Expression Level Polymorphisms Research Articles

Association between polymorphisms in NOBOX and litter size traits in Xiangsu pigs.

The newborn ovary homeobox gene (NOBOX) regulates ovarian and early oocyte development, and thus plays an essential role in reproduction. In this study, the mRNA expression level and single nucleotide polymorphism (SNP) of NOBOX in various tissues of Xiangsu pigs were studied to explore the relationship between its polymorphism and litter size traits. Also, bioinformatics was used to evaluate the effects of missense substitutions on protein structure and function. The results revealed that NOBOX is preferentially expressed in the ovary. Six mutations were detected in the NOBOX sequence, including g.1624 T>C, g.1858 G>A, g.2770 G>A, g.2821 A>G, g.5659 A>G, and g.6025 T>A, of which g.1858 G>A was a missense mutation. However, only g.1858 G>A, g.5659 A>G, and g.6025 T>A were significantly associated with litter size traits (p < 0.05). Further prediction of the effect of the missense mutation g.1858 G>A on protein function revealed that p.V82M is a non-conservative mutation that significantly reduces protein stability and thus alters protein function. Overall, these findings suggest that NOBOX polymorphism is closely related to the litter size of Xiangsu pigs, which may provide new insights into pig breeding.

Crucial Role of Foxp3 Gene Expression and Mutation in Systemic Lupus Erythematosus, Inferred from Computational and Experimental Approaches.

The impaired suppressive function of regulatory T cells is well-understood in systemic lupus erythematosus. This is likely due to changes in Foxp3 expression that are crucial for regulatory T-cell stability and function. There are a few reports on the correlation between the Foxp3 altered expression level and single-nucleotide polymorphisms within the Foxp3 locus. Moreover, some studies showed the importance of Foxp3 expression in the same diseases. Therefore, to explore the possible effects of single-nucleotide polymorphisms, here, we evaluated the association of IVS9+459/rs2280883 (T>C) and -2383/rs3761549 (C>T) Foxp3 polymorphisms with systemic lupus erythematosus. Moreover, through machine-learning and deep-learning methods, we assessed the connection of the expression level of the gene with the disease. Single-nucleotide polymorphisms of Foxp3 (IVS9+459/rs2280883 (T>C) and -2383/rs3761549 (C>T)) were, respectively, genotyped using allele-specific PCR and direct sequencing and polymerase chain reaction-restriction fragment length polymorphism, in 199 systemic lupus erythematosus patients and 206 healthy age- and sex-matched controls. The Statistical Package for the Social Sciences version 19 and Fisher's exact and chi-square tests were used to analyze the data. Moreover, six machine-learning models and two sequential deep-learning models were designed to classify patients from normal people in the E-MTAB-11191 dataset through the expression level of Foxp3 and its correlated genes. The allele and genotype frequencies of both polymorphisms in question were found to be significantly associated with an increased risk of systemic lupus erythematosus. Furthermore, both of the two single-nucleotide polymorphisms were associated with some systemic-lupus-erythematosus-related risk factors. Three SVM models and the logistic regression model showed an 81% accuracy in classification problems. In addition, the first deep-learning model showed an 83% and 89% accuracy for the training and validation data, respectively, while the second model had an 85% and 79% accuracy for the training and validation datasets. In this study, we are prompted to represent the predisposing loci for systemic lupus erythematosus pathogenesis and strived to provide evidence-based support to the application of machine learning for the identification of systemic lupus erythematosus. It is predicted that the recruiting of machine-learning algorithms with the simultaneous measurement of the applied single nucleotide polymorphisms will increased the diagnostic accuracy of systemic lupus erythematosus, which will be very helpful in providing sufficient predictive value about individual subjects with systemic lupus erythematosus.

Abstract A010: ANO7 expression changes in prostate cancer progression — Association with an aggressive phenotype?

