Li Wang1, Meng Guo2, Kai Wang1, Lei Zhang1. 1. Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China. 2. Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China.
Abstract
Purpose: Metabolic alterations are crucial for tumor progression and response to therapy. The comprehensive model of combined central carbon metabolism-associated genes that contribute to the outcomes of glioma and astrocytoma is not well understood. Method: We studied the profiles of 63 genes involved in central carbon metabolism in 514 relatively low-grade glioma patients. The different distributions of gene expression in gliomas and astrocytoma were identified. The differential gene expression between each cohort and the correlations with prognosis were detected. Finally, we built a tentative model to detect the prognostic roles of carbon metabolism-associated genes in astrocytoma. Result: Two primary clusters and four subclusters with significantly different overall survival were identified in low-grade glioma. The differences of histological diagnoses, grade, tumor site, and age were detected between each cluster. Comparing with other histological types, patients with astrocytoma exhibited the worst prognosis. Between astrocytoma patients with poor and favorable prognoses, expression profiles of 11 genes were significantly discrepant. We detected that 18 genes were respectively correlated with overall survival in astrocytoma; moreover, four genes (RAF1, AKT3, IDH1, and FGFR1) were detected as dependent variables for the prediction of the survival status of astrocytoma patients and were capable to predict the survival. Conclusion: Central carbon metabolism-associated genes are differentially expressed in all patients with glioma and histological subtype astrocytoma. The gene expression profile is significantly associated with clinical manifestations. These results suggested that both the multigene expression patterns and individual central carbon metabolism-associated genes were potentially capable to predict the prognosis of patients with low-grade glioma.
Purpose: Metabolic alterations are crucial for tumor progression and response to therapy. The comprehensive model of combined central carbon metabolism-associated genes that contribute to the outcomes of glioma and astrocytoma is not well understood. Method: We studied the profiles of 63 genes involved in central carbon metabolism in 514 relatively low-grade gliomapatients. The different distributions of gene expression in gliomas and astrocytoma were identified. The differential gene expression between each cohort and the correlations with prognosis were detected. Finally, we built a tentative model to detect the prognostic roles of carbon metabolism-associated genes in astrocytoma. Result: Two primary clusters and four subclusters with significantly different overall survival were identified in low-grade glioma. The differences of histological diagnoses, grade, tumor site, and age were detected between each cluster. Comparing with other histological types, patients with astrocytoma exhibited the worst prognosis. Between astrocytomapatients with poor and favorable prognoses, expression profiles of 11 genes were significantly discrepant. We detected that 18 genes were respectively correlated with overall survival in astrocytoma; moreover, four genes (RAF1, AKT3, IDH1, and FGFR1) were detected as dependent variables for the prediction of the survival status of astrocytomapatients and were capable to predict the survival. Conclusion: Central carbon metabolism-associated genes are differentially expressed in all patients with glioma and histological subtype astrocytoma. The gene expression profile is significantly associated with clinical manifestations. These results suggested that both the multigene expression patterns and individual central carbon metabolism-associated genes were potentially capable to predict the prognosis of patients with low-grade glioma.
