Increased Sleep Latency and Decreased Sleep Duration are Associated With Elevated Risk of Bed Sharing Among Mother-Infant Dyads

Bed sharing increases risk of sleep-related infant deaths. We hypothesized that infant sleep difficulties increase bed sharing, independent of social determinants of health (SDOH). In total, 191 mother-infant dyads in a prospective, longitudinal cohort study completed the Brief Infant Sleep Questionnaire at 1, 4, 6, and 12 months. Sleep characteristics at 1 month (latency, duration, night awakenings) were compared between dyads with/without bed sharing in the first 12 months. Infants who participated in bed sharing slept fewer hours at night (7.1 ± 1.7 hours vs 8.3 ± 1.5 hours, P = .001, d = -0.79), and took longer to fall asleep (0.7 ± 0.6 hours vs 0.5 ± 0.5 hours, P = .021, d = 0.43), even when controlling for SDOH variables that influence bed sharing. Maternal perception of sleep problems did not differ between groups (P = .12). Our findings suggest that infants with quantifiable sleep difficulties at 1 month are more likely to bed share.

Comparison of Symptom Duration Between Children With SARS-CoV-2 and Peers With Other Viral Illnesses During the COVID-19 Pandemic

Some children and young people (CYP) with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) experience persistent symptoms, commonly called "long COVID." It remains unclear whether symptoms of SARS-CoV-2 persist longer than those of other respiratory viruses, particularly in young children. This cross-sectional study involved 372 CYP (0-15 years) tested for SARS-CoV-2. Character and duration of symptoms (cough, runny nose, sore throat, rash, diarrhea, vomiting, sore muscles, fatigue, fever, loss of smell) were compared between CYP with a positive test (n = 100) and those with a negative test (n = 272), while controlling for medical/demographic covariates. The average duration of symptoms for CYP with a positive SARS-CoV-2 test (8.5 ± 10 days) did not differ from that of CYP with a negative test (7.2 ± 5 days, P = .71, d = 0.046). A positive SARS-CoV-2 test did not increase the risk (36/372, 10%) of symptoms persisting for ≥3 weeks (odds ratio = 0.96, 95% confidence interval = 0.45-2.0). These results suggest CYP with non-SARS-CoV-2 infections experience a similar duration of symptoms as peers with SARS-CoV-2 infection.

Infant Saliva Microbiome Activity Modulates Nutritional Impacts on Neurodevelopment

Neurodevelopment is influenced by complex interactions between environmental factors, including social determinants of health (SDOH), nutrition, and even the microbiome. This longitudinal cohort study of 142 infants tested the hypothesis that microbial activity modulates the effects of nutrition on neurodevelopment. Salivary microbiome activity was measured at 6 months using RNA sequencing. Infant nutrition was assessed longitudinally with the Infant Feeding Practices survey. The primary outcome was presence/absence of neurodevelopmental delay (NDD) at 18 months on the Survey of Wellbeing in Young Children. A logistic regression model employing two microbial factors, one nutritional factor, and two SDOH accounted for 33.3% of the variance between neurodevelopmental groups (p < 0.001, AIC = 77.7). NDD was associated with Hispanic ethnicity (OR 18.1, 2.36-139.3; p = 0.003), no fish consumption (OR 10.6, 2.0-54.1; p = 0.003), and increased Candidatus Gracilibacteria activity (OR 1.43, 1.00-2.07; p = 0.007). Home built after 1977 (OR 0.02, 0.001-0.53; p = 0.004) and Chlorobi activity (OR 0.76, 0.62-0.93, p = 0.001) were associated with reduced risk of NDD. Microbial alpha diversity modulated the effect of fish consumption on NDD (X2 = 5.7, p = 0.017). These data suggest the benefits of fish consumption for neurodevelopment may be mediated by microbial diversity. Confirmation in a larger, randomized trial is required.

Saliva microRNA Profile in Children with and without Severe SARS-CoV-2 Infection

Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) may impair immune modulating host microRNAs, causing severe disease. Our objectives were to determine the salivary miRNA profile in children with SARS-CoV-2 infection at presentation and compare the expression in those with and without severe outcomes. Children <18 years with SARS-CoV-2 infection evaluated at two hospitals between March 2021 and February 2022 were prospectively enrolled. Severe outcomes included respiratory failure, shock or death. Saliva microRNAs were quantified with RNA sequencing. Data on 197 infected children (severe = 45) were analyzed. Of the known human miRNAs, 1606 (60%) were measured and compared across saliva samples. There were 43 miRNAs with ≥2-fold difference between severe and non-severe cases (adjusted p-value < 0.05). The majority (31/43) were downregulated in severe cases. The largest between-group differences involved miR-4495, miR-296-5p, miR-548ao-3p and miR-1273c. These microRNAs displayed enrichment for 32 gene ontology pathways including viral processing and transforming growth factor beta and Fc-gamma receptor signaling. In conclusion, salivary miRNA levels are perturbed in children with severe COVID-19, with the majority of miRNAs being down regulated. Further studies are required to validate and determine the utility of salivary miRNAs as biomarkers of severe COVID-19.

Refinement of saliva microRNA biomarkers for sports-related concussion

BACKGROUND

Recognizing sport-related concussion (SRC) is challenging and relies heavily on subjective symptom reports. An objective, biological marker could improve recognition and understanding of SRC. There is emerging evidence that salivary micro-ribonucleic acids (miRNAs) may serve as biomarkers of concussion; however, it remains unclear whether concussion-related miRNAs are impacted by exercise. We sought to determine whether 40 miRNAs previously implicated in concussion pathophysiology were affected by participation in a variety of contact and non-contact sports. Our goal was to refine a miRNA-based tool capable of identifying athletes with SRC without the confounding effects of exercise.

METHODS

This case-control study harmonized data from concussed and non-concussed athletes recruited across 10 sites. Levels of salivary miRNAs within 455 samples from 314 individuals were measured with RNA sequencing. Within-subjects testing was used to identify and exclude miRNAs that changed with either (a) a single episode of exercise (166 samples from 83 individuals) or (b) season-long participation in contact sports (212 samples from 106 individuals). The miRNAs that were not impacted by exercise were interrogated for SRC diagnostic utility using logistic regression (172 samples from 75 concussed and 97 non-concussed individuals).

RESULTS

Two miRNAs (miR-532-5p and miR-182-5p) decreased (adjusted p < 0.05) after a single episode of exercise, and 1 miRNA (miR-4510) increased only after contact sports participation. Twenty-three miRNAs changed at the end of a contact sports season. Two of these miRNAs (miR-26b-3p and miR-29c-3p) were associated (R > 0.50; adjusted p < 0.05) with the number of head impacts sustained in a single football practice. Among the 15 miRNAs not confounded by exercise or season-long contact sports participation, 11 demonstrated a significant difference (adjusted p < 0.05) between concussed and non-concussed participants, and 6 displayed moderate ability (area under curve > 0.70) to identify concussion. A single ratio (miR-27a-5p/miR-30a-3p) displayed the highest accuracy (AUC = 0.810, sensitivity = 82.4%, specificity = 73.3%) for differentiating concussed and non-concussed participants. Accuracy did not differ between participants with SRC and non-SRC (z = 0.5, p = 0.60).

CONCLUSION

Salivary miRNA levels may accurately identify SRC when not confounded by exercise. Refinement of this approach in a large cohort of athletes could eventually lead to a non-invasive, sideline adjunct for SRC assessment.

The Association between Infant Colic and the Multi-Omic Composition of Human Milk

Infant colic is a common condition with unclear biologic underpinnings and limited treatment options. We hypothesized that complex molecular networks within human milk (i.e., microbes, micro-ribonucleic acids (miRNAs), cytokines) would contribute to colic risk, while controlling for medical, social, and nutritional variables. This hypothesis was tested in a cohort of 182 breastfed infants, assessed with a modified Infant Colic Scale at 1 month. RNA sequencing was used to interrogate microbial and miRNA features. Luminex assays were used to measure growth factors and cytokines. Milk from mothers of infants with colic (n = 28) displayed higher levels of Staphylococcus (adj. p = 0.038, d = 0.30), miR-224-3p (adj. p = 0.023, d = 0.33), miR-125b-5p (adj. p = 0.028, d = 0.29), let-7a-5p (adj. p = 0.028, d = 0.27), and miR-205-5p (adj. p = 0.029, d = 0.26) compared to milk from non-colic mother-infant dyads (n = 154). Colic symptom severity was directly associated with milk hepatocyte growth factor levels (R = 0.21, p = 0.025). A regression model involving let-7a-5p, miR-29a-3p, and Lactobacillus accurately modeled colic risk (X² = 16.7, p = 0.001). Molecular factors within human milk may impact colic risk, and provide support for a dysbiotic/inflammatory model of colic pathophysiology.

