Immune checkpoint inhibitors (ICI) have revolutionized the field of cancer therapy in the last decade. By re-activating the body`s immune response to the tumor, ICI has improved therapeutic benefit for several solid tumors including melanoma.
Still, a significant number of tumors do not respond to ICI. Reasons for this are insufficient T-cell responses, e.g. due to the lack of (neo)antigens, and a positive selection for the activation of immune evasion mechanisms. Interestingly, classic oncogenes such as BRAF, RAS and MYC were demonstrated to convey active immune evasion in addition to their well-characterized cell-autonomous effects. Recently, we were able to show that the targeted pharmacological inhibition of the MAPK pathway modulates the detection of tumor cells by autologous T cells in an antigen-specific manner. The aim of this project is to investigate how immune evasion is mediated by oncogenes and how new combination immunotherapeutic therapies can be developed from these findings.
To this end, we will employ a mass spectrometric analysis of tumor antigens from MHC I complexes in melanoma. In preliminary experiments, we observed that a large proportion of the peptides presented on tumors do not result from the degradation of known proteins, but can be assigned to non-coding sequence elements. These "cryptic peptides" (CP) derive, for example, from short open reading frames in UTR sequences, long non-coding RNAs and introns. The observation is relevant because we recently found that the oncogene MYC regulates the cellular pool of transcripts globally. In the presence of high MYC levels, RNA polymerase primarily produces coding mRNA, while the inhibition of MYC leads to the strong transcription of non-coding antisense RNAs, eRNAs, and mRNAs (= pervasive transcription).
We therefore propose a model in which MYC suppresses pervasive transcription and thus also the presentation of CP. At the same time, the examination of the peptide pool before and after MAPK inhibition is planned. Since strategies have already been developed to pharmacologically inhibit the expression of MYC and studies combining targeted therapy and ICI are being conducted, the results obtained might become clinically relevant in the foreseeable future.
Multiple Myeloma is a cancer formed by malignant plasma cells that is characterized by complex genetic heterogeneity. To date, most genomic analyses in multiple myeloma have been conducted on untreated patients, and the resistance mechanisms underlying disease relapse are poorly understood.
This project thus focuses on the clonal evolution of Multiple Myeloma patients after relapse from treatment. We aim to systematically interrogate the mutational profiles of these patients, identify tumorigenic driver mutations, and elucidate their functional and structural consequences. Our particular focus is on ubiquitin ligases in the HECT family that have emerged as key players in tumor biology, but have generally not been exploited for therapeutic benefit.
By revealing the pathways in which disease-associated mutations in HECT ligase genes take effect and the consequences of these mutations for the conformational dynamics, interaction patterns, and catalytic activities of HECT ligases, we aim to render this undercharacterized class of enzymes accessible for targeted therapeutic strategies in Multiple Myeloma.
Colorectal cancer is one of the leading causes of cancer related death in the world. Throughout the last years, an increase in tumour incidence in patients <50 years could be observed. Hence, increasing research efforts regarding treatment options are required to identify new vulnerabilities and therapeutic options.
Despite advances in the characterisation of the underlying genetic alterations via ‘Next Generation Sequencing’, suitable in vivo models for research and treatment validation are lacking. Our aim is to close this gap and establish in vivo model systems with common genetic alterations found in patients with colorectal cancer. By depletion of various tumour suppressors, we aim to understand the effects on proliferation, differentiation, invasion and metastasis. As various mutations can have significant impact on immunotherapy, we want to investigate the recruitment of immune cells depending on the genetics of the primary tumour.
This project is intended as an interdisciplinary project, including the collaboration with the MPI-junior research groups of Prof. Gasteiger and Kastenmueller. Here, we will focus on the interplay between tumours (with various genetic modulations) and the immune system.
We are intending to utilise the CRISPR/Cas9 system to establish primary tumours in otherwise wild type animals. The flexibility of genetic engineering with CRISPR/Cas9 will help us to quickly adopt new genetic combinations and enables us to make use of any available mouse model system, e.g. immune-specific reporter strains. While classic mouse models have extensively contributed to our understanding of colorectal cancer, genetic shortcomings make limit their use for he planned experiments. CRISPR/Cas9 will enable us to generate primary tumours in patient-relevant locations in the intestinal tract.
Developing tumours will be analysed according to WHO-standards in close collaboration with human patient samples (PD Dr. Armin Wiegering, surgeon, & Dr. Mathias Rosenfeldt, pