Logic-based modeling and drug repurposing for the prediction of novel therapeutic targets and combination regimens against E2F1-driven melanoma progression

Melanoma presents increasing prevalence and poor outcomes. Progression to aggressive stages is characterized by overexpression of the transcription factor E2F1 and activation of downstream prometastatic gene regulatory networks (GRNs). Appropriate therapeutic manipulation of the E2F1-governed GRNs holds the potential to prevent metastasis however, these networks entail complex feedback and feedforward regulatory motifs among various regulatory layers, which make it difficult to identify druggable components. To this end, computational approaches such as mathematical modeling and virtual screening are important tools to unveil the dynamics of these signaling networks and identify critical components that could be further explored as therapeutic targets. Herein, we integrated a well-established E2F1-mediated epithelial-mesenchymal transition (EMT) map with transcriptomics data from E2F1-expressing melanoma cells to reconstruct a core regulatory network underlying aggressive melanoma. Using logic-based in silico perturbation experiments of a core regulatory network, we identified that simultaneous perturbation of Protein kinase B (AKT1) and oncoprotein murine double minute 2 (MDM2) drastically reduces EMT in melanoma. Using the structures of the two protein signatures, virtual screening strategies were performed with the FDA-approved drug library. Furthermore, by combining drug repurposing and computer-aided drug design techniques, followed by molecular dynamics simulation analysis, we identified two potent drugs (Tadalafil and Finasteride) that can efficiently inhibit AKT1 and MDM2 proteins. We propose that these two drugs could be considered for the development of therapeutic strategies for the management of aggressive melanoma.

Abstract 1895: A conserved E2F1-activated gene regulatory network encompassing monocarboxylic acid transporter-1, its co-operating antisense lncRNA SLC16A1-AS1 and their common downstream targets mediates bladder cancer invasiveness

AIM: The therapeutic arsenal against muscle-invasive bladder cancer (BC) is poor, leading to fatal outcomes and necessitating next-generation targeted therapeutics. A causative event of BC progression is activation of the gene regulatory networks (GRN) of the transcription factor E2F1. LncRNAs are emerging integral components of the E2F1-regulated GRNs, but their implication in BC progression is unknown. Our study focuses on lncRNAs that participate in E2F1-activated GRNs underlying BC progression and the therapeutic exploitation thereof.

METHODS: We applied bioinformatics on BC patient cohorts to identify clinically relevant lncRNAs upregulated in invasive stages. Of those, the E2F1-responsive lncRNAs were defined by subjecting T24 clones inducibly overexpressing E2F1 to HTA2.0 RNA arrays. Candidates in close proximity to oncogenes/tumor-suppressors were further selected, based on an emerging “guilt-by-association” rule of lncRNA biology. LncRNAs were qPCR-validated and E2F1-transactivation was shown by ChIP and reporter assays. The SLC16A1-AS1 lncRNA was functionally characterized by CRISPR/Cas9 knockout in invasive BC cells, followed by migration/invasion/metabolic assays, transcriptomics and mice in vivo experimentation. SLC16A1-AS1 homologues across species were predicted by comparative genomics.

RESULTS: Our pipeline unveiled SLC16A1-AS1 lncRNA located nearby and antisense to SLC16A1 protein-coding gene. SLC16A1 synthesizes the membrane-bound Monocarboxylic Acid Transporter-1 (MCT1), a key metabolic regulator that mediates lactate uptake and glycolytic flux and favors BC invasiveness; while SLC16A1-AS1 function was unknown to date. SLC16A1 and SLC16A1-AS1 present a ‘head-to-head’ gene arrangement, with a bidirectional E2F1-responsive promoter. This ‘operon-like’ gene cluster is conserved across mammals, implying functional relevance of MCT1/E2F1/SLC16A1-AS1. In invasive BC cells, E2F1 transactivates SLC16A1-AS1, which remains in the nucleus exerting gene regulatory functions, as well as MCT1, which localizes in the cytoplasm to control lactate flux. SLC16A1-AS1 induces EMT-independent invasiveness by regulating expression of downstream cell migration-related targets which are co-modulated by MCT1.

CONCLUSIONS: MCT1 and SLC16A1-AS1 constitute a composite, E2F1-responsive functional unit, co-operatively regulating common cell-migration related downstream targets. Their conserved gene arrangement, which ensures simultaneous transcription upon E2F1 upregulation, could facilitate co-ordination between metabolism reprogramming and cell migration to establish aggressive phenotypes. Combining SLC16A1-AS1 suppression with formulated MCT1 inhibitors might provide a therapeutic basis against progressive BC.

Citation Format: Berdien A. Jansen, Stella Logotheti, Dirk Heckl, Jan-Henning Klusmann, Dirk Kozcan, Laila Taher, Georg Fuellen, David Engelmann, Brigitte Pützer. A conserved E2F1-activated gene regulatory network encompassing monocarboxylic acid transporter-1, its co-operating antisense lncRNA SLC16A1-AS1 and their common downstream targets mediates bladder cancer invasiveness [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1895. doi:10.1158/1538-7445.AM2017-1895

Comprehensive genomic profiles of small cell lung cancer

We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Δex2/3. In rare cases, SCLC tumours exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signalling in a pre-clinical SCLC mouse model strikingly reduced the number of tumours and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.