Genetic-Epigenetic Interactions in Asthma Revealed by a Genome-Wide Gene-Centric Search

OBJECTIVES

There is evidence to suggest that asthma pathogenesis is affected by both genetic and epigenetic variation independently, and there is some evidence to suggest that genetic-epigenetic interactions affect risk of asthma. However, little research has been done to identify such interactions on a genome-wide scale. The aim of this studies was to identify genes with genetic-epigenetic interactions associated with asthma.

METHODS

Using asthma case-control data, we applied a novel nonparametric gene-centric approach to test for interactions between multiple SNPs and CpG sites simultaneously in the vicinities of 18,178 genes across the genome.

RESULTS

Twelve genes, PF4, ATF3, TPRA1, HOPX, SCARNA18, STC1, OR10K1, UPK1B, LOC101928523, LHX6, CHMP4B, and LANCL1, exhibited statistically significant SNP-CpG interactions (false discovery rate = 0.05). Of these, three have previously been implicated in asthma risk (PF4, ATF3, and TPRA1). Follow-up analysis revealed statistically significant pairwise SNP-CpG interactions for several of these genes, including SCARNA18, LHX6, and LOC101928523 (p = 1.33E-04, 8.21E-04, 1.11E-03, respectively).

CONCLUSIONS

Joint effects of genetic and epigenetic variation may play an important role in asthma pathogenesis. Statistical methods that simultaneously account for multiple variations across chromosomal regions may be needed to detect these types of effects on a genome-wide scale.

High-performance small- and wide-angle X-ray scattering (SAXS/WAXS) experiments on a multi-functional laboratory goniometer platform with easily exchangeable X-ray modules

Small-angle X-ray scattering (SAXS) is a well-established, versatile technique for the analysis of nanoscale structures and dimensions, e.g., in liquid dispersions, thin solid objects or powder samples. When combined with wide-angle X-ray scattering (WAXS), complementary information about the atomic structure can be obtained. SAXS experiments traditionally require dedicated instruments to achieve the desired angular resolution, sensitivity, stability, and speed of measurement. Here we demonstrate how a multi-functional laboratory goniometer platform, as widely being used for powder X-ray diffraction and for a variety of related techniques, can be configured with pre-aligned X-ray modules that enable advanced SAXS/WAXS experiments, without compromising the exceptional versatility of the instrument. Line and point collimation setups, as well as quick and easy switching between them, are readily possible. Key components are a detachable, evacuated beam path and a high-resolution, low-noise hybrid pixel area detector, in combination with a hardware interface design that allows to configure the instrument with different X-ray modules without the need for re-alignment. Software for SAXS data reduction and analysis was developed. The good SAXS/WAXS performance and the derived analytical results were verified on various test samples, such as gold nanoparticles, colloidal silica, liposomes, dilute protein solutions, and solid polymer samples. It is believed that this novel approach to SAXS/WAXS instrumentation will help to make this powerful structure analysis technique more widely accessible and affordable for multi-user laboratories.

C-Terminal Truncated α-Synuclein Fibrils Contain Strongly Twisted β-Sheets

C-terminal truncations of monomeric wild-type alpha-synuclein (henceforth WT-αS) have been shown to enhance the formation of amyloid aggregates both in vivo and in vitro and have been associated with accelerated progression of Parkinson’s disease (PD). The correlation with PD may not solely be a result of faster aggregation, but also of which fibril polymorphs are preferentially formed when the C-terminal residues are deleted. Considering that different polymorphs are known to result in distinct pathologies, it is important to understand how these truncations affect the organization of αS into fibrils. Here we present high-resolution microscopy and advanced vibrational spectroscopy studies that indicate that the C-terminal truncation variant of αS, lacking residues 109–140 (henceforth referred to as 1–108-αS), forms amyloid fibrils with a distinct structure and morphology. The 1–108-αS fibrils have a unique negative circular dichroism band at ∼230 nm, a feature that differs from the canonical ∼218 nm band usually observed for amyloid fibrils. We show evidence that 1–108-αS fibrils consist of strongly twisted β-sheets with an increased inter-β-sheet distance and a higher solvent exposure than WT-αS fibrils, which is also indicated by the pronounced differences in the 1D-IR (FTIR), 2D-IR, and vibrational circular dichroism spectra. As a result of their distinct β-sheet structure, 1–108-αS fibrils resist incorporation of WT-αS monomers.

Combined Prenatal Pesticide Exposure and Folic Acid Intake in Relation to Autism Spectrum Disorder

BACKGROUND

Maternal folic acid (FA) protects against developmental toxicity from certain environmental chemicals.

OBJECTIVE

We examined combined exposures to maternal FA and pesticides in relation to autism spectrum disorder (ASD).

METHODS

Participants were California children born from 2000-2007 who were enrolled in the Childhood Autism Risks from Genetics and the Environment (CHARGE) case-control study at age 2-5 y, were clinically confirmed to have ASD (n=296) or typical development (n=220), and had information on maternal supplemental FA and pesticide exposures. Maternal supplemental FA and household pesticide product use were retrospectively collected in telephone interviews from 2003-2011. High vs. low daily FA intake was dichotomized at 800μg (median). Mothers' addresses were linked to a statewide database of commercial applications to estimate agricultural pesticide exposure.

