Speaker: Susan Lynch
The session focused on the ongoing work in the field concerning whether the gut microbiome might be considered a viable target for preventing or treating allergies, including food allergies. Additionally, the speaker discussed a trial design for testing a microbial therapeutic for preventing allergic disease. It was noted that the field of human microbiome research, which began 20 years ago, has significantly transformed our understanding of human biology. Over these decades, it has been recognized that humans are superorganisms colonized by a diverse range of microbes on both the skin and internal mucosal surfaces. The gastrointestinal tract, in particular, harbors the greatest burden and diversity of these microbes, which collectively possess more than 150 times the genetic capacity of the human genome. This microbial pan-genome plays a crucial role in maintaining human health by performing various activities not encoded in the human genome. The human microbiome was considered highly manipulable compared to the human genome, despite arguments that Crispr Cas engineering allows for direct manipulation of human cells. Factors influencing microbiomes, especially in the gastrointestinal tract, were known to shape them significantly. By leveraging these factors, microbiomes could be manipulated to promote population health. The gastrointestinal microbiome had long been primarily associated with metabolizing dietary compounds, such as complex carbohydrates and fibers, into essential products like short-chain fatty acids, crucial for gastrointestinal cell energy and anti-inflammatory properties. Additionally, gut microbes metabolized various other substances, including drugs, xenobiotics, and processed food components, which could adversely affect human health.
The gut microbiome is responsible for most small molecules found in feces or the gastrointestinal tract lumen and over 50% of metabolites found in circulation. It is regarded as a crucial auxiliary pan-genomic organ that metabolizes not only food but also other substances in the intestinal tract. The production of small molecules influences the development and function of the immune system, shaping cellular immune phenotypes. Studies across large birth cohorts indicate that disturbances to the gut microbiome in early infancy are associated with allergic diseases and asthma in later childhood, suggesting that early-life perturbations strongly influence the development of these conditions.
A recent study, presented and published last year by Sapinda Banyanovic's group, demonstrated the relationship between early microbiome profiles and the development of peanut allergy in later childhood. The study utilized infant and mid-childhood samples from a cohort of 122 individuals. Microbiome profiling using 16S sequencing was conducted in infancy, observing subsequent peanut allergy development. The findings indicated that significant perturbations to the microbiome, specifically a depletion of Clostridia and increased Streptococcus, were associated with later peanut allergy development. In mid-childhood, although there were minimal microbiological differences in fecal samples between children who did and did not develop peanut allergy, those who developed the allergy showed a depletion of Bifidobacterium species. These microbial differences were more pronounced in early infancy, suggesting that early microbial exposures may influence the likelihood of developing peanut allergy later in childhood.
The metabolic productivity of these microbiomes was examined, with a particular focus on short-chain anti-inflammatory fatty acids. It was found that in infancy, higher concentrations of short-chain fatty acids, including butyrate and isovalerate, were observed in the stool samples of infants who later developed peanut allergy, contrary to expected outcomes. This suggests that excessive production of short-chain fatty acids might have been detrimental to protection against peanut allergy. Additionally, mouse models have demonstrated similar findings. Short-chain fatty acids were traditionally regarded as exclusively anti-inflammatory; however, it has been revealed that the optimal concentration of these acids is crucial for their anti-inflammatory efficacy. Excessive production of short-chain fatty acids appears to contribute to the development of peanut allergy, alongside reduced concentrations.
