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Baek IK, Cheong HS, Namgoong S, Kim JH, Kang SG, Yoon SJ, Kim SH, Chang JH, Kim LH, Shin HD. Two independent variants of epidermal growth factor receptor associated with risk of glioma in a Korean population. Sci Rep 2022; 12:19014. [PMID: 36347915 PMCID: PMC9643523 DOI: 10.1038/s41598-022-23217-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022] Open
Abstract
Gliomas are the most common primary tumors in the brain and spinal cord. In previous GWASs, SNPs in epidermal growth factor receptor (EGFR) have been reported as risk loci for gliomas. However, EGFR variants associated with gliomas in the Korean population remain unstudied. This study explored the association of EGFR SNPs with the risk of glioma. We genotyped 13 EGFR exon SNPs in a case-control study that included 324 Korean patients diagnosed with glioma and 480 population-based controls. Statistical analyses of the association between EGFR SNPs and glioma risk were conducted using logistic regression. Both stepwise analysis and conditional logistic analysis were performed to identify independent associations among genotyped variants. We confirmed that two SNPs (rs2227983, rs1050171) were significantly associated with glioma (rs2227983: odds ratio = 1.42, Pcorr = 0.009; rs1050171: odds ratio = 1.68, Pcorr = 0.005). Additionally, the stepwise analysis and conditional logistic analysis indicated that both SNPs created variants with independent genetic effects. This study is the first to show evidence that functional variants of EGFR, namely, rs2227983 (K521R) and rs1050171 (Q787Q), are associated with an increased risk of glioma in the Korean population. Future work should confirm the functional association between EGFR variants and glioma.
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Affiliation(s)
- In Ki Baek
- grid.263736.50000 0001 0286 5954Department of Life Science, Sogang University, Seoul, 04107 Republic of Korea
| | - Hyun Sub Cheong
- Research Institute for Life Science, GW Vitek, Inc., Seoul, Republic of Korea
| | - Seok Namgoong
- Research Institute for Life Science, GW Vitek, Inc., Seoul, Republic of Korea
| | - Jeong-Hyun Kim
- grid.267370.70000 0004 0533 4667Department of Medicine, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seok-Gu Kang
- grid.15444.300000 0004 0470 5454Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seon-Jin Yoon
- grid.15444.300000 0004 0470 5454Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea ,grid.15444.300000 0004 0470 5454Department of Biochemistry and Molecular Biology, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Se Hoon Kim
- grid.15444.300000 0004 0470 5454Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hee Chang
- grid.15444.300000 0004 0470 5454Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Lyoung Hyo Kim
- Research Institute for Life Science, GW Vitek, Inc., Seoul, Republic of Korea
| | - Hyoung Doo Shin
- grid.263736.50000 0001 0286 5954Department of Life Science, Sogang University, Seoul, 04107 Republic of Korea ,grid.263736.50000 0001 0286 5954Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
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Dissecting Molecular Features of Gliomas: Genetic Loci and Validated Biomarkers. Int J Mol Sci 2020; 21:ijms21020685. [PMID: 31968687 PMCID: PMC7014190 DOI: 10.3390/ijms21020685] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 02/07/2023] Open
Abstract
Recently, several studies focused on the genetics of gliomas. This allowed identifying several germline loci that contribute to individual risk for tumor development, as well as various somatic mutations that are key for disease classification. Unfortunately, none of the germline loci clearly confers increased risk per se. Contrariwise, somatic mutations identified within the glioma tissue define tumor genotype, thus representing valid diagnostic and prognostic markers. Thus, genetic features can be used in glioma classification and guided therapy. Such copious genomic variabilities are screened routinely in glioma diagnosis. In detail, Sanger sequencing or pyrosequencing, fluorescence in-situ hybridization, and microsatellite analyses were added to immunohistochemistry as diagnostic markers. Recently, Next Generation Sequencing was set-up as an all-in-one diagnostic tool aimed at detecting both DNA copy number variations and mutations in gliomas. This approach is widely used also to detect circulating tumor DNA within cerebrospinal fluid from patients affected by primary brain tumors. Such an approach is providing an alternative cost-effective strategy to genotype all gliomas, which allows avoiding surgical tissue collection and repeated tumor biopsies. This review summarizes available molecular features that represent solid tools for the genetic diagnosis of gliomas at present or in the next future.
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Abstract
Incidence, prevalence, and survival for brain tumors varies by histologic type, age at diagnosis, sex, and race/ethnicity. Significant progress has been made in identifying potential risk factors for brain tumors, although more research is warranted. The strongest risk factors that have been identified thus far include allergies/atopic disease, ionizing radiation, and heritable genetic factors. Further analysis of large, multicenter, epidemiologic studies, as well as well annotated omic datasets (including genomic, epigenomic, transcriptomic, proteomic, or metabolomics data) can potentially lead to further understanding of the relationship between gene and environment in the process of brain tumor development.
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Fahmideh MA, Lavebratt C, Schüz J, Röösli M, Tynes T, Grotzer MA, Johansen C, Kuehni CE, Lannering B, Prochazka M, Schmidt LS, Feychting M. Common genetic variations in cell cycle and DNA repair pathways associated with pediatric brain tumor susceptibility. Oncotarget 2016; 7:63640-63650. [PMID: 27613841 PMCID: PMC5325391 DOI: 10.18632/oncotarget.11575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/15/2016] [Indexed: 01/11/2023] Open
Abstract
Knowledge on the role of genetic polymorphisms in the etiology of pediatric brain tumors (PBTs) is limited. Therefore, we investigated the association between single nucleotide polymorphisms (SNPs), identified by candidate gene-association studies on adult brain tumors, and PBT risk.The study is based on the largest series of PBT cases to date. Saliva DNA from 245 cases and 489 controls, aged 7-19 years at diagnosis/reference date, was genotyped for 68 SNPs. Data were analyzed using unconditional logistic regression.The results showed EGFRrs730437 and EGFRrs11506105 may decrease susceptibility to PBTs, whereas ERCC1rs3212986 may increase risk of these tumors. Moreover, stratified analyses indicated CHAF1Ars243341, CHAF1Ars2992, and XRCC1rs25487 were associated with a decreased risk of astrocytoma subtype. Furthermore, an increased risk of non-astrocytoma subtype associated with EGFRrs9642393, EME1rs12450550, ATMrs170548, and GLTSCRrs1035938 as well as a decreased risk of this subtype associated with XRCC4rs7721416 and XRCC4rs2662242 were detected.This study indicates SNPs in EGFR, ERCC1, CHAF1A, XRCC1, EME1, ATM, GLTSCR1, and XRCC4 may be associated with the risk of PBTs. Therefore, cell cycle and DNA repair pathways variations associated with susceptibility to adult brain tumors also seem to be associated with PBT risk, suggesting pediatric and adult brain tumors might share similar etiological pathways.
