Copy Number Polymorphisms Research Articles

Determinants of expression variability

The amount of tissue-specific expression variability (EV) across individuals is an essential characteristic of a gene and believed to have evolved, in part, under functional constraints. However, the determinants and functional implications of EV are only beginning to be investigated. Our analyses based on multiple expression profiles in 41 primary human tissues show that a gene’s EV is significantly correlated with a number of features pertaining to the genomic, epigenomic, regulatory, polymorphic, functional, structural and network characteristics of the gene. We found that (i) EV of a gene is encoded, in part, by its genomic context and is further influenced by the epigenome; (ii) strong promoters induce less variable expression; (iii) less variable gene loci evolve under purifying selection against copy number polymorphisms; (iv) genes that encode inherently disordered or highly interacting proteins exhibit lower variability; and (v) genes with less variable expression are enriched for house-keeping functions, while genes with highly variable expression tend to function in development and extra-cellular response and are associated with human diseases. Thus, our analysis reveals a number of potential mediators as well as functional and evolutionary correlates of EV, and provides new insights into the inherent variability in eukaryotic gene expression.

GABAA Receptor Genetics and Clinical Pharmacology

GABAA receptors (GABAARs) are Cl−-selective ligand-gated ion channels that mediate both fast synaptic inhibition and persistent tonic inhibition in the CNS. The receptor is composed of subunits that affect biophysical and pharmacological properties of the channel. A growing number of studies have examined copy number variations, mutations, and polymorphisms in genes encoding GABAAR subunits and found that changes in subunit function and expression are linked to a variety of neurological disorders. GABAARs are targets for a wide range of pharmaceutical agents including benzodiazepines, barbiturates, general anesthetics, and neurosteroids. It remains to be fully determined how genetic variations in GABAA subunits affect clinical pharmacology. Conversely, there is growing interest in the use of GABAergic drugs to treat disorders with an etiology arising from genetic variations in GABAA subunits.

Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations.

BackgroundHyperuricemia is associated with multiple diseases, including gout, cardiovascular disease, and renal disease. Serum urate is highly heritable, yet association studies of single nucleotide polymorphisms (SNPs) and serum uric acid explain a small fraction of the heritability. Whether copy number polymorphisms (CNPs) contribute to uric acid levels is unknown.ResultsWe assessed copy number on a genome-wide scale among 8,411 individuals of European ancestry (EA) who participated in the Atherosclerosis Risk in Communities (ARIC) study. CNPs upstream of the urate transporter SLC2A9 on chromosome 4p16.1 are associated with uric acid (, p=3.19×10-23). Effect sizes, expressed as the percentage change in uric acid per deleted copy, are most pronounced among women (3.974.935.87 [ 2.55097.5 denoting percentiles], p=4.57×10-23) and independent of previously reported SNPs in SLC2A9 as assessed by SNP and CNP regression models and the phasing SNP and CNP haplotypes (). Our finding is replicated in the Framingham Heart Study (FHS), where the effect size estimated from 4,089 women is comparable to ARIC in direction and magnitude (1.414.707.88, p=5.46×10-03).ConclusionsThis is the first study to characterize CNPs in ARIC and the first genome-wide analysis of CNPs and uric acid. Our findings suggests a novel, non-coding regulatory mechanism for SLC2A9-mediated modulation of serum uric acid, and detail a bioinformatic approach for assessing the contribution of CNPs to heritable traits in large population-based studies where technical sources of variation are substantial.

Insertion-deletions burden in copy number polymorphisms of the Tibetan population.

