TRAF3IP2-IL-17 Axis Strengthens the Gingival Defense against Pathogens

Recent genome-wide association studies have suggested novel risk loci associated with periodontitis, which is initiated by dysbiosis in subgingival plaque and leads to destruction of teeth-supporting structures. One such genetic locus was the tumor necrosis factor receptor-associated factor 3 interacting protein 2 (TRAF3IP2), a gene encoding the gate-keeping interleukin (IL)-17 receptor adaptor. In this study, we first determined that carriers of the lead exonic variant rs13190932 within the TRAF3IP2 locus combined with a high plaque microbial burden was associated with more severe periodontitis than noncarriers. We then demonstrated that TRAF3IP2 is essential in the IL-17-mediated CCL2 and IL-8 chemokine production in primary gingival epithelial cells. Further analysis suggested that rs13190932 may serve a surrogate variant for a genuine loss-of-function variant rs33980500 within the same gene. Traf3ip2 null mice (Traf3ip2^-/-) were more susceptible than wild-type (WT) mice to the Porphyromonas gingivalis-induced periodontal alveolar bone loss. Such bone loss was associated with a delayed P. gingivalis clearance and an attenuated neutrophil recruitment in the gingiva of Traf3ip2^-/- mice. Transcriptomic data showed decreased expression of antimicrobial genes, including Lcn2, S100a8, and Defb1, in the Traf3ip2^-/- mouse gingiva in comparison to WT mice prior to or upon P. gingivalis oral challenge. Further 16S ribosomal RNA sequencing analysis identified a distinct microbial community in the Traf3ip2^-/- mouse oral plaque, which was featured by a reduced microbial diversity and an overabundance of Streptococcus genus bacteria. More P. gingivalis was observed in the Traf3ip2^-/- mouse gingiva than WT control animals in a ligature-promoted P. gingivalis invasion model. In agreement, neutrophil depletion resulted in more local gingival tissue invasion by P. gingivalis. Thus, we identified a homeostatic IL-17-TRAF3IP2-neutrophil axis underpinning host defense against a keystone periodontal pathogen.

DNA methylation differences in monozygotic twins with Van der Woude syndrome

Introduction

Van der Woude Syndrome (VWS) is an autosomal dominant disorder responsible for 2% of all syndromic orofacial clefts (OFCs) with IRF6 being the primary causal gene (70%). Cases may present with lip pits and either cleft lip, cleft lip with cleft palate, or cleft palate, with marked phenotypic discordance even among individuals carrying the same mutation. This suggests that genetic or epigenetic modifiers may play additional roles in the syndrome's etiology and variability in expression. We report the first DNA methylation profiling of 2 pairs of monozygotic twins with VWS. Our goal is to explore epigenetic contributions to VWS etiology and variable phenotypic expressivity by comparing DNAm profiles in both twin pairs. While the mutations that cause VWS in these twins are known, the additional mechanism behind their phenotypic risk and variability in expression remains unclear.

Methods

We generated whole genome DNAm data for both twin pairs. Differentially methylated positions (DMPs) were selected based on: (1) a coefficient of variation in DNAm levels in unaffected individuals < 20%, and (2) intra-twin pair absolute difference in DNAm levels >5% (delta beta > | 0.05|). We then divided the DMPs in two subgroups for each twin pair for further analysis: (1) higher methylation levels in twin A (Twin A > Twin B); and (2) higher methylation levels in twin B (Twin B >Twin A).

Results and Discussion

Gene ontology analysis revealed a list of enriched genes that showed significant differential DNAm, including clef-associated genes. Among the cleft-associated genes, TP63 was the most significant hit (p=7.82E-12). Both twin pairs presented differential DNAm levels in CpG sites in/near TP63 (Twin 1A > Twin 1B and Twin 2A < Twin 2B). The genes TP63 and IRF6 function in a biological regulatory loop to coordinate epithelial proliferation and differentiation in a process that is critical for palatal fusion. The effects of the causal mutations in IRF6 can be further impacted by epigenetic dysregulation of IRF6 itself, or genes in its pathway. Our data shows evidence that changes in DNAm is a plausible mechanism that can lead to markedly distinct phenotypes, even among individuals carrying the same mutation.

