Gut bacteria-derived serotonin promotes immune tolerance in early life

The gut microbiota promotes immune system development in early life, but the interactions between the gut metabolome and immune cells in the neonatal gut remain largely undefined. Here, we demonstrate that the neonatal gut is uniquely enriched with neurotransmitters, including serotonin, and that specific gut bacteria directly produce serotonin while down-regulating monoamine oxidase A to limit serotonin breakdown. We found that serotonin directly signals to T cells to increase intracellular indole-3-acetaldehdye and inhibit mTOR activation, thereby promoting the differentiation of regulatory T cells, both ex vivo and in vivo in the neonatal intestine. Oral gavage of serotonin into neonatal mice resulted in long-term T cell-mediated antigen-specific immune tolerance toward both dietary antigens and commensal bacteria. Together, our study has uncovered an important role for specific gut bacteria to increase serotonin availability in the neonatal gut and identified a function of gut serotonin in shaping T cell response to dietary antigens and commensal bacteria to promote immune tolerance in early life.

The Gut-Liver Axis in Pediatric Liver Health and Disease

There has been growing interest in the complex host-microbe interactions within the human gut and the role these interactions play in systemic health and disease. As an essential metabolic organ, the liver is intimately coupled to the intestinal microbial environment via the portal venous system. Our understanding of the gut-liver axis comes almost exclusively from studies of adults; the gut-liver axis in children, who have unique physiology and differing gut microbial communities, remains poorly understood. Here, we provide a comprehensive overview of common pediatric hepatobiliary conditions and recent studies exploring the contributions of the gut microbiota to these conditions or changes of the gut microbiota due to these conditions. We examine the current literature regarding the microbial alterations that take place in biliary atresia, pediatric non-alcoholic fatty liver disease, Wilson's disease, cystic fibrosis, inflammatory bowel disease, and viral hepatitis. Finally, we propose potential therapeutic approaches involving modulation of the gut microbiota and the gut-liver axis to mitigate the progression of pediatric liver disease.

Gut microbiome regulates serotonin production in the neonatal intestine to promote immune tolerance in early life

The gut microbiome in neonates is vastly different from that in adults due to dietary changes and gut maturation. However, the neonatal gut metabolome, largely shaped by gut bacteria, remains largely undefined. Using high-throughput metabolomics, we compared >500 metabolites in the ileum of specific pathogen-free (SPF) wild-type neonatal and adult mice. We found that most metabolites at significantly higher levels in neonates were neurotransmitters, including serotonin (5-HT), a neurotransmitter critical in the regulation of gut motility and mood stabilization. SPF neonates had significantly higher 5-HT levels in the ileum compared to both SPF adults and germ-free (GF) neonates, suggesting the gut microbiome as a key driver of generation in the neonatal intestine. Gut bacteria in neonates modulate the enzymes TPH-1 and MAO-A involved in the synthesis and breakdown of 5-HT. In addition, unlike in the adult intestine where 5-HT is produced primarily by enterochromaffin cells, gut bacteria are major producers of 5-HT in the neonatal intestine. The immunomodulatory role of 5-HT in the neonatal intestine has not been explored. We demonstrate that 5-HT directly promotes the differentiation regulatory T cells while diminishing interferon gamma and interleukin-17 produced in CD4 T cells, ex vivo and in vivo, in the neonatal intestine. Oral gavage of 5-HT into neonatal mice enhanced immune tolerance toward both commensal bacteria and dietary antigens. Our study has elucidated unique mechanisms by gut microbiota to regulate 5-HT generation in the neonatal intestine, and a novel immunomodulatory role for intestinal 5-HT to promote immune tolerance towards both dietary antigens and commensal bacteria during the early developmental stage.

Exploring background mutational processes to decipher cancer genetic heterogeneity

Much remains unknown about the progression and heterogeneity of mutational processes in different cancers and their diagnostic and clinical potential. A growing body of evidence supports mutation rate dependence on the local DNA sequence context for various types of mutations. We propose several tools for the analysis of cancer context-dependent mutations, which are implemented in an online computational framework MutaGene. The framework explores DNA context-dependent mutational patterns and underlying somatic cancer mutagenesis, analyzes mutational profiles of cancer samples, identifies the combinations of underlying mutagenic processes including those related to infidelity of DNA replication and repair machinery, and various other endogenous and exogenous mutagenic factors. As a result, the combination of mutagenic processes can be identified in any query sample with subsequent comparison to mutational profiles derived from malignant and benign samples. In addition, mutagen or cancer-specific mutational background models are applied to calculate expected DNA and protein site mutability to decouple relative contributions of mutagenesis and selection in carcinogenesis, thus elucidating the site-specific driving events in cancer. MutaGene is freely available at https://www.ncbi.nlm.nih.gov/projects/mutagene/.