Diffuse low-grade gliomas are the most common primary malignancies in adults and include astrocytomas, oligodendrogliomas, and oligoastrocytomas (Brat et al., 2015). Different histological subtypes of glioma were undistinguishable; however, large differences in clinical behavior and response to therapy suggest that difference among the histological types is crucial (Smith et al., 2000). Even within each subtype, there are large differences in clinical performance among individual patients. Surgery resection is the primary therapeutic method for low-grade gliomas, but the outcomes are less than satisfactory because of the highly infiltrative nature of glioma, and the presence of residual tumor tissue results in recurrence and malignant progression (Dixit and Raizer, 2017). The prognosis of patients with relatively low-grade glioma varies widely, with some patients living for more than 5 years, while others survive less than 1 year (Bush and Chang, 2016). A more precise method of predicting the outcomes of relatively low-grade glioma is urgently needed to be developed.Metabolic reprogramming is a central hallmark of cancer. Dysregulation of metabolism-related genes leads to cellular transformation and tumor progression. Warburg (1956) revealed differences in the central metabolic pathways in solid tumors and noted that cancer cells require a large amount of glucose to maintain a high rate of glycolysis even in the presence of adequate oxygen and that they convert a majority of that glucose into lactic acid (the Warburg effect). More recently, it has been recognized that the “Warburg effect” contains a similarly increased utilization of glutamine (Reitzer et al., 1979). Previous studies have detected some variations in the genes, such as IDH1/2, GLUT1, and GLUT3, involved in tumor metabolism in gliomas (Yan et al., 2009; Verhaak et al., 2010; Labak et al., 2016). High-throughput sequencing has substantially advanced the understanding of the metabolic changes in low-grade gliomas by detecting changes in metabolism-associated genes (Brennan et al., 2013). Profiling holistic gene expression not only facilitates the investigation of subgroups with low-grade glioma but also enables the identification of the predictors of overall survival (OS) (Chen et al., 2016). Which pattern of expression of metabolism-associated genes in tumor tissue contributes to glioma is not well understood. The Cancer Genome Atlas (TCGA) provided a standardized gene expression dataset for the study of the expression pattern of metabolism-related genes, which enables the investigation of correlations between clinical manifestations and carbon metabolism–associated genes in glioma (The Cancer Genome Atlas Research Network et al., 2008; Sanborn et al., 2013).In this study, we investigated the expression patterns of central carbon metabolism–associated genes in adult patients with diffuse low-grade glioma, including astrocytoma, oligodendroglioma, and oligoastrocytoma. Moreover, we respectively detected the prognostic roles of individual gene and the multiple-gene combination. These results will facilitate an integral understanding of the metabolic alterations in glioma and provide a novel perspective to manage and treat this lethal cancer.
Methods
Samples and Database
We obtained transcriptome data and the corresponding clinical data of 514 relatively low-grade gliomapatients from TCGA from the cBioPortal for Cancer Genomics (http://cbioportal.org) (Gao et al., 2013). We filtered the data based on whether the mRNA z-score data, histological diagnosis, and OS data were comprehensive. Collectively, the studied dataset included 194 astrocytoma samples, 130 oligoastrocytoma samples, and 190 oligodendroglioma samples.Central carbon metabolism–related genes in the cancer-associated gene panel (hsa05230) were derived from the KEGG pathway database (http://www.kegg.jp/kegg/), as previously described (Kanehisa et al., 2017). In total, 65 central carbon metabolism–associated genes were listed; however, transcriptome information was missing for MYC and HKDC1, and the remaining 63 candidate genes were included after filtration. The gene expression levels were calculated from the mRNA z scores and compared to the expression distribution of each gene from tumors that were diploid for the genes in 514 patients with glioma (RNA-Seq V2 RSEM), based on TCGA data.
Bioinformatics
A cluster analysis of the 63 genes expressed in each histological type was used to distinguish samples based on gene expression patterns. Samples with different gene expression patterns were identified from the whole dataset. The transcriptional levels were shown as mRNA z scores and clustered using the hierarchical clustering algorithm in the Gene Cluster 3.0 program (De Hoon et al., 2004). The cluster heat map and pattern according to tumor stage were generated with the Java Treeview program (Saldanha, 2004).
Prognostic Implication Analyses
To investigate the prognostic role of the cancer metabolism–associated genes, we used GraphPad Prism 6 for Windows (GraphPad Software, Inc., CA, US; version 6.01, 2012) to perform comparisons of the overall survivals in different clusters. Additionally, an analysis of the difference in OS between the cohorts with low and high expression levels of differentially expressed genes was conducted with GraphPad Prism 6.
Statistical Analysis
Survival curves were plotted according to the Kaplan–Meier method and compared using the log-rank test in GraphPad Prism 6. Associations between clinical characteristics and the variables used to determine the clusters of patients were analyzed by Fisher exact test and the Pearson/Spearman correlation. Differences in gene expression levels between clusters were analyzed by analysis of variance. Correlations between variable were determined by regression analyses. All tests were performed with SPSS 19.0 (IBM, Inc., NY, US). P < 0.05 was considered statistically significant.
