scholarly journals Association of TP53 Alteration with Tissue Specificity and Patient Outcome of IDH1-Mutant Glioma

Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 2116
Author(s):  
Balazs Murnyak ◽  
L. Eric Huang
Keyword(s):  
Patient Outcome ◽  
Tissue Specificity ◽  
Human Cancer ◽  
Lower Grade ◽  
Isocitrate Dehydrogenase 1 ◽  
Who Grade ◽  
Lower Grade Glioma ◽  
Incidence Studies ◽  
Idh1 Mutations ◽  
Tp53 Status

Since the initial discovery of recurrent isocitrate dehydrogenase 1 (IDH1) mutations at Arg132 in glioma, IDH1 hotspot mutations have been identified in cholangiocarcinoma, chondrosarcoma, leukemia, and various other types of cancer of sporadic incidence. Studies in glioma and leukemia have helped promote the theory that IDH1 mutations are an oncogenic event that drives tumorigenesis in general. Through bioinformatic analysis of more than 45,000 human pan-cancer samples from three independent datasets, we show here that IDH1 mutations are rare events in human cancer but are exclusively prevalent in WHO grade II and grade III (lower-grade) glioma. Interestingly, alterations in the tumor-suppressor gene TP53 (tumor protein p53) co-occur significantly with IDH1 mutations and show a tendency of exclusivity to IDH2 mutations. The co-occurrence of IDH1 mutation and TP53 alteration is widespread in glioma, particularly in those harboring IDH1R132H, IDH1R132G, and IDH1R132S, whereas co-occurrence of IDH1R132C and TP53 alteration can be found sporadically in other cancer types. In keeping with the importance of p53 in tumor suppression, TP53 status is an independent predictor of overall survival irrespective of histological and molecular subgroups in lower-grade glioma. Together, these results indicate tissue specificity of IDH1 hotspot mutation and TP53 alteration and the importance of TP53 status as a predictor of patient outcome in lower-grade glioma.

scholarly journals IMT-01 THERAPEUTIC EFFECT AGAINST LOWER GRADE GLIOMA INDUCED BY DENDRITIC CELL BASED IMMUNOTHERAPY

2019 ◽  
Vol 1 (Supplement_2) ◽  
pp. ii17-ii17
Author(s):  
Yasuharu Akasaki ◽  
Jun Takei ◽  
Yuko Kamata ◽  
Yohei Yamamoto ◽  
Ryosuke Mori ◽  
...  
Keyword(s):  
Glioma Cells ◽  
Progression Free Survival ◽  
Cervical Region ◽  
Lower Grade ◽  
Mri Findings ◽  
Who Grade ◽  
Lower Grade Glioma ◽  
Major Interest ◽  
Grade Ii

Abstract BACKGROUND This trial was designed to evaluate the safety and clinical responses to an immunotherapy with fusions of dendritic and glioma cells in patients with lower grade glioma (LGG; WHO grade II-III glioma). METHOD Autologous cultured glioma cells obtained from surgical specimens were fused with autologous dendritic cells (DC) using polyethylene glycol. The fusion cells (FC) were inoculated intradermally in the cervical region of subjects. Toxicity, progression-free survival (PFS), overall survival (OS), and MRI findings were evaluated. DNA for whole exome and RNA for whole transcriptome extracted from HLA-A*24:02 positive glioma cells were analyzed by next generation sequencer. Variant peptides showing strong binding affinity to HLA-A*24:02 but not the corresponding wild type peptides were selected as candidate of neo-antigens. RESULTS The number of subjects of this trial were 24 (initially diagnosed cases: 20, recurrence cases: 4). WHO grade III cases were 20, and grade II cases were 4. Male were 15, and female were 9. Mean of follow up periods were 53.0 months (the longest follow up period: 1322 months). The number of events on PFS and OS were 8 and 6, respectively. Mean of candidate of neo-antigen peptides in HLA-A*24:02 positive patients (n=8) was 34. Among these candidates, twelve types of common neo-antigen peptide were identified. Neo-antigen peptides specifically expressed in the glioma cells from the effective group were not identified. CONCLUSIONS These results indicate that the efficacy of FC-immunotherapy may not always depend on the number of gene mutations or the expression of the specific neo-antigens. FC-immunotherapy, as a means of producing specific immunity against neo-antigens may safely induce anti-tumor effects in patients with LGG. Analysis of prognostic factor in glioma immunotherapy may be the next area of major interest.

