A structured evaluation of cryopreservation in generating single-cell transcriptomes from cerebrospinal fluid.

Area of Science:

• Immunology
• Neuroscience
• Genomics

Background:

• Single-cell transcriptomics offers deep insights into cerebrospinal fluid (CSF) cellular composition.
• Fragile CSF cells pose challenges for immediate processing, potentially limiting large-scale studies.

Purpose of the Study:

• To develop and validate a robust cryopreservation protocol for CSF cells.
• To assess the impact of cryopreservation on CSF cell viability, transcriptomic profiles, and immune cell clonotypes for single-cell RNA sequencing (scRNA-seq).

Main Methods:

• Collected CSF samples from 21 participants across two sites.
• Split samples into fresh processing and cryopreservation groups.
• Performed scRNA-seq and B and T cell receptor sequencing on both fresh and cryopreserved samples.

Main Results:

• High recovery rates of all known CSF cell types after cryopreservation and thawing.
• No significant differences in cell type proportions or cellular transcriptomes between fresh and cryopreserved cells.
• Consistent results across different sites and scRNA-seq chemistries; clonotype diversity remained unaffected.

Conclusions:

• The developed cryopreservation protocol is effective for preserving CSF cells for scRNA-seq.
• This method provides a reliable alternative to immediate processing, enabling large-scale studies of CSF cells.