Abstract Introduction The expression level and single nucleotide polymorphisms of the prostate-specific gene ANO7 have been shown to correlate with prostate cancer (PrCa) outcome. Very little is known about ANO7, apart from its expression profile in tissues and that the protein is either a calcium-activated ion channel or a lipid scramblase. Our results suggest that ANO7 likely has a role in PrCa progression and that loss of ANO7 is associated with malignant PrCa. Materials and methods Sections of a prostate cancer formalin-fixed paraffin-embedded tissue microarray were used for ANO7 mRNA and protein detection. mRNA was detected with fluorescent in situ hybridization (FISH). Protein was detected with immunohistochemistry (IHC) using a polyclonal anti-ANO7 antibody (HPA035730). mRNA from fresh radical prostatectomy primary tumor samples were sequenced and subsequent gene expression levels were analyzed for co-expression with ANO7. The sample set consisted of a matched tumor and benign tissue sample (15+15) from each patient. Results The FISH images indicated explicitly that ANO7 mRNA is exclusively expressed in the luminal cells of the prostatic glandular epithelium. ANO7 mRNA is expressed in all cancerous lumina-forming glandular structures, but not in poorly-formed glands or sheets of cancer, in which ANO7 mRNA expression is very low or non-existent. Morphologically benign glands amidst cancerous tissue showed no expression, in contrast to tissue in which benign glands are predominating. The IHC showed a similar staining pattern to FISH.ANO7 co-expression gene set enrichment analysis resulted in 19 positively correlating and 77 negatively correlating pathways in KEGG (Kyoto Encyclopedia of Genes and Genomes) terms. Most of the positively correlating terms relate to metabolism, whereas among the negatively correlating terms, there were many signal transduction and cell growth and death-related pathways, such as Hippo, Ras, and p53 signaling pathways. Conclusions ANO7 mRNA and protein expression correlate spatially in the tissue, showing that the expression is specific to differentiated luminal cells and highly reduced in high-grade cancer. This notion is supported by the co-expressed gene-set enrichment analysis, which is showing a negative correlation of ANO7 with many pathways that are associated with aggressive PrCa. Mainly metabolism-related processes were positively correlated with ANO7, which could indicate that ANO7 is linked to the reprogramming of metabolism in the cells during cancer progression. Further research aims to identify the pathways in which ANO7 plays a significant role and to elucidate how the ANO7 protein functionally alters signaling related to PrCa progression. Citation Format: Olli Metsälä, Gudrun Wahlström, Pekka Taimen, Johanna Schleutker. ANO7 expression changes in prostate cancer progression — Association with an aggressive phenotype? [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A010.

Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly.

Natural isolates of the potato and tomato pathogen Phytophthora infestans exhibit substantial variation in virulence, chemical sensitivity, ploidy, and other traits. A chromosome-scale assembly was developed to expand genomic resources for this oomyceteous microbe, and used to explore the basis of variation. Using PacBio and Illumina data, a long-range linking library, and an optical map, an assembly was created and coalesced into 15 pseudochromosomes spanning 219 Mb using SNP-based genetic linkage data. De novo gene prediction combined with transcript evidence identified 19,981 protein-coding genes, plus about eight thousand tRNA genes. The chromosomes were comprised of a mosaic of gene-rich and gene-sparse regions plus very long centromeres. Genes exhibited a biased distribution across chromosomes, especially members of families encoding RXLR and CRN effectors which clustered on certain chromosomes. Strikingly, half of F1 progeny of diploid parents were polyploid or aneuploid. Substantial expression level polymorphisms between strains were identified, much of which could be attributed to differences in chromosome dosage, transposable element insertions, and adjacency to repetitive DNA. QTL analysis identified a locus on the right arm of chromosome 3 governing sensitivity to the crop protection chemical metalaxyl. Strains heterozygous for resistance often experienced megabase-sized deletions of that part of the chromosome when cultured on metalaxyl, increasing resistance due to loss of the sensitive allele. This study sheds light on diverse phenomena affecting variation in P. infestans and relatives, helps explain the prevalence of polyploidy in natural populations, and provides a new foundation for biologic and genetic investigations.

IDF21-0381 Expression Levels and Genetic Polymorphism of Scavenger Receptor Class B Type 1 as a Biomarker of Type 2 Diabetes

