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1.
Curr Oncol Rep ; 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38822929

ABSTRACT

PURPOSE OF REVIEW: Homologous recombination repair deficiency (HRD) increases breast cancer susceptibility and influences both prophylactic and active management of breast cancer. This review evaluates HRD testing and the therapeutic implications of HRD in a global context. RECENT FINDINGS: Ongoing research efforts have highlighted the importance of HRD beyond BRCA1/2 as a potential therapeutic target in breast cancer. However, despite the improved affordability of next-generation sequencing (NGS) and the discovery of PARP inhibitors, economic and geographical barriers in access to HRD testing and breast cancer screening do not allow all patients to benefit from the personalized treatment approach they provide. Advancements in HRD testing modalities and targeted therapeutics enable tailored breast cancer management. However, inequalities in access to testing and optimized treatments are contributing to widening health disparities globally.

2.
J Natl Cancer Inst ; 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38852945

ABSTRACT

BACKGROUND: Breast cancer brain metastasis is a rising occurrence, necessitating a better understanding of the mechanisms involved for effective management. Breast cancer brain metastases diverge notably from the primary tumor, with gains in kinase and concomitant losses of steroid signaling observed. In this study, we explored the role of the kinase receptor RET in promoting breast cancer brain metastases and provide a rationale for targeting this receptor. METHODS: RET expression was characterized in a cohort of patients with primary and brain metastatic tumors. RET functionality was assessed using pharmacological inhibition and gene silencing in patient-derived brain metastatic tumor explants and in vivo models, organoid models, and brain organotypic cultures. RNA sequencing was used to uncover novel brain metastatic relevant RET mechanisms of action. RESULTS: A statistically significant enrichment of RET in brain metastases was observed in estrogen receptor-positive breast cancer, where it played a role in promoting cancer cell adhesion, survival, and outgrowth in the brain. In vivo, RET overexpression enhanced brain metastatic competency in patient-derived models. At a mechanistic level, RET overexpression was found to enhance the activation of gene programs involved in cell adhesion, requiring EGFR cooperation to deliver a pro-brain metastatic phenotype. CONCLUSION: Our results illustrate, for the first time, the role of RET in regulating colonization and outgrowth of breast cancer brain metastasis and provide data to support the use of RET inhibitors in the management strategy for patients with breast cancer brain metastases.

3.
Curr Oncol Rep ; 26(2): 103-113, 2024 02.
Article in English | MEDLINE | ID: mdl-38236558

ABSTRACT

PURPOSE OF REVIEW: In the last decade, poly (ADP-ribose) polymerase (PARP) inhibitors have been approved in the treatment of several cancers, such as breast and ovarian cancer. This article aims to discuss the current uses, limitations, and future directions for PARP inhibitors (PARPis) in the treatment of breast cancer. RECENT FINDINGS: Following the results of the OlympiAD and EMBRACA trials, PARPis were approved in HER2-negative breast cancer with a germline BRCA mutation. We reviewed this class of drugs' mechanism of action, efficacy, and limitations, as well as further studies that discussed resistance, impaired homologous recombination repair (HRR), and the combination of PARPis with other drugs. Improving understanding of HRR, increasing the ability to target resistance, and combining PARPis with other novel agents are continuing to increase the clinical utility of PARPis.


Subject(s)
Breast Neoplasms , Ovarian Neoplasms , Female , Humans , Poly(ADP-ribose) Polymerase Inhibitors/therapeutic use , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , Breast Neoplasms/drug therapy , Breast Neoplasms/genetics , Poly(ADP-ribose) Polymerases/genetics , DNA Repair , Ovarian Neoplasms/drug therapy
4.
EMBO Mol Med ; 15(12): e17737, 2023 Dec 07.
Article in English | MEDLINE | ID: mdl-37902007

ABSTRACT

Glucocorticoid receptor (GR) is a transcription factor that plays a crucial role in cancer biology. In this study, we utilized an in silico-designed GR activity signature to demonstrate that GR relates to the proliferative capacity of numerous primary cancer types. In breast cancer, the GR activity status determines luminal subtype identity and has implications for patient outcomes. We reveal that GR engages with estrogen receptor (ER), leading to redistribution of ER on the chromatin. Notably, GR activation leads to upregulation of the ZBTB16 gene, encoding for a transcriptional repressor, which controls growth in ER-positive breast cancer and associates with prognosis in luminal A patients. In relation to ZBTB16's repressive nature, GR activation leads to epigenetic remodeling and loss of histone acetylation at sites proximal to cancer-driving genes. Based on these findings, epigenetic inhibitors reduce viability of ER-positive breast cancer cells that display absence of GR activity. Our findings provide insights into how GR controls ER-positive breast cancer growth and may have implications for patients' prognostication and provide novel therapeutic candidates for breast cancer treatment.