Infant Saliva Levels of microRNA miR-151a-3p Are Associated with Risk for Neurodevelopmental Delay

Prompt recognition of neurodevelopmental delay is critical for optimizing developmental trajectories. Currently, this is achieved with caregiver questionnaires whose sensitivity and specificity can be limited by socioeconomic and cultural factors. This prospective study of 121 term infants tested the hypothesis that microRNA measurement could aid early recognition of infants at risk for neurodevelopmental delay. Levels of four salivary microRNAs implicated in childhood autism (miR-125a-5p, miR-148a-5p, miR-151a-3p, miR-28-3p) were measured at 6 months of age, and compared between infants who displayed risk for neurodevelopmental delay at 18 months (n = 20) and peers with typical development (n = 101), based on clinical evaluation aided by the Survey of Wellbeing in Young Children (SWYC). Accuracy of microRNAs for predicting neurodevelopmental concerns at 18 months was compared to the clinical standard (9-month SWYC). Infants with neurodevelopmental concerns at 18 months displayed higher levels of miR-125a-5p (d = 0.30, p = 0.018, adj p = 0.049), miR-151a-3p (d = 0.30, p = 0.017, adj p = 0.048), and miR-28-3p (d = 0.31, p = 0.014, adj p = 0.048). Levels of miR-151a-3p were associated with an 18-month SWYC score (R = -0.19, p = 0.021) and probability of neurodevelopmental delay at 18 months (OR = 1.91, 95% CI, 1.14-3.19). Salivary levels of miR-151a-3p enhanced predictive accuracy for future neurodevelopmental delay (p = 0.010, X² = 6.71, AUC = 0.71) compared to the 9-month SWYC score alone (OR = 0.56, 95% CI, 0.20-1.58, AUC = 0.567). This pilot study provides evidence that miR-151a-3p may aid the identification of infants at risk for neurodevelopmental delay. External validation of these findings is necessary.

Multi-Omic Factors Associated with Frequency of Upper Respiratory Infections in Developing Infants

Susceptibility to upper respiratory infections (URIs) may be influenced by host, microbial, and environmental factors. We hypothesized that multi-omic analyses of molecular factors in infant saliva would identify complex host-environment interactions associated with URI frequency. A cohort study involving 146 infants was used to assess URI frequency in the first year of life. Saliva was collected at 6 months for high-throughput multi-omic measurement of cytokines, microRNAs, transcripts, and microbial RNA. Regression analysis identified environmental (daycare attendance, atmospheric pollution, breastfeeding duration), microbial (Verrucomicrobia, Streptococcus phage), and host factors (miR-22-5p) associated with URI frequency (p < 0.05). These results provide pathophysiologic clues about molecular factors that influence URI susceptibility. Validation of these findings in a larger cohort could one day yield novel approaches to detecting and managing URI susceptibility in infants.

Infant consumption of microRNA miR-375 in human milk lipids is associated with protection from atopy

BACKGROUND

Human milk is thought to reduce infant atopy risk. The biologic mechanism for this protective effect is not fully understood.

OBJECTIVES

We tested the hypothesis that infant consumption of 4 microRNAs (miR-146b-5p, miR-148b-3p, miR-21-5p, and miR-375-3p) in human milk would be associated with reduced atopy risk.

METHODS

The Breast Milk Influence of the Microtranscriptome Profile on Atopy in Children over Time (IMPACT) study involved a cohort of mother-infant dyads who planned to breastfeed beyond 4 mo. Infant consumption of the 4 human milk microRNAs (miRNAs) in the first 6 mo was calculated as the product of milk miRNA concentration and the number of human milk feeds, across 3 lactation stages: early milk (0-4 wk), transitional milk (4-16 wk), and mature milk (16-24 wk). The primary outcome was infant atopy in the first year, defined as atopic dermatitis (AD), food allergies, or wheezing. The final analysis included 432 human milk samples and 7824 wk of longitudinal health data from 163 dyads.

RESULTS

Seventy-three infants developed atopy. Forty-one were diagnosed with AD (25%), 33 developed food allergy (20%), and 10 had wheezing (6%). Eleven developed >1 condition (7%). Infants who did not develop atopy consumed higher concentrations of miR-375-3p (d = 0.18, P = 0.022, adj P = 0.044) and miR-148b-3p (d = 0.23, P = 0.007, adj P = 0.028). The consumption of miR-375-3p (X2 = 5.7, P = 0.017, OR: 0.92, 95% CI: 0.86, 0.99) was associated with reduced atopy risk. Concentrations of miR-375-3p increased throughout lactation (r = 0.46, F = 132.3, P = 8.4 × 10-34) and were inversely associated with maternal body mass (r = -0.11, t = -2.1, P = 0.032).

CONCLUSIONS

This study provides evidence that infant consumption of miR-375-3p may reduce atopy risk.

Confounding Factors Impacting microRNA Expression in Human Saliva: Methodological and Biological Considerations

There is growing interest in saliva microRNAs (miRNAs) as non-invasive biomarkers for human disease. Such an approach requires understanding how differences in experimental design affect miRNA expression. Variations in technical methodologies, coupled with inter-individual variability may reduce study reproducibility and generalizability. Another barrier facing salivary miRNA biomarker research is a lack of recognized “control miRNAs”. In one of the largest studies of human salivary miRNA to date (922 healthy individuals), we utilized 1225 saliva samples to quantify variability in miRNA expression resulting from aligner selection (Bowtie1 vs. Bowtie2), saliva collection method (expectorated vs. swabbed), RNA stabilizer (presence vs. absence), and individual biological factors (sex, age, body mass index, exercise, caloric intake). Differential expression analyses revealed that absence of RNA stabilizer introduced the greatest variability, followed by differences in methods of collection and aligner. Biological factors generally affected a smaller number of miRNAs. We also reported coefficients of variations for 643 miRNAs consistently present in saliva, highlighting several salivary miRNAs to serve as reference genes. Thus, the results of this analysis can be used by researchers to optimize parameters of salivary miRNA measurement, exclude miRNAs confounded by numerous biologic factors, and identify appropriate miRNA controls.

Defining Biological Phenotypes of Mild Traumatic Brain Injury Using Saliva MicroRNA Profiles

Concussion is a heterogeneous injury that relies predominantly on subjective symptom reports for patient assessment and treatment. Developing an objective, biological test could aid phenotypic categorization of concussion patients, leading to advances in personalized treatment. This prospective multi-center study employed saliva micro-ribonucleic acid (miRNA) levels to stratify 251 individuals with concussion into biological subgroups. Using miRNA biological clusters, our objective was to assess for differences in medical/demographic characteristics, symptoms, and functional measures of balance and cognition. The miRNAs that best defined each cluster were used to identify physiological pathways that characterized each cluster. The 251 participants (mean age: 18 ± 7 years; 57% male) were optimally grouped into 10 clusters based on 22 miRNA levels. The clusters differed in age (χ² = 19.1, p = 0.024), days post-injury at the time of saliva collection (χ² = 22.6; p = 0.007), and number of prior concussions (χ² = 17.6, p = 0.040). The clusters also differed in symptom reports for fatigue (χ² = 17.7; p = 0.039), confusion (χ² = 22.3; p = 0.008), difficulty remembering (χ² = 22.0; p = 0.009), and trouble falling asleep (χ² = 17.2; p = 0.046), but not objective balance or cognitive performance (p > 0.05). The miRNAs that defined concussion clusters regulate 16 physiological pathways, including adrenergic signaling, estrogen signaling, fatty acid metabolism, GABAergic signaling, synaptic vesicle cycling, and transforming growth factor (TGF)-β signaling. These results show that saliva miRNA levels may stratify individuals with concussion based on underlying biological perturbations that are relevant to both symptomology and pharmacological targets. If validated in a larger cohort, miRNA assessment could aid individualized, biology-driven concussion treatment.

Understanding immunological origins of atopic dermatitis through multi-omic analysis

BACKGROUND

The pathophysiology of atopic dermatitis (AD) is multifactorial, impacted by individual medical, demographic, environmental, and immunologic factors. This study used multi-omic analyses to assess how host and microbial factors could contribute to infant AD development.

METHODS

This longitudinal cohort study included 129 term infants, identified as AD (n = 37) or non-AD (n = 92) using the Infant Feeding Practices-II survey and review of medical records. Standardized surveys were used to assess medical and demographic traits (gestational age, sex, race, maternal AD, and atopy family history), and environmental exposures (delivery method, maternal tobacco use, pets, breastfeeding duration, and timing of solid food introduction). Saliva was collected at 6 months for multi-omic assessment of cytokines, microRNAs, mRNAs, and the microbiome. The contribution of each factor to AD status was assessed with logistic regression.

RESULTS

Medical, demographic, and environmental factors did not differ between AD and non-AD infants. Five "omic" factors (IL-8/IL-6, miR-375-3p, miR-21-5p, bacterial diversity, and Proteobacteria) differed between groups (p < .05). The severity of AD was positively associated with levels of miR-375-3p (R = .17, p = .049) and Proteobacteria (R = .22, p = .011), and negatively associated with levels of miR-21-5p (R = .20, p = .022). Multi-omic features accounted for 17% of variance between groups, significantly improving an AD risk model employing medical, demographic, and environmental factors (X²  = 32.47, p = .006).

CONCLUSION

Interactions between the microbiome and host signaling may predispose certain infants to AD by promoting a pro-inflammatory environment.

