The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer

Three-dimensional (3D) epigenome remodeling is an important mechanism of gene deregulation in cancer. However, its potential as a target to counteract therapy resistance remains largely unaddressed. Here, we show that epigenetic therapy with decitabine (5-Aza-mC) suppresses tumor growth in xenograft models of pre-clinical metastatic estrogen receptor positive (ER+) breast tumor. Decitabine-induced genome-wide DNA hypomethylation results in large-scale 3D epigenome deregulation, including de-compaction of higher-order chromatin structure and loss of boundary insulation of topologically associated domains. Significant DNA hypomethylation associates with ectopic activation of ER-enhancers, gain in ER binding, creation of new 3D enhancer-promoter interactions and concordant up-regulation of ER-mediated transcription pathways. Importantly, long-term withdrawal of epigenetic therapy partially restores methylation at ER-enhancer elements, resulting in a loss of ectopic 3D enhancer-promoter interactions and associated gene repression. Our study illustrates the potential of epigenetic therapy to target ER+ endocrine-resistant breast cancer by DNA methylation-dependent rewiring of 3D chromatin interactions, which are associated with the suppression of tumor growth.

DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity

DNA replication timing and three-dimensional (3D) genome organization are associated with distinct epigenome patterns across large domains. However, whether alterations in the epigenome, in particular cancer-related DNA hypomethylation, affects higher-order levels of genome architecture is still unclear. Here, using Repli-Seq, single-cell Repli-Seq, and Hi-C, we show that genome-wide methylation loss is associated with both concordant loss of replication timing precision and deregulation of 3D genome organization. Notably, we find distinct disruption in 3D genome compartmentalization, striking gains in cell-to-cell replication timing heterogeneity and loss of allelic replication timing in cancer hypomethylation models, potentially through the gene deregulation of DNA replication and genome organization pathways. Finally, we identify ectopic H3K4me3-H3K9me3 domains from across large hypomethylated domains, where late replication is maintained, which we purport serves to protect against catastrophic genome reorganization and aberrant gene transcription. Our results highlight a potential role for the methylome in the maintenance of 3D genome regulation.

Abstract PS18-17: Mdm2 inhibition synergises with endocrine therapy or cdk4/6 inhibition for the treatment of estrogen receptor-positive breast cancer

Background: Resistance to endocrine therapy is a major clinical challenge in the management of estrogen receptor (ER)-positive breast cancer. In this setting p53 is frequently wildtype and its activity may be suppressed via upregulation of its key regulator MDM2. This underlies our rationale to evaluate MDM2 inhibition as a therapeutic strategy in treatment resistant ER-positive breast cancer.

Methods: We used the MDM2 inhibitor NVP-CGM097 to treat in vitro and in vivo models alone and in combination with fulvestrant or palbociclib. We perform cell viability, cell cycle, apoptosis and senescence assays to evaluate antitumor effects in p53 wildtype and p53 mutant ER positive cell lines (MCF-7, ZR75-1, T-47D) and MCF-7 lines resistant to endocrine therapy and to CDK4/6 inhibition. We further assess the drug effects in patient-derived xenograft (PDX) models of endocrine-sensitive and -resistant ER positive breast cancer.

Results: We demonstrate that MDM2 inhibition results in cell cycle arrest and increased apoptosis in p53-wildtype in vitro and in vivo breast cancer models, leading to potent anti-tumour activity. We find that endocrine therapy or CDK4/6 inhibition synergises with MDM2 inhibition but does not further enhance apoptosis. Instead, combination treatments result in profound regulation of cell cycle-related transcriptional programmes, with synergy achieved through increased antagonism of cell cycle progression. Combination therapy pushes cell lines resistant to fulvestrant or palbociclib to become senescent and significantly reduces tumour growth in a fulvestrant resistant patient derived xenograft model.

Conclusions: We conclude that MDM2 inhibitors in combination with ER degraders or CDK4/6 inhibitors represent a rational strategy for treating advanced, endocrine resistant ER-positive breast cancer, operating through synergistic activation of cell cycle co-regulatory programs.

Citation Format: Neil Portman, Heloisa Milioli, Sarah Alexandrou, Rhiannon Coulson, Aliza Yong, Kristine Fernandez, KeeMing Chia, Ensar Halilovic, Davendra Segara, Andrew Parker, Sue Haupt, Ygal Haupt, Wayne Tilley, Alex Swarbrick, Liz Caldon, Elgene Lim. Mdm2 inhibition synergises with endocrine therapy or cdk4/6 inhibition for the treatment of estrogen receptor-positive breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS18-17.