Subject(s)
Breast Neoplasms , Female , Humans , Breast Neoplasms/genetics , Breast Neoplasms/drug therapy , Cell Line, Tumor , Gene Expression Regulation, Neoplastic , Receptors, Estrogen/genetics , Receptors, Estrogen/metabolism , Receptors, Glucocorticoid/genetics , Receptors, Glucocorticoid/metabolism
6.
Nat Med ; 28(4): 752-765, 2022 04.
Article in English | MEDLINE | ID: mdl-35411077

ABSTRACT

Whole-brain radiotherapy (WBRT) is the treatment backbone for many patients with brain metastasis; however, its efficacy in preventing disease progression and the associated toxicity have questioned the clinical impact of this approach and emphasized the need for alternative treatments. Given the limited therapeutic options available for these patients and the poor understanding of the molecular mechanisms underlying the resistance of metastatic lesions to WBRT, we sought to uncover actionable targets and biomarkers that could help to refine patient selection. Through an unbiased analysis of experimental in vivo models of brain metastasis resistant to WBRT, we identified activation of the S100A9-RAGE-NF-κB-JunB pathway in brain metastases as a potential mediator of resistance in this organ. Targeting this pathway genetically or pharmacologically was sufficient to revert the WBRT resistance and increase therapeutic benefits in vivo at lower doses of radiation. In patients with primary melanoma, lung or breast adenocarcinoma developing brain metastasis, endogenous S100A9 levels in brain lesions correlated with clinical response to WBRT and underscored the potential of S100A9 levels in the blood as a noninvasive biomarker. Collectively, we provide a molecular framework to personalize WBRT and improve its efficacy through combination with a radiosensitizer that balances therapeutic benefit and toxicity.


Subject(s)
Brain Neoplasms , Melanoma , Brain Neoplasms/secondary , Cranial Irradiation , Humans , Melanoma/radiotherapy
7.
Pharmacol Res Perspect ; 10(2): e00923, 2022 04.
Article in English | MEDLINE | ID: mdl-35289104

ABSTRACT

Obesity is highly prevalent in breast cancer patients and is associated with increased recurrence and breast cancer-specific mortality. Glucocorticoids (GC) are used as an adjuvant in cancer treatment and are associated with promoting breast cancer metastasis through activation of stemness-related pathways. Therefore, we utilized the synergetic allograft E0771 breast cancer model to investigate if treatment with GCs had differential effects on promoting cancer stem cells in lean and diet-induced obese mice. Indeed, both lean mice treated with dexamethasone and obese mice with no treatment had no effect on the ex vivo colony-forming ability, mammosphere formation, or aldehyde dehydrogenase (ALDH) bright subpopulation. However, treatment of obese mice with dexamethasone resulted in a significant increase in ex vivo colony formation, mammosphere formation, ALDH bright subpopulation, and expression of pluripotency transcription factors. GC transcriptionally regulated genes were not altered in the dexamethasone-treated groups compared to treatment controls. In summary, these results provide initial evidence that obesity presents a higher risk of GC-induced cancer stemness via non-genomic GC signaling which is of potential translational significance.


Subject(s)
Breast Neoplasms , Aldehyde Dehydrogenase/metabolism , Animals , Breast Neoplasms/drug therapy , Breast Neoplasms/genetics , Cell Line, Tumor , Dexamethasone/pharmacology , Female , Humans , Mice , Neoplastic Stem Cells/metabolism , Neoplastic Stem Cells/pathology , Obesity/metabolism
8.
EMBO Mol Med ; 14(3): e14552, 2022 03 07.
Article in English | MEDLINE | ID: mdl-35174975

ABSTRACT

We report a medium-throughput drug-screening platform (METPlatform) based on organotypic cultures that allows to evaluate inhibitors against metastases growing in situ. By applying this approach to the unmet clinical need of brain metastasis, we identified several vulnerabilities. Among them, a blood-brain barrier permeable HSP90 inhibitor showed high potency against mouse and human brain metastases at clinically relevant stages of the disease, including a novel model of local relapse after neurosurgery. Furthermore, in situ proteomic analysis applied to metastases treated with the chaperone inhibitor uncovered a novel molecular program in brain metastasis, which includes biomarkers of poor prognosis and actionable mechanisms of resistance. Our work validates METPlatform as a potent resource for metastasis research integrating drug-screening and unbiased omic approaches that is compatible with human samples. Thus, this clinically relevant strategy is aimed to personalize the management of metastatic disease in the brain and elsewhere.


