Variants In Key Genes Research Articles

Genetic Variations Related to Angiotensin II Production and Risk for Basal Cell Carcinoma.

Basal cell carcinoma (BCC) is the most prevalent human neoplasm, with constantly increasing annual incidence. Despite its slow growth, BCC is locally invasive and, if left untreated, can cause severe complications, including metastasis and death. The renin-angiotensin system (RAS) plays a key role in electrolyte balance, atrial pressure, tissue development, homeostasis, and inflammation, but also in cancer development. After binding to its type 1 receptor (AT1R), angiotensin II (ANGII), the system's principal hormonal effector, regulates cancer pathways spanning from the formation of the initial cancer cell to the construction and nutrition of the tumor microenvironment, angiogenesis, proliferation, and metastasis. Although the role of RAS in the development of skin pathologies has not been widely researched, RAS-targeting antihypertensive medications have been shown to have a chemoprotective effect against BCC. Based on those findings, our group conducted a series of genetic association studies to investigate the association between common functional variations in key genes related to ANGII production (AGT, ACE, ACE2, AT1R, AT2R, and CMA1) and the risk of BCC occurrence. This review provides a summary of the current understanding of the ANGII involvement in BCC development. The reliable and easily assessed pool of genetic biomarkers may be used for predictive testing and prevention purposes in high-risk individuals.

Abstract P6-02-10: Prevalence of breast cancer predisposing variants in patients with breast carcinoma in situ

Abstract Background. Carcinoma in situ (CIS) of the breast is a non-obligatory pre-malignant breast lesion and a highly suspected precursor of invasive cancer. Although the selection criteria for referral to genetic testing are well established for patients diagnosed with invasive breast cancer, these are not clear for patients diagnosed with CIS. Our goal is to assess the prevalence of predisposing pathogenic variants in key genes, as well as to describe factors in patients with CIS that might be associated with genetic predisposition. Methods. A total of 267 patients solely diagnosed with CIS (mean age 43.65 years, range 18-74) through years 2010-2022, were referred for genetic testing and were analyzed, following their informed consent, implementing a 42-gene panel. Of these, 81.5%, 12.4% and 5.8% were ductal, lobular and mixed CIS, respectively. Patients having a synchronous invasive breast cancer diagnosis were not included in the study. Of patients with known grade, 52.28%, 28.9% and 18.8% were grade 3, 2 and 1, respectively. Strong family history for breast cancer (>2 close family relatives) was positive in 28% (75/267) of patients, while 67.8% of CIS were hormone receptor positive. Results. A total of 12.7% (34/267) of patients carried pathogenic variants in seven clinically actionable genes, i.e. CHEK2 (10), BRCA2 (9), BRCA1 (5), ATM (5), PALB2 (2), MSH6 (2) and TP53 (1). Mean age at diagnosis of carriers was 42.1 years (range 29-61 years, p=0.26), 60% of patients had a grade 3 CIS diagnosis (OR 1.1, 95% 0.589-2.1, p=0.73), 96% had a hormone positive diagnosis (OR 1.4, 95% 0.78-2.50, p=0.24), while 73.5% (25/34) reported as having at least two close family relatives with breast cancer (OR 2.9, 95% 1.6-5.1, p=0.0001). The vast majority of carriers had a ductal CIS (DCIS) diagnosis, i.e. 91.2% (31/34) although this did not reach statistical significance (OR 1.087, 95% 0.64-1.82, p=0.72), probably due to small numbers. Notably, carriers were more likely to have a diagnosis with comedo characteristics, although this parameter has not been monitored closely for the whole cohort. Conclusion. Herein, an important fraction of patients with breast CIS carried pathogenic variants in clinically actionable genes, with the most frequent being CHEK2, BRCA2, BRCA1 and ATM. Notably, the prevalence is comparable to that of patients with invasive breast cancer. Strong family history for breast cancer was strongly associated with the identification of predisposing variants. Other factors, such as high grade, hormone positivity, age at diagnosis and others might also be associated with predisposition to CIS, but larger, prospective, studies are needed to confirm these. This is one of the few studies evaluating the inherited predisposition associated with both high and moderate penetrant breast cancer genes, highlighting that individuals with CIS diagnosis and strong family history for breast cancer should be offered the option to genetic testing via multigene panel. Citation Format: Florentia Fostira, Dimitrios Nasikas, Paraskevi Apostolou, Vassiliki Dellatola, Anna Fokianou, Panagiota Kontogianni, Romina Alevizou, Sofia Filippidou, Dimitrios Maniatis, Lazaros Papadopoulos, Emmanouil Pavlakis, Panagiota Ntasiou, Sofia Karageorgopoulou, Grigorios Xepapadakis. Prevalence of breast cancer predisposing variants in patients with breast carcinoma in situ [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-02-10.

