Spatial Cross-Talk between Oxidative Stress and DNA Replication in Human Fibroblasts

MS-based proteomics has been applied
to a differential network
analysis of the nuclear–cytoplasmic subcellular distribution
of proteins between cell-cycle arrest: (a) at the origin activation
checkpoint for DNA replication, or (b) in response to oxidative stress.
Significant changes were identified for 401 proteins. Cellular response
combines changes in trafficking and in total abundance to vary the
local compartmental abundances that are the basis of cellular response.
Appreciable changes for both perturbations were observed for 245 proteins,
but cross-talk between oxidative stress and DNA replication is dominated
by 49 proteins that show strong changes for both. Many nuclear processes
are influenced by a spatial switch involving the proteins {KPNA2,
KPNB1, PCNA, PTMA, SET} and heme/iron proteins HMOX1 and FTH1. Dynamic
spatial distribution data are presented for proteins involved in caveolae,
extracellular matrix remodelling, TGFβ signaling, IGF pathways,
emerin complexes, mitochondrial protein import complexes, spliceosomes,
proteasomes, and so on. The data indicate that for spatially heterogeneous
cells cross-compartmental communication is integral to their system
biology, that coordinated spatial redistribution for crucial protein
networks underlies many functional changes, and that information on
dynamic spatial redistribution of proteins is essential to obtain
comprehensive pictures of cellular function. We describe how spatial
data of the type presented here can provide priorities for further
investigation of crucial features of high-level spatial coordination
across cells. We suggest that the present data are related to increasing
indications that much of subcellular protein transport is constitutive
and that perturbation of these constitutive transport processes may
be related to cancer and other diseases. A quantitative, spatially
resolved nucleus–cytoplasm interaction network is provided
for further investigations.