Dual targeting of the androgen receptor and PI3K/AKT/mTOR pathways in prostate cancer models improves antitumor efficacy and promotes cell apoptosis

Prostate cancer is a frequent malignancy in older men and has a very high 5-year survival rate if diagnosed early. The prognosis is much less promising if the tumor has already spread outside the prostate gland. Targeted treatments mainly aim at blocking androgen receptor (AR) signaling and initially show good efficacy. However, tumor progression due to AR-dependent and AR-independent mechanisms is often observed after some time, and novel treatment strategies are urgently needed. Dysregulation of the PI3K/AKT/mTOR pathway in advanced prostate cancer and its implication in treatment resistance has been reported. We compared the impact of PI3K/AKT/mTOR pathway inhibitors with different selectivity profiles on in vitro cell proliferation and on caspase 3/7 activation as a marker for apoptosis induction, and observed the strongest effects in the androgen-sensitive prostate cancer cell lines VCaP and LNCaP. Combination treatment with the AR inhibitor darolutamide led to enhanced apoptosis in these cell lines, the effects being most pronounced upon cotreatment with the pan-PI3K inhibitor copanlisib. A subsequent transcriptomic analysis performed in VCaP cells revealed that combining darolutamide with copanlisib impacted gene expression much more than individual treatment. A comprehensive reversal of the androgen response and the mTORC1 transcriptional programs as well as a marked induction of DNA damage was observed. Next, an in vivo efficacy study was performed using the androgen-sensitive patient-derived prostate cancer (PDX) model LuCaP 35 and a superior efficacy was observed after the combined treatment with copanlisib and darolutamide. Importantly, immunohistochemistry analysis of these treated tumors showed increased apoptosis, as revealed by elevated levels of cleaved caspase 3 and Bcl-2-binding component 3 (BBC3). In conclusion, these data demonstrate that concurrent blockade of the PI3K/AKT/mTOR and AR pathways has superior antitumor efficacy and induces apoptosis in androgen-sensitive prostate cancer cell lines and PDX models.

Preclinical Anticipation of On- and Off-Target Resistance Mechanisms to Anti-Cancer Drugs: A Systematic Review

The advent of targeted therapies has led to tremendous improvements in treatment options and their outcomes in the field of oncology. Yet, many cancers outsmart precision drugs by developing on-target or off-target resistance mechanisms. Gaining the ability to resist treatment is the rule rather than the exception in tumors, and it remains a major healthcare challenge to achieve long-lasting remission in most cancer patients. Here, we discuss emerging strategies that take advantage of innovative high-throughput screening technologies to anticipate on- and off-target resistance mechanisms before they occur in treated cancer patients. We divide the methods into non-systematic approaches, such as random mutagenesis or long-term drug treatment, and systematic approaches, relying on the clustered regularly interspaced short palindromic repeats (CRISPR) system, saturated mutagenesis, or computational methods. All these new developments, especially genome-wide CRISPR-based screening platforms, have significantly accelerated the processes for identification of the mechanisms responsible for cancer drug resistance and opened up new avenues for future treatments.

Grade Group 1 Prostate Cancers Exhibit Tumor-defining Androgen Receptor-driven Programs

Grade group 1 (GG1) primary prostate cancers with a pathologic Gleason score of 6 are considered indolent and generally not associated with fatal outcomes, so treatment is not indicated for most cases. These low-grade cancers have an overall negligible risk of locoregional progression and metastasis to distant organs, which is why there is an ongoing debate about whether these lesions should be reclassified as "noncancerous". However, the underlying molecular activity of key disease drivers, such as the androgen receptor (AR), have thus far not been thoroughly characterized in low-grade tumors. Therefore, we set out to delineate the AR chromatin-binding landscape in low-grade GG1 prostate cancers to gain insights into whether these AR-driven programs are actually tumor-specific or are normal prostate epithelium-like. These analyses showed that GG1 tumors do not harbor a distinct AR cistrome and, similar to higher-grade cancers, AR preferentially binds to tumor-defining cis-regulatory elements. Furthermore, the enhancer activity of these regions and the expression of their respective target genes were not significantly different in GG1 tumors. From an epigenetic perspective, this finding supports the cancer designation currently given to these low-grade tumors and clearly distinguishes them from noncancerous benign tissue. PATIENT SUMMARY: We characterized the molecular activity of the androgen receptor protein, which drives prostate cancer disease, in low-grade tumors. Our results show that these tumors are true cancers and are clearly separate from benign prostate tissue despite their low clinical aggressiveness.

Targeting fatty acid oxidation via Acyl-CoA binding protein hinders glioblastoma invasion

The diffuse nature of Glioblastoma (GBM) tumors poses a challenge to current therapeutic options. We have previously shown that Acyl-CoA Binding Protein (ACBP, also known as DBI) regulates lipid metabolism in GBM cells, favoring fatty acid oxidation (FAO). Here we show that ACBP downregulation results in wide transcriptional changes affecting invasion-related genes. In vivo experiments using patient-derived xenografts combined with in vitro models demonstrated that ACBP sustains GBM invasion via binding to fatty acyl-CoAs. Blocking FAO mimics ACBP^KD-induced immobility, a cellular phenotype that can be rescued by increasing FAO rates. Further investigation into ACBP-downstream pathways served to identify Integrin beta-1, a gene downregulated upon inhibition of either ACBP expression or FAO rates, as a mediator for ACBP's role in GBM invasion. Altogether, our findings highlight a role for FAO in GBM invasion and reveal ACBP as a therapeutic vulnerability to stall FAO and subsequent cell invasion in GBM tumors.

Development of machine learning–powered models for prostate cancer HRD prediction

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Background: In prostate cancer, homologous recombination deficiency (HRD) is associated with poor prognosis, and sensitivity to DNA damaging agents and DNA damage repair (DDR) inhibitors. As new classes of DDR inhibitors become available, identifying patients with HRD will be critical for treatment selection. Here, we present machine learning (ML)-based models trained to predict HRD status directly from hematoxylin and eosin (H&E) whole slide images (WSI). Methods: ML models were trained to predict and segment cells and tissue regions within the tumor microenvironment (TME) using annotated (N=91,021 annotations) WSI of H&E-stained resections from the cancer genome atlas prostate adenocarcinoma (TCGA PRAD) dataset (N=401) and needle core biopsies from a proprietary dataset (N=1,000). Quantified Human Interpretable Features (HIFs) that describe the TME composition were extracted. Three models were trained to predict HRD status using 373 WSI with known HRD score (TCGA PRAD; train N=259, validation N=76, and test N=38). Two models used input from the TME model: An HIF multivariate logistic regression model, and a graph neural network (GNN) where predictions are based on the complex spatial relationships within the TME. An end-to-end (E2E) multiple instance learning model predicted directly from the WSI. Two cutoffs for HRD were defined using Gaussian Mixture Models, resulting in 99 WSI (train N=72, validation N=18, and test N=9) positive for the Genomic Instability (>16 events) cutoff, and 58 WSI (train N=44, validation N=10, test N=4) positive for the Genomic Instability (>22 events) cutoff. An independent validation set of 45 biopsies and 16 resections from a biobank of metastatic castration resistant prostate cancer with HRD status determined by whole-exome sequencing was compared to ML model H&E-based HRD prediction. Results: In the TCGA test set of resection samples, all three models moderately or strongly predicted HRD status, with the HIF model showing the best performance (AUROC 0.87, sensitivity 0.88, specificity 0.62). The same HIF model performed equally well (AUROC 0.85, Sensitivity 0.93, specificity 0.67) in the resection samples from the independent validation set. However, the model performance went down (AUROC 0.69, sensitivity 0.91, specificity: 0.3) when both resection and needle biopsy samples were included, highlighting the importance of a representative training set to achieve robust performance in a real world setting. Further model training and validation with a more diverse dataset is required to accurately assess the performance of the model on needle biopsies. Conclusions: ML models trained on resection prostate cancer samples performed well in predicting HRD status when applied to the same sample type, demonstrating the potential of ML models to predict genomic biomarkers status in surgical specimens for treatment decision.

How well do polygenic risk scores identify men at high risk for prostate cancer? Systematic review and meta-analysis

OBJECTIVES

Genome-wide association studies have revealed over 200 genetic susceptibility loci for prostate cancer (PCa). By combining them, polygenic risk scores (PRS) can be generated to predict risk of PCa. We summarize the published evidence and conduct meta-analyses of PRS as a predictor of PCa risk in Caucasian men.

PATIENTS AND METHODS

Data were extracted from 59 studies, with 16 studies including 17 separate analyses used in the main meta-analysis with a total of 20,786 cases and 69,106 controls identified through a systematic search of ten databases. Random effects meta-analysis was used to obtain pooled estimates of area under the receiver-operating characteristic curve (AUC). Meta-regression was used to assess the impact of number of single-nucleotide polymorphisms (SNPs) incorporated in PRS on AUC. Heterogeneity is expressed as I² scores. Publication bias was evaluated using funnel plots and Egger tests.

RESULTS

The ability of PRS to identify men with PCa was modest (pooled AUC 0.63, 95% CI 0.62-0.64) with moderate consistency (I² 64%). Combining PRS with clinical variables increased the pooled AUC to 0.74 (0.68-0.81). Meta-regression showed only negligible increase in AUC for adding incremental SNPs. Despite moderate heterogeneity, publication bias was not evident.