Subject(s)
Antineoplastic Agents , Brain Neoplasms , Animals , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Blood-Brain Barrier , Brain Neoplasms/drug therapy , Mice , Neoplasm Recurrence, Local , Proteomics
9.
Nat Commun ; 13(1): 514, 2022 01 26.
Article in English | MEDLINE | ID: mdl-35082299

ABSTRACT

The molecular events and transcriptional plasticity driving brain metastasis in clinically relevant breast tumor subtypes has not been determined. Here we comprehensively dissect genomic, transcriptomic and clinical data in patient-matched longitudinal tumor samples, and unravel distinct transcriptional programs enriched in brain metastasis. We report on subtype specific hub genes and functional processes, central to disease-affected networks in brain metastasis. Importantly, in luminal brain metastases we identify homologous recombination deficiency operative in transcriptomic and genomic data with recurrent breast mutational signatures A, F and K, associated with mismatch repair defects, TP53 mutations and homologous recombination deficiency (HRD) respectively. Utilizing PARP inhibition in patient-derived brain metastatic tumor explants we functionally validate HRD as a key vulnerability. Here, we demonstrate a functionally relevant HRD evident at genomic and transcriptomic levels pointing to genomic instability in breast cancer brain metastasis which is of potential translational significance.


Subject(s)
Brain Neoplasms/genetics , Brain Neoplasms/metabolism , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Neoplasm Metastasis , Adult , Breast , Female , Gene Regulatory Networks , Genes, p53/genetics , Humans , Middle Aged , Mutation , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , Transcriptome
10.
Oncogene ; 40(7): 1318-1331, 2021 02.
Article in English | MEDLINE | ID: mdl-33420368

ABSTRACT

Steroid regulated cancer cells use nuclear receptors and associated regulatory proteins to orchestrate transcriptional networks to drive disease progression. In primary breast cancer, the coactivator AIB1 promotes estrogen receptor (ER) transcriptional activity to enhance cell proliferation. The function of the coactivator in ER+ metastasis however is not established. Here we describe AIB1 as a survival factor, regulator of pro-metastatic transcriptional pathways and a promising actionable target. Genomic alterations and functional expression of AIB1 associated with reduced disease-free survival in patients and enhanced metastatic capacity in novel CDX and PDX ex-vivo models of ER+ metastatic disease. Comparative analysis of the AIB1 interactome with complementary RNAseq characterized AIB1 as a transcriptional repressor. Specifically, we report that AIB1 interacts with MTA2 to form a repressive complex, inhibiting CDH1 (encoding E-cadherin) to promote EMT and drive progression. We further report that pharmacological and genetic inhibition of AIB1 demonstrates significant anti-proliferative activity in patient-derived models establishing AIB1 as a viable strategy to target endocrine resistant metastasis. This work defines a novel role for AIB1 in the regulation of EMT through transcriptional repression in advanced cancer cells with a considerable implication for prognosis and therapeutic interventions.


Subject(s)
Breast Neoplasms/drug therapy , Cadherins/genetics , Histone Deacetylases/genetics , Nuclear Receptor Coactivator 3/genetics , Repressor Proteins/genetics , Antigens, CD/genetics , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Cell Proliferation/genetics , Disease-Free Survival , Epithelial-Mesenchymal Transition/drug effects , Estrogen Receptor alpha/genetics , Female , Gene Expression Regulation, Neoplastic/drug effects , Humans , MCF-7 Cells , Neoplasm Metastasis , Nuclear Receptor Coactivator 3/antagonists & inhibitors , Phenotype , Prognosis , Tamoxifen/pharmacology
11.
BMC Med ; 18(1): 349, 2020 11 19.
Article in English | MEDLINE | ID: mdl-33208158