scholarly journals NI-06 MOLECULAR DIAGNOSIS, 11C-METHIONINE UPTAKE AND PROGNOSIS IN GRADE 2 AND 3 GLIOMAS

2019 ◽  
Vol 1 (Supplement_2) ◽  
pp. ii26-ii26
Author(s):  
Kaoru Tamura ◽  
Yaeko Furuhashi ◽  
Motoki Inaji ◽  
Daisuke Kobayashi ◽  
Takahiro Ogishima ◽  
...  
Keyword(s):  
Who Classification ◽  
Genetic Alterations ◽  
Normal Brain ◽  
Lower Grade ◽  
Who Grade ◽  
Oligodendroglial Tumors ◽  
Integrated Diagnosis ◽  
Lower Grade Glioma ◽  
Methionine Uptake ◽  
Grade 3

Abstract OBJECT The revised 2016 WHO Classification of Tumours of the Central Nervous System incorporates genetic alterations into the classification system, with the goal of creating more homogenous disease categories with greater prognostic value. In this study, we reclassified 103 consecutive lower grade gliomas using the revised 2016 WHO classification and examined for 11C-methionine uptake and prognosis. METHODS 103 consecutive lower grade glioma patients (Grade 2 in 41 patients, Grade 3 in 62 patients) treated at Tokyo Medical and Dental University Hospital from 2000 to 2018 were included in this study. The IDH1/2, ATRX and 1p19q status were analyzed using tumor samples. The tumor-to-normal ratio (T/N) of 11 C-methionine uptake was calculated by dividing the maximum standardized uptake value (SUV) for the tumor by the mean SUV of the normal brain. RESULT In the integrated diagnosis, 11 astrocytomas and 17 anaplastic astrocytomas were diagnosed as “IDH-mutant”, while 14 astrocytomas and 29 anaplastic astrocytomas were diagnosed as “IDH-wild”. In the 32 oligodendroglial tumors, 12 oligodendrogliomas and 9 anaplastic oligodendrogliomas were diagnosed as “IDH-mutant and 1p/19q-codeleted”. The concordance rate with 1p19q co-deletion and ATRX retention was 94.7%. The median T/N ratios in oligodendroglial tumors with “IDH-mutant and 1p/19q-codeleted” were 1.83 in Grade 2 and 2.83 in grade 3, which were significantly higher than those in astrocytic tumors with “IDH-mutant” (G2: 1.38, G3:1.62). Kaplan-Meier survival analysis revealed that oligodendroglial tumors with “IDH-mutant and 1p/19q-codeleted” had significantly better outcomes regardless of WHO grade. Overall survival was 90.9% at 5 years and 77.9% at 10 years in oligodendroglial tumors with “IDH-mutant and 1p/19q-codeleted”. CONCLUSIONS The results indicated that lower grade glioma categories reclassified with molecular classification correlate with the T/N ratio of methionine and the prognosis.

scholarly journals Transcriptomic Analysis of Glioma Based on IDH Status Identifies ACAA2 as a Prognostic Factor in Lower Grade Glioma

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Chenxing Wu ◽  
Hongwang Song ◽  
Xiaojun Fu ◽  
Shouwei Li ◽  
Tao Jiang
Keyword(s):  
Prognostic Factor ◽  
Network Analysis ◽  
Targeted Therapies ◽  
Correlation Network ◽  
Lower Grade ◽  
Gene Expressions ◽  
Who Grade ◽  
Lower Grade Glioma ◽  
Idh Mutations ◽  
Weighted Correlation

