Abstract 4261: Development of quantitative multi-platform tests for easy readout of AR, ER, PI3K and MAPK pathway activity to unravel pathophysiology across cancer and tissue types

Introduction: Currently, the selection of targeted therapy is commonly based on genetic data, such as well-known gene mutations, but these mutations do not provide conclusive evidence for the functional activation of the affected pathway. For this reason, we have developed computational models to assess the molecular phenotype of individual tumors, determining the functional activity of oncogenic signaling pathways based on mRNA expression levels of the direct target genes of the respective pathway transcription factors (Verhaegh et al., Cancer Res 2014; Van Ooijen et al., Am J Pathol 2018; Van de Stolpe et al., Sci Rep 2019). For a broader application of these models, we translated them to RT-qPCR, RNA sequencing and microarray tests, for a quantitative and reproducible assessment of signaling pathway activity.

Materials and methods: Focusing on the AR, ER, PI3K-FOXO and MAPK-AP1 pathways, we developed PCR primers and probes to assess mRNA expression levels of the pathways' direct target genes. For model parameter calibration, we performed controlled cell line experiments in which the respective pathways were inactivated and activated, to have calibration samples with known pathway activity status. Per pathway, the same set of calibration samples and the same set of target genes were used to develop RT-qPCR, RNA sequencing and microarray tests, to maximize similarity. The resulting OncoSignal tests can be used for a quantitative assessment of pathway activity on individual samples, giving a score on a 0-100 scale. We verified these tests on independent samples with known pathway status. We ran repeat experiments to assess the reproducibility within each platform, and tested the same samples on all three platforms to assess cross-platform concordance.

Results: Using the OncoSignal score, low activity test samples were clearly separated from highly active ones. For example, AR-PCR scores went from 19±3 on androgen-deprived LNCaP cell lines to 70±2 after stimulation with DHT, and went down again to 33±1 and 23±1 when subsequently treated with bicalutamide and enzalutamide, respectively. PI3K-FOXO-microarray scores went from 12±1 on control MCF7 experiments to 50±4 after alpelisib treatment. Measurements on 100+ samples on all three platforms showed Pearson correlations between 0.93 and 0.99 in OncoSignal scores, with absolute differences typically below 10.

Conclusion: We developed broadly applicable tests to assess AR, ER, PI3K-FOXO and MAPK-AP1 pathway activity in a quantitative manner on individual samples, with good reproducibility on repeat experiments and good concordance between PCR, RNA sequencing and microarray measurements. These tests can be used to unravel disease pathophysiology in (pre-)clinical samples. The added value of OncoSignal for therapy response prediction is currently being evaluated in different studies.

Citation Format: Martijn Akse, Henk van Ooijen, Anke Pierik, Sandra van den Bosch, Hans van Zon, Laurent Holtzer, Anne van Brussel, Márcia Inda, Yvonne Wesseling-Rozendaal, Wim Verhaegh, Eveline den Biezen-Timmermans. Development of quantitative multi-platform tests for easy readout of AR, ER, PI3K and MAPK pathway activity to unravel pathophysiology across cancer and tissue types [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4261.

SPECT/CT imaging of temperature-sensitive liposomes for MR-image guided drug delivery with high intensity focused ultrasound

The goal of this study was to investigate the blood kinetics and biodistribution of temperature-sensitive liposomes (TSLs) for MR image-guided drug delivery. The co-encapsulated doxorubicin and [Gd(HPDO3A)(H₂O)] as well as the ¹¹¹In-labeled liposomal carrier were quantified in blood and organs of tumor bearing rats. After TSL injection, mild hyperthermia (T=42 °C) was induced in the tumor using high intensity focused ultrasound under MR image-guidance (MR-HIFU). The biodistribution of the radiolabeled TSLs was investigated using SPECT/CT imaging, where the highest uptake of ¹¹¹In-labeled TSLs was observed in the spleen and liver. The MR-HIFU-treated tumors showed 4.4 times higher liposome uptake after 48 h in comparison with controls, while the doxorubicin concentration was increased by a factor of 7.9. These effects of HIFU-treatment are promising for applications in liposomal drug delivery to tumors.

Temperature-sensitive liposomes for doxorubicin delivery under MRI guidance

Local drug delivery of doxorubicin holds promise to improve the therapeutic efficacy and to reduce toxicity profiles. Here, we investigated the release of doxorubicin and [Gd(HPDO3A)(H(2)O)] from different temperature-sensitive liposomes for applications in temperature-induced drug delivery under magnetic resonance image guidance. In particular, two temperature-sensitive systems composed of DPPC:MPPC:DPPE-PEG2000 (low temperature-sensitive liposomes, LTSL) and DPPC:HSPC:cholesterol:DPPE-PEG2000 (traditional temperature-sensitive liposomes, TTSL) were investigated. The co-encapsulation of [Gd(HPDO3A)(H(2)O)], a clinically approved MRI contrast agent, did not influence the encapsulation and release of doxorubicin. The LTSL system showed a higher leakage of doxorubicin at 37 degrees C, but a faster release of doxorubicin at 42 degrees C compared to the TTSL system. Furthermore, the rapid release of both doxorubicin and the MRI contrast agent from the liposomes occurred near the melting phase transition temperature, making it possible to image the release of doxorubicin using MRI.

Comparing the DNA hypermethylome with gene mutations in human colorectal cancer

We have developed a transcriptome-wide approach to identify genes affected by promoter CpG island DNA hypermethylation and transcriptional silencing in colorectal cancer. By screening cell lines and validating tumor-specific hypermethylation in a panel of primary human colorectal cancer samples, we estimate that nearly 5% or more of all known genes may be promoter methylated in an individual tumor. When directly compared to gene mutations, we find larger numbers of genes hypermethylated in individual tumors, and a higher frequency of hypermethylation within individual genes harboring either genetic or epigenetic changes. Thus, to enumerate the full spectrum of alterations in the human cancer genome, and to facilitate the most efficacious grouping of tumors to identify cancer biomarkers and tailor therapeutic approaches, both genetic and epigenetic screens should be undertaken.

Loss of gene expression in association with aberrant accumulation of 5-methylcytosine in gene promoter CpG islands is a common feature of human cancer. Here, we describe a method to discover these genes that permits identification of hundreds of novel candidate cancer genes in any cancer cell line. We now estimate that as much as 5% of colon cancer genes may harbor aberrant gene hypermethylation and we term these the cancer “promoter CpG island DNA hypermethylome.” Multiple mutated genes recently identified via cancer resequencing efforts are shown to be within this hypermethylome and to be more likely to undergo epigenetic inactivation than genetic alteration. Our approach allows derivation of new potential tumor biomarkers and potential pathways for therapeutic intervention. Importantly, our findings illustrate that efforts aimed at complete identification of the human cancer genome should include analyses of epigenetic, as well as genetic, changes.