The glioma proteome


Intracranial tumors comprise approximately 2% of all adult cancers, but form a larger fraction within the group of childhood tumors. Gliomas account for approximately 60% of all intracranial tumors and are classified according to the suggested cell of origin, differentiation and malignancy grade. The prognosis for high-grade gliomas is poor due to limited possibilities of curative treatment.

Gliomas are tumors of neuroepithelial tissue and comprise a complex and heterogeneous group of tumors representing counterparts to various normal inhabitant cells of the central nervous system (CNS). The most common form of glioma is astrocytoma, representing approximately half of all brain tumors.

The 5-year survival rate for glioma patients in general is usually less than 10%, with children reaching a rate of almost 25%. Grade IV astrocytoma, also known as glioblastoma or glioblastoma multiforme (GBM) is the most common and aggressive glioma with a very poor 5-year survival (less than 5%), a majority of patients survive less than 3 months, and accounts for about 15% of all brain tumors. There is currently no cure for GBM but it is normally treated with surgery followed by chemotherapy and radiotherapy to increase the length of survival.

Here, we explore the glioma proteome using TCGA transcriptomics data and antibody based protein data. 263 genes are suggested as prognostic based on transcriptomics data from 153 patients; 195 genes associated with unfavourable prognosis and 68 genes associated with favourable prognosis.

TCGA data analysis


In this metadata study we focused on the GBM data available from TCGA. The transcriptomics data was available from 153 patients; 54 female and 99 male, 30 were still alive and 123 patients deceased at the time of data collection. Information on stage distribution was missing.

Unfavourable prognostic genes in glioma


For unfavourable genes, higher relative expression levels at diagnosis gives significantly lower overall survival for the patients. There are 195 genes associated with unfavourable prognosis in glioma. In Table 1, the top 20 most significant genes related to unfavourable prognosis are listed.

REEP2 is a gene associated with unfavourable prognosis in glioma. The best separation is achieved by an expression cutoff at 38.3 fpkm which divides the patients into two groups with 0% 3-year survival for patients with high expression versus 10% for patients with low expression, p-value: 3.43e-4. Immunohistochemical staining using an antibody targeting REEP2 (HPA031813) shows differential expression pattern in glioma samples.

REEP2 - survival analysis p<0.001
REEP2 - high expression
REEP2 - low expression

Table 1. The 20 genes with highest significance associated with unfavourable prognosis in glioma.

Gene Description Predicted localization mRNA (cancer) p-value
PODNL1 podocan like 1 Intracellular,Secreted 1.4 2.06e-8
SLC6A6 solute carrier family 6 member 6 Membrane 3.5 1.09e-7
PTPRN protein tyrosine phosphatase, receptor type N Intracellular,Membrane 5.3 2.45e-7
MT1H metallothionein 1H Intracellular 2.2 4.29e-7
RPL39L ribosomal protein L39 like Intracellular 8.8 9.50e-7
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Favourable prognostic genes in glioma


For favourable genes, higher relative expression levels at diagnosis gives significantly higher overall survival for the patients. There are 68 genes associated with favourable prognosis in glioma. In Table 2, the top 20 most significant genes related to favourable prognosis are listed.

PHGDH is a gene associated with favourable prognosis in glioma. The best separation is achieved by an expression cutoff at 17.9 fpkm which divides the patients into two groups with 9% 3-year survival for patients with high expression versus 0% for patients with low expression, p-value: 2.26e-4. Immunohistochemical staining using an antibody targeting PHGDH (CAB003681) shows differential expression pattern in glioma samples.

PHGDH - survival analysis p<0.001
PHGDH - high expression
PHGDH - low expression

Table 2. The 20 genes with highest significance associated with favourable prognosis in glioma.