Maternal Variants in the MFGE8 Gene are Associated with Perceived Breast Milk Supply

Background: The World Health Organization recommends exclusive breastfeeding for ≥6 months, but many mothers are unable to meet this goal. A major reason why mothers undergo early, unplanned breastfeeding cessation is perceived inadequate of milk supply (PIMS). We hypothesized that defining genetic polymorphisms associated with PIMS could aid early identification of at-risk mothers, providing an opportunity for targeted lactation support. Materials and Methods: This prospective observational cohort study followed 221 breastfeeding mothers for 12 months, collecting medical, demographic, and breastfeeding characteristics. Eighteen mammary secretory genes were assessed for single-nucleotide polymorphisms in 88 women (45 with PIMS and 43 with perceived adequate milk supply [PAMS]), matched by age/race/parity. Hierarchical regressions were used to assess the ability of genotype to aid PIMS prediction. Results: Mothers with PIMS exclusively breastfed for a shorter period (7 ± 12 weeks; p = 0.001) and reported lower milk production (17.6 ± 13.3 oz/day; p = 0.001), and their infants displayed reduced weight-for-length Z-score gains (0.74 ± 1.4; p = 0.038) relative to mothers with PAMS (22 ± 19 weeks; 27.03 ± 12.2 oz/day; 1.4 ± 1.5). Maternal genotype for the rs2271714 variant within milk fat globule EGF and factor V/VIII domain containing gene (MFGE8) was associated with PIMS status (p = 0.009, adjusted p = 0.09, likelihood ratio = 9.33) and duration of exclusive breastfeeding (p = 0.009, adjusted p = 0.09, χ² = 9.39). Addition of MFGE8 genotype to a model employing maternal characteristics (age, parity, previous breast-feeding duration, body mass index, education, and depression status) significantly increased predictive accuracy for PIMS status (p = 0.001; χ² = 13.5; area under the curve = 0.813 versus 0.725). Conclusions: Genotyping one lactogenic gene aided identification of mothers at risk for PIMS. If validated in a larger cohort, such an approach could be used to identify mothers who may benefit from increased lactation support.

Levels of Breast Milk MicroRNAs and Other Non-Coding RNAs Are Impacted by Milk Maturity and Maternal Diet

There is emerging evidence that non-coding RNAs (ncRNAs) within maternal breast milk (MBM) impart unique metabolic and immunologic effects on developing infants. Most studies examining ncRNAs in MBM have focused on microRNAs. It remains unclear whether microRNA levels are related to other ncRNAs, or whether they are impacted by maternal characteristics. This longitudinal cohort study examined 503 MBM samples from 192 mothers to: 1) identify the most abundant ncRNAs in MBM; 2) examine the impact of milk maturity on ncRNAs; and 3) determine whether maternal characteristics affect ncRNAs. MBM was collected at 0, 1, and 4 months post-delivery. High throughput sequencing quantified ncRNAs within the lipid fraction. There were 3069 ncRNAs and 238 microRNAs with consistent MBM presence (≥10 reads in ≥10% samples). Levels of 17 ncRNAs and 11 microRNAs accounted for 80% of the total RNA content. Most abundant microRNAs displayed relationships ([R]>0.2, adj p< 0.05) with abundant ncRNAs. A large proportion of ncRNAs (1269/3069; 41%) and microRNAs (206/238; 86%) were affected by MBM maturity. The majority of microRNAs (111/206; 54%) increased from 0-4 months. Few ncRNAs and microRNAs were affected (adj p < 0.05) by maternal age, race, parity, body mass index, gestational diabetes, or collection time. However, nearly half of abundant microRNAs (4/11) were impacted by diet. To our knowledge this is the largest study of MBM ncRNAs, and the first to demonstrate a relationship between MBM microRNAs and maternal diet. Such knowledge could guide nutritional interventions aimed at optimizing metabolic and immunologic microRNA profiles within MBM.

Associations between stool micro-transcriptome, gut microbiota, and infant growth

Rapid infant growth increases the risk for adult obesity. The gut microbiome is associated with early weight status; however, no study has examined how interactions between microbial and host ribonucleic acid (RNA) expression influence infant growth. We hypothesized that dynamics in infant stool micro-ribonucleic acids (miRNAs) would be associated with both microbial activity and infant growth via putative metabolic targets. Stool was collected twice from 30 full-term infants, at 1 month and again between 6 and 12 months. Stool RNA were measured with high-throughput sequencing and aligned to human and microbial databases. Infant growth was measured by weight-for-length z-score at birth and 12 months. Increased RNA transcriptional activity of Clostridia (R = 0.55; Adj p = 3.7E-2) and Burkholderia (R = -0.820, Adj p = 2.62E-3) were associated with infant growth. Of the 25 human RNAs associated with growth, 16 were miRNAs. The miRNAs demonstrated significant target enrichment (Adj p < 0.05) for four metabolic pathways. There were four associations between growth-related miRNAs and growth-related phyla. We have shown that longitudinal trends in gut microbiota activity and human miRNA levels are associated with infant growth and the metabolic targets of miRNAs suggest these molecules may regulate the biosynthetic landscape of the gut and influence microbial activity.

Longitudinal stability of salivary microRNA biomarkers in children and adolescents with autism spectrum disorder

BACKGROUND

Autism spectrum disorder (ASD) is a complex neurological condition with increasing prevalence. Few tools accurately predict the developmental trajectory of children with ASD. Such tools would allow clinicians to provide accurate prognoses and track the efficacy of therapeutic interventions. Salivary RNAs that reflect the genetic-environmental interactions underlying ASD may provide objective measures of symptom severity and developmental outcomes. This study investigated whether salivary RNAs previously identified in childhood ASD remain perturbed in older children. We also explored whether RNA candidates changed with therapeutic intervention.

METHOD

A case-control design was used to characterize levels of 78 saliva RNA candidates among 96 children (48 ASD, 48 non-ASD, mean age: 11 years). Thirty-one children (22 ASD, 9 non-ASD developmental delay, mean age: 4 years) were followed longitudinally to explore changes of RNA candidates during early intervention. Saliva RNA and standardized behavioral assessments were collected for each participant. Associations between candidate RNAs and behavioral scores were determined in both groups via Spearman Correlation. Changes in candidate RNAs across two time-points were assessed in the younger cohort via Wilcoxon rank-sum test.

RESULTS

Seven RNAs were associated with VABS-II and BASC scores in the older group ([R] >0.25, FDR< 0.15). Within the younger cohort, 12 RNAs displayed significant changes over time (FDR< 0.05). Three microRNAs were associated with behavioral scores and changed over time (miR-182-5p, miR-146b-5p, miR-374a-5p).

CONCLUSION

Several salivary RNAs are strongly associated with autistic behaviors in older individuals with ASD and change as early as three months after therapy initiation in younger children. These molecules could be used to track treatment effectiveness and provide prognoses. Further validation is necessary.

Early influenza vaccination rates decline in children during the COVID-19 pandemic

BACKGROUND

This investigation sought to determine whether early season rates of pediatric influenza vaccination changed in a season when there was a concurrent COVID-19 pandemic.

METHODS

This study used cohort and cross sectional data from an academic primary care division in Southcentral Pennsylvania that serves approximately 17,500 patients across 4 practice sites. Early season (prior to November 1) vaccination rates in 2018, 2019 and 2020 were recorded for children, age 6 months to 17 years. To explore the impact of COVID-19 on vaccination, we fit a model with a logit link (estimated via generalized estimating equations to account for clustering by patient over time) on calendar year, adjusted for race, ethnicity, age, and insurance type. We examined interaction effects of demographic covariates with calendar year.

RESULTS

Early vaccination rates were lower in 2020 (29.7%) compared with 2018 and 2019 (34.2% and 33.3%). After adjusting for covariates and accounting for clustering over time, the odds of early vaccination in 2020 were 19% lower compared to 2018 (OR 0.81, 95% CI: 0.78-0.85). In 2020, children with private insurance were more likely to receive early vaccination than in 2018 (OR 1.51, 95% CI: 1.04-1.15), whereas children with public insurance were less likely to receive early vaccination in 2020 than in 2018 (OR 0.62, 95% CI: 1.38-1.65).

CONCLUSIONS

Early influenza vaccination rates declined in a year with a concurrent COVID-19 pandemic. Modeling that accounts for individual trends and demographic variables identified specific populations with lower odds of early vaccination in 2020. Additional research is needed to investigate whether the COVID-19 pandemic impacted parental intent to obtain the influenza vaccine, or introduced barriers to healthcare access.

Evidence-based use of scalable biomarkers to increase diagnostic efficiency and decrease the lifetime costs of autism

Challenges associated with the current screening and diagnostic process for autism spectrum disorder (ASD) in the US cause a significant delay in the initiation of evidence-based interventions at an early age when treatments are most effective. The present study shows how implementing a second-order diagnostic measure to high risk cases initially flagged positive from screening tools can further inform clinical judgment and substantially improve early identification. We use two example measures for the purposes of this demonstration; a saliva test and eye-tracking technology, both scalable and easy-to-implement biomarkers recently introduced in ASD research. Results of the current cost-savings analysis indicate that lifetime societal cost savings in special education, medical and residential care are estimated to be nearly $580,000 per ASD child, with annual cost savings in education exceeding $13.3 billion, and annual cost savings in medical and residential care exceeding $23.8 billion (of these, nearly $11.2 billion are attributable to Medicaid). These savings total more than $37 billion/year in societal savings in the US. Initiating appropriate interventions faster and reducing the number of unnecessary diagnostic evaluations can decrease the lifetime costs of ASD to society. We demonstrate the value of implementing a scalable highly accurate diagnostic in terms of cost savings to the US. LAY SUMMARY: This paper demonstrates how biomarkers with high accuracy for detecting autism spectrum disorder (ASD) could be used to increase the efficiency of early diagnosis. Results also show that, if more children with ASD are identified early and referred for early intervention services, the system would realize substantial costs savings across the lifespan.

