Known glioma risk loci are associated with glioma with a family history of brain tumours -- a case-control gene association study

Pertinence of glioma and single nucleotide polymorphism of TERT, CCDC26, CDKN2A/B and RTEL1 genes in glioma: a meta-analysis

Background

Previous genetic-epidemiological studies considered TERT (rs2736100), CCDC26 (rs4295627), CDKN2A/B (rs4977756) and RTEL1 (rs6010620) gene polymorphisms as the risk factors specific to glioma. However, the data samples of previous genetic-epidemiological studies are modest to determine whether they have definite association with glioma.

Method

The study paid attention to systematically searching databases of PubMed, Embase, Web of Science (WoS), Scopus, Cochrane Library and Google Scholars. Meta-analysis under 5 genetic models, namely recessive model (RM), over-dominant model (O-DM), allele model (AM), co-dominant model (C-DM) and dominant model (DM) was conducted for generating odds ratios (ORs) and 95% confidence intervals (CIs). That was accompanied by subgroup analyses according to various racial groups. The software STATA 17.0 MP was implemented in the study.

Result

21 articles were collected. According to data analysis results, in four genetic models (AM, RM, DM and C-DM) TERT gene rs2736100 polymorphism, CCDC26 gene rs4295627 polymorphism, CDKN2A/B gene rs4977756 polymorphism and RTEL1 gene rs6010620 polymorphisms increased the risk of glioma in Caucasians to different degrees. In Asian populations, the CCDC26 gene rs4295627 polymorphism and CDKN2A/B gene rs4977756 polymorphism did not exhibit a relevance to the risk of glioma. It is suggested to cautiously explain these results as the sample size is small.

Conclusion

The current meta-analysis suggested that the SNP of TERT (rs2736100), CCDC26 (rs4295627), CDKN2A/B (rs4977756) and RTEL1 (rs6010620) genes in glioma might increase risk of glioma, but there are ethnic differences. Further studies evaluating these polymorphisms and glioma risk are warranted.

Traumatic brain injury and subsequent brain tumor development: a systematic review of the literature

The role of prior head trauma in stimulating brain tumor development has been previously described in the literature but continues to be debated. The goal of this study was to conduct a systematic review interrogating the contemporary literature to delineate any possible relationship between traumatic brain injury and brain tumor development. A systematic review exploring development of post-TBI brain tumor was conducted by searching electronic databases. Abstracts from articles were read and selected for full-text review according to criteria previously established in the scientific literature. Relevant full-text articles were divided into case reports and single-arm studies and epidemiological studies. Of 1070 resultant articles, 18 case reports and single-arm studies (level of evidence of IV and V) with 45 patients were included. The most common cause of TBI was traffic accidents. The average period between TBI and subsequent tumor diagnosis was 12.8 years. Meningiomas represented the largest share of tumors, followed by gliomas. Most post-TBI brain tumors developed in the frontal and temporal lobes. Fifteen epidemiological studies were also interrogated from a variety of countries (level of evidence of III). Case-control studies were more common than cohort studies. There were 9 of 15 studies proposed a possible relationship between history of head trauma and development of brain tumor. The relationship between head trauma and neoplastic growth continues to be heavily debated. There are certainly case reports and epidemiological studies in the literature that suggest a correlational relationship between the two. However, there is no concrete evidence of a causal relationship between TBI and brain tumors. More research is needed to definitively delineate the extent of any such relationship.

Genetic alterations in non-syndromic, familial gliomas in first degree relatives: A systematic review

OBJECTIVE

Despite numerous reports in syndromic gliomas, the underlying genetic and molecular basis of familial, non-syndromic gliomas, in first degree relatives, remains unclear. This rare cohort of patients harboring invasive primary brain tumors with poor prognosis may provide a potential substrate of understanding the complex genetic cascade triggering tumorigenesis.

METHODS

A systematic review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocols (PRISMA-P) 2015 and The Cochrane Handbook of Systematic Reviews of Interventions. PubMed/MEDLINE, Embase and CENTRAL databases were accessed with set inclusion and exclusion criteria.

RESULTS

Following returns of 6756 articles, systematic analysis resulted in 48 papers, with 18 case series, 4 linkage analysis, 3 case-control studies, 1 cohort study, and 22 case reports. A total of 164 first degree relatives of 72 families were analyzed. The most common genetic alterations associated with non-syndromic familial gliomas reported to affect chromosomes 17 (51.1 % germline and 9.3 % tumor mutations), 22 (15.6 % germline and 6 % tumor mutations) and 1 and 19 (4.4 % germline and 9.3 % tumor mutations), with the most commonly affected genes TP53 (8.5 %) and NF2 (3.7 %). Tumor suppressors or cell-cycle regulators, cell signaling and transcription regulation or methylation were the most common gene function categories.

