FANS Unfixed: Isolation and Proteomic Analysis of Mouse Cell Type-Specific Brain Nuclei

Epigenetic-mediated gene regulation orchestrates brain
cell-type
gene expression programs, and epigenetic dysregulation is a major
driver of aging and disease-associated changes. Proteins that mediate
gene regulation are mostly localized to the nucleus; however, nuclear-localized
proteins are often underrepresented in gene expression studies and
have been understudied in the context of the brain. To address this
challenge, we have optimized an approach for nuclei isolation that
is compatible with proteomic analysis. This was coupled to a mass
spectrometry protocol for detecting proteins in low-concentration
samples. We have generated nuclear proteomes for neurons, microglia,
and oligodendrocytes from the mouse brain cortex and identified cell-type
nuclear proteins associated with chromatin structure and organization,
chromatin modifiers such as transcription factors, and RNA-binding
proteins, among others. Our nuclear proteomics platform paves the
way for assessing brain cell type changes in the nuclear proteome
across health and disease, such as neurodevelopmental, aging, neurodegenerative,
and neuroinflammatory conditions. Data are available via ProteomeXchange
with the identifier PXD053515.