Background. Glioma is the most common and lethal tumor in the central nervous system (CNS). More than 70% of WHO grade II/III gliomas were found to harbor isocitrate dehydrogenase (IDH) mutations which generated targetable metabolic vulnerabilities. Focusing on the metabolic vulnerabilities, some targeted therapies, such as NAMPT, have shown significant effects in preclinical and clinical trials. Methods. We explored the TCGA as well as CGGA database and analyzed the RNA-seq data of lower grade gliomas (LGG) with the method of weighted correlation network analysis (WGCNA). Differential expressed genes were screened, and coexpression relationships were grouped together by performing average linkage hierarchical clustering on the topological overlap. Clinical data were used to conduct Kaplan–Meier analysis. Results. In this study, we identified ACAA2 as a prognostic factor in IDH mutation lower grade glioma with the method of weighted correlation network analysis (WGCNA). The difference of ACAA2 gene expressions between the IDH wild-type (IDH-WT) group and the IDH mutant (IDH-MUT) group suggested that there may be different potential targeted therapies based on the fatty acid metabolic vulnerabilities, which promoted the personalized treatment for LGG patients.

scholarly journals MPC-2 Clinical course and prognosis of lower-grade glioma, IDH wildtype and pTERT mutant

2021 ◽  
Vol 3 (Supplement_6) ◽  
pp. vi16-vi16
Author(s):  
Yoshinobu Takahashi ◽  
Hayato Takeuchi ◽  
Seisuke Tanigawa ◽  
Takanari Okamoto ◽  
Naoya Hashimoto
Keyword(s):  
Median Survival ◽  
Lower Grade ◽  
Diffuse Astrocytoma ◽  
Who Grade ◽  
Female Ratio ◽  
Astrocytic Glioma ◽  
Tert Promoter ◽  
Lower Grade Glioma ◽  
Idh Mutations ◽  
Astrocytic Gliomas

Abstract Background and Purpose: In the cIMPACT-Now update 3, it was proposed that grade 2 astrocytic gliomas without IDH-mutations and grade 3 astrocytic gliomas with TERT promoter mutations should be designated as diffuse IDH wildtype astrocytic glioma with molecular features of WHO grade IV glioblastoma. Therefore, we investigated whether this group of tumors actually corresponds to grade IV prognostically in cases that we encountered ourselves. Cases and Methods: Among the 65 patients having primary astrocytic glioma who were operated in our hospital from January 2016 to March 2021, the prognostic values of seven patients with lower-grade glioma, IDH wildtype, and pTERT mutant were investigated. Results: Among the seven patients, the median age was 59 years (50–66 years). Four of them had anaplastic astrocytoma, two had diffuse astrocytoma, and no tumor lesion could be identified upon histological examination for one patient. The male-to-female ratio was 1:6. MGMT methylation was observed in two patients (29%). The median survival was 20 months, with a significantly worse prognosis when compared with lower-grade glioma without the TERT promoter mutation (13 patients: median survival 40 months), but a better prognosis when compared with glioblastoma (45 patients: median survival 13 months) (Log-rank p = 0.0051). Conclusion: Although EGFR amplification, combined whole chromosome 7 gain, and whole chromosome 10 loss were not examined, the prognostic value of lower-grade glioma, IDH wildtype, and pTERT mutant was not as poor as that of glioblastoma. Further investigation is required to confirm whether these groups of tumors should be treated in the same way as grade IV glioblastoma.