BACKGROUND:Many studies have been conducted to identify either insertions-deletions (inDels) or copy number variations (CNVs) in humans, but few studies have been conducted to identify both of these forms coexisting in the same region.AIMS AND OBJECTIVES:To map the functionally significant sites within human genes that are likely to influence human traits and diseases.MATERIALS AND METHODS:In this report, we describe an inDel map in the 1051 Tibetan CNV regions obtained through CNV genotyping using Affymetrix Genome-wide single nucleotide polymorphism 6.0 chip. InDel polymorphisms in these copy number polymorphism regions were identified with a computational approach using the 2500 deoxyribonucleic acid sequences obtained from the 1000 Genome Project.RESULTS:The study identified a total of 95935 inDels that range from 1 bp to several bps in length which were found scattered across regulatory regions, exons and in introns of genes underlying the CNVs. A study on the distribution of inDels revealed that the majority of inDels were found in coding regions of the genome than the noncoding, while within the genes, inDels in intron regions were more followed by exonic regions and finally the regulatory regions.CONCLUSION:Study of inDels in CNV regions contribute to the enhanced understanding of the role played by the two variations and their collective influence on the genome. Further, a collection of these inDel genetic markers will aid in genetic mapping, further understanding of the phenotypic variability, identification of disease genes and in detecting novel CNVs.

Identification of ethnically specific genetic variations in pan-asian ethnos.

Asian populations contain a variety of ethnic groups that have ethnically specific genetic differences. Ethnic variants may be highly relevant in disease and human differentiation studies. Here, we identified ethnically specific variants and then investigated their distribution across Asian ethnic groups. We obtained 58,960 Pan-Asian single nucleotide polymorphisms of 1,953 individuals from 72 ethnic groups of 11 Asian countries. We selected 9,306 ethnic variant single nucleotide polymorphisms (ESNPs) and 5,167 ethnic variant copy number polymorphisms (ECNPs) using the nearest shrunken centroid method. We analyzed ESNPs and ECNPs in 3 hierarchical levels: superpopulation, subpopulation, and ethnic population. We also identified ESNP- and ECNP-related genes and their features. This study represents the first attempt to identify Asian ESNP and ECNP markers, which can be used to identify genetic differences and predict disease susceptibility and drug effectiveness in Asian ethnic populations.

Validation for Clinical Use of, and Initial Clinical Experience with, a Novel Approach to Population-Based Carrier Screening using High-Throughput, Next-Generation DNA Sequencing

Traditional carrier screening assays are designed to look for only the most common mutations within a gene owing to cost considerations. Although this can yield high detection rates in specific populations for specific genes (such as cystic fibrosis in Caucasians), they are suboptimal for other ethnicities or for patients of mixed or unknown ethnic background. Next-generation DNA sequencing provides an opportunity to provide carrier screening using more comprehensive mutation panels that are limited primarily by information about the clinical impact of detected sequence changes. We describe a next-generation DNA sequencing-based assay capable of reliably screening patient samples in a timely and comprehensive manner. The analytic accuracy in a research setting has been documented. Here, we describe the additional studies performed to ensure the accuracy (analytic validity) and robustness of our assay for use in clinical practice and provide data from our experience offering this testing. Our clinical experience using this approach to screen 11,691 invitro fertilization patients has identified 449 mutant alleles: 447 in carriers and 2 in an affected individual. In total, we found 87 distinct mutations in 14 different genes. Approximately one quarter of the mutations found are not included in traditional, limited, mutation panels, including 16 known mutations unique to our panel, and novel truncating mutations in several genes.

Short Copy Number Variations Potentially Associated with Tonic Immobility Responses in Newly Hatched Chicks

IntroductionTonic immobility (TI) is fear-induced freezing that animals may undergo when confronted by a threat. It is principally observed in prey species as defence mechanisms. In our preliminary research, we detected large inter-individual variations in the frequency and duration of freezing behavior among newly hatched domestic chicks (Gallus gallus). In this study we aim to identify the copy number variations (CNVs) in the genome of chicks as genetic candidates that underlie the behavioral plasticity to fearful stimuli.MethodsA total of 110 domestic chicks were used for an association study between TI responses and copy number polymorphisms. Array comparative genomic hybridization (aCGH) was conducted between chicks with high and low TI scores using an Agilent 4×180 custom microarray. We specifically focused on 3 genomic regions (>60 Mb) of chromosome 1 where previous quantitative trait loci (QTL) analysis showed significant F-values for fearful responses.ResultsACGH successfully detected short CNVs within the regions overlapping 3 QTL peaks. Eleven of these identified loci were validated by real-time quantitative polymerase chain reaction (qPCR) as copy number polymorphisms. Although there wkas no significant p value in the correlation analysis between TI scores and the relative copy number within each breed, several CNV loci showed significant differences in the relative copy number between 2 breeds of chicken (White Leghorn and Nagoya) which had different quantitative characteristics of fear-induced responses.ConclusionOur data shows the potential CNVs that may be responsible for innate fear response in domestic chicks.