Risk Factors and Medical Symptoms Associated With Electronic Vapor Product Use Among Adolescents and Young Adults

The use of electronic vapor products (EVPs) has increased dramatically in the past decade. The objectives of our study were to examine the frequency of EVP use; to identify demographic characteristics, risk-taking behaviors, and beliefs about vaping; and to determine symptoms associated with EVPs among adolescents. A questionnaire addressing these objectives was administered to a convenience sample of subjects aged 12 to 23 years. Among 494 completed questionnaires, 80% of responders were considered experimenters/nonusers (never tried or tried one time) and 20% were considered frequent users (at least once a month). We identified demographic features and risk-taking behaviors associated with EVP use. In the previous 6 months, frequent users were more likely to report headache, cough, sleep disturbances, dehydration, weakness, racing heart, chest pain, and tremors. Our findings provide evidence to support efforts to decrease EVP use through screening, education, and preventative strategies.

Discrepancies in child and parent reporting of concussion symptoms

Objective: To assess discrepancies between child and parent symptom reports following concussion.Methods: Prospective cohort study involving 61 patients, age 7-21 years, diagnosed with a concussion within the previous 14 days. Children/parents completed the Child SCAT-3 symptom inventory at enrollment and 4 weeks post-injury. A within-subjects t-test was used to compare differences in child/parent response for each of 20 individual symptoms, 4 symptom domains, and total symptom severity. Pearson correlations were used to measure agreement between child/parent responses. A repeated measures analysis of variance assessed the effect of time on child/parent symptom discrepancy.Results: At enrollment, children reported higher symptom severity for 'distracted easily' (adj. p = .015) and 'confused' (adj. p = .015). There was moderate-to-high (r > 0.3) agreement between children and parents for more individual symptoms at enrollment (18/20) than at 4 weeks post-injury (14/20). Age had no effect (p > .05) on the discrepancy between child/parent reports.Conclusions: Although there was moderate-to-strong agreement between child/parent reports of concussion symptoms, discrepancies in individual cognitive symptom reports exist, in both children and adolescents. Therefore, collection of parent scales may provide useful information when tracking cognitive symptoms in adolescent patients, who may under-report or under-recognize cognitive deficits.

Saliva RNA Biomarkers of Gastrointestinal Dysfunction in Children With Autism and Neurodevelopmental Disorders: Potential Implications for Precision Medicine

Gastrointestinal (GI) disorders are common in children with neurodevelopmental disorders such as autism spectrum disorder (ASD). A limited understanding of the biologic factors that predispose this population to GI disorders has prevented development of individualized therapies to address this important medical issue. The goal of the current study was to determine if elements of the salivary micro-transcriptome could provide insight into the biologic perturbations unique to children with ASD-related GI disturbance. This cohort study included 898 children (ages 18-73 months) with ASD, non-ASD developmental delay (DD), or typical development (TD). The saliva micro-transcriptome of each child was assessed with RNA-seq. Outputs were aligned to microbial and human databases. A Kruskal Wallis analysis of variance (ANOVA) was used to compare levels of 1821 micro-transcriptome features across neurodevelopmental status (ASD, DD, or TD) and GI presence or absence. An ANOVA was also used to compare micro-transcriptome levels among GI sub-groups (constipation, reflux, food intolerance, other GI condition, no GI condition), and to identify RNAs that differed among children taking three common GI medications (probiotics, reflux medication, or laxatives). Relationships between features identified in ANOVA testing were examined for associations with scores on the Autism Diagnostic Observation Schedule, 2nd Edition (ADOS-2) and the Vineland Adaptive Behavior Scales. GI disturbance rates were higher among children with ASD than peers with TD but were similar to those with DD. Five piwi-interacting RNAs and three microbial RNAs displayed an interaction between developmental status and GI disturbance. Fifty-seven salivary RNAs differed between GI sub-groups-with microRNA differences between food intolerance and reflux groups being most common. Twelve microRNAs displayed an effect of GI disturbance and showed association with GI medication uses and measures of behavior. These 12 microRNAs displayed enrichment for 13 physiologic pathways, including metabolism/digestion long-term depression, and neurobiology of addiction. This study identifies salivary micro-transcriptome features with differential expression among children with ASD-related GI disturbance. A subset of the RNAs displays relationships with treatment modality and are associated with autistic behaviors. The pathobiologic targets of the micro-transcriptome markers may serve as targets for individualized therapeutic interventions aimed at easing pain and behavioral difficulties seen in ASD-related GI disturbance.

Parent Perspectives Towards Genetic and Epigenetic Testing for Autism Spectrum Disorder

Examining community views on genetic/epigenetic research allows collaborative technology development. Parent perspectives toward genetic/epigenetic testing for autism spectrum disorder (ASD) are not well-studied. Parents of children with ASD (n = 131), non-ASD developmental delay (n = 39), and typical development (n = 74) completed surveys assessing genetic/epigenetic knowledge, genetic/epigenetic concerns, motives for research participation, and attitudes/preferences toward ASD testing. Most parents (96%) were interested in saliva-based molecular testing for ASD. Some had concerns about privacy (14%) and insurance-status (10%). None (0%) doubted scientific evidence behind genetic/epigenetic testing. Most reported familiarity with genetics (88%), but few understood differences from epigenetics (19%). Child developmental status impacted insurance concerns (p = 0.01). There is broad parent interest in a genetic/epigenetic test for ASD. It will be crucial to carefully consider and address bioethical issues surrounding this sensitive topic while developing such technology.

Diagnosing mild traumatic brain injury using saliva RNA compared to cognitive and balance testing

BACKGROUND

Early, accurate diagnosis of mild traumatic brain injury (mTBI) can improve clinical outcomes for patients, but mTBI remains difficult to diagnose because of reliance on subjective symptom reports. An objective biomarker could increase diagnostic accuracy and improve clinical outcomes. The aim of this study was to assess the ability of salivary noncoding RNA (ncRNA) to serve as a diagnostic adjunct to current clinical tools. We hypothesized that saliva ncRNA levels would demonstrate comparable accuracy for identifying mTBI as measures of symptom burden, neurocognition, and balance.

METHODS

This case-control study involved 538 individuals. Participants included 251 individuals with mTBI, enrolled ≤14 days postinjury, from 11 clinical sites. Saliva samples (n = 679) were collected at five time points (≤3, 4-7, 8-14, 15-30, and 31-60 days post-mTBI). Levels of ncRNAs (microRNAs, small nucleolar RNAs, and piwi-interacting RNAs) were quantified within each sample using RNA sequencing. The first sample from each mTBI participant was compared to saliva samples from 287 controls. Samples were divided into testing (n = 430; mTBI = 201 and control = 239) and training sets (n = 108; mTBI = 50 and control = 58). The test set was used to identify ncRNA diagnostic candidates and create a diagnostic model. Model accuracy was assessed in the naïve test set.

RESULTS

A model utilizing seven ncRNA ratios, along with participant age and chronic headache status, differentiated mTBI and control participants with a cross-validated area under the curve (AUC) of .857 in the training set (95% CI, .816-.903) and .823 in the naïve test set. In a subset of participants (n = 321; mTBI = 176 and control = 145) assessed for symptom burden (Post-Concussion Symptom Scale), as well as neurocognition and balance (ClearEdge System), these clinical measures yielded cross-validated AUC of .835 (95% CI, .782-.880) and .853 (95% CI, .803-.899), respectively. A model employing symptom burden and four neurocognitive measures identified mTBI participants with similar AUC (.888; CI, .845-.925) as symptom burden and four ncRNAs (.932; 95% CI, .890-.965).

CONCLUSION

Salivary ncRNA levels represent a noninvasive, biologic measure that can aid objective, accurate diagnosis of mTBI.

"Flu-Floppers": Factors Influencing Families' Fickle Flu Vaccination Patterns

While influenza vaccination in the prior year is a strong predictor of subsequent vaccination, many families do not have static vaccination patterns. This study examined factors guiding influenza vaccination decisions among parents whose children sporadically received the influenza vaccination (flu-floppers). We administered surveys to 141 flu-flopper families. Surveys included 21 factors associated with vaccine decision making. A conceptual framework of "passive" and "active" decision making was used to assess parental motivators behind vaccine decisions. The most common reason for vaccinating was a desire to prevent influenza (45%). The most common reason for not vaccinating was a belief that influenza vaccination is not effective (29%). Most parents (88%) reported an active reason in years when their child was vaccinated, while only 43% reported an active reason when their child was not vaccinated (P < .00001). These findings may guide efforts to increase influenza vaccination rates in children most amenable to vaccination.

Oral microbiota and autism spectrum disorder (ASD)

Autism spectrum disorder (ASD) is associated with several oropharyngeal abnormalities, including dysbiosis in the oral microbiota. Since the oral cavity is the start of the gastrointestinal tract, this strengthens and extends the notion of a microbial gut-brain axis in ASD and even raises the question whether a microbial oral-brain axis exists. It is clear that oral bacteria can find their way to the brain through a number of pathways following routine dental procedures. A connection between the oral microbiota and a number of other brain disorders has been reported. As the evidence so far for an association between the oral microbiota and ASDs rests on a few reports only, further studies in this field are necessary. The current review discusses a possible relationship between oral bacteria and the biologic and symptomologic aspects of ASD, focusing on the clinical implications for diagnostic and therapeutic development.

The Transcriptional Signature of a Runner's High

INTRODUCTION

Endorphins, endocannabinoids, monoamines, and neurotrophins have all been implicated in the euphoric response to endurance running, known as a runner's high (RH). The epitranscriptional mechanisms regulating this effect have not been defined. Here, we investigate peripheral micro-ribonucleic acid (miRNA) changes unique to athletes experiencing postrun euphoria, yielding insights into gene networks that control an RH.