The perturbations to the gut microbiome in early infancy associated with later peanut allergic development were examined to determine if they were responsible for driving the condition. Evidence supporting this notion was derived from an independent study by Catherine Nagler's group at the University of Chicago. This study utilized germ-free or notobiotic mice, animals raised without their microbiome. These animals were inoculated with human feces to mimic the effects of a diverse microbiome on the mammalian immune response. The feces of a cow's milk-allergic infant and healthy control were used to inoculate these germ-free animals. The results demonstrated that the feces from the cow's milk allergic infant induced phenotypic features of cow's milk allergy in the inoculated animals. This confirmed that the metabolic activities of microbes in the feces and the gut lumen were sufficient to drive cow's milk allergy in a mammalian model of disease. The research group further investigated specific microbial and host features associated with cow's milk allergy development in this model system. Key pathways, such as arachidonic and linoleic metabolism, were enriched in the feces or gut microbiome of animals that developed cow's milk allergy. This finding was particularly significant given a previous study that observed high lipid enrichment called 12,13 DiHOME linoleic acid metabolite in one-month-old infants who developed atopic disease and asthma. The lipid was shown to predict the odds ratio for developing atopy or asthma in later childhood. It was demonstrated that this prediction was based on an analysis of one-month-old fecal samples. The increase in these concentrations in the feces and the molecular implications of these products were sought to be understood. Shotgun metagenomic analysis of infant fecal samples was leveraged, and two species, Bifidobacterium bifidum and Enterococcus fecalis, were identified as encoding a specific gene called an epoxide hydrolase that produces 12,13 DiHOME. It was demonstrated for the first time that the pool of this lipid present in the fecal samples of these infants, who were on the trajectory to allergy and asthma, was being produced by specific strains of microbes in their gut microbiomes
The dendritic and T cell co-culture assays were leveraged to demonstrate that as the concentration of this lipid was increased, the frequency of T regulatory cells and their capacity to produce IL-10 were decreased. It was shown to be the immunological crux of allergic disease development. It was further demonstrated that this microbial-derived lipid was sufficient to reduce the capacity to downregulate allergic inflammation in vitro. Additionally, this effect was demonstrated in vivo in animal models of airway allergic inflammation. The antigen-presenting cell populations were examined, revealing that this lipid increased the expression of fatty acid transport genes and the metabolism of fatty acids. It was found that this lipid acted as a PPAR gamma activator and significantly decreased the presentation of lipid molecules on the surface of dendritic cells and IL-10 production.
Furthermore, incubating dendritic cells with this lipid resulted in physiological changes that ultimately led to the downregulation or reduced frequency of T-regulatory cells in the system. The influence of this lipid on macrophages, the other major antigen-presenting cell population, was also explored. It was noted that macrophages, crucial in controlling microbial colonization and clearing pathogens throughout life, could also process antigens affected by this lipid. When macrophages derived from monocytes are co-incubated with the 12,13 diHOME lipid, their ability to clear pathogens is reduced. Additionally, their production of IL-10 is diminished, and they exhibit an inflammatory phenotype characterized by the expression of IL-1 beta, NF kappa beta, and TNF alpha. It was found that these changes have long-term effects on the clinical phenotype observed in children, suggesting that early-life metabolic interactions may epigenetically alter antigen-presenting cells. Specifically, co-incubation with the lipid induces epigenetic modifications in interferon response elements crucial for combating intracellular pathogens.
Consequently, these macrophages lose their ability to mount an interferon-mediated response when exposed to bacterial products or peanut antigens later on. It underscores how early life microbial metabolism in the gut influences the metabolic environment, significantly impacting the functional characteristics of various immune cells through epigenetic modifications, predisposing them towards inflammatory phenotypes and affecting their responsiveness to stimuli.
The speaker emphasized that early-life microbial exposure plays a crucial role in developing immune function and susceptibility to allergies later in childhood. Microbes acquired in infancy, especially in the gut, educate the immune system. The research emphasizes the importance of early microbial exposures in shaping an individual's allergic predisposition. To address this, rather than using single-species probiotics, a multi-species live microbial therapy is proposed to reprogram immune responses and promote appropriate microbiome and metabolic development in the early gut microbiome. This approach aims to enhance immune tolerance and prevent allergic diseases by shaping the immune productivity of the gut microbiome. The research utilized various datasets, including longitudinal studies on infants receiving probiotic supplementation. Results consistently show that infants at risk for allergies and asthma exhibit lower microbial diversity in their gut microbiome during their first year of life than healthy infants.