Background: Type 2 Diabetes Mellitus (T2DM) persists to be a major health problem worldwide and it is well accepted that T2DM is a metabolic disorder caused by hyperglycemia, which arises from insufficient pancreatic insulin secretion to peripheral tissues. Moreover, scavenger receptor class B type 1 (SRB1) protein plays a major role in the uptake of cholesteryl ester from high-density lipoprotein (HDL) and eliminates extra cholesterol from peripheral tissues as bile by the process of reverse cholesterol transport (RCT) Lack of SRB1 protein can result in an imbalance of cholesterol, dyslipidemia and eventually lead to insulin resistance. Aim: The present study aimed to determine whether the expression level and genetic polymorphism scavenger receptor class B type 1 (SRB1) rs5888 may be used as biological markers in type 2 diabetes mellitus (T2DM). Method: A total of 600 individuals, including 300 T2DM and 300 healthy individuals, were enrolled in the study from April 2016 to April 2017. Blood samples were collected from each T2DM and healthy individual. Total proteins were determined using western blot analysis. Also, restriction fragment length polymorphism (RFLP) analysis was achieved to detect the incidence of genetic polymorphisms. Results: Western blot analysis results revealed that the protein expression of SRB1 was significantly decreased in T2DM of SRB1 CC variant as compared with controls. The genotype distribution and the allelic frequencies for the SRB1 polymorphism were significantly different than T2DM and controls. CC genotype of the SRB1 polymorphism showed a potential association with the incidence of T2DM (OR = 1.19, 95% CI 0.63 - 2.25, P = 0.577). Discussion: In the present study, SRB1 CC variant had decreased SRB1 protein expression which might be due to variation in the regulatory region of the SRB1 gene that could involve in differential expression of SRB1 as the variant was located in the promoter region of the gene and could hinder the binding of transcriptional factor. Additionally, previous reports also found that the rs5888 SNP affected SRBI RNA secondary structure, which changed its ability to undergo productive protein translation leading ultimately to significantly lower SRB1 protein expression.

Study on the Relationship between lncRNA Gene Polymorphism and Systemic Lupus Erythematosus.

Background Systemic lupus erythematosus (SLE) is an autoimmune disease that can cause damage to multiple systems of the body. A number of studies have shown that long-chain noncoding RNA (lncRNA) can participate in the occurrence and development of a variety of autoimmune diseases. This study is aimed at detecting the expression levels of 5 lncRNAs in SLE patients and healthy controls and at exploring the relationship between expression levels and clinical symptoms and laboratory indicators. Methods The design type of this study is a case-control study. A total of 76 SLE patients and 71 healthy controls were included in the first phase of the study. Real-time fluorescence quantitative polymerase chain reaction was used to detect the expression level of 5 kinds of lncRNAs including lnc7514, lnc0640, lncagf, nc3643, and lnc5150 in PBMCs of two groups of patients; the expression of lncRNAs in the case group and the control group was analyzed. We analyzed the differences in the expression levels of lncRNAs between case and control groups, and explored the association of expression levels with clinical manifestations and laboratory characteristics. SPSS23.0 was used to analyze the expression level and gene polymorphism results; the statistical analysis test level α = 0.05. Results The expression level of lnc0640 in PBMCs of SLE patient group was higher than that of healthy control group (Z = −3.56, P = 0.03). However, lnc5150 was lower than in healthy controls (Z = −7.16, P < 0.001). lnc3643 expression levels were lower in SLE patients of SLE patients with pleurisy was lower than that of patients without pleurisy (Z = −2.44, P = 0.02). Low lnc3643 expression levels were observed in PBMCs with SLE patients with rash symptoms (Z = −2.75, P = 0.013). SLE expressed lower lnc3643 levels in PBMCs with SLE compared with those without pleurisy (Z = −2.42, P = 0.02). The above differences were statistically significant. Association analysis of lncRNA expression levels and clinical manifestations in SLE patients found that SLE was lower than those without rash or pleurisy (both P < 0.05); association analysis of lncRNA expression level and laboratory results found a negative correlation between lnc3643, lnc7514, and SLE disease activity score (SLEDAI-2K), blood sink (ESR), and C-reactive protein (CRP) (all P < 0.05). Conclusions lnc0640 was overexpressed in PBMCs in SLE patients compared with healthy controls. lnc3643 was negatively correlated with SLEDAI, and expression levels were associated with SLE patients with arthritis, rash, and pleuritis.

Expression Levels and Genetic Polymorphism of Scavenger Receptor Class B Type 1 as a Biomarker of Type 2 Diabetes Mellitus

ObjectivesThis study aimed to determine whether the expression level and genetic polymorphism scavenger receptor class B type 1 (SCARB1) rs5888 may be used as biological markers in type 2 diabetes mellitus (T2DM).MethodsThis case-control study was conducted at King George’s Medical University, Lucknow, India, from September 2018 to December 2019. Blood samples were collected from each individual with T2DM and each healthy individual. Total proteins were determined using western blot analysis. Additionally, restriction fragment length polymorphism analysis was achieved to detect the incidence of genetic polymorphisms.ResultsA total of 600 individuals, including 300 individuals with T2DM and 300 healthy individuals, were enrolled in the study. Western blot analysis results revealed that the protein expression of SRB1 was significantly decreased in T2DM of SCARB1 CC variant when compared with controls (P = 0.007). The genotype distribution and the allelic frequencies for the SRB1 polymorphism were significantly different between T2DM and controls (P = 0.03). The CC genotype of the SCARB1 polymorphism showed a potential association with the incidence of T2DM (odds ratio = 1.19, 95% confidence interval = 0.63–2.25; P = 0.577).ConclusionThe expression levels and genetic polymorphisms of the SCARB1 CC variant may be potential biomarkers for the occurrence of T2DM.

Expression GWAS of PGIP1 Identifies STOP1-Dependent and STOP1-Independent Regulation of PGIP1 in Aluminum Stress Signaling in Arabidopsis.

To elucidate the unknown regulatory mechanisms involved in aluminum (Al)-induced expression of POLYGALACTURONASE-INHIBITING PROTEIN 1 (PGIP1), which is one of the downstream genes of SENSITIVE TO PROTON RHIZOTOXICITY 1 (STOP1) regulating Al-tolerance genes, we conducted a genome-wide association analysis of gene expression levels (eGWAS) of PGIP1 in the shoots under Al stress using 83 Arabidopsis thaliana accessions. The eGWAS, conducted through a mixed linear model, revealed 17 suggestive SNPs across the genome having the association with the expression level variation in PGIP1. The GWAS-detected SNPs were directly located inside transcription factors and other genes involved in stress signaling, which were expressed in response to Al. These candidate genes carried different expression level and amino acid polymorphisms. Among them, three genes encoding NAC domain-containing protein 27 (NAC027), TRX superfamily protein, and R-R-type MYB protein were associated with the suppression of PGIP1 expression in their mutants, and accordingly, the system affected Al tolerance. We also found the involvement of Al-induced endogenous nitric oxide (NO) signaling, which induces NAC027 and R-R-type MYB genes to regulate PGIP1 expression. In this study, we provide genetic evidence that STOP1-independent NO signaling pathway and STOP1-dependent regulation in phosphoinositide (PI) signaling pathway are involved in the regulation of PGIP1 expression under Al stress.

Expression genome-wide association study identifies that phosphatidylinositol-derived signalling regulates ALUMINIUM SENSITIVE3 expression under aluminium stress in the shoots of Arabidopsis thaliana

To identify unknown regulatory mechanisms leading to aluminium (Al)-induction of the Al tolerance gene ALS3, we conducted an expression genome-wide association study (eGWAS) for ALS3 in the shoots of 95 Arabidopsis thaliana accessions in the presence of Al. The eGWAS was conducted using a mixed linear model with 145,940 genome-wide single nucleotide polymorphisms (SNPs) and the association results were validated using reverse genetics. We found that many SNPs from the eGWAS were associated with genes related to phosphatidylinositol metabolism as well as stress signal transduction, including Ca2+signals, inter-connected in a co-expression network. Of these, PLC9, CDPK32, ANAC071, DIR1, and a hypothetical protein (AT4G10470) possessed amino acid sequence/ gene expression level polymorphisms that were significantly associated with ALS3 expression level variation. Furthermore, T-DNA insertion mutants of PLC9, CDPK32, and ANAC071 suppressed shoot ALS3 expression in the presence of Al. This study clarified the regulatory mechanisms of ALS3 expression in the shoot and provided genetic evidence of the involvement of phosphatidylinositol-derived signal transduction under Al stress.

A single-population GWAS identified AtMATE expression level polymorphism caused by promoter variants is associated with variation in aluminum tolerance in a local Arabidopsis population.