CONCLUSION

Typically, PRS accuracy is comparable to PSA or family history with a pooled AUC value 0.63 indicating mediocre performance for PRS alone.

Abstract 651: Combination of the androgen receptor inhibitor darolutamide and the PI3K inhibitor copanlisib leads to improved anti-tumor efficacy and apoptosis in prostate cancer models

Prostate cancer is mainly driven by androgen receptor (AR) signaling so that drugs directly inhibiting this pathway such as GnRH ligands and AR inhibitors are now established as mainstay treatments. Unfortunately, treatment resistance often develops and combination therapies may represent potential strategies to prolong disease remission. The PI3K/Akt/mTOR signaling pathway plays an essential role in prostate cancer and is upregulated in about 30-50% of patients. Loss of the PI3K/Akt/mTOR pathway inhibitor PTEN is observed in up to 40% of late-stage prostate cancer patients. Compounds inhibiting PI3K or Akt have shown promising efficacy in preclinical prostate cancer models, and advanced clinical trials with these inhibitors are currently ongoing in metastatic castration-resistant prostate cancer, often in combination with AR inhibitors. Here we examined the impact of combining the AR inhibitor darolutamide with the pan class I PI3K inhibitor copanlisib on preclinical models in vitro and in vivo. We found that treating different androgen-dependent prostate cancer cell lines with darolutamide and copanlisib had a very strong synergistic inhibitory effect. Induction of apoptosis was observed in the PARP cleavage and caspase 3/7 activation assays after treatment with copanlisib and more so after treatment with copanlisib plus darolutamide. Expression analysis showed that darolutamide strongly down-regulated AR target genes such as KLK3, FKBP5 and TMPRSS2, but copanlisib had no additional impact. However, when examining genes involved in the apoptotic pathway we found that the down-regulation of pro-apoptotic genes that follows androgen treatment was strongly reversed by the combined darolutamide and copanlisib treatment. Finally, in vivo efficacy studies showed that the LuCaP 96 prostate cancer patient-derived (PDX) xenograft, which has a non-functional PTEN gene, strongly responded to darolutamide, but additional treatment with copanlisib did not increase anti-tumor efficacy. In the LuCaP 35 PDX model, which expresses PTEN at low level, darolutamide or copanlisib treatment alone showed only limited efficacy, while the combination exhibited tumor inhibitory effects. In conclusion, we found that combining darolutamide with copanlisib strongly inhibited the proliferation of prostate cancer models in vitro. This was linked to strong induction of cell apoptosis and prevention of pro-apoptotic gene down-regulation. Superior efficacy was also observed in the LuCaP 35 PDX xenograft model in vivo. Additional data are needed to explore the underlying molecular mechanisms. Together these results further support the exploration of the impact of combining AR and PI3K signaling inhibitors in late-stage prostate cancer patients.

Citation Format: Tatsuo Sugawara, Holly NGuyen, Eva Corey, Ekaterina Nevedomskaya, Oliver Politz, Dominik Mumberg, Bernard Haendler. Combination of the androgen receptor inhibitor darolutamide and the PI3K inhibitor copanlisib leads to improved anti-tumor efficacy and apoptosis in prostate cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 651.

From Omics to Multi-Omics Approaches for In-Depth Analysis of the Molecular Mechanisms of Prostate Cancer

Cancer arises following alterations at different cellular levels, including genetic and epigenetic modifications, transcription and translation dysregulation, as well as metabolic variations. High-throughput omics technologies that allow one to identify and quantify processes involved in these changes are now available and have been instrumental in generating a wealth of steadily increasing data from patient tumors, liquid biopsies, and from tumor models. Extensive investigation and integration of these data have led to new biological insights into the origin and development of multiple cancer types and helped to unravel the molecular networks underlying this complex pathology. The comprehensive and quantitative analysis of a molecule class in a biological sample is named omics and large-scale omics studies addressing different prostate cancer stages have been performed in recent years. Prostate tumors represent the second leading cancer type and a prevalent cause of cancer death in men worldwide. It is a very heterogenous disease so that evaluating inter- and intra-tumor differences will be essential for a precise insight into disease development and plasticity, but also for the development of personalized therapies. There is ample evidence for the key role of the androgen receptor, a steroid hormone-activated transcription factor, in driving early and late stages of the disease, and this led to the development and approval of drugs addressing diverse targets along this pathway. Early genomic and transcriptomic studies have allowed one to determine the genes involved in prostate cancer and regulated by androgen signaling or other tumor-relevant signaling pathways. More recently, they have been supplemented by epigenomic, cistromic, proteomic and metabolomic analyses, thus, increasing our knowledge on the intricate mechanisms involved, the various levels of regulation and their interplay. The comprehensive investigation of these omics approaches and their integration into multi-omics analyses have led to a much deeper understanding of the molecular pathways involved in prostate cancer progression, and in response and resistance to therapies. This brings the hope that novel vulnerabilities will be identified, that existing therapies will be more beneficial by targeting the patient population likely to respond best, and that bespoke treatments with increased efficacy will be available soon.

Abstract 1008: Comparative proteomics and transcriptomics analysis of the impact of androgen stimulation and darolutamide inhibition in a prostate cancer model

Androgen receptor (AR) signaling is the major driver in prostate cancer. Darolutamide is a high-affinity AR inhibitor recently approved for non-metastatic castration-resistant prostate cancer. The impact of the AR on gene transcription has been extensively examined but the downstream effects on protein levels are still poorly understood. Here we generated for the first time comprehensive quantitative proteomic and transcriptomic data from the androgen-sensitive, prostate cancer cell line VCaP treated with the androgen R1881 and darolutamide. For the proteomic analysis, a comprehensive and quantitative label-free protein expression profiling was performed using nanoscale liquid chromatography coupled to tandem mass spectrometry. For the transcriptomic analysis, sequencing was performed via single-end, 50 base-pair reads with an average depth of 21 million reads per sample. FASTQ reads were mapped with STAR aligner to the human genome GRCh38 and quantified with RSEM. Further analysis was performed in R statistical software. We investigated the expression levels of 12900 protein-coding genes and 8721 translated proteins. Androgen treatment resulted in increased expression of known androgen response genes, as well as of genes from the mTORC1 pathway, cell cycle and other pathways previously shown to be affected by androgens. This was paralleled by upregulation of the corresponding protein levels in the majority of cases. Importantly, a detailed comparative analysis of transcriptomic and proteomic data revealed a few notable differences in regulation. In androgen-treated prostate cancer cells, there was a strong increase of FOLH1, AMACR and FKBP5 transcript levels (10 to 40-fold) but only a moderate increase of the corresponding protein levels (2 to 6-fold). Additional darolutamide treatment led to strong down-regulation of androgen-induced gene expression and of the corresponding protein levels. Here also there were a few instances where protein and transcript levels were differentially regulated. The discrepancy in transcript and protein levels seen after androgen and anti-androgen treatment suggests differential post-transcriptional regulation of protein abundance to occur in some instances. In conclusion, we found that darolutamide strongly reversed androgen-induced activation of gene expression programs related to cell proliferation and survival, both at the transcript and protein levels. We furthermore identified for the first time androgen-activated genes whose function is additionally regulated at the post-transcription level.

Citation Format: Ekaterina Nevedomskaya, Simon J. Baumgart, Tatsuo Sugawara, Ralf Lesche, Dominik Mumberg, Bernard Haendler. Comparative proteomics and transcriptomics analysis of the impact of androgen stimulation and darolutamide inhibition in a prostate cancer model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1008.

The potent AMPK inhibitor BAY-3827 shows strong efficacy in androgen-dependent prostate cancer models

PURPOSE

5' adenosine monophosphate-activated kinase (AMPK) is an essential regulator of cellular energy homeostasis and has been associated with different pathologies, including cancer. Precisely defining the biological role of AMPK necessitates the availability of a potent and selective inhibitor.

METHODS

High-throughput screening and chemical optimization were performed to identify a novel AMPK inhibitor. Cell proliferation and mechanistic assays, as well as gene expression analysis and chromatin immunoprecipitation were used to investigate the cellular impact as well as the crosstalk between lipid metabolism and androgen signaling in prostate cancer models. Also, fatty acid turnover was determined by examining lipid droplet formation.

RESULTS

We identified BAY-3827 as a novel and potent AMPK inhibitor with additional activity against ribosomal 6 kinase (RSK) family members. It displays strong anti-proliferative effects in androgen-dependent prostate cancer cell lines. Analysis of genes involved in AMPK signaling revealed that the expression of those encoding 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase (HMGCR), fatty acid synthase (FASN) and 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 (PFKFB2), all of which are involved in lipid metabolism, was strongly upregulated by androgen in responsive models. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) analysis identified several androgen receptor (AR) binding peaks in the HMGCR and PFKFB2 genes. BAY-3827 strongly down-regulated the expression of lipase E (LIPE), cAMP-dependent protein kinase type II-beta regulatory subunit (PRKAR2B) and serine-threonine kinase AKT3 in responsive prostate cancer cell lines. Also, the expression of members of the carnitine palmitoyl-transferase 1 (CPT1) family was inhibited by BAY-3827, and this was paralleled by impaired lipid flux.

