Polymorphisms in transcription factor binding sites and enhancer regions and pancreatic ductal adenocarcinoma risk

Genome-wide association studies (GWAS) are a powerful tool for detecting variants associated with complex traits and can help risk stratification and prevention strategies against pancreatic ductal adenocarcinoma (PDAC). However, the strict significance threshold commonly used makes it likely that many true risk loci are missed. Functional annotation of GWAS polymorphisms is a proven strategy to identify additional risk loci. We aimed to investigate single-nucleotide polymorphisms (SNP) in regulatory regions [transcription factor binding sites (TFBSs) and enhancers] that could change the expression profile of multiple genes they act upon and thereby modify PDAC risk. We analyzed a total of 12,636 PDAC cases and 43,443 controls from PanScan/PanC4 and the East Asian GWAS (discovery populations), and the PANDoRA consortium (replication population). We identified four associations that reached study-wide statistical significance in the overall meta-analysis: rs2472632(A) (enhancer variant, OR 1.10, 95%CI 1.06,1.13, p = 5.5 × 10−8), rs17358295(G) (enhancer variant, OR 1.16, 95%CI 1.10,1.22, p = 6.1 × 10−7), rs2232079(T) (TFBS variant, OR 0.88, 95%CI 0.83,0.93, p = 6.4 × 10−6) and rs10025845(A) (TFBS variant, OR 1.88, 95%CI 1.50,1.12, p = 1.32 × 10−5). The SNP with the most significant association, rs2472632, is located in an enhancer predicted to target the coiled-coil domain containing 34 oncogene. Our results provide new insights into genetic risk factors for PDAC by a focused analysis of polymorphisms in regulatory regions and demonstrating the usefulness of functional prioritization to identify loci associated with PDAC risk.</p

Polymorphisms in transcription factor binding sites and enhancer regions and pancreatic ductal adenocarcinoma risk

Genome-wide association studies (GWAS) are a powerful tool for detecting variants associated with complex traits and can help risk stratification and prevention strategies against pancreatic ductal adenocarcinoma (PDAC). However, the strict significance threshold commonly used makes it likely that many true risk loci are missed. Functional annotation of GWAS polymorphisms is a proven strategy to identify additional risk loci. We aimed to investigate single-nucleotide polymorphisms (SNP) in regulatory regions [transcription factor binding sites (TFBSs) and enhancers] that could change the expression profile of multiple genes they act upon and thereby modify PDAC risk. We analyzed a total of 12,636 PDAC cases and 43,443 controls from PanScan/PanC4 and the East Asian GWAS (discovery populations), and the PANDoRA consortium (replication population). We identified four associations that reached study-wide statistical significance in the overall meta-analysis: rs2472632(A) (enhancer variant, OR 1.10, 95%CI 1.06,1.13, p = 5.5 × 10−8), rs17358295(G) (enhancer variant, OR 1.16, 95%CI 1.10,1.22, p = 6.1 × 10−7), rs2232079(T) (TFBS variant, OR 0.88, 95%CI 0.83,0.93, p = 6.4 × 10−6) and rs10025845(A) (TFBS variant, OR 1.88, 95%CI 1.50,1.12, p = 1.32 × 10−5). The SNP with the most significant association, rs2472632, is located in an enhancer predicted to target the coiled-coil domain containing 34 oncogene. Our results provide new insights into genetic risk factors for PDAC by a focused analysis of polymorphisms in regulatory regions and demonstrating the usefulness of functional prioritization to identify loci associated with PDAC risk.</p

Genetic determinants of telomere length and risk of pancreatic cancer: A PANDoRA study