METHODS

A cohort study involving 25 collegiate runners (48% females, age = 20 ± 1 yr) examined salivary RNA levels before and after a long-distance run. Participants were divided into RH and nonrunner's high (NRH) groups based on surveys of four criteria (mood, lost sense of time, run quality, and euphoria). Physiological measures were also recorded (temperature, heart rate, blood pressure, pupillary dilatation, and salivary serotonin). Levels of miRNAs and their messenger RNA targets were compared across pre- and postrun samples from RH and NRH groups with two-way ANOVA. Representation of opioid, gamma-aminobutyic acid (GABA), endocannabinoid, neurotrophin, serotonergic, and dopaminergic pathways was assessed in DIANA miRPath. Pearson's correlation analyses examined relationships between miRNAs and RH indices.

RESULTS

RH participants (n = 13) demonstrated postrun mydriasis (P = 0.046) and hypothermia (P = 0.043) relative to NRH participants (n = 12) but had no difference in serotonin dynamics (P = 0.88). Six miRNAs (miR-194-5p, miR-4676-3p, miR-4254, miR-4425, miR-1273-3p, miR-6743-5p) exhibited significant effects (false discovery rate P value < 0.05) across pre- or postrun and RH/NRH groups. These miRNAs displayed target enrichment for opioid (P = 2.74E-06) and GABA (P = 0.00016) pathways. miR-1237-3p levels were related with lost sense of time (R = 0.40). Mitogen-activated protein kinase (MAPK11), an endocannabinoid target of miR-1273-3p, was nominally elevated in RH participants (false discovery rate P value = 0.11).

CONCLUSIONS

Unique dynamics in miRNA concentration occur in athletes with subjective/objective evidence of RH, targeting genes implicated endorphin, endocannabinoid, and GABAergic signaling.

An Adaptive Multivariate Two-Sample Test With Application to Microbiome Differential Abundance Analysis

Differential abundance analysis is a crucial task in many microbiome studies, where the central goal is to identify microbiome taxa associated with certain biological or clinical conditions. There are two different modes of microbiome differential abundance analysis: the individual-based univariate differential abundance analysis and the group-based multivariate differential abundance analysis. The univariate analysis identifies differentially abundant microbiome taxa subject to multiple correction under certain statistical error measurements such as false discovery rate, which is typically complicated by the high-dimensionality of taxa and complex correlation structure among taxa. The multivariate analysis evaluates the overall shift in the abundance of microbiome composition between two conditions, which provides useful preliminary differential information for the necessity of follow-up validation studies. In this paper, we present a novel Adaptive multivariate two-sample test for Microbiome Differential Analysis (AMDA) to examine whether the composition of a taxa-set are different between two conditions. Our simulation studies and real data applications demonstrated that the AMDA test was often more powerful than several competing methods while preserving the correct type I error rate. A free implementation of our AMDA method in R software is available at https://github.com/xyz5074/AMDA.

Saliva MicroRNA Differentiates Children With Autism From Peers With Typical and Atypical Development

OBJECTIVE

Clinical diagnosis of autism spectrum disorder (ASD) relies on time-consuming subjective assessments. The primary purpose of this study was to investigate the utility of salivary microRNAs for differentiating children with ASD from peers with typical development (TD) and non-autism developmental delay (DD). The secondary purpose was to explore microRNA patterns among ASD phenotypes.

METHOD

This multicenter, prospective, case-control study enrolled 443 children (2-6 years old). ASD diagnoses were based on DSM-5 criteria. Children with ASD or DD were assessed with the Autism Diagnostic Observation Schedule II and Vineland Adaptive Behavior Scales II. MicroRNAs were measured with high-throughput sequencing. Differential expression of microRNAs was compared among the ASD (n = 187), TD (n = 125), and DD (n = 69) groups in the training set (n = 381). Multivariate logistic regression defined a panel of microRNAs that differentiated children with ASD and those without ASD. The algorithm was tested in a prospectively collected naïve set of 62 samples (ASD, n = 37; TD, n = 8; DD, n = 17). Relations between microRNA levels and ASD phenotypes were explored.

RESULT

Fourteen microRNAs displayed differential expression (false discovery rate < 0.05) among ASD, TD, and DD groups. A panel of 4 microRNAs (controlling for medical/demographic covariates) best differentiated children with ASD from children without ASD in training (area under the curve = 0.725) and validation (area under the curve = 0.694) sets. Eight microRNAs were associated (R > 0.25, false discovery rate < 0.05) with social affect, and 10 microRNAs were associated with restricted/repetitive behavior.

CONCLUSION

Salivary microRNAs are "altered" in children with ASD and associated with levels of ASD behaviors. Salivary microRNA collection is noninvasive, identifying ASD-status with moderate accuracy. A multi-"omic" approach using additional RNA families could improve accuracy, leading to clinical application.

CLINICAL TRIAL REGISTRATION INFORMATION

A Salivary miRNA Diagnostic Test for Autism; https://clinicaltrials.gov/; NCT02832557.

Ethanol-induced DNA repair in neural stem cells is transforming growth factor β1-dependent

Following neurotoxic damage, cells repair their DNA, and survive or undergo apoptosis. This study tests the hypothesis that ethanol induces a DNA damage response (DDR) in neural stem cells (NSCs) that promotes excision repair (ER) and this repair is influenced by the growth factor environment. Non-immortalized NSCs treated with fibroblast growth factor 2 or transforming growth factor (TGF) β1 were exposed to ethanol. Ethanol increased total DNA damage, reactive oxygen species, and oxidized DNA bases. TGFβ1 potentiated these toxic effects. Transcriptional analyses of cultured NSCs revealed ethanol-induced increases in transcripts related to the DDR (e.g., Hus1 and p53), base ER (e.g., Mutyh and Nthl1), and nucleotide ER (e.g., Xpc), particularly in the presence of TGFβ1. Expression and activity of ER proteins were affected by ethanol. Similar changes occurred in proliferating cells of ethanol-treated mouse fetuses. Ethanol-induced DNA repair in NSCs depends on the ambient growth factors. Gene products for DNA repair in stem cells are among the first biomarkers identifying fetal alcohol-induced damage.

A Review of MicroRNA Biomarkers in Traumatic Brain Injury

There is growing public concern surrounding traumatic brain injury (TBI). TBI can cause significant morbidity, and the long-term sequelae are poorly understood. TBI diagnosis and management rely on patient-reported symptoms and subjective clinical assessment. There are no biologic tools to detect mild TBI or to track brain recovery. Emerging evidence suggests that microRNAs (miRNAs) may provide information about the injured brain. These tiny epigenetic molecules are expressed throughout the body. However, they are particularly important in neurons, can cross the blood-brain barrier, and are securely transported from cell to cell, where they regulate gene expression. miRNA levels may identify patients with TBI and predict symptom duration. This review synthesizes miRNA findings from 14 human studies. We distill more than 291 miRNAs to 17 biomarker candidates that overlap across multiple studies and multiple biofluids. The goal of this review is to establish a collective understanding of miRNA biology in TBI and identify clinical priorities for future investigations of this promising biomarker.

Comparison of serum and saliva miRNAs for identification and characterization of mTBI in adult mixed martial arts fighters

Traumatic brain injury (TBI) is a major cause of death and disability worldwide, with mild TBI (mTBI) accounting for 85% of cases. mTBI is also implicated in serious long-term sequelae including second impact syndrome and chronic traumatic encephalopathy. mTBI often goes undiagnosed due to delayed symptom onset and limited sensitivity of conventional assessment measures compared with severe TBI. Current efforts seek to identify accurate and reliable non-invasive biomarkers associated with functional measures relevant to long-term outcomes. Here we evaluated the utility of serum and salivary microRNAs (miRNAs) to serve as sensitive and specific peripheral biomarkers of possible mTBI. Our primary objectives were to establish the relationship between peripheral measures of miRNA, objective quantification of head impacts, and sensitive indices of balance and cognitive function in healthy young adult athletes. A secondary objective was to compare the sensitivity of miRNA versus commonly used blood-based protein biomarkers. 50 amateur mixed martial arts (MMA) fighters participated. 216 saliva and serum samples were collected at multiple time points, both pre- and post-fight. Levels of 10 serum proteins were compared in a subset of the fighters (n = 24). Levels of miRNAs were obtained by next generation sequencing. Functional outcomes were evaluated using a computerized assessment system that measured cognitive performance, body sway, and combined cognitive performance and body sway during dual task completion. Data were analyzed using multivariate logistic regression for predictive classification, analysis of variance, correlation analysis and principal component analysis. We identified a subset of salivary and serum miRNAs that showed robust utility at predicting TBI likelihood and demonstrated quantitative associations with head impacts as well as cognitive and balance measures. In contrast, serum proteins demonstrated far less utility. We also found that the timing of the responses varies in saliva and serum, which is a critical observation for biomarker studies to consider.

Validation of a Salivary RNA Test for Childhood Autism Spectrum Disorder

Background: The diagnosis of autism spectrum disorder (ASD) relies on behavioral assessment. Efforts to define biomarkers of ASD have not resulted in an objective, reliable test. Studies of RNA levels in ASD have demonstrated potential utility, but have been limited by a focus on single RNA types, small sample sizes, and lack of developmental delay controls. We hypothesized that a saliva-based poly-“omic” RNA panel could objectively distinguish children with ASD from their neurotypical peers and children with non-ASD developmental delay.