Results
Expression Profile of Central Carbon Metabolism–Associated Genes in Diffuse Gliomas
To investigate central carbon metabolism programming in diffuse gliomas, we first examined the transcriptional distributions of carbon metabolism–associated genes. In total, 63 genes that have been widely reported to be key players in metabolic reprogramming were included (Soga, 2013). The patients with diffuse glioma were sorted by differences in the gene expression according to the RNA-Seq data. Following filtration, 514 patients with survival data were included in the cluster analysis (). The preliminary analysis showed that there were two clusters, and strikingly, the 101 patients in cluster 1 had much worse prognoses than the patients in cluster 2 (OS of 48.65 vs 105.12 months, P < 0.0001) (, ). Between the two clusters, there was a significant difference in the expression levels (P < 0.05) of 49 genes (). A comparison of the clinical characteristics of clusters 1 and 2 showed that the parameters of histological diagnoses, tumor grade, tumor site, and age were vastly different between the two clusters (P < 0.001), as shown in .
Figure 1
The expression profile of central carbon metabolism–associated genes in glioma patients. (A) In total, 514 patients were primarily divided into two clusters. The expression values of 63 genes corresponding to the individual patient were arrayed in the columns according to the expression affinity. Patients with similar gene expression patterns were clustered and grouped using the hierarchical clustering algorithm and arrayed in the rows. (B) The patients in cluster 1 had much worse prognoses than the patients in cluster 2, of which overall survival (OS) was 48.65 months compared to 105.12 months. (C) There were 49 genes that showed a significant difference in the expression levels between the two clusters P < 0.05. (D) The studied cohort was further subdivided into four subclusters, among which the subcluster 1 was with the worst OS and subcluster 4 showed the most favorable outcome. (E) The differential expression analysis revealed that 52 metabolism-associated genes were significantly different between subcluster 1 and subcluster 4.
Table 1
Overall survival differences of each cluster.
Cluster
Significance (P)
1
2
Number
158
356
<0.0001
Median survival
48.65
105.12
Table 2
Characteristics of glioma patients in clustered groups 1 and 2.
Clinical features
Cluster
Total
P
1
2
Histological diagnosis
Astrocytoma
92
102
194
2.96E−10***
Oligoastrocytoma
34
96
130
Oligodendroglioma
32
158
190
Grade
Unknown
0
1
1
<0.001***
G2
52
196
248
G3
106
159
265
Age
≤41
53
215
268
1.37E−8***
>41
105
141
246
Tumor site
Unknown
0
1
1
<0.001***
Posterior fossa, brain stem
1
0
1
Posterior fossa, cerebellum
2
0
2
Supratentorial, frontal lobe
73
229
302
Supratentorial, not otherwise specified
7
1
8
Supratentorial, occipital lobe
0
8
8
Supratentorial, parietal lobe
18
28
46
Supratentorial, temporal lobe
57
89
146
Laterality
Unknown
1
4
5
0.412
Left
79
171
250
Midline
4
3
7
Right
74
178
252
Supratentorial localization
Unknown
7
22
29
0.853
Cerebral cortex
43
98
141
Deep gray
1
2
3
Not listed in medical Record
73
149
222
White matter
34
85
119
Sex
Female
74
155
229
0.275
Male
84
201
285
History neoadjuvant
No
158
353
511
0.719
Yes
0
3
3
***P < 0.001.
The expression profile of central carbon metabolism–associated genes in gliomapatients. (A) In total, 514 patients were primarily divided into two clusters. The expression values of 63 genes corresponding to the individual patient were arrayed in the columns according to the expression affinity. Patients with similar gene expression patterns were clustered and grouped using the hierarchical clustering algorithm and arrayed in the rows. (B) The patients in cluster 1 had much worse prognoses than the patients in cluster 2, of which overall survival (OS) was 48.65 months compared to 105.12 months. (C) There were 49 genes that showed a significant difference in the expression levels between the two clusters P < 0.05. (D) The studied cohort was further subdivided into four subclusters, among which the subcluster 1 was with the worst OS and subcluster 4 showed the most favorable outcome. (E) The differential expression analysis revealed that 52 metabolism-associated genes were significantly different between subcluster 1 and subcluster 4.Overall survival differences of each cluster.Characteristics of gliomapatients in clustered groups 1 and 2.***P < 0.001.To detect the subtler differences among further stratified cohorts, we subdivided the 514 patients into four subclusters based on the expression of the 63 genes. We detected that extreme differences in prognosis were shown among those subclusters (P < 0.0001) (, ). Subcluster 1 was associated with the worst OS, while subcluster 4 showed a much favorable outcome than other subclusters (). Comparison of the gene expression variations revealed that the expression levels of 52 metabolism-associated genes were significantly different between the two prognostic-discrepant cohorts (). Additionally, we compared the clinical characteristics of the subclusters. Similar with the previous result, clear significant differences were found with regard to the parameters of histological diagnoses, tumor grade, tumor site, and age (P < 0.001) ().
