Table 2. Pros and cons of established biomarkers in autoimmune encephalitis.

AE: autoimmune encephalitis, CSF: cerebrospinal fluid, MRI: magnetic resonance imaging, EEG: electroencephalogram, IL-6: interleukin-6, TNF-α: tumor necrosis factor-alpha, FDG-PET: fluorodeoxyglucose positron emission tomography

Biomarker	Pros	Cons
Autoantibodies (e.g., anti-NMDAR, anti-LGI1, anti-CASPR2)	High specificity for AE subtypes. Directly linked to pathogenesis. Can guide treatment decisions.	Not all patients with AE have detectable antibodies (seronegative cases). Testing can be time-consuming and may not correlate well with disease severity or prognosis in all cases.
CSF analysis (pleocytosis, protein levels, oligoclonal bands)	Widely available and can support the diagnosis of the inflammatory process	Low specificity for AE. Can be normal in some AE cases. Requires invasive lumbar puncture
MRI findings	Non-invasive and can exclude other pathologies. Specific patterns can suggest AE.	Can be normal in early stages or some AE subtypes. Findings can be non-specific Limited sensitivity in some AE cases.
EEG changes	Can detect subclinical seizures. Specific patterns (e.g., extreme delta brush in anti-NMDAR encephalitis) can be suggestive.	Low specificity for AE. Requires expertise for interpretation. Findings can be variable and non-specific.
Inflammatory markers (e.g., IL-6, TNF-α)	Can indicate ongoing inflammation and may correlate with disease activity	Low specificity for AE. Can be elevated in various inflammatory conditions. Limited availability of testing in some settings
FDG-PET	Can show abnormalities before structural MRI changes and may help in monitoring the treatment response	Limited availability and high-cost exposure to radiation. Patterns can overlap with other conditions.