CONCLUSION

Four specific chromosomes (17, 22, 1 and 19) and two specific genes (TP53 and NF2) appear to be most commonly involved. This appears to be the first systematic review of genetic factors underlying non-syndromic glioma clustering in families. The defined list of genetic abnormalities, linked to familial gliomas, may facilitate therapeutic targets and future treatment design.

The rs498872 polymorphism is associated with an elevated susceptibility to glioma: a meta-analysis of 36,264 subjects

Several genome-wide association studies have already explored the associations between rs498872 polymorphism and glioma, but the results of these studies were not consistent. Consequently, we conducted a meta-analysis of relevant studies to better analyze the effects of rs498872 polymorphism on individual susceptibility to glioma. PubMed, Web of Science and Embase were searched for eligible studies. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated. Totally, 12 studies with 36,264 subjects were analyzed. A significant association with glioma was observed for the rs498872 polymorphism in CC versus CT + TT (dominant comparison, p < 0.0001, OR = 0.81, 95% CI 0.76-0.85), TT versus CC + CT (recessive comparison, p < 0.0001, OR = 1.23, 95% CI 1.13-1.34), CT versus CC + TT (overdominant comparison, p < 0.0001, OR = 1.15, 95% CI 1.09-1.21) and C versus T (allele comparison, p < 0.0001, OR = 0.86, 95% CI 0.84-0.90). Further subgroup analyses yielded similar positive results in both Asians and Caucasians. Our findings suggested that the rs498872 polymorphism may serve as a potential genetic biomarker of glioma in both Asians and Caucasians.

Beginning at the ends: telomeres and human disease

Studies of rare and common illnesses have led to remarkable progress in the understanding of the role of telomeres (nucleoprotein complexes at chromosome ends essential for chromosomal integrity) in human disease. Telomere biology disorders encompass a growing spectrum of conditions caused by rare pathogenic germline variants in genes encoding essential aspects of telomere function. Dyskeratosis congenita, a disorder at the severe end of this spectrum, typically presents in childhood with the classic triad of abnormal skin pigmentation, nail dystrophy, and oral leukoplakia, accompanied by a very high risk of bone marrow failure, cancer, pulmonary fibrosis, and other medical problems. In contrast, the less severe end of the telomere biology disorder spectrum consists of middle-age or older adults with just one feature typically seen in dyskeratosis congenita, such as pulmonary fibrosis or bone marrow failure. In the common disease realm, large-scale molecular epidemiology studies have discovered novel associations between illnesses, such as cancer, heart disease, and mental health, and both telomere length and common genetic variants in telomere biology genes. This review highlights recent findings of telomere biology in human disease from both the rare and common disease perspectives. Multi-disciplinary collaborations between clinicians, basic scientists, and epidemiologist are essential as we seek to incorporate new telomere biology discoveries to improve health outcomes.

Associations between EGFR gene polymorphisms and susceptibility to glioma: a systematic review and meta-analysis from GWAS and case-control studies

The results of genome-wide association studies (GWAS) and case-control studies performed to investigate the associations between epidermal growth factor receptor (EGFR) gene polymorphisms and glioma risk are controversial. The aim of this systematic review and meta-analysis is to determine whether EGFR gene polymorphisms are associated with glioma risk by searching 'PubMed', 'EMBASE', 'Web of Science', 'Cochrane Library' and 'China WeiPu Library' to retrieve studies that investigated associations between EGFR gene polymorphisms and glioma risk. Four GWAS containing 35 studies and 7 case-control studies meeting the inclusion criteria were finally recruited, and 11 single-nucleotide polymorphisms (SNPs) were analyzed. The results showed a significant positive association between rs730437/rs845552 and glioma risk in Asians, and a significant negative association between them in Caucasians. In addition, rs11506105 was significantly associated with an increased risk of glioma in both Asians and Caucasians, and rs11979158 decreased the risk of glioma in Caucasians. However, no significant association was observed between rs12718945/rs17172432/rs4947492 and glioma risk in Asians, between rs2252586 and glioma risk in Caucasians, and between rs3752651 and glioma risk in either Asians or Caucasians. In conclusion, different SNPs in EGFR gene might have different impacts on the risk of glioma in various ethnicities, which offers new insights into the treatment with a target-oriented approach.