Table 3
Overall survival differences of each subcluster
Subcluster
Significance (P)
1
2
3
4
Number
101
57
123
233
<0.0001
Median survival
24.38
62.12
87.39
130.68
Table 4
Characteristics of glioma patients in subdivided clusters.
Clinical features
Subcluster
Total
P
1
2
3
4
Histological diagnosis
Astrocytoma
67
25
60
42
194
5.94E−21***
Oligoastrocytoma
19
15
40
56
130
Oligodendroglioma
15
17
23
135
190
Grade
Unknown
0
0
0
1
1
3.88E−08***
G2
20
32
60
136
248
G3
81
25
63
96
265
Age
≤41
32
21
84
131
268
5.32E−8***
>41
69
36
39
102
246
Tumor site
Unknown
0
0
0
1
1
<0.001***
Posterior fossa, brain stem
1
0
0
0
1
Posterior fossa, cerebellum
2
0
0
0
2
Supratentorial, frontal lobe
40
33
71
158
302
Supratentorial, not otherwise specified
4
3
0
1
8
Supratentorial, occipital lobe
0
0
3
5
8
Supratentorial, parietal lobe
11
7
15
13
46
Supratentorial, temporal lobe
43
14
34
55
146
Laterality
Unknown
1
0
2
2
5
0.235
Left
44
35
60
111
250
Midline
4
0
1
2
7
Right
52
22
60
118
252
Supratentorial localization
Unknown
4
3
6
16
29
0.910
Cerebral cortex
24
19
32
66
141
Deep gray
1
0
0
2
3
Not listed in medical record
50
23
55
94
222
White matter
22
12
30
55
119
Sex*
Female
45
29
47
108
229
0.357
Male
56
28
76
125
285
History neoadjuvant
No
100
55
119
225
499
0.453
Yes
1
2
4
8
15
***represent P < 0.001.
Overall survival differences of each subclusterCharacteristics of gliomapatients in subdivided clusters.***represent P < 0.001.
Variations in Metabolism-Associated Gene Expression Levels in Different Histological Types
According to the binary comparisons among different gene expression cohorts, histological type was revealed as the variable associated with the largest differences in gene expression. We compared the OS of patients with astrocytoma, oligoastrocytoma, and oligodendroglioma, and significant differences were detected (). The median survival times of patients with astrocytoma (66.12 months), oligoastrocytoma 5.12 months), and oligodendroglioma (95.5 months) were markedly distinguishing (P = 0.0084). Further analysis of differences in gene expression demonstrated that 45 metabolism-associated genes were differentially expressed among the histological types (, ).
Figure 2
The differences in prognoses of patients with astrocytoma, oligoastrocytoma, and oligodendroglioma were significant. (A) The prognoses of patients with astrocytoma, oligoastrocytoma, and oligodendroglioma were significant. (B) Differential expression analysis demonstrated that 45 metabolism-associated genes were discrepantly expressed among the three histological types.
The differences in prognoses of patients with astrocytoma, oligoastrocytoma, and oligodendroglioma were significant. (A) The prognoses of patients with astrocytoma, oligoastrocytoma, and oligodendroglioma were significant. (B) Differential expression analysis demonstrated that 45 metabolism-associated genes were discrepantly expressed among the three histological types.
Differences in the Expression Levels of Metabolism-Associated Genes in Astrocytoma
The above results showed that among the histological types of glioma, astrocytoma showed the worst prognosis. To study the expression profiles of metabolism-associated genes in the poor-prognosis histological types, we grouped the patients with astrocytoma according to the metabolism-associated genes transcriptional data. Among the patients, two primary clusters that showed distinguishing median survival times of 43.99 and 73.42 months were identified (P = 0.0064) (). Further, four subclusters were divided according to fine grouping. The comparison of the OS showed that the difference in prognosis was even more marked (P < 0.0001) (). Subcluster 2 had the worse prognosis (median of 24.9 months) than other subclusters (median of 67.41 months), P < 0.0001 (). We respectively detected the gene expression differences between cluster 1 versus cluster 2; among different subclusters and subcluster 2 versus the other subclusters, the results revealed that the expressions of 33 metabolism-associated genes were significantly varied ().
