The section Molecular Cell Biology (Prof. Hüttelmaier) characterizes RNA-guided mechanisms controlling gene expression in cancer. These studies center on RNA-binding proteins (RBPs) as well as non-coding RNAs, such as microRNAs.  The main goals of this research are to identify, evaluate and progress (1) new biomarkers for tumor diagnostics, (2) therapeutic targets, as well as (3) therapeutic concepts for targeted cancer therapy based on small molecule drugs and circular RNAs.

Main Projects

The human IGF2 mRNA binding protein (IGF2BPs) family comprises three members, IGF2BP1-3. IGF2BP1 und 3 are bona fide oncofetal proteins. They are highly abundant  in embryogenesis, barely observed in adult tissues, but severely upregulated or even de novo synthesized in several cancers. In various tumor models, IGF2BP1/3 promote tumor growth and metastasis by regulating mRNA turnover and translation. Our recent work unravels the huge potential of IGF2BP1 and 3 in cancer diagnosis, especially aggressive cancer subtypes, and their suitability as targets for cancer therapy. In current studies, we further characterize the molecular basis of IGF2BP function in cancer. These studies aim to set the stage and support ongoing efforts to develop IGF2BP-centered targeted therapies  based on small molecule drugs as well as PROTACs (proteolysis targeting chimeras).  Main cancers this research focuses on comprise lung cancer, neuroblastoma, ovarian cancer, pancreatic cancer, and anaplastic thyroid cancer.

Open positions (Master, PhD students, Postdocs as well as Technicians)

MicroRNAs (miRNAs) control the vast majority of mRNAs by promoting their decay and impairing translation. In tumors a variety of oncomiRs have been identified. Their main role is to interfere with the expression of tumor suppressors. In tumor models, we recently have demonstrated that such oncomiRs can be inhibited by circular RNA decoys (ciRs). Application of ciRs formulated in polymeric nanoparticles are effectively transported in cancer cells where they reprogram gene expression – of major interest is the reactivation of tumor suppressor synthesis. This is associated with severely reduced tumor growth in animal tumor models. Current projects aim to identify oncomiRs druggable by ciRs and to improve the efficiency and applicability of ciR-based therapies in cancer treatment. Main cancers this research focuses on comprise lung carcinomas, neuroblastoma, ovarian cancer, pancreatic cancer, and anaplastic thyroid carcinoma.

Open positions (Master, PhD students, Postdocs as well as Technicians)

Identification and characterization of oncoRBPs

The characterization of IGF2 mRNA binding proteins (IGF2BPs) in cancer unraveled the huge diagnostic and therapeutic potential of RBPs in cancer therapy. RBPs promoting cancer initiation and/or progression, like IGF2BPs, are termed oncoRBPs. In current projects, we aim to identify additional oncoRBPs in solid cancers and evaluate their suitability as diagnostic markers and therapeutic targets in cancer treatment. Next to IGF2BPs, these studies currently focus on the MEX3 und MSI RBP families and the following cancers: lung carcinomas, neuroblastoma, ovarian cancer, pancreatic cancer, and anaplastic thyroid carcinoma.

Therapeutic inhibition of oncoRBPs by covalent inhibitors

The inhibition of oncoRBPs remains challenging due to the common lack of catalytic activity and high conservation of RNA-binding domains. To overcome these limitations, we develop an innovative and efficient approach based on developing RBP-inhibitors utilizing covalent protein modification. Preliminary studies already led to a covalent IGF2BP1 inhibitor, termed J5 (EU-Patent application, EP20159945) and initiated the development of covalent PROTACs (proteolysis targeting chimera).

Therapeutic inhibition of oncoRBPs by reversible inhibitors

Next to covalent inhibitors, we established interdisciplinary research efforts aiming to develop reversible inhibitors of oncoRBPs, mainly IGF2BPs. In current studies the therapeutic potential of such inhibitors (lead compounds) was validated in experimental animal tumor models. Current projects aim to improve the potency, efficacy and specificity of these lead compounds. Next to the direct inhibition of protein function, we also evaluate PROTACs (proteolysis targeting chimera) to induce degradation of target oncoRBPs.

OncoRBP-Inhibitors in combined therapies

Oncofetal RBPs (oncoRBPs) regulate various cancer hallmark pathways. In recent analyses, we could demonstrate that oncoRBPs not only promote tumor cell proliferation and impair apoptosis, but also promote tumor cell immune evasion (Dr. Bley). In current studies, we characterize the molecular mechanisms underlying these regulatory roles.  These efforts set the stage to explore the synergy of oncoRBPs inhibition with other targeted cancer therapies, including PD-L1/PD1 immunotherapies.