TMOD-06. CREATION OF PATIENT-DERIVED LOWER GRADE GLIOMA ORGANOID MODELS FOR PERSONALIZED TREATMENT RESPONSE ASSESSMENT

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi216-vi217
Author(s):  
Kalil Abdullah ◽  
Joseph Buehler ◽  
Cylaina Bird ◽  
MIlan Savani ◽  
Alex Sternisha ◽  
...  
Keyword(s):  
Treatment Response ◽  
Genetic Alterations ◽  
Lower Grade ◽  
High Grade ◽  
Who Grade ◽  
Oncology Research ◽  
Genetically Engineered Mice ◽  
Lower Grade Glioma ◽  
Idh Mutations

Abstract Creating in vitro models of lower grade glioma represents a major challenge in neuro-oncology research. There are few such models that are tractable and widely used, which has hindered understanding of the biology of these tumors. Recently, substantial progress has been made in generating patient-derived in vitro organoid models of high grade glioma, but modeling lower grade disease remains difficult. Based on our experience creating neurosphere cultures of lower grade astrocytomas from genetically engineered mice, we hypothesized that modifying patient-derived organoid generation protocols to incorporate physiological oxygen levels would allow establishment and propagation of lower grade glioma organoids. In this study, we show that this approach supports efficient organoid model generation from primary glioma specimens across all histological subtypes and tumor grades (WHO Grade I-IV, n = 20). These organoid models retain key characteristics of their respective parental tumors, including IDH mutations and other genetic alterations, metabolite profiles, intratumoral heterogeneity, cellular composition, and cytoarchitectural features. Importantly, lower grade glioma organoids can be cultured for months and reanimated after biobanking. Our high success rate ( >90%) in establishing organoid models from primary lower grade glioma tissue samples further highlighted opportunities for treatment response assessments. To perform longitudinal measurements of therapy-induced changes in glioma organoid viability, we designed a novel, non-invasive imaging assay (termed rapid apex imaging) to determine real-time treatment response in low and high grade gliomas. We evaluated longitudinal responses of glioblastoma and IDH1 R132H-positive Grade II astrocytoma organoids to temozolomide and olaparib with and without radiation treatment. We quantified topological changes in organoid structure by building a bioinformatics tool to translate imaging data into a cellularity metric as a biomarker of organoid response. Our work unveils an effective new method to create in vitro, personalized models of lower grade glioma that supports elucidation of treatment sensitivity profiles.

scholarly journals Survival of diffuse astrocytic glioma, IDH1/2 wildtype, with molecular features of glioblastoma, WHO grade IV: a confirmation of the cIMPACT-NOW criteria

2019 ◽  
Vol 22 (4) ◽  
pp. 515-523 ◽  
Author(s):  
C Mircea S Tesileanu ◽  
Linda Dirven ◽  
Maarten M J Wijnenga ◽  
Johan A F Koekkoek ◽  
Arnaud J P E Vincent ◽  
...  
Keyword(s):  
Proportional Hazards ◽  
Proportional Hazards Model ◽  
Cox Proportional Hazards ◽  
Cox Proportional Hazards Model ◽  
World Health ◽  
Lower Grade ◽  
Isocitrate Dehydrogenase 1 ◽  
Who Grade ◽  
Astrocytic Glioma ◽  
Molecular Features