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Affiliation(s)
- Maral Adel Fahmideh
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Catharina Lavebratt
- Neurogenetics Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, and Center for Molecular Medicine, Karolinska University Hospital, L8:00, SE-171 76 Stockholm, Sweden
| | - Joachim Schüz
- Section of Environment and Radiation, International Agency for Research on Cancer (IARC), 69372 Lyon, France
| | - Martin Röösli
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, 4002 Basel, Switzerland
- University of Basel, 4003 Basel, Switzerland
| | - Tore Tynes
- The Cancer Registry of Norway, NO-0379 Oslo, Norway
- National Institute of Occupational Health, NO-0360 Oslo, Norway
| | - Michael A. Grotzer
- Department of Oncology, University Children's Hospital of Zurich, 8032 Zurich, Switzerland
| | - Christoffer Johansen
- Unit of Survivorship, The Danish Cancer Society Research Centre, DK-2100 Copenhagen, Denmark
- Oncology Department, Finsen Centre, Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Claudia E Kuehni
- Swiss Childhood Cancer Registry, Institute of Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland
| | - Birgitta Lannering
- Childrens Cancer Center, Queen Silvia Childrens Hospital, SE-416 85 Gothenburg, Sweden
| | - Michaela Prochazka
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Lisbeth S Schmidt
- Department of Clinical Genetics, University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Maria Feychting
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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Ghasimi S, Wibom C, Dahlin AM, Brännström T, Golovleva I, Andersson U, Melin B. Genetic risk variants in the CDKN2A/B, RTEL1 and EGFR genes are associated with somatic biomarkers in glioma. J Neurooncol 2016; 127:483-92. [PMID: 26839018 PMCID: PMC4835517 DOI: 10.1007/s11060-016-2066-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/22/2016] [Indexed: 01/22/2023]
Abstract
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.
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Affiliation(s)
- Soma Ghasimi
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Carl Wibom
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden.,Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Anna M Dahlin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden.,Computational Life Science Cluster (CLiC), Umeå University, Umeå, Sweden
| | - Thomas Brännström
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Irina Golovleva
- Department of Medical Bioscience, Medical and Clinical Genetics, Umeå University, Umeå, Sweden
| | - Ulrika Andersson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden.
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
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6
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Fung C, Zhou P, Joyce S, Trent K, Yuan JM, Grandis JR, Weissfeld JL, Romkes M, Weeks DE, Egloff AM. Identification of epidermal growth factor receptor (EGFR) genetic variants that modify risk for head and neck squamous cell carcinoma. Cancer Lett 2014; 357:549-56. [PMID: 25511740 DOI: 10.1016/j.canlet.2014.12.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/03/2014] [Accepted: 12/04/2014] [Indexed: 01/30/2023]
Abstract
EGFR polymorphisms have not been thoroughly evaluated for association with head and neck squamous cell carcinoma (HNSCC) risk. We genotyped 578 HNSCC patients and 588 cancer-free controls for 60 EGFR single nucleotide polymorphisms (SNPs) and tested associations with HNSCC risk. EGFR intronic SNPs rs12535536, rs2075110, rs1253871, rs845561 and rs6970262 and synonymous SNP rs2072454 were associated with HNSCC risk among all subjects (p < 0.05). SNPs rs12538371, rs845561, and rs6970262 were significantly associated with HNSCC risk (p < 0.05) among never tobacco users. We identified EGFR variants that likely modify risk for HNSCC including three variants that contribute to tobacco-independent risk.
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Affiliation(s)
- Christopher Fung
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Pei Zhou
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sonali Joyce
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kerry Trent
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jian-Min Yuan
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jennifer R Grandis
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joel L Weissfeld
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Marjorie Romkes
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel E Weeks
- Department of Human Genetics and Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ann Marie Egloff
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA.
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7
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Thakkar JP, Dolecek TA, Horbinski C, Ostrom QT, Lightner DD, Barnholtz-Sloan JS, Villano JL. Epidemiologic and molecular prognostic review of glioblastoma. Cancer Epidemiol Biomarkers Prev 2014; 23:1985-96. [PMID: 25053711 DOI: 10.1158/1055-9965.epi-14-0275] [Citation(s) in RCA: 809] [Impact Index Per Article: 80.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most common and aggressive primary central nervous system malignancy with a median survival of 15 months. The average incidence rate of GBM is 3.19/100,000 population, and the median age of diagnosis is 64 years. Incidence is higher in men and individuals of white race and non-Hispanic ethnicity. Many genetic and environmental factors have been studied in GBM, but the majority are sporadic, and no risk factor accounting for a large proportion of GBMs has been identified. However, several favorable clinical prognostic factors are identified, including younger age at diagnosis, cerebellar location, high performance status, and maximal tumor resection. GBMs comprise of primary and secondary subtypes, which evolve through different genetic pathways, affect patients at different ages, and have differences in outcomes. We report the current epidemiology of GBM with new data from the Central Brain Tumor Registry of the United States 2006 to 2010 as well as demonstrate and discuss trends in incidence and survival. We also provide a concise review on molecular markers in GBM that have helped distinguish biologically similar subtypes of GBM and have prognostic and predictive value.