Abstract P6-20-04: Activation of AR inhibits growth of endocrine-resistant breast cancer

Introduction

Resistance to endocrine therapy is a major clinical problem in estrogen receptor positive (ER+) breast cancer. The androgen receptor (AR) is expressed in ˜90% of all ER+ breast cancers and high expression of AR is associated with a better patient outcome in this subtype. In agreement, AR activation in breast cancer cell line models reduces proliferation of cells via antagonism of ER signaling. However, uncertainty surrounding the role of AR in endocrine resistance is reflected in current clinical trials in which both AR agonists and antagonists are being investigated. In this study, we sought to investigate the optimal approach in targeting AR in endocrine-resistant breast cancer.

Methods

We evaluated the consequences of AR activation, using AR cognate ligand 5α-dihydrotestosterone (DHT) and selective AR modulator enobosarm, and AR antagonism using enzalutamide on in vitro and in vivo models of endocrine-resistance. The efficacy of these AR modulators were assessed in vitro using tamoxifen-resistant (TamR) and long-term estrogen derived (LTED) models of MCF7 cells, and in vivo using ESR1 mutant E2-dependent (HCI-005) and ESR1 wild-type E2-independent (Gar15-13) endocrine-resistant PDX models

Results

Treatment with DHT and enobosarm inhibited the growth of MCF7 TamR and LTED cells but enzalutamide had no effect. AR activation was associated with loss of ER in MCF7 TamR cells and loss of ER-regulated PR expression in MCF7 LTED which suggests that this growth suppression was mediated through the antagonism of ER signaling. Notably, an additive anti-proliferative effect was observed with the combination of enobosarm and CDK4/6 inhibitor palbocilib in the MCF7 TamR cells. A similar pattern was observed in vivo with DHT strongly inhibiting the proliferation of both PDX models. Enobosarm similarly suppressed the proliferation of HCI-005, and to a lesser extent in Gar15-13. The benefit of enobosarm in Gar15-13 was significant given that this model is fulvestrant-resistant. Antagonizing AR with enzalutamide had no effect on growth of Gar15-13 model, similar to our in vitro data. AR agonists reduced expression levels of ER and PR in HCI-005, and transcriptomic analysis of AR agonist-treated Gar15-13 identified significant negative enrichment of genes related to proliferation and estrogen response. These observations indicate that the growth-suppressive effects of AR activation in vivo were mediated through inhibiting ER signaling. We identified an AR gene signature, through RNA-seq analysis of DHT-treated Gar15-13 PDX, which is strongly associated with good outcome in the METABRIC dataset, supporting the hypothesis that an active canonical AR signaling is tumor suppressive in both endocrine-sensitive and -resistant disease contexts. Lastly, we present in vivo data demonstrating enhanced suppression of Ki-67 with the combination of enobosarm and palbociclib in the Gar15-13 PDX.

Conclusion

We have demonstrated that activating AR is an effective therapeutic approach in endocrine-resistant breast cancer, and the combination of an AR agonist with a CDK4/6 inhibitor warrants further investigation in this breast cancer subtype.

Citation Format: Chia KM, Milioli H, Portman N, Laven-Law G, Yong A, Swarbrick A, Caldon L, Tilley W, Hickey T, Lim E. Activation of AR inhibits growth of endocrine-resistant breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-20-04.