Figure 3
The expression profile of central carbon metabolism–associated genes in patients with astrocytoma. (A) According to expression profiling, two primary clusters and additionally four subdivided clusters were identified. The comparison of median survival between two primary clusters (B) and five subdivided clusters (C) showed significant difference. In addition, patients in subcluster 2 showed the worst prognosis comparing to other patients, P < 0.0001 (D). (E) Differential expression analysis demonstrated that 33 metabolism-associated genes were significantly variated in all contrast of clusters 1 and 2, subcluster 2 and the other subclusters, and five subclusters.
The expression profile of central carbon metabolism–associated genes in patients with astrocytoma. (A) According to expression profiling, two primary clusters and additionally four subdivided clusters were identified. The comparison of median survival between two primary clusters (B) and five subdivided clusters (C) showed significant difference. In addition, patients in subcluster 2 showed the worst prognosis comparing to other patients, P < 0.0001 (D). (E) Differential expression analysis demonstrated that 33 metabolism-associated genes were significantly variated in all contrast of clusters 1 and 2, subcluster 2 and the other subclusters, and five subclusters.
The Prognostic Role of Metabolism-Associated Genes in Astrocytoma
We uncovered that the expression pattern of metabolism-associated genes was closely related to the prognosis of patients with astrocytoma. To investigate the effect of individual metabolism-associated gene on the prognosis of astrocytomapatients, we divided the subjects into two cohorts according to the OS: poor prognosis group and good prognosis group. We further investigated the differences in the expression levels of the metabolism-associated genes. It was detected that 11 genes, namely, FGFR1, ERBB2, PGAM4, PGAM1, G6PD, RET, AKT3, PTEN, RAF1, PKM, and LDHA, had significantly different expression levels between patients with poor and favorable OS times (, ).
Figure 4
The prognostic role of metabolism-associated genes in astrocytoma. (A) There are 11 differentially expressed genes, containing FGFR1, ERBB2, PGAM4, PGAM1, G6PD, RET, AKT3, PTEN, RAF1, PKM, and LDHA, which were detected to be significantly discrepant between patients with poor and favorable overall survival (OS) times. (B) According to study correlation of individual gene expression and survival, the expression levels of nine genes positively correlated with OS (r > .2, P < 0.05), and the expression levels of the other nine genes were negatively correlated with OS (r < –0.2, P < 0.05).
The prognostic role of metabolism-associated genes in astrocytoma. (A) There are 11 differentially expressed genes, containing FGFR1, ERBB2, PGAM4, PGAM1, G6PD, RET, AKT3, PTEN, RAF1, PKM, and LDHA, which were detected to be significantly discrepant between patients with poor and favorable overall survival (OS) times. (B) According to study correlation of individual gene expression and survival, the expression levels of nine genes positively correlated with OS (r > .2, P < 0.05), and the expression levels of the other nine genes were negatively correlated with OS (r < –0.2, P < 0.05).Additionally, we detected the pertinences between the trend of metabolism-associated gene expression differential and survival variation. According to study correlation of individual gene expression and survival, positive correlations were detected between the respective expression levels of nine genes containing PGAM1, PGAM4, RAF1, PDHB, AKT3, PTEN, PIK3R1, RET, and MAPK3 with OS (r > 0.2, P < 0.05); on the other hand, the expression levels of nine genes containing EGFR, IDH1, GCK, PKM, LDHA, G6PD, TIGAR, ERBB2, and FGFR1 were detected negatively correlated to survival (r < −0.2, P < 0.05) (). In addition to their associations with survival, the expression levels of the genes are closely correlated between the two sets ().
Table 5
The correlation of overall survival (OS) of astrocytoma and expressing variation of individual gene.