Integrated Analysis of ECT2 and COL17A1 as Potential Biomarkers for Pancreatic Cancer.

Background Pancreatic cancer (PC) is a malignant tumor of the digestive tract. It presents with atypical clinical symptoms and lacks specific diagnostic indicators. This study is aimed at exploring the potential biomarkers of PC. Methods TCGA database pancreatic cancer dataset was normalized and used to identify differentially expressed genes (DEGs). Survival, independent prognostic, and clinical correlation analyses were performed on DEGs to screen for key genes. DNA methylation, mutation, and copy number variation (CNV) analyses were used to analyze genetic variants in key genes. GSEA was performed to explore the functional enrichment of the key genes. Based on the expression of key genes, construction of a competing endogenous RNA (ceRNA) network, analysis of the tumor microenvironment (TME), and prediction of chemotherapeutic drug sensitivity were performed. Furthermore, the GEO database was used to validate the reliability of key genes. Results Two key genes (ECT2 and COL17A1) were identified, which were highly expressed in PC. The mRNA expression of ECT2 and COL17A1 was associated with DNA methylation and CNV. The cell cycle, proteasome, and pathways in cancer were enriched in the high-COL17A1 and ECT2 groups. The TME results showed that immune scores were decreased in the high-ECT2 group. CeRNA network results showed that there were eleven miRNAs were involved in the regulation of ECT2 and COL17A1. Moreover, pRRophetic analysis showed that 20 chemotherapeutic drugs were associated with ECT2 and COL17A1 expression. Conclusions Collectively, ECT2 and COL17A1 may be potential biomarkers for PC, providing a new direction for clinical diagnosis and treatment.

Germline genetics of prostate cancer.

An important fraction (>/~10%) of men with high-risk, localized prostate cancer and metastatic prostate cancer carry germline (heritable) pathogenic and likely pathogenic variants (also known as mutations) in DNA repair genes. These can represent known or suspected autosomal dominant cancer predisposition syndromes. Growing evidence suggests that pathogenic variants in key genes involved in homologous recombination and mismatch DNA repair are important in prostate cancer initiation and/or the development of metastases. Here we provide a comprehensive review regarding individual genes and available literature regarding risks for developing prostate cancer, and discuss current national guidelines for germline genetic testing in the prostate cancer population and treatment implications. The association with prostate cancer risk and treatment implications is best understood for those with germline mutations of BRCA2, with emerging data supporting associations with ATM, CHEK2, BRCA1, HOXB13, MSH2, MSH6, PALB2, TP53 and NBN. Treatment implications in the metastatic castration resistant prostate cancer setting include rucaparib and olaparib, and pembrolizumab with potential clinical trial opportunities in earlier disease settings. The data summarized in this review has led to the expansion of national guidelines for germline genetic testing in prostate cancer. We review these guidelines, and discuss the importance of cascade genetic testing of relatives, diverse populations with attention to inclusion, as well as prostate cancer screening updates and clinical trial opportunities for men who carry genetic risk factors for prostate cancer.

Epichlo\xeb scottii sp. nov., a new endophyte isolated from Melica uniflora is the missing ancestor of Epichlo\xeb disjuncta

Here we describe a new, haploid and stroma forming species within the genus Epichloë, as Epichloë scottii sp. nov. The fungus was isolated from Melica uniflora growing in Bad Harzburg, Germany. Phylogenetic reconstruction using a combined dataset of the tubB and tefA genes strongly support that E. scottii is a distinct species and the so far unknown ancestor species of the hybrid E. disjuncta. A distribution analysis showed a high infection rate in close vicinity of the initial sampling site and only two more spots with low infection rates. Genetic variations in key genes required for alkaloid production suggested that E. scottii sp. nov. might not be capable of producing any of the major alkaloids including ergot alkaloid, loline, indole-diterpene and peramine. All isolates and individuals found in the distribution analysis were identified as mating-type B explaining the lack of mature stromata during this study. We further release a telomere-to-telomere de novo assembly of all seven chromosomes and the mitogenome of E. scottii sp. nov.

Genetic Predisposition to the Mortality in Septic Shock Patients: From GWAS to the Identification of a Regulatory Variant Modulating the Activity of a CISH Enhancer.