CONCLUSIONS

The availability of the potent inhibitor BAY-3827 will contribute to a better understanding of the role of AMPK signaling in cancer, especially in prostate cancer.

Darolutamide antagonizes androgen signaling by blocking enhancer and super-enhancer activation

Prostate cancer (PCa) is one of the most frequent tumor types in the male Western population. Early-stage PCa and late-stage PCa are dependent on androgen signaling, and inhibitors of the androgen receptor (AR) axis represent the standard therapy. Here, we studied in detail the global impact of darolutamide, a newly approved AR antagonist, on the transcriptome and AR-bound cistrome in two PCa cell models. Darolutamide strongly depleted the AR from gene regulatory regions and abolished AR-driven transcriptional signaling. Enhancer activation was blocked at the chromatin level as evaluated by H3K27 acetylation (H3K27ac), H3K4 monomethylation (H3K4me1), and FOXA1, MED1, and BRD4 binding. We identified genomic regions with high affinities for the AR in androgen-stimulated, but also in androgen-depleted conditions. A similar AR affinity pattern was observed in healthy and PCa tissue samples. High FOXA1, BRD4, H3K27ac, and H3K4me1 levels were found to mark regions showing AR binding in the hormone-depleted setting. Conversely, low FOXA1, BRD4, and H3K27ac levels were observed at regulatory sites that responded strongly to androgen stimulation, and AR interactions at these sites were blocked by darolutamide. Beside marked loss of AR occupancy, FOXA1 recruitment to chromatin was also clearly reduced after darolutamide treatment. We furthermore identified numerous androgen-regulated super-enhancers (SEs) that were associated with hallmark androgen and cell proliferation-associated gene sets. Importantly, these SEs are also active in PCa tissues and sensitive to darolutamide treatment in our models. Our findings demonstrate that darolutamide is a potent AR antagonist blocking genome-wide AR enhancer and SE activation, and downstream transcription. We also show the existence of a dynamic AR cistrome that depends on the androgen levels and on high AR affinity regions present in PCa cell lines and also in tissue samples.

Abstract A29: Genome-wide CRISPR/Cas9 screens for the identification of novel YAP1/TAZ modulators

Aberrant activation of the Hippo pathway effectors YAP1/TAZ promotes cell proliferation and tumorigenesis. To identify novel regulators of YAP1/TAZ in cancer, we established a FACS-based screening system monitoring YAP1/TAZ activity in MDA-MB-231 breast cancer cells. Using these cells, we performed pooled genome-wide CRISPR/Cas9 knockout and CRISPR activation/interference (a/i) screens. The list of hits included previously known YAP1/TAZ modulators such as LATS2, AJUBA, and TAZ itself, demonstrating the robustness of the screen. Moreover, we identified about 30 novel candidate genes with potential inhibitory activity on YAP1/TAZ and about 50 candidate genes that may play a role in YAP1/TAZ activation. These genes represent diverse cellular functions such as regulation of actin cytoskeleton, integrin signaling, and ER protein processing, among others. Modulation of endogenous YAP1/TAZ target genes was assessed by individual gene knockout using crRNAs. Functional characterization of the novel potential YAP1/TAZ modulators will aid to the further understanding of YAP1/TAZ biology in health and disease.

Citation Format: Jan Naujoks, Lisette Potze, Julia Kuehnlenz, Atanas Kamburov, Ekaterina Nevedomskaya, Andreas Steffen, Claudia Luther, Anna Anurin, Anne Buttgereit, Stefan Prechtl, Benjamin Bader, Ralf Lesche, Peter Staller, Martin Lange, Barbara Nicke. Genome-wide CRISPR/Cas9 screens for the identification of novel YAP1/TAZ modulators [abstract]. In: Proceedings of the AACR Special Conference on the Hippo Pathway: Signaling, Cancer, and Beyond; 2019 May 8-11; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(8_Suppl):Abstract nr A29.

Epigenetic profiling demarcates molecular subtypes of muscle-invasive bladder cancer

Muscle-invasive bladder cancer (MIBC) is a heterogeneous disease that often recurs despite aggressive treatment with neoadjuvant chemotherapy and (radical) cystectomy. Basal and luminal molecular subtypes have been identified that are linked to clinical characteristics and have differential sensitivities to chemotherapy. While it has been suggested that epigenetic mechanisms play a role in defining these subtypes, a thorough understanding of the biological mechanisms is lacking. This report details the first genome-wide analysis of histone methylation patterns of human primary bladder tumours by chromatin immunoprecipitations and next-generation sequencing (ChIP-seq). We profiled multiple histone marks: H3K27me3, a marker for repressed genes, and H3K4me1 and H3K4me3, which are indicators of active enhancers and active promoters. Integrated analysis of ChIP-seq data and RNA sequencing revealed that H3K4 mono-methylation demarcates MIBC subtypes, while no association was found for the other two histone modifications in relation to basal and luminal subtypes. Additionally, we identified differentially methylated H3K4me1 peaks in basal and luminal tumour samples, suggesting that active enhancers play a role in defining subtypes. Our study is the first analysis of histone modifications in primary bladder cancer tissue and provides an important resource for the bladder cancer community.

Androgen modulation of XBP1 is functionally driving part of the AR transcriptional program

Prostate cancer development and progression is largely dependent on androgen receptor (AR) signaling. AR is a hormone-dependent transcription factor, which binds to thousands of sites throughout the human genome to regulate expression of directly responsive genes, including pro-survival genes that enable tumor cells to cope with increased cellular stress. ERN1 and XBP1 - two key players of the unfolded protein response (UPR) - are among such stress-associated genes. Here, we show that XBP1 levels in primary prostate cancer are associated with biochemical recurrence in five independent cohorts. Patients who received AR-targeted therapies had significantly lower XBP1 expression, whereas expression of the active form of XBP1 (XBP1s) was elevated. In vitro results show that AR-induced ERN1 expression led to increased XBP1s mRNA and protein levels. Furthermore, ChIP-seq analysis revealed that XBP1s binds enhancers upon stress stimuli regulating genes involved in UPR processes, eIF2 signaling and protein ubiquitination. We further demonstrate genomic overlap of AR- and XBP1s-binding sites, suggesting genomic conversion of the two signaling cascades. Transcriptomic effects of XBP1 were further studied by knockdown experiments, which lead to decreased expression of androgen-responsive genes and UPR genes. These results suggest a two-step mechanism of gene regulation, which involves androgen-induced expression of ERN1, thereby enhancing XBP1 splicing and transcriptional activity. This signaling cascade may prepare the cells for the increased protein folding, mRNA decay and translation that accompanies AR-regulated tumor cell proliferation.

Abstract 3055: Genome-wide CRISPR/Cas9 screen for the identification of novel YAP1/TAZ modulators

Aberrant activation of the Hippo pathway effectors YAP1/TAZ promotes cell proliferation and tumorigenesis. To identify novel regulators of YAP1/TAZ as a possible means to treat cancer, we established a novel, FACS-based screening system monitoring YAP1/TAZ activity in MDA-MB-231 breast cancer cells. Using these cells, we performed a pooled genome-wide CRISPR/Cas9 knockout screen. We identified approximately 50 genes potentially activating YAP1/TAZ with functions in the Actin Cytoskeleton signaling, p53 signaling, cell polarity or ER stress, amongst others. Moreover, we identified about 30 potential targets which when knocked out induce activity of YAP1/TAZ. The list of hits included genes known to affect the YAP1/TAZ activity such as AJUBA, LATS2 and TEAD, demonstrating the validity of the screen. Functional validation of the novel potential YAP1/TAZ modulators will aid to the further understanding of YAP1/TAZ biology and may open the door to new therapeutic avenues for targeting YAP1/TAZ in cancer.

Citation Format: Jan Naujoks, Lisette Potze, Anna Anurin, Julia Kuehnlenz, Ralf Lesche, Atanas Kamburov, Ekaterina Nevedomskaya, Andreas Steffen, Martin Lange, Barbara Nicke. Genome-wide CRISPR/Cas9 screen for the identification of novel YAP1/TAZ modulators [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3055.

Abstract 5210: Darolutamide impairs prostate cancer growth by altering chromatin conformation and transcriptional activity of genes involved in cell proliferation and survival

Androgen signalling is essential for early and late stage prostate cancer (PCa), as demonstrated by the efficacy of androgen receptor (AR) antagonists. The AR gene and its regulatory element are frequently amplified in castration-resistant tumors for which improved treatments are highly needed. Recent findings underscore that gene regulatory elements play an important role in tumor development due to their impact on chromatin conformation and gene regulation. Here we describe the genome-wide effects of darolutamide, a novel AR antagonist which just completed a pivotal clinical phase III trial, by analyzing AR occupancy and its impact on chromatin looping, histone H3K27 acetylation and downstream gene regulation. Genome-wide RNA-seq and ChIP-seq were used to analyze the androgen-sensitive cell lines VCaP, LAPC4 and LNCaP treated with R1881, or with R1881 and darolutamide. Binding of AR and of the pioneer factor FOXA1, as well as histone H3K27 acetylation were determined. Chromatin conformation was detected using the HiChIP method with an AR-specific antibody. Differential gene expression was analyzed by DESeq2 and Gene Set Enrichment Analyses. ChIP-seq peak identification was done by MACS2. HiChIP analysis was performed with the hichipper pipeline. Darolutamide efficiently blocked AR signalling at the level of transcriptional regulation and altered chromatin landscape interaction. Analysis of transcriptomic data showed a strong reduction of the androgen response, as well as down-regulation of proliferation and cell cycle genes by darolutamide. Concordantly, AR occupancy was decreased genome-wide compared to androgen stimulation. Importantly, no binding cluster was identified which showed increased AR occupancy after darolutamide treatment, as reported for other AR antagonists. Interestingly, we observed in darolutamide-treated samples a parallel reduction of FOXA1 occupancy at AR sites, which argues for a co-dependence between this pioneer factor and the AR. Also, we found that H3K27 acetylation, a histone mark linked to active regions, was markedly down-regulated at specific enhancer and gene regions following darolutamide treatment, further pointing to reduced activity of enhancer regions recognized by the AR. Finally, determination of chromatin looping mediated by the AR between enhancers and gene promoters showed a dense network at genes involved in prostate cancer survival. The loss of AR binding at these regions was in line with the significantly reduced transcriptional response observed following darolutamide treatment. In conclusion, we found that darolutamide strongly prevented genome-wide AR binding in multiple hormone-sensitive cellular PCa models, importantly at genes involved in cell proliferation and survival. We furthermore highlight the cross-talk between the pioneer factor FOXA1 and the AR.