ABSTRACT

BACKGROUND: Metastatic breast cancer is a major cause of cancer-related deaths in woman. Brain metastasis is a common and devastating site of relapse for several breast cancer molecular subtypes, including oestrogen receptor-positive disease, with life expectancy of less than a year. While efforts have been devoted to developing therapeutics for extra-cranial metastasis, drug penetration of blood-brain barrier (BBB) remains a major clinical challenge. Defining molecular alterations in breast cancer brain metastasis enables the identification of novel actionable targets. METHODS: Global transcriptomic analysis of matched primary and metastatic patient tumours (n = 35 patients, 70 tumour samples) identified a putative new actionable target for advanced breast cancer which was further validated in vivo and in breast cancer patient tumour tissue (n = 843 patients). A peptide mimetic of the target's natural ligand was designed in silico and its efficacy assessed in in vitro, ex vivo and in vivo models of breast cancer metastasis. RESULTS: Bioinformatic analysis of over-represented pathways in metastatic breast cancer identified ADAM22 as a top ranked member of the ECM-related druggable genome specific to brain metastases. ADAM22 was validated as an actionable target in in vitro, ex vivo and in patient tumour tissue (n = 843 patients). A peptide mimetic of the ADAM22 ligand LGI1, LGI1MIM, was designed in silico. The efficacy of LGI1MIM and its ability to penetrate the BBB were assessed in vitro, ex vivo and in brain metastasis BBB 3D biometric biohybrid models, respectively. Treatment with LGI1MIM in vivo inhibited disease progression, in particular the development of brain metastasis. CONCLUSION: ADAM22 expression in advanced breast cancer supports development of breast cancer brain metastasis. Targeting ADAM22 with a peptide mimetic LGI1MIM represents a new therapeutic option to treat metastatic brain disease.


Subject(s)
ADAM Proteins/metabolism , Biomimetic Materials/pharmacology , Brain Neoplasms/drug therapy , Brain Neoplasms/secondary , Breast Neoplasms/drug therapy , Intracellular Signaling Peptides and Proteins/metabolism , Nerve Tissue Proteins/metabolism , Peptides/pharmacology , ADAM Proteins/biosynthesis , ADAM Proteins/genetics , Animals , Brain Neoplasms/genetics , Brain Neoplasms/metabolism , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Breast Neoplasms/pathology , Female , Gene Expression Profiling , Humans , Molecular Targeted Therapy , Neoplasm Recurrence, Local/metabolism , Nerve Tissue Proteins/biosynthesis , Nerve Tissue Proteins/genetics
12.
Cancer Res ; 80(20): 4314-4323, 2020 10 15.
Article in English | MEDLINE | ID: mdl-32641416

ABSTRACT

Spread of cancer to the brain remains an unmet clinical need in spite of the increasing number of cases among patients with lung, breast cancer, and melanoma most notably. Although research on brain metastasis was considered a minor aspect in the past due to its untreatable nature and invariable lethality, nowadays, limited but encouraging examples have questioned this statement, making it more attractive for basic and clinical researchers. Evidences of its own biological identity (i.e., specific microenvironment) and particular therapeutic requirements (i.e., presence of blood-brain barrier, blood-tumor barrier, molecular differences with the primary tumor) are thought to be critical aspects that must be functionally exploited using preclinical models. We present the coordinated effort of 19 laboratories to compile comprehensive information related to brain metastasis experimental models. Each laboratory has provided details on the cancer cell lines they have generated or characterized as being capable of forming metastatic colonies in the brain, as well as principle methodologies of brain metastasis research. The Brain Metastasis Cell Lines Panel (BrMPanel) represents the first of its class and includes information about the cell line, how tropism to the brain was established, and the behavior of each model in vivo. These and other aspects described are intended to assist investigators in choosing the most suitable cell line for research on brain metastasis. The main goal of this effort is to facilitate research on this unmet clinical need, to improve models through a collaborative environment, and to promote the exchange of information on these valuable resources.


