ABSTRACT
Genome-wide association studies (GWAS) have contributed to our understanding of glioma susceptibility. To date, 25 risk loci for development of any of the glioma subtypes are known. However, GWAS studies reveal little about the molecular processes that lead to increased risk, especially for non-coding single nucleotide polymorphisms (SNP). A particular SNP in intron 2 of LRIG1, rs11706832, has been shown to increase the susceptibility for IDH1 mutated low-grade gliomas (LGG). Leucine-rich repeats and immunoglobulin-like domains protein 1 (LRIG1) is important in cancer development as it negatively regulates the epidermal growth factor receptor (EGFR); however, the mechanism responsible for this particular risk SNP and its potential effect on LRIG1 are not known. Using CRISPR-CAS9, we edited rs11706832 in HEK293T cells. Four HEK293T clones with the risk allele were compared to four clones with the non-risk allele for LRIG1 and SLC25A26 gene expression using RT-qPCR, for global gene expression using RNA-seq, and for metabolites using gas chromatography-mass spectrometry (GC-MS). The experiment did not reveal any significant effect of the SNP on the expression levels or splicing patterns of LRIG1 or SLC25A26. The global gene expression analysis revealed that the risk allele C was associated with upregulation of several mitochondrial genes. Gene enrichment analysis of 74 differentially expressed genes in the genome revealed a significant enrichment of type I interferon response genes, where many genes were downregulated for the risk allele C. Gene expression data of IDH1 mutated LGGs from the cancer genome atlas (TCGA) revealed a similar under expression of type I interferon genes associated with the risk allele. This study found the expression levels and splicing patterns of LRIG1 and SLC25A26 were not affected by the SNP in HEK293T cells. However, the risk allele was associated with a downregulation of genes involved in the innate immune response both in the HEK293T cells and in the LGG data from TCGA.
Subject(s)
Glioma , Interferon Type I , Humans , Cell Proliferation , Membrane Glycoproteins/metabolism , Interferon Type I/metabolism , Genome-Wide Association Study , HEK293 Cells , Polymorphism, Single Nucleotide , Cell Line, Tumor , Glioma/genetics , Glioma/metabolism , Calcium-Binding Proteins/genetics , Amino Acid Transport Systems/geneticsABSTRACT
BACKGROUND: Although recent sequencing studies have revealed that 10% of childhood gliomas are caused by rare germline mutations, the role of common variants is undetermined and no genome-wide significant risk loci for pediatric central nervous system tumors have been identified to date. METHODS: Meta-analysis of 3 population-based genome-wide association studies comprising 4069 children with glioma and 8778 controls of multiple genetic ancestries. Replication was performed in a separate case-control cohort. Quantitative trait loci analyses and a transcriptome-wide association study were conducted to assess possible links with brain tissue expression across 18 628 genes. RESULTS: Common variants in CDKN2B-AS1 at 9p21.3 were significantly associated with astrocytoma, the most common subtype of glioma in children (rs573687, P-value of 6.974e-10, OR 1.273, 95% CI 1.179-1.374). The association was driven by low-grade astrocytoma (P-value of 3.815e-9) and exhibited unidirectional effects across all 6 genetic ancestries. For glioma overall, the association approached genome-wide significance (rs3731239, P-value of 5.411e-8), while no significant association was observed for high-grade tumors. Predicted decreased brain tissue expression of CDKN2B was significantly associated with astrocytoma (P-value of 8.090e-8). CONCLUSIONS: In this population-based genome-wide association study meta-analysis, we identify and replicate 9p21.3 (CDKN2B-AS1) as a risk locus for childhood astrocytoma, thereby establishing the first genome-wide significant evidence of common variant predisposition in pediatric neuro-oncology. We furthermore provide a functional basis for the association by showing a possible link to decreased brain tissue CDKN2B expression and substantiate that genetic susceptibility differs between low- and high-grade astrocytoma.
Subject(s)
Astrocytoma , Glioma , RNA, Long Noncoding , Humans , Child , Genome-Wide Association Study , Glioma/genetics , Genotype , Genetic Predisposition to Disease , Astrocytoma/genetics , Polymorphism, Single NucleotideABSTRACT
Background: Understanding the trajectory and development of disease is important and the knowledge can be used to find novel targets for therapy and new diagnostic tools for early diagnosis. Methods: Large cohorts from different parts of the world are unique assets for research as they have systematically collected plasma and DNA over long-time periods in healthy individuals, sometimes even with repeated samples. Over time, the population in the cohort are diagnosed with many different diseases, including brain tumors. Results: Recent studies have detected genetic variants that are associated with increased risk of glioblastoma and lower grade gliomas specifically. The impact for genetic markers to predict disease in a healthy population has been deemed low, and a relevant question is if the genetic variants for glioma are associated with risk of disease or partly consist of genes associated to survival. Both metabolite and protein spectra are currently being explored for early detection of cancer. Conclusions: We here present a focused review of studies of genetic variants, metabolomics, and proteomics studied in prediagnostic glioma samples and discuss their potential in early diagnostics.
