Clinical Features, Antibody Profiles, and Prognostic Factors in Autoimmune Encephalitis: A Single-Center Study

<b>Background/Objectives</b>: Autoimmune encephalitis (AIE) comprises a heterogeneous group of inflammatory central nervous system (CNS) disorders characterized by variable clinical presentations and antibody profiles. This study aimed to identify poor prognostic factors in AIE by retrospectively evaluating patients diagnosed based on clinical, radiological, and serological findings. <b>Methods</b>: Forty-four patients diagnosed with AIE between 2014 and 2024 were included. Demographic, clinical, radiological, and serological data were collected retrospectively. Patients were grouped based on antibody localization (intracellular, surface, and seronegative) and classified by treatment response. Poor prognosis was defined as a lack of objective clinical improvement to treatment or death. <b>Results</b>: The mean age was 57.8 ± 13.6 years, with a female-to-male ratio of approximately 1:1. Limbic encephalitis (LE) was the most common clinical presentation (43.2%). Malignancy was detected in 33.3% of patients, most frequently in those with SOX1 (83.3%), anti-Hu (60.0%), and anti-Yo (50.0%) antibodies. Anti-SOX1 positivity was significantly associated with both malignancy (OR = 27.5, <i>p</i> = 0.007) and mortality (OR = 13.2, <i>p</i> = 0.009), while anti-LGI1 positivity correlated with the absence of malignancy (<i>p</i> = 0.036). Patients with LE showed significantly better treatment responses (OR = 14.0, <i>p</i> = 0.019). Mortality was 20.1% overall and highest among anti-SOX1-positive patients (66.7%). The presence of multiple antibodies was associated with higher mortality and poorer prognosis, although not statistically significantly. <b>Conclusions</b>: Anti-SOX1 positivity is a key indicator of poor prognosis in AIE and is strongly associated with both malignancy and mortality. In contrast, LE presentation was linked to a better treatment response. Antibody profile, clinical features, and malignancy screening are critical for risk stratification and guiding management in AIE.