In Adult Philadelphia Chromosome Positive Acute Lymphoblastic Leukemia, The Negative Prognostic Impact Of IKZF1, CDKN2A/B and PAX5 Deletions Is Not Abrogated By Allogeneic Stem Cell Transplantation In First Complete Remission

Philadelphia chromosome positive (Ph+) acute lymphoblastic leukemia (ALL) is traditionally considered the subtype with the worst prognosis, despite recent improvements in long-term survival brought about by the use of tyrosine kinase inhibitors (TKI) such as imatinib or dasatinib. Allogeneic stem cell transplantation (aSCT) remains the most effective curative post-remission therapy in adults but appears to be less critical in children, indicating a substantial clinical and biological heterogeneity within the subgroup of Ph+ ALL. The ability to segregate Ph+ ALL into subgroups with different prognosis on the basis of reductions of BCR-ABL1 transcript levels during therapy lends further support to the heterogeneity of this type of leukemia, for which the genetic basis is not known. Microarray-based genome-wide profiling studies conducted predominantly in pediatric ALL patients have recently revealed novel recurrent submicroscopic aberrations of genes involved in B-cell development and cell cycle regulation, such as CDKN2A/B, IKZF1, PAX5, ETV6, RB1, BTG1 and EBF1. Deletions of IKZF1, CDKN2A/B and PAX genes have received the most attention due to their high frequency particularly in BCR-ABL1-positive ALL and their association with an inferior prognosis in the setting of combined TKI and chemotherapy. Their prognostic relevance in the setting of allogeneic SCT for adult or pediatric high risk BCP-ALL is not known. We therefore examined whether the negative prognostic role of IKZF1 aberrations and other frequent microdeletions of genes associated with B-cell development can be overcome by allogeneic SCT in CR1.A total of 137 newly diagnosed Ph+ ALL pts. (median age 42 years, range 18-64y, 79 male 58 female) treated within the prospective multicenter GMALL study 07/03 were analyzed. 96 of these patients underwent aSCT in first complete remission (CR), 8 pts. were primary refractory, 12 CR pts. did not undergo aSCT and relapsed, 11 pts. died during induction. Genome-wide copy number analysis in search for acquired copy number alterations (CNA) was performed with Affymetrix SNP 6.0 arrays with anonymous references. Copy number polymorphisms were excluded from the data by comparison with known copy number polymorphisms registered in the UCSC genome browser http://genome.ucsc.edu/, (hg-18). Putatively acquired CNAs were validated by multiplex ligation-dependent probe amplification (MLPA) and germline matched SNP array analysis of n=20 samples within the study.Of the 96 pts. transplanted in CR1, 48 remain in CR (CCR), 30 pts. relapsed after aSCT and 7 died of treatment related causes, survival data only are available for one patient. CDKN2A/B genomic alterations were identified in 41% (40/97) of patients, deletions of IKZF1 and PAX5 were observed in 61% (59/97) and 39% (38/97) of pts., respectively.Univariate analysis of the complete cohort revealed that deletion of CDKN2A/B was the only aberration with a statistically significant negative effect on overall survival (OS) (p=0.003). Among patients transplanted in CR1, IKZF1-deletions were associated with inferior median time to relapse after SCT (56 mos vs. n.r., p=0.01), DFS from SCT (15.6 mos. vs. n.r.; p=0.024) and OS (median 40 mos. vs. not reached (n.r.) p=0.04) compared with the IKZF1 wildtype cohort. Similarly, the prognosis of pts. with CDKN2A/B deletions was inferior in terms of DFS (median 10.6 mos. vs. n.r.; p=0.022) and OS (median 25 mos. vs. n.r.; p=0.01), but not of remission duration from SCT. PAX5 (p=0.07) but not the combination of all three lesions (p=0.14) showed a trend to a worse prognosis. Of the more uncommon genetic aberrations BTLA, EBF1, ETV6, RB1 and BTG1, only the latter was associated with a lower probability of remaining in CR (0% vs. 67% at 5 years; p=0.012) or DFS (0% vs. 52% at 5 years; p=0.043), with a trend towards shorter OS (median 35 mos. vs. 87 mos; p=0.078).In conclusion, genomic lesions of IKZF1, CDKN2 and PAX5 identify a subgroup of Ph+ ALL pts. who have an inferior survival despite undergoing aSCT in CR1. Their poor outcome is attributable primarily to a high relapse rate after SCT, emphasizing the need to introduce additional treatment elements prior to and after aSCT. Disclosures:No relevant conflicts of interest to declare.