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Affiliation(s)
- Jigisha P Thakkar
- Department of Medicine, University of Kentucky, Lexington, Kentucky. Department of Neurology, University of Kentucky, Lexington, Kentucky
| | - Therese A Dolecek
- Division of Epidemiology and Biostatistics and Institute for Health Research and Policy, School of Public Health, University of Illinois at Chicago, Chicago, Illinois
| | - Craig Horbinski
- Department of Pathology, University of Kentucky, Lexington, Kentucky
| | - Quinn T Ostrom
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Donita D Lightner
- Department of Neurology and Pediatrics, University of Kentucky, Lexington, Kentucky
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - John L Villano
- Department of Medicine, University of Kentucky, Lexington, Kentucky. Department of Neurology, University of Kentucky, Lexington, Kentucky.
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Ostrom QT, Bauchet L, Davis FG, Deltour I, Fisher JL, Langer CE, Pekmezci M, Schwartzbaum JA, Turner MC, Walsh KM, Wrensch MR, Barnholtz-Sloan JS. The epidemiology of glioma in adults: a "state of the science" review. Neuro Oncol 2014; 16:896-913. [PMID: 24842956 PMCID: PMC4057143 DOI: 10.1093/neuonc/nou087] [Citation(s) in RCA: 1419] [Impact Index Per Article: 141.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/09/2014] [Indexed: 12/14/2022] Open
Abstract
Gliomas are the most common primary intracranial tumor, representing 81% of malignant brain tumors. Although relatively rare, they cause significant mortality and morbidity. Glioblastoma, the most common glioma histology (∼45% of all gliomas), has a 5-year relative survival of ∼5%. A small portion of these tumors are caused by Mendelian disorders, including neurofibromatosis, tuberous sclerosis, and Li-Fraumeni syndrome. Genomic analyses of glioma have also produced new evidence about risk and prognosis. Recently discovered biomarkers that indicate improved survival include O⁶-methylguanine-DNA methyltransferase methylation, isocitrate dehydrogenase mutation, and a glioma cytosine-phosphate-guanine island methylator phenotype. Genome-wide association studies have identified heritable risk alleles within 7 genes that are associated with increased risk of glioma. Many risk factors have been examined as potential contributors to glioma risk. Most significantly, these include an increase in risk by exposure to ionizing radiation and a decrease in risk by history of allergies or atopic disease(s). The potential influence of occupational exposures and cellular phones has also been examined, with inconclusive results. We provide a “state of the science” review of current research into causes and risk factors for gliomas in adults.
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Pandey JP, Kaur N, Costa S, Amorim J, Nabico R, Linhares P, Vaz R, Viana-Pereira M, Reis RM. Immunoglobulin genes implicated in glioma risk. Oncoimmunology 2014; 3:e28609. [PMID: 25097800 PMCID: PMC4091592 DOI: 10.4161/onci.28609] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 03/11/2014] [Accepted: 03/20/2014] [Indexed: 12/26/2022] Open
Abstract
Both genetic and environmental factors are thought to be causal in gliomagenesis. Several genes have been implicated in glioma development, but the putative role of a major immunity-related gene complex member, immunoglobulin heavy chain γ (IGHG) has not been evaluated. Prior observations that IGHG-encoded γ marker (GM) allotypes exhibit differential sensitivity to an immunoevasion strategy of cytomegalovirus, a pathogen implicated as a promoter of gliomagenesis, has lead us to hypothesize that these determinants are risk factors for glioma. To test this hypothesis, we genotyped the IGHG locus comprising the GM alleles, specifically GM alleles 3 and 17, of 120 glioma patients and 133 controls via TaqMan® genotyping assay. To assess the associations between GM genotypes and the risk of glioma, we applied an unconditional multivariate logistic regression analysis adjusted for potential confounding variables. In comparison to subjects who were homozygous for the GM 17 allele, the GM 3 homozygotes were over twice as likely, and the GM 3/17 heterozygotes were over three times as likely, to develop glioma. Similar results were achieved when analyzed by combining the data corresponding to alleles GM 3 and GM 3/17 in a dominant model. The GM 3/17 genotype and the combination of GM 3 and GM 3/17 were found to be further associated with over 3 times increased risk for high-grade astrocytoma (grades III-IV). Allele frequency analyses also showed an increased risk for gliomas and high-grade astrocytoma in association with GM 3. Our findings support the premise that the GM 3 allele may present risk for the development of glioma, possibly by modulating immunity to cytomegalovirus.
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Affiliation(s)
- Janardan P Pandey
- Department of Microbiology and Immunology; Medical University of South Carolina; Charleston, SC USA
| | - Navtej Kaur
- Department of Microbiology and Immunology; Medical University of South Carolina; Charleston, SC USA
| | - Sandra Costa
- Life and Health Sciences Research Institute; University of Minho; Campus de Gualtar; Braga, Portugal ; ICVS/3B's-PT Government Associate Laboratory; Campus de Gualtar, Braga, Portugal
| | - Julia Amorim
- Department of Oncology; Hospital de Braga; Sete Fontes-São Victor; Braga, Portugal
| | - Rui Nabico
- Department of Oncology; Hospital de Braga; Sete Fontes-São Victor; Braga, Portugal
| | - Paulo Linhares
- Department of Neurosurgery; Hospital S. João; Porto, Portugal ; Faculty of Medicine; Oporto University; Porto, Portugal
| | - Rui Vaz
- Department of Neurosurgery; Hospital S. João; Porto, Portugal ; Faculty of Medicine; Oporto University; Porto, Portugal
| | - Marta Viana-Pereira
- Life and Health Sciences Research Institute; University of Minho; Campus de Gualtar; Braga, Portugal ; ICVS/3B's-PT Government Associate Laboratory; Campus de Gualtar, Braga, Portugal
| | - Rui M Reis
- Life and Health Sciences Research Institute; University of Minho; Campus de Gualtar; Braga, Portugal ; ICVS/3B's-PT Government Associate Laboratory; Campus de Gualtar, Braga, Portugal ; Molecular Oncology Research Center; Barretos Cancer Hospital; Barretos, SP Brazil
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10
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Dong YS, Hou WG, Li XL, Jin TB, Li Y, Feng DY, Liu DB, Gao GD, Yin ZM, Qin HZ. Genetic association of CHEK2, GSTP1, and ERCC1 with glioblastoma in the Han Chinese population. Tumour Biol 2014; 35:4937-41. [PMID: 24532427 DOI: 10.1007/s13277-014-1648-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 01/12/2014] [Indexed: 11/28/2022] Open
Abstract
Glioblastoma (GBM), a deadly brain tumor, is the most malignant glioma. It mainly occurs in adults and occurs significantly more in males than in females. We genotyped 19 tag single nucleotide polymorphisms (tSNPs) from 13 genes in a case-control study of the Han Chinese population to identify genetic factors contributing to the risk of GBM. These tSNPs were genotyped by Sequenom MassARRAY RS1000. Statistical analysis was performed using χ(2) test and SNPStats, a website software. Using χ(2) test, we found that the distribution of two tSNPs (rs2267130 in checkpoint kinase 2 (CHEK2), p = 0.040; rs1695 in GSTP1, p = 0.023) allelic frequencies had significant difference between cases and controls. When we analyzed all of the tSNPs using the SNPStats software, we found that rs1695 in GSTP1 decreased the risk of GBM in log-additive model (OR = 0.56, 95% CI, 0.34-0.94, p = 0.022). Besides, we found that there is an interaction between rs3212986 in excision repair cross-complementing group 1 (ERCC1) and gender under codominant and recessive models. The gene polymorphisms in CHEK2, GSTP1, and ERCC1 may be involved in GBM in the Han Chinese population. Since our sample size is small, further investigation needs to be performed.