Genome-Wide Scan for Parent-of-Origin Effects in a sub-Saharan African Cohort With Nonsyndromic Cleft Lip and/or Cleft Palate (CL/P)

OBJECTIVE

Nonsyndromic cleft lip and/or cleft palate (NSCL/P) have multifactorial etiology where genetic factors, gene-environment interactions, stochastic factors, gene-gene interactions, and parent-of-origin effects (POEs) play cardinal roles. POEs arise when the parental origin of alleles differentially impacts the phenotype of the offspring. The aim of this study was to identify POEs that can increase risk for NSCL/P in humans using a genome-wide dataset.

METHODS

The samples (174 case-parent trios from Ghana, Ethiopia, and Nigeria) included in this study were from the African only genome wide association studies (GWAS) that was published in 2019. Genotyping of individual DNA using over 2 million multiethnic and African ancestry-specific single-nucleotide polymorphisms from the Illumina Multi-Ethnic Genotyping Array v2 15070954 A2 (genome build GRCh37/hg19) was done at the Center for Inherited Diseases Research. After quality control checks, PLINK was employed to carry out POE analysis employing the pooled subphenotypes of NSCL/P.

RESULTS

We observed possible hints of POEs at a cluster of genes at a 1 mega base pair window at the major histocompatibility complex class 1 locus on chromosome 6, as well as at other loci encompassing candidate genes such as ASB18, ANKEF1, AGAP1, GABRD, HHAT, CCT7, DNMT3A, EPHA7, FOXO3, lncRNAs, microRNA, antisense RNAs, ZNRD1, ZFAT, and ZBTB16.

CONCLUSION

Findings from our study suggest that some loci may increase the risk for NSCL/P through POEs. Additional studies are required to confirm these suggestive loci in NSCL/P etiology.

Genome-wide Gene-by-Sex Interaction Studies Identify Novel Nonsyndromic Orofacial Clefts Risk Locus

Risk loci identified through genome-wide association studies have explained about 25% of the phenotypic variations in nonsyndromic orofacial clefts (nsOFCs) on the liability scale. Despite the notable sex differences in the incidences of the different cleft types, investigation of loci for sex-specific effects has been understudied. To explore the sex-specific effects in genetic etiology of nsOFCs, we conducted a genome-wide gene × sex (GxSex) interaction study in a sub-Saharan African orofacial cleft cohort. The sample included 1,019 nonsyndromic orofacial cleft cases (814 cleft lip with or without cleft palate and 205 cleft palate only) and 2,159 controls recruited from 3 sites (Ethiopia, Ghana, and Nigeria). An additive logistic model was used to examine the joint effects of the genotype and GxSex interaction. Furthermore, we examined loci with suggestive significance (P < 1E-5) in the additive model for the effect of the GxSex interaction only. We identified a novel risk locus on chromosome 8p22 with genome-wide significant joint and GxSex interaction effects (rs2720555, p_2df = 1.16E-08, p_GxSex = 1.49E-09, odds ratio [OR] = 0.44, 95% CI = 0.34 to 0.57). For males, the risk of cleft lip with or without cleft palate at this locus decreases with additional copies of the minor allele (p < 0.0001, OR = 0.60, 95% CI = 0.48 to 0.74), but the effect is reversed for females (p = 0.0004, OR = 1.36, 95% CI = 1.15 to 1.60). We replicated the female-specific effect of this locus in an independent cohort (p = 0.037, OR = 1.30, 95% CI = 1.02 to 1.65), but no significant effect was found for the males (p = 0.29, OR = 0.86, 95% CI = 0.65 to 1.14). This locus is in topologically associating domain with craniofacially expressed and enriched genes during embryonic development. Rare coding mutations of some of these genes were identified in nsOFC cohorts through whole exome sequencing analysis. Our study is additional proof that genome-wide GxSex interaction analysis provides an opportunity for novel findings of loci and genes that contribute to the risk of nsOFCs.