Prognostic value of mitochondrial DNA content and G10398A polymorphism in non-small cell lung cancer

Non-small cell lung cancer (NSCLC) is one of the leading causes of cancer-related mortality worldwide. Mitochondrial dysfunction has been postulated to render cancer cells resistant to apoptosis based on the Warburg hypothesis. However, few studies have investigated the prognostic value of mitochondrial DNA (mtDNA) content and G10398A polymorphism in NSCLC patients. mtDNA copy number and G10398A polymorphism in 128 NSCLC tissue samples were assessed by real-time PCR (RT-PCR) and PCR-RFLP respectively, and their relationship to prognosis were analyzed by survival analysis and Cox proportional hazards model. In vitro, an mtDNA deletion A549 ρ(0) cell model was utilized to assess the function of mtDNA on radiosensitivity. Cell cycle distribution and reactive oxygen species (ROS) were analyzed to elucidate the potential mechanisms. For the whole group, the median follow-up time and overall survival time were 22.5 and 23.4 months, respectively. Patients with high mtDNA content had a marginally longer survival time than patients with low mtDNA content (P=0.053). Moreover, patients with high mtDNA content plus 10398G had a significantly longer overall survival time compared with those having low mtDNA content plus 10398A (47 vs. 27 months, P<0.05). In addition, multivariate analysis showed that stage and low mtDNA content plus 10398A were the two most independent prognostic factors. In vitro, the A549 ρ(0) cells showed more resistance to radiation than ρ(+) cells. Following radiation, ρ(0) cells showed delayed G2 arrest and lower ROS level as compared to ρ(+) cells. In conclusion, the present study suggests that in patients with NSCLC, low mtDNA content plus 10398A could be a marker of poor prognosis which is associated with resistance to anticancer treatment caused by low mtDNA content plus 10398A polymorphism resulting in mitochondrial dysfunction.

Acetylcholine-metabolizing butyrylcholinesterase (BCHE) copy number and single nucleotide polymorphisms and their role in attention-deficit/hyperactivity syndrome