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Affiliation(s)
- Yu-Shu Dong
- Department of Neurosurgery, Tangdu Hospital, The Fourth Military Medical University, No. 1, Xinsi Road, Xi'an, 710038, China
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11
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Antihistamine use and immunoglobulin E levels in glioma risk and prognosis. Cancer Epidemiol 2013; 37:908-12. [PMID: 23994286 DOI: 10.1016/j.canep.2013.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 07/30/2013] [Accepted: 08/05/2013] [Indexed: 01/09/2023]
Abstract
OBJECTIVE An inverse association between personal history of allergies/asthma and glioma risk has been fairly consistently reported in the epidemiologic literature. However, the role of regular antihistamine use remains controversial due to a small number of studies reporting contradictory findings. We evaluated the association between regular use of oral antihistamines and glioma risk, adjusting for a number of relevant factors (e.g., immunoglobulin E levels and history of chickenpox). METHODS We used a subset of the Harris County Case-Control Study, which included 362 pathologically confirmed glioma cases and 462 cancer-free controls, to evaluate this association using unconditional multivariable logistic regression. These models were run among the overall study population and stratified by allergy status. Cox regression was utilized to examine whether antihistamine use was associated with mortality among all cases and separately among high-grade cases. RESULTS Antihistamine use was strongly associated with glioma risk among those with a positive allergy/asthma history (OR: 4.19, 95% CI: 2.06-8.51), but not among those with a negative history (OR: 1.59, 95% CI: 0.95-2.67). There were no significant associations between antihistamine use and survival among cases. CONCLUSION The current study implies that regular antihistamine use may increase glioma risk. However, several larger studies are necessary before definitive conclusions can be drawn.
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12
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Sintupisut N, Liu PL, Yeang CH. An integrative characterization of recurrent molecular aberrations in glioblastoma genomes. Nucleic Acids Res 2013; 41:8803-21. [PMID: 23907387 PMCID: PMC3799430 DOI: 10.1093/nar/gkt656] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most common and malignant primary brain tumor in adults. Decades of investigations and the recent effort of the Cancer Genome Atlas (TCGA) project have mapped many molecular alterations in GBM cells. Alterations on DNAs may dysregulate gene expressions and drive malignancy of tumors. It is thus important to uncover causal and statistical dependency between ‘effector’ molecular aberrations and ‘target’ gene expressions in GBMs. A rich collection of prior studies attempted to combine copy number variation (CNV) and mRNA expression data. However, systematic methods to integrate multiple types of cancer genomic data—gene mutations, single nucleotide polymorphisms, CNVs, DNA methylations, mRNA and microRNA expressions and clinical information—are relatively scarce. We proposed an algorithm to build ‘association modules’ linking effector molecular aberrations and target gene expressions and applied the module-finding algorithm to the integrated TCGA GBM data sets. The inferred association modules were validated by six tests using external information and datasets of central nervous system tumors: (i) indication of prognostic effects among patients; (ii) coherence of target gene expressions; (iii) retention of effector–target associations in external data sets; (iv) recurrence of effector molecular aberrations in GBM; (v) functional enrichment of target genes; and (vi) co-citations between effectors and targets. Modules associated with well-known molecular aberrations of GBM—such as chromosome 7 amplifications, chromosome 10 deletions, EGFR and NF1 mutations—passed the majority of the validation tests. Furthermore, several modules associated with less well-reported molecular aberrations—such as chromosome 11 CNVs, CD40, PLXNB1 and GSTM1 methylations, and mir-21 expressions—were also validated by external information. In particular, modules constituting trans-acting effects with chromosome 11 CNVs and cis-acting effects with chromosome 10 CNVs manifested strong negative and positive associations with survival times in brain tumors. By aligning the information of association modules with the established GBM subclasses based on transcription or methylation levels, we found each subclass possessed multiple concurrent molecular aberrations. Furthermore, the joint molecular characteristics derived from 16 association modules had prognostic power not explained away by the strong biomarker of CpG island methylator phenotypes. Functional and survival analyses indicated that immune/inflammatory responses and epithelial-mesenchymal transitions were among the most important determining processes of prognosis. Finally, we demonstrated that certain molecular aberrations uniquely recurred in GBM but were relatively rare in non-GBM glioma cells. These results justify the utility of an integrative analysis on cancer genomes and provide testable characterizations of driver aberration events in GBM.