Subject(s)
Brain Neoplasms/pathology , Brain Neoplasms/secondary , Neoplasms, Experimental/pathology , Animals , Blood-Brain Barrier/drug effects , Cell Culture Techniques/methods , Cell Line, Tumor , Humans , Mice , Rats , Tropism , Tumor Microenvironment , Xenograft Model Antitumor Assays
13.
Nat Protoc ; 15(8): 2503-2518, 2020 08.
Article in English | MEDLINE | ID: mdl-32591768

ABSTRACT

Fixed-tissue ChIP-seq for H3K27 acetylation (H3K27ac) profiling (FiTAc-seq) is an epigenetic method for profiling active enhancers and promoters in formalin-fixed, paraffin-embedded (FFPE) tissues. We previously developed a modified ChIP-seq protocol (FiT-seq) for chromatin profiling in FFPE. FiT-seq produces high-quality chromatin profiles particularly for methylated histone marks but is not optimized for H3K27ac profiling. FiTAc-seq is a modified protocol that replaces the proteinase K digestion applied in FiT-seq with extended heating at 65 °C in a higher concentration of detergent and a minimized sonication step, to produce robust genome-wide H3K27ac maps from clinical samples. FiTAc-seq generates high-quality enhancer landscapes and super-enhancer (SE) annotation in numerous archived FFPE samples from distinct tumor types. This approach will be of great interest for both basic and clinical researchers. The entire protocol from FFPE blocks to sequence-ready library can be accomplished within 4 d.


Subject(s)
Chromatin Immunoprecipitation Sequencing/methods , Histones/chemistry , Histones/metabolism , Lysine/metabolism , Paraffin Embedding , Tissue Fixation , Acetylation , Animals , Liver/cytology , Mice
14.
J Neural Transm (Vienna) ; 127(2): 213-230, 2020 02.
Article in English | MEDLINE | ID: mdl-31894418

ABSTRACT

6-Hydroxydopamine (6-OHDA), which is a neurotoxin that selectively destroys catecholaminergic nerves in sympathetically innervated tissues, has been used to provide a model of Parkinson's disease in experimental animals. It is rapidly autoxidised to yield potentially toxic products and reactive oxygen species. Its ability to release Fe(II) from protein storage sites also results in the formation of hROS. This account will consider how this family of toxic products may contribute to the observed effects of 6-OHDA.


Subject(s)
Disease Models, Animal , Neurotoxins/pharmacology , Oxidopamine/pharmacology , Parkinson Disease , Animals , Humans , Neurotoxins/toxicity , Oxidopamine/toxicity
15.
Sci Rep ; 9(1): 18518, 2019 12 06.
Article in English | MEDLINE | ID: mdl-31811234

ABSTRACT

Breast cancer brain metastasis (BCBM) is an area of unmet clinical need. MicroRNAs (miRNAs) have been linked to the metastatic process in breast cancer (BC). In this study, we aim to determine differentially-expressed miRNAs utilising primary BCs that did not relapse (BCNR, n = 12), primaries that relapsed (BCR) and their paired (n = 40 pairs) brain metastases (BM) using the NanoString™ nCounter™ miRNA Expression Assays. Significance analysis of microarrays identified 58 and 11 differentially-expressed miRNAs between BCNR vs BCR and BCR vs BM respectively and pathway analysis revealed enrichment for genes involved in invasion and metastasis. Four miRNAs, miR-132-3p, miR-199a-5p, miR-150-5p and miR-155-5p, were differentially-expressed within both cohorts (BCNR-BCR, BCR-BM) and receiver-operating characteristic curve analysis (p = 0.00137) and Kaplan-Meier survival method (p = 0.0029, brain metastasis-free survival; p = 0.0007, overall survival) demonstrated their potential use as prognostic markers. Ingenuity pathway enrichment linked them to the MET oncogene, and the cMET protein was overexpressed in the BCR (p < 0.0001) and BM (p = 0.0008) cases, compared to the BCNRs. The 4-miRNAs panel identified in this study could be potentially used to distinguish BC patients with an increased risk of developing BCBM and provide potential novel therapeutic targets, whereas cMET-targeting warrants further investigation in the treatment of BCBM.


Subject(s)
Brain Neoplasms/genetics , Brain Neoplasms/mortality , Breast Neoplasms/mortality , Gene Expression Regulation, Neoplastic , MicroRNAs/genetics , Biomarkers, Tumor/genetics , Brain Neoplasms/secondary , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Female , Gene Expression Profiling , Humans , Kaplan-Meier Estimate , Neoplasm Invasiveness , Neoplasm Recurrence, Local , Normal Distribution , Oligonucleotide Array Sequence Analysis , Principal Component Analysis , Prognosis , ROC Curve , Risk , Treatment Outcome
16.
Clin Cancer Res ; 25(23): 7139-7150, 2019 12 01.
Article in English | MEDLINE | ID: mdl-31409615

ABSTRACT

PURPOSE: Invasive lobular carcinoma (ILC) is a subtype of breast cancer accounting for 10% of breast tumors. The majority of patients are treated with endocrine therapy; however, endocrine resistance is common in estrogen receptor-positive breast cancer and new therapeutic strategies are needed. Bromodomain and extraterminal inhibitors (BETi) are effective in diverse types of breast cancer but they have not yet been assessed in ILC. EXPERIMENTAL DESIGN: We assessed whether targeting the BET proteins with JQ1 could serve as an effective therapeutic strategy in ILC in both 2D and 3D models. We used dynamic BH3 profiling and RNA-sequencing (RNA-seq) to identify transcriptional reprograming enabling resistance to JQ1-induced apoptosis. As part of the RATHER study, we obtained copy-number alterations and RNA-seq on 61 ILC patient samples. RESULTS: Certain ILC cell lines were sensitive to JQ1, while others were intrinsically resistant to JQ1-induced apoptosis. JQ1 treatment led to an enhanced dependence on antiapoptotic proteins and a transcriptional rewiring inducing fibroblast growth factor receptor 1 (FGFR1). This increase in FGFR1 was also evident in invasive ductal carcinoma (IDC) cell lines. The combination of JQ1 and FGFR1 inhibitors was highly effective at inhibiting growth in both 2D and 3D models of ILC and IDC. Interestingly, we found in the RATHER cohort of 61 ILC patients that 20% had FGFR1 amplification and we showed that high BRD3 mRNA expression was associated with poor survival specifically in ILC. CONCLUSIONS: We provide evidence that BETi either alone or in combination with FGFR1 inhibitors or BH3 mimetics may be a useful therapeutic strategy for recurrent ILC patients.


Subject(s)
Aniline Compounds/pharmacology , Antineoplastic Agents/pharmacology , Azepines/pharmacology , Breast Neoplasms/drug therapy , Carcinoma, Lobular/drug therapy , Gene Expression Regulation, Neoplastic/drug effects , Sulfonamides/pharmacology , Transcription Factors/antagonists & inhibitors , Triazoles/pharmacology , Apoptosis , Breast Neoplasms/metabolism , Breast Neoplasms/pathology , Carcinoma, Lobular/metabolism , Carcinoma, Lobular/pathology , Cell Cycle , Cell Proliferation , Cohort Studies , Female , Humans , Neoplasm Invasiveness , Prognosis , Receptor, ErbB-2/metabolism , Receptors, Estrogen/metabolism , Receptors, Progesterone/metabolism , Survival Rate , Tumor Cells, Cultured
17.
Mol Cancer Ther ; 18(10): 1731-1743, 2019 10.
Article in English | MEDLINE | ID: mdl-31289138

ABSTRACT

Divergent roles for androgen receptor (AR) in breast cancer have been reported. Following aromatase inhibitor (AI) treatment, the conversion of circulating androgens into estrogens can be diminished by >99%. We wished to establish whether the steroid environment can dictate the role of AR and the implications of this for subsequent therapy. This study utilizes models of AI resistance to explore responsiveness to PI3K/mTOR and anti-AR therapy when cells are exposed to unconverted weak androgens. Transcriptomic alterations driven by androstenedione (4AD) were assessed by RNA-sequencing. AR and estrogen receptor (ER) recruitment to target gene promoters was evaluated using ChIP, and relevance to patient profiles was performed using publicly available data sets. Although BEZ235 showed decreased viability across AI-sensitive and -resistant cell lines, anti-AR treatment elicited a decrease in cell viability only in the AI-resistant model. Serum and glucocorticoid-regulated kinase 3 (SGK3) and cAMP-dependent protein kinase inhibitor ß (PKIB) were confirmed to be regulated by 4AD and shown to be mediated by AR; crucially, reexposure to estradiol suppressed expression of these genes. Meta-analysis of transcript levels showed high expression of SGK3 and PKIB to be associated with poor response to endocrine therapy (HR = 2.551, P = 0.003). Furthermore, this study found levels of SGK3 to be sustained in patients who do not respond to AI therapy. This study highlights the importance of the tumor steroid environment. SGK3 and PKIB are associated with poor response to endocrine therapy and could have utility in tailoring therapeutic approaches.