OS positively correlated genes
OS negatively correlated genes
Pearson correlation coefficient (r)
Significant(P)
Pearson correlation coefficient (r)
Significant(P)
PGAM1
0.41
< 0.001***
FGFR1
−0.45
<0.001***
PGAM4
0.40
0.001**
ERBB2
−0.39
0.001**
RAF1
0.36
0.003**
TIGAR
−0.37
0.002**
PDHB
0.29
0.012*
G6PD
−0.33
0.006**
AKT3
0.28
0.016*
LDHA
−0.32
0.007**
PTEN
0.27
0.020*
PKM
−0.28
0.017*
PIK3R1
0.26
0.025*
IDH1
−0.27
0.021*
RET
0.25
0.029*
GCK
−0.27
0.018*
MAPK3
0.25
0.031*
EGFR
−0.23
0.039*
*P < 0.05; **P < 0.01; ***P < 0.001.
The correlation of overall survival (OS) of astrocytoma and expressing variation of individual gene.*P < 0.05; **P < 0.01; ***P < 0.001.To address the prognostic roles of those survival-related genes, we separately split the astrocytomapatients into two groups according to the single gene expression and additionally compared the prognosis between the two groups (). Except to AKT3 and PIK3R1, 16 genes showed a significant association with prognosis. Patients with low expression levels of RET and PGAM1 were associated with a greater hazard ratio (HR) for death than that of patients with high expression levels of RET and PGAM1 (P < 0.0001). In contrast, patients with high expression levels of TIGAR, ERBB2, EGFR, and FGFR1 had a higher HR for death than that of patients with low expression levels of those genes (P < 0.0001) ().
Figure 5
The correlation of singular gene expression difference with the astrocytoma prognosis.
Table 6
The prognostic roles of single metabolism associated gene in astrocytoma.
The correlation of singular gene expression difference with the astrocytoma prognosis.The prognostic roles of single metabolism associated gene in astrocytoma.*P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001.To evaluate the effects of differences in gene expression on the prediction of the outcome of astrocytoma, we ranked the expression data of 18 genes to construct a regression model. Based on the ranking results, four genes (RAF1, AKT3, IDH1, and FGFR1) were independent predictors of the survival status of astrocytomapatients (). To integrate these four genes into a single panel, multivariate Cox regression analysis was employed to obtain the coefficient. The risk score was calculated as follows: the risk score was equal to the expression of RAF1∗1.801 plus the expression of AKT3∗1.545 plus the expression of IDH1∗1.569 plus the expression of FGFR1∗1.035 (). As shown in , the area under the receiver operating characteristic curve of the four-gene panel for the prediction of the long- or short-term outcomes of astrocytoma was 0.9407, with a 95% confidence interval of 0.8864 to 0.9949 and a P < 0.0001.
Figure 6
Four-gene panel was utilized to potentially predict the outcomes of patients with astrocytoma. (A) The score of the four-gene model including RAF1, AKT3, IDH1, and FGFR1 was positively correlated with overall survival and showed a linearity. (B) The area under the receiver operating characteristic curve of the four-gene panel for the prediction of the long- or short-term outcomes of astrocytoma was 0.9407, with a 95% confidence interval of 0.8864 to 0.9949 and P < 0.0001.
Four-gene panel was utilized to potentially predict the outcomes of patients with astrocytoma. (A) The score of the four-gene model including RAF1, AKT3, IDH1, and FGFR1 was positively correlated with overall survival and showed a linearity. (B) The area under the receiver operating characteristic curve of the four-gene panel for the prediction of the long- or short-term outcomes of astrocytoma was 0.9407, with a 95% confidence interval of 0.8864 to 0.9949 and P < 0.0001.
