The gut microbiome associated with LGI1- and CASPR2-antibody encephalitis

Autoimmune encephalitis is a cause of brain inflammation characterised by auto-antibodies which target cell surface neuronal proteins, and lead to neuronal dysfunction. In older people, common forms are encephalitis with autoantibodies to leucine-rich glioma inactivated protein 1 ( LGI1 ) and contactin associated protein like 2 ( CASPR2 ), whose presentation includes frequent focal seizures. The exact cause of these autoantibodies remain unknown, but established predispositions include overrepresented human leukocyte antigen (HLA) alleles. Yet, these alleles are themselves common in the healthy ancestry-matched population. One potential aetiological hypothesis is that an environmental trigger, such as the gut microbiome, interacts with a genetically predisposed individual. To investigate this, we studied 47 patients with leucine-rich glioma-inactivated 1 (LGI1)- or contactin-associated protein 2 (CAPSR2)-antibody encephalitis (LGI1/CASPR2-Ab-E) and 37 familial/environmentally matched controls, and performed metagenomic shotgun sequencing, to describe compositional and functional differences in the gut microbiome. We observed that LGI1/CASPR2-Ab-E gut microbiomes exhibited a significant reduction in the ratio of Firmicutes and Bacteroidetes phyla, which associated with dosage of HLA susceptibility alleles in LGI1-Ab-E patients. Furthermore, we identified differences in functional gene profiles in the gut microbiome that led to a reduction of neuroinflammatory protective short-chain-fatty-acids (SCFA) in LGI1-Ab-E patients. Taken together, our results suggest that a compositional shift in the gut microbiome of LGI1/CASPR2-Ab-E associates with a neuroinflammatory state, possibly through the reduction of SCFA production. Our study highlights the potential of the gut microbiome to explain some of the complex condition and unravel aetiological questions. Validation studies with greater sample sizes are recommended.