Gene Description Predicted localization mRNA (cancer) p-value
SAMD13 sterile alpha motif domain containing 13 Intracellular 1.2 2.06e-8
MIER1 MIER1 transcriptional regulator Intracellular,Secreted 4.7 6.18e-8
STARD7 StAR related lipid transfer domain containing 7 Intracellular,Secreted 58.8 5.94e-6
ZBTB6 zinc finger and BTB domain containing 6 Intracellular 4.5 9.75e-6
RCOR3 REST corepressor 3 Intracellular 4.8 1.92e-5
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The glioma transcriptome


The transcriptome analysis shows that 72% (n=14021) of all human genes (n=19479) are expressed in glioma. All genes were classified according to the glioma-specific expression into one of five different categories, based on the ratio between mRNA levels in glioma compared to the mRNA levels in the other 16 analyzed cancer tissues. 640 genes show some level of elevated expression in glioma compared to other cancers (Figure 1). The elevated category is further subdivided into three categories as shown in Table 3.

Figure 1. The distribution of all genes across the five categories based on transcript abundance in glioma as well as in all other cancer tissues.

Table 3. Number of genes in the subdivided categories of elevated expression in glioma.

Category Number of genes Description
Tissue enriched 219 At least five-fold higher mRNA levels in a particular cancer as compared to all other cancers
Group enriched 175 At least five-fold higher mRNA levels in a group of 2-7 cancers
Tissue enhanced 246 At least five-fold higher mRNA levels in a particular cancer as compared to average levels in all cancers
Total 640 Total number of elevated genes in glioma

Additional information


The classification of gliomas is based on cell type, grade and location. Cell type classification is divided into 6 main categories; astrocytoma, oligodendrogliomas, brain stem gliomas, ependymomas, oligo-astrocytomas and optic pathway gliomas. Grade classification is divided inte low-grade (benign tendencies) and high-grade gliomas (malignant). Gliomas can also be classified according whether they are above or below the tentorium, a membrane in the brain that separates the cerebrum from the cerebellum. The classification is supertentorium (cerebrum) and infratentorium (cerebellum), there is also one more known as pontine tumors and is located in the brainstem.

Astrocytomas represent almost half of all brain tumors and are defined based on morphological features such as cellularity, nuclear atypia, mitotic rate, endothelial proliferation and necrosis.Astrocytomas are assigned to grades I-IV according to the current WHO classification system. These include pilocytic astrocytoma (Grade I), astrocytoma (Grade II), anaplastic astrocytoma (Grade III), and glioblastoma (Grade IV). The various forms of glioma are highly variable and several phenotypically different cell types exist, including gemistocytic glioma cells. Gemistocytic cells resemble a morphological alteration that can also be found in reactive astrocytes and is characterized by eosinophilic staining of a large, swollen cytoplasm.

Approximately 15% of gliomas are oligodendrogliomas. Histologically, oligodendrogliomas commonly show uniform cell architecture with increased numbers of delicate blood vessels. The tumor cell nuclei are mainly round and regular, and often surrounded by an artifactual perinuclear clearing that results in the so called "fried egg" appearance. High-grade oligodendrogliomas (anaplastic oligodendrogliomas) are recognized by features such as increased cellularity, mitotic activity and nuclear pleomorphism, as well as necrosis and endothelial proliferation.

The distinction between different forms of brain tumors is mainly based on morphological features, but immunohistochemistry plays an important role to distinguish between different tumor types, in particular when the tumor is poorly differentiated. In neuropathological diagnostics, antibodies directed towards proteins such as Glial Fibrillary Acidic Protein, Synaptophysin, EGFR, p53 and the proliferation marker Ki-67 are commonly used.

Relevant links and publications


Uhlen M et al, 2017. A pathology atlas of the human cancer transcriptome. Science.
PubMed: 28818916 DOI: 10.1126/science.aan2507

Cancer Genome Atlas Research Network et al, 2013. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet.
PubMed: 24071849 DOI: 10.1038/ng.2764

Uhlén M et al, 2015. Tissue-based map of the human proteome. Science
PubMed: 25613900 DOI: 10.1126/science.1260419

Sjöstedt E et al, 2015. Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex. PLoS One.
PubMed: 26076492 DOI: 10.1371/journal.pone.0130028

MedScape - Glioblastoma Multiforme

National Cancer institute - Glioblastoma Multiforme

Histology dictionary - Glioma