Citation Format: Simon J. Baumgart, Ekaterina Nevedomskaya, Ralf Lesche, Bernard Haendler. Darolutamide impairs prostate cancer growth by altering chromatin conformation and transcriptional activity of genes involved in cell proliferation and survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5210.

Functional diversity of inhibitors tackling the differentiation blockage of MLL-rearranged leukemia

Introduction

The chromosomal rearrangements of the mixed-lineage leukemia gene MLL (KMT2A) have been extensively characterized as a potent oncogenic driver in leukemia. For its oncogenic function, most MLL-fusion proteins exploit the multienzyme super elongation complex leading to elevated expression of MLL target genes. High expression of MLL target genes overwrites the normal hematopoietic differentiation program, resulting in undifferentiated blasts characterized by the capacity to self-renew. Although extensive resources devoted to increased understanding of therapeutic targets to overcome de-differentiation in ALL/AML, the inter-dependencies of targets are still not well described. The majority of inhibitors potentially interfering with MLL-fusion protein driven transformation have been characterized in individual studies, which so far hindered their direct cross-comparison.

Methods

In our study, we characterized head-to-head clinical stage inhibitors for BET, DHODH, DOT1L as well as two novel inhibitors for CDK9 and the Menin-MLL interaction with a focus on differentiation induction. We profiled those inhibitors for global gene expression effects in a large cell line panel and examined cellular responses such as inhibition of proliferation, apoptosis induction, cell cycle arrest, surface marker expression, morphological phenotype changes, and phagocytosis as functional differentiation readout. We also verified the combination potential of those inhibitors on proliferation and differentiation level.

Results

Our analysis revealed significant differences in differentiation induction and in modulating MLL-fusion target gene expression. We observed Menin-MLL and DOT1L inhibitors act very specifically on MLL-fused leukemia cell lines, whereas inhibitors of BET, DHODH and P-TEFb have strong effects beyond MLL-fusions. Significant differentiation effects were detected for Menin-MLL, DOT1L, and DHODH inhibitors, whereas BET and CDK9 inhibitors primarily induced apoptosis in AML/ALL cancer models. For the first time, we explored combination potential of the abovementioned inhibitors with regards to overcoming the differentiation blockage.

Conclusion

Our findings show substantial diversity in the molecular activities of those inhibitors and provide valuable insights into the further developmental potential as single agents or in combinations in MLL-fused leukemia.

Electronic supplementary material

The online version of this article (10.1186/s13045-019-0749-y) contains supplementary material, which is available to authorized users.

Darolutamide is a potent androgen receptor antagonist with strong efficacy in prostate cancer models

Darolutamide is a novel androgen receptor (AR) antagonist with a distinct chemical structure compared to other AR antagonists and currently in clinical Phase 3 trials for prostate cancer. Using cell‐based transactivation assays, we demonstrate that darolutamide, its diastereomers and its main metabolite keto‐darolutamide are strong, competitive antagonists for AR wild type, and also for several mutants identified in prostate cancer patients for which other AR antagonists show reduced antagonism or even agonism. Darolutamide, its two diastereomers and main metabolite are also strong antagonists in assays measuring AR N/C interaction and homodimerization. Molecular modeling suggests that the flexibility of darolutamide allows accommodation in the W742C/L mutated AR ligand‐binding pocket while for enzalutamide the loss of the important hydrophobic interaction with W742 leads to reduced AR interaction. This correlates with an antagonistic pattern profile of coregulator recruitment for darolutamide. In vitro efficacy studies performed with androgen‐dependent prostate cancer cell lines show that darolutamide strongly reduces cell viability and potently inhibits spheroid formation. Also, a marked down‐regulation of androgen target genes paralleled by decreased AR binding to gene regulatory regions is seen. In vivo studies reveal that oral dosing of darolutamide markedly reduces growth of the LAPC‐4 cell line‐derived xenograft and of the KuCaP‐1 patient‐derived xenograft. Altogether, these results substantiate a unique antagonistic profile of darolutamide and support further development as a prostate cancer drug.

What's new?

Comparison of genomic landscapes from primary prostate cancer and metastatic tumor shows that resistance mechanisms are centered on androgen signaling and increased synthesis. Here, the novel androgen receptor (AR) antagonist darolutamide shows strong in vitro and in vivo efficacy in different prostate cancer models. Darolutamide retains its antagonistic properties at elevated androgen levels and for several AR mutants identified in therapy‐resistant patients. A unique binding profile inside the AR ligand‐binding domain linked to the flexibility of darolutamide is proposed. Altogether, these results substantiate a unique antagonistic profile of darolutamide and support further development as a prostate cancer drug.

Urinary metabolites predict prolonged duration of delayed graft function in DCD kidney transplant recipients

Extending kidney donor criteria, including donation after circulatory death (DCD), has resulted in increased rates of delayed graft function (DGF) and primary nonfunction. Here, we used Nuclear Magnetic Resonance (NMR) spectroscopy to analyze the urinary metabolome of DCD transplant recipients at multiple time points (days 10, 42, 180, and 360 after transplantation). The aim was to identify markers that predict prolonged duration of functional DGF (fDGF). Forty-seven metabolites were quantified and their levels were evaluated in relation to fDGF. Samples obtained at day 10 had a different profile than samples obtained at the other time points. Furthermore, at day 10 there was a statistically significant increase in eight metabolites and a decrease in six metabolites in the group with fDGF (N = 53) vis-à-vis the group without fDGF (N = 22). In those with prolonged fDGF (≥21 days) (N = 17) urine lactate was significantly higher and pyroglutamate lower than in those with limited fDGF (<21 days) (N = 36). In order to further distinguish prolonged fDGF from limited fDGF, the ratios of all metabolites were analyzed. In a logistic regression analysis, the sum of branched-chain amino acids (BCAAs) over pyroglutamate and lactate over fumarate, predicted prolonged fDGF with an AUC of 0.85. In conclusion, kidney transplant recipients with fDGF can be identified based on their altered urinary metabolome. Furthermore, two ratios of urinary metabolites, lactate/fumarate and BCAAs/pyroglutamate, adequately predict prolonged duration of fDGF.

Optimized ChIP-seq method facilitates transcription factor profiling in human tumors

This study presents an optimized ChIP-seq protocol to enhance transcription factor profiling in human tumours, enabling the analysis of highly challenging samples, including core needle biopsies.

Chromatin immunoprecipitation (ChIP)-seq analyses of transcription factors in clinical specimens are challenging due to the technical limitations and low quantities of starting material, often resulting in low enrichments and poor signal-to-noise ratio. Here, we present an optimized protocol for transcription factor ChIP-seq analyses in human tissue, yielding an ∼100% success rate for all transcription factors analyzed. As proof of concept and to illustrate general applicability of the approach, human tissue from the breast, prostate, and endometrial cancers were analyzed. In addition to standard formaldehyde fixation, disuccinimidyl glutarate was included in the procedure, greatly increasing data quality. To illustrate the sensitivity of the optimized protocol, we provide high-quality ChIP-seq data for three independent factors (AR, FOXA1, and H3K27ac) from a single core needle prostate cancer biopsy specimen. In summary, double-cross-linking strongly improved transcription factor ChIP-seq quality on human tumor samples, further facilitating and enhancing translational research on limited amounts of tissue.

Loss of androgen receptor signaling in prostate cancer-associated fibroblasts (CAFs) promotes CCL2- and CXCL8-mediated cancer cell migration

Fibroblasts are abundantly present in the prostate tumor microenvironment (TME), including cancer‐associated fibroblasts (CAFs) which play a key role in cancer development. Androgen receptor (AR) signaling is the main driver of prostate cancer (PCa) progression, and stromal cells in the TME also express AR. High‐grade tumor and poor clinical outcome are associated with low AR expression in the TME, which suggests a protective role of AR signaling in the stroma against PCa development. However, the mechanism of this relation is not clear. In this study, we isolated AR‐expressing CAF‐like cells. Testosterone (R1881) exposure did not affect CAF‐like cell morphology, proliferation, or motility. PCa cell growth was not affected by culturing in medium from R1881‐exposed CAF‐like cells; however, migration of PCa cells was inhibited. AR chromatin immune precipitation sequencing (ChIP‐seq) was performed and motif search suggested that AR in CAF‐like cells bound the chromatin through AP‐1‐elements upon R1881 exposure, inducing enhancer‐mediated AR chromatin interactions. The vast majority of chromatin binding sites in CAF‐like cells were unique and not shared with AR sites observed in PCa cell lines or tumors. AR signaling in CAF‐like cells decreased expression of multiple cytokines; most notably CCL2 and CXCL8 and both cytokines increased migration of PCa cells. These results suggest direct paracrine regulation of PCa cell migration by CAFs through AR signaling.