Organic acids (OA) are released from roots in response to aluminum (Al), conferring an Al tolerance to plants that is regulated by OA transporters such as ALMT (Al‐activated malate transporter) and multi‐drug and toxic compound extrusion (MATE). We have previously reported that the expression level polymorphism (ELP) of AtALMT1 is strongly associated with variation in Al tolerance among natural accessions of Arabidopsis. However, although AtMATE is also expressed following Al exposure and contributes to Al tolerance, whether AtMATE contributes to the variation of Al tolerance and the molecular mechanisms of ELP remains unclear. Here, we dissected the natural variation in AtMATE expression level in response to Al at the root using diverse natural accessions of Arabidopsis. Phylogenetic analysis revealed that more than half of accessions belonging to the Central Asia (CA) population show markedly low AtMATE expression levels, while the majority of European populations show high expression levels. The accessions of the CA population with low AtMATE expression also show significantly weakened Al tolerance. A single‐population genome‐wide association study (GWAS) of AtMATE expression in the CA population identified a retrotransposon insertion in the AtMATE promoter region associated with low gene expression levels. This may affect the transcriptional regulation of AtMATE by disrupting the effect of a cis‐regulatory element located upstream of the insertion site, which includes AtSTOP1 (sensitive to proton rhizotoxicity 1) transcription factor‐binding sites revealed by chromatin immunoprecipitation‐qPCR analysis. Furthermore, the GWAS performed without the accessions expressing low levels of AtMATE, excluding the effect of AtMATE promoter polymorphism, identified several candidate genes potentially associated with AtMATE expression.

Genome-Wide Association Study and Genomic Prediction Elucidate the Distinct Genetic Architecture of Aluminum and Proton Tolerance in Arabidopsis thaliana.

Under acid soil conditions, Al stress and proton stress can occur, reducing root growth and function. However, these stressors are distinct, and tolerance to each is governed by multiple physiological processes. To better understand the genes that underlie these coincidental but experimentally separable stresses, a genome-wide association study (GWAS) and genomic prediction (GP) models were created for approximately 200 diverse Arabidopsis thaliana accessions. GWAS and genomic prediction identified 140/160 SNPs associated with Al and proton tolerance, respectively, which explained approximately 70% of the variance observed. Reverse genetics of the genes in loci identified novel Al and proton tolerance genes, including TON1-RECRUITING MOTIF 28 (AtTRM28) and THIOREDOXIN H-TYPE 1 (AtTRX1), as well as genes known to be associated with tolerance, such as the Al-activated malate transporter, AtALMT1. Additionally, variation in Al tolerance was partially explained by expression level polymorphisms of AtALMT1 and AtTRX1 caused by cis-regulatory allelic variation. These results suggest that we successfully identified the loci that regulate Al and proton tolerance. Furthermore, very small numbers of loci were shared by Al and proton tolerance as determined by the GWAS. There were substantial differences between the phenotype predicted by genomic prediction and the observed phenotype for Al tolerance. This suggested that the GWAS-undetectable genetic factors (e.g., rare-allele mutations) contributing to the variation of tolerance were more important for Al tolerance than for proton tolerance. This study provides important new insights into the genetic architecture that produces variation in the tolerance of acid soil.

Gene amplification as a form of population-level gene expression regulation.

Organisms cope with change by taking advantage of transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. Here, we investigate whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations in Escherichia coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy-number and, therefore, expression-level polymorphisms. This amplification-mediated gene expression tuning (AMGET) occurs on timescales that are similar to canonical gene regulation and can respond to rapid environmental changes. Mathematical modelling shows that amplifications also tune gene expression in stochastic environments in which transcription-factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune the expression of any gene, without leaving any genomic signature.

Evaluation of tumor necrosis factor (TNF)-α mRNA expression level and the rs1799964 polymorphism of the TNF-α gene in peripheral mononuclear cells of patients with inflammatory bowel diseases.

Crohn's disease (CD) and ulcerative colitis (UC) are types of chronic inflammatory bowel disease (IBD) of which the actual causes remain unknown. Emerging data indicate that alterations in cytokine synthesis may be involved in IBD pathogenesis. The aim of the present study was to determine whether the tumor necrosis factor (TNF)-α mRNA expression level and rs1799964 polymorphism are the genetic susceptibility component of IBD development. The TNF-α mRNA expression level of peripheral blood mononuclear cells (PBMCs) was measured using comparative reverse-transcription quantitative polymerase chain reaction (PCR). Genomic DNA from 201 individuals (CD: n=15; UC: n=86; control subjects: n=100) was analyzed for the presence of the TNF-α-1031 polymorphism by PCR-restriction fragment length polymorphism. An increased TNF-α mRNA expression level was additionally observed in the CC genotype of the -1031 TNF-α gene polymorphism compared with the TC and TT genotypes (P<0.05). Furthermore, the present results revealed that there was no significant difference in the genotype/allele frequencies of the -1031 TNF-α gene polymorphism in Iranian IBD patients. By comparison, the TNF-α mRNA expression level was evaluated in patients with a history of taking medications and demonstrated a significant association in the group that received the 5-ASA + Pred + AZA,5. 5-ASA + Pred + AZA + IFX when compared with the other groups (P<0.05). Thus, these results support the hypothesis that overexpression of the TNF-α gene, which correlated with the CC genotype, may represent a genetic risk factor for Iranian IBD.