The high mortality rate in septic shock patients is likely due to environmental and genetic factors, which influence the host response to infection. Two genome-wide association studies (GWAS) on 832 septic shock patients were performed. We used integrative bioinformatic approaches to annotate and prioritize the sepsis-associated single nucleotide polymorphisms (SNPs). An association of 139 SNPs with death based on a false discovery rate of 5% was detected. The most significant SNPs were within the CISH gene involved in cytokine regulation. Among the 139 SNPs associated with death and the 1311 SNPs in strong linkage disequilibrium with them, we investigated 1439 SNPs within non-coding regions to identify regulatory variants. The highest integrative weighted score (IW-score) was obtained for rs143356980, indicating that this SNP is a robust regulatory candidate. The rs143356980 region is located in a non-coding region close to the CISH gene. A CRISPR-Cas9-mediated deletion of this region and specific luciferase assays in K562 cells showed that rs143356980 modulates the enhancer activity in K562 cells. These analyses allowed us to identify several genes associated with death in patients with septic shock. They suggest that genetic variations in key genes, such as CISH, perturb relevant pathways, increasing the risk of death in sepsis patients.

Rare Variants in the DNA Repair Pathway and the Risk of Colorectal Cancer.

Inherited susceptibility is an important contributor to colorectal cancer risk, and rare variants in key genes or pathways could account in part for the missing proportion of colorectal cancer heritability. We conducted an exome-wide association study including 2,327 cases and 2,966 controls of European ancestry from three large epidemiologic studies. Single variant associations were tested using logistic regression models, adjusting for appropriate study-specific covariates. In addition, we examined the aggregate effects of rare coding variation at the gene and pathway levels using Bayesian model uncertainty techniques. In an exome-wide gene-level analysis, we identified ST6GALNAC2 as the top associated gene based on the Bayesian risk index (BRI) method [summary Bayes factor (BF)BRI = 2604.23]. A rare coding variant in this gene, rs139401613, was the top associated variant (P = 1.01 × 10-6) in an exome-wide single variant analysis. Pathway-level association analyses based on the integrative BRI (iBRI) method found extreme evidence of association with the DNA repair pathway (BFiBRI = 17852.4), specifically with the nonhomologous end joining (BFiBRI = 437.95) and nucleotide excision repair (BFiBRI = 36.96) subpathways. The iBRI method also identified RPA2, PRKDC, ERCC5, and ERCC8 as the top associated DNA repair genes (summary BFiBRI ≥ 10), with rs28988897, rs8178232, rs141369732, and rs201642761 being the most likely associated variants in these genes, respectively. We identified novel variants and genes associated with colorectal cancer risk and provided additional evidence for a role of DNA repair in colorectal cancer tumorigenesis. This study provides new insights into the genetic predisposition to colorectal cancer, which has potential for translation into improved risk prediction.

Set-theory based benchmarking of three different variant callers for targeted sequencing

BackgroundNext generation sequencing (NGS) technologies have improved the study of hereditary diseases. Since the evaluation of bioinformatics pipelines is not straightforward, NGS demands effective strategies to analyze data that is of paramount relevance for decision making under a clinical scenario. According to the benchmarking framework of the Global Alliance for Genomics and Health (GA4GH), we implemented a new simple and user-friendly set-theory based method to assess variant callers using a gold standard variant set and high confidence regions. As model, we used TruSight Cardio kit sequencing data of the reference genome NA12878. This targeted sequencing kit is used to identify variants in key genes related to Inherited Cardiac Conditions (ICCs), a group of cardiovascular diseases with high rates of morbidity and mortality.ResultsWe implemented and compared three variant calling pipelines (Isaac, Freebayes, and VarScan). Performance metrics using our set-theory approach showed high-resolution pipelines and revealed: (1) a perfect recall of 1.000 for all three pipelines, (2) very high precision values, i.e. 0.987 for Freebayes, 0.928 for VarScan, and 1.000 for Isaac, when compared with the reference material, and (3) a ROC curve analysis with AUC > 0.94 for all cases. Moreover, significant differences were obtained between the three pipelines. In general, results indicate that the three pipelines were able to recognize the expected variants in the gold standard data set.ConclusionsOur set-theory approach to calculate metrics was able to identify the expected ICCs related variants by the three selected pipelines, but results were completely dependent on the algorithms. We emphasize the importance to assess pipelines using gold standard materials to achieve the most reliable results for clinical application.

Exploration of a Resequenced Tomato Core Collection for Phenotypic and Genotypic Variation in Plant Growth and Fruit Quality Traits.

