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Retromer is a heteropentameric complex that plays a specialized role in endosomal protein sorting and trafficking. Here, we report a reduction in the retromer proteins—vacuolar protein sorting 35 (VPS35), VPS26A, and VPS29—in patients with amyotrophic lateral sclerosis (ALS) and in the ALS model provided by transgenic (Tg) mice expressing the mutant superoxide dismutase-1 G93A. These changes are accompanied by a reduction of levels of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor subunit GluA1, a proxy of retromer function, in spinal cords from Tg SOD1 G93A mice. Correction of the retromer deficit by a viral vector expressing VPS35 exacerbates the paralytic phenotype in Tg SOD1 G93A mice. Conversely, lowering Vps35 levels in Tg SOD1 G93A mice ameliorates the disease phenotype. In light of these findings, we propose that mild alterations in retromer inversely modulate neurodegeneration propensity in ALS.

Background DNA methylation of CpG sites on genetic loci has been linked to increased risk of asthma in children exposed to elevated ambient air pollutants (AAPs). Further identification of specific CpG sites and the pollutants that are associated with methylation of these CpG sites in immune cells could impact our understanding of asthma pathophysiology. In this study, we sought to identify some CpG sites in specific genes that could be associated with asthma regulation (Foxp3 and IL10) and to identify the different AAPs for which exposure prior to the blood draw is linked to methylation levels at these sites. We recruited subjects from Fresno, California, an area known for high levels of AAPs. Blood samples and responses to questionnaires were obtained (n = 188), and in a subset of subjects (n = 33), repeat samples were collected 2 years later. Average measures of AAPs were obtained for 1, 15, 30, 90, 180, and 365 days prior to each blood draw to estimate the short-term vs. long-term effects of the AAP exposures. Results Asthma was significantly associated with higher differentially methylated regions (DMRs) of the Foxp3 promoter region (p = 0.030) and the IL10 intronic region (p = 0.026). Additionally, at the 90-day time period (90 days prior to the blood draw), Foxp3 methylation was positively associated with NO2, CO, and PM2.5 exposures (p = 0.001, p = 0.001, and p = 0.012, respectively). In the subset of subjects retested 2 years later (n = 33), a positive association between AAP exposure and methylation was sustained. There was also a negative correlation between the average Foxp3 methylation of the promoter region and activated Treg levels (p = 0.039) and a positive correlation between the average IL10 methylation of region 3 of intron 4 and IL10 cytokine expression (p = 0.030). Conclusions Short-term and long-term exposures to high levels of CO, NO2, and PM2.5 were associated with alterations in differentially methylated regions of Foxp3. IL10 methylation showed a similar trend. For any given individual, these changes tend to be sustained over time. In addition, asthma was associated with higher differentially methylated regions of Foxp3 and IL10. Electronic supplementary material The online version of this article (10.1186/s13148-017-0433-4) contains supplementary material, which is available to authorized users.

Chronic exposure to mouse allergen may contribute greatly to the inner-city asthma burden. We hypothesized that reducing mouse allergen exposure may modulate the immunopathology underlying symptomatic pediatric allergic asthma, and that this occurs through epigenetic regulation. To test this hypothesis, we studied a cohort of mouse sensitized, persistent asthmatic inner-city children undergoing mouse allergen-targeted integrated pest management (IPM) vs education in a randomized controlled intervention trial. We found that decreasing mouse allergen exposure, but not cockroach, was associated with reduced FOXP3 buccal DNA promoter methylation, but this was unrelated to mouse specific IgE production. This finding suggests that the environmental epigenetic regulation of an immunomodulatory gene may occur following changing allergen exposures in some highly exposed cohorts. Given the clinical and public health importance of inner-city pediatric asthma and the potential impact of environmental interventions, further studies will be needed to corroborate changes in epigenetic regulation following changing exposures over time, and determine their impact on asthma morbidity in susceptible children.

Primers for PCR and pyrosequencing experiments. Table S2. Correlations of day 1 vs. day 6 FOXP3 methylation and mRNA expression. Table S3. Among children with high BC exposure, there is a trend towards active children (coded 1) having a greater odds of lower methylation compared to non-active children (coded 0). Table S4. Higher FOXP3 promoter 2 methylation is associated with overall lower lung function (nâ =â 135). Table S5. The relationship between FOXP3 promoter 2 methylation and lung function does not significantly vary by high vs. low BC exposure. Table S6. Among children with high BC, the association between physical activity and FOXP3 promoter methylation is greater in females. Table S7. The relationship between FOXP3 promoter methylation and lung function is greater among females compared to that among males.

Primers for PCR and pyrosequencing experiments. Table S2. Correlations of day 1 vs. day 6 FOXP3 methylation and mRNA expression. Table S3. Among children with high BC exposure, there is a trend towards active children (coded 1) having a greater odds of lower methylation compared to non-active children (coded 0). Table S4. Higher FOXP3 promoter 2 methylation is associated with overall lower lung function (nâ =â 135). Table S5. The relationship between FOXP3 promoter 2 methylation and lung function does not significantly vary by high vs. low BC exposure. Table S6. Among children with high BC, the association between physical activity and FOXP3 promoter methylation is greater in females. Table S7. The relationship between FOXP3 promoter methylation and lung function is greater among females compared to that among males.

Sampling scheme for accelerometer, black carbon (BC), buccal swabs for DNA and RNA analysis and spirometry. Figure S2. Schematic representation of the FOXP3 gene and the six CpG sites in the promoter region that were investigated. TSS transcription start site, TSDR Treg-specific demethylated region, CNS conserved non-coding sequence. Figure S3. Correlations of FOXP3 methylation across promoter regions and with mRNA relative expression. Figure S4. Distribution of FOXP3 promoter methylation in females vs. males stratified by physical activity (active vs. non-active). Females have lower FOXP3 promoter methylation compared to males. Figure S5. Distribution of FOXP3 promoter methylation in females vs. males stratified by BC concentration (low vs. high). Females have lower FOXP3 promoter methylation compared to males. Figure S6. Distribution of FOXP3 promoter methylation stratified by combined activity and BC concentration in females (n = 67). Figure S7. Distribution of FOXP3 promoter methylation stratified by combined activity and BC concentration in males (n = 68).

Sampling scheme for accelerometer, black carbon (BC), buccal swabs for DNA and RNA analysis and spirometry. Figure S2. Schematic representation of the FOXP3 gene and the six CpG sites in the promoter region that were investigated. TSS transcription start site, TSDR Treg-specific demethylated region, CNS conserved non-coding sequence. Figure S3. Correlations of FOXP3 methylation across promoter regions and with mRNA relative expression. Figure S4. Distribution of FOXP3 promoter methylation in females vs. males stratified by physical activity (active vs. non-active). Females have lower FOXP3 promoter methylation compared to males. Figure S5. Distribution of FOXP3 promoter methylation in females vs. males stratified by BC concentration (low vs. high). Females have lower FOXP3 promoter methylation compared to males. Figure S6. Distribution of FOXP3 promoter methylation stratified by combined activity and BC concentration in females (n = 67). Figure S7. Distribution of FOXP3 promoter methylation stratified by combined activity and BC concentration in males (n = 68).

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