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Affiliation(s)
- Nardnisa Sintupisut
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan, ROC and Institute of Information Science, Academia Sinica, Taipei, Taiwan, ROC
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Rice T, Zheng S, Decker PA, Walsh KM, Bracci P, Xiao Y, McCoy LS, Smirnov I, Patoka JS, Hansen HM, Hsuang G, Wiemels JL, Tihan T, Pico AR, Prados MD, Chang SM, Berger MS, Caron A, Fink S, Kollmeyer T, Rynearson A, Voss J, Kosel ML, Fridley BL, Lachance DH, Eckel-Passow JE, Sicotte H, O'Neill BP, Giannini C, Wiencke JK, Jenkins RB, Wrensch MR. Inherited variant on chromosome 11q23 increases susceptibility to IDH-mutated but not IDH-normal gliomas regardless of grade or histology. Neuro Oncol 2013; 15:535-41. [PMID: 23361564 PMCID: PMC3635511 DOI: 10.1093/neuonc/nos324] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 10/02/2012] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION Recent discoveries of inherited glioma risk loci and acquired IDH mutations are providing new insights into glioma etiology. IDH mutations are common in lower grade gliomas and secondary glioblastomas and uncommon in primary glioblastomas. Because the inherited variant in 11q23 has been associated with risk of lower grade glioma and not with glioblastomas, we hypothesized that this variant increases susceptibility to IDH-mutated gliomas, but not to IDH-wild-type gliomas. METHODS We tested this hypothesis in patients with glioma and controls from the San Francisco Adult Glioma Study, the Mayo Clinic, and Illumina controls (1102 total patients, 5299 total controls). Case-control additive associations of 11q23 risk alleles (rs498872, T allele) were calculated using logistic regression, stratified by tumor IDH status (mutated or wild-type) and by histology and grade. We also adjusted for the recently discovered 8q24 glioma risk locus rs55705857 G allele. RESULTS The 11q23 glioma risk locus was associated with increased risk of IDH-mutated gliomas of all histologies and grades (odds ratio [OR] = 1.50; 95% confidence interval [CI] = 1.29-1.74; P = 1.3X10(-7)) but not with IDH-wild-type gliomas of any histology or grade (OR = 0.91; 95% CI = 0.81-1.03; P = 0.14). The associations were independent of the rs55705857 G allele. CONCLUSION A variant at the 11q23 locus increases risk for IDH-mutated but not IDH-wild-type gliomas, regardless of grade or histology.
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Affiliation(s)
- Terri Rice
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94107, USA.
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14
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Okada H, Scheurer ME, Sarkar SN, Bondy ML. Integration of epidemiology, immunobiology, and translational research for brain tumors. Ann N Y Acad Sci 2013; 1284:17-23. [PMID: 23651189 PMCID: PMC3648859 DOI: 10.1111/nyas.12115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We recently identified a pivotal role for the host type I interferon (IFN) pathway in immunosurveillance against de novo mouse glioma development, especially through the regulation of immature myeloid cells (IMCs) in the glioma microenvironment. The present paper summarizes our published work in a number of areas. We have identified single-nucleotide polymorphisms (SNPs) in human IFN genes that dictate altered prognosis of patients with glioma. One of these SNPs (rs12553612) is located in the promoter of IFNA8 and influences its activity. Conversely, recent epidemiologic data show that chronic use of nonsteroidal anti-inflammatory drugs lowers the risk of glioma. We translated these findings back to our de novo glioma model and found that cyclooxygenase-2 inhibition enhances antiglioma immunosurveillance by reducing glioma-associated IMCs. Taken together, these findings suggest that alterations in myeloid cell function condition the brain for glioma development. Finally, in preliminary work, we have begun applying novel immunotherapeutic approaches to patients with low-grade glioma with the aim of preventing malignant transformation. Future research will hopefully better integrate epidemiological, immunobiological, and translational techniques to develop novel, preventive approaches for malignant gliomas.
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Affiliation(s)
- Hideho Okada
- University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA.
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15
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Walsh KM, Anderson E, Hansen HM, Decker PA, Kosel ML, Kollmeyer T, Rice T, Zheng S, Xiao Y, Chang JS, McCoy LS, Bracci PM, Wiemels JL, Pico AR, Smirnov I, Lachance DH, Sicotte H, Eckel-Passow JE, Wiencke JK, Jenkins RB, Wrensch MR. Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies. Genet Epidemiol 2013; 37:222-8. [PMID: 23280628 PMCID: PMC3670948 DOI: 10.1002/gepi.21707] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 11/13/2012] [Accepted: 11/22/2012] [Indexed: 01/07/2023]
Abstract
Genomewide association studies (GWAS) and candidate-gene studies have implicated single-nucleotide polymorphisms (SNPs) in at least 45 different genes as putative glioma risk factors. Attempts to validate these associations have yielded variable results and few genetic risk factors have been consistently replicated. We conducted a case-control study of Caucasian glioma cases and controls from the University of California San Francisco (810 cases, 512 controls) and the Mayo Clinic (852 cases, 789 controls) in an attempt to replicate previously reported genetic risk factors for glioma. Sixty SNPs selected from the literature (eight from GWAS and 52 from candidate-gene studies) were successfully genotyped on an Illumina custom genotyping panel. Eight SNPs in/near seven different genes (TERT, EGFR, CCDC26, CDKN2A, PHLDB1, RTEL1, TP53) were significantly associated with glioma risk in the combined dataset (P < 0.05), with all associations in the same direction as in previous reports. Several SNP associations showed considerable differences across histologic subtype. All eight successfully replicated associations were first identified by GWAS, although none of the putative risk SNPs from candidate-gene studies was associated in the full case-control sample (all P values > 0.05). Although several confirmed associations are located near genes long known to be involved in gliomagenesis (e.g., EGFR, CDKN2A, TP53), these associations were first discovered by the GWAS approach and are in noncoding regions. These results highlight that the deficiencies of the candidate-gene approach lay in selecting both appropriate genes and relevant SNPs within these genes.
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Affiliation(s)
- Kyle M Walsh
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.
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16
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Goodenberger ML, Jenkins RB. Genetics of adult glioma. Cancer Genet 2012; 205:613-21. [PMID: 23238284 DOI: 10.1016/j.cancergen.2012.10.009] [Citation(s) in RCA: 567] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Revised: 10/22/2012] [Accepted: 10/26/2012] [Indexed: 12/13/2022]
Abstract
Gliomas make up approximately 30% of all brain and central nervous system tumors and 80% of all malignant brain tumors. Despite the frequency of gliomas, the etiology of these tumors remains largely unknown. Diffuse gliomas, including astrocytomas and oligodendrogliomas, belong to a single pathologic class but have very different histologies and molecular etiologies. Recent genomic studies have identified separate molecular subtypes within the glioma classification that appear to correlate with biological etiology, prognosis, and response to therapy. The discovery of these subtypes suggests that molecular genetic tests are and will be useful, beyond classical histology, for the clinical classification of gliomas. While a familial susceptibility to glioma has been identified, only a small percentage of gliomas are thought to be due to single-gene hereditary cancer syndromes. Through the use of linkage studies and genome-wide association studies, multiple germline variants have been identified that are beginning to define the genetic susceptibility to glioma.
