A new potential therapeutic target for prostate cancer has been discovered using in silico analysis to identify potential synthetic-lethal gene interactions in this disease.

In this investigation, the authors established and validated an in silico approach for identifying potential synthetic-lethal interactions. Using information from TGCA database they searched for mutually exclusive gene deletion patterns in the cancer genome. Specifically, they sought genes that were occasionally deleted in some cancers, but were always retained if a specific gene was deleted, suggesting that it might be needed for cancer-promoting behaviour (termed synthetic-essential genes). The investigators theorized that targeting the synthetic-essential genes could inhibit the growth and survival of tumours with a specific gene mutation.

Focussing on PTEN, which is frequently mutated in prostate cancer, the researchers discovered a synthetic-essential relationship with CHD1 on performing large-scale genomic analyses of data from the prostate cancer TGCA and other prostate cancer databases. A significant negative correlation between expression of PTEN and CHD1 was observed between BPH and prostate cancer samples. Furthermore, CHD1 expression positively correlated with Gleason grade and is increased in Pten-deficient mouse prostate epithelium, indicating that CDH1 might be required for the progression of PTEN-deficient prostate cancer.

Depletion of CHD1 using short hairpin RNA (shRNA) or CRISPR-directed nullizygous mutation in PTEN-deficient human and mouse prostate cancer cell lines inhibited colony formation and induced cell death. In vivo, suppression of CDH1 expression reduced growth and cell proliferation and increased apoptosis of cell-line-derived xenografts in mice. In patient-derived xenograft models, treatment with CDH1-targeting short interfering RNA (shRNA) inhibited tumour progression. However, these results were not recapitulated in cell lines with intact PTEN expression. Moreover, CRISPR-mediated knockout of PTEN sensitized cells to CDH1 depletion in vitro and in vivo. PTEN re-expression in PTEN-null prostate cancer cell lines resulted in decreased CDH1 protein expression, but did not affect mRNA levels. Furthermore, treatment with an AKT inhibitor reduced CDH1 expression in PC3 cells and the stability of CDH1 was increased in PTEN-deficient cells.

depletion of β-TrCP using shRNA resulted in CDH1 accumulation and decreased ubiquitination

Inhibiting the proteasome in PTEN-wild-type BPH cells resulted in intracellular accumulation of CDH1. Further analysis showed that endogenous CDH1 was modified by ubiquitination, which was enhanced by PTEN overexpression. Consensus-sequence scanning of E3 ligase interaction domains revealed two evolutionarily conserved putative β-TrCP consensus binding motifs, and coimmunoprecipitation experiments confirmed the interaction between β-TrCP and CDH1. Overexpression of β-TrCP resulted in reduced CDH1 levels and increased its ubiquitination. Moreover, depletion of β-TrCP using shRNA resulted in CDH1 accumulation and decreased ubiquitination. Both conserved β-TrCP binding motifs harbour a GSK3β consensus sequence, which is a direct target of AKT that is inhibited on AKT activation. Overexpression of GSK3β or its constitutively active mutant in vitro increased CDH1 phosphorylation and reduced its expression.

Further coimmunoprecipitation experiments showed that CHD1 binds H3K4me3, which is associated with transcriptional activity, and a substantial reduction in this mark was observed on CHD1 depletion in vitro. Chromatin immunoprecipitation followed by sequencing identified 8,468 CDH1 binding sites and 26,826 H3K4me3-enriched regions in prostate cancer cells in vitro. Analysis of genes regulated by CDH1–H3k4me3 showed enrichment of those involved in the TNF–NFκB pathway, which was activated in Pten-null mouse prostate tissue and downregulated in CDH1-deficient cells.

These data show that epigenetic regulation of CDH1 is a therapeutic target in PTEN-deficient prostate cancer and identify a novel pathway connecting PTEN and the regulation of the NFκB pathway. This in silico method could be used to discover other therapeutic targets in this disease.

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