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.

基于质谱的蛋白质组学（MS-based proteomics）已被用于细胞周期阻滞状态下蛋白质的核质亚细胞分布差异网络分析：（a）处于DNA复制起始激活检查点的细胞周期阻滞，或（b）响应氧化应激的细胞周期阻滞。研究共鉴定出401个存在显著表达变化的蛋白质。细胞应答过程通过整合细胞内转运与总丰度的变化，以改变局部区室的蛋白质丰度，而这正是细胞应答的核心基础。针对两种扰动处理，共有245个蛋白质出现了显著变化；而氧化应激与DNA复制之间的信号串扰，则主要由49个在两种处理下均表现出强烈变化的蛋白质所主导。诸多核过程受到包含{KPNA2、KPNB1、PCNA、PTMA、SET}以及血红素/铁蛋白HMOX1和FTH1的蛋白质空间转换机制的调控。本研究提供了参与小窝、细胞外基质重塑、转化生长因子β（TGFβ）信号通路、胰岛素样生长因子（IGF）通路、Emerin复合物、线粒体蛋白质输入复合物、剪接体以及蛋白酶体等过程的蛋白质的动态空间分布数据。研究数据表明，对于空间异质性细胞而言，跨区室通讯是其系统生物学特性不可或缺的组成部分；关键蛋白质网络的协同空间重分布是诸多功能变化的分子基础；而获取蛋白质动态空间分布的相关信息，对于全面解析细胞功能而言至关重要。本研究阐述了此类空间分布数据如何可为进一步研究细胞间高级空间协调的关键特征提供优先级方向。我们提出，本研究所得数据与越来越多的研究结论相一致：即多数亚细胞蛋白质转运过程是组成型的，而这些组成型转运过程的紊乱可能与癌症及其他疾病相关。本研究提供了一个定量空间分辨的核质相互作用网络，以供后续研究使用。