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. ### Competing Interest Statement SRI has received honoraria/research support from UCB, Immunovant, MedImmun, Roche, Janssen, Cerebral therapeutics, ADC therapeutics, Brain, CSL Behring, and ONO Pharma, and receives licensed royalties on patent application WO/2010/046716 entitled "Neurological Autoimmune Disorders". And has filed two other patents entitled "Diagnostic method and therapy" (WO2019211633 and US-2021-0071249-A1; PCT application WO202189788A1) and "Biomarkers" (PCT/GB2022/050614 and WO202189788A1). ### Funding Statement This work was funded by a grant from the Medical Research Charities Group, the Health Research Board, Ireland, and Epilepsy Ireland (grant code: MRCG-2018-005), and Science Foundation Ireland (SFI) under Grant Number 16/RC/3948 and co-funded under the European Regional Development Fund and by FutureNeuro industry partners. A senior clinical fellowship (to SFI) from the Medical Research Council [MR/V007173/1], Wellcome Trust Fellowship [104079/Z/14/Z], the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC) (The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: This study was approved by ethics committees at the Royal College of Surgeons in Ireland (under protocol REC1631), and Oxford University (under protocol number 16/YH/0013). Ethics for this study was approved in the UK by Yorkshire & The Humber - Leeds East Research Ethics Committee (16/YH/0013). All patients gave written informed consent. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The raw metagenomic sequence data will be made accessible on the European Genome-Phenome Archive (EGA) upon publication and will be referred to here.