A tomato core collection consisting of 122 gene bank accessions, including landraces, old cultivars, and wild relatives, was explored for variation in several plant growth, yield and fruit quality traits. The resequenced accessions were also genotyped with respect to a number of mutations or variations in key genes known to underlie these traits. The yield-related traits fruit number and fruit weight were much higher in cultivated varieties when compared to wild accessions, while, in wild tomato accessions, Brix was higher than in cultivated varieties. Known mutations in fruit size and shape genes could well explain the fruit size variation, and fruit colour variation could be well explained by known mutations in key genes of the carotenoid and flavonoid pathway. The presence and phenotype of several plant architecture affecting mutations, such as self-pruning (sp), compound inflorescence (s), jointless-2 (j-2), and potato leaf (c) were also confirmed. This study provides valuable phenotypic information on important plant growth- and quality-related traits in this collection. The allelic distribution of known genes that underlie these traits provides insight into the role and importance of these genes in tomato domestication and breeding. This resource can be used to support (precision) breeding strategies for tomato crop improvement.

Genetic Polymorphisms in Multispecific Transporters Mitigate Mercury Nephrotoxicity in an Artisanal and Small-Scale Gold Mining Community in Colombia.

In artisanal and small-scale gold mining, occupational exposure to mercury (Hg) vapor is related to harmful effects on several organs, including the kidneys. We previously reported significantly increased levels of Hg in blood and urine despite normal kidney function in individuals from Colombia occupationally exposed to Hg compared with those nonexposed. We evaluated the contribution of 4 genetic variants in key genes encoding the transporters solute carrier (SLC; rs4149170 and rs4149182) and ATP-binding cassette(ABC; rs1202169 and rs1885301) in the pathogenesis of nephrotoxicity due to Hg exposure in these groups. Regression analysis was performed to determine the association between the blood- and urine-Hg concentration with SLC and ABC polymorphisms in 281 Colombian individuals (160 exposed and 121 nonexposed to Hg). We found an enrichment of ABCB1 rs1202169-T allele in the exposed group (p = .011; OR= 2.05; 95% CI = 1.18-3.58) compared with the nonexposure group. We also found that carriers of SLC22A8 rs4149182-G and ABCB1 rs1202169-T alleles had a higher urinary clearance rate of Hg than noncarriers (β = 0.13, p = .04), whereas carriers of SLC22A6 rs4149170-A and ABCB1 rs1202169-C alleles showed abnormal levels of estimated glomerular filtration rate (β = -84.96, p = .040) and beta-2-microglobulin (β = 743.38, p < .001). Our results suggest that ABCB1 rs1202169 and its interaction with SLC22A8 rs4149182 and SLC22A6 rs4149170 could mitigate Hg nephrotoxicity by controlling the renal proximal tubule cell accumulation of inorganic Hg. This will be useful to estimate the risk of kidney toxicity associated to Hg and the genetic selection to aid adaptation to Hg-rich environments.

Genetic Associations with Aging Muscle: A Systematic Review.

The age-related decline in skeletal muscle mass, strength and function known as ‘sarcopenia’ is associated with multiple adverse health outcomes, including cardiovascular disease, stroke, functional disability and mortality. While skeletal muscle properties are known to be highly heritable, evidence regarding the specific genes underpinning this heritability is currently inconclusive. This review aimed to identify genetic variants known to be associated with muscle phenotypes relevant to sarcopenia. PubMed, Embase and Web of Science were systematically searched (from January 2004 to March 2019) using pre-defined search terms such as “aging”, “sarcopenia”, “skeletal muscle”, “muscle strength” and “genetic association”. Candidate gene association studies and genome wide association studies that examined the genetic association with muscle phenotypes in non-institutionalised adults aged ≥50 years were included. Fifty-four studies were included in the final analysis. Twenty-six genes and 88 DNA polymorphisms were analysed across the 54 studies. The ACTN3, ACE and VDR genes were the most frequently studied, although the IGF1/IGFBP3, TNFα, APOE, CNTF/R and UCP2/3 genes were also shown to be significantly associated with muscle phenotypes in two or more studies. Ten DNA polymorphisms (rs154410, rs2228570, rs1800169, rs3093059, rs1800629, rs1815739, rs1799752, rs7412, rs429358 and 192 bp allele) were significantly associated with muscle phenotypes in two or more studies. Through the identification of key gene variants, this review furthers the elucidation of genetic associations with muscle phenotypes associated with sarcopenia.

