SUMMARYRNA sequencing (RNA-seq) detects estrogen receptor alpha gene (ESR1) fusion transcripts in estrogen receptor-positive (ER+) breast cancer, but their role in disease pathogenesis remains unclear. We examined multiple ESR1 fusions and found that two, both identified in advanced endocrine treatment-resistant disease, encoded stable and functional fusion proteins. In both examples, ESR1-e6>YAP1 and ESR1-e6>PCDH11X, ESR1 exons 1–6 were fused in frame to C-terminal sequences from the partner gene. Functional properties include estrogen-independent growth, constitutive expression of ER target genes, and anti-estrogen resistance. Both fusions activate a metastasis-associated transcriptional program, induce cellular motility, and promote the development of lung metastasis. ESR1-e6>YAP1- and ESR1-e6>PCDH11X-induced growth remained sensitive to a CDK4/6 inhibitor, and a patient-derived xenograft (PDX) naturally expressing the ESR1-e6>YAP1 fusion was also responsive. Transcriptionally active ESR1 fusions therefore trigger both endocrine therapy resistance and metastatic progression, explaining the association with fatal disease progression, although CDK4/6 inhibitor treatment is predicted to be effective.

Breast cancer is the leading cause of cancer and mortality in women worldwide. Recent studies have argued that there is a close relationship between lipid synthesis and cancer progression because some enzymes related to lipid synthesis are overexpressed in breast cancer tissues. However, lipid distribution in breast cancer tissues has not been investigated. We aimed to visualize phosphatidylcholines (PCs) and lysoPCs (LPCs) in human breast cancer tissues by performing matrix assisted laser desorption/ionization-imaging mass spectrometry (MALDI-IMS), which is a novel technique that enables the visualization of molecules comprehensively. Twenty-nine breast tissue samples were obtained during surgery and subjected to MALDI-IMS analysis. We evaluated the heterogeneity of the distribution of PCs and LPCs on the tissues. Three species [PC(32∶1), PC(34∶1), and PC(36∶1)] of PCs with 1 mono-unsaturated fatty acid chain and 1 saturated fatty acid chain (MUFA-PCs) and one [PC(34∶0)] of PCs with 2 saturated fatty acid chains (SFA-PC) were relatively localized in cancerous areas rather than the rest of the sections (named reference area). In addition, the LPCs did not show any biased distribution. The relative amounts of PC(36∶1) compared to PC(36∶0) and that of PC(36∶1) to LPC(18∶0) were significantly higher in the cancerous areas. The protein expression of stearoyl-CoA desaturase-1 (SCD1), which is a synthetic enzyme of MUFA, showed accumulation in the cancerous areas as observed by the results of immunohistochemical staining. The ratios were further analyzed considering the differences in expressions of the estrogen receptor (ER), human epidermal growth factor receptor 2 (HER2), and Ki67. The ratios of the signal intensity of PC(36∶1) to that of PC(36∶0) was higher in the lesions with positive ER expression. The contribution of SCD1 and other enzymes to the formation of the observed phospholipid composition is discussed.