Abstract A26: The distribution pattern of ERα expression, VEGFR2 expression level and its genetic variation as potential biomarkers for tamoxifen resistance

Abstract Background. The crosstalk between estrogen receptor alpha (ERα) and growth factor receptors is an essential part of tamoxifen resistance and the vascular endothelial growth factor/ tyrosine kinase domain receptor (VEGF/KDR) signaling pathway is clinically significant in the mechanisms of this resistance. The aim of the present study was to analyze the association of distribution pattern of ERα expression, VEGFR2 expression level, ESR1 and KDR single nucleotide polymorphisms (SNPs) with tamoxifen response in hormone receptor-positive primary breast cancer. Material and methods. Formalin-fixed paraffin-embedded and fresh frozen breast cancer tissue of the primary tumor was obtained from 97 hormone receptor-positive breast cancer patients treated with adjuvant tamoxifen at the Tomsk Cancer Research Institute. The distribution patterns of ERα expression and Ki-67 protein expression were determined by immunohistochemistry. The quantitative expression levels of VEGFR2 (CD309) and p-Akt473 was measured using a flow cytometry. TaqMan SNP assays were used for genotyping ESR1+30T&amp;gt;C (rs2077647), ESR1 2014G&amp;gt;A (rs2228480), KDR-604T&amp;gt;C (rs2071559) and KDR 1192G&amp;gt;A (rs2305948) polymorphisms. Progression-free survival (PFS) was used as end-point for survival analyses. Results. Patients who did not benefit from tamoxifen treatment (tamoxifen resistance group -TR) showed significantly higher heterogeneous ERα expression than tamoxifen sensitive patients (TS; 81.1% and 58.3% respectively, P = 0.021). We found that ESR12014A mutant allele carriers were more prevalent in TR patients than in TS group (26.3% vs. 8.0%, respectively, P = 0.009). Similarly, the KDR -604T allele of rs2071559 was statistically significant related with tamoxifen resistance (P = 0.034). However, the KDR 1192G allele of rs2305948 were significantly less common in the tamoxifen progressive group compared to the tamoxifen sensitive patients (38.0% vs. 90.0%, respectively, P = 0.035). In addition, the variant homozygote KDR 1192GG (vs. AA) of rs2305948 was associated with VEGFR2 expression (r = -0.524, p = 0.012). VEGFR2 expression levels also showed borderline significant correlation with p-Akt473 expression (r = 0.368, p = 0.070). The Kaplan-Meier survival analysis demonstrated a significant relationship of heterogeneous distribution of ERα expression with poor survival of tamoxifen treated patients (log-rank P = 0.009). Moreover, the PFS for the patients with the KDR -604TT genotypes of rs2071559 were worse than for the patients with the CC genotype (log-rank P = 0.123). Conclusion. The distribution pattern of ERα expression, VEGFR2 expression level and its genetic variation can serve as potential predictors for hormone receptor-positive breast cancer patients treated with adjuvant tamoxifen and thus provide more information for optimizing patient's selection to tamoxifen adjuvant therapy. Citation Format: Nataliya Babyshkina, Sergey Vtorushin, Stanislav Patalyak, Tatyana Dronova, Elena Slonimskaya, Nadejda Cherdyntseva. The distribution pattern of ERα expression, VEGFR2 expression level and its genetic variation as potential biomarkers for tamoxifen resistance. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr A26.