Abstract Background The Consortium to Inform Molecular and Practical Approaches to CNS Tumor Taxonomy (cIMPACT-NOW) has recommended that isocitrate dehydrogenase 1 and 2 wildtype (IDH1/2wt) diffuse lower-grade gliomas (LGGs) World Health Organization (WHO) grade II or III that present with (i) a telomerase reverse transcriptase promoter mutation (pTERTmt), and/or (ii) gain of chromosome 7 combined with loss of chromosome 10, and/or (iii) epidermal growth factor receptor (EGFR) amplification should be reclassified as diffuse astrocytic glioma, IDH1/2 wildtype, with molecular features of glioblastoma, WHO grade IV (IDH1/2wt astrocytomas WHO IV). This paper describes the overall survival (OS) of IDH1/2wt astrocytoma WHO IV patients, and more in detail patients with tumors with pTERTmt only. Methods In this retrospective multicenter study, we compared the OS of 71 IDH1/2wt astrocytomas WHO IV patients, with radiological characteristics of LGGs, with the OS of 197 IDH1/2wt glioblastoma patients. Moreover, we compared the OS of 22 pTERTmt only astrocytoma patients with the OS of the IDH1/2wt glioblastoma patients. Results Median OS was similar for IDH1/2wt astrocytoma WHO IV patients (23.8 mo) and IDH1/2wt glioblastoma patients (19.2 mo) (Cox proportional hazards model: hazard ratio [HR] 1.27, 95% CI: 0.85–1.88, P = 0.242). OS was also similar in patients with IDH1/2wt astrocytomas WHO IV, pTERTmt only, and IDH1/2wt glioblastomas (HR 1.15, 95% CI: 0.64–2.10, P = 0.641). Conclusions The presented data confirm the cIMPACT-NOW recommendation and we propose that IDH1/2wt astrocytomas WHO IV in the absence of other qualifying mutations should be classified as IDH1/2wt glioblastomas.

scholarly journals ACT-17 Protocol design of a matrix-type of novel clinical trial for lower-grade gliomas

2020 ◽  
Vol 2 (Supplement_3) ◽  
pp. ii8-ii9
Author(s):  
Yoshihiro Muragaki ◽  
Masayuki Nitta ◽  
Taiichi Saito ◽  
Shunsuke Tsuzuki ◽  
Atsushi Fukui ◽  
...  
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
High Risk ◽  
Low Risk ◽  
Observational Research ◽  
Lower Grade ◽  
Who Grade ◽  
Lower Grade Glioma ◽  
The Matrix

Abstract Introduction: Differentiation between glioma grade 2 and 3 was performed based on histological findings. The current grade is an important prognostic factor due to its widespread use, economic efficiency, and data accumulation, but analog elements remain and the genetic marker is unknown. The concept of Lower-grade glioma including G2/3 is spreading. On the other hand, WHO grade is the criteria of clinical trials, and evidence is established for G2 with low risk and high risk, G3 alone or with G4. In Japan, JCOG 1303 and 1016 have been implemented for high-risk G2 and G3, respectively and will be finished next year. Therefore, we examined the feasibility and design of novel clinical trial for patients with grade 2/3 glioma. Method: With reference to clinical trials of high evidence level and public database registration, we researched trials, arms, and designs for each of 3 genotypes, oligodendroglioma (OD), astrocytoma IDH mutant and IDH wild (A-IDHm, A-IDHw). Results: The standard arm common to all genotypes is follow-up (EORTC22845) for G2 low-risk, and chemoradiotherapy (CRT) for G3. Standard arm for G2 high risk, depending on a genotype, is follow-up (EORTC22845), radiation alone (A-IDHm and IDHw, A-IDHw: RTOG9802 subanalysis), or PCV chemoradiotherapy (OD and A-IDHm: 9802). Furthermore, the standard arm and the test arm were replaced by the matrix-like method on each genotype. Results in the G2/3-targeted trial, there was no standard arm all in the three genotypes. In addition, there were a design of master protocols for many genotype and a design that has arms of randomization and observation. Conclusion: Applying the master protocol, the possibility of novel G2/3 target trial in which the arms existing in MATRIX form was suggested. With the improvement of the genetic analysis infrastructure, prospective observational research and a well-designed intervention research plan for each genotype are required.

scholarly journals Identification of Iron Metabolism-Related Genes as Prognostic Indicators for Lower-Grade Glioma

2021 ◽  
Vol 11 ◽  
Author(s):  
Shenbin Xu ◽  
Zefeng Wang ◽  
Juan Ye ◽  
Shuhao Mei ◽  
Jianmin Zhang
Keyword(s):  
Overall Survival ◽  
High Risk ◽  
Risk Score ◽  
Iron Metabolism ◽  
Risk Group ◽  
High Risk Group ◽  
Lower Grade ◽  
Who Grade ◽  
Lower Grade Glioma ◽  
Score Model