Non-canonical AR activity facilitates endocrine resistance in breast cancer

The role of androgen receptor (AR) in endocrine-resistant breast cancer is controversial and clinical trials targeting AR with an AR antagonist (e.g., enzalutamide) have been initiated. Here, we investigated the consequence of AR antagonism using in vitro and in vivo models of endocrine resistance. AR antagonism in MCF7-derived tamoxifen-resistant (TamR) and long-term estrogen-deprived breast cancer cell lines were achieved using siRNA-mediated knockdown or pharmacological inhibition with enzalutamide. The efficacy of enzalutamide was further assessed in vivo in an estrogen-independent endocrine-resistant patient-derived xenograft (PDX) model. Knockdown of AR inhibited the growth of the endocrine-resistant cell line models. Microarray gene expression profiling of the TamR cells following AR knockdown revealed perturbations in proliferative signaling pathways upregulated in endocrine resistance. AR loss also increased some canonical ER signaling events and restored sensitivity of TamR cells to tamoxifen. In contrast, enzalutamide did not recapitulate the effect of AR knockdown in vitro, even though it inhibited canonical AR signaling, which suggests that it is the non-canonical AR activity that facilitated endocrine resistance. Enzalutamide had demonstrable efficacy in inhibiting AR activity in vivo but did not affect the growth of the endocrine-resistant PDX model. Our findings implicate non-canonical AR activity in facilitating an endocrine-resistant phenotype in breast cancer. Unlike canonical AR signaling which is inhibited by enzalutamide, non-canonical AR activity is not effectively antagonized by enzalutamide, and this has important implications in the design of future AR-targeted clinical trials in endocrine-resistant breast cancer.

A novel ATM-dependent checkpoint defect distinct from loss of function mutation promotes genomic instability in melanoma

Melanomas have high levels of genomic instability that can contribute to poor disease prognosis. Here, we report a novel defect of the ATM-dependent cell cycle checkpoint in melanoma cell lines that promotes genomic instability. In defective cells, ATM signalling to CHK2 is intact, but the cells are unable to maintain the cell cycle arrest due to elevated PLK1 driving recovery from the arrest. Reducing PLK1 activity recovered the ATM-dependent checkpoint arrest, and over-expressing PLK1 was sufficient to overcome the checkpoint arrest and increase genomic instability. Loss of the ATM-dependent checkpoint did not affect sensitivity to ionizing radiation demonstrating that this defect is distinct from ATM loss of function mutations. The checkpoint defective melanoma cell lines over-express PLK1, and a significant proportion of melanomas have high levels of PLK1 over-expression suggesting this defect is a common feature of melanomas. The inability of ATM to impose a cell cycle arrest in response to DNA damage increases genomic instability. This work also suggests that the ATM-dependent checkpoint arrest is likely to be defective in a higher proportion of cancers than previously expected.

Targeting the androgen receptor in breast cancer

The androgen receptor (AR) is expressed in the majority of breast cancer and across the three main breast cancer subtypes. Historically, the oncogenic role of AR has best been described in molecular apocrine breast cancers, an estrogen receptor (ER)-/AR+ subtype which has a steroid response signature similar to that in the ER-positive breast cancer. The signalling effect of AR is likely to be different across breast cancer subtypes, and particularly important is its interaction with ER signalling. Despite the high frequency of AR expression in breast cancer, it is still not a standard clinical practice to use AR antagonists as therapy. Older trials of AR-directed therapies in breast cancer have had generally been disappointing. More recently, more potent, next-generation, AR-directed therapies have been developed in the context of prostate cancer. Here, we will review the emerging literature dissecting the role of AR signalling in a context-dependent manner in breast cancer and the renewed interest and wave of clinical trials targeting the AR in breast cancer.

Finally, how histone deacetylase inhibitors disrupt mitosis!

The disruption of normal mitosis by histone deacetylase inhibitors is a significant contributor to the anticancer effects of these drugs. However, the mechanism by which these drugs affect mitosis is poorly understood. A number of recent papers have now thrown considerable light onto how these drugs elicit this very distinctive cell cycle disruption.

Clinical significance of enhanced sensitivity in detecting HBsAg by Biotin-Avidin ELISA

The Biotin-Avidin System (BAS) was incorporated into enzyme-linked immunosorbent assay (ELISA) technique to increase the sensitivity of the standard ELISA for the detection of HBsAg. We compared the sensitivity of Biotin-Avidin ELISA (BA-ELISA) with monoclonal antibody reverse passive hemagglutination assay (McAB RPHA), standard ELISA and solid phase radioimmunoassay (SPRIA). BA-ELISA was most sensitive. Out of 276 healthy individuals who were HBsAg negative by polyclonal antibody RPHA (PcAB-RPHA), 10(3.60%) were HBsAg positive by the BA-ELISA. Out of 123 acute hepatitis patients who were HBsAg negative by PcAb-RPHA and anti-HBc positive by ELISA, 64(52.03%) were found to be HBsAg positive by BA-ELISA. This study indicates that enhanced sensitivity of BA-ELISA in detecting HBsAg significantly increases the correctness of diagnosis of HBV infection.