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Affiliation(s)
- McKinsey L Goodenberger
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
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17
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EGFR gene variants are associated with specific somatic aberrations in glioma. PLoS One 2012; 7:e47929. [PMID: 23236348 PMCID: PMC3517607 DOI: 10.1371/journal.pone.0047929] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 09/18/2012] [Indexed: 11/25/2022] Open
Abstract
A number of gene variants have been associated with an increased risk of developing glioma. We hypothesized that the reported risk variants may be associated with tumor genomic instability. To explore potential correlations between germline risk variants and somatic genetic events, we analyzed matched tumor and blood samples from 95 glioma patients by means of SNP genotyping. The generated genotype data was used to calculate genome-wide allele-specific copy number profiles of the tumor samples. We compared the copy number profiles across samples and found two EGFR gene variants (rs17172430 and rs11979158) that were associated with homozygous deletion at the CDKN2A/B locus. One of the EGFR variants (rs17172430) was also associated with loss of heterozygosity at the EGFR locus. Our findings were confirmed in a separate dataset consisting of matched blood and tumor samples from 300 glioblastoma patients, compiled from publically available TCGA data. These results imply there is a functional effect of germline EGFR variants on tumor progression.
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18
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Wiencke JK, Accomando WP, Zheng S, Patoka J, Dou X, Phillips JJ, Hsuang G, Christensen BC, Houseman EA, Koestler DC, Bracci P, Wiemels JL, Wrensch M, Nelson HH, Kelsey KT. Epigenetic biomarkers of T-cells in human glioma. Epigenetics 2012; 7:1391-402. [PMID: 23108258 DOI: 10.4161/epi.22675] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Immune factors are thought to influence glioma risk and outcomes, but immune profiling studies to further our understanding of the immune response are limited by current immunodiagnostic methods. We developed a new assay to capture glioma immune biology based on quantitative methylation specific PCR (qMSP) of two T-cell genes (CD3Z: T-cells, and FOXP3: Tregs). Flow cytometry of T-cells correlated well with the CD3Z demethylation assay (r = 0.93; p < 2.2 × 10 (-16) ), demonstrating the validity of the assay. Furthermore, there was a high correlation between qMSP and immunohistochemistry (IHC) in quantifying tumor infiltrating T-cells (r = 0.85; p = 3.4 × 10 (-11) ). Applying our qMSP methods to archival whole blood from 65 glioblastoma multiforme (GBM) cases and 94 non-diseased controls, GBM cases had highly statistically significantly lower T-cells (p = 1.7 × 10 (-9) ) as well as Tregs (p = 5.2 × 10 (-11) ) and a modestly lower ratio of Tregs/T-cells (p = 0.024). Applying the methods to 120 excised glioma tumors, we observed that tumor infiltrating CD3+ T-cells were positively correlated with glioma tumor grade (p = 5.7 × 10 (-7) ), and that Tregs were enriched in tumors compared with peripheral blood indicating active chemoattraction of suppressive Tregs into the tumor compartment. Poorer patient survival was correlated with higher levels of tumor infiltrating T-cells (p = 0.01) and Tregs (p = 0.04). DNA methylation based immunodiagnostics represent a new generation of powerful laboratory tools offering many advantages over conventional methods that will facilitate large clinical epidemiologic studies and capitalize on stored archival blood and tissue banks.
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Affiliation(s)
- John K Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA USA.
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Increased microglia/macrophage gene expression in a subset of adult and pediatric astrocytomas. PLoS One 2012; 7:e43339. [PMID: 22937035 PMCID: PMC3425586 DOI: 10.1371/journal.pone.0043339] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 07/19/2012] [Indexed: 12/11/2022] Open
Abstract
Glioblastoma (GBM) is a highly malignant brain tumor with a dismal prognosis. Gene expression profiling of GBM has revealed clinically relevant tumor subtypes, and this provides exciting opportunities to better understand disease pathogenesis. Results from an increasing number of studies demonstrate a role for the immune response in cancer progression, yet it is unclear how the immune response differs across tumor subtypes and how it affects outcome. Utilizing gene expression data from The Cancer Genome Atlas Project and the Gene Expression Omnibus database, we demonstrate an enrichment of immune response-related gene expression in the mesenchymal subtype of adult GBM (n = 173) and pediatric high-grade gliomas (n = 53). In an independent cohort of pediatric astrocytomas (n = 24) from UCSF, we stratified tumors into subtypes and confirmed these findings. Using novel immune cell-specific gene signatures we demonstrate selective enrichment of microglia/macrophage-related genes in adult and pediatric GBM tumors of the mesenchymal subtype. Furthermore, immunostaining of adult GBM tumors showed significantly higher cell numbers of microglia/macrophages in mesenchymal versus non-mesenchymal tumors (p = 0.04). Interestingly, adult GBM tumors with the shortest survival had significant enrichment of microglia/macrophage-related genes but this was not true for pediatric GBMs. Consistent with an association with poor outcome, immune response-related genes were highly represented in an adult poor prognosis gene signature, with the expression of genes related to macrophage recruitment and activation being most strongly associated with survival (p<0.05) using CoxBoost multivariate modeling. Using a microglia/macrophage high gene signature derived from quantification of tumor-infiltrating cells in adult GBM, we identified enrichment of genes characteristic of CD4 T cells, granulocytes, and microglia/macrophages (n = 573). These studies support a role for the immune response, particularly the microglia/macrophage response, in the biology of an important subset of GBM. Identification of this subset may be important for future therapeutic stratification.
