Selected Articles from This Issue

Women with germline BRCA1 or BRCA2 gene mutations experience elevated breast cancer risks. Previous studies have demonstrated that breast epithelial cell differentiation is altered in BRCA1/2 mutant preneoplastic tissues, but underlying mechanisms remain undefined. In their study, Caputo and colleagues assessed non-BRCA mutant and preneoplastic BRCA1/2 mutant breast tissues using spatial transcriptomics to decipher molecular interactions that might dictate epithelial cell differentiation in each case. Ligand-receptor pair correlation analysis revealed autocrine β1-integrin interactions favoring extracellular matrix (ECM) breakdown on BRCA1 mutant epithelial cells. Conversely, autocrine β1-integrin interactions on BRCA2 mutant epithelial cells were associated with ECM remodeling and mechano-signaling. The authors validated these findings in vitro by querying β1-integrin activation and ERK activation in primary human breast epithelial cells expressing BRCA1- or BRCA2-specific siRNAs. Paracrine ligand-receptor analysis between epithelial and stromal cells also identified enhanced integrin-dependent signaling in BRCA1/2 mutant breast tissues, and the authors confirmed several associations ex vivo using indirect immunofluorescence analysis. Altogether, this study unveils molecular interactions unique to BRCA1 and BRCA2 mutant breast tissues that could inform breast cancer chemoprevention strategies.

Detecting and characterizing rare driver mutations could inform novel targeted therapeutic approaches, but doing so is challenging given limited cohort sizes and dataset and analytical limitations. To address those challenges, Balasooriya and colleagues developed a machine learning tool that integrates patient genome sequencing data, clinical annotations, and global posttranslational modification (PTM) proteomics data. The tool identified both known and unknown driver mutations and corresponding PTM disruptions. To test the utility of their algorithm, the authors assessed a novel driver mutation featured prominently in their tool – a frameshift mutation in activated CDC42 kinase-1 (ACK1) termed p633fs*. ACK1 p633fs* mutant transduction into a murine pro-B cell line revealed that the mutant promoted oncogenic transformation. Using a cell model in which exogenous ACK1 mutants were integrated via Flp recombinase, the authors showed that p633fs*-mediated ACK1 truncation and corresponding exclusion of its Mig6 homology region and ubiquitin-association domain enhanced ACK1 kinase activity and protein stability, respectively. Overall, this study provides a novel driver mutation discovery tool and demonstrates its functionality by characterizing a newly identified oncogenic ACK1 mutation.

Recent studies have found that mTOR interacts with androgen receptor (AR) transcriptional complexes in prostate cancer. How transcription factor FOXA1 might regulate mTOR-containing AR transcriptional complexes is unknown, as are differential functional characteristics of nuclear and cytoplasmic mTOR (nmTOR and cmTOR, respectively). In their study, Chen and colleagues separately queried nmTOR and cmTOR functions by stably transfecting mTOR tagged with nuclear localization or export sequences, respectively, into an androgen-dependent prostate cancer cell line. RNA-sequencing analysis contrasting nmTOR- and cmTOR-expressing cell lines demonstrated that nmTOR decreased AR target gene expression, while cmTOR augmented cell cycle gene transcript abundances. Reversal of the latter finding by pharmacologic mTOR inhibitors demonstrated that cmTOR promoted cell cycle transcriptomic enrichment in a kinase-dependent manner. Conversely, lack of transcriptional changes in cells expressing a kinase-defective nmTOR mutant showed that nmTOR transcriptional activity was kinase independent. ChIP-sequencing revealed that shRNA-mediated FOXA1 ablation altered nmTOR genomic localization, and RNA-sequencing identified corresponding transcriptomic changes. Taken together, this study delineates nmTOR and cmTOR functions, and shows that FOXA1 regulates nmTOR-containing AR transcriptional complex activity.

Nuclear protein kinase C delta (PKCδ) promotes irradiation-induced apoptosis, and PKCδ inhibition confers radioprotection to normal tissue. How PKCδ might regulate the irradiation-induced DNA damage response (DDR), though, remains unclear. In their study, Affandi and colleagues modulated PKCδ expression using transient PKCδ construct transfection and shRNA-mediated PRKCD abrogation in immortalized, non-transformed cell lines. Integrated homologous recombination (HR) and non-homologous end-joining (NHEJ) reporters in cells harboring transfected endonuclease-inflicted DNA damage and altered PKCδ levels demonstrated that PKCδ inhibits HR and NHEJ. Nuclease sensitivity assays showed that PKCδ decreased chromatin accessibility. The authors queried PKCδ-associated histone modifications using mass spectrometry-based epiproteomic analysis and found that PKCδ ablation increased H3K36 dimethylation, a DDR-associated modification. Further analysis revealed that PKCδ expression negatively correlated with that of sirtuin 6 (SIRT6), a deacetylase that can displace Jumonji demethylase KDM2A to augment H3K36 dimethylation. Accordingly, PKCδ abrogation decreased chromatin-bound KDM2A levels, and shRNA-mediated SIRT6 silencing inhibited the PKCδ loss-mediated DDR. In sum, this study presents a novel epigenetic mechanism by which PKCδ regulates the DDR.