Plasma proteome in LGI-1 autoimmune encephalitis

Leucine-rich glioma-inactivated antibody associated autoimmune encephalitis (LGI-1 AE) is a rare immune mediated neuroinflammatory disease resulting in seizures and cognitive impairment. LGI-1 AE can respond well to immunotherapy, however residual symptoms, particularly cognitive dysfunction may persist despite treatment. We have previously identified perturbations of peripheral innate immune cells (monocytes) in LGI-1 AE in the treated (chronic) phase of the disease. To further understand these peripheral changes, we performed a proteomic analysis of plasma from individuals with LGI-1 AE in the untreated (acute) and chronic phase of the illness.

High-throughput proteomic profiling was performed on plasma samples from nine acute and 27 chronic LGI-1 AE participants and 16 age- and sex-matched controls using the SomaLogic 11 k proteomic panel. Differentially expressed proteins (DEP) were identified using limma with false discovery rate (FDR) < 0.05. Bulk RNA sequencing was performed on isolated monocytes from ten of the participants with chronic LGI-1 AE and 28 controls. Differential gene analysis was performed using DESeq2 with FDR < 0.1. Pathway analysis was performed on the transcriptomic and proteomic datasets with gene set enrichment analysis using the Gene Ontology Biological Processes database and FDR < 0.05.

The plasma analysis identified 215 overexpressed and 1015 suppressed proteins in the acute cohort compared with the healthy cohort. Upregulated proteins included proteins related to innate immune activation, chemoattractants for myeloid cells, components of the complement cascade as well as lymphocyte signalling and activation molecules. Significantly downregulated pathways included those related to autophagy. There were no significantly differentially expressed proteins (DEP) between the acute and chronic or chronic and control cohorts. Monocyte transcriptomic analysis revealed 18 upregulated and 170 downregulated genes, highlighting interleukin (IL)-6 and downstream IL-6 pathway signalling as key dysregulated pathways.

This study identified IL-6 signalling and activation of the terminal complement cascade as potential pathophysiological immune mechanisms, highlighting opportunities for therapeutic repurposing using existing agents in LGI-1 AE. In addition, the observed suppression of autophagy- related pathways suggests a previously underappreciated mechanism that may contribute to disease pathogenesis, warranting further investigations into the role of autophagy dysregulation in CNS autoimmunity associated with LGI-1 AE.