Abstract 1798: A detailed comparison between second-generation AR antagonists reveals differences in the overall impact on gene regulation patterns in prostate cancer cells

Androgen receptor (AR) signaling is essential at all prostate cancer stages and is clinically addressed by surgical or chemical castration, AR antagonists and androgen synthesis inhibitors. Second-generation AR antagonists include the approved drug enzalutamide and the late-stage clinical investigational oral compounds apalutamide and darolutamide. Comparing the gene expression patterns and the overarching epigenetic modifications elicited by AR antagonists will be essential for a detailed understanding of the molecular mode of action of these compounds.

Methods: The transcriptome and AR binding patterns were analyzed by RNA-seq and qPCR, respectively. Genome-wide changes of the active transcription histone modification H3K27 acetylation were determined by ChIP-seq.

Results: RNA-seq was performed in the androgen-dependent VCaP and LNCaP cell lines for a detailed analysis of the genome-wide transcriptional effects of the AR antagonists darolutamide, enzalutamide and apalutamide. Gene set enrichment analysis indicated that many genes involved in androgen response were up- or down-regulated by androgen treatment with R1881. Principal component analysis showed that treatment with pharmacologically relevant doses of AR antagonists had similar effects at the 8-hour time point, however some differences were visible at the 22-hour time point. A strong expression down-regulation of a number of genes from the Wnt and epithelial-mesenchymal transition (EMT) pathways was observed for darolutamide as compared to enzalutamide and apalutamide treatment in the VCaP cell line. In LNCaP cells the major differences between the AR antagonists were observed in the androgen-regulated genes, which is consistent with varying degrees of inhibition by the drugs in this cell line. Next we determined the global H3K27 acetylation profiles which characterize open chromatin and active transcription. ChIP-seq analysis performed in LNCaP cells revealed a strong impact of androgen treatment on the H3K27 acetylation profiles of numerous genes involved in hormonal regulation. Darolutamide significantly reversed genome-wide H3K27 acetylation patterns, almost to non-androgen stimulated levels. More specifically, a reduction of H3K27 peaks was observed at KLK3 and FKBP5 regulatory elements. In addition, we determined the impact of AR antagonists on AR binding at the KLK2 and KLK3 regulatory elements. Darolutamide and enzalutamide strongly reduced androgen-stimulated AR binding whereas the impact of apalutamide was slightly lower.

Conclusions: AR antagonists strongly reversed the effects of the androgen R1881, both at the level of gene expression, and of H3K27 acetylation and AR binding. A detailed comparison between second-generation AR antagonists showed interesting differences in the regulation of genes in the Wnt and EMT pathways.

Citation Format: Simon J. Baumgart, Ekaterina Nevedomskaya, Ralf Lesche, Henrik Seidel, Bernard Haendler. A detailed comparison between second-generation AR antagonists reveals differences in the overall impact on gene regulation patterns in prostate cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1798.

Recent Advances in Prostate Cancer Treatment and Drug Discovery

Novel drugs, drug sequences and combinations have improved the outcome of prostate cancer in recent years. The latest approvals include abiraterone acetate, enzalutamide and apalutamide which target androgen receptor (AR) signaling, radium-223 dichloride for reduction of bone metastases, sipuleucel-T immunotherapy and taxane-based chemotherapy. Adding abiraterone acetate to androgen deprivation therapy (ADT) in order to achieve complete androgen blockade has proven highly beneficial for treatment of locally advanced prostate cancer and metastatic hormone-sensitive prostate cancer (mHSPC). Also, ADT together with docetaxel treatment showed significant benefit in mHSPC. Ongoing clinical trials for different subgroups of prostate cancer patients include the evaluation of the second-generation AR antagonists enzalutamide, apalutamide and darolutamide, of inhibitors of the phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) pathway, of inhibitors of DNA damage response, of targeted alpha therapy and of prostate-specific membrane antigen (PSMA) targeting approaches. Advanced clinical studies with immune checkpoint inhibitors have shown limited benefits in prostate cancer and more trials are needed to demonstrate efficacy. The identification of improved, personalized treatments will be much supported by the major progress recently made in the molecular characterization of early- and late-stage prostate cancer using “omics” technologies. This has already led to novel classifications of prostate tumors based on gene expression profiles and mutation status, and should greatly help in the choice of novel targeted therapies best tailored to the needs of patients.

mTOR pathway activation is a favorable prognostic factor in human prostate adenocarcinoma

Prostate cancer patients with localized disease are treated with curative intent. However, the disease will recur in approximately 30% of patients with a high incidence of morbidity and mortality. Prognostic biomarkers are needed to identify patients with high risk of relapse. mTOR pathway activation is reported in prostate cancer, but clinical trials testing efficacy of mTOR inhibitors were unsuccessful. To explain this clinical observation, we studied the expression and prognostic impact of mTOR-S2448 phosphorylation in localized prostate carcinomas. mTOR-S2448 phosphorylation is indicative for an activated mTOR pathway in prostate cancer. Surprisingly, the mTOR signaling pathway is activated specifically in prostate cancer patients with a favorable outcome. Since tumors from poor-outcome patients have low levels of mTOR-S2448 phosphorylation, this may explain why mTOR inhibitors proved unsuccessful in prostate cancer trials.

Neoadjuvant tamoxifen synchronizes ERα binding and gene expression profiles related to outcome and proliferation

Estrogen receptor alpha (ERα)-positive breast cancers are frequently treated with tamoxifen, but resistance is common. It remains elusive how tamoxifen resistance occurs and predictive biomarkers for treatment outcome are needed. Because most biomarker discovery studies are performed using pre-treatment surgical resections, the effects of tamoxifen therapy directly on the tumor cell in vivo remain unexamined. In this study, we assessed DNA copy number, gene expression profiles and ERα/chromatin binding landscapes on breast tumor specimens, both before and after neoadjuvant tamoxifen treatment. We observed neoadjuvant tamoxifen treatment synchronized ERα/chromatin interactions and downstream gene expression, indicating that hormonal therapy reduces inter-tumor molecular variability. ERα-synchronized sites are associated with dynamic FOXA1 action at these sites, which is under control of growth factor signaling. Genes associated with tamoxifen-synchronized sites are capable of differentiating patients for tamoxifen benefit. Due to the direct effects of therapeutics on ERα behavior and transcriptional output, our study highlights the added value of biomarker discovery studies after neoadjuvant drug exposure.

The adaptive immune system promotes initiation of prostate carcinogenesis in a human c-Myc transgenic mouse model

Increasing evidence from epidemiological and pathological studies suggests a role of the immune system in the initiation and progression of multiple cancers, including prostate cancer. Reports on the contribution of the adaptive immune system are contradictive, since both suppression and acceleration of disease development have been reported. This study addresses the functional role of lymphocytes in prostate cancer development using a genetically engineered mouse model (GEMM) of human c-Myc driven prostate cancer (Hi-Myc mice) combined with B and T cell deficiency (RAG1^-/- mice). From a pre-cancerous stage on, Hi-Myc mice showed higher accumulation of immune cells in their prostates then wild-type mice, of which macrophages were the most abundant. The onset of invasive adenocarcinoma was delayed in Hi-MycRAG1^-/- compared to Hi-Myc mice and associated with decreased infiltration of leukocytes into the prostate. In addition, lower levels of the cytokines CXCL2, CCL5 and TGF-β1 were detected in Hi-MycRAG1^-/- compared to Hi-Myc mouse prostates. These results from a GEMM of prostate cancer provide new insights into the promoting role of the adaptive immune system in prostate cancer development. Our findings indicate that the endogenous adaptive immune system does not protect against de novo prostate carcinogenesis in Hi-Myc transgenic mice, but rather accelerates the formation of invasive adenocarcinomas. This may have implications for the development of novel treatment strategies.

Endogenous androgen receptor proteomic profiling reveals genomic subcomplex involved in prostate tumorigenesis

Androgen receptor (AR) is a key player in prostate cancer development and progression. Here we applied immunoprecipitation mass spectrometry of endogenous AR in LNCaP cells to identify components of the AR transcriptional complex. In total, 66 known and novel AR interactors were identified in the presence of synthetic androgen, most of which were critical for AR-driven prostate cancer cell proliferation. A subset of AR interactors required for LNCaP proliferation were profiled using chromatin immunoprecipitation assays followed by sequencing, identifying distinct genomic subcomplexes of AR interaction partners. Interestingly, three major subgroups of genomic subcomplexes were identified, where selective gain of function for AR genomic action in tumorigenesis was found, dictated by FOXA1 and HOXB13. In summary, by combining proteomic and genomic approaches we reveal subclasses of AR transcriptional complexes, differentiating normal AR behavior from the oncogenic state. In this process, the expression of AR interactors has key roles by reprogramming the AR cistrome and interactome in a genomic location-specific manner.