e Histone acetyltransferase binding to ORC-1 (HBO1) is a critically important histone acetyltransferase for forming the prereplicative complex (pre-RC) at the replication origin. Pre-RC formation is completed by loading of the MCM2-7 heterohexameric complex, which functions as a helicase in DNA replication. HBO1 recruited to the replication origin by CDT1 acetylates histone H4 to relax the chromatin conformation and facilitates loading of the MCM complex onto replication origins. However, the acetylation status and mechanism of regulation of histone H3 at replication origins remain elusive. HBO1 positively regulates cell proliferation under normal cell growth conditions. Whether HBO1 regulates proliferation in response to DNA damage is poorly understood. In this study, we demonstrated that HBO1 was degraded after DNA damage to suppress cell proliferation. Ser50 and Ser53 of HBO1 were phosphorylated in an ATM/ATR DNA damage sensor-dependent manner after UV treatment. ATM/ATRdependently phosphorylated HBO1 preferentially interacted with DDB2 and was ubiquitylated by CRL4 DDB2 . Replacement of endogenous HBO1 in Ser50/53Ala mutants maintained acetylation of histone H3K14 and impaired cell cycle regulation in response to UV irradiation. Our findings demonstrate that HBO1 is one of the targets in the DNA damage checkpoint. These results show that ubiquitin-dependent control of the HBO1 protein contributes to cell survival during UV irradiation.T ight regulation of genome maintenance processes, including DNA repair, checkpoints, apoptosis, and cell cycle control, prevents DNA instability after DNA damage. Mammalian cells coordinately operate these systems for organism survival, in part through ataxia telangiectasia mutated (ATM) and ATM-and RAD3-related protein (ATR), two critical kinases that function as regulators of major checkpoint pathways. ATM is primarily activated by DNA double-strand breaks (DSBs) (1), and ATR is activated in response to inhibition of DNA replication (2). Activated ATM and ATR phosphorylate histone H2AX to recruit DNA repair proteins (3) and also checkpoint kinase 1 (Chk1) to suppress cell cycle progression (4, 5). Chk1 indirectly inhibits dephosphorylation of Tyr15 of cyclin-dependent kinase 2 (CDK2) (6) and CDC2 via Cdc25A degradation (7). ATM and ATR also phosphorylate the p53 tumor suppressor to increase its protein stability (8). p53 is a critical cellular factor that induces apoptosis genes (9) and the p21 CDK inhibitor gene (10, 11). Thus, substrates of ATM and ATR are involved in arresting the cell cycle, repairing DNA, and eliminating damaged cells by apoptosis.Histone acetyltransferase binding to ORC-1 (HBO1) was originally identified as an ORC1 binding protein (12) and acts as a cofactor in the prereplicative complex (pre-RC) (13). This histone acetyltransferase (HAT) associates with distinct complexes to acetylate histones H3 and H4 (14, 15). HBO1 is also involved in cell proliferation control through regulating the expression of multiple genes in the p53 pathway (16). A previous ...

HBO1, a histone acetyl transferase, is a co-activator of DNA pre-replication complex formation. We recently reported that HBO1 is phosphorylated by ATM and/or ATR and binds to DDB2 after ultraviolet irradiation. Here, we show that phosphorylated HBO1 at cyclobutane pyrimidine dimer (CPD) sites mediates histone acetylation to facilitate recruitment of XPC at the damaged DNA sites. Furthermore, HBO1 facilitates accumulation of SNF2H and ACF1, an ATP-dependent chromatin remodelling complex, to CPD sites. Depletion of HBO1 inhibited repair of CPDs and sensitized cells to ultraviolet irradiation. However, depletion of HBO1 in cells derived from xeroderma pigmentosum patient complementation groups, XPE, XPC and XPA, did not lead to additional sensitivity towards ultraviolet irradiation. Our findings suggest that HBO1 acts in concert with SNF2H–ACF1 to make the chromosome structure more accessible to canonical nucleotide excision repair factors.

SignificanceMass spectrometry-based proteogenomics of patient-derived xenografts (PDXs) identified dihydropyrimidinase-like-3 (DPYSL3) as a multilevel (RNA/protein/phosphoprotein) expression outlier specific to a claudin-low (CLOW) PDX. DPYSL3 has established functions in neural cell migration and axon outgrowth but is understudied in breast cancer. Here, we demonstrate that loss of DPYSL3 promotes cell-cycle arrest, multinucleation, and collapse of the vimentin microfilament network associated with increased phospho-vimentin. DPYSL3 is also a negative regulator of p21-activated kinase (PAK) and suppresses epithelial-to-mesenchymal transition (EMT). In turn, EMT regulators induce DPYSL3, suggesting that DPYSL3 provides negative feedback on EMT. DPYSL3 therefore serves as a biomarker for CLOW tumors that exhibit PAK-dependent motility and EMT and is also susceptible to therapeutic approaches that promote vimentin phosphorylation during mitosis.