Methods: This multi-center cross-sectional study included 456 children, ages 19–83 months. Children were either neurotypical (n = 134) or had a diagnosis of ASD (n = 238), or non-ASD developmental delay (n = 84). Comprehensive human and microbial RNA abundance was measured in the saliva of all participants using unbiased next generation sequencing. Prior to analysis, the sample was randomly divided into a training set (82% of subjects) and an independent validation test set (18% of subjects). The training set was used to develop an RNA-based algorithm that distinguished ASD and non-ASD children. The validation set was not used in model development (feature selection or training) but served only to validate empirical accuracy.

Results: In the training set (n = 372; mean age 51 months; 75% male; 51% ASD), a set of 32 RNA features (controlled for demographic and medical characteristics), identified ASD status with a cross-validated area under the curve (AUC) of 0.87 (95% CI: 0.86–0.88). In the completely separate validation test set (n = 84; mean age 50 months; 85% male; 60% ASD), the algorithm maintained an AUC of 0.88 (82% sensitivity and 88% specificity). Notably, the RNA features were implicated in physiologic processes related to ASD (axon guidance, neurotrophic signaling).

Conclusion: Salivary poly-omic RNA measurement represents a novel, non-invasive approach that can accurately identify children with ASD. This technology could improve the specificity of referrals for ASD evaluation or provide objective support for ASD diagnoses.

Impact of a "No Mobile Device" Policy on Developmental Surveillance in a Pediatric Clinic

Children commonly use mobile devices at pediatric office visits. This practice may affect patient-provider interaction and undermine accuracy of developmental surveillance. A randomized, provider-blinded, controlled trial examined whether a policy prohibiting mobile device use in a pediatric clinic improved accuracy of pediatricians' developmental surveillance. Children, aged 18 to 36 months, were randomized to device-prohibited (intervention; n = 58) or device-allowed (control; n = 54) groups. After a 30-minute well-visit, development was evaluated as "normal," "borderline," or "delayed" in 5 categories using the Ages and Stages Questionnaire (ASQ-3). ASQ-3 results were compared with providers' clinical assessment in each category. Provider-ASQ discrepancies were more common for intervention participants ( P = .025). Providers "missed" more ASQ-3 "delayed" scores ( P = .005) in the intervention group, particularly in the fine motor domain ( P = .018). Prohibiting mobile device use at well-visits did not improve accuracy of providers' developmental surveillance. Mobile devices may entertain children at well-visits, allowing opportunities for parent-provider discussion, or observation of fine motor skills.

Oral microbiome activity in children with autism spectrum disorder

Autism spectrum disorder (ASD) is associated with several oropharyngeal abnormalities, including buccal sensory sensitivity, taste and texture aversions, speech apraxia, and salivary transcriptome alterations. Furthermore, the oropharynx represents the sole entry point to the gastrointestinal (GI) tract. GI disturbances and alterations in the GI microbiome are established features of ASD, and may impact behavior through the "microbial-gut-brain axis." Most studies of the ASD microbiome have used fecal samples. Here, we identified changes in the salivary microbiome of children aged 2-6 years across three developmental profiles: ASD (n = 180), nonautistic developmental delay (DD; n = 60), and typically developing (TD; n = 106) children. After RNA extraction and shotgun sequencing, actively transcribing taxa were quantified and tested for differences between groups and within ASD endophenotypes. A total of 12 taxa were altered between the developmental groups and 28 taxa were identified that distinguished ASD patients with and without GI disturbance, providing further evidence for the role of the gut-brain axis in ASD. Group classification accuracy was visualized with receiver operating characteristic curves and validated using a 50/50 hold-out procedure. Five microbial ratios distinguished ASD from TD participants (79.5% accuracy), three distinguished ASD from DD (76.5%), and three distinguished ASD children with/without GI disturbance (85.7%). Taxonomic pathways were assessed using the Kyoto Encyclopedia of Genes and Genomes microbial database and compared with one-way analysis of variance, revealing significant differences within energy metabolism and lysine degradation. Together, these results indicate that GI microbiome disruption in ASD extends to the oropharynx, and suggests oral microbiome profiling as a potential tool to evaluate ASD status. Autism Res 2018, 11: 1286-1299. © 2018 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: Previous research suggests that the bacteria living in the human gut may influence autistic behavior. This study examined genetic activity of microbes living in the mouth of over 300 children. The microbes with differences in children with autism were involved in energy processing and showed potential for identifying autism status.

Diurnal oscillations in human salivary microRNA and microbial transcription: Implications for human health and disease

The microbiome plays a vital role in human health and disease. Interaction between human hosts and the microbiome occurs through a number of mechanisms, including transcriptomic regulation by microRNA (miRNA). In animal models, circadian variations in miRNA and microbiome elements have been described, but patterns of co-expression and potential diurnal interaction in humans have not. We investigated daily oscillations in salivary miRNA and microbial RNA to explore relationships between these components of the gut-brain-axis and their implications in human health. Nine subjects provided 120 saliva samples at designated times, on repeated days. Samples were divided into three sets for exploration and cross-validation. Identification and quantification of host miRNA and microbial RNA was performed using next generation sequencing. Three stages of statistical analyses were used to identify circadian oscillators: 1) a two-way analysis of variance in the first two sample sets identified host miRNAs and microbial RNAs whose abundance varied with collection time (but not day); 2) multivariate modeling identified subsets of these miRNAs and microbial RNAs strongly-associated with collection time, and evaluated their predictive ability in an independent hold-out sample set; 3) regulation of circadian miRNAs and microbial RNAs was explored in data from autistic children with disordered sleep (n = 77), relative to autistic peers with typical sleep (n = 63). Eleven miRNAs and 11 microbial RNAs demonstrated consistent diurnal oscillation across sample sets and accurately predicted collection time in the hold-out set. Associations among five circadian miRNAs and four circadian microbial RNAs were observed. We termed the 11 miRNAs CircaMiRs. These CircaMiRs had 1,127 predicted gene targets, with enrichment for both circadian gene targets and metabolic signaling processes. Four CircaMiRs had "altered" expression patterns among children with disordered sleep. Thus, novel and correlated circadian oscillations in human miRNA and microbial RNA exist and may have distinct implications in human health and disease.

Distance running alters peripheral microRNAs implicated in metabolism, fluid balance, and myosin regulation in a sex-specific manner

Microribonucleic acids (miRNAs) mediate adaptive responses to exercise and may serve as biomarkers of exercise intensity/capacity. Expression of miRNAs is altered in skeletal muscle, plasma, and saliva following exertion. Women display unique physiologic responses to endurance exercise, and miRNAs respond to pathologic states in sex-specific patterns. However sex-specific miRNA responses to exercise remain unexplored. This study utilized high-throughput RNA sequencing to measure changes in salivary RNA expression among 25 collegiate runners following a single long-distance run. RNA concentrations in pre- and post-run saliva was assessed through alignment and quantification of 4,694 miRNAs and 27,687 mRNAs. Pair-wise Wilcoxon rank-sum test identified miRNAs with significant [false discovery rate (FDR) < 0.05] post-run changes. Associations between miRNA levels and predicted mRNA targets were explored with Pearson correlations. Differences in miRNA patterns between men ( n = 13) and women ( n = 12) were investigated with two-way analysis of variance. Results revealed 122 salivary miRNAs with post-run changes. The eight miRNAs with the largest changes were miR-3671, miR-5095 (downregulated); and miR-7154-3p, miR-200b-5p, miR-5582-3p, miR-6859-3p, miR-6751-5p, miR-4419a (upregulated). Predicted mRNA targets for these miRNAs represented 15 physiologic processes, including glycerophospholipid metabolism (FDR = 0.042), aldosterone-regulated sodium reabsorption (FDR = 0.049), and arrhythmogenic ventricular cardiomyopathy (FDR = 0.018). Twenty-six miRNA/mRNA pairs had associated changes in post-run levels. Three miRNAs (miR-4675, miR-6745, miR-6746-3p) demonstrated sex-specific responses to exercise. Numerous salivary miRNAs change in response to endurance running and target the expression of genes involved in metabolism, fluid balance, and musculoskeletal adaptations. A subset of miRNAs may differentiate the metabolic response to exercise in men and women.

Association of Salivary MicroRNA Changes With Prolonged Concussion Symptoms

IMPORTANCE

Approximately one-third of children who experience a concussion develop prolonged concussion symptoms. To our knowledge, there are currently no objective or easily administered tests for predicting prolonged concussion symptoms. Several studies have identified alterations in epigenetic molecules known as microRNAs (miRNAs) following traumatic brain injury. No studies have examined whether miRNA expression can detect prolonged concussion symptoms.

OBJECTIVE

To evaluate the efficacy of salivary miRNAs for identifying children with concussion who are at risk for prolonged symptoms.

DESIGN, SETTING, AND PARTICIPANTS

This prospective cohort study at the Penn State Medical Center observed 52 patients aged 7 to 21 years presenting for evaluation of concussion within 14 days of initial head injury, with follow-up at 4 and 8 weeks.

EXPOSURES

All patients had a clinical diagnosis of concussion.

MAIN OUTCOMES AND MEASURES

Salivary miRNA expression was measured at the time of initial clinical presentation in all patients. Patients with a Sport Concussion Assessment Tool (SCAT3) symptom score of 5 or greater on self-report or parent report 4 weeks after injury were designated as having prolonged symptoms.