Abstract 5368: The evolutionary history of human colitis-associated colorectal cancer

Abstract Introduction: Inflammatory bowel disease (IBD) confers an increased lifetime risk of developing colorectal cancer (CRC). Our study aimed to compare the molecular and genetic features of colitis-associated CRC (CA-CRC) to the more common sporadic CRC (S-CRC), and to dissect the evolutionary history of CA-CRC using multi-region next generation sequencing. Methods: Fresh frozen colectomy specimens were collected from 12 patients with CA-CRC. For each case, whole exome sequencing was performed on multiple regions of tumor, adjacent normal mucosa and blood. Variants in key genes were validated by Sanger sequencing and BaseScope in situ hybridization, and copy numbers were validated by FISH. Copy number profiling (by SNP array or low-pass whole genome sequencing) was performed on low grade dysplasia (LGD; n=28), high grade dysplasia (HGD; n=13), mixed LGD/HGD (n=7) and CA-CRC (n=15). Phylogenetic trees were reconstructed for each case, and evolutionary analysis was used to reveal the temporal sequence of events leading to CA-CRC. Results: The majority of sequenced tumors (10/12) were microsatellite stable, and these had a median mutation rate of 3.0 single nucleotide alterations (SNAs) per Mb, ~20% higher than that of S-CRC. Mutational signatures identified ‘accelerated ageing' in the colitic bowel, likely a consequence of repeated inflammation and regeneration cycles. There was considerable mutational burden in non-dysplastic IBD mucosa (median 47 SNAs), with a median of 24% of these SNAs also clonal within the neighboring CA-CRC, indicating a mutational field. In CA-CRC the most commonly mutated gene was TP53, occurring more frequently than in S-CRC (80% vs. 58%), whereas APC mutations were significantly less common (40% vs. 75%, p=0.03). We analyzed the genetic heterogeneity of CA-CRCs and found that the number of clonal SNAs per tumor was not significantly different to S-CRCs, however CA-CRCs had significantly more SNAs that were unique to one region (p=0.04); this increase in diversity is likely due to an elevated mutation rate. CA- CRCs were often near-triploid (42%) or near-tetraploid (21%), with many other recurrent copy-number alterations that were distinct from those observed in S-CRC. Phylogenetic analysis revealed that copy number alterations (CNAs) accrue in non-dysplastic bowel, but the transition from LGD to HGD involves a punctuated ‘catastrophic' increase in CNA burden. Conclusions: Multi-region sequencing of CA-CRC has revealed a distinct pathway of colon carcinogenesis, with an increase in mutational burden and heterogeneity compared to S-CRC. Copy-number profiling indicated extensive genomic alterations, with dramatic accrual at the LGD to HGD transition. The significant mutational burden in surrounding normal mucosa indicates field cancerization, which is an encouraging prospect for screening programs; however the likelihood of punctuated evolution may offer a limited window for early detection. Citation Format: Ann-Marie Baker, William Cross, Kathleen Curtius, Chang-ho Ryan Choi, Ibrahim Al-Bakir, Daniel Temko, Pierre Martinez, Marc Williams, Hayley Davis, Sujata Biswas, Nicholas A. Wright, Morgan Moorghen, Stephen J. Hayes, Manuel Rodriguez-Justo, Andrew Silver, Lai Mun Wang, Marnix Jansen, Ailsa L. Hart, Simon J. Leedham, Trevor A. Graham. The evolutionary history of human colitis-associated colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5368.

Comparative Genome Analysis of 2 Mycobacterium Tuberculosis Strains from Pakistan: Insights Globally Into Drug Resistance, Virulence, and Niche Adaptation.

Multidrug-resistant Mycobacterium tuberculosis is a global threat particularly in developing countries like Pakistan. In this study, we identified 2 M tuberculosis strains, mnpk and swlpk, by 16S RNA genes, sequenced their draft genome, and compared the 2 genomes with reference strain H37Rv and gene expression analysis of selected virulent genes. Phylogenetic analysis of M tuberculosis strains, mnpk and swlpk, using 16S RNA genes revealed that the strains are closely related with reference strain H37Rv. The draft genome sequence of mnpk and swlpk contains 4305 and 4295 protein-coding genes, respectively, having 99.9% with high collinearity when compared with H37Rv. Although some important drug-resistant genes such as fabG, faDE24, and iniA were missing, genome mining also revealed key drug-resistant genes such as katG, inhA, rpoA, rpoB, and rpoC against first-line isoniazid and rifampicin drug. The strain mnpk and swlpk encodes 257 putative and 86 verified virulent genes including type 7 secretion system (T7SS) key genes. The variation in the expression profile of selected T7SS genes, particularly low expression level of EspK, raised concern that the mechanism of virulence of mnpk and swlpk might be different from H37Rv strains as espK is associated with ATPase EccC1a and EccC1b which showed high expression level. Briefly, this study shows that the strains mnpk and swlpk are linked with H37Rv having 99% similarity in genomes, but the absence of drug-resistant genes and variation in key genes’ expression profile espK, EccE1, PPE41, and espC provide a rationale for the future investigation of M tuberculosis mnpk and swlpk pathogenesis via RNA sequencing, single-nucleotide polymorphisms, as well as gene manipulation.

