Genes, environment, and developmental timing: New insights from translational approaches to understand early origins of respiratory diseases

High TSLP responses in the human infant airways are associated with pre-activated airway epithelial IFN antiviral immunity

Thymic stromal lymphopoietin (TSLP) is a primarily epithelial-derived cytokine that drives type 2 allergic immune responses. Early life viral respiratory infections elicit high TSLP production, which leads to the development of type 2 inflammation and airway hyperreactivity. The goal of this study was to examine in vivo and in vitro the human airway epithelial responses leading to high TSLP production during viral respiratory infections in early infancy. A total of 129 infants (<1-24 m, median age 10 m) with severe viral respiratory infections were enrolled for in vivo (n = 113), and in vitro studies (n = 16). Infants were classified as 'high TSLP' or 'low TSLP' for values above or below the 50th percentile. High versus low TSLP groups were compared in terms of type I-III IFN responses and production of chemokines promoting antiviral (CXCL10), neutrophilic (CXCL1, CXCL5, CXCL8), and type 2 responses (CCL11, CCL17, CCL22). Human infant airway epithelial cell (AEC) cultures were used to define the transcriptomic (RNAseq) profile leading to high versus low TSLP responses in vitro in the absence (baseline) or presence (stimulated) of a viral mimic (poly I:C). Infants in the high TSLP group had greater in vivo type III IFN airway production (median type III IFN in high TSLP 183.2 pg/mL vs. 63.4 pg/mL in low TSLP group, p = 0.007) and increased in vitro type I-III IFN AEC responses after stimulation with a viral mimic (poly I:C). At baseline, our RNAseq data showed that infants in the high TSLP group had significant upregulation of IFN signature genes (e.g., IFIT2, IFI6, MX1) and pro-inflammatory chemokine genes before stimulation. Infants in the high TSLP group also showed a baseline AEC pro-inflammatory state characterized by increased production of all the chemokines assayed (e.g., CXCL10, CXCL8). High TSLP responses in the human infant airways are associated with pre-activated airway epithelial IFN antiviral immunity and increased baseline AEC production of pro-inflammatory chemokines. These findings present a new paradigm underlying the production of TSLP in the human infant airway epithelium following early life viral exposure and shed light on the long-term impact of viral respiratory illnesses during early infancy and beyond childhood.

Multi-omic factors associated with future wheezing in infants

BACKGROUND

The pathophysiology of wheezing is multifactorial, impacted by medical, demographic, environmental, and immunologic factors. We hypothesized that multi-omic analyses of host and microbial factors in saliva would enhance the ability to identify infants at risk for wheezing.

METHODS

This longitudinal cohort study included 161 term infants. Infants who developed wheezing (n = 27) within 24 months of delivery were identified using the International Study of Asthma and Allergies in Childhood Written Questionnaire and review of the medical record. Standardized surveys were used to assess infant traits and environmental exposures. Saliva was collected for multi-omic assessment of cytokines, microRNAs, mRNAs, and microbiome/virome RNAs.

RESULTS

Two infant factors (daycare attendance, family history of asthma) and three salivary "omic" features (miR-26a-5p, Elusimicrobia, Streptococcus phage phiARI0131-1) differed between the two groups (adjusted p < 0.05). miR-26a-5p levels were correlated with Elusimicrobia (R = -0.87, p = 3.7 × 10^-31). A model employing the three omic features plus daycare attendance and family asthma history yielded the highest predictive accuracy for future wheezing episodes (AUC = 0.74, 95% CI: 0.703-0.772, 77% sensitivity, 62% specificity).

CONCLUSIONS

Host-microbiome interactions in saliva may yield pathophysiologic clues about the origins of wheezing and aid identification of infants at risk of future wheezing episodes.

IMPACT

Wheezing is multi-factorial, but the relative contributions of infant traits, environment, and underlying biology are poorly understood. This multi-omic study identifies three molecular factors, including salivary microRNAs, microbes, and viral phages associated with increased risk of infant wheezing. Measurement of these molecular factors enhanced predictive accuracy for future wheezing when combined with family asthma history and daycare attendance. Validation of this approach could be used to identify infants at risk for wheezing and guide personalized medical management.

Long-term effects of wildfire smoke exposure during early life on the nasal epigenome in rhesus macaques

BACKGROUND

Wildfire smoke is responsible for around 20% of all particulate emissions in the U.S. and affects millions of people worldwide. Children are especially vulnerable, as ambient air pollution exposure during early childhood is associated with reduced lung function. Most studies, however, have focused on the short-term impacts of wildfire smoke exposures. We aimed to identify long-term baseline epigenetic changes associated with early-life exposure to wildfire smoke. We collected nasal epithelium samples for whole genome bisulfite sequencing (WGBS) from two groups of adult female rhesus macaques: one group born just before the 2008 California wildfire season and exposed to wildfire smoke during early-life (n = 8), and the other group born in 2009 with no wildfire smoke exposure during early-life (n = 14). RNA-sequencing was also performed on a subset of these samples.

RESULTS

We identified 3370 differentially methylated regions (DMRs) (difference in methylation ≥ 5%, empirical p < 0.05) and 1 differentially expressed gene (FLOT2) (FDR < 0.05, fold of change ≥ 1.2). The DMRs were annotated to genes significantly enriched for synaptogenesis signaling, protein kinase A signaling, and a variety of immune processes, and some DMRs significantly correlated with gene expression differences. DMRs were also significantly enriched within regions of bivalent chromatin (top odds ratio = 1.46, q-value < 3 × 10^-6) that often silence key developmental genes while keeping them poised for activation in pluripotent cells.

CONCLUSIONS

These data suggest that early-life exposure to wildfire smoke leads to long-term changes in the methylome over genes impacting the nervous and immune systems. Follow-up studies will be required to test whether these changes influence transcription following an immune/respiratory challenge.

Airway Wall Remodeling in Childhood Asthma-A Personalized Perspective from Cell Type-Specific Biology

Airway wall remodeling is a pathology occurring in chronic inflammatory lung diseases including asthma, chronic obstructive pulmonary disease, and fibrosis. In 2017, the American Thoracic Society released a research statement highlighting the gaps in knowledge and understanding of airway wall remodeling. The four major challenges addressed in this statement were: (i) the lack of consensus to define “airway wall remodeling” in different diseases, (ii) methodologic limitations and inappropriate models, (iii) the lack of anti-remodeling therapies, and (iv) the difficulty to define endpoints and outcomes in relevant studies. This review focuses on the importance of cell-cell interaction, especially the bronchial epithelium, in asthma-associated airway wall remodeling. The pathology of “airway wall remodeling” summarizes all structural changes of the airway wall without differentiating between different pheno- or endo-types of asthma. Indicators of airway wall remodeling have been reported in childhood asthma in the absence of any sign of inflammation; thus, the initiation event remains unknown. Recent studies have implied that the interaction between the epithelium with immune cells and sub-epithelial mesenchymal cells is modified in asthma by a yet unknown epigenetic mechanism during early childhood.