RESULTS

Of the 52 included participants, 22 (42%) were female, and the mean (SD) age was 14 (3) years. Participants were split into the prolonged symptom group (n = 30) and acute symptom group (n = 22). Concentrations of 15 salivary miRNAs spatially differentiated prolonged and acute symptom groups on partial least squares discriminant analysis and demonstrated functional relationships with neuronal regulatory pathways. Levels of 5 miRNAs (miR-320c-1, miR-133a-5p, miR-769-5p, let-7a-3p, and miR-1307-3p) accurately identified patients with prolonged symptoms on logistic regression (area under the curve, 0.856; 95% CI, 0.822-0.890). This accuracy exceeded accuracy of symptom burden on child (area under the curve, 0.649; 95% CI, 0.388-0.887) or parent (area under the curve, 0.562; 95% CI, 0.219-0.734) SCAT3 score. Levels of 3 miRNAs were associated with specific symptoms 4 weeks after injury; miR-320c-1 was associated with memory difficulty (R, 0.55; false detection rate, 0.02), miR-629 was associated with headaches (R, 0.47; false detection rate, 0.04), and let-7b-5p was associated with fatigue (R, 0.45; false detection rate, 0.04).

CONCLUSIONS AND RELEVANCE

Salivary miRNA levels may identify the duration and character of concussion symptoms. This could reduce parental anxiety and improve care by providing a tool for concussion management. Further validation of this approach is needed.

Overlapping MicroRNA Expression in Saliva and Cerebrospinal Fluid Accurately Identifies Pediatric Traumatic Brain Injury

To assess the accuracy and physiological relevance of circulating microRNA (miRNA) as a biomarker of pediatric concussion, we compared changes in salivary miRNA and cerebrospinal fluid (CSF) miRNA concentrations after childhood traumatic brain injury (TBI). A case-cohort design was used to compare longitudinal miRNA concentrations in CSF of seven children with severe TBI against three controls without TBI. The miRNAs "altered" in CSF were interrogated in saliva of 60 children with mild TBI and compared with 18 age- and sex-matched controls. The miRNAs with parallel changes (Wilcoxon rank sum test) in CSF and saliva were interrogated for predictive accuracy of TBI status using a multivariate regression technique. Spearman rank correlation identified relationships between miRNAs of interest and clinical features. Functional analysis with DIANA mirPath identified related mRNA pathways. There were 214 miRNAs detected in CSF, and 135 (63%) were also present in saliva. Six miRNAs had parallel changes in both CSF and saliva (miR-182-5p, miR-221-3p, mir-26b-5p, miR-320c, miR-29c-3p, miR-30e-5p). These miRNAs demonstrated an area under the curve of 0.852 for identifying mild TBI status. Three of the miRNAs exhibited longitudinal trends in CSF and/or saliva after TBI, and all three targeted mRNAs related to neuronal development. Concentrations of miR-320c were directly correlated with child and parent reports of attention difficulty. Salivary miRNA represents an easily measured, physiologically relevant, and accurate potential biomarker for TBI. Further studies assessing the influence of orthopedic injury and exercise on peripheral miRNA patterns are needed.

Metabolism-related microRNAs in maternal breast milk are influenced by premature delivery

BackgroundMaternal breast milk (MBM) is enriched in microRNAs, factors that regulate protein translation throughout the human body. MBM from mothers of term and preterm infants differs in nutrient, hormone, and bioactive-factor composition, but the microRNA differences between these groups have not been compared. We hypothesized that gestational age at delivery influences microRNA in MBM, particularly microRNAs involved in immunologic and metabolic regulation.MethodsMBM from mothers of premature infants (pMBM) obtained 3-4 weeks post delivery was compared with MBM from mothers of term infants obtained at birth (tColostrum) and 3-4 weeks post delivery (tMBM). The microRNA profile in lipid and skim fractions of each sample was evaluated with high-throughput sequencing.ResultsThe expression profiles of nine microRNAs in lipid and skim pMBM differed from those in tMBM. Gene targets of these microRNAs were functionally related to elemental metabolism and lipid biosynthesis. The microRNA profile of tColostrum was also distinct from that of pMBM, but it clustered closely with tMBM. Twenty-one microRNAs correlated with gestational age demonstrated limited relationships with method of delivery, but not other maternal-infant factors.ConclusionPremature delivery results in a unique MBM microRNA profile with metabolic targets. This suggests that preterm milk may have adaptive functions for growth in premature infants.

Neurodevelopmental Delay Diagnosis Rates Are Increased in a Region with Aerial Pesticide Application

A number of studies have implicated pesticides in childhood developmental delay (DD) and autism spectrum disorder (ASD). The influence of the route of pesticide exposure on neurodevelopmental delay is not well defined. To study this factor, we examined ASD/DD diagnoses rates in an area near our regional medical center that employs yearly aerial pyrethroid pesticide applications to combat mosquito-borne encephalitis. The aim of this study was to determine if areas with aerial pesticide exposure had higher rates of ASD/DD diagnoses. This regional study identified higher rates of ASD/DD diagnoses in an area with aerial pesticides application. Zip codes with aerial pyrethroid exposure were 37% more likely to have higher rates of ASD/DD (adjusted RR = 1.37, 95% CI = 1.06-1.78, p = 0.02). A Poisson regression model controlling for regional characteristics (poverty, pesticide use, population density, and distance to medical center), subject characteristics (race and sex), and local birth characteristics (prematurity, low birthweight, and birth rates) identified a significant relationship between aerial pesticide use and ASD/DD rates. The relationship between pesticide application and human neurodevelopment deserves additional study to develop safe and effective methods of mosquito prevention, particularly as communities develop plans for Zika virus control.

A Comparative Review of microRNA Expression Patterns in Autism Spectrum Disorder

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by a wide spectrum of deficits in social interaction, communication, and behavior. There is a significant genetic component to ASD, yet no single gene variant accounts for >1% of incidence. Posttranscriptional mechanisms such as microRNAs (miRNAs) regulate gene expression without altering the genetic code. They are abundant in the developing brain and are dysregulated in children with ASD. Patterns of miRNA expression are altered in the brain, blood, saliva, and olfactory precursor cells of ASD subjects. The ability of miRNAs to regulate broad molecular pathways in response to environmental stimuli makes them an intriguing player in ASD, a disorder characterized by genetic predisposition with ill-defined environmental triggers. In addition, the availability and extracellular stability of miRNAs make them an ideal candidate for biomarker discovery. Here, we discuss 27 miRNAs with overlap across ASD studies, including 3 miRNAs identified in 3 or more studies (miR-23a, miR-146a, and miR-106b). Together, these 27 miRNAs have 1245 high-confidence mRNA targets, a significant number of which are expressed in the brain. Furthermore, these mRNA targets demonstrate over-representation of autism-related genes with enrichment of neurotrophic signaling molecules. Brain-derived neurotrophic factor, a molecule involved in hippocampal neurogenesis and altered in ASD, is targeted by 6 of the 27 miRNAs of interest. This neurotrophic pathway represents one intriguing mechanism by which perturbations in miRNA signaling might influence central nervous system development in children with ASD.

Alterations in serum microRNA in humans with alcohol use disorders impact cell proliferation and cell death pathways and predict structural and functional changes in brain

BACKGROUND

There is currently a lack of reliable, minimally invasive biomarkers that could predict the extent of alcoholism-induced CNS damage. Developing such biomarkers may prove useful in reducing the prevalence of alcohol use disorders (AUDs). Extracellular microRNAs (miRNAs) can be informative molecular indicators of changes in neuronal gene expression. In this study, we performed a global analysis of extracellular miRNAs to identify robust biomarkers of early CNS damage in humans diagnosed with DSM-IV AUDs. We recruited a relatively young set of 20 AUD subjects and 10 age-matched controls. They were subjected to comprehensive medical, neuropsychological and neuroimaging tests, followed by comparison of miRNA levels found in peripheral blood serum. Employing a conservative strategy to identify candidate biomarkers, miRNAs were quantified using two independent high-throughput methods: microarray and next-generation RNA-sequencing. This improved our capacity to discover and validate relevant miRNAs.

RESULTS

Our results identified several miRNAs with significant and reproducible expression changes in AUD subjects versus controls. Moreover, several significant associations between candidate miRNA biomarkers and various medical, neuropsychological and neuroimaging parameters were identified using Pearson correlation and unbiased hierarchical clustering analyses. Some of the top candidate biomarkers identified, such as mir-92b and mir-96 have established roles in neural development. Cross-species validation of miRNA expression was performed using two different in vivo rat drinking models and two different in vitro mouse neural stem cell exposure models. A systems level analysis revealed a remarkable degree of convergence in the top changes seen in all of these data sets, specifically identifying cell death, cell proliferation and cell cycle processes as most consistently affected. Though not necessarily the same molecules, the affected miRNAs within these pathways clearly influence common genes, such as p53 and TNF, which stand out as potential keystone molecules. Lastly, we also examined the potential tissue origins of these biomarkers by quantifying their levels in 15 different tissue types and show that several are highly-enriched in the brain.

CONCLUSIONS

Collectively, our results suggest that serum miRNA expression changes can directly relate to alterations in CNS structure and function, and may do so through effects on highly specific cellular pathways.

Evaluation of cell proliferation, apoptosis, and DNA-repair genes as potential biomarkers for ethanol-induced CNS alterations

Background

Alcohol use disorders (AUDs) lead to alterations in central nervous system (CNS) architecture along with impaired learning and memory. Previous work from our group and that of others suggests that one mechanism underlying these changes is alteration of cell proliferation, apoptosis, and DNA-repair in neural stem cells (NSCs) produced as a consequence of ethanol-induced effects on the expression of genes related to p53-signaling. This study tests the hypothesis that changes in the expression of p53-signaling genes represent biomarkers of ethanol abuse which can be identified in the peripheral blood of rat drinking models and human AUD subjects and posits that specific changes may be correlated with differences in neuropsychological measures and CNS structure.