A previous genome-wide screen for copy number variations (CNVs) in attention deficit/hyperactivity disorder (ADHD) revealed a de novo chromosome 3q26.1 deletion in one of the patients. Candidate genes at this locus include the acetylcholine-metabolizing butyrylcholinesterase (BCHE) expressing gene (OMIM #177400), which is of particular interest. The present study investigates the hypothesis that the heterozygous deletion of the BCHE gene is associated with adult ADHD (aADHD). Ina first step, we screened 348 aADHD patients and 352 controls for stretches of loss of heterozygosity (LOH) across the entire BCHE gene to screen for the deletion. Our second aim was to clarify whether BCHE single nucleotide polymorphisms (SNPs) themselves influence the risk towards ADHD. Putative functional consequences of associated SNPs as well as their un-typed proxies were predicted by several bioinformatic tools. 96 individuals displayed entirely homozygous genotype reads in all 12examined SNPs, making them possible candidates to harbor a heterozygous BCHE deletion. DNA from these 96 probands was further analyzed by real-time PCR using a BCHE-specific CNV assay. However, no deletion was found. Of the 12 tag SNPs that passed inclusion criteria, rs4680612 and rs829508were significantly associated with aADHD, as their minor alleles occurred more often in cases than in controls (p = 0.018 and p = 0.039, respectively). The risk variant rs4680612 is located in the transcriptional control region of the gene and predicted to disrupt a binding site for MYT-1, which has previously been associated with mental disorders. However, when examining a second independent adult ADHD sample of 353 cases, the association did not replicate. When looking up the deletion in three genome-wide screens for CNV in ADHD and combining it with the present study, it became apparent that 3 from a total of 1030 ADHD patients, but none of 5787 controls, featured a deletion of the BCHE promoter region including rs4680612 (p = 0.00004). Taken together, there are several lines of evidence suggesting a potential involvement of BCHE in the etiopathology of ADHD, as a rare hemizygous deletion as well as a common SNP in the same region are associated with disease, although with different penetrance. Both variations result in the disruption of the binding site of the transcription factor MYT-1 suggesting epistatic effects of BCHE and MYT-1 in the pathogenesis of ADHD. As we were not able to replicate the SNP association, our findings should be considered preliminary and call for larger studies in extended phenotypes.

Copy number polymorphism in plant genomes

Copy number variants (CNVs) are genomic rearrangements resulting from gains or losses of DNA segments. Typically, the term refers to rearrangements of sequences larger than 1 kb. This type of polymorphism has recently been shown to be a key contributor to intra-species genetic variation, along with single-nucleotide polymorphisms and short insertion-deletion polymorphisms. Over the last decade, a growing number of studies have highlighted the importance of copy number variation (CNV) as a factor affecting human phenotype and individual CNVs have been linked to risks for severe diseases. In plants, the exploration of the extent and role of CNV is still just beginning. Initial genomic analyses indicate that CNVs are prevalent in plants and have greatly affected plant genome evolution. Many CNV events have been observed in outcrossing and autogamous species. CNVs are usually found on all chromosomes, with CNV hotspots interspersed with regions of very low genetic variation. Although CNV is mainly associated with intergenic regions, many CNVs encompass protein-coding genes. The collected data suggest that CNV mainly affects the members of large families of functionally redundant genes. Thus, the effects of individual CNV events on phenotype are usually modest. Nevertheless, there are many cases in which CNVs for specific genes have been linked to important traits such as flowering time, plant height and resistance to biotic and abiotic stress. Recent reports suggest that CNVs may form rapidly in response to stress.

MHC class IIB exon 2 polymorphism in the Grey partridge (Perdix perdix) is shaped by selection, recombination and gene conversion.

Among bird species, the most studied major histocompatibility complex (MHC) is the chicken MHC. Although the number of studies on MHC in free-ranging species is increasing, the knowledge on MHC variation in species closely related to chicken is required to understand the peculiarities of bird MHC evolution. Here we describe the variation of MHC class IIB (MHCIIB) exon 2 in a population of the Grey partridge (Perdix perdix), a species of high conservation concern throughout Europe and an emerging galliform model in studies of sexual selection. We found 12 alleles in 108 individuals, but in comparison to other birds surprisingly many sites show signatures of historical positive selection. Individuals displayed between two to four alleles both on genomic and complementary DNA, suggesting the presence of two functional MHCIIB loci. Recombination and gene conversion appear to be involved in generating MHCIIB diversity in the Grey partridge; two recombination breakpoints and several gene conversion events were detected. In phylogenetic analysis of galliform MHCIIB, the Grey partridge alleles do not cluster together, but are scattered through the tree instead. Thus, our results indicate that the Grey partridge MHCIIB is comparable to most other galliforms in terms of copy number and population polymorphism.

