and five lncRNAs (CTD-2140B24.6, LINC02015, AC068888.1, CERNA1, LINC00618) were screened out by a risk score model and formed a PCG-lncRNA signature for its predictive power was strongest (AUC = 0.78 in the training dataset). The PCG-lncRNA signature could divide patients into high- risk or low-risk group with significantly different survival (median 7.47 vs. 18.27 months, log-rank test P < 0.001) in the training dataset. Similar result was observed in the test dataset (median 11.40 vs. 16.80 months, log-rank test P = 0.001) and the independent set (median 8.93 vs. 16.22 months, log-rank test P = 0.007). Multivariable Cox regression analysis verified that it was an independent prognostic factor for the postsurgical patients with GBM. Compared with IDH mutation status, O-(6)-methylguanine DNA methyltransferase promoter methylation status and age, the signature was proved to have a superior predictive power. And stratified analysis found that the signature could further separated postoperative GBM patients who received TMZ-chemoradiation into high- and low-risk groups in TCGA and GEO dataset.

Conclusions

The PCG-lncRNA signature was a novel prognostic marker to predict survival and TMZ-chemoradiation response in GBM patients after surgery.

Electronic supplementary material

The online version of this article (10.1186/s12967-018-1744-8) contains supplementary material, which is available to authorized users.

CD24 expression as a marker for predicting clinical outcome in human gliomas

CD24 is overexpressed in glioma cells in vitro and in vivo. However, the correlation of its expression with clinicopathological parameters of gliomas and its prognostic significance in this tumor remain largely unknown. To address this problem, 151 glioma specimens and 10 nonneoplastic brain tissues were collected. Quantitative real-time PCR, immunochemistry assay, and Western blot analysis were carried out to investigate the expression of CD24. As per the results, CD24 was overexpressed in gliomas. Its expression levels in glioma tissues with higher grade (P < 0.001) and lower KPS (P < 0.001) were significantly higher than those with lower grade and higher KPS, respectively. Cox multifactor analysis showed that CD24 (P = 0.02) was an independent prognosis factor for human glioma. Our data provides convincing evidence for the first time that the overexpression of CD24 at gene and protein levels is correlated with advanced clinicopathological parameters and poor prognosis in patients with glioma.

Stratifin expression is a novel prognostic factor in human gliomas

Stratifin (14-3-3σ or SFN) is a member of the 14-3-3 family of proteins which play critical roles in different cellular signaling processes. Stratifin as a potential tumor suppressor gene plays an important role in carcinogenesis and metastasis. The aim of this study was to investigate the expression of Stratifin in human gliomas and to analyze its expression profile with respect to tumor development. The expression pattern of Stratifin was analyzed by immunohistochemistry and/or Western blotting in tumor samples from 186 patients with different grades of gliomas. Prognostic significance was assessed using Kaplan-Meier survival estimates and Cox regression analyses. The expression pattern of Stratifin was correlated with the pathological and clinical characteristics of the patients with gliomas. Western blot analysis indicated that the average optical densitometry (OD) ratio of Stratifin in high-grade gliomas (World Health Organization [WHO] grade III/IV) was lower than in low-grade tumors (WHO grade I/II, p=0.026). In addition, statistical analysis showed that patients expressing a high level of Stratifin have favorable overall survival rates relative to those expressing a low level of this protein. Cox multi-factor analysis showed that Stratifin (p=0.02) was an independent prognosis factor for human gliomas. Our results provide convincing evidence that the expression of Stratifin is down-regulated in human gliomas. Its expression level is correlated with the clinicopathological parameters and prognosis in patients with gliomas. Pending validation targeting, Stratifin might also be a novel opportunity to improve the therapy of this tumor.

Sp1 is upregulated in human glioma, promotes MMP-2-mediated cell invasion and predicts poor clinical outcome

Sp1, the first identified transcription factor, has been reported to be associated with the development and progression of various human cancer types. However, the clinical significance and biological role of Sp1 in glioma are less well understood. In this study, we found that the expression of Sp1 was markedly elevated in glioma cell lines and tissues. Immunohistochemistry analysis revealed that the vast majority of 222 paraffin-embedded archival glioma specimens tested displayed positive Sp1 expression, and 58.6% exhibited high-level Sp1 expression. Statistical analysis suggested that the high Sp1 expression was correlated strongly with the WHO grading (p < 0.001) and survival status (p < 0.001) of glioma patients. Patients with lower Sp1 expression had better overall survival than those with higher Sp1 expression. Multivariate analysis suggested that Sp1 expression might be an independent prognostic indicator of the survival of patients with glioma. Furthermore, overexpression of Sp1 in glioma cells was found to increase their invasiveness, and in contrast, silencing Sp1 by siRNA caused an inhibition of cell invasion. Moreover, we demonstrated that the up-regulation of Sp1 could increase activity and expression of MMP-2. Collectively, our data suggest that Sp1 might represent a valuable prognostic marker for glioma and is involved in modulation of tumor invasion.

Prognostic significance of histological grading, p53 status, YKL-40 expression, and IDH1 mutations in pediatric high-grade gliomas

The objective of this study was to evaluate, in a series of 43 pediatric high-grade gliomas (21 anaplastic astrocytoma WHO grade III and 22 glioblastoma WHO grade IV), the prognostic value of histological grading and expression of p53 and YKL-40. Moreover, mutational screening for TP53 and IDH1 was performed in 27 of 43 cases. The prognostic stratification for histological grading showed no difference in overall (OS) and progression-free survival (PFS) between glioblastomas and anaplastic astrocytomas. Overexpression of YKL40 was detected in 25 of 43 (58%) cases, but YKL-40 expression was not prognostic in terms of OS and PFS. p53 protein expression was observed in 13 of 43 (31%) cases but was not prognostic. TP53 mutations were detected in five of 27 (18%) cases (four glioblastomas and one anaplastic astrocytoma). Patients with TP53 mutation had a shorter median OS (9 months) and PFS (8 months) than those without mutations (OS, 17 months; PFS, 16 months), although this trend did not reach statistical significance (p = 0.07). IDH1 mutations were not detected in any of the cases analyzed. Our results suggest that in pediatric high-grade gliomas: (i) histological grading does not have strong prognostic significance, (ii) YKL-40 overexpression is less frequent than adult high-grade gliomas and does not correlate with a more aggressive behavior, (iii) TP53 mutations but not p53 expression may correlate with a more aggressive behavior, and (iv) IDH1 mutations are absent. These observations support the concept that, despite identical histological features, the biology of high-grade gliomas in children differs from that in adults, and therefore different prognostic factors are needed.