Impact of novel SNPs identified in Cynara cardunculus genes on functionality of proteins regulating phenylpropanoid pathway and their association with biological activities

BackgroundCynara cardunculus L. offers a natural source of phenolic compounds with the predominant molecule being chlorogenic acid. Chlorogenic acid is gaining interest due to its involvement in various biological properties such as, antibacterial, antifungal, antioxidant, hepatoprotective, and anticarcinogenic activities.ResultsIn this work we screened a Cynara cardunculus collection for new allelic variants in key genes involved in the chlorogenic acid biosynthesis pathway. The target genes encode p-coumaroyl ester 3′-hydroxylase (C3′H) and hydroxycinnamoyl-CoA: quinate hydroxycinnamoyl transferase (HQT), both participating in the synthesis of chlorogenic acid. Using high-resolution melting, the C3′H gene proved to be highly conserved with only 4 haplotypes while, for HQT, 17 haplotypes were identified de novo. The putative influence of the identified polymorphisms in C3′H and HQT proteins was further evaluated using bioinformatics tools. We could identify some polymorphisms that may lead to protein conformational changes. Chlorogenic acid content, antioxidant and antithrombin activities were also evaluated in Cc leaf extracts and an association analysis was performed to assess a putative correlation between these traits and the identified polymorphisms.ConclusionIn this work we identified allelic variants with putative impact on C3′H and HQT proteins which are significantly associated with chlorogenic acid content and antioxidant activity. Further study of these alleles should be explored to assess putative relevance as genetic markers correlating with Cynara cardunculus biological properties with further confirmation by functional analysis.

Identification of novel alleles induced by EMS-mutagenesis in key genes of kernel hardness and starch biosynthesis in wheat by TILLING

To identify novel allelic variations in key genes of wheat quality, the present study used the targeting induced local lesions in genomes platform to detect point mutations in target genes. The wheat variety Longfumai 17 was treated by the mutagen ethyl methanesulfonate to produce a bulk M2 generation, and the population included 1122 plants. A total length of 3906.80 kb nucleotides was analyzed, and the average mutation density was 1/244.17 kb. The identified mutations included G>A substitutions (43.75%), C>T substitutions (31.25%), A insertions (12.50%), T insertions (6.25%), and deletions (6.25%). These point mutations led to changes in amino acids and thus the encoded protein sequences, ultimately producing 18.75% of missense mutations, 12.50% of frame shift mutations, 6.25% of nonsense mutations, 25.00% of silent mutations and 37.50% of non-coding region mutations. In the kernel hardness gene Pinb and 3 starch synthesis genes waxy, Agp2 and SSIIa-A, we detected 16 different point mutations in 25 mutant lines. The Pinb gene harbored two missense mutations and a nonsense mutation; the C>T missense mutation resulted in a novel allele, this novel allele and the nonsense mutation alerted protein 3D structure; the waxy gene presented missense and frame shift mutations; the Agp2 gene carried a missense mutation; the SSIIa-A incurred a missense mutation and a frame shift mutation that resulted in premature protein termination. All the frame shift mutations, nonsense mutations and the Pinb novel allele resulted in allelic variation of their corresponding genes, which in turn affected their gene functions. The identified mutant lines can be used as intermediate materials in wheat quality improvement schemes.

Polymorphic Variants of SCN1A and EPHX1 Influence Plasma Carbamazepine Concentration, Metabolism and Pharmacoresistance in a Population of Kosovar Albanian Epileptic Patients.