Subject(s)
Aromatase Inhibitors/therapeutic use , Breast Neoplasms/drug therapy , Breast Neoplasms/genetics , Drug Resistance, Neoplasm , Gene Expression Regulation, Neoplastic , Receptors, Androgen/metabolism , Steroids/metabolism , Adaptation, Physiological/drug effects , Androstenedione/pharmacology , Aromatase Inhibitors/pharmacology , Cell Survival/drug effects , Disease-Free Survival , Drug Resistance, Neoplasm/genetics , Estradiol/pharmacology , Gene Expression Regulation, Neoplastic/drug effects , Humans , Imidazoles/pharmacology , Imidazoles/therapeutic use , Intracellular Signaling Peptides and Proteins/metabolism , MCF-7 Cells , Phosphatidylinositol 3-Kinases/metabolism , Postmenopause/drug effects , Promoter Regions, Genetic/genetics , Protein Serine-Threonine Kinases/metabolism , Quinolines/pharmacology , Quinolines/therapeutic use , RNA, Messenger/genetics , RNA, Messenger/metabolism , Receptors, Estrogen/metabolism , Signal Transduction/drug effects , Transcriptome/drug effects , Transcriptome/genetics , Up-Regulation/drug effects
18.
J Natl Cancer Inst ; 111(4): 388-398, 2019 04 01.
Article in English | MEDLINE | ID: mdl-29961873

ABSTRACT

BACKGROUND: Breast cancer brain metastases (BrMs) are defined by complex adaptations to both adjuvant treatment regimens and the brain microenvironment. Consequences of these alterations remain poorly understood, as does their potential for clinical targeting. We utilized genome-wide molecular profiling to identify therapeutic targets acquired in metastatic disease. METHODS: Gene expression profiling of 21 patient-matched primary breast tumors and their associated brain metastases was performed by TrueSeq RNA-sequencing to determine clinically actionable BrM target genes. Identified targets were functionally validated using small molecule inhibitors in a cohort of resected BrM ex vivo explants (n = 4) and in a patient-derived xenograft (PDX) model of BrM. All statistical tests were two-sided. RESULTS: Considerable shifts in breast cancer cell-specific gene expression profiles were observed (1314 genes upregulated in BrM; 1702 genes downregulated in BrM; DESeq; fold change > 1.5, Padj < .05). Subsequent bioinformatic analysis for readily druggable targets revealed recurrent gains in RET expression and human epidermal growth factor receptor 2 (HER2) signaling. Small molecule inhibition of RET and HER2 in ex vivo patient BrM models (n = 4) resulted in statistically significantly reduced proliferation (P < .001 in four of four models). Furthermore, RET and HER2 inhibition in a PDX model of BrM led to a statistically significant antitumor response vs control (n = 4, % tumor growth inhibition [mean difference; SD], anti-RET = 86.3% [1176; 258.3], P < .001; anti-HER2 = 91.2% [1114; 257.9], P < .01). CONCLUSIONS: RNA-seq profiling of longitudinally collected specimens uncovered recurrent gene expression acquisitions in metastatic tumors, distinct from matched primary tumors. Critically, we identify aberrations in key oncogenic pathways and provide functional evidence for their suitability as therapeutic targets. Altogether, this study establishes recurrent, acquired vulnerabilities in BrM that warrant immediate clinical investigation and suggests paired specimen expression profiling as a compelling and underutilized strategy to identify targetable dependencies in advanced cancers.


Subject(s)
Biomarkers, Tumor/genetics , Brain Neoplasms/genetics , Breast Neoplasms/genetics , Gene Expression Regulation, Neoplastic , Neoplasm Recurrence, Local/genetics , Transcriptome , Adult , Animals , Brain Neoplasms/secondary , Breast Neoplasms/pathology , Case-Control Studies , Female , Follow-Up Studies , Gene Expression Profiling , Humans , Longitudinal Studies , Mice , Middle Aged , Neoplasm Recurrence, Local/pathology , Prognosis , Survival Rate , Xenograft Model Antitumor Assays
19.
J Mol Med (Berl) ; 96(10): 1025-1037, 2018 10.
Article in English | MEDLINE | ID: mdl-30069746