Telomere deregulation is a hallmark of cancer. Telomere length measured in lymphocytes (LTL) has been shown to be a risk marker for several cancers. For pancreatic ductal adenocarcinoma (PDAC) consensus is lacking whether risk is associated with long or short telomeres. Mendelian randomization approaches have shown that a score built from SNPs associated with LTL could be used as a robust risk marker. We explored this approach in a large scale study within the PANcreatic Disease ReseArch (PANDoRA) consortium. We analyzed 10 SNPs (ZNF676-rs409627, TERT-rs2736100, CTC1-rs3027234, DHX35-rs6028466, PXK-rs6772228, NAF1-rs7675998, ZNF208-rs8105767, OBFC1-rs9420907, ACYP2-rs11125529 and TERC-rs10936599) alone and combined in a LTL genetic score (“teloscore”, which explains 2.2% of the telomere variability) in relation to PDAC risk in 2,374 cases and 4,326 controls. We identified several associations with PDAC risk, among which the strongest were with the TERT-rs2736100 SNP (OR = 1.54; 95%CI 1.35–1.76; p = 1.54 × 10−10) and a novel one with the NAF1-rs7675998 SNP (OR = 0.80; 95%CI 0.73–0.88; p = 1.87 × 10−6, ptrend = 3.27 × 10−7). The association of short LTL, measured by the teloscore, with PDAC risk reached genome-wide significance (p = 2.98 × 10−9 for highest vs. lowest quintile; p = 1.82 × 10−10 as a continuous variable). In conclusion, we present a novel genome-wide candidate SNP for PDAC risk (TERT-rs2736100), a completely new signal (NAF1-rs7675998) approaching genome-wide significance and we report a strong association between the teloscore and risk of pancreatic cancer, suggesting that telomeres are a potential risk factor for pancreatic cancer

Toxicity of parked motor vehicle indoor air

The interior of motor vehicles is made of a wide variety of synthetic materials, which emit volatile organic compounds (VOC). We tested the health effects of emissions from vehicles exposed to "parked in sunshine" conditions. A new and a 3 year old vehicle with identical interior were exposed to 14 000 W of light. Indoor air was analyzed by GC-MS. Toxicity of extracts of indoor air was assayed in human primary keratinocytes, human lung epithelial A549 cell line, and Chinese hamster V79 lung fibroblasts. In addition, toxicity after metabolic activation by CYP1A1, CYP1A2, CYP1B1, CYP2A6, CYP2B6, and CYP2E1 was assayed. The effect on type I allergic reaction (IgE-mediated immune response), type IV allergic reaction (T-cell mediated immune response), and irritative potential was evaluated also. A total of 10.9 and 1.2 mg/m(3) VOC were found in new and used motor vehicle indoor air, respectively. The major compounds in the new vehicle were o,m,p-xylenes, C-3 and C-4-alkylbenzenes, dodecane, tridecane, and methylpyrrolidinone. In the used vehicle they were acetone, methylpyrrolidinone, methylcyclohexane, acetaldehyde, o,m,p-xylenes, ethylhexanol, and toluene. No toxicity was observed in any cell line with or without metabolic activation. Neither did we find an effect on type IV sensitization or an irritative potential. A slight but statistically significant aggravating effect on IgE-mediated immune response of only the new vehicle indoor air was determined (p < 0.05). The IgE-response modulating effect of indoor air might be relevant for atopic individuals. Else no direct toxicity, no toxicity after metabolic activation by cytochrome P450, and no irritative or type IV sensitizing potential of motor vehicle indoor air were found, neither from the new nor used vehicle. Our investigations indicated no apparent health hazard of parked motor vehicle indoor air

ATM protein-dependent phosphorylation of Rad50 protein regulates DNA repair and cell cycle control

