[Show abstract][Hide abstract] ABSTRACT: The extent to which heritable genetic variants can affect tumor development has yet to be fully elucidated. Tumor selection of single nucleotide polymorphism (SNP) risk alleles, a phenomenon called preferential allelic imbalance (PAI), has been demonstrated in some cancer types. We developed a novel application of digital PCR termed Somatic Mutation Allelic Ratio Test using Droplet Digital PCR (SMART-ddPCR) for accurate assessment of tumor PAI, and have applied this method to test the hypothesis that heritable SNPs associated with childhood acute lymphoblastic leukemia (ALL) may demonstrate tumor PAI. These SNPs are located at CDKN2A (rs3731217) and IKZF1 (rs4132601), genes frequently lost in ALL, and at CEBPE (rs2239633), ARID5B (rs7089424), PIP4K2A (rs10764338), and GATA3 (rs3824662), genes located on chromosomes gained in high-hyperdiploid ALL. We established thresholds of AI using constitutional DNA from SNP heterozygotes, and subsequently measured allelic copy number in tumor DNA from 19-142 heterozygote samples per SNP locus. We did not find significant tumor PAI at these loci, though CDKN2A and IKZF1 SNPs showed a trend towards preferential selection of the risk allele (p = 0.17 and p = 0.23, respectively). Using a genomic copy number control ddPCR assay, we investigated somatic copy number alterations (SCNA) underlying AI at CDKN2A and IKZF1, revealing a complex range of alterations including homozygous and hemizygous deletions and copy-neutral loss of heterozygosity, with varying degrees of clonality. Copy number estimates from ddPCR showed high agreement with those from multiplex ligation-dependent probe amplification (MLPA) assays. We demonstrate that SMART-ddPCR is a highly accurate method for investigation of tumor PAI and for assessment of the somatic alterations underlying AI. Furthermore, analysis of publicly available data from The Cancer Genome Atlas identified 16 recurrent SCNA loci that contain heritable cancer risk SNPs associated with a matching tumor type, and which represent candidate PAI regions warranting further investigation.
PLoS ONE 11/2015; 10(11):e0143343. DOI:10.1371/journal.pone.0143343 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Leukemia is one of the leading journals in hematology and oncology. It is published monthly and covers all aspects of the research and treatment of leukemia and allied diseases. Studies of normal hemopoiesis are covered because of their comparative relevance.
[Show abstract][Hide abstract] ABSTRACT: Background:
The prediction of clinical behavior, response to therapy, and outcome of infiltrative glioma is challenging. On the basis of previous studies of tumor biology, we defined five glioma molecular groups with the use of three alterations: mutations in the TERT promoter, mutations in IDH, and codeletion of chromosome arms 1p and 19q (1p/19q codeletion). We tested the hypothesis that within groups based on these features, tumors would have similar clinical variables, acquired somatic alterations, and germline variants.
We scored tumors as negative or positive for each of these markers in 1087 gliomas and compared acquired alterations and patient characteristics among the five primary molecular groups. Using 11,590 controls, we assessed associations between these groups and known glioma germline variants.
Among 615 grade II or III gliomas, 29% had all three alterations (i.e., were triple-positive), 5% had TERT and IDH mutations, 45% had only IDH mutations, 7% were triple-negative, and 10% had only TERT mutations; 5% had other combinations. Among 472 grade IV gliomas, less than 1% were triple-positive, 2% had TERT and IDH mutations, 7% had only IDH mutations, 17% were triple-negative, and 74% had only TERT mutations. The mean age at diagnosis was lowest (37 years) among patients who had gliomas with only IDH mutations and was highest (59 years) among patients who had gliomas with only TERT mutations. The molecular groups were independently associated with overall survival among patients with grade II or III gliomas but not among patients with grade IV gliomas. The molecular groups were associated with specific germline variants.
Gliomas were classified into five principal groups on the basis of three tumor markers. The groups had different ages at onset, overall survival, and associations with germline variants, which implies that they are characterized by distinct mechanisms of pathogenesis. (Funded by the National Institutes of Health and others.).