Association between RTEL1 gene polymorphisms and COPD susceptibility in a Chinese Han population

Objective

We investigated the association between single-nucleotide polymorphisms in regulation of telomere elongation helicase 1 (RTEL1), which has been associated with telomere length in several brain cancers and age-related diseases, and the risk of chronic obstructive pulmonary disease (COPD) in a Chinese Han population.

Methods

In a case–control study that included 279 COPD cases and 290 healthy controls, five single-nucleotide polymorphisms in RTEL1 were selected and genotyped using the Sequenom MassARRAY platform. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using unconditional logistic regression after adjusting for age and gender.

Results

In the genotype model analysis, we determined that rs4809324 polymorphism had a decreased effect on the risk of COPD (CC versus TT: OR =0.28; 95% CI =0.10–0.82; P=0.02). In the genetic model analysis, we found that the “C/C” genotype of rs4809324 was associated with a decreased risk of COPD based on the codominant model (OR =0.33; 95% CI =0.13–0.86; P=0.022) and recessive model (OR =0.32; 95% CI =0.12–0.80; P=0.009).

Conclusion

Our data shed new light on the association between genetic polymorphisms of RTEL1 and COPD susceptibility in the Chinese Han population.

A Comparative Study of the Molecular Characteristics of Familial Gliomas and Other Cancers

BACKGROUND

Familial cancers are those that co-occur among first-degree relatives without showing Mendelian patterns of inheritance.

MATERIALS AND METHODS

In this analysis, we compare the genomic characteristics of familial and sporadic cancers, with a focus on low-grade gliomas (LGGs) using sequence and expression data from the Cancer Genome Atlas.

RESULTS

Familial cancers show similar genomic and molecular biomarker profiles to sporadic cancers, consistent with the similarity in their clinical features. There are no statistically significant differences among somatic mutation, copy number variant, or gene expression patterns between familial and sporadic cancers; methylation profiles are the only class of molecular data to show significant differences.

CONCLUSION

Familial cancers are likely driven by multiple, individually weak contributions to familiality (i.e. large numbers of alleles and/or shared environmental risks). Consequently, these risk factors tend to be obscured by stronger confounding variables such as clinical or molecular variation among cancer subtypes.

The role of the RTEL1 rs2297440 polymorphism in the risk of glioma development: a meta-analysis

The regulator of the telomere elongation helicase1 (RTEL1) gene plays a crucial role in the DNA double-stand break-repair pathway by maintaining genomic stability. Recent epidemiological studies showed that the rs2297440 polymorphism in the RTEL1 gene was a potential risk locus for glioma development, but the results were inconclusive. To clarify the association between this polymorphism and the risk of glioma, we performed a comprehensive meta-analysis. The PubMed, EMBASE, Web of Science, and China National Knowledge Infrastructure databases were systematically searched to identify all relevant published studies up to 30 August 2015. Four eligible studies were finally included. The pooled results indicated that the RTEL1 rs2297440 polymorphism moderately increased the risk of glioma in all genetic models. A comparison of the dominant model CT + CC versus TT (OR 1.40; 95 % CI 1.24-1.60; p < 0.001) indicated that having the C allele conferred a 40 % increased risk of developing glioma. In a subgroup analysis based on geographic location (Europe, Asia, and America), there was an association between the rs2297440 polymorphism and the risk of glioma in all three areas. The results of the subgroup analysis based on source of control indicated an elevated risk of glioma in population-based control studies. This meta-analysis demonstrates that the RTEL1 rs2297440 polymorphism plays a moderate, but significant role in the risk of glioma. Further studies with larger sample sizes are necessary to confirm this finding.

Effect of CDKN2A/B rs4977756 polymorphism on glioma risk: a meta-analysis of 16 studies including 24077 participants

