410 - Longitudinal transcriptome changes during S. epidermidis CSF shunt infection

Monday, May 1, 2023

9:30 AM – 11:30 AM ET

Poster Number: 410
Publication Number: 410.417

Gwenn L. Skar, University of Nebraska Medical Center, Omaha, NE, United States; Matthew Beaver, UNMC, Omaha, NE, United States; Richard C. Crist, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States; Benjamin C.. Reiner, University of Pennsylvania, Philadelphia, PA, United States; Samar N. Chehimi, University of Pennsylvania, Philadelphia, PA, United States

Presenting Author(s)

Gwenn L. Skar, MD

Assistant Professor
University of Nebraska Medical Center
Omaha, Nebraska, United States

Background: Thousands of CSF shunts are placed each year to treat hydrocephalus, however, this is often complicated by infection. Tragically, these infections are associated with significant long-term neurologic morbidity. The cellular mechanisms underlying this neurologic morbidity are poorly understood.

Objective: Using single nucleus nuclear RNA sequencing (snRNAseq) we identified acute and chronic transcriptome changes that occur in the brain following CSF shunt infection, providing potential insight into causes of neurologic morbidity.

Design/Methods:

Silicone catheters were precoated with S. epidermidis and implanted into the lateral ventricle of the brain in C57BL/6 mice. At days 3 and 56 post-infection brain tissue immediately surrounding the catheter was removed and snap frozen for storage and nuclei isolation. SnRNAseq libraries were generated using the 10x Genomics Chromium Controller and sequenced on a NovaSeq 6000. The R package Seurat was used for quality control and to cluster nuclei based on transcriptomic data. Cluster identities were determined by expression of canonical cell-specific genes. Pseudobulk analysis was performed in the R package Libra, allowing identification of differentially expressed genes. Ingenuity Pathway Analysis was used for analysis of canonical pathways and upstream regulators.

Results:

Twenty-two transcriptomically distinct clusters of nuclei were identified. Differentially expressed genes (DEGs) at day 3 post-infection were observed in both neuronal and glial populations. The top DEGs included genes with known connections to regulation of inflammation and infection (e.g. Saa3, Acod1, Atp5g1). These genes were not differentially expressed at day 56 post-infection. At day 56 post-infection, the majority of DEGs were identified in neuronal clusters. Genes encoding components of the complement system (e.g. C4b, C1qa, C1qc) were upregulated in specific neuronal subtypes. Pathway analysis of DEGs observed at day 56 post-infection also revealed an overrepresentation of genes involved in neuronal development.

Conclusion(s):

These data indicate that S. epidermidis CSF shunt infection results in both short- and long-term transcriptomic changes that differ by cell population. The identification of DEGs and activated pathways with connections to cognitive function and neuronal development provide potential targets for future work to explore cell type-specific roles in influencing the long-term consequences of pediatric CNS infection.