New England Journal of Medicine 06/2015; 372(26). DOI:10.1056/NEJMoa1407279 · 55.87 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Reactivation of telomerase reverse transcriptase (TERT) expression enables cells to overcome replicative senescence and escape apoptosis, which are fundamental steps in the initiation
of human cancer. Multiple cancer types, including up to 83% of glioblastomas (GBMs), harbor highly recurrent TERT promoter mutations of unknown function but specific to two nucleotide positions. We identified the functional consequence
of these mutations in GBMs to be recruitment of the multimeric GA-binding protein (GABP) transcription factor specifically
to the mutant promoter. Allelic recruitment of GABP is consistently observed across four cancer types, highlighting a shared
mechanism underlying TERT reactivation. Tandem flanking native E26 transformation-specific motifs critically cooperate with these mutations to activate
TERT, probably by facilitating GABP heterotetramer binding. GABP thus directly links TERT promoter mutations to aberrant expression in multiple cancers.
[Show abstract][Hide abstract] ABSTRACT: Lower-grade (World Health Organization Grades II and III) gliomas vary widely in clinical behavior and are classified as astrocytic, oligodendroglial, or mixed. Anaplasia depends greatly on mitotic activity, with CDKN2A loss considered as the most common mechanism for cell cycle dysregulation. We investigated whether loss of the CDKN2A gene is associated with overall survival across pathologically and genetically defined glioma subtypes. After adjustment for IDH mutation, sex, and age, CDKN2A deletion was strongly associated with poorer overall survival in astrocytomas but not in oligodendrogliomas or oligoastrocytomas. Molecular classification of astrocytomas by IDH mutation, TP53 mutation, and /or ATRX loss of expression revealed that CDKN2A loss in IDH/TP53 mutated tumors was strongly associated with worse overall survival. CDKN2A loss in IDH mutated tumors with ATRX loss was only weakly associated with worse overall survival. These findings suggest that CDKN2A testing may provide further clinical aid in lower-grade glioma substratification beyond IDH mutation and 1p19q codeletion status, particularly in IDH/TP53 mutated astrocytomas.
[Show abstract][Hide abstract] ABSTRACT: Genome-wide association studies focusing on European-ancestry populations have identified ALL risk loci on IKZF1, ARID5B, and CEBPE. To capture the impacts of these genes on ALL risk in the California Hispanic population, we comprehensively assessed the variation within the genes and further assessed the joint effects between the genetic variation and surrogates for early-life infections (the presence of older siblings, daycare attendance, and ear infections).
Genotypic data for 323 Hispanic ALL cases and 454 controls from the California Childhood Leukemia Study were generated using Illumina OmniExpress v1 platform. Logistic regression assuming a log-additive model estimated odds ratios (OR) associated with each SNP, adjusted for age, sex, and the first five principal components. In addition, we examined potential interactions between six ALL risk alleles and surrogates for early-life infections using logistic regression models that included an interaction term.
Significant associations between genotypes at IKZF1, ARID5B, and CEBPE and ALL risk were identified: rs7780012, OR 0.50, 95 % confidence interval (CI) 0.35-0.71 (p = 0.004); rs7089424, OR 2.12, 95 % CI 1.70-2.65 (p = 1.16 × 10(-9)); rs4982731, OR 1.69, 95 % CI 1.37-2.08 (p = 2.35 × 10(-6)), respectively. Evidence for multiplicative interactions between genetic variants and surrogates for early-life infections with ALL risk was not observed.
Consistent with findings in non-Hispanic White population, our study showed that variants within IKZF1, ARID5B, and CEBPE were associated with increased ALL risk, and the effects for ARID5B and CEBPE were most prominent in the high-hyperdiploid ALL subtype in the California Hispanic population. Results implicate the ARID5B, CEBPE, and IKZF1 genes in the pathogenesis of childhood ALL.