So far, epidemiological studies have been performed to investigate the association of CDKN2A/B rs4977756 polymorphism and glioma risk. However, the results from different studies remain inconsistent. To clarify these conflicts and to quantitatively evaluate the effect of rs4977756 polymorphism on glioma risk, a meta-analysis was conducted using relevant published clinical studies about rs4977756 polymorphisms and glioma risk. Relevant studies concerning the association between rs4977756 polymorphism and risk of glioma were included in this meta-analysis. Odds ratio (OR) and 95 % confidence interval (CI) were calculated under fixed or random effects models when appropriate. Subgroup analyses were performed by race. This meta-analysis included 13 studies with a total of 8129 cases and 15,858 controls. The pooled results showed that there was an obvious association of CDKN2A/B rs4977756 polymorphism with risk of glioma in all four comparison models (dominant model/AG + GG vs. AA: OR = 1.36, 95 %CI = 1.20-1.54, p < 0.01; heterozygote comparison/AG vs. AA: OR = 1.31, 95 %CI = 1.12-1.53, p < 0.01; homozygote comparison/GG versus AA: OR = 1.49, 95 %CI = 1.36-1.64, p < 0.01; additive model/G vs. A: OR = 1.23, 95 %CI = 1.18-1.28, p < 0.01, respectively). For the subgroup analyses of ethnicities, similar results were observed in Caucasians. However, the association was not found between rs4977756 polymorphism and the risk of glioma in all models for the Asian studies. The CDKN2A/B rs4977756 polymorphism is obvious increase the risk of glioma in Caucasians. Future studies are needed to confirm the results in other ethnic populations.

DNA repair gene ERCC1 polymorphisms and glioma susceptibility among Chinese population: a meta-analysis

BACKGROUND

Excision repair cross complementation group 1 (ERCC1) has been shown to be involved in the progression of glioma susceptibility. However, the results remain conflict. The aim of this study was to systematically review and evaluate the role of ERCC1 C118T and C8092A polymorphisms in glioma risk among Chinese population.

METHODS

Related case-control studies were searched in online electronic databases. Odds ratio (OR) with its 95% confidence interval (CI) were employed to calculate the extracted data.

RESULTS

Total seven articles were retrieved, including 4426 subjects (1926 were glioma patients and 2500 were matched controls). No significant heterogeneity was found between studies (I(2)=0%, P>0.01). Our results demonstrated that A allele and AA genotype of ERCC1 C8092A polymorphism have a positive association with increasing the risk of glioma in the fixed-effect model (A vs. C: OR=1.13, 95% CI=1.02-1.25, P=0.02; AA vs. CC: OR=1.29, 95% CI=1.04-1.61, P=0.02; AA vs. CA+CC: OR=1.25, 95% CI=1.01-1.55, P=0.04). However, no significant relationship was found between C118T variant and glioma susceptibility.

CONCLUSIONS

Our results indicated that ERCC1 C8092A, not C118T polymorphism might be a biomarker for patients with glioma among Chinese population. Future studies with more ethnicities are needed to explore the precise association.

Molecular Markers in Low-Grade Glioma-Toward Tumor Reclassification

Low-grade diffuse gliomas are a heterogeneous group of primary glial brain tumors with highly variable survival. Currently, patients with low-grade diffuse gliomas are stratified into risk subgroups by subjective histopathologic criteria with significant interobserver variability. Several key molecular signatures have emerged as diagnostic, prognostic, and predictor biomarkers for tumor classification and patient risk stratification. In this review, we discuss the effect of the most critical molecular alterations described in diffuse (IDH1/2, 1p/19q codeletion, ATRX, TERT, CIC, and FUBP1) and circumscribed (BRAF-KIAA1549, BRAF(V600E), and C11orf95-RELA fusion) gliomas. These molecular features reflect tumor heterogeneity and have specific associations with patient outcome that determine appropriate patient management. This has led to an important, fundamental shift toward developing a molecular classification of World Health Organization grade II-III diffuse glioma.

CCDC26 rs4295627 polymorphism and glioma risk: a meta-analysis

Several studies have examined the association of CCDC26 rs4295627 polymorphism and glioma risk. However, the results were conflicting. Thus, a meta-analysis was conducted. We searched for relevant studies up to Dec 2014 in both English and Chinese through the PubMed/MEDLINE, EMBASE, the China National Knowledge Infrastructure (CNKI) platforms, WanFang and VIP database. Overall, 14 studies with 17419 cases and 28465 controls were selected for final meta-analysis. CCDC26 rs4295627 polymorphism was significantly associated with an increased risk of glioma (OR = 1.25, 95% CI 1.15-1.36, P < 0.00001). Interestingly, CCDC26 rs4295627 polymorphism might decrease the risk of glioma in Asians (OR = 0.92, 95% CI 0.82-1.03, P = 0.15). However, Caucasians with CCDC26 rs4295627 polymorphism showed an increased risk of glioma (OR = 1.33, 95% CI 1.25-1.46, P < 0.00001). Subgroup analysis was performed by histology. Significant associations were observed among astrocytoma patients (OR = 1.31, 95% CI 1.17-1.47, P < 0.00001) and oligodendroglioma patients (OR = 1.79, 95% CI 1.47-2.17, P < 0.00001). No significant association was found between this polymorphism and glioblastoma risk (OR = 0.11, 95% CI 0.92-1.33, P = 0.28). This meta-analysis suggested that CCDC26 rs4295627 polymorphism was a risk factor for glioma.

