Applying novel technologies to the cerebrospinal fluid and its cells for the benefit of improved diagnosis and treatment prediction in neuro-immunological diseases and cerebral infections

The cerebrospinal fluid (CSF) contains soluble molecules such as protein, sugar and lipids, and – at least in the healthy situation – only few cellular components, i.e up to 3 cells per microliter.  The analysis of CSF could be performed by many different methods, such as fluorescent-activated-cell-sorting (FACS), single cell transcriptomics (scRNAseq), or mass-spectrometry (MS/MS). However, in clinical practice only a differential blood cell count, some limited clinical chemistry measures, and immunoglobulin analysis is routinely being used (1). This routine analysis serves many purposes, but has its limitation in e.g. differentiating a viral CNS infection from an autoimmune CNS process.

In our CSF study, we analyze and compare the following methods, for an improved characterization of the content of the CSF, and hence the benefit of our patients:

1. The cell type characterization by flow cytometry (FACS)
2. A novel epigenetic analysis of the cellular components of the CSF (developed by the company EPIMUNE) will be compared to
3. As a gold standard, single-cell RNA sequencing for the comprehensive analysis of cells in the CSF will be performed in selected samples.

In collaboration with the Departments of Neurology (Prof. S. Rauer), Psychiatry (Prof. L. Tebartz van Elst), and Gastroenterology (Dr. Sagar) we are examining the CSF of patients with a broad variety of neurological diseases, including but not limited to viral and bacterial infections and several autoimmune conditions. We postulate that different cell types can be measured when the total cell count in the CSF is high. We suspect that in certain patient groups, numerical differences in cell types will emerge. The CSF of these patients is spun down into a cellular pellet, which are then being analyzed by the following methods:

1. Flow cytometry
   A routinely-used method to count difference cell subsets in blood is flow cytometry. Despite its challenge to detect low numbers of cells in samples, we have developed a methodological approach to overcome these problems: Utilizing the advanced capabilities of the Sony ID7000 Spectral Cell Analyzer allows for a precise interrogation of an antibody panel consisting of 21 different antibodies in a single sample. This strategic selection enables comprehensive phenotypic profiling of different leukocyte subsets beyond the traditional scope of analysis, ensuring optimal resolution and accuracy in our analytical assessments.