 

Open positions (Master, PhD students, Postdocs as well as Technicians)

The RNA-binding protein RAVER1 was described by Hüttelmaier et al. in 2001. RAVER1 associates with the splicing regulator PTB in membrane-free (liquid droplet-like) perinucleolar compartments (PNC) and influences alternative splicing. In cancer models, RAVER1 serves pro-oncogenic roles involving the regulation of interferon-, NFKB-, and potentially TP53-signaling. In studies funded within the framework of the RTG2467, the role of RAVER1 in cancer and its regulation via intrinsically disordered regions (IDRs), mediating association with PTB, is investigated.

Open positions (Master, PhD students, Postdocs as well as Technicians)

RNA-binding proteins (RBPs) are key modulators of tumor cell fate and influence inflammatory signaling. Studies funded within the framework of the RTG2751 , aim to characterize the role of RBPs in early, inflammation-driven carcinogenesis of pancreatic cancer as well as immune evasion mechanisms.

Open positions (Master, PhD students, Postdocs as well as Technicians)

Currently funded projects

P05 of the RU5433 will address the role and therapeutic target potential of the RBP MEX3A in lung adenocarcinoma (LUAD), which still accounts for the vast majority of cancer-associated mortality worldwide. MEX3A is a bona fide oncofetal RBP with reported E3-ubiqutin ligase activity. Unpublished findings by the applicants indicate that MEX3A promotes tumor growth in LUAD cell and animal models by enhancing major oncogenic drivers like MYC and impairing tumor suppressive pathways and regulators, e.g. TP53 and PDCD4. Therapeutic target potential of MEX3A was recently validated by revealing impaired tumor growth upon MEX3A depletion in experimental LUAD xenograft models. With the studies proposed, P05 will characterize the mechanisms underlying the presumably interconnected roles of MEX3A in controlling RNA fate (RNA-binding) and ubiquitin-dependent modulation (E3-ligase) of protein function and turnover. These efforts benefit from long standing collaboration and complementary expertise of the applicants: Hüttelmaier, the role and therapeutic target potential of ncRNAs and RBPs in cancer; Sinz, analyses of protein abundance, modification and ligand-association (incl. RBPs) by quantitative and cross-linking mass spectrometry.

P09 of the RU5433 aims at the SAR-guided development of RBP-directed small molecule inhibitors for cancer therapy. In previous studies, IGF2 mRNA binding proteins (IGF2BPs) were demonstrated to promote tumor progression in a conserved manner. IGF2BP1, the most potent oncofetal RBP of the IGF2BP family, impairs the mostly miRNA- and m6A-dependent (N6-methyladenosine) inhibition of tumor promoting factors, such as E2F1, LIN28B, MYC/N and SRF. This post-transcriptional enhancement of pro-oncogenic factors is effectively inhibited in cells and animal tumor models by reversible as well as covalent cysteine-directed small molecules interfering with IGF2BP1-RNA association (patents: EP20159945.3, EP202118071.1). Based on the complementary expertise in structural biology (Balbach), RBP-centered R3oGE in tumor biology (Hüttelmaier) and medicinal chemistry (Sippl), P09 will pursue the SAR-guided development and refinement of IGF2BP1/3-directed reversible, irreversible (covalent) inhibitors as well as PROTACs (proteolysis targeting chimeras) and will initiate the development of covalent inhibitors directed against other oncofetal RBPs like MEX3A (also see P05in the RU5433). These efforts provide a platform and technologies for exploring small molecule inhibition of other oncoRBPs characterized by the RU5433 consortium.

In addition to administration of the research program of the RU5433, the coordination project (P10) of the RU5433 will implement research training concepts and will provide research support in: i) NGS (next generation sequencing); ii) MSI (multi-spectral imaging); iii) MST (microscale thermophoresis) and ISS (isothermal spectral shift). Leitmotivs and conceptual settings for research training were derived and evolved from the RTG1591 (2010-2019; speaker, Prof. Hüttelmaier). Administrative tasks of P10 include the managing of all central funds allocated to projects upon request, support in the recruitment of staff, and implementation as well as organization of research training concepts. The spokesperson (Hüttelmaier) of the RU5433 will coordinate the research consortium. He will be supported by the deputy spokesperson (Klusmann), Alexander Rausch (scientific coordination) and Tanja Wolf (administrative coordination). Research training and support will further benefit from implementation of Dr. Bley (P08 in the RU5433), the scientific head of the Core Facility Imaging (CFI), and two bioinformaticians, Dr. Glaß and Dr. Misiak, leading the CFI-associated core unit for NGS analytics.

Neuroblastoma accounts for approximately 8% of all childhood cancers and 15% of cancer-related death in infants. Typically, neuroblastoma initiates from one of the adrenals or along the spine. Despite intense research, the outcome of high-risk neuroblastoma (HR NBL) with an overall survival of less than 15% remains dismal. Clinically neuroblastoma represents heterogeneous and in various cases as an aggressive disease due to enhanced chemoresistant and high self-renewal potential.

