Identification and functional characterization of long non-coding RNAs as epigenetic determinants of therapy resistance in BRAF-driven cancers

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BRAF-mediated activation of the mitogen-activated protein kinase (MAPK) pathway represents an oncogenic hallmark in several cancer types including melanoma (MM) and pilocytic astrocytoma (PA). The contribution of long non-coding RNAs (lncRNA) as regulators of the MAPK pathway and, particularly, of therapy resistance to MAPK inhibition remains poorly understood, but could represent a novel powerful target in oncology. As expression of many lncRNAs is confined to specific developmental programs or cellular states, these transcripts are particularly promising as predictive biomarkers and therapeutic targets. We have successfully established a bioinformatic pipeline to reveal lncRNA candidates in multi-omics datasets in medulloblastomas (mutational data, RNA sequencing and gene expression profiling). Here, we propose to identify and functionally characterize lncRNAs that are specifically expressed in BRAF-mutant tumors and impede the therapeutic response to BRAF inhibitors. We plan to discover the signaling networks that correlate with these lncRNAs using our established systems biology pipeline. While the mutational landscape of MM is highly complex, PA harbors very limited recurrent mutations mostly in BRAF and other MAPK pathway intermediates causing much lower mutational noise in experimental analysis. We will overlay the BRAF-dependent lncRNA expression profiles from primary MM and PA samples. Subsequently, we will determine the cancer-related role of selected lncRNA candidates using functional genomics approaches upon candidate gene overexpression or depletion in patient-derived cell models and established cell lines from PA and MM, the latter being provided by collaborations within the PhenoTImE consortium. Specifically, we will reveal differential lncRNA expression upon BRAF inhibition and then modulate the expression of the most promising lncRNA candidates to potentially overcome drug resistance. Using clinically annotated tumor samples from MM and PA patients, the resulting lncRNA profiles will be also evaluated regarding their potential as predictive biomarkers for therapy. Lastly, we will utilize a systems biology approach for proteogenomic data combined with high-throughput drug screening to identify and validate synergistic combination therapies with MAPK inhibitors to overcome therapy resistance. We expect from these studies straightforward translational rationales for the design of future clinical trials and for the establishment of further translational biomarker programs alongside. The common goals of the Clinical Research Unit PhenoTImE serve as a fundamental basis for a powerful collaborative network with highly complementary expertise to elucidate lncRNAs as crucial modulators of MAPK signaling in BRAF mutant tumors. Likewise, we will contribute our bioinformatic expertise and high-throughput drug screening platform to ensure rapid translation of the profound biological insights into clinical applications.