AhR expression and polymorphisms are associated with risk of coronary arterial disease in Chinese population

The aryl hydrocarbon receptor (AhR) mediates the control of environmental toxicity, and modulates the development and pathogenesis of the cardiovascular system. However, little is known about the role of AhR in coronary arterial disease (CAD) susceptibility. We therefore conducted a case-control study in a Chinese population, and assessed the potential association between AhR variants and CAD susceptibility. Compared with the controls, circulating AhR expression was found to be significantly increased in patients with CAD and its subtypes including ST-segment and non-ST-segment elevation myocardial infarction, and stable and unstable angina pectoris. Receiver operating characteristic (ROC) analysis to evaluate the effect of AhR on CAD progression showed it to be a potent biomarker for CAD. Genotype frequencies of AhR rs2066853 differed significantly between CAD and control subjects, while smoking and hyperlipidemia markedly promoted CAD risk relative to the AhR polymorphism. Moreover, a significant difference in AhR variant distribution was observed between the four CAD subtypes with different severities. The expression level and functional polymorphisms of circulating AhR may affect the susceptibility and progression of CAD in Chinese populations. This provides a novel view of the etiology and epidemiology of CAD, and will contribute to the diagnosis and therapy of this severe disease.

Isolation and characterization of the omega-6 fatty acid desaturase (FAD2) gene family in the allohexaploid oil seed crop Crambe abyssinica Hochst

Crambe (Crambe abyssinica Hochst ex. R. E. Fries) is an ideal crop for industrial oil production because of its high erucic acid content (C22:1, approx. 60 %) in its seed oil. The value of crambe oil can be improved by increasing C22:1 content or reducing polyunsaturated fatty acids (PUFA). The FAD2 gene plays a critical role in PUFA biosynthesis. To identify targets for breeding, we characterized FAD2 in crambe for copy number and expression profile. Seven copies of FAD2 were detected in allohexaploid crambe. Three genes (CaFAD2-C1, -C2 and -C3) were expressed in multiple tissues, including root, seedling, leaf, flower, bud and developing seeds. In developing seeds, the expression of these genes was upregulated with CaFAD2-C3, being expressed predominantly with a peak at 20 days after pollination. This gene is therefore a promising candidate gene for determining PUFA levels in seed oil. Four other FAD2 genes were considered to be “pseudo-genes” as they harbour internal stop codons and were not expressed. Among the six crambe varieties with consistent variation in oil composition, no nucleotide polymorphisms were found in the CaFAD2-C1, -C2 and -C3 genes. In seeds at 30 days after pollination, statistically significant expression level polymorphisms for only one gene, CaFAD2-C2, was found among the varieties. However, although significantly different, the difference in expression was small and did not explain the variation in oil composition. Given the absence of genetic variation in CaFAD2 genes in crambe breeding lines, breeding for high erucic acid content calls for a molecular breeding approach whereby mutations are chemically induced to increase the genetic variation.

Bimodal expression level polymorphisms in Arabidopsis thaliana

Differences in gene expression are termed expression level polymorphisms (ELPs). Here, we propose a new ELP class, bimodal ELPs (bELPs), as a criterion to screen for genes that are responsible for natural phenotypic variation and/or that are targeted by balancing selection. bELP genes are characterized by two expression level modes. Genomic scans based on nucleotide sequences are not ideal for identifying genes targeted for selection. A critical concern is that several genes can be present in the selection-targeted regions identified by such scans. This situation indicates the importance of integrating genomic sequence data and other information, such as gene expression data. Comparative transcriptomics is useful for determining evolutionarily and ecologically important polymorphisms. In a genome-wide expression screen of 34 accessions, we identified 344 Arabidopsis thaliana genes exhibiting bELPs. Population genetic analysis revealed that bELP genes had high nucleotide diversities and long linkage disequilibriums. The highest nucleotide diversity (11-fold greater than the genomic mean) was found in the At1g23780 gene, which encodes a putative F-box protein. We observed a clear association between the expression mode and sequence type of the At1g23780 gene. Our results suggest that bELPs will be useful for the screening and functional analysis of genes responsible for phenotypic polymorphisms. Such a “multi-omics” approach has the potential to facilitate the scanning of genes relevant to balanced polymorphisms not only in A. thaliana, but also in other model and non-model organisms.

A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1.

The genetic model plant Arabidopsis thaliana, like many plant species, experiences a range of edaphic conditions across its natural habitat. Such heterogeneity may drive local adaptation, though the molecular genetic basis remains elusive. Here, we describe a study in which we used genome-wide association mapping, genetic complementation, and gene expression studies to identify cis-regulatory expression level polymorphisms at the AtHKT1;1 locus, encoding a known sodium (Na+) transporter, as being a major factor controlling natural variation in leaf Na+ accumulation capacity across the global A. thaliana population. A weak allele of AtHKT1;1 that drives elevated leaf Na+ in this population has been previously linked to elevated salinity tolerance. Inspection of the geographical distribution of this allele revealed its significant enrichment in populations associated with the coast and saline soils in Europe. The fixation of this weak AtHKT1;1 allele in these populations is genetic evidence supporting local adaptation to these potentially saline impacted environments.