AB0006 CNStream2: a powerful tool for the study of the genetic basis of rheumatic diseases

BackgroundIn the last years, high throughput genotyping techniques have widely used for the characterization of new genetic variants associated with rheumatic diseases. Amongst these, Illumina Beadchip microarrays have been widely...

Determining the Population Frequency of the CFHR3/CFHR1 Deletion at 1q32

In this study we have used multiplex ligation-dependent probe amplification (MLPA) to measure the copy number of CFHR3 and CFHR1 in DNA samples from 238 individuals from the UK and 439 individuals from the HGDP-CEPH Human Genome Diversity Cell Line Panel. We have then calculated the allele frequency and frequency of homozygosity for the copy number polymorphism represented by the CFHR3/CFHR1 deletion. There was a highly significant difference between geographical locations in both the allele frequency (X2 = 127.7, DF = 11, P-value = 4.97x10-22) and frequency of homozygosity (X2 = 142.3, DF = 22, P-value = 1.33x10-19). The highest frequency for the deleted allele (54.7%) was seen in DNA samples from Nigeria and the lowest (0%) in samples from South America and Japan. The observed frequencies in conjunction with the known association of the deletion with AMD, SLE and IgA nephropathy is in keeping with differences in the prevalence of these diseases in African and European Americans. This emphasises the importance of identifying copy number polymorphism in disease.

Widespread Divergence of the CEACAM/PSG Genes in Vertebrates and Humans Suggests Sensitivity to Selection

In mammals, carcinoembryonic antigen cell adhesion molecules (CEACAMs) and pregnancy-specific glycoproteins (PSGs) play important roles in the regulation of pathogen transmission, tumorigenesis, insulin signaling turnover, and fetal–maternal interactions. However, how these genes evolved and to what extent they diverged in humans remain to be investigated specifically. Based on syntenic mapping of chordate genomes, we reveal that diverging homologs with a prototypic CEACAM architecture–including an extracellular domain with immunoglobulin variable and constant domain-like regions, and an intracellular domain containing ITAM motif–are present from cartilaginous fish to humans, but are absent in sea lamprey, cephalochordate or urochordate. Interestingly, the CEACAM/PSG gene inventory underwent radical divergence in various vertebrate lineages: from zero in avian species to dozens in therian mammals. In addition, analyses of genetic variations in human populations showed the presence of various types of copy number variations (CNVs) at the CEACAM/PSG locus. These copy number polymorphisms have 3–80% frequency in select populations, and encompass single to more than six PSG genes. Furthermore, we found that CEACAM/PSG genes contain a significantly higher density of nonsynonymous single nucleotide polymorphism (SNP) compared to the chromosome average, and many CEACAM/PSG SNPs exhibit high population differentiation. Taken together, our study suggested that CEACAM/PSG genes have had a more dynamic evolutionary history in vertebrates than previously thought. Given that CEACAM/PSGs play important roles in maternal–fetal interaction and pathogen recognition, these data have laid the groundwork for future analysis of adaptive CEACAM/PSG genotype-phenotypic relationships in normal and complicated pregnancies as well as other etiologies.

Abstract 3171: Analysis of copy number and LOH in germline samples from different tumor types in The Cancer Genome Atlas (TCGA) project.