RESULTS

High FA intake (≥800μg) during the first pregnancy month and no known pesticide exposure was the reference group for all analyses. Compared with this group, ASD was increased in association with <800μg FA and any indoor pesticide exposure {adjusted odds ratio [OR]=2.5 [95% confidence interval (CI): 1.3, 4.7]} compared with low FA [OR=1.2 (95% CI: 0.7, 2.2)] or indoor pesticides [OR=1.7 (95% CI: 1.1, 2.8)] alone. ORs for the combination of low FA and regular pregnancy exposure (≥6 mo) to pet pesticides or to outdoor sprays and foggers were 3.9 (95% CI: 1.4, 11.5) and 4.1 (95% CI: 1.7, 10.1), respectively. ORs for low maternal FA and agricultural pesticide exposure 3 mo before or after conception were 2.2 (95% CI: 0.7, 6.5) for chlorpyrifos, 2.3 (95% CI: 0.98, 5.3) for organophosphates, 2.1 (95% CI: 0.9, 4.8) for pyrethroids, and 1.5 (95% CI: 0.5, 4.8) for carbamates. Except for carbamates, these ORs were approximately two times greater than those for either exposure alone or for the expected ORs for combined exposures under multiplicative or additive models.

CONCLUSIONS

In this study population, associations between pesticide exposures and ASD were attenuated among those with high versus low FA intake during the first month of pregnancy. Confirmatory and mechanistic studies are needed. https://doi.org/10.1289/EHP604.

Evidence for Intramolecular Antiparallel Beta-Sheet Structure in Alpha-Synuclein Fibrils from a Combination of Two-Dimensional Infrared Spectroscopy and Atomic Force Microscopy

The aggregation of the intrinsically disordered protein alpha-synuclein (αS) into amyloid fibrils is thought to play a central role in the pathology of Parkinson’s disease. Using a combination of techniques (AFM, UV-CD, XRD, and amide-I 1D- and 2D-IR spectroscopy) we show that the structure of αS fibrils varies as a function of ionic strength: fibrils aggregated in low ionic-strength buffers ([NaCl] ≤ 25 mM) have a significantly different structure than fibrils grown in higher ionic-strength buffers. The observations for fibrils aggregated in low-salt buffers are consistent with an extended conformation of αS molecules, forming hydrogen-bonded intermolecular β-sheets that are loosely packed in a parallel fashion. For fibrils aggregated in high-salt buffers (including those prepared in buffers with a physiological salt concentration) the measurements are consistent with αS molecules in a more tightly-packed, antiparallel intramolecular conformation, and suggest a structure characterized by two twisting stacks of approximately five hydrogen-bonded intermolecular β-sheets each. We find evidence that the high-frequency peak in the amide-I spectrum of αS fibrils involves a normal mode that differs fundamentally from the canonical high-frequency antiparallel β-sheet mode. The high sensitivity of the fibril structure to the ionic strength might form the basis of differences in αS-related pathologies.

A New Method for the Synthesis of Organopolyoxometalate Hybrid Compounds

The reaction of a quaternary ammonium salt of the tin chloride-substituted polyoxometalate, [PSn(Cl)W11O39]4-, with a variety of n-nucleophiles including primary, secondary, and tertiary amines and a tertiary phosphine, yielded tin-centered Lewis acid-base adducts, [PSn(Cl)W11O39]4--n-nucleophile; with more nucleophilic secondary amines such as diisopropylamine, apparently some [PSnN[CH(CH3)2]2W11O39]4- was formed as a minor product. The compounds were identified by 1H, 119Sn, 15N, 31P, and 183W NMR, ESI-MS, and elemental analyses. The key connectivity of the Sn-Cl center with the amine was clarified by the observation of 3J Sn-H couplings (Sn from the polyoxometalate cluster and H from the amine moiety) in a 2D 119Sn-1H heteronuclear multiple-bond correlation NMR experiment. This new, rather simple synthetic method was also utilized for preparing amino acid-polyoxometalate hybrid compounds.

Regioselective Alkene Carbon−Carbon Bond Cleavage to Aldehydes and Chemoselective Alcohol Oxidation of Allylic Alcohols with Hydrogen Peroxide Catalyzed by [cis-Ru(II)(dmp)2(H2O)2]2+ (dmp = 2,9-dimethylphenanthroline)

[reaction: see text] [cis-Ru(II)(dmp)2(H2O)2]2+ (dmp = 2,9-dimethylphenanthroline) was found to be a selective oxidation catalyst using hydrogen peroxide as oxidant. Thus, primary alkenes were very efficiently oxidized via direct carbon-carbon bond cleavage to the corresponding aldehydes as an alternative to ozonolysis. Secondary alkenes were much less reactive, leading to regioselective oxidation of substrates such as 4-vinylcyclohexene and 7-methyl-1,6-octadiene at the terminal position. Primary allylic alcohols were chemoselectively oxidized to the corresponding allylic aldehydes, e.g., geraniol to citral.

Carbon-carbon and carbon-nitrogen coupling reactions catalyzed by palladium nanoparticles derived from a palladium substituted Keggin-type polyoxometalate

Palladium 15-20 nm particles stabilized by a Keggin-type polyoxometalate were prepared by reduction of K(5)PPdW(11)O(39) with H(2). The nanoparticles were shown to be effective catalysts for Suzuki-, Heck-, and Stille-type carbon-carbon coupling and carbon-nitrogen coupling reactions of bromoarenes in aqueous media. Chloroarenes were also reactive in reaction media without solvent. [reaction: see text]