ABSTRACT
No strong aetiological factors have been established for glioma aside from genetic mutations and variants, ionising radiation and an inverse relationship with asthmas and allergies. Our aim was to investigate the association between pre-diagnostic immune protein levels and glioma risk. We conducted a case-control study nested in the Northern Sweden Health and Disease Study cohort. We analysed 133 glioma cases and 133 control subjects matched by age, sex and date of blood donation. ELISA or Luminex bead-based multiplex assays were used to measure plasma levels of 19 proteins. Conditional logistic regression models were used to estimate the odds ratios and 95% CIs. To further model the protein trajectories over time, the linear mixed-effects models were conducted. We found that the levels of sVEGFR2, sTNFR2, sIL-2Rα and sIL-6R were associated with glioma risk. After adjusting for the time between blood sample collection and glioma diagnosis, the odds ratios were 1.72 (95% CI = 1.01-2.93), 1.48 (95% CI = 1.01-2.16) and 1.90 (95% CI = 1.14-3.17) for sTNFR2, sIL-2Rα and sIL-6R, respectively. The trajectory of sVEGFR2 concentrations over time was different between cases and controls (p-value = 0.031), increasing for cases (0.8% per year) and constant for controls. Our findings suggest these proteins play important roles in gliomagenesis.
Subject(s)
Glioma , Case-Control Studies , Cohort Studies , Glioma/diagnosis , Glioma/epidemiology , Glioma/etiology , Humans , Logistic Models , Odds RatioABSTRACT
BACKGROUND: Heart failure is a rare condition in the paediatric population, associated with high morbidity and mortality. When medical therapy is no longer sufficient, mechanical circulatory support such as a ventricular assist device can be used to bridge these children to transplant or recovery. Coagulation-related complications such as thrombi, embolism and bleeding events represent the greatest challenge in paediatric patients on mechanical support. We aimed to describe the outcomes and coagulation-related complications in this patient population at our institution. METHODS: A total of 20 patients with either Berlin Heart EXCOR® or HeartWare® implantation were reviewed in this retrospective study. Study endpoints were survival to heart transplant, weaning due to recovery or death. Thrombotic events were defined as thrombus formation in the device or in the patient, or cardioembolic strokes. Bleeding events were defined as events requiring interventional surgery or transfusion of red blood cells. RESULTS: The aetiology of heart failure included cardiomyopathy (n = 12), end-stage congenital heart disease (n = 6) and myocarditis (n = 2). Of the 20 patients, 12 were bridged to transplant, 7 recovered and could be weaned and 1 died. The median duration of mechanical support was 84 days (range: 20-524 days). At least one major or minor bleeding event occurred in 45% of the patients. Thrombotic events occurred 21 times in 10 patients. Four of the patients (20%) had no bleeding or thromboembolic event. CONCLUSION: In all, 95% of the patients were successfully bridged to transplant or recovery. Bleeding events and thrombotic events were common.
Subject(s)
Heart Failure , Heart Transplantation , Heart-Assist Devices , Child , Heart-Assist Devices/adverse effects , Humans , Retrospective Studies , Treatment OutcomeABSTRACT
The number of national reference populations that are whole-genome sequenced are rapidly increasing. Partly driving this development is the fact that genetic disease studies benefit from knowing the genetic variation typical for the geographical area of interest. A whole-genome sequenced Swedish national reference population (n = 1000) has been recently published but with few samples from northern Sweden. In the present study we have whole-genome sequenced a control population (n = 300) (ACpop) from Västerbotten County, a sparsely populated region in northern Sweden previously shown to be genetically different from southern Sweden. The aggregated variant frequencies within ACpop are publicly available (DOI 10.17044/NBIS/G000005) to function as a basic resource in clinical genetics and for genetic studies. Our analysis of ACpop, representing approximately 0.11% of the population in Västerbotten, indicates the presence of a genetic substructure within the county. Furthermore, a demographic analysis showed that the population from which samples were drawn was to a large extent geographically stationary, a finding that was corroborated in the genetic analysis down to the level of municipalities. Including ACpop in the reference population when imputing unknown variants in a Västerbotten cohort resulted in a strong increase in the number of high-confidence imputed variants (up to 81% for variants with minor allele frequency < 5%). ACpop was initially designed for cancer disease studies, but the genetic structure within the cohort will be of general interest for all genetic disease studies in northern Sweden.
