Violeta de Anca Prado: Early life metabolic disruption: multigenerational consequences on the genome, epigenome and microbiota

Abstract

Obesity and metabolic syndrome are rising worldwide, having a prevalence increased not only in adults, but also in children. The consequences of a metabolic impact during early life can last throughout the adult life, impacting further generations. How that impact affects might be explain by two concepts: epigenetics, the molecular mechanism by which environmental exposures affect the phenotype, and the holobiont, in which the microbiota acts as an extended genotype and phenotype. This thesis investigated the consequences of repeated early life metabolic disruption across generations on genetic and epigenetic factors, and on the microbiome. 

We employed a murine model for childhood obesity based on litter size reduction: 8 pups per dam in the control group, 4 in the overnutrition group. The overnutrition group developed neonatal obesity and signs of metabolic syndrome later in life. The nutritional challenge was maintained for three generations in two cohorts, in which the maternal and the paternal lineage were followed.  DNA methylation, genetic analyses were performed in both germ cells and somatic tissues, while the faecal microbiome metagenome was also investigated.

This thesis in composed of three studies. The first study benchmarked bioinformatic tools used to analysed data produced by Genotype-by-Sequence combined with Methylated DNA immune-precipitation (GBS-MeDIP), the methodology later used in the second study. We found that the combination of featureCounts and the non-parametric statistical method Mann-Whitney U test was the most suitable to analyse GBS-MeDIP generated data. The second study investigated the consequences of an early life metabolic disruption on the sperm methylome and genome as well as their interaction. We found that germ line genetic but not methylomic variation across generations was indicative of treatment response, with only a few methylation sites being altered across generation and an important effect on copy number variations. In the third study, we investigated the role of the sustained metabolic disruption across generation on the methylome of epididymal white adipose tissue (eWAT) and on the gut microbiota. We identified one factor which separated the early life the treatment from control animals and explained more variance in males. The affected microbial functions included short-chain fatty acid biosynthesis, relevant for host immunometabolism and energy regulation. Methylation patterns of metabolic pathways in eWAT were also affected, and these effects persisted stably across generations.

Overall, this thesis shows that a multigenerational metabolic challenge during the neonatal phase promotes changes in the soma, germline and functional gut microbiota, that the germline methylome and genome are intertwined across generations, and that gut microbiota has an important role in environmental exposures. This work could help understand the molecular mechanisms involved in obesity and their long-term functional consequences.