Ultrathin metal-organic framework membrane production by gel-vapour deposition

Ultrathin, molecular sieving membranes composed of microporous materials offer great potential to realize high permeances and selectivities in separation applications, but strategies for their production have remained a challenge. Here we show a route for the scalable production of nanometre-thick metal–organic framework (MOF) molecular sieving membranes, specifically via gel–vapour deposition, which combines sol–gel coating with vapour deposition for solvent-/modification-free and precursor-/time-saving synthesis. The uniform MOF membranes thus prepared have controllable thicknesses, down to ~17 nm, and show one to three orders of magnitude higher gas permeances than those of conventional membranes, up to 215.4 × 10⁻⁷ mol m⁻² s⁻¹ Pa⁻¹ for H₂, and H₂/C₃H₈, CO₂/C₃H₈ and C₃H₆/C₃H₈ selectivities of as high as 3,400, 1,030 and 70, respectively. We further demonstrate the in situ scale-up processing of a MOF membrane module (30 polymeric hollow fibres with membrane area of 340 cm²) without deterioration in selectivity.

MOF-based membranes have shown great promise in separation applications, but producing thin membranes that allow for high fluxes remains challenging. Here, the authors use a gel–vapour deposition strategy to fabricate composite membranes with less than 20 nm thicknesses and high gas permeances and selectivities.

Properties and cellular effects of particulate matter from direct emissions and ambient sources

The pollution of particulate matter (PM) is of great concern in China and many other developing countries. It is generally recognized that the toxicity of PM is source and property dependent. However, the relationship between PM properties and toxicity is still not well understood. In this study, PM samples from direct emissions of wood, straw, coal, diesel combustion, cigarette smoking and ambient air were collected and characterized for their physicochemical properties. Their expression of intracellular reactive oxygen species (ROS) and levels of inflammatory cytokines (i.e., tumor necrosis factor-α (TNF-α)) was measured using a RAW264.7 cell model. Our results demonstrated that the properties of the samples from different origins exhibited remarkable differences. Significant increases in ROS were observed when the cells were exposed to PMs from biomass origins, including wood, straw and cigarettes, while increases in TNF-α were found for all the samples, particularly those from ambient air. The most important factor associated with ROS generation was the presence of water-soluble organic carbon, which was extremely abundant in the samples that directly resulted from biomass combustion. Metals, endotoxins and PM size were the most important properties associated with increases in TNF-α expression levels. The association of the origins of PM particles and physicochemical properties with cytotoxic properties is illustrated using a cluster analysis.

Pharmacokinetics of LJP 993, a tetrameric conjugate of domain 1 of beta2-glycoprotein I for antiphospholipid syndrome

beta2-glycoprotein I is the best-characterized antigenic target for antiphospholipid autoantibodies. We synthesized a tetrameric conjugate of the domain 1 of beta2-glycoprotein I (LJP 993) aimed at developing the conjugate as a Toleragen to suppress antiphospholipid syndrome. The present studies focused on determining the stability, tissue distribution, plasma concentration-time profile and excretion of the LJP 993 in mice. The stability of LJP 993 in mouse plasma was quantitatively evaluated using strong cation-exchange high performance liquid chromatography. ( 125)I-labeled LJP 993 was intravenously injected to mice, and levels of (125)I-labeled LJP 993 in plasma, tissues, urine and feces were determined at known intervals. Incubation of LJP 993 with mouse serum at 37 degrees C for 8 h resulted in a decrease by 34% of LJP 993 concentration. No degradation fragment was observed during the incubation. After a single intravenous administration of (125)I-LJP 993 (0.5 and 5 mg/kg) to mice, both C(max) and area-under-curve values increased in a dose-proportional manner, and blood radioactivity disappeared in a bi-exponential manner with the distribution half-lives equal to 1.7 min, and the elimination half-lives 188 and 281 min, respectively. The (125)I-LJP 993 was moderately distributed into organs and tissues with the exception that brain level of ( 125)I-LJP 993 was negligible. The major sites of (125)I-LJP 993 uptake were the kidney (at 30 min post dosing), and kidney, lung, liver, heart, spleen, skin, muscle and fat tissues (at 4 h post dosing). Cumulative urinary and fecal radioactivity for 0-48 h post dosing accounted for 44.7% and 4.2% of the administered dose, respectively, with the fast rate of urinal excretion occurring within the first 8 h. In summary, LJP 993 was fairly stable in mouse plasma. After administration to mice, (125)I-LJP 993 was taken up mainly by kidney and then distributed extensively to tissues except brain. Both C(max) and area-under-curve values increased in a dose-proportional manner. It was predominantly excreted in the urine with an elimination half-life longer than 3 h. Kidney is a major route to excrete the tetrameric conjugate.