AimThe present study aimed to evaluate the effects of gene variants in key genes influencing pharmacokinetic and pharmacodynamic of carbamazepine (CBZ) on the response in patients with epilepsy.Materials & MethodsFive SNPs in two candidate genes influencing CBZ transport and metabolism, namely ABCB1 or EPHX1, and CBZ response SCN1A (sodium channel) were genotyped in 145 epileptic patients treated with CBZ as monotherapy and 100 age and sex matched healthy controls. Plasma concentrations of CBZ, carbamazepine-10,11-epoxide (CBZE) and carbamazepine-10,11-trans dihydrodiol (CBZD) were determined by HPLC-UV-DAD and adjusted for CBZ dosage/kg of body weight.ResultsThe presence of the SCN1A IVS5-91G>A variant allele is associated with increased epilepsy susceptibility. Furthermore, carriers of the SCN1A IVS5-91G>A variant or of EPHX1 c.337T>C variant presented significantly lower levels of plasma CBZ compared to carriers of the common alleles (0.71±0.28 vs 1.11±0.69 μg/mL per mg/Kg for SCN1A IVS5-91 AA vs GG and 0.76±0.16 vs 0.94±0.49 μg/mL per mg/Kg for EPHX1 c.337 CC vs TT; P<0.05 for both). Carriers of the EPHX1 c.416A>G showed a reduced microsomal epoxide hydrolase activity as reflected by a significantly decreased ratio of CBZD to CBZ (0.13±0.08 to 0.26±0.17, p<0.05) also of CBZD to CBZE (1.74±1.06 to 3.08±2.90; P<0.05) and CDRCBZD (0.13±0.08 vs 0.24±0.19 μg/mL per mg/Kg; P<0.05). ABCB1 3455C>T SNP and SCN1A 3148A>G variants were not associated with significant changes in CBZ pharmacokinetic. Patients resistant to CBZ treatment showed increased dosage of CBZ (657±285 vs 489±231 mg/day; P<0.001) but also increased plasma levels of CBZ (9.84±4.37 vs 7.41±3.43 μg/mL; P<0.001) compared to patients responsive to CBZ treatment. CBZ resistance was not related to any of the SNPs investigated.ConclusionsThe SCN1A IVS5-91G>A SNP is associated with susceptibility to epilepsy. SNPs in EPHX1 gene are influencing CBZ metabolism and disposition. CBZ plasma levels are not an indicator of resistance to the therapy.

69 Association of TERC Related Genetic Variation and Telomerase Activity with Ventricular Arrhythmias in Ischaemic Cardiomtyopathy

<h3>Introduction</h3> Implantable cardioverter defibrillators (ICD) reduce mortality in ischaemic cardiomyopathy patients at a high risk of ventricular arrhythmias (VA), which are the commonest cause of sudden death. However, ICDs are associated with morbidity and mortality. Importantly 67% of patients never receive an appropriate shock after ICD implantation under current guidelines, suggesting a need for better risk stratification. Telomere and telomerase activity (TA) in leukocytes have recently been shown to correlate with biological ageing and pathogenesis of cardiovascular diseases. Telomerase maintains telomere length and is composed of reverse transcriptase TERT and RNA template TERC. Evidence suggests that genetic variation in key genes has a key impact on TA. Association of SNP12696304 on chromosome 3q26 (at a locus that includes TERC) with telomere length has been shown. We investigated the association between genetic variation in SNP12696304 and leukocyte TA with incidence of VA in ischaemic cardiomyopathy patients. <h3>Methods</h3> 90 ischaemic cardiomyopathy Caucasian patients with primary prevention ICDs were recruited. Genomic DNA was isolated from venous blood samples. TA was measured by the telomere repeat amplification protocol and genotyping done using Taqman SNP assay. Continuous data were compared by unpaired T-test and categorical data by Chi-square test. Logistic regression was used to determine correlation of genotype and TA with VA. <h3>Results</h3> There was no significant difference in baseline demographics between patients with VA(Cases) and no-VA(Controls) as shown in Table 1. The TA was significantly higher in the cases and correlated with incidence of VA (p-value 0.02). No significant correlation between the genotype and VA was identified (C/C OR 1; C/G OR 0.54, CI 0.21 – 1.417, p-value 0.343; G/G OR 0.80, CI 0.198 – 3.236, p-value 0.907). There was a significant correlation between risk of VA and TA increase in C/C genotype (OR7.5, CI1–56.6, p-value 0.04). This correlation was not significant in the G/G or C/G genotype as shown in Figure 1. <h3>Conclusion</h3> There is a significant correlation between TA and VA in ischaemic cardiomyopathy patients. Moreover, homozygosity for C allele of SNP 12696304 (encoding TERC) significantly effects telomerase expression. Thus, increased TA predisposes individuals with C/C genotype to a higher incidence of VA. TA in this genotype can be developed as a biomarker to predict VA and guide ICD prescription in ischaemic cardiomyopathy.

