Integrative analysis of blood and gut microbiota data suggests a non-alcoholic fatty liver disease (NAFLD)-related disorder in French SLAdd minipigs

Abstract

Minipigs are a group of small-sized swine lines, which show a broad range of phenotype variation and which often tend to be obese. the SLA dd (DD) minipig line was created by the niH and selected as homozygous at the SLA locus. It was brought to France more than 30 years ago and maintained inbred ever since. in this report, we characterized the physiological status of a herd of french DD pigs by measuring intermediate phenotypes from blood and faeces and by using Large White (LW) pigs as controls. three datasets were produced, i.e. complete blood counts (cBcs), microarray-based blood transcriptome, and faecal microbiota obtained by 16S rRNA sequencing. CBCs and expression profiles suggested a non-alcoholic fatty liver disease (nAfLD)-related pathology associated to comorbid cardiac diseases. The characterization of 16S sequencing data was less straightforward, suggesting only a potential weak link to obesity. The integration of the datasets identified several fine-scale associations between CBCs, gene expression, and faecal microbiota composition. NAFLD is a common cause of chronic liver disease in Western countries and is linked to obesity, type 2 diabetes mellitus and cardiac pathologies. Here we show that the French DD herd is potentially affected by this syndrome. Minipigs are a group of small-sized swine lines, which started to be developed in the 1940s for biomedical research. They present many advantages over conventional pigs, like size, ease of handling and decreased feed requirements 1. Today, a large variety of breeds is available for very different applications. Minipig lines are maintained using specific breeding strategies, which minimize inbreeding while keeping the genetic integrity of the population 2. Examples of minipigs include the MeLiM line, a model to study an inheritable form of melanoma undergoing spontaneous regression 3 and the Yucatan strain, used for research on cardiovascular pathologies and diabetes 1. Minipig lines homozygous at the major histocompatibility locus (MHC, also known as Swine Leukocyte Antigen or SLA in pigs) were also produced by the NIH, mostly for immunology studies and transplantation programs 4. Non-alcoholic fatty liver disease is the most common cause of chronic liver disease in developed countries 5,6. It spans a spectrum of pathologies ranging from hepatic steatosis to non-alcoholic steatohepatitis (NASH) and cirrhosis 6-8. While NAFLD was traditionally seen as a pathology affecting mainly the liver, it has recently been shown that its burden is not limited to this organ. There is increasing evidence that NAFLD is multisystemic, involving extra-hepatic organs and pathways. It is associated with obesity 9 , type 2 diabetes mellitus, insulin resistance, metabolic syndrome and cardiovascular diseases 5-7,10-12. Despite the complexity of this pathology, many NAFLD-related molecular pathways are known 13-15 , and its development is usually modelled using the "two-hit hypothesis" 12,13. The "first hit" corresponds to insulin resistance-mediated fat accumulation in h...