Strong sorption of phenanthrene by condensed organic matter in soils and sediments

The nonhydrolyzable carbon (NHC) and black carbon (BC) in three contaminated soils and seven sediments from the Pearl River Delta and Estuary, China, were isolated upon treatments with an acid hydrolysis method and with a combustion method at 375 degrees C, respectively, and their sorption isotherms for phenanthrene (Phen) were established. It was found that NHC is chemically and structurally different from the biopolymer and humic substances and consists mainly of aliphatic and aromatic carbon using elemental analysis, 13C nuclear magnetic resonance spectroscopy (13C NMR), and Fourier transformed infrared spectroscopy (FTIR). All the sorption isotherms are nonlinear and are well fitted by the Freundlich model. The single-point organic carbon-normalized distribution coefficient (K(oc)) measured for the isolated NHC is 1.3-7.7 times higher than that for the bulk samples at the same aqueous concentration of Phen. The NHC fractions play a dominant role to the overall sorption in the bulk samples. The bulk soils and their NHC fractions have lower sorption capacity than the bulk sediments and their NHC fractions, relating to the different source of organic matter between soils and sediments. The Phen sorption capacity in the NHC samples is related significantlyto H/C ratios and aliphatic carbon, but negatively to aromatic carbon, demonstrating the important role of aliphatic carbon to the Phen sorption and the fate in the investigated soils and sediments.

[Distribution of polybrominated diphenyl ethers in aquatic species from the Pearl River Estuary]

Polybrominated diphenyl ethers (PBDEs) were detected in biota samples collected from the Pearl River Estuary. The concentrations of sigma10 PBDEs (BDE28, 47, 66, 100, 99, 85, 154, 153, 138, 183) in fish species (including Platycephalus indicus, Pseudosiaena crocea , Pampus argenteus, Cynoglossus robustus, and Harpodon nehereus), shrimps (including Metapenaeus ensis and Metapenaeus affinis) and Squilla oratoria were from 37.8 ng x g(-1) to 407.1 ng x g(-1) (normalized to lipid), from 49.0 ng x g(-1) to 239.1 ng x g(-1) and from 142 ng x g(-1) to 444.5 ng x g(-1), respectively. BDE47 was the dominant congener in all biota samples, with a contribution to sigma10 PBDEs ranging from 53.7% to 66.9%. Differences in concentrations of PBDEs and PBDE patterns in different species may be related to the different feeding habit, living environment and uptaking or elimination rate. High ratios of concentrations of PBDEs in liver /muscle in fish species indicated that PBDEs tended to accumulate more in liver than in muscle.

Butyltins in sediments from Santa Monica and San Pedro basins, California

Butyltins have been measured for the first time in sediments from the deeper waters of the Santa Monica and San Pedro (SM/SP) basins of Southern California borderland. Core samples were collected from water depths ranging from 458 m in the shelf to 906 m in the central basin. Surficial and a few subsurface sections from selected cores were analyzed for butyltins. The dominant components are generally dibutyl and monobutyltins (DBT and MBT, respectively). Microbial degradation of Tributyltin (TBT, the most toxic of the butyltin species) to DBT and MBT during the long range transport to deeper basins, as well as a lack of continuing inputs of TBT in the present times could justify the butyltins signatures found in the region. The levels of butyltins are in the lower range (below detection level, <1, to 14 ng of Sn g(-1)) relative to nearshore sediments. However, the results demonstrate that the butyltins are, indeed, found even in the sediments of the central basins of the Southern California borderland suggesting that deeper global oceanic regimes need to be further investigated for these compounds.