Voľba lesného reprodukčného materiálu v podmienkach klimatickej zmeny / Choice of forest reproductive material under conditions of climate change

AbstractClimate change may endanger not only yield and fulfilling the social functions of European forests, but even the survival of several tree species. The study emphasises the complexity of climatic factors and physiological mechanisms, which may potentially endanger the persistence of tree populations and which cannot be reduced to problems of drought and temperature increase. A substantial inter-population variation in traits associated with the response to climatic stress, observed in provenance experiments, is a prerequisite for the choice of proper forest reproductive material (FRM) in reforestation as a strategy of climate-change mitigation. Assisted migration, i.e., transfer of FRM from source regions, currently characterised by such climate characteristics, which are expected in the target regions in the future, requires knowledge of key stress factors (depending on the climate scenario), physiological processes associated with the adaptation to this stress, identification of genes and eventually epigenetic mechanisms, controlling adaptation processes, and finally mapping of genetic and/or epigenetic variation in key genes. For most tree species, such information is not yet available. Therefore, assisted migration under such information uncertainty needs to be complemented by in situ gene conservation measures to preserve the possibility of reversing the effects of eventual erroneous decisions on FRM transfer.

23Association of TERC related genetic variation and telomerase activity with ventricular arrhythmias in ischaemic cardiomyopathy

Introduction: Implantable cardioverter defibrillators (ICD) reduce mortality in ischaemic cardiomyopathy patients at a high risk of ventricular arrhythmias (VA), which are the commonest cause of sudden death. However, ICDs are associated with morbidity and mortality. Importantly, 67% of patients never receive an appropriate shock after ICD implantation under current guidelines, suggesting a need for better risk stratification.Telomere and telomerase activity (TA) in leukocytes have recently been shown to correlate with biological ageing and pathogenesis of cardiovascular diseases. Telomerase maintains telomere length and is composed of a reverse transcriptase, TERT, and an RNA template, TERC. Evidence suggests that genetic variation in key genes has a key impact on TA. Association of SNP12696304 on chromosome 3q26 (at a locus that includes TERC) with telomere length has been shown. We investigated the association between genetic variation in SNP12696304 and leukocyte TA with incidence of VA in ischaemic cardiomyopathy patients. Methods: 90 ischaemic cardiomyopathy Caucasian patients with primary prevention ICDs were recruited. Genomic DNA was isolated from venous blood samples. TA was measured by the telomere repeat amplification (TRAP) protocol and genotyping done using Taqman SNP assay. Continuous data were compared by unpaired T-test and categorical data by Chi-square test. Logistic regression was used to determine correlation of genotype and TA with VA. Results: There was no significant difference in baseline demographics including age, WCC, gender, LVEF, GFR and follow up since ICD implant between patients with VA (Cases) and no-VA (Controls). The TA was significantly higher in the cases and correlated with incidence of VA (p-value 0.02). No significant correlation between the genotype and VA was identified (C/C OR 1; C/G OR 0.54, CI 0.21–1.417, p-value 0.343; G/G OR 0.80, CI 0.198–3.236, p-value 0.907). There was a significant correlation between risk of VA and TA increase in C/C genotype (OR7.5, CI1-56.6, p-value 0.04). This correlation was not significant in the G/G or C/G genotype as shown in Conclusion: There is a significant correlation between TA and VA in ischaemic cardiomyopathy patients. Moreover, homozygosity for C-allele of SNP12696304 (encoding TERC) signifcantly effects telomerase expression. Thus, increased TA predisposes individuals with C/C genotype to a higher incidence of VA. This needs to be validated in prospective studies for clinical use. ![Graphic][1] Figure 1 TA and genotype - cases vs controls [1]: /embed/inline-graphic-1.gif

Genetic variation in key genes associated with statin therapy in the Azores Islands (Portugal) healthy population

Background: Inter-individual variation in response to statins (efficacy and toxicity) has been described and may be due to polymorphisms implicated in drug pharmacokinetics or pharmacodynamics.Aim: This study investigates clinically relevant pharmacogenes underlying statin response in 170 healthy Azoreans.Methods: Eight SNPs in candidate genes—HMGCR (rs3846662, rs17238540, rs17244841), CETP (rs708272), APOE (rs7412, rs429358) and SLCO1B1 (rs2306283, rs4149056)—were genotyped.Results: The allele frequencies were similar to those reported for European derived populations, excepting SLCO1B1 c.388A>G (rs2306283), which has a significant difference when compared with the HapMap CEU population (p = 1 × 10−8). The results of statin efficacy showed that 9.1% of Azoreans are APOE4 carriers. This allele has been associated with lower LDLc reduction from statin therapy and also higher LDLc levels at baseline. Regarding SLCO1B1, associated with statin toxicity, 1.8% of individuals have two reduced-function alleles (c.521CC).Conclusion: The results contribute to overcome the lack of knowledge regarding the frequency of pharmacogenetic SNPs and their corresponding haplotypes in targeted populations, such as Azores islands. Moreover, the present work constitutes an initial step to implementing pharmacogenomics in clinical practice where physicians could use a patient’s genetic make-up to optimize statin therapy, regarding efficiency and myopathy risk.