Abstract Using data from The Cancer Genome Atlas (TCGA) project and HapMap consortium, we examined the hypothesis that existing copy number polymorphisms might predispose individuals to cancer and if different common CNVs bias toward different cancer types. This analysis was performed using a subset of the TCGA data, obtained from blood derived “normal” samples of cancer patients. All the data was generated using Affymetrix SNP 6.0 arrays (Affymetrix, Inc.) and processed using Nexus Copy Number ver. 6.1 (BioDiscovery, Inc.). The project contained 451 Glioblastoma (GBM), 353 Colon cancer, and 245 Skin cancer samples in addition to 211 HapMap samples which we used as reference since these individuals were supposed to be healthy. Using Fisher's Exact test, we compared each different cancer types to the HapMap samples to identify regions of copy number change with FDR corrected p-value of less than 0.05 and difference in frequency between each population of at least 10%. Many of the regions found in this process encompass regions identified as common CNV polymorphisms as reported in the Database of Genomic Variance (DGV). For example, a polymorphic region on 8p23.1 containing a number of genes from the Beta defensin family involved in defense response to bacterium were seen significantly gained in germline samples obtained from cancer patients as compared to the HapMap samples (11% in HapMap, 42% in Colon Cancer, 28% in GBM, and 32% in Skin cancer). Additionally, some interesting regions were identified that were not seen as polymorphic in the general population, did not show up in the HapMap samples or reported in DGV, but had high prevalence in the blood derived normal samples from cancer patients. Using gene enrichment analysis on genes discovered in these regions we identified a number of known cancer specific pathways that were highly enriched (e.g. KEGG Glioma and Melanoma pathways being statistically significantly enriched). Looking at the effected genes in these pathways we identified small focal and recurrent events that often only spanned a small portion of a gene covering a few exons. This included genes such as PIK3CA where a focal gain covering exons 10-14 were observed in none of the HapMap samples but in 21% of the germline of patients with Colon cancer, 9% of GBM and 14% of Skin cancer patients. A similar focal and recurrent gain was observed in KIT covering exons 2-7 with no gains in the HapMap samples and 55% in Colon, 15% in GBM, and 50% in Skin cancer patients. Similar observations were also made for other well-known cancer genes such as RAF1 and EGFR but to a lesser extent. We are in a process of comparing matched tumor/normal cases to further investigate possible evolution of these changes from the germline to the surrounding tissue (also available from the TCGA database) to the primary tumor samples. Citation Format: Soheil Shams, Raja Keshavan, Joshua D. Schiffman. Analysis of copy number and LOH in germline samples from different tumor types in The Cancer Genome Atlas (TCGA) project. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3171. doi:10.1158/1538-7445.AM2013-3171

Epstein–Barr virus latent membrane protein 1 increases genomic instability through Egr-1-mediated up-regulation of activation-induced cytidine deaminase in B-cell lymphoma

Epstein–Barr virus (EBV)-encoded latent membrane protein-1 (LMP1) is a transmembrane protein essential for EBV-induced immortalization and transformation of B cells. Activation-induced cytidine deaminase (AID) triggers somatic hypermutation and recombination, in turn contributing to lymphomagenesis. Here, we report an intracellular mechanism by which LMP1 contributes to B cell lymphomagenesis via AID expression. In our experiments, LMP1 increased AID mRNA expression and promoter activity. The AID promoter region contains a binding site for Egr-1, a prominent transcription factor that is reported to be up-regulated by LMP1. In promoter activity analysis, Egr-1 enhanced the reporter activity of the wild-type AID promoter, but not that containing a mutated Egr-1 binding site. Egr-1 knockdown abrogated LMP-1-mediated up-regulation of AID promoter reporter activity in EBV-negative BJAB cells and reduced AID promoter reporter activity in EBV-positive SKW6.4 cells. AID induced down-regulation of the nuclear factor-κB (NFκB) inhibitory tumor suppressor Rassf6, suggesting that AID functions as an upstream regulator of the NFκB inhibitory Rassf6. Moreover, Egr-1 expression was associated with an increased number of genomic lesions in genome-wide analysis using single nucleotide polymorphism (SNP) microarray and copy number variation (CNV). Collectively, LMP1 induces AID up-regulation and genomic instability via Egr-1. Increased AID expression may, in turn, promote down-regulation of the NFκB inhibitor, Rassf6, thereby further increasing the survival of genetically destabilized B-cell lymphoma cells.