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Amirian ES, Scheurer ME. Chromosomally-integrated human herpesvirus 6 in familial glioma etiology. Med Hypotheses 2012; 79:193-6. [PMID: 22591997 DOI: 10.1016/j.mehy.2012.04.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 04/20/2012] [Indexed: 01/28/2023]
Abstract
Human herpesvirus 6 (HHV-6) is a highly neurotropic beta-herpesvirus with demonstrated transformative properties. HHV-6 infection has been implicated in the etiologies of cancers, including lymphoma and leukemia; conditions with brain involvement, including epilepsy and encephalitis; and other disorders. HHV-6 is also the only human herpesvirus that has been proven to integrate into the chromosomes of a proportion (1-12%) of infected individuals. Because several traditional genetic association studies have failed to identify a variant that can account for the established relationship between family history and glioma risk, the possibility that chromosomally-integrated HHV-6 (CI-HHV-6), as a heritable factor, may explain a proportion of familial glioma cases warrants evaluation. To test this hypothesis, the prevalence of CI-HHV-6 in familial glioma cases and related and unrelated cancer-free control groups should be compared. Among glioma-affected families, the inheritance pattern of CI-HHV-6 could be evaluated by constructing pedigrees. If CI-HHV-6 is found to be associated with familial glioma risk, this knowledge could potentially lead to the future development of novel therapeutic and preventive approaches, including vaccines and immunotherapies targeted at the HHV-6 sequences.
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Affiliation(s)
- E Susan Amirian
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
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21
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Recent advances in the molecular understanding of glioblastoma. J Neurooncol 2012; 108:11-27. [PMID: 22270850 PMCID: PMC3337398 DOI: 10.1007/s11060-011-0793-0] [Citation(s) in RCA: 294] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2011] [Accepted: 12/27/2011] [Indexed: 01/04/2023]
Abstract
Glioblastoma is the most common and most aggressive primary brain tumor. Despite maximum treatment, patients only have a median survival time of 15 months, because of the tumor’s resistance to current therapeutic approaches. Thus far, methylation of the O6-methylguanine-DNA methyltransferase (MGMT) promoter has been the only confirmed molecular predictive factor in glioblastoma. Novel “genome-wide” techniques have identified additional important molecular alterations as mutations in isocitrate dehydrogenase 1 (IDH1) and its prognostic importance. This review summarizes findings and techniques of genetic, epigenetic, transcriptional, and proteomic studies of glioblastoma. It provides the clinician with an up-to-date overview of current identified molecular alterations that should ultimately lead to new therapeutic targets and more individualized treatment approaches in glioblastoma.
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22
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Amlin-Van Schaick JC, Kim S, DiFabio C, Lee MH, Broman KW, Reilly KM. Arlm1 is a male-specific modifier of astrocytoma resistance on mouse Chr 12. Neuro Oncol 2012; 14:160-74. [PMID: 22234937 DOI: 10.1093/neuonc/nor206] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
While many cancers show a sex bias, the genetic basis and molecular mechanisms underlying sex bias are not always clear. Astrocytoma and glioblastoma show male predominance in humans. We have shown previously that glial tumors forming in the Nf1-/+; Trp53-/+cis (NPcis) mouse model also show a sex bias in some genetic contexts. Using cross-species comparisons we have identified candidate male-specific modifiers of astrocytoma/glioblastoma. Linkage analysis of B6X(B6X129)-NPcis mice identifies a modifier of astrocytoma resistance specific to males, named Arlm1, on distal mouse Chr 12. Arlm1 is syntenic to human Chr 7p15, 7p21, 7q36, and 14q32 regions that are altered in human glioblastoma. A subset of these genes shows male-specific correlations to glioblastoma patient survival time and represents strong candidates for the Arlm1 modifier gene. Identification of male-specific modifier genes will lead to a better understanding of the molecular basis of male predominance in astrocytoma and glioblastoma.
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Affiliation(s)
- Jessica C Amlin-Van Schaick
- Mouse Cancer Genetics Program, National Cancer Institute, West 7th St at Fort Detrick, Frederick, MD 21702, USA
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23
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Abstract
PURPOSE OF REVIEW A small percentage of gliomas are caused by inheritance in cancer syndromes but there is also a general familial aggregation of glioma. Recently, low penetrant genes associated with glioma risk have been identified. RECENT FINDINGS Seven independent chromosomal loci have robustly been associated with glioma risk: 5p15.33 (rs2736100, TERT), 8q24.21 (rs4295627, CCDC26), 9p21.3 (rs4977756, CDKN2A-CDKN2B), 20q13.33 (rs6010620, RTEL1), and 11q23.3 (rs498872, PHLDB1), and two loci at 7p11.2 (rs11979158 and rs2252586, EGFR). Several of these genes are obvious candidates in their role for chromosomal integrity and glioma progression. Moreover, all loci but the EGFR and CDKN2A genes display a pattern of association to certain glioma subtypes. SUMMARY The causes of glioma have until recently been unknown for most cases, partly due to lack of statistically powered studies enabling subclassification of glioma subtypes. The novel chromosomal loci associated with different glioma subtypes have provided us with an additional understanding of causes of glioma. All low penetrant genes contribute with a modest increased risk and cannot by themselves be used for risk prediction. Nevertheless, they could provide a tool to understand the underlying biology of glioma progression and to be used in future studies of gene-environment studies of specific glioma subtypes.
