Introduction
Encephalitis continues to exert a strong disease burden and to present diagnostic challenges. The incidence of encephalitis is about 10–20 per 100,000 in the United States [
1], and approximately 7 of 100.000 are hospitalized due to encephalitis [
2]. Etiology remains unspecified in about half the cases [
3], but 20–50% of cases with known etiology are caused by viruses. Incidence and pathogen spectrum vary significantly depending on geographic region. In the United States and Europe most of the cases can be attributed to herpes simplex virus (HSV), followed by varicella zoster virus (VZV) and enteroviruses. The prognosis depends strongly on timely diagnosis and institution of correct treatments. For example, HSV encephalitis-associated lethality is 70–100% in untreated patients but 20–30% in patients receiving virus specific therapy [
4]. Therefore, attempts have been made to improve the detection of viral pathogens. Besides PCR and multiplex assays, metagenomic next-generation sequencing (mNGS) could prove useful, but it appears to be less accurate for the detection of viral (AUC = 0.5–0.7) than bacterial pathogens (AUC = 0.85) [
5].
Despite the sequelae evoked by the primary virus infection itself, viral relapses can occur as well as secondary autoimmune processes leading to autoimmune neuroinflammation. In the case of HSV encephalitis, about 25% of all patients experience a relapse either by virus reactivation or, in 15–20% by an autoimmune anti-n-methyl-D-aspartate-receptor (NMDAr) encephalitis [
6,
7]. In autoimmune encephalitis the host immune system targets self-antigens expressed in the central nervous system (CNS) [
8]. The symptoms vary based on the specific autoantibody involved, yet shared characteristics collectively suggest the likelihood of autoimmune-driven encephalitis [
9]. However, symptoms of viral and autoimmune CNS inflammation are similar (e.g. altered mental status, seizures) and the etiology can therefore not be differentiated on the basis of clinical findings.
Advances in diagnostics have enabled us to identify several well-characterized autoantibodies that cause autoimmune encephalitis, but the results are not available in the acute setting, as turnaround time may be up to 1–2 weeks depending on work flows in diagnostic laboratories. Moreover, about 50% of encephalitis patients remain without etiological diagnosis and it is unknown how many of these actually suffer from an autoimmune encephalitis. Considering that viral and autoimmune encephalitis require completely different treatments (antivirals vs. immune suppression/apheresis), there is a clear need for diagnostic biomarkers to distinguish between these two entities as soon as possible after lumbar puncture. Apart from the detection of a viral pathogen or a specific autoantibody, there are several biomarkers that aid to differentiate viral from autoimmune encephalitis. CSF leukocyte count is one of the best-known CSF markers, and together with clinical parameters (subacute/chronic presentation; Charlson comorbidity index < 2 and psychiatric/memory complaints) the absence of inflammatory changes in CSF has been used to generate a risk score for autoimmune encephalitis (area under the ROC curve, AUC, 0.92 [95% CI, 0.87–0.97]) [
10]. CSF oligoclonal bands are more common in patients with autoimmune encephalitis than viral encephalitis, yet can be found in non-inflammatory diseases as well [
11]. Cytokines such as M-CSF and the B-cell markers CXCL13 and BAFF tend to be elevated in autoantibody-associated disorders, whereas interferon gamma (IFN-γ) is elevated mainly in viral encephalitis [
12,
13].
Quantifying metabolites in cerebrospinal fluid (CSF) is a promising approach to identify novel biomarkers for infectious and inflammatory CNS disorders, as CSF is in intimate contact with the target organ and has been evaluated as “liquid biopsy” for CNS pathology essentially since development of lumbar puncture in the nineteenth century. Moreover, small molecules can potentially be developed to rapid diagnostics that can be performed after lumbar puncture at the bedside or in an acute services lab and thus have the potential to provide shorter turn-around time than detection of pathogenic viruses and autoantibodies. We have previously applied a targeted metabolomics approach to measure 188 small molecules in CSF from 221 patients with infectious, autoimmune, and non-inflammatory CNS disorders. In previous publications we reported the identification of accurate biomarkers for CNS involvement in varicella-zoster virus reactivation [
14], for enterovirus meningitis in patients without CSF pleocytosis [
15], and for the differentiation between bacterial and viral meningitis [
16,
17]. We have now expanded the analysis of this cohort to screen for CSF metabolite biomarkers that can accurately distinguish between viral CNS infections and autoimmune meuroinflammation and may reveal pathophysiological differences between the two.
Discussion
We performed a targeted metabolomic analysis of CSF samples from patients with viral CNS infections, autoimmune neuroinflammation, and noninflamed controls and found that CSF metabolites were more accurate biomarkers than standard diagnostic CSF parameter for the differentiation between viral CNS infections and autoimmune neuroinflammation, whereby the short-chain acylcarnitines C4 (isobutyrylcarnitine) and C5 (isovalerylcarnitine) were among the best metabolite biomarkers.