The Mre11/Rad50/NBN complex plays a central role in coordinating the cellular response to DNA double-strand breaks. The importance of Rad50 in that response is evident from the recent description of a patient with Rad50 deficiency characterized by chromosomal instability and defective ATM-dependent signaling. We report here that ATM (defective in ataxia-telangiectasia) phosphorylates Rad50 at a single site (Ser-635) that plays an important adaptor role in signaling for cell cycle control and DNA repair. Although a Rad50 phosphosite-specific mutant (S635G) supported normal activation of ATM in Rad50-deficient cells, it was defective in correcting DNA damage-induced signaling through the ATM-dependent substrate SMC1. This mutant also failed to correct radiosensitivity, DNA double-strand break repair, and an S-phase checkpoint defect in Rad50-deficient cells. This was not due to disruption of the Mre11/Rad50/NBN complex revealing for the first time that phosphorylation of Rad50 plays a key regulatory role as an adaptor for specific ATM-dependent downstream signaling through SMC1 for DNA repair and cell cycle checkpoint control in the maintenance of genome integrity

Bioavailability of vitamins A and E from whole and vitamin-fortified milks in control subjects

Background: Dairy products fortified with vitamins and minerals represent a growing market that is of interest to those sectors of the population with unbalanced diets and increased needs. However, there is little information on the bioavailability of micronutrients in milk products at dietary intake levels. Aim of the study: To evaluate the bioavailability of vitamins A and E in whole milk and fortified whole and skimmed milk in control subjects.Methods: A single-dose bioavailability study was performed using three commercially available milks (unfortified whole milk and whole and skimmed milk fortified with vitamins A and E). Nineteen volunteers (10 women and 9 men) ingested 430 ml of each milk on different days. The contents of retinol and α-tocopherol provided in the milks and the retinyl esters and α-tocopherol in triglyceride-rich lipoprotein fractions (TRL) from plasma collected for 6.5 h postprandially were assayed using a quality-controlled HPLC method. The relative absorption of vitamins A and E from milks was calculated on the basis of area under the curve (AUC) versus time curve estimations, adjusted for plasma volume and expressed as percentage of the amount of nutrient provided. Results: The total amounts of retinol and α-tocopherol provided ranged between 0.48 and 4.15 μmol and 0.41 and 32.49 μmol, respectively. The AUC value of retinyl palmitate in TRL was higher for fortified whole milk than for the other two milks (unfortified whole and fortified skimmed milk). The percent relative absorption of vitamin A did not differ among the three types of milk. The AUC for α-tocopherol was no different after the ingestion of any of these milks. Conclusion: The mean percentage of retinol absorption was apparently similar for the three types of milk, regardless of the amount of fat ingested with each type of milk and the vitamin A provided. © 2006 Steinkopff Verlag.Peer Reviewe

A WAO - ARIA - GA²LEN consensus document on molecular-based allergy diagnostics.

Molecular-based allergy (MA) diagnostics is an approach used to map the allergen sensitization of a patient at a molecular level, using purified natural or recombinant allergenic molecules (allergen components) instead of allergen extracts. Since its introduction, MA diagnostics has increasingly entered routine care, with currently more than 130 allergenic molecules commercially available for in vitro specific IgE (sIgE) testing.MA diagnostics allows for an increased accuracy in allergy diagnosis and prognosis and plays an important role in three key aspects of allergy diagnosis: (1) resolving genuine versus cross-reactive sensitization in poly-sensitized patients, thereby improving the understanding of triggering allergens; (2) assessing, in selected cases, the risk of severe, systemic versus mild, local reactions in food allergy, thereby reducing unnecessary anxiety for the patient and the need for food challenge testing; and (3) identifying patients and triggering allergens for specific immunotherapy (SIT).Singleplex and multiplex measurement platforms are available for MA diagnostics. The Immuno-Solid phase Allergen Chip (ISAC) is the most comprehensive platform currently available, which involves a biochip technology to measure sIgE antibodies against more than one hundred allergenic molecules in a single assay. As the field of MA diagnostics advances, future work needs to focus on large-scale, population-based studies involving practical applications, elucidation and expansion of additional allergenic molecules, and support for appropriate test interpretation. With the rapidly expanding evidence-base for MA diagnosis, there is a need for allergists to keep abreast of the latest information. The aim of this consensus document is to provide a practical guide for the indications, determination, and interpretation of MA diagnostics for clinicians trained in allergology