Androgen receptor profiling predicts prostate cancer outcome

Prostate cancer is the second most prevalent malignancy in men. Biomarkers for outcome prediction are urgently needed, so that high-risk patients could be monitored more closely postoperatively. To identify prognostic markers and to determine causal players in prostate cancer progression, we assessed changes in chromatin state during tumor development and progression. Based on this, we assessed genomewide androgen receptor/chromatin binding and identified a distinct androgen receptor/chromatin binding profile between primary prostate cancers and tumors with an acquired resistance to therapy. These differential androgen receptor/chromatin interactions dictated expression of a distinct gene signature with strong prognostic potential. Further refinement of the signature provided us with a concise list of nine genes that hallmark prostate cancer outcome in multiple independent validation series. In this report, we identified a novel gene expression signature for prostate cancer outcome through generation of multilevel genomic data on chromatin accessibility and transcriptional regulation and integration with publically available transcriptomic and clinical datastreams. By combining existing technologies, we propose a novel pipeline for biomarker discovery that is easily implementable in other fields of oncology.

Comparative Cistromics Reveals Genomic Cross-talk between FOXA1 and ERα in Tamoxifen-Associated Endometrial Carcinomas

Tamoxifen, a small-molecule antagonist of the transcription factor estrogen receptor alpha (ERα) used to treat breast cancer, increases risks of endometrial cancer. However, no parallels of ERα transcriptional action in breast and endometrial tumors have been found that might explain this effect. In this study, we addressed this issue with a genome-wide assessment of ERα-chromatin interactions in surgical specimens obtained from patients with tamoxifen-associated endometrial cancer. ERα was found at active enhancers in endometrial cancer cells as marked by the presence of RNA polymerase II and the histone marker H3K27Ac. These ERα binding sites were highly conserved between breast and endometrial cancer and enriched in binding motifs for the transcription factor FOXA1, which displayed substantial overlap with ERα binding sites proximal to genes involved in classical ERα target genes. Multifactorial ChIP-seq data integration from the endometrial cancer cell line Ishikawa illustrated a functional genomic network involving ERα and FOXA1 together with the enhancer-enriched transcriptional regulators p300, FOXM1, TEAD4, FNFIC, CEBP8, and TCF12. Immunohistochemical analysis of 230 primary endometrial tumor specimens showed that lack of FOXA1 and ERα expression was associated with a longer interval between breast cancer and the emergence of endometrial cancer, exclusively in tamoxifen-treated patients. Our results define conserved sites for a genomic interplay between FOXA1 and ERα in breast cancer and tamoxifen-associated endometrial cancer. In addition, FOXA1 and ERα are associated with the interval time between breast cancer and endometrial cancer only in tamoxifen-treated breast cancer patients. Cancer Res; 76(13); 3773-84. ©2016 AACR.

Abstract P6-08-06: Neoadjuvant tamoxifen therapy synchronizes ERα binding and gene expression profiles

Background: The majority of breast cancer patients are diagnosed with ERα-positive breast cancer. Most ERα-positive patients are treated with adjuvant endocrine therapy — typically tamoxifen or aromatase inhibitors — to block cellular proliferation. Although these treatments are considered successful, resistance is common. Notably, cross-resistance between the two types of therapies is not always observed suggesting molecular heterogeneity and underlining the need for development of personalized treatments. The Anastrozole, Fulvestrant or Tamoxifen Exposure — Response in molecular profile study (AFTER study, NCT00738777) aims to investigate prospectively whether short-term treatment can induce molecular changes indicative of pre-operative therapy response. Study Design: ERα-positive breast cancer patients are included in this open-label multicenter study. Post-menopausal patients are randomized between tamoxifen, anastrozole and fulvestrant and pre-menopausal and male patients receive tamoxifen. Treatment occurs during the pre-operative window between diagnosis and surgery (4±2 weeks). Clinical characteristics collected are ERα/PR and HER2 status as well as lymph-node status. The primary endpoint is the decrease in tumor cell proliferation, as assessed by Ki67 gene expression and published cell proliferation gene expression signatures. All data are collected from both pre- and post-treatment samples. Additionally, we will compare the changes induced by treatment in gene expression, ERα/DNA binding interactions, DNA copy number, endoxifen and estradiol levels. Results: Among 67 patients currently enrolled, we examined the data from the subset of 28 tamoxifen treated patients. ERα and PR levels did not differ significantly between pre- and post-treatment. All tumors were HER2-negative. Proliferation examined by Ki67 (IHC and gene expression, MKI67) was significantly lower in post-treatment samples (P &lt; 0.01). A significant association was identified with the change in gene expression proliferation signature score and change in MKI67 (rho = 0.7, P &lt; 0.001). We identified two samples, which changed from MammaPrint (MP) low-risk to high-risk among 17 pairs with data. One sample's score was on the cutoff for high-risk definition. Interestingly, the second sample also had an increase in Ki67 gene expression and proliferation gene signature score in the post-treatment sample. Overall, ERα/DNA binding interaction regions overlapped significantly more among post-treatment samples as compared to pre-treatment samples (P &lt;0.001). There were 3 samples that increased in MKI67 gene expression after drug exposure. Among these, only the MP low- to high-risk sample had an increase in proliferation gene signature and decrease in ERα/DNA binding interactions. Conclusions: Pre-treatment samples were more variable for both proliferation gene expression signatures and ERα/DNA binding interactions indicating the underlying molecular heterogeneity of the group prior to therapy. This inter-tumor heterogeneity appears to have been lowered by exposure to tamoxifen. Interestingly, not all samples were uniform in their response to tamoxifen exposure as measured by Ki67 and MP scores suggesting samples taken after treatment exposure may be useful for predictive biomarker discovery.

Citation Format: Linn SC, Severson TM, Nevedomskaya E, Peeters J, van Rossum A, Kuilman T, Krijgsman O, Goossens I, Glas A, Koornstra R, Peeper D, Wesseling J, Simon I, Wessels L, Zwart W. Neoadjuvant tamoxifen therapy synchronizes ERα binding and gene expression profiles. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-08-06.

Mastermind-Like 3 Controls Proliferation and Differentiation in Neuroblastoma

Neuroblastoma cell lines can differentiate upon treatment with retinoic acid (RA), a finding that provided the basis for the clinical use of RA to treat neuroblastoma. However, resistance to RA is often observed, which limits its clinical utility. Using a gain-of-function genetic screen, we identified an unexpected link between RA signaling and mastermind-like 3 (MAML3), a known transcriptional coactivator for NOTCH. Our findings indicate that MAML3 expression leads to the loss of activation of a subset of RA target genes, which hampers RA-induced differentiation and promotes resistance to RA. The regulatory DNA elements of this subset of RA target genes show overlap in binding of MAML3 and the RA receptor, suggesting a direct role for MAML3 in the regulation of these genes. In addition, MAML3 has RA-independent functions, including the activation of IGF1R and downstream AKT signaling via upregulation of IGF2, resulting in increased proliferation. These results demonstrate an important mechanistic role for MAML3 in proliferation and RA-mediated differentiation.

IMPLICATIONS

MAML3 coordinates transcription regulation with receptor tyrosine kinase pathway activation, shedding new light on why this gene is mutated in multiple cancers. Mol Cancer Res; 14(5); 411-22. ©2016 AACR.

SRC3 Phosphorylation at Serine 543 Is a Positive Independent Prognostic Factor in ER-Positive Breast Cancer

PURPOSE

The steroid receptor coactivator SRC3 is essential for the transcriptional activity of estrogen receptor α (ERα). SRC3 is sufficient to cause mammary tumorigenesis, and has also been implicated in endocrine resistance. SRC3 is posttranslationally modified by phosphorylation, but these events have not been investigated with regard to functionality or disease association. Here, we investigate the spatial selectivity of SRC3-pS543/DNA binding over the human genome and its expression in primary human breast cancer in relation with outcome.

EXPERIMENTAL DESIGN

Chromatin immunoprecipitation, coupled with sequencing, was used to determine the chromatin binding patterns of SRC3-pS543 in the breast cancer cell line MCF7 and two untreated primary breast cancers. IHC was used to assess the expression of SRC3 and SRC3-pS543 in 1,650 primary breast cancers. The relationship between the expression of SRC3 and SRC3-pS543, disease-free survival (DFS), and breast cancer specific survival (BCSS) was assessed.

RESULTS

Although total SRC3 is selectively found at enhancer regions, SRC3-pS543 is recruited to promoters of ERα responsive genes, both in the MCF7 cell line and primary breast tumor specimens. SRC3-pS543 was associated with both improved DFS (P = 0.003) and BCSS (P = 0.001) in tamoxifen untreated high-risk patients, such a correlation was not seen in tamoxifen-treated cases, the interaction was statistically significant (P = 0.001). Multivariate analysis showed SRC3-pS543 to be an independent prognostic factor.

CONCLUSIONS

Phosphorylation of SRC3 at S543 affects its genomic interactions on a genome-wide level, where SRC3-pS543 is selectively recruited to promoters of ERα-responsive genes. SRC3-pS543 is a prognostic marker, and a predictive marker of response to endocrine therapy.

Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

Systematic identification of noncoding regulatory elements has, to date, mainly relied on large-scale reporter assays that do not reproduce endogenous conditions. We present two distinct CRISPR-Cas9 genetic screens to identify and characterize functional enhancers in their native context. Our strategy is to target Cas9 to transcription factor binding sites in enhancer regions. We identified several functional enhancer elements and characterized the role of two of them in mediating p53 (TP53) and ERα (ESR1) gene regulation. Moreover, we show that a genomic CRISPR-Cas9 tiling screen can precisely map functional domains within enhancer elements. Our approach expands the utility of CRISPR-Cas9 to elucidate the functions of the noncoding genome.

Androgen receptor DNA binding and chromatin accessibility profiling in prostate cancer

Prostate cancer (PCa) is the second most common cancer in men. The Androgen Receptor (AR) is the major driver of PCa and the main target of therapy in the advanced setting. AR is a nuclear receptor that binds the chromatin and regulates transcription of genes involved in cancer cell proliferation and survival. In a study by Stelloo et al. (1) we explored prostate cancer on the level of transcriptional regulation by means of Formaldehyde-Assisted Isolation of Regulatory Elements and Chromatin Immunoprecipitation coupled with massive parallel sequencing (FAIRE-seq and ChIP-seq, respectively). We employed these data for the assessment of differences in transcriptional regulation at distinct stages of PCa progression and to construct a prognostic gene expression classifier. Genomics data includes FAIRE-seq data from normal prostate tissue as well as primary, hormone therapy resistant and metastatic PCa. Furthermore, ChIP-seq data from primary and resistant PCa were generated, along with multiple input controls. The data are publicly available through NCBI GEO database with accession number GSE65478. Here we describe the genomics and clinical data in detail and provide comparative analysis of FAIRE-seq and ChIP-seq data.

A Systems Oncology Approach Identifies NT5E as a Key Metabolic Regulator in Tumor Cells and Modulator of Platinum Sensitivity

Altered metabolism in tumor cells is required for rapid proliferation but also can influence other phenotypes that affect clinical outcomes such as metastasis and sensitivity to chemotherapy. Here, a genome-wide association study (GWAS)-guided integration of NCI-60 transcriptome and metabolome data identified ecto-5'-nucleotidase (NT5E or CD73) as a major determinant of metabolic phenotypes in cancer cells. NT5E expression and associated metabolome variations were also correlated with sensitivity to several chemotherapeutics including platinum-based treatment. NT5E mRNA levels were observed to be elevated in cells upon in vitro and in vivo acquisition of platinum resistance in ovarian cancer cells, and specific targeting of NT5E increased tumor cell sensitivity to platinum. We observed that tumor NT5E levels were prognostic for outcomes in ovarian cancer and were elevated after treatment with platinum, supporting the translational relevance of our findings. In this work, we integrated and analyzed a plethora of public data, demonstating the merit of such a systems oncology approach for the discovery of novel players in cancer biology and therapy. We experimentally validated the main findings of the NT5E gene being involved in both intrinsic and acquired resistance to platinum-based drugs. We propose that the efficacy of conventional chemotherapy could be improved by NT5E inhibition and that NT5E expression may be a useful prognostic and predictive clinical biomarker.

APOBEC3B-Mediated Cytidine Deamination Is Required for Estrogen Receptor Action in Breast Cancer

Estrogen receptor α (ERα) is the key transcriptional driver in a large proportion of breast cancers. We report that APOBEC3B (A3B) is required for regulation of gene expression by ER and acts by causing C-to-U deamination at ER binding regions. We show that these C-to-U changes lead to the generation of DNA strand breaks through activation of base excision repair (BER) and to repair by non-homologous end-joining (NHEJ) pathways. We provide evidence that transient cytidine deamination by A3B aids chromatin modification and remodelling at the regulatory regions of ER target genes that promotes their expression. A3B expression is associated with poor patient survival in ER+ breast cancer, reinforcing the physiological significance of A3B for ER action.

Abstract 5075: The composition and interactions in the microenvironment of human prostate cancer

Background: Prostate cancer is a heterogeneous disease both genetically and in its clinical behavior. It is widely accepted that a tumor does not only consist of cancer cells but also contains many other non-malignant cells, including immune cells and cancer associated fibroblasts. These non-malignant cells create the tumor microenvironment. It is previously suggested that the tumor microenvironment modulates the behavior of various cancers, including prostate cancer. Little is known about the exact interactions between prostate cancer cells and its micro environment. In this study we aim to gain insight into the composition of the microenvironment and the interaction between malignant and non-malignant cells. Moreover, these interactions might hold a predictive signature for disease progression and metastatic disease.

Methods: Biopsies were obtained from Formalin Fixed Paraffin Embedded (FFPE) human prostate cancers from 10 patients with pelvic lymph node metastases and 10 gleason score (7-8-9) matched patients with non-metastatic disease. RNA was isolated from the FFPE samples and sequenced. A tissue micro array was constructed from the same prostate cancers. Fresh prostate cancer biopsies were taken right after radical prostatectomy, and fibroblast cells were isolated for short term culture.

Results: The RNA sequencing of FFPE prostate biopsies revealed an increased expression of cancer related stroma genes in tumor tissue compared to non-tumorous tissue. Presence of various cell types was confirmed by immunohistochemistry (IHC). The subtypes of various immune cell populations could be identified, including regulatory T cells and pro-tumorous M2-like macrophages. The percentage of M2-like macrophages identified by the CD163 marker showed a significant increase in tumor tissue compared to non-tumorous tissue, which was unique for patients with metastatic disease. Furthermore we could confirm that decreased stromal Androgen Receptor (AR) expression correlated with disease progression and also correlated with metastatic disease. To investigate which stromal cells were AR positive we performed double stainings of PDGFR beta and AR. Costaining of both markers confirmed AR expression in fibroblasts. The stromal cells cultured from the fresh prostate cancer biopsies were morphologically fibroblasts and expressed AR, Smooth Muscle Actin and PDGFR beta, suggesting a cancer associated phenotype. Testosterone stimulation of these fibroblasts showed increased chromatin binding of the AR. This suggests that the AR is functional in these cancer associated fibroblasts.

Conclusions: This study gained insight into the composition of the prostate cancer microenvironment. The increased expression of CD163 and the decreased expression of stromal AR was related to pelvic lymph node metastases.

Citation Format: Monique Melis, Bianca Cioni, Ekaterina Nevedomskaya, Johan van Burgsteden, Emma Hodel, Annegien Broeks, Henk van der Poel, Jeroen de Jong, Andre Bergman. The composition and interactions in the microenvironment of human prostate cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5075. doi:10.1158/1538-7445.AM2015-5075

CopywriteR: DNA copy number detection from off-target sequence data

Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting 'off-target' sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools.

Exploratory analysis of urinary tract infection using a GC-APCI-MS platform

This study shows the first application of GC-APCI-MS in a clinical setting specifically in the context of urinary tract infection.

Phosphorylation of activating transcription factor-2 (ATF-2) within the activation domain is a key determinant of sensitivity to tamoxifen in breast cancer

Activating transcription factor-2 (ATF-2) has been implicated as a tumour suppressor in breast cancer (BC). c-JUN N-terminal kinase (JNK) and p38 MAPK phosphorylate ATF-2 within the activation domain (AD), which is required for its transcriptional activity. To date, the role of ATF-2 in determining response to endocrine therapy has not been explored. Effects of ATF-2 loss in the oestrogen receptor (ER)-positive luminal BC cell line MCF7 were explored, as well as its role in response to tamoxifen treatment. Genome-wide chromatin binding patterns of ATF-2 when phosphorylated within the AD in MCF-7 cells were determined using ChIP-seq. The expression of ATF-2 and phosphorylated ATF-2 (pATF-2-Thr71) was determined in a series of 1,650 BC patients and correlated with clinico-pathological features and clinical outcome. Loss of ATF-2 diminished the growth-inhibitory effects of tamoxifen, while tamoxifen treatment induced ATF-2 phosphorylation within the AD, to regulate the expression of a set of 227 genes for proximal phospho-ATF-2 binding, involved in cell development, assembly and survival. Low expression of both ATF-2 and pATF-2-Thr71 was significantly associated with aggressive pathological features. Furthermore, pATF-2 was associated with both p-p38 and pJNK1/2 (< 0.0001). While expression of ATF-2 is not associated with outcome, pATF-2 is associated with longer disease-free (p = 0.002) and BC-specific survival in patients exposed to tamoxifen (p = 0.01). Furthermore, multivariate analysis confirmed pATF-2-Thr71 as an independent prognostic factor. ATF-2 is important for modulating the effect of tamoxifen and phosphorylation of ATF-2 within the AD at Thr71 predicts for improved outcome for ER-positive BC receiving tamoxifen.