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Costa BM, Viana-Pereira M, Fernandes R, Costa S, Linhares P, Vaz R, Pinheiro C, Lima J, Soares P, Silva A, Pardal F, Amorim J, Nabiço R, Almeida R, Alegria C, Pires MM, Pinheiro C, Carvalho E, Oliveira P, Lopes JM, Reis RM. Impact of EGFR Genetic Variants on Glioma Risk and Patient Outcome. Cancer Epidemiol Biomarkers Prev 2011; 20:2610-7. [DOI: 10.1158/1055-9965.epi-11-0340] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Amirian ES, Scheurer ME, Liu Y, D'Amelio AM, Houlston RS, Etzel CJ, Shete S, Swerdlow AJ, Schoemaker MJ, McKinney PA, Fleming SJ, Muir KR, Lophatananon A, Bondy ML. A novel approach to exploring potential interactions among single-nucleotide polymorphisms of inflammation genes in gliomagenesis: an exploratory case-only study. Cancer Epidemiol Biomarkers Prev 2011; 20:1683-1689. [PMID: 21724854 DOI: 10.1158/1055-9965.epi-11-0203] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Despite extensive research on the topic, glioma etiology remains largely unknown. Exploration of potential interactions between single-nucleotide polymorphisms (SNP) of immune genes is a promising new area of glioma research. The case-only study design is a powerful and efficient design for exploring possible multiplicative interactions between factors that are independent of one another. The purpose of our study was to use this exploratory design to identify potential pair wise SNP-SNP interactions from genes involved in several different immune-related pathways for investigation in future studies. METHODS The study population consisted of two case groups: 1,224 histologic confirmed, non-Hispanic white glioma cases from the United States and a validation population of 634 glioma cases from the United Kingdom. Polytomous logistic regression, in which one SNP was coded as the outcome and the other SNP was included as the exposure, was utilized to calculate the ORs of the likelihood of cases simultaneously having the variant alleles of two different SNPs. Potential interactions were examined only between SNPs located in different genes or chromosomes. RESULTS Using this data mining strategy, we found 396 significant SNP-SNP interactions among polymorphisms of immune-related genes that were present in both the U.S. and U.K. study populations. CONCLUSION This exploratory study was conducted for the purpose of hypothesis generation, and thus has provided several new hypotheses that can be tested using traditional case-control study designs to obtain estimates of risk. IMPACT This is the first study, to our knowledge, to take this novel approach to identifying SNP-SNP interactions relevant to glioma etiology.
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Affiliation(s)
- E Susan Amirian
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael E Scheurer
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Yanhong Liu
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Anthony M D'Amelio
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Richard S Houlston
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey, UK
| | - Carol J Etzel
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Sanjay Shete
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Anthony J Swerdlow
- Section of Epidemiology, Institute of Cancer Research, Sutton, Surrey, UK
| | | | | | - Sarah J Fleming
- Centre for Epidemiology and Biostatistics, University of Leeds, Leeds, UK
| | - Kenneth R Muir
- Health Sciences Research Institute, Warwick Medical School, University of Warwick, Coventry, UK
| | - Artitaya Lophatananon
- Health Sciences Research Institute, Warwick Medical School, University of Warwick, Coventry, UK
| | - Melissa L Bondy
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
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Sanson M, Hosking FJ, Shete S, Zelenika D, Dobbins SE, Ma Y, Enciso-Mora V, Idbaih A, Delattre JY, Hoang-Xuan K, Marie Y, Boisselier B, Carpentier C, Wang XW, Di Stefano AL, Labussière M, Gousias K, Schramm J, Boland A, Lechner D, Gut I, Armstrong G, Liu Y, Yu R, Lau C, Di Bernardo MC, Robertson LB, Muir K, Hepworth S, Swerdlow A, Schoemaker MJ, Wichmann HE, Müller M, Schreiber S, Franke A, Moebus S, Eisele L, Försti A, Hemminki K, Lathrop M, Bondy M, Houlston RS, Simon M. Chromosome 7p11.2 (EGFR) variation influences glioma risk. Hum Mol Genet 2011; 20:2897-904. [PMID: 21531791 DOI: 10.1093/hmg/ddr192] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
While gliomas are the most common primary brain tumors, their etiology is largely unknown. To identify novel risk loci for glioma, we conducted genome-wide association (GWA) analysis of two case-control series from France and Germany (2269 cases and 2500 controls). Pooling these data with previously reported UK and US GWA studies provided data on 4147 glioma cases and 7435 controls genotyped for 424 460 common tagging single-nucleotide polymorphisms. Using these data, we demonstrate two statistically independent associations between glioma and rs11979158 and rs2252586, at 7p11.2 which encompasses the EGFR gene (population-corrected statistics, P(c) = 7.72 × 10(-8) and 2.09 × 10(-8), respectively). Both associations were independent of tumor subtype, and were independent of EGFR amplification, p16INK4a deletion and IDH1 mutation status in tumors; compatible with driver effects of the variants on glioma development. These findings show that variation in 7p11.2 is a determinant of inherited glioma risk.
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Affiliation(s)
- Marc Sanson
- Université Pierre et Marie Curie-Paris 6, Centre de Recherche de l’Institut du Cerveau et de la Moëlle épinière/UMR-S975, GH Pitié-Salpêtrière, 47 boulevard de l'Hôpital, Paris, France
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27
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Scheurer ME, Amirian ES, Davlin SL, Rice T, Wrensch M, Bondy ML. Effects of antihistamine and anti-inflammatory medication use on risk of specific glioma histologies. Int J Cancer 2011; 129:2290-6. [PMID: 21190193 DOI: 10.1002/ijc.25883] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 12/08/2010] [Indexed: 01/08/2023]
Abstract
Several studies have shown a decrease in glioma risk associated with a personal history of allergic conditions and the medications used to treat the symptoms. However, few studies have been able to examine risk within histological subgroups of glioma. Case-control data from M. D. Anderson Cancer Center and University of California, San Francisco were pooled to conduct the analysis stratified by histological subtype. A risk prediction model considering inflammation-related variables and antihistamine use was built using logistic regression. Of the subtypes examined, long-term antihistamine use was associated with increased risk of anaplastic gliomas, especially when length of use was considered in conjunction with history of asthma or allergy. Anaplastic cases with no history of asthma or allergy were 2.94 times more likely than controls to report antihistamine use for 10 years or more; whereas anaplastic cases with a history of asthma or allergy were 2.34 times more likely than controls to report antihistamine use for 10 years or more. Furthermore, anti-inflammatory medication use was associated with a protective effect against glioblastoma (OR = 0.80; 95% CI: 0.65, 0.99), especially among individuals with no history of asthma or allergies. No statistically significant effects of anti-inflammatory drugs or antihistamines were evident for the other histological subtypes. Thus, modulation of the immune system by the use of common drugs, such as antihistamines or nonsteroidal anti-inflammatory drugs, may contribute to the development of certain types of brain tumors.
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Affiliation(s)
- Michael E Scheurer
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.
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