Acetylcholinesterase of Rhipicephalus (Boophilus) microplus and Phlebotomus papatasi: Gene identification, expression, and biochemical properties of recombinant proteins

The southern cattle tick Rhipicephalus (Boophilus) microplus (Bm) is a vector of bovine babesiosis and anaplasmosis. Tick resistance to organophosphate (OP) acaricide involves acetylcholinesterase (AChE) insensitivity to OP and metabolic detoxification. Sequencing and in vitro expression of Bm genes encoding AChE allowed biochemical characterization of three BmAChEs expressed in tick synganglion. rBmAChE1, rBmAChE2 and rBmAChE3 exhibited substrate preference for acetylthiocholine, high substrate inhibition and sensitivity to AChE-specific inhibitors. OP-insensitivity mutations were demonstrated in rBmAChE1 and rBmAChE3. Gene silencing suggested functional complementation of BmAChEs in vivo. BmAChE genes were amplified in copy number and multiple transcript polymorphisms were expressed in individual tick synganglia for each of the BmAChEs, suggesting allelic diversity within individuals. Studies also identified a gene encoding AChE of the sand fly, Phlebotomus papatasi, a vector of leishmaniasis in humans and animals. Expression of recombinant P. papatasi AChE (rPpAChE) enabled biochemical characterization and identification of effective inhibitors that selectively target rPpAChE.

A novel FCGR3A intragenic haplotype is associated with increased FcγRIIIa/CD16a cell surface density and population differences

FcγRIIIa (CD16a) cell surface density affects immune complex binding and initiation of effector mechanisms. Investigations into the clinical relevance of variable FcγRIIIa surface density require baseline data from healthy individuals. In this study, proportions of FcγRIIIa-positive leukocyte subsets and corresponding FcγRIIIa cell surface densities were determined in whole blood from 53 healthy individuals (22 Black individuals, 31 Caucasians). Compared to Caucasians, Black individuals had significantly lower proportions of FcγRIIIa-positive natural killer (NK) cells (95.2% vs. 96.9%) and CD8(+) T lymphocytes (9.6% vs. 11.7%), whereas the opposite was true for monocytes (24.2% vs. 16.3%). However, Black individuals had significantly lower FcγRIIIa surface densities on monocytes and NK cells compared to Caucasians (P<0.001). We investigated FCGR3A gene copy number and novel polymorphisms, obtained from full gene sequencing, in relation to FcγRIIIa expression levels on NK cells. The broad range of FcγRIIIa surface densities was not attributed to variable FCGR3A gene copy number (all individuals had 2 gene copies except for 2/53 (3.8%) with one extra copy). However, a novel 3-SNP/1-indel FCGR3A intragenic haplotype may account for the significantly increased FcγRIIIa surface densities (P<0.0001) and may explain the population differences. This genetic determinant may serve as predictive marker for a high-expressing FcγRIIIa phenotype.

Gene Copy-Number Polymorphism Caused by Retrotransposition in Humans

The era of whole-genome sequencing has revealed that gene copy-number changes caused by duplication and deletion events have important evolutionary, functional, and phenotypic consequences. Recent studies have therefore focused on revealing the extent of variation in copy-number within natural populations of humans and other species. These studies have found a large number of copy-number variants (CNVs) in humans, many of which have been shown to have clinical or evolutionary importance. For the most part, these studies have failed to detect an important class of gene copy-number polymorphism: gene duplications caused by retrotransposition, which result in a new intron-less copy of the parental gene being inserted into a random location in the genome. Here we describe a computational approach leveraging next-generation sequence data to detect gene copy-number variants caused by retrotransposition (retroCNVs), and we report the first genome-wide analysis of these variants in humans. We find that retroCNVs account for a substantial fraction of gene copy-number differences between any two individuals. Moreover, we show that these variants may often result in expressed chimeric transcripts, underscoring their potential for the evolution of novel gene functions. By locating the insertion sites of these duplicates, we are able to show that retroCNVs have had an important role in recent human adaptation, and we also uncover evidence that positive selection may currently be driving multiple retroCNVs toward fixation. Together these findings imply that retroCNVs are an especially important class of polymorphism, and that future studies of copy-number variation should search for these variants in order to illuminate their potential evolutionary and functional relevance.