Complex formation and function of estrogen receptor α in transcription requires RIP140

RIP140 is a transcriptional coregulator involved in energy homeostasis, ovulation, and mammary gland development. Although conclusive evidence is lacking, reports have implicated a role for RIP140 in breast cancer. Here, we explored the mechanistic role of RIP140 in breast cancer and its involvement in estrogen receptor α (ERα) transcriptional regulation of gene expression. Using ChIP-seq analysis, we demonstrate that RIP140 shares more than 80% of its binding sites with ERα, colocalizing with its interaction partners FOXA1, GATA3, p300, CBP, and p160 family members at H3K4me1-demarcated enhancer regions. RIP140 is required for ERα-complex formation, ERα-mediated gene expression, and ERα-dependent breast cancer cell proliferation. Genes affected following RIP140 silencing could be used to stratify tamoxifen-treated breast cancer cohorts, based on clinical outcome. Importantly, this gene signature was only effective in endocrine-treated conditions. Cumulatively, our data suggest that RIP140 plays an important role in ERα-mediated transcriptional regulation in breast cancer and response to tamoxifen treatment.

Genome-wide epigenetic profiling of breast cancer tumors treated with aromatase inhibitors

Aromatase inhibitors (AI) are extensively used in the treatment of estrogen receptor-positive breast cancers, however resistance to AI treatment is commonly observed. Apart from Estrogen receptor (ERα) expression, no predictive biomarkers for response to AI treatment are clinically applied. Yet, since other therapeutic options exist in the clinic, such as tamoxifen, there is an urgent medical need for the development of treatment-selective biomarkers, enabling personalized endocrine treatment selection in breast cancer. In the described dataset, ERα chromatin binding and histone marks H3K4me3 and H3K27me3 were assessed in a genome-wide manner by Chromatin Immunoprecipitation (ChIP) combined with massive parallel sequencing (ChIP-seq). These datasets were used to develop a classifier to stratify breast cancer patients on outcome after AI treatment in the metastatic setting. Here we describe in detail the data and quality control metrics, as well as the clinical information associated with the study, published by Jansen et al. [1]. The data is publicly available through the GEO database with accession number GSE40867.

VAV3 mediates resistance to breast cancer endocrine therapy

Introduction

Endocrine therapies targeting cell proliferation and survival mediated by estrogen receptor α (ERα) are among the most effective systemic treatments for ERα-positive breast cancer. However, most tumors initially responsive to these therapies acquire resistance through mechanisms that involve ERα transcriptional regulatory plasticity. Herein we identify VAV3 as a critical component in this process.

Methods

A cell-based chemical compound screen was carried out to identify therapeutic strategies against resistance to endocrine therapy. Binding to ERα was evaluated by molecular docking analyses, an agonist fluoligand assay and short hairpin (sh)RNA–mediated protein depletion. Microarray analyses were performed to identify altered gene expression. Western blot analysis of signaling and proliferation markers, and shRNA-mediated protein depletion in viability and clonogenic assays, were performed to delineate the role of VAV3. Genetic variation in VAV3 was assessed for association with the response to tamoxifen. Immunohistochemical analyses of VAV3 were carried out to determine its association with therapeutic response and different tumor markers. An analysis of gene expression association with drug sensitivity was carried out to identify a potential therapeutic approach based on differential VAV3 expression.

Results

The compound YC-1 was found to comparatively reduce the viability of cell models of acquired resistance. This effect was probably not due to activation of its canonical target (soluble guanylyl cyclase), but instead was likely a result of binding to ERα. VAV3 was selectively reduced upon exposure to YC-1 or ERα depletion, and, accordingly, VAV3 depletion comparatively reduced the viability of cell models of acquired resistance. In the clinical scenario, germline variation in VAV3 was associated with the response to tamoxifen in Japanese breast cancer patients (rs10494071 combined P value = 8.4 × 10⁻⁴). The allele association combined with gene expression analyses indicated that low VAV3 expression predicts better clinical outcome. Conversely, high nuclear VAV3 expression in tumor cells was associated with poorer endocrine therapy response. Based on VAV3 expression levels and the response to erlotinib in cancer cell lines, targeting EGFR signaling may be a promising therapeutic strategy.

Conclusions

This study proposes VAV3 as a biomarker and a rationale for its use as a signaling target to prevent and/or overcome resistance to endocrine therapy in breast cancer.

(1)H NMR-based metabolic profiling of urinary tract infection: combining multiple statistical models and clinical data

Urinary tract infection (UTI) encompasses a variety of clinical syndromes ranging from mild to life-threatening conditions. As such, it represents an interesting model for the development of an analytically based scoring system of disease severity and/or host response. Here we test the feasibility of this concept using (1)H NMR based metabolomics as the analytical platform. Using an exhaustively clinically characterized cohort and taking advantage of the multi-level study design, which opens possibilities for case-control and longitudinal modeling, we were able to identify molecular discriminators that characterize UTI patients. Among those discriminators a number (e.g. acetate, trimethylamine and others) showed association with the degree of bacterial contamination of urine, whereas others, such as, for instance, scyllo-inositol and para-aminohippuric acid, are more likely to be the markers of morbidity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-012-0411-y) contains supplementary material, which is available to authorized users.

Fibrinogen alpha chain O-glycopeptides as possible markers of urinary tract infection

Urinary tract infection (UTI) is the most common bacterial infection leading to substantial morbidity and considerable health care expenditures across all ages. Here we present an exploratory UPLC-MS study of human urine in the context of febrile, complicated urinary tract infection aimed to reveal and identify possible markers of a host response on infection. A UPLC-MS based workflow, taking advantage of Ultra High Resolution (UHR) Qq-ToF-MS, and multivariate data handling were applied to a carefully selected group of 39 subjects with culture-confirmed febrile Escherichia coli UTI. Using a combination of unsupervised and supervised multivariate modeling we have pinpointed a number of peptides specific for UTI. An unequivocal structural identification of these peptides, as O-glycosylated fragments of the human fibrinogen alpha 1 chain, required MS2 and MS3 experiments on two different MS platforms: ESI-UHR-Qq-ToF and ESI-ion trap, a blast search and, finally, confirmation was achieved by matching experimental tandem mass spectra with those of custom synthesized candidate-peptides. In conclusion, exploiting non-targeted UPLC-MS based approach for the investigation of UTI related changes in urine, we have identified and structurally characterized unique O-glycopeptides, which are, to our knowledge, the first demonstration of O-glycosylation of human fibrinogen alpha 1-chain.

Cross-platform analysis of longitudinal data in metabolomics

Metabolic profiling is considered to be a very promising tool for diagnostic purposes, for assessing nutritional status and response to drugs. However, it is also evident that human metabolic profiles have a complex nature, influenced by many external factors. This, together with the understanding of the difficulty to assign people to distinct groups and a general move in clinical science towards personalized medicine, raises the interest to explore individual and variable metabolic features for each individual separately in longitudinal study design. In the current paper we have analyzed a set of metabolic profiles of a selection of six urine samples per person from a set of healthy individuals by (1)H NMR and reversed-phase UPLC-MS. We have demonstrated that the method for recovery of individual metabolic phenotypes can give complementary information to another established method for analysis of longitudinal data--multilevel component analysis. We also show that individual metabolic signatures can be found not only in (1)H NMR data, as has been demonstrated before, but also even more strongly in LC-MS data.

CE-MS for metabolic profiling of volume-limited urine samples: application to accelerated aging TTD mice

Metabolic profiling of biological samples is increasingly used to obtain more insight into the pathophysiology of diseases. For translational studies, biological samples from animal models are explored; however, the volume of these samples can be a limiting factor for metabolic profiling studies. For instance, only a few microliters of urine is often available from small animals like mice. Hence, there is a need for a tailor-made analytical method for metabolic profiling of volume-limited samples. In the present study, the feasibility of capillary electrophoresis time-of-flight mass spectrometry (CE-ToF-MS) for metabolic profiling of urine from mice is evaluated. Special attention is paid to the analytical workflow; that is, such aspects as sample preparation, analysis, and data treatment are discussed from the metabolomics viewpoint. We show that metabolites belonging to several chemical families can be analyzed in mouse urine with the CE-ToF-MS method using minimal sample pretreatment and an in-capillary preconcentration procedure. This exemplifies the advantages of CE-ToF-MS for metabolic profiling of volume-limited samples as loss of material is minimized. The feasibility of the CE-ToF-MS-based workflow for metabolic profiling is illustrated by the analysis of urine samples from wild-type as well as from TTD mutant mice, which are a model for the accelerated aging, with osteoporosis being one of the main hallmarks.

Evaluation of GC-APCI/MS and GC-FID as a complementary platform

With a development of the metabolomics field, complementary cross-platform approaches started to attract attention, as none of the contemporary analytical methods had the capacity to cover the entire space of the human metabolome. In the current manuscript, we have evaluated an online coupling of gas chromatography (GC)-mass spectrometry (MS) and flame ionization detector (FID) as ways of cross-detector analysis. The possible value of this combination was recognized from the very first days of GC-MS history but was never explored in detail. We have compared the basic analytical parameters of both detectors, such as limit of detection (LOD) and limit of quantification, with intra- and interday reproducibility. We show that for the majority of the tested compounds, MS detector demonstrates lower LOD. At the same time, FID appeared to be more robust, showing lower relative standard deviations (RSDs) for intra- and interday reproducibility. We conclude that the gain of this dual detector acquisition appears to be most evident for complex biological samples, where wide dynamic range and predictable response of FID are useful for an initial quantitative overview of sample composition and estimation of molar proportions of different metabolites. MS provides reliable, structural information and superior, at least in the case of atmospheric pressure chemical ionization, sensitivity. Taken together, both detectors represent a flexible tool for explorative studies and if supported by a powerful data-processing algorithm, would appear to be useful in any metabolic profiling study.