Aiming to identify potentially targetable oncogenic networks promoting high-risk neuroblastoma, we conducted a thorough analysis of neuroblastoma transcriptomes and chromosomal aberrations including RNA-seq, small RNA-seq, and shallow whole genome sequencing (sWGS) of 100 primary tumor samples. Findings were correlated with a pan-cancer survey of publicly available loss-of-function CRISPR screen data, including MYCN-amplified neuroblastoma cell lines. These comprehensive investigations revealed a significant number of essential genes on chromosome 17q, frequently gained in high-risk neuroblastoma. Among these genes, we identified IGF2BP1, an oncofetal RNA-binding protein, acting as a pro-oncogenic driver in neuroblastoma. Studies in cellulo, xenograft as well as transgenic neuroblastoma mouse models indicate that IGF2BP1 promotes an aggressive, high-risk neuroblastoma phenotype by fostering MYCN-driven gene expression. Preliminary analyses of MYCN/IGF2BP1-driven effectors suggest various targetable proteins, e.g. Survivin (BIRC5) located on chromosome 17q. In preliminary studies, we observed that BIRC5 inhibition is IGF2BP1-dependent. Accordingly, we expect that the concomitant pharmacological impairment of MYCN/IGF2BP1 and their effectors has therapeutic benefit.

With the project funded by the German cancer aid, we wish to: 1) characterize the role and therapeutic target potential of MYCN/IGF2BP1-driven gene expression in high-risk neuroblastoma and 2) will evaluate novel therapeutic strategies aiming to target the MYCN/IGF2BP1-driven expression of oncogenic factors. These pre-clinical efforts ultimately aim to improve the therapy and outcome of high-risk neuroblastoma patients.

The anaplastic thyroid carcinoma (ATC) is rare, but the most fatal malignancy of the thyroid gland with average survival probability of only up to six month upon diagnosis. Despite substantial research efforts, the molecular mechanism underlying the progression of well-differentiated thyroid carcinomas of follicular origin (WDTC) to ATC are only poorly understood, and effective ATC treatment regimens are still lacking. In the interest of patients, it is thus mandatory to explore new avenues to treat this fatal malignancy.

In recent studies, supported by the German cancer aid, we unraveled gene expression programs and the first positive markers, in particular IGF2BP1, distinguishing ATC from other malignancies of the thyroid. The oncofetal IGF2 mRNA binding protein 1 (IGF2BP1) is de novo synthesized in ATC and promotes the expression of various oncogenes like MYC by stabilizing the respective mRNAs. Deletion of IGF2BP1 in human ATC cell lines severely impairs their vitality and tumor growth in nude mouse models. In accord, the overexpression of IGF2BP1 in the murine thyroid promotes hyperplasia and induces aggressive carcinomas in synergy with mutant KRAS, one major driving mutation in various human cancers including ATC. Aiming to impair IGF2BP1 oncogenic functions, we developed two lines of small molecule compounds impairing the RNA-binding of IGF2BP1 and consequently pro-oncogenic roles of IGF2BP1 in experimental ATC models.

With the studies funded by the German cancer aid, we wish to further explore molecular mechanism and therapeutic target potential of IGF2BP1-driven gene expression in thyroid cancer initiation and progression using transgenic mouse models and human ATC cell models. Aiming to unravel mechanisms underlying the severe shift in gene expression characteristic for ATC, we will use IGF2BP1 de novo synthesis as a handle to identify key transcriptional and epigenetic regulators of ATC gene expression using CRISPR-screening. This may unravel novel therapeutic targets which will be explored next to benefits of improved IGF2BP1 inhibitors and combined treatment regimens in pre-clinical ATC models. In sum, we expect the proposed studies to provide substantial new insights into the molecular basis of thyroid carcinoma progression and will highlight new avenues in ATC treatment.

The RNA-binding protein RAVER1 was described by Hüttelmaier et al. in 2001. RAVER1 associates with the splicing regulator PTB in membrane-free (liquid droplet-like) perinucleolar compartments (PNC) and influences alternative splicing. In cancer models, RAVER1 serves pro-oncogenic roles involving the regulation of interferon-, NFKB-, and potentially TP53-signaling. In studies funded within the framework of the RTG2467, the role of RAVER1 in cancer and its regulation via intrinsically disordered regions (IDRs), mediating association with PTB, is investigated.

Open positions (Master, PhD students, Postdocs as well as Technicians)

RNA-binding proteins (RBPs) are key modulators of tumor cell fate and influence inflammatory signaling. Studies funded within the framework of the RTG2751 , aim to characterize the role of RBPs in early, inflammation-driven carcinogenesis of pancreatic cancer as well as immune evasion mechanisms.

Open positions (Master, PhD students, Postdocs as well as Technicians)

Research Funding