Furthermore, these at-risk infants demonstrate deficiencies in metabolic pathways critical for immune function. Statistical analyses identified groups of microbes that collaborate in the healthy infant gut, forming the basis for developing potential microbial therapies, which are now undergoing preclinical testing in animal models.
The first cocktail tested by researchers contained five bacterial members. It was tested in a mouse model of airway allergy, where mice were challenged with cockroach antigens. This model induces allergic airway inflammation. Six treatment groups were examined: controls without cockroach exposure, those exposed to cockroach antigen plus PBS, and a therapeutic consortium containing a specific Lactobacillus species. Another group received the Lactobacillus species alone, while another group had the therapeutic consortium without this species. A group received a heat-killed therapeutic consortium as well. The hypothesis tested was the requirement for metabolically active microbes to protect against allergic inflammation. Results showed distinct differences among the groups: animals treated with the therapeutic consortium showed pristine airways similar to those not exposed to allergens. Treatment with Lactobacillus alone was insufficient for protection. Removing Lactobacillus from the consortium eliminated airway protection, indicating the necessity of microbial interactions for full effectiveness. Additionally, only metabolically active microbial groups provided protection; the heat-killed consortium did not. Staining demonstrated differences in nucleated cell presence around air spaces, reinforcing these findings.
It was observed that reduced levels of MUC5AC, eotaxin, IL-13, IL-4, and IL-10 in the airways were seen only in the group treated with the therapeutic consortium. Consistent findings indicated that an IL-10 response may not be necessary if allergic inflammation is absent in the airways of these animals. Another criterion was emphasized: manipulating the microbiome of the participants targeted for use. It was demonstrated that the gut microbiota composition of animals receiving the therapeutic consortium differed notably from those exposed only to cockroach allergen challenge and PBS and those receiving neither. The introduction of these live organisms notably altered the gut microbiome's composition and metabolic output, as evident in the metabolic profiles depicted in the lower graphs. Additionally, the circulating metabolites in these animals were altered by introducing this group of live organisms.
In 2017, funds were raised, and STMC Therapeutics was established to investigate whether a therapeutic consortium could demonstrate efficacy in preventing allergic disease. The aim was to treat neonates with a cocktail of organisms from early postnatal stages to influence their immune response and microbiome development throughout infancy. Due to the vulnerability of neonates, safety needed to be demonstrated in a descending age manner, starting from adults to adolescents and then down to children aged two. Each group was treated daily with the therapeutic consortium for a month, followed by a washout, during which no severe adverse events associated with the treatment were observed. Additionally, significant differences in the gut microbiome were observed in individuals treated with the consortium compared to those in the placebo group. A significant reduction in two linoleic acid metabolites, including the 12, 13 DiHOME metabolite, which was demonstrated to be a potent modulator of pro-allergic and inflammatory phenotypes, was observed.
Additionally, during both the treatment and washout periods, a decrease in eotaxin was noted among those treated with the cocktail, a phenomenon not observed in the placebo group. These findings suggest that the cocktail may possess therapeutic potential for established allergic diseases. Subsequently, the interest has shifted towards investigating whether early introduction of this organism cocktail in neonates can prevent allergic disease, leading to the initiation of the adored trial or the Allergic Disease Onset Prevention Study. Coordination with the FDA facilitated the implementation of two additional safety trials targeting descending age groups, the first involving children aged six to twelve months, followed by those aged twelve months to one month. Enrollment of 238 infants was completed by December last year, with daily treatment administered throughout their first year of life. The primary endpoint focuses on atopic dermatitis, with secondary assessments encompassing food allergies, respiratory issues, and other allergic conditions. Top-line data is expected in Q1 of the upcoming year, with final results slated for evaluation at two years of age, marking the culmination of the study.
European Academy of Allergy and Clinical Immunology (EAACI), 2024 31st May-3rd June, Valencia