Subject(s)
Genome, Human , Polymorphism, Genetic , Population/genetics , Aged , Aged, 80 and over , Databases, Genetic , Female , Humans , Male , Middle Aged , Sweden , Whole Genome SequencingABSTRACT
INTRODUCTION: Numerous prior studies, even from countries with free access to care, have associated long travel time to care with poor survival in patients with colorectal cancer. METHODS: This is a data-linkage study of all 3718 patients with colorectal cancer, diagnosed between 2007 and 2013 in Northern Sweden, one of the most sparsely populated areas in Europe. Travel time to nearest hospital was calculated based on GPS coordinates and multivariable Cox regression was used to analyse possible associations between travel time and cause-specific survival. RESULTS: No association between travel time and survival was observed, either in univariable analysis (colon HR 1.00 [95% CI 0.998-1.003]; rectal HR 0.998; [95% CI 0.995-1.002]) or in multivariable Cox regression analysis (colon HR 0.999 [95% CI 0.997-1.002]; rectal HR 0.997 [95% CI 0.992-1.002]). CONCLUSIONS: In contrast to most other studies, no association between travel time and colorectal cancer survival was found; despite that longer travel time was associated with known risk factors for poorer outcome. In the Swedish health care setting, travel time does not appear to represent a barrier to care or to negatively influence outcomes.
Subject(s)
Colorectal Neoplasms/mortality , Aged , Colorectal Neoplasms/diagnosis , Colorectal Neoplasms/pathology , Databases, Factual , Educational Status , Female , Humans , Information Storage and Retrieval , Kaplan-Meier Estimate , Male , Middle Aged , Neoplasm Staging , Proportional Hazards Models , Registries , Risk Factors , Time FactorsABSTRACT
INTRODUCTION: Medulloblastoma is a malignant embryonal tumor of the cerebellum that occurs predominantly in children. To find germline genetic variants associated with medulloblastoma risk, we conducted a genome-wide association study (GWAS) including 244 medulloblastoma cases and 247 control subjects from Sweden and Denmark. METHODS: Genotyping was performed using Illumina BeadChips, and untyped variants were imputed using IMPUTE2. RESULTS: Fifty-nine variants in 11 loci were associated with increased medulloblastoma risk (p < 1 × 10-5), but none were statistically significant after adjusting for multiple testing (p < 5 × 10-8). Thirteen of these variants were genotyped, whereas 46 were imputed. Genotyped variants were further investigated in a validation study comprising 249 medulloblastoma cases and 629 control subjects. In the validation study, rs78021424 (18p11.23, PTPRM) was associated with medulloblastoma risk with OR in the same direction as in the discovery cohort (ORT = 1.59, pvalidation = 0.02). We also selected seven medulloblastoma predisposition genes for investigation using a candidate gene approach: APC, BRCA2, PALB2, PTCH1, SUFU, TP53, and GPR161. The strongest evidence for association was found for rs201458864 (PALB2, ORT = 3.76, p = 3.2 × 10-4) and rs79036813 (PTCH1, ORA = 0.42, p = 2.6 × 10-3). CONCLUSION: The results of this study, including a novel potential medulloblastoma risk loci at 18p11.23, are suggestive but need further validation in independent cohorts.
Subject(s)
Biomarkers, Tumor/genetics , Cerebellar Neoplasms/genetics , Genetic Predisposition to Disease , Genome-Wide Association Study , Medulloblastoma/genetics , Polymorphism, Single Nucleotide , Case-Control Studies , Cerebellar Neoplasms/pathology , Cohort Studies , Genotype , Humans , Medulloblastoma/pathology , PrognosisABSTRACT
Genome-wide association studies have identified 25 germline genetic loci that increase the risk of glioma. The somatic tumor molecular alterations, including IDH-mutation status and 1p/19q co-deletion, have been included into the WHO 2016 classification system for glioma. To investigate how the germline genetic risk variants correlate with the somatic molecular subtypes put forward by WHO, we performed a meta-analysis that combined findings from 330 Swedish cases and 876 controls with two other recent studies. In total, 5,103 cases and 10,915 controls were included. Three categories of associations were found. First, variants in TERT and TP53 were associated with increased risk of all glioma subtypes. Second, variants in CDKN2B-AS1, EGFR, and RTEL1 were associated with IDH-wildtype glioma. Third, variants in CCDC26 (the 8q24 locus), C2orf80 (close to IDH), LRIG1, PHLDB1, ETFA, MAML2 and ZBTB16 were associated with IDH-mutant glioma. We therefore propose three etiopathological pathways in gliomagenesis based on germline variants for future guidance of diagnosis and potential functional targets for therapies. Future prospective clinical trials of patients with suspicion of glioma diagnoses, using the genetic variants as biomarkers, are necessary to disentangle how strongly they can predict glioma diagnosis.