Discussion
Low-grade glioma has complicated characteristics and diverse histologic types. Although the histopathological classification of low-grade gliomas is reliable, it varies between observers and is insufficient to predict clinical outcomes (Louis et al., 2016). Recently, the molecular analysis of tumors has become a critical part of tumor classification and prognostication, and increasing evidence has suggested that defining tumor subtypes based on differences in gene expression in low-grade glioma is meaningful (Verhaak et al., 2010; Eckel-Passow et al., 2015; Louis et al., 2016). In this study, we found that metabolism-associated gene profiling was able to define two primary clusters and four subclusters of patients with low-grade glioma regardless of histologic type. Overall survival differed between the primary clusters and subclusters. We identified 44 genes with significant differences in expression levels between the groups of patients with the worst and best prognoses (). Some of those genes participate in the regulation of intracellular signal transduction, and others are involved in the metabolism of glucose and other carbohydrates. In addition to the differences in gene expression, we found that the groups had significant differences in histological types, tumor grades, tumor sites, and age. The results showed the specific expression profiles of metabolism-associated genes in patients with low-grade glioma.Astrocytomas, oligoastrocytomas, and oligodendrogliomas are the three histologic subtypes of low-grade glioma; the subtypes have always been difficult to define according to clinical features (Louis et al., 2014). In the current dataset, patients with astrocytoma had worse prognoses than those of patients with the other two subtypes. We detected the differentially expressed genes in patients with different histological types of glioma, and 45 genes were significantly differentially expressed among the three subtypes. Moreover, 80% of those genes (35 genes) overlapped with the gene set (44 genes) that was associated with different subgroups. Specifically, we determined the expression profiles of metabolism-associated genes in astrocytomas. The results showed that 33 genes had significantly different expression levels, and those differences in expression were closely correlated with OS in patients with astrocytomas. These differences in the expression of metabolism-associated genes not only reveal metabolic differences among the histological subtypes but also suggest that there is metabolic heterogeneity within a single subtype.In patients with astrocytomas, we identified 11 genes that varied significantly in expression between patients with poor and favorable OS. Additionally, we detected genes with expression levels that were positively and negatively associated with OS, and a correlation existed between the expression levels of these two sets of genes. According to the survival analysis, 16 genes were significantly associated with prognosis. Patients with low expression levels of RET and PGAM1 and high expression levels of TIGAR, ERBB2, EGFR, and FGFR1 had elevated HRs with regard to survival. The RET gene encodes a transmembrane receptor that is a member of the tyrosine protein kinase family of proteins. It has been reported that the mRNA levels of RET are elevated in astrocytomapatients with IDH mutations, who are known to have prolonged survival (Zhang et al., 2018). PGAM1 is involved in tumor cell glycolysis and biosynthesis, and this protein had elevated expression levels in high-grade astrocytomas (Liu et al., 2018). Increased expression of these two genes in astrocytomas might inhibit metabolic pathways crucial to the development and progression of tumors.Low-grade glioma is one of the most malignant human diseases, with a very poor prognosis and scant available information about its biological properties. This study provided new information about the metabolism events affected by the identified genes with differential expression levels. We divided the patients into different subgroups according to their metabolism-associated gene expression patterns. The expression levels of those genes were strongly correlated with the prognosis of patients with astrocytoma, possibly because of their effect on the regulation of the biological behavior of the tumor. This study increases our understanding of the prognostic roles of central carbon metabolism–associated genes in patients with low-grade glioma.
Data Availability
The datasets analyzed for this study can be found in the cBioPortal for Cancer Genomics (http://cbioportal.org).
Ethics Statement
Data obtained from the TCGA open-access database was collected from tumors of patients who provided informed consent based on the guidelines from the TCGA Ethics, Law and Policy Group.
Author Contributions
LZ designed the current study. MG collected the data and performed the statistical test. KW sorted the clinical information and interpreted the result. LW wrote the manuscript. All authors read and approved the final manuscript.
Funding
This work was funded by the National Natural Science Foundation of China (no. 81702355).
Conflict of Interest Statement
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Authors: Roel G W Verhaak; Katherine A Hoadley; Elizabeth Purdom; Victoria Wang; Yuan Qi; Matthew D Wilkerson; C Ryan Miller; Li Ding; Todd Golub; Jill P Mesirov; Gabriele Alexe; Michael Lawrence; Michael O'Kelly; Pablo Tamayo; Barbara A Weir; Stacey Gabriel; Wendy Winckler; Supriya Gupta; Lakshmi Jakkula; Heidi S Feiler; J Graeme Hodgson; C David James; Jann N Sarkaria; Cameron Brennan; Ari Kahn; Paul T Spellman; Richard K Wilson; Terence P Speed; Joe W Gray; Matthew Meyerson; Gad Getz; Charles M Perou; D Neil Hayes Journal: Cancer Cell Date: 2010-01-19 Impact factor: 31.743
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