Lower-grade glioma (LGG) is characterized by genetic and transcriptional heterogeneity, and a dismal prognosis. Iron metabolism is considered central for glioma tumorigenesis, tumor progression and tumor microenvironment, although key iron metabolism-related genes are unclear. Here we developed and validated an iron metabolism-related gene signature LGG prognosis. RNA-sequence and clinicopathological data from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) were downloaded. Prognostic iron metabolism-related genes were screened and used to construct a risk-score model via differential gene expression analysis, univariate Cox analysis, and the Least Absolute Shrinkage and Selection Operator (LASSO)-regression algorithm. All LGG patients were stratified into high- and low-risk groups, based on the risk score. The prognostic significance of the risk-score model in the TCGA and CGGA cohorts was evaluated with Kaplan-Meier (KM) survival and receiver operating characteristic (ROC) curve analysis. Risk- score distributions in subgroups were stratified by age, gender, the World Health Organization (WHO) grade, isocitrate dehydrogenase 1 (IDH1) mutation status, the O6‐methylguanine‐DNA methyl‐transferase (MGMT) promoter-methylation status, and the 1p/19q co-deletion status. Furthermore, a nomogram model with a risk score was developed, and its predictive performance was validated with the TCGA and CGGA cohorts. Additionally, the gene set enrichment analysis (GSEA) identified signaling pathways and pathological processes enriched in the high-risk group. Finally, immune infiltration and immune checkpoint analysis were utilized to investigate the tumor microenvironment characteristics related to the risk score. We identified a prognostic 15-gene iron metabolism-related signature and constructed a risk-score model. High risk scores were associated with an age of > 40, wild-type IDH1, a WHO grade of III, an unmethylated MGMT promoter, and 1p/19q non-codeletion. ROC analysis indicated that the risk-score model accurately predicted 1-, 3-, and 5-year overall survival rates of LGG patients in the both TCGA and CGGA cohorts. KM analysis showed that the high-risk group had a much lower overall survival than the low-risk group (P < 0.0001). The nomogram model showed a strong ability to predict the overall survival of LGG patients in the TCGA and CGGA cohorts. GSEA analysis indicated that inflammatory responses, tumor-associated pathways, and pathological processes were enriched in high-risk group. Moreover, a high risk score correlated with the infiltration immune cells (dendritic cells, macrophages, CD4+ T cells, and B cells) and expression of immune checkpoint (PD1, PDL1, TIM3, and CD48). Our prognostic model was based on iron metabolism-related genes in LGG, can potentially aid in LGG prognosis, and provides potential targets against gliomas.

scholarly journals MPC-18 CATEGORIZATION OF LOWER GRADE GLIOMA USING ONCOPANEL

2019 ◽  
Vol 1 (Supplement_2) ◽  
pp. ii25-ii25
Author(s):  
Hiroyuki Uchida ◽  
Toshiaki Akahane ◽  
Nayuta Higa ◽  
Mari Kirishima ◽  
Tsubasa Hiraki ◽  
...  
Keyword(s):  
Genetic Alterations ◽  
Lower Grade ◽  
Diffuse Glioma ◽  
Diffuse Astrocytoma ◽  
Idh Mutation ◽  
Who Grade ◽  
Egfr Amplification ◽  
Integrated Diagnosis ◽  
Lower Grade Glioma ◽  
Tert Mutation