Results

Remarkably, microarray analysis of 350 genes related to p53-signaling in peripheral blood leukocytes (PBLs) of binge-drinking rats revealed 190 genes that were significantly altered after correcting for multiple testing. Moreover, 40 of these genes overlapped with those that we had previously observed to be changed in ethanol-exposed mouse NSCs. Expression changes in nine of these genes were tested for independent confirmation by a custom QuantiGene Plex (QGP) assay for a subset of p53-signaling genes, where a consistent trend for decreased expression of mitosis-related genes was observed. One mitosis-related gene (Pttg1) was also changed in human lymphoblasts cultured with ethanol. In PBLs of human AUD subjects seven p53-signaling genes were changed compared with non-drinking controls. Correlation and principal components analysis were then used to identify significant relationships between the expression of these seven genes and a set of medical, demographic, neuropsychological and neuroimaging measures that distinguished AUD and control subjects. Two genes (Ercc1 and Mcm5) showed a highly significant correlation with AUD-induced decreases in the volume of the left parietal supramarginal gyrus and neuropsychological measures.

Conclusions

These results demonstrate that alcohol-induced changes in genes related to proliferation, apoptosis, and DNA-repair are observable in the peripheral blood and may serve as a useful biomarker for CNS structural damage and functional performance deficits in human AUD subjects.

Effects of ethanol on transforming growth factor Β1-dependent and -independent mechanisms of neural stem cell apoptosis

Stem cell vitality is critical for the growth of the developing brain. Growth factors can define the survival of neural stem cells (NSCs) and ethanol can affect growth factor-mediated activities. The present study tested two hypotheses: (a) ethanol causes the apoptotic death of NSCs and (b) this effect is influenced by the ambient growth factor. Monolayer cultures of non-immortalized NS-5 cells were exposed to fibroblast growth factor (FGF) 2 or transforming growth factor (TGF) β1 in the absence or presence of ethanol for 48 h. Ethanol killed NSCs as measured by increases in the numbers of ethidium bromide+ and annexin V+ cells and decreases in the number of calcein AM+ (viable) cells. These toxic effects were promoted by TGFβ1. A quantitative polymerase chain reaction array of apoptosis-related mRNAs revealed an ethanol-induced increase (≥2-fold change; p<0.05) in transcripts involved in Fas ligand (FasL) and tumor necrosis factor (TNF) signaling. These effects, particularly the FasL pathway, were potentiated by TGFβ1. Immunocytochemical analyses of NS-5 cells showed that transcriptional alterations translated into consistent up-regulation of protein expression. Experiments with the neocortical proliferative zones harvested from fetal mice exposed to ethanol showed that ethanol activated similar molecular systems in vivo. Thus, ethanol induces NSC death through two distinct molecular mechanisms, one is initiated by TGFβ1 (FasL) and another (through TNF) which is TGFβ1-independent.

Ethanol-induced methylation of cell cycle genes in neural stem cells

Ethanol inhibits the proliferation of neural precursors by altering mitogenic and anti-mitogenic growth factor signaling and can affect global methylation activity in the fetus. We tested the hypothesis that epigenetic modification of specific cell cycle genes underlies the ethanol-induced inhibition of growth factor-regulated cell cycle progression. Monolayer cultures of neural stem cells (NSCs) were treated with fibroblast growth factor 2 or transforming growth factor (TGF) β1 in the absence or presence of ethanol. Ethanol increased the total length of the cell cycle by elongating the amount of time spent in the gap 1 (G1) and synthesis (S) phases of the cell cycle. Ethanol induced the hypermethylation of multiple cell cycle genes associated with the G1/S and gap 2/mitotic phase (G2/M) checkpoints and increased the expression and activity of DNA methyltransferases. These changes were most pronounced in the presence of TGFβ1. Epigenetic alterations paralleled the down-regulation of associated transcripts and other checkpoint-related mRNAs both in vitro (NS-5 cell culture) and in vivo (fetal mouse cortex). Ethanol-induced hypermethylation was accompanied by decreases in the proportion of NSCs expressing associated cell cycle proteins. Thus, ethanol disrupts growth factor-related cell cycle progression by inducing checkpoint restriction at the G1/S transition through a feed-forward system involving the methylation of G2/M regulators.

Hypothermia differentially increases extracellular signal-regulated kinase and stress-activated protein kinase/c-Jun terminal kinase activation in the hippocampus during reperfusion after asphyxial cardiac arrest

Mitogen-activated protein kinases are signal transduction mediators that have been implicated in cell survival and cell death. This study characterized the activation of pathways in the hippocampus during reperfusion after global cerebral ischemia, as well as the influence of a regimen of hypothermia that reduces ischemic cell death in the hippocampus. Circulatory arrest was induced in rats by 8 min of asphyxia. Relative levels of phosphorylated and total extracellular signal-regulated kinase, stress-activated protein kinase/c-Jun N-terminal kinase and p38 mitogen-activated protein kinase were measured in the hippocampus after 6, 12 or 24h of reperfusion using immunoblotting. Asphyxia induced a progressive increase in phosphorylated extracellular signal-regulated kinase and stress-activated protein kinase/c-Jun N-terminal kinase, but no change in phosphorylated p38 mitogen-activated protein kinase. Induction of mild hypothermia (33 degrees C) during reperfusion increased extracellular signal-regulated kinase phosphorylation and produced a smaller increase in stress-activated protein kinase/c-Jun N-terminal kinase phosphorylation at 24h. Hypothermia did not alter extracellular signal-regulated kinase activation in rats not subjected to ischemia. Extracellular signal-regulated kinase activation was associated with an increase in phosphorylation of the mitogen-activated protein kinase kinase 1/2, and was inhibited by administration of the specific mitogen-activated protein kinase kinase 1/2 inhibitor SL327. Immunohistochemical staining showed an increase in active extracellular signal-regulated kinase in the CA1, CA2, CA3 and dentate gyrus regions of the hippocampus after ischemia and reperfusion. In contrast, active stress-activated protein kinase/c-Jun N-terminal kinase immunoreactivity was most intense in the CA3 and dentate gyrus regions. These data demonstrate that both extracellular signal-regulated kinase and stress-activated protein kinase/c-Jun N-terminal kinase pathways are activated during the first 24h of reperfusion after global cerebral ischemia, and that hypothermia increases the activation of extracellular signal-regulated kinase relative to stress-activated protein kinase/c-Jun N-terminal kinase. Thus, an increase in extracellular signal-regulated kinase activation may be associated with improved neuronal survival after ischemic injury.

Hypothermia during reperfusion after asphyxial cardiac arrest improves functional recovery and selectively alters stress-induced protein expression

This study examined whether prolonged hypothermia induced 1 hour after resuscitation from asphyxial cardiac arrest would improve neurologic outcome and alter levels of stress-related proteins in rats. Rats were resuscitated from 8 minutes of asphyxia resulting in cardiac arrest. Brain temperature was regulated after resuscitation in three groups: normothermia (36.8 degrees C x 24 hours), immediate hypothermia (33 degrees C x 24 hours, beginning immediately after resuscitation), and delayed hypothermia (33 degrees C x 24 hours, beginning 60 minutes after resuscitation). Mortality and neurobehavioral deficits were improved in immediate and delayed hypothermia rats relative to normothermia rats. Furthermore, both immediate and delayed hypothermia improved neuronal survival in the CA1 region of the hippocampus assessed at 14 days. In normothermia rats, the 70-kDa heat shock protein (Hsp70) and 40-kDa heat shock protein (Hsp40) were increased within 12 hours after resuscitation in the hippocampus. Delayed hypothermia attenuated the increase in Hsp70 levels in the hippocampus but did not affect Hsp70 induction in the cerebellum. Hippocampal expression of Hsp40 was not affected by hypothermia. These data indicate that prolonged hypothermia during later reperfusion improves neurologic outcome after experimental global ischemia and is associated with selective changes in the pattern of stress-induced protein expression.

Normoxic ventilation during resuscitation and outcome from asphyxial cardiac arrest in rats

The formation of reactive oxygen species during reperfusion is one trigger for neuronal injury after global cerebral ischemia. Because formation of reactive oxygen species requires delivery of molecular oxygen to ischemic tissue, restricting inspired oxygen during reperfusion may decrease neurological damage. This study examined whether ventilation with room air rather than pure oxygen during resuscitation would improve neurological recovery after cardiac arrest in rats. Adult, male rats were subjected to 8 min of asphyxia resulting in cardiac arrest. During resuscitation, rats were ventilated either with hyperoxia (FiO2 = 1.0) or normoxia (FiO2 = 0.21, room air). Neurobehavioral deficits were scored daily for 72 h after resuscitation, after which brains were collected for histology. Normoxia decreased arterial oxygen content. Other physiological parameters and mortality did not differ between groups. All surviving rats exhibited behavioral and histological signs of brain damage. Neurological deficit scores did not differ between normoxia and hyperoxia conditions at any time point. The number of ischemic neurons in the hippocampus also did not differ between groups. These data indicate neither benefit nor detriment of reducing inspired oxygen concentration during resuscitation from asphyxial cardiac arrest in rats.