ABSTRACT
BACKGROUND: The Mono-amine oxidase-A (MAO-A) enzyme is involved in the degradation and regulation of catecholamines such as serotonin, dopamine, epinephrine and nor-epinephrine. Preclinical studies suggest that this enzyme may contribute to an environment favorable for growth of malignant glioma. The MAO-A gene is located on the X-chromosome and has at least one functional genetic polymorphism. The aim of the present study was to explore possible effects of MAO-A genotype on development of glioblastoma in males. METHODS: Genotypes for 437 glioma cases and 876 population-based controls from the Swedish Glioma International Case-Control study (GICC) were compared. We analyzed the germline DNA using the Illumina Oncoarray. We selected seven single nucleotide polymorphisms (SNPs) located in the MAO-A gene, and imputed genotypes based on data from the 1000 genomes project. We used 1579 male glioblastoma cases and 1875 controls comprising the whole GICC cohort for subsequent validation of findings. RESULTS: The rs144551722 SNP was a significant predictor of development of glioblastoma in males (p-value = 0.0056) but not in females even after correction for multiple testing. We conducted haplotype analysis to confirm an association between MAO-A gene and risk of glioblastoma (p-value = 0.016). We found similar results in the validation sample. CONCLUSIONS: These results suggest the possibility of a role for the MAO-A enzyme and the MAO-A gene in the development of glioblastoma in males.
Subject(s)
Brain Neoplasms/genetics , Glioblastoma/genetics , Monoamine Oxidase/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Brain Neoplasms/enzymology , Case-Control Studies , Female , Genotype , Glioblastoma/enzymology , Humans , Male , Middle Aged , Polymorphism, Single Nucleotide , Sex Characteristics , Young AdultABSTRACT
BACKGROUND: Genome-wide association studies have identified germline genetic variants in 25 genetic loci that increase the risk of developing glioma in adulthood. It is not known if these variants increase the risk of developing glioma in children and adolescents and young adults (AYA). To date, no studies have performed genome-wide analyses to find novel genetic variants associated with glioma risk in children and AYA. METHODS: We investigated the association between 8,831,628 genetic variants and risk of glioma in 854 patients diagnosed up to the age of 29 years and 3,689 controls from Sweden and Denmark. Recruitment of patients and controls was population based. Genotyping was performed using Illumina BeadChips, and untyped variants were imputed with IMPUTE2. We selected 41 established adult glioma risk variants for detailed investigation. RESULTS: Three adult glioma risk variants, rs634537, rs2157719, and rs145929329, all mapping to the 9p21.3 (CDKN2B-AS1) locus, were associated with glioma risk in children and AYA. The strongest association was seen for rs634537 (odds ratioG = 1.21; 95% confidence interval = 1.09-1.35; P = 5.8 × 10-4). In genome-wide analysis, an association with risk was suggested for 129 genetic variants (P <1 × 10-5). CONCLUSIONS: Carriers of risk alleles in the 9p21.3 locus have an increased risk of glioma throughout life. The results from genome-wide association analyses require validation in independent cohorts. IMPACT: Our findings line up with existing evidence that some, although not all, established adult glioma risk variants are associated with risk of glioma in children and AYA. Validation of results from genome-wide analyses may reveal novel susceptibility loci for glioma in children and AYA.
