Hippocampal proteome profiling of a mouse model with dysfunctional STAT1 signaling

Signal transduction via the Signal Transducer and Activator of Transcription 1 (STAT1) pathway is indispensable for mediating the intracellular effects of interferon-α (IFN-α), interferon-γ (IFN-γ) and other cytokines in the brain and, thereby, crucial for antiviral and antibacterial responses during potential life-threatening CNS infections. However, the role of STAT1 signaling beyond the known IFN-α and IFN-γ effects in immediate antimicrobial defense is highly context-dependent, and studies in the existing literature using STAT1-targeted mouse models under normal physiological conditions remain scarce. Here, we characterized a STAT1 targeted-disruption mouse model (STAT1-/- mice) in the absence of infectious stimuli by quantitative proteome analysis. Soluble hippocampal protein extracts from five female animals per condition (WT, STAT1-/-) were processed with replicate injection, resulting in two technical replicates per biological replicate and, thus, in a total of 20 LC-MS runs to be compared. We utilized an ion mobility-enhanced version of a data-independent acquisition (DIA) workflow with alternating low and elevated energy (referred to as UDMSE). Label-free protein quantification revealed numerous differentially regulated proteins, many of which classified as products of IFN-regulated genes according to Interferome V2.01 (https://interferome.org/interferome/home.jspx), and/or of STAT1 target genes according to the ENCODE transcription factor targets dataset (https://maayanlab.cloud/Harmonizome/dataset/ENCODE+Transcription+Factor+Targets). By integration of transcriptome and proteome data, we detected significant alterations in hippocampal gene and protein expression profiles implicated in neuroinflammatory processes and neuroprotection.