ABSTRACT

Elevated levels of the anti-apoptotic BCL2 protein associate with favourable outcome in breast cancer. We investigated whether executioner caspase activation downstream of mitochondrial apoptosis was associated with, or independent, of BCL2's prognostic signature in breast cancer. Levels of pro- and anti-apoptotic BCL2 family proteins were quantified in triple negative breast cancer (TNBC) samples and utilised to calculate BCL2 profiles of 845 breast cancer patients. Biomarkers including single apoptosis proteins and network-enriched apoptosis system signatures were evaluated using uni- and multi-variate Cox-models. In both TNBC and non-TNBC breast cancer, the anti-apoptotic BCL2 protein was particularly abundant when compared to other solid tumours. High BCL2 protein levels were prognostic of favourable outcome across all breast cancers (HR 0.4, 95% CI 0.2-0.6, Wald p < 0.0001). Although BCL2 and cleaved caspase-7 levels were negatively correlated, levels of cleaved caspase-7 were also associated with favourable outcome (HR 0.4, 95% CI 0.3-0.7, Wald p = 0.001). A combination of low BCL2 and low cleaved caspase-7 protein levels was highly prognostic of unfavourable outcome across all breast cancers (HR 11.29, 95% CI 2.20-58.23, Wald p = 0.01). A combination of BCL2 and cleaved caspase-7 levels is a promising prognostic biomarker in breast cancer patients. KEY MESSAGE: BCL2 levels are elevated in breast cancer where they are marker of good prognosis. BCL2 and active caspase levels correlate negatively; yet, active caspases indicate good outcome. Low BCL2 and low caspase-7 are highly prognostic of unfavourable outcome across all breast cancers. BCL2 levels indicate molecular subtype and tumour proliferation status in breast cancer.


Subject(s)
Biomarkers, Tumor/metabolism , Breast Neoplasms/metabolism , Caspase 7/metabolism , Proto-Oncogene Proteins c-bcl-2/metabolism , Female , Humans , Prognosis
20.
Clin Cancer Res ; 24(15): 3692-3703, 2018 08 01.
Article in English | MEDLINE | ID: mdl-29567811

ABSTRACT

Purpose: Despite the clinical utility of endocrine therapies for estrogen receptor-positive (ER) breast cancer, up to 40% of patients eventually develop resistance, leading to disease progression. The molecular determinants that drive this adaptation to treatment remain poorly understood. Methylome aberrations drive cancer growth yet the functional role and mechanism of these epimutations in drug resistance are poorly elucidated.Experimental Design: Genome-wide multi-omics sequencing approach identified a differentially methylated hub of prodifferentiation genes in endocrine resistant breast cancer patients and cell models. Clinical relevance of the functionally validated methyl-targets was assessed in a cohort of endocrine-treated human breast cancers and patient-derived ex vivo metastatic tumors.Results: Enhanced global hypermethylation was observed in endocrine treatment resistant cells and patient metastasis relative to sensitive parent cells and matched primary breast tumor, respectively. Using paired methylation and transcriptional profiles, we found that SRC-1-dependent alterations in endocrine resistance lead to aberrant hypermethylation that resulted in reduced expression of a set of differentiation genes. Analysis of ER-positive endocrine-treated human breast tumors (n = 669) demonstrated that low expression of this prodifferentiation gene set significantly associated with poor clinical outcome (P = 0.00009). We demonstrate that the reactivation of these genes in vitro and ex vivo reverses the aggressive phenotype.Conclusions: Our work demonstrates that SRC-1-dependent epigenetic remodeling is a 'high level' regulator of the poorly differentiated state in ER-positive breast cancer. Collectively these data revealed an epigenetic reprograming pathway, whereby concerted differential DNA methylation is potentiated by SRC-1 in the endocrine resistant setting. Clin Cancer Res; 24(15); 3692-703. ©2018 AACR.


Subject(s)
Breast Neoplasms/drug therapy , Cell Differentiation/drug effects , Receptors, Estrogen/genetics , src-Family Kinases/genetics , Breast/drug effects , Breast/pathology , Breast Neoplasms/genetics , Breast Neoplasms/pathology , CRISPR-Cas Systems/genetics , Cell Proliferation/drug effects , DNA Methylation/genetics , Disease-Free Survival , Drug Resistance, Neoplasm/genetics , Epigenomics , Female , Gene Expression Regulation, Neoplastic/drug effects , Gene Silencing , Heterografts , Humans , MCF-7 Cells , Microarray Analysis , Neoplasm Invasiveness/genetics , Neoplasm Invasiveness/pathology , Neoplasm Metastasis
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