TNFR1 mRNA Expression Level and TNFR1 Gene Polymorphisms are Predictive Markers for Susceptibility to Develop Invasive Pulmonary Aspergillosis

Tumour necrosis factor (TNF) is primarily secreted by monocytes/macrophages and activated T lymphocytes in response to fungal infections. TNF acts through TNF receptor 1 (TNFR1) triggering a pro-inflammatory response, and therefore plays a pivotal role in immune regulation and host immune responses. We hypothesized that single nucleotide polymorphisms (SNPs) in TNFR1 gene may influence the innate immune response against Aspergillus. Three SNPs were genotyped in 275 individuals (144 immunocompromised haematological patients with high-risk of developing IPA and 131 healthy controls): TNFR1(-383(A/C)) (rs2234649) and TNFR1(-609(G/T)) (rs4149570) in the 5 prime UTR region, and TNFR1(+36(A/G)) SNP (rs767455) in the first exon of the gene. Of the 144 haematological patients, 77 patients developed Invasive Pulmonary Aspergillosis (IPA) infection and the remaining 67 patients were not infected. TNFR1(+36(A/G)) and TNFR1(-609(G/T)) were associated with IPA susceptibility (p=0.033 and p=0.018, respectively). A role of TNFR1 genetic variants in the susceptibility of patients to develop IPA was also supported by the significantly lower TNFR1 mRNA expression level in IPA than in IPA-resistant patients and the strong correlation between the TNFR1(-609) genetic variant and the expression levels of TNFR1. There was also a tendency for a higher frequency of galactomannan (GM) positivity in patients with TNFR1(-609G/G) genotype than in patients with TNFR1(-609G/T) (p=0.0909) or TNFR1(-609T/T) (p=0.0913) genotype. Predictive sequence analysis of the effects of TNFR1(-609) promoter polymorphism revealed that this SNP might play a critical role in modifying the affinity of ICSBP/IRF-8, a transcription factor that is involved in the TNFR1-mediated activation of NFkappaB signalling pathway. Taken together, these data suggest that TNFR1 polymorphisms influence the risk of IPA disease and might be useful for risk stratification strategies. These findings need to be confirmed in validation studies with larger samples of haematological patients.

Gene Expression Profiles Deciphering Rice Phenotypic Variation between Nipponbare (Japonica) and 93-11 (Indica) during Oxidative Stress

Rice is a very important food staple that feeds more than half the world's population. Two major Asian cultivated rice (Oryza sativa L.) subspecies, japonica and indica, show significant phenotypic variation in their stress responses. However, the molecular mechanisms underlying this phenotypic variation are still largely unknown. A common link among different stresses is that they produce an oxidative burst and result in an increase of reactive oxygen species (ROS). In this study, methyl viologen (MV) as a ROS agent was applied to investigate the rice oxidative stress response. We observed that 93-11 (indica) seedlings exhibited leaf senescence with severe lesions under MV treatment compared to Nipponbare (japonica). Whole-genome microarray experiments were conducted, and 1,062 probe sets were identified with gene expression level polymorphisms between the two rice cultivars in addition to differential expression under MV treatment, which were assigned as Core Intersectional Probesets (CIPs). These CIPs were analyzed by gene ontology (GO) and highlighted with enrichment GO terms related to toxin and oxidative stress responses as well as other responses. These GO term-enriched genes of the CIPs include glutathine S-transferases (GSTs), P450, plant defense genes, and secondary metabolism related genes such as chalcone synthase (CHS). Further insertion/deletion (InDel) and regulatory element analyses for these identified CIPs suggested that there may be some eQTL hotspots related to oxidative stress in the rice genome, such as GST genes encoded on chromosome 10. In addition, we identified a group of marker genes individuating the japonica and indica subspecies. In summary, we developed a new strategy combining biological experiments and data mining to study the possible molecular mechanism of phenotypic variation during oxidative stress between Nipponbare and 93-11. This study will aid in the analysis of the molecular basis of quantitative traits.