Cancer Causes and Control 03/2015; 26(4). DOI:10.1007/s10552-015-0550-3 · 2.74 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Significant gaps exist in our understanding of the causes and clinical management of glioma. One of the biggest gaps is how best to manage low-grade (World Health Organization [WHO] Grade II) glioma. Low-grade glioma (LGG) is a uniformly fatal disease of young adults (mean age 41 years), with survival averaging approximately 7 years. Although LGG patients have better survival than patients with high-grade (WHO Grade III or IV) glioma, all LGGs eventually progress to high-grade glioma and death. Data from the Surveillance, Epidemiology and End Results (SEER) program of the National Cancer Institute suggest that for the majority of LGG patients, overall survival has not significantly improved over the past 3 decades, highlighting the need for intensified study of this tumor. Recently published research suggests that historically used clinical variables are not sufficient (and are likely inferior) prognostic and predictive indicators relative to information provided by recently discovered tumor markers (e.g., 1p/19q deletion and IDH1 or IDH2 mutation status), tumor expression profiles (e.g., the proneural profile) and/or constitutive genotype (e.g., rs55705857 on 8q24.21). Discovery of such tumor and constitutive variation may identify variables needed to improve randomization in clinical trials as well as identify patients more sensitive to current treatments and targets for improved treatment in the future. This article reports on survival trends for patients diagnosed with LGG within the United States from 1973 through 2011 and reviews the emerging role of tumor and constitutive genetics in refining risk stratification, defining targeted therapy, and improving survival for this group of relatively young patients.
[Show abstract][Hide abstract] ABSTRACT: The majority of gliomas are sporadic in origin. Familial gliomas have been reported, though they are exceptionally rare. Several familial cancer syndromes are associated with autosomal dominant glioma risk, typically with incomplete penetrance. When two siblings are affected in the absence of a known dominantly inherited cancer syndrome, an autosomal recessive condition may be suspected (e.g. constitutional mismatch repair syndrome). We present two separate sets of siblings, one set with low grade gliomas, and the other with high grade gliomas. Histology for all tumors were either oligodendroglioma or had features of oligodendroglioma. Interestingly, there is a nearly identical histopathology and anatomical localization noted in these clinical presentations. For one family, genetic testing and family inquiry have resulted in no identifiable genetic pattern of disease. High-penetrance familial mutations and common low-penetrance susceptibility loci (e.g. single-nucleotide polymorphism (SNPs)) may contribute to familial glioma risk. We present two instances of familial glioma without an identifiable genetic cause. These cases implicate a potential heritable etiology for glioma families in which Mendelian disorders have not been identified. Further investigation should focus on identifying the potential genetic links involved with cases such as the ones presented here.
Journal of Neuro-Oncology 09/2014; 121(1). DOI:10.1007/s11060-014-1611-2 · 3.07 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Glioblastoma, the most common and aggressive form of glioma, has a median survival time of just 15 months. Both inherited and acquired genetic variation influence gliomagenesis. Previous genome-wide association studies (GWAS) have discovered seven glioma risk loci, including two in genes involved in telomere structure and function (TERT and RTEL1).
[Show abstract][Hide abstract] ABSTRACT: Meningiomas represent the most frequently diagnosed primary brain tumor in the United States accounting for approximately one third of such tumors in adults. To date the sole consistently identified risk factor remains exposure to ionizing radiation with risks from 6-10 fold reported. Persons diagnosed with meningioma after exposure to therapeutic ionizing radiation likely represent a genetically-sensitive subpopulation of patients. Currently, radiation-associated meningiomas (RAM) are the most common form of radiation-induced neoplasm yet no sequencing data exist for this class of tumor.
[Show abstract][Hide abstract] ABSTRACT: In 2012, using a genome-wide association study (GWAS) of UCSF Adult Glioma Study patients and replication in patients from the Mayo Clinic, TCGA and GliomaSE, we showed that a SNP in SSBP2 on chromosome 5 was associated with survival of glioblastoma (GBM) patients who received standard of care (SOC). Since then we have examined 41 SNPs that were potentially associated with survival after glioma diagnosis based on our preliminary results or published results of others.