Acylcarnitines are intermediates of beta-oxidation, i. e. the metabolism of fatty acids to acetyl-CoA, which is fed into the tricarboxylic acid cycle as energy source and building block. Elevated extracellular levels of short-chain acylcarnitines usually reflect a dysfunction of beta-oxidation of saturated fatty acids in mitochondria, which leads to the conjugation of accumulating fatty acid fragments to the carrier molecule carnitine. These acylcarnitine complexes are then extruded into the cytoplasm and subsequently into the extracellular environment [
28]. In our study we noted that the highest C4 and C5 concentrations in CSF were found in HSE, which is known to interfere considerably more strongly with cell homeostasis (and cause organ damage) than VZV or enteroviruses. A plausible explanation would, therefore, be that the viruses, and particularly HSV, compromise mitochondrial utilization of fatty acids in the CNS, favoring glycolysis as a readily available energy source. This is also supported by higher lactate concentrations in viral CNS infections than autoimmune neuroinflammation (Table
2). There also is experimental evidence that both HSV and VZV induce mitochondrial dysfunction in human cells [
29,
30]. This mitochondrial dysfunction may also result from interferon responses triggered by these viruses. Deleting interferon-γ stimulated gene 15 (ISG15) in human cells results in hyperactive interferon signaling, mimicking a viral infection. ISG15-deficient cells have an interferon-driven defect in mitochondrial respiration, which leads to compromised fatty acid oxidation and elevated acylcarnitine levels [
31,
32], and pharmacologic inhibition of interferon signaling leads to a normalization of fatty acid oxidation in the ISG15-deficient cells [
32].
All other accurate biomarkers for viral CNS infections vs. autoimmune neuroinflammation were membrane phospholipids, and their concentrations were always higher in viral CNS infections. This agrees well with our previous observations that, even though the highest phospholipid levels in CSF are found in bacterial meningitis [
17], elevated concentrations of specific phospholipid species are also found in viral infections, as compared to noninflamed control samples [
14,
15]. Viruses interact with host cell membranes in complex ways. Cell damage in the sense of a cytopathic effect would be the simplest explanation for the release of membrane phospholipids during viral infections, and this agrees well with our observation that levels were highest in HSE. However, more subtle mechanisms such as differences in membrane signaling or perturbations during viral entry and budding are also plausible.
Using LC–MS/MS analysis of the same cohort, we have previously reported that CSF kynurenine and the tryptophan/kynurenine ratio constitute biomarkers for the differentiation between viral CNS infections and autoimmune neuroinflammation [
18], which was subsequently corroborated using a simple immunoassay for these analytes [
33]. Kynurenine was studied in [
18] because it had been detected > LOD preferentially in infected samples and therefore held promise as a biomarker for infectious CNS processes, but it was excluded from the present analysis because it was detected > LOD in < 80% of the samples. The AUCs for kynurenine and tryptophan/kynurenine ratio in [
18] for the differentiation between viral CNS infections and autoimmune neuroinflammation were 0.8 and 0.79, respectively, which is substantially lower than the AUCs of the CSF metabolite biomarkers identified in the present study. However, the AUCs for both kynurenine and tryptophan/kynurenine ratio increased to 0.95 when CSF cell count was added in a logistic regression model. Future studies should investigate whether logistic regression models containing selected CSF metabolite biomarkers described herein and standard CSF parameters result in a similar improvement of diagnostic potential.
The diagnosis of Bell’s palsy is made in individuals with acute onset of paralysis of the facial nerve after excluding known causes of facial neuritis including infections with, e.g.,
Borrelia sp. or VZV [
34]. Major risk factors are diabetes, hypertension, pregnancy, and obesity. In the Bell’s palsy patients in our cohort, common infectious etiologies had been excluded. However, concentrations of certain CSF metabolite biomarkers for viral CNS infections was slightly higher than in the Tourette syndrome controls, suggesting an inflammatory etiology even though CSF cell counts were normal in all Bell’s palsy samples. This also agrees with our previous observation that phospholipid levels are elevated in CSF samples from enterovirus meningitis with normal cell counts [
15]. Taken together, these results support the common concept that Bell’s palsy often has an inflammatory origin, such as post-infectious processes after infections with pathogens that are not usually tested for in clinical practice.
Limitations and strengths of the study
Our study is limited in that the samples were collected at a single center and we could, therefore, not perform an external validation, which would provide stronger evidence for the validity of the biomarkers. The results should, therefore, be replicated in an independent cohort before further development to a clinical diagnostic can be considered. In addition, the exact molecular identity of some of the identified phosphatidylcholines needs to be defined further, as some of them correspond to more than one isobar or isomer. This metabolomics analysis targeted only a selection of metabolite classes, and other markers for mitochondrial function (e.g., tricarboxylic acid intermediates, cytochrome C, ATP, NADH) or membrane perturbation (e.g., ceramides) were not included. The Human Metabolome Database (hmdb.ca) lists 468 endogenous CSF metabolites, and a broader screen might detect additional biomarkers. On the other hand, a clear strength of the study is that all specimens were collected using a standardized protocol and that definitive diagnoses according to viral pathogen and inflammatory disorder were available.
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