Subject(s)
Genetic Loci/genetics , Glioma/genetics , Polymorphism, Single Nucleotide/genetics , Adolescent , Adult , Case-Control Studies , Child , Child, Preschool , Female , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Infant , Infant, Newborn , Male , Risk Factors , Young AdultABSTRACT
PURPOSE: Previous studies have suggested an association between relative leukocyte telomere length (rLTL) and glioma risk. This association may be influenced by several factors, including allergies, BMI, and smoking. Previous studies have shown that individuals with asthma and allergy have shortened relative telomere length, and decreased risk of glioma. Though, the details and the interplay between rLTL, asthma and allergies, and glioma molecular phenotype is largely unknown. METHODS: rLTL was measured by qPCR in a Swedish population-based glioma case-control cohort (421 cases and 671 controls). rLTL was related to glioma risk and health parameters associated with asthma and allergy, as well as molecular events in glioma including IDH1 mutation, 1p/19q co-deletion, and EGFR amplification. RESULTS: Longer rLTL was associated with increased risk of glioma (OR = 1.16; 95% CI 1.02-1.31). Similar to previous reports, there was an inverse association between allergy and glioma risk. Specific, allergy symptoms including watery eyes was most strongly associated with glioma risk. High body mass index (BMI) a year prior diagnosis was significantly protective against glioma in our population. Adjusting for allergy, asthma, BMI, and smoking did not markedly change the association between longer rLTL and glioma risk. rLTL among cases was not associated with IDH1 mutation, 1p/19q co-deletion, or EGFR amplification, after adjusting for age at diagnosis and sex. CONCLUSIONS: In this Swedish glioma case-control cohort, we identified that long rLTL increases the risk of glioma, an association not confounded by allergy, BMI, or smoking. This highlights the complex interplay of the immune system, rLTL and cancer risk.
Subject(s)
Brain Neoplasms/epidemiology , Glioma/epidemiology , Leukocytes , Telomere , Adult , Aged , Aged, 80 and over , Body Mass Index , Brain Neoplasms/genetics , Case-Control Studies , Confounding Factors, Epidemiologic , Female , Glioma/genetics , Humans , Hypersensitivity/epidemiology , Male , Middle Aged , Phenotype , Risk Factors , Smoking/epidemiology , Sweden/epidemiologyABSTRACT
OBJECTIVES: To investigate the molecular and structural patterns of bone healing during guided bone regeneration (GBR), comparing two resorbable non-cross-linked collagen membranes. MATERIALS AND METHODS: Trabecular bone defects in rat femurs were filled with deproteinized bovine bone (DBB) and covered with either a membrane comprising collagen and elastin (CXP) or collagen (BG). Samples were harvested after 3 and 21 days for histology/histomorphometry and gene expression analysis. Gene expression analysis was performed on the membrane (at 3 days) and the underlying defect compartment (at 3 and 21 days). RESULTS: At the total defect level, no differences in bone area percentage were found between the CXP and BG. When evaluating the central area of the defect, a higher percentage of de novo bone formation was seen for the CXP membrane (34.9%) compared to BG (15.5%) at 21 days (p = .01). Gene expression analysis revealed higher expression of bone morphogenetic protein-2 (Bmp2) in the membrane compartment at 3 days in the BG group. By contrast, higher Bmp2 expression was found in the defect compartment treated with the CXP membrane, both at 3 and 21 days. A significant temporal increase (from 3 to 21 days) in the remodeling activity, cathepsin K (Catk) and calcitonin receptor (Calcr), was found in the CXP group. Molecular analysis demonstrated expression of several growth factors and cytokines in the membrane compartment irrespective of the membrane type. Bmp2 expression in the membrane correlated positively with Bmp2 expression in the defect, whereas fibroblast growth factor-2 (Fgf2) expression in the membrane correlated positively with inflammatory cytokines, tumor necrosis factor-alpha (Tnfa) and interleukin-6 (Il6) in the defect. CONCLUSIONS: The results provide histological and molecular evidence that different resorbable collagen membranes contribute differently to the GBR healing process. In the BG group, bone formation was primarily localized to the peripheral part of the defect. By contrast, the CXP group demonstrated significantly higher de novo bone formation in the central portion of the defect. This increase in bone formation was reflected by triggered expression of potent osteogenic growth factor, Bmp2, in the defect. These findings suggest that the CXP membrane may have a more active role in regulating the bone healing dynamics.