Abstract PURPOSE We are developing a 48-gene OncoPanel (Kagoshima Brain Tumor 48 OncoPanel) specializing in glioma diagnosis. Clinical application of genetic diagnosis derived from genetic alterations detected by OncoPanel, including IDH mutation, 1p/19q-codeletion, and other gene mutations in lower-grade glioma was verified. METHODS The 48 genes consist of 24 genes related to glioma and 24 genes on chromosomes 1 and 19. DNA was extracted from tumor FFPE samples and blood samples, and then single nucleotide variants and copy number variants were detected using next-generation sequencer. RESULTS Among the 99 diffuse glioma cases that had undergone OncoPanel analysis by July 2019, 40 cases diagnosed histologically as WHO grade 2 or 3 diffuse glioma were included. The integrated diagnosis by conventional gene analysis were Diffuse astrocytoma 10 cases, anaplastic astrocytoma 11 cases, oligodendroglioma 10 cases, anaplastic oligodendroglioma 9 cases. IDH1 mutation was detected in 30 cases, of which in 19 cases 1p/19q-codeletion was detected, all with TERT mutation. Among 11 cases with 1p/19q-non-codeletion, ATRX mutation was detected in 10 cases and was almost mutually exclusive with TERT mutation. In 10 cases without IDH mutation, EGFR amplification or mutation was detected in 6 cases, of which 4 cases were accompanied by TERT mutation. DISCUSSION KBT48 can detect TERT and ATRX mutations in a mutually exclusive manner and can improve the classification accuracy of oligodendroglioma and astrocytoma. Groups with gene profiles similar to glioblastoma with EGFR amplification/mutation and TERT mutation can also be classified. CONCLUSIONS In the diagnostic classification of lower-grade glioma, KBT48 can well classify into oligodendroglioma group, astrocytoma group and glioblastoma-like group, and is considered to be applicable in clinical practice.

scholarly journals Identification of a Prognostic Hypoxia-Associated Gene Set in IDH-Mutant Glioma

2018 ◽  
Vol 19 (10) ◽  
pp. 2903 ◽  
Author(s):  
Philip Dao Trong ◽  
Saskia Rösch ◽  
Heimo Mairbäurl ◽  
Stefan Pusch ◽  
Andreas Unterberg ◽  
...  
Keyword(s):  
Culture Conditions ◽  
The Cancer Genome Atlas ◽  
Lower Grade ◽  
Isocitrate Dehydrogenase 1 ◽  
Who Grade ◽  
Survival Score ◽  
Hypoxic Conditions ◽  
Glioma Growth ◽  
Selection Operator ◽  
Related Survival

Glioma growth is often accompanied by a hypoxic microenvironment favorable for the induction and maintenance of the glioma stem cell (GSC) phenotype. Due to the paucity of cell models of Isocitrate Dehydrogenase 1 mutant (IDH1mut) GSCs, biology under hypoxic conditions has not been sufficiently studied as compared to IDH1 wildtype (IDH1wt) GSCs. We therefore grew well-characterized IDH1mut (n = 4) and IDH1wt (n = 4) GSC lines under normoxic (20%) and hypoxic (1.5%) culture conditions and harvested mRNA after 72 h. Transcriptome analyses were performed and hypoxia regulated genes were further analyzed using the expression and clinical data of the lower grade glioma cohort of The Cancer Genome Atlas (LGG TCGA) in a confirmatory approach and to test for possible survival associations. Results show that global expression changes were more pronounced in IDH1wt than in IDH1mut GSCs. However, when focusing on known hypoxia-regulated gene sets, enrichment analyses showed a comparable regulation in both IDH1mut and IDH1wt GSCs. Of 272 significantly up-regulated genes under hypoxic conditions in IDH1mut GSCs a hypoxia-related survival score (HRS-score) of five genes (LYVE1, FAM162A, WNT6, OTP, PLOD1) was identified by the Least Absolute Shrinkage and Selection Operator (LASSO) algorithm which was able to predict survival independent of age, 1p19q co-deletion status and WHO grade (II vs. III) in the LGG TCGA cohort and in the Rembrandt dataset. Altogether, we were able to identify and validate a novel hypoxia-related survival score in IDH1mut GSCs consisting of five hypoxia-regulated genes which was significantly associated with patient survival independent of known prognostic confounders.

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