Postnatal Mouse Brain Region-Resolved Peptidomic Resource of Conditional Ndel1 Loss: Comparison of Acidic and Alcoholic Extraction Strategies

Abstract

The oligopeptidase Ndel1 (NudE neurodevelopment protein 1 like 1) is a multifunctional protein implicated in neurodevelopmental processes, intensively investigated as a potential biomarker in psychiatric disorders. While its roles in regulating the cytoskeleton are well-studied, the global consequences of its loss on the brain's peptide landscape are unknown. This study presents a comprehensive, region-resolved peptidomic resource detailing the consequences of postnatal Ndel1 loss in the mouse cortex, hippocampus, striatum, and cerebellum. We also validated this method of microwave protease inactivation followed by acidic and organic extractions by means of this peptidome analysis across several brain regions. More specifically, using a conditional knockout mouse model with Ndel1 deletion in forebrain excitatory neurons, we employed complementary acidic and alcoholic extraction workflows coupled to liquid chromatography–tandem mass spectrometry (LC–MS/MS). We generated a comparative atlas of differentially abundant peptides (DAPs), identifying hundreds of peptide changes across the different brain regions and extraction methods. Gene Ontology analysis of the inferred source proteins revealed alterations in pathways related to cytoskeletal organization, synaptic function, and cellular metabolism. This dataset provides a foundational resource for generating new hypotheses about Ndel1's region-specific functions and serves as a valuable reference for the neurodevelopmental and neuropeptidomics communities. Understanding these Ndel1-driven changes is crucial, providing valuable insights into the pathophysiology of neurodevelopmental and mental disorders linked to reduced Ndel1 activity, such as schizophrenia, autism, and bipolar disorder. This holistic view may reveal novel therapeutic targets for these complex conditions. (Figure presented.).