Subject(s)
Bone Regeneration/physiology , Collagen , Femur/physiology , Guided Tissue Regeneration , Animals , Bone Morphogenetic Proteins/genetics , Bone Morphogenetic Proteins/metabolism , Cathepsin K/genetics , Cathepsin K/metabolism , Cytokines/genetics , Cytokines/metabolism , Elastin , Femur/anatomy & histology , Femur/metabolism , Gene Expression Profiling , Male , Models, Animal , Osteocalcin/genetics , Osteocalcin/metabolism , Rats , Rats, Sprague-Dawley , Receptors, Calcitonin/genetics , Receptors, Calcitonin/metabolismABSTRACT
OBJECTIVE: The objective of this study was to estimate the area fraction of different ratios of Bio-Oss® and bone, prior to grafting in an in vitro model to demonstrate a histomorphometric baseline. METHODS: Bio-Oss® particles were mixed with autogenous bone from pig jaw in three different ratios (50:50, 80:20 and 100:0) and packed in rice paper in a standardized procedure. Histomorphometric analyses were performed in 25 specimens and 74 regions of interest. The area percentage of Bio-Oss® , bone, and non-mineralized tissue (NMT) were calculated. Results were reported as mean values and 95% confidence interval (CI). RESULTS: The mean area fraction of Bio-Oss® was 20.6% (CI: 18.2-23) in the 50:50 mixture, 33.6% (CI: 29.7-37.6) in the 80:20 mixture, and 43.4% (CI: 40.5-46.3) in the 100:0 mixture. The mean area fraction of NMT was 60.5% (CI: 57.9-63.1) in the 50:50 mixture, 59.6% (CI: 56.4-62.7) in the 80:20 mixture, and 56.6% (CI: 53.7-59.5) in the 100:0 mixture. The mean area fraction of bone was 18.9% (CI: 16.9-20.9) in the 50:50 mixture and 6.8% (CI: 5-8.6) in the 80:20 mixture. CONCLUSION: There is a great difference in the clinically estimated percentage and the histomorphometrically evaluated percentage of Bio-Oss® at baseline, prior to grafting. The area fraction of different tissues presented in this study may be beneficial as guidance for histomorphometrical baseline calculations when different mixtures of Bio-Oss® and autogenous bone are used as grafting materials.
Subject(s)
Bone Transplantation/methods , Minerals/therapeutic use , Animals , In Vitro Techniques , Jaw/pathology , Minerals/administration & dosage , Orthognathic Surgical Procedures , SwineABSTRACT
Genome-wide association studies and candidate gene studies have identified several genetic variants that increase glioma risk. The majority of these variants are non-coding and the mechanisms behind the increased risk in carriers are not known. In this study, we hypothesize that some of the established glioma risk variants induce aberrant DNA methylation in the developing tumor, either locally (gene-specific) or globally (genome-wide). In a pilot data set including 77 glioma patients, we used Illumina beadchip technology to analyze genetic variants in blood and DNA methylation in matched tumor samples. To validate our findings, we used data from the Cancer Genome Atlas, including 401 glioblastoma patients. Consensus clustering identified the glioma CpG island methylator phenotype (gCIMP) and two additional subgroups with distinct patterns of global DNA methylation. In the pilot dataset, gCIMP was associated with two genetic variants in CDKN2B-AS1, rs1412829 and rs4977756 (9p21.3, p = 8.1 x 10-7 and 4.8 x 10-5, respectively). The association was in the same direction in the TCGA dataset, although statistically significant only when combining individuals with AG and GG genotypes. We also investigated the relation between glioma risk variants and DNA methylation in the promoter region of genes located within 30 kb of each variant. One association in the pilot dataset, between the TERT risk variant rs2736100 and lower methylation of cg23827991 (in TERT; p = 0.001), was confirmed in the TCGA dataset (p = 0.001). In conclusion, we found an association between rs1412829 and rs4977756 (9p21.3, CDKN2B-AS1) and global DNA methylation pattern in glioma, for which a trend was seen also in the TCGA glioblastoma dataset. We also found an association between rs2736100 (in TERT) and levels of methylation at cg23827991 (localized in the same gene, 3.3 kbp downstream of the risk variant), which was validated in the TCGA dataset. Except for this one association, we did not find strong evidence for gene-specific DNA methylation mediated by glioma risk variants.