Targeted sequencing in chromosome 17q linkage region identifies familial glioma candidates in the Gliogene Consortium

Glioma is a rare, but highly fatal, cancer that accounts for the majority of malignant primary brain tumors. Inherited predisposition to glioma has been consistently observed within non-syndromic families. Our previous studies, which involved non-parametric and parametric linkage analyses, both yielded significant linkage peaks on chromosome 17q. Here, we use data from next generation and Sanger sequencing to identify familial glioma candidate genes and variants on chromosome 17q for further investigation. We applied a filtering schema to narrow the original list of 4830 annotated variants down to 21 very rare (<0.1% frequency), non-synonymous variants. Our findings implicate the MYO19 and KIF18B genes and rare variants in SPAG9 and RUNDC1 as candidates worthy of further investigation. Burden testing and functional studies are planned.

RTEL1: functions of a disease-associated helicase

DNA secondary structures that arise during DNA replication, repair, and recombination (3R) must be processed correctly to prevent genetic instability. Regulator of telomere length 1 (RTEL1) is an essential DNA helicase that disassembles a variety of DNA secondary structures to facilitate 3R processes and to maintain telomere integrity. The past few years have witnessed the emergence of RTEL1 variants that confer increased susceptibility to high-grade glioma, astrocytomas, and glioblastomas. Mutations in RTEL1 have also been implicated in Hoyeraal-Hreidarsson syndrome, a severe form of the bone-marrow failure and cancer predisposition disorder, dyskeratosis congenita. We review these recent findings and highlight its crucial link between DNA secondary-structure metabolism and human disease.

Genetics in glioma: lessons learned from genome-wide association studies

PURPOSE OF REVIEW

The purpose of this review is to describe the recent knowledge gathered from the identification of seven genomic regions that have been linked to the risk of developing malignant glioma.

RECENT FINDINGS

The recent novel discoveries in fine mapping and genotype-phenotype studies will be highlighted. Through imputation and next-generation sequencing a novel genetic variant, rs55705857, with a strong association at 8q24 has been discovered and validated in two studies. This locus is specifically associated with IDH1-mutated and IDH2-mutated tumors and oligodendroglial tumors, albeit the specific mechanism of tumor development is not understood. The genetic variants associated with the risk of glioma in the EGFR gene have also been associated with specific somatic aberrations, including loss at the CDKN2A/B locus and allele specific loss of EGFR in the tumors. A specific TP53 low frequency variant has also been associated with glioma risk and validated in a separate data set. The genetic risk in the telomere regulating genes TERT and RTEL appear to be associated with higher grade tumors without IDH mutations.

SUMMARY

The link of genetic loci to specific tumor subtypes may have relevance for understanding glioma biology, and for developing new diagnostic tools and targeted therapy for glioma.

Association between telomerase reverse transcriptase rs2736100 polymorphism and risk of glioma

BACKGROUND

Epidemiological studies have been conducted to investigate the association of telomerase reverse transcriptase (TERT) rs2736100 polymorphism with glioma risk. The aim of the present study was to evaluate the association of TERT rs2736100 polymorphism with glioma risk using a meta-analysis approach.

MATERIALS AND METHODS

All eligible studies were identified through a search of PubMed, EMBASE, China National Knowledge Infrastructure, Database of Chinese Scientific and Technical Periodicals, and China Biology Medical literature database before January 2014. The association between the TERT rs2736100 polymorphism and glioma risk was estimated by odds ratio (OR) and 95% confidence interval (CI).

RESULTS

A total of nine case-control studies including 9411 cases and 13,708 controls were eventually collected. Overall, we found that TERT rs2736100 polymorphism was significantly associated with the risk of glioma (OR = 1.29, 95% CI 1.24-1.34, P < 0.001). In the subgroup analysis based on ethnicity, the significant association was found in Caucasians (OR = 1.29, 95% CI 1.24-1.34, P < 0.001). In subgroup analyses by histology, the associations were significant in glioblastoma (OR = 1.45, 95% CI 1.32-1.60, P < 0.001), astrocytoma (OR = 1.41, 95% CI 1.26-1.58, P < 0.001), and oligodendroglioma (OR = 1.20, 95% CI 1.05-1.37, P = 0.008).

CONCLUSIONS

Taken together, these data suggested that TERT rs2736100 polymorphism may contribute to glioma susceptibility.