Targeting nuclear pore protein, NUP210, reduces metastasis through heterochromatin-mediated silencing of mechanosensitive genes

Mechanical signals from the extracellular microenvironment have been shown to promote tumor and metastasis progression. It remains unclear how these signals are transmitted to the nucleus to regulate gene expression necessary for metastatic progression. In a genome-wide screen for metastasis-associated polymorphism in the non-coding regulatory region of the genome, we found NUP210, a nuclear pore complex protein as a metastasis susceptibility gene and a cellular mechanosensor. Depletion of NUP210 in metastatic cancer cells significantly reduces lung metastasis in mouse orthotopic transplantation models. Mechanistically, NUP210 interacts with histone H3.1/3.2 (preferentially enriched at the poised/bivalent gene promoters) at the nuclear periphery. To investigate how NUP210 regulates metastasis, we performed combined ChIP-seq and RNA-seq analysis to identify the NUP210-dependent downstream signaling pathways necessary for metastatic progression. Interestingly, RNA-seq analysis revealed that the loss of NUP210 in cancer cells significantly decreased the expression of mechanosensitive, cell adhesion/migration-related pro-metastatic genes. ChIP-seq analysis of H3K4me3 (transcriptional activation mark) and H3K27me3 (transcriptionally repressive, heterochromatin mark) in NUP210 WT/KO cells revealed that NUP210 loss resulted in increased heterochromatinization of mechanosensitive, cell migration-related genes associated at the nuclear periphery. Our results provide a new insight into the role of nuclear pore protein in regulating cellular mechanosensation and metastasis. For RNA-seq, 4T1 cells were grown in tissue culture dishes. After 48 h of incubation, total RNA was isolated using RNeasy mini kit (Qiagen). On-column DNase I treatment was performed to eliminate genomic DNA contamination. For chromatin immunoprecipitation, 4T1 cells were cultured for 48h. Chromatin was prepared using ChIP-IT Express Enzymatic kit (Active Motif) according to manufacturer’s instructions.