Subject(s)
Brain Neoplasms/genetics , DNA Methylation , Glioma/genetics , Polymorphism, Single Nucleotide , RNA, Long Noncoding/genetics , Telomerase/genetics , CpG Islands , Databases, Genetic , Genetic Predisposition to Disease , Genome-Wide Association Study , Glioblastoma/genetics , Humans , Oligodendroglioma/genetics , Pilot Projects , Promoter Regions, GeneticABSTRACT
Genetic variants have been associated with the risk of developing glioma, but functional mechanisms on disease phenotypic traits remain to be investigated. One phenotypic trait of glioblastoma is the mutation and amplification of the epidermal growth factor receptor (EGFR) gene. We investigated associations between pre-diagnostic serum protein concentrations of EGFR and ErbB2, both members of the EGFR family, and future risk of glioma. Further, we studied if EGFR glioma risk variants were associated with EGFR and ErbB2 serum levels. We assessed the associations between genetic glioma risk variants and serum concentrations of EGFR and ErbB2, as measured in pre-diagnostic cohort serum samples of 593 glioma patients and 590 matched cancer-free controls. High serum EGFR and ErbB2 levels were associated with risk of developing glioblastoma (P = 0.008; OR = 1.58, 95 % CI = 1.13-2.22 and P = 0.017, OR = 1.63, 95 % CI = 1.09-2.44, respectively). High serum ErbB2 concentration was also associated with glioma risk overall (P = 0.049; OR = 1.39, 95 % CI = 1.00-1.93). Glioma risk variants were not associated with high serum protein abundance. In contrast, the EGFR risk variant rs4947986 (T) was correlated with decreased EGFR serum levels (study cohort P = 0.024 and controls P = 0.009). To our knowledge, this is the first study showing an association of EGFR and ErbB2 serum levels with glioma more than a decade before diagnosis, indicating that EGFR and ErbB2 serum proteins are important in early gliomagenesis. However, we did not find evidence that glioma risk variants were associated with high pre-diagnostic serum concentrations of EGFR and ErbB2.
Subject(s)
Brain Neoplasms/blood , Brain Neoplasms/genetics , ErbB Receptors/blood , Glioma/blood , Glioma/genetics , Receptor, ErbB-2/blood , Adolescent , Adult , Aged , Biomarkers, Tumor/blood , Case-Control Studies , Female , Genetic Predisposition to Disease/genetics , Genotype , Humans , Male , Middle Aged , Polymorphism, Single Nucleotide , Young AdultABSTRACT
During the last years, genome wide association studies have discovered common germline genetic variants associated with specific glioma subtypes. We aimed to study the association between these germline risk variants and tumor phenotypes, including copy number aberrations and protein expression. A total of 91 glioma patients were included. Thirteen well known genetic risk variants in TERT, EGFR, CCDC26, CDKN2A, CDKN2B, PHLDB1, TP53, and RTEL1 were selected for investigation of possible correlations with the glioma somatic markers: EGFR amplification, 1p/19q codeletion and protein expression of p53, Ki-67, and mutated IDH1. The CDKN2A/B risk variant, rs4977756, and the CDKN2B risk variant, rs1412829 were inversely associated (p = 0.049 and p = 0.002, respectively) with absence of a mutated IDH1, i.e., the majority of patients homozygous for the risk allele showed no or low expression of mutated IDH1. The RTEL1 risk variant, rs6010620 was associated (p = 0.013) with not having 1p/19q codeletion, i.e., the majority of patients homozygous for the risk allele did not show 1p/19q codeletion. In addition, the EGFR risk variant rs17172430 and the CDKN2B risk variant rs1412829, both showed a trend for association (p = 0.055 and p = 0.051, respectively) with increased EGFR copy number, i.e., the majority of patients homozygote for the risk alleles showed chromosomal gain or amplification of EGFR. Our findings indicate that CDKN2A/B risk genotypes are associated with primary glioblastoma without IDH mutation, and that there is an inverse association between RTEL1 risk genotypes and 1p/19q codeletion, suggesting that these genetic variants have a molecular impact on the genesis of high graded brain tumors. Further experimental studies are needed to delineate the functional mechanism of the association between genotype and somatic genetic aberrations.
Subject(s)
Biomarkers, Tumor/genetics , Cyclin-Dependent Kinase Inhibitor p15/genetics , Cyclin-Dependent Kinase Inhibitor p16/genetics , DNA Helicases/genetics , ErbB Receptors/genetics , Glioma/genetics , Polymorphism, Single Nucleotide/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Brain Neoplasms/genetics , Brain Neoplasms/pathology , Female , Follow-Up Studies , Genetic Predisposition to Disease , Glioma/pathology , Humans , Immunoenzyme Techniques , In Situ Hybridization, Fluorescence , Male , Middle Aged , Mutation/genetics , Neoplasm Grading , Prognosis , Risk Factors , Survival Rate , Young AdultABSTRACT
Recent studies have described a number of genes that are frequently altered in medulloblastoma tumors and that have putative key roles in the development of the disease. We hypothesized that common germline genetic variations in these genes may be associated with medulloblastoma development. Based on recent publications, we selected 10 genes that were frequently altered in medulloblastoma: CCND2, CTNNB1, DDX3X, GLI2, SMARCA4, MYC, MYCN, PTCH1, TP53, and MLL2 (now renamed as KMT2D). Common genetic variants (single nucleotide polymorphisms) annotating these genes (n = 221) were genotyped in germline DNA (neonatal dried blood spot samples) from 243 childhood medulloblastoma cases and 247 control subjects from Sweden and Denmark. Eight genetic variants annotating three genes in the sonic hedgehog signaling pathway; CCND2, PTCH1, and GLI2, were found to be associated with the risk of medulloblastoma (P(combined) < 0.05). The findings were however not statistically significant following correction for multiple testing by the very stringent Bonferroni method. The results do not support our hypothesis that common germline genetic variants in the ten studied genes are associated with the risk of developing medulloblastoma.
Subject(s)
Brain Neoplasms/genetics , Cyclin D2/genetics , Genetic Predisposition to Disease/genetics , Kruppel-Like Transcription Factors/genetics , Medulloblastoma/genetics , Nuclear Proteins/genetics , Polymorphism, Single Nucleotide/genetics , Receptors, Cell Surface/genetics , Adolescent , Child , Child, Preschool , Denmark , Female , Genetic Association Studies , Humans , Male , Patched Receptors , Patched-1 Receptor , Retrospective Studies , Sweden , Young Adult , Zinc Finger Protein Gli2ABSTRACT
BACKGROUND: Although glioma etiology is poorly understood in general, growing evidence indicates a genetic component. Four large genome-wide association studies (GWAS) have linked common genetic variants with an increased glioma risk. However, to date, these studies are based largely on a case-control design, where cases have been recruited at the time of or after diagnosis. They may therefore suffer from a degree of survival bias, introduced when rapidly fatal cases are not included. METHODS: To confirm glioma risk variants in a prospective setting, we have analyzed 11 previously identified risk variants in a set of prediagnostic serum samples with 598 cases and 595 matched controls. Serum samples were acquired from The Janus Serum Bank, a Norwegian population-based biobank reserved for cancer research. RESULTS: We confirmed the association with glioma risk for variants within five genomic regions: 8q24.21 (CCDC26), 9p21.3 (CDKN2B-AS1), 11q23.3 (PHLDB1), 17p13.1 (TP53), and 20q13.33 (RTEL1). However, previously identified risk variants within the 7p11.2 (EGFR) region were not confirmed by this study. CONCLUSIONS: Our results indicate that the risk variants that were confirmed by this study are truly associated with glioma risk and may, consequently, affect gliomagenesis. Though the lack of positive confirmation of EGFR risk variants may be attributable to relatively limited statistical power, it nevertheless raises the question whether they truly are risk variants or markers for glioma prognosis. IMPACT: Our findings indicate the need for further studies to clarify the role of glioma risk loci with respect to prolonged survival versus etiology.
Subject(s)
Brain Neoplasms/genetics , Genetic Variation/genetics , Glioma/genetics , Adult , Aged , Brain Neoplasms/mortality , Case-Control Studies , DNA Helicases/genetics , Female , Genes, erbB-1/genetics , Glioma/mortality , Humans , Intracellular Signaling Peptides and Proteins/genetics , Male , Middle Aged , Nerve Tissue Proteins/genetics , Polymerase Chain Reaction , Polymorphism, Single Nucleotide/genetics , Prospective Studies , RNA, Long Noncoding/genetics , Registries , Risk Factors , Survival Rate , Tumor Suppressor Protein p53/genetics , Young AdultABSTRACT
An active stroma is important for cancer cell invasion and metastasis. We investigated the expression of fibroblast activation protein (FAP) in relation to patient prognosis in colorectal cancer. Colorectal cancer specimens from 449 patients were immunohistochemically stained with a FAP antibody and evaluated in the tumor center and tumor front using a semiquantitative four-level scale. FAP was expressed by fibroblasts in 85-90 % of the tumors examined. High versus no/low expression in the tumor center was associated with poor prognosis (multivariate hazard ratio, HR = 1.72; 95 % CI 1.07-2.77, p = 0.025). FAP expression in the tumor front, though more frequent than in the tumor center, was not associated with prognosis. FAP expression in the tumor center was more common in specimens with positive microsatellite instability (MSI) screening status and in patients with high CpG island methylator phenotype (CIMP) status. However, inclusion of MSI screening status and CIMP status in the multivariate analysis strengthened the risk estimates for high FAP expression in the tumor center (HR = 1.89; 95 % CI 1.13-3.14; p = 0.014), emphasizing the role of FAP as an independent prognostic factor. Stromal FAP expression is common in colorectal cancer, and we conclude that high FAP expression in the tumor center, but not the tumor front, is an independent negative prognostic factor.