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A 73-year-old man developed subacute cognitive impairment, status epilepticus and reduced level of consciousness requiring mechanical ventilation. An MR scan of the brain showed multifocal inflammatory lesions, but with normal cerebrospinal fluid (CSF); blood results showed positive antinuclear antibody (ANA) and anti-double-stranded DNA (anti-dsDNA) antibodies (Abs), but normal complement and urine analysis. Commercial kit for cell-surface antineuronal antibodies, including anti-NMDAR (anti-N-Methyl-D-Aspartate Receptor antibody), anti-LGI1 (anti-Leucine-Rich Glioma-Inactivated 1 antibody), anti-CASPR2 (anti-Contactin-Associated Protein-Like 2 antibody), anti-GABA-BR (anti-Gamma-Aminobutyric Acid Type B Receptor antibody), anti-AMPAR (anti-α-Amino-3-Hydroxy-5-Methyl-4-Isoxazolepropionic Acid Receptor antibody) and anti-DPPX (anti-Dipeptidyl-Peptidase-Like Protein-6 antibody), was negative in serum and CSF. We gave methylprednisolone, plasma exchange, rituximab and cyclophosphamide. However, despite initial improvement, he had five relapses. We reassessed the diagnosis and identified a thymoma; also, research laboratory testing with tissue-based and cell-based assays identified anti-GABA-AR Abs. He improved following thymectomy and with tocilizumab. This case underscores the complexity and varied presentations of anti-GABA-AR encephalitis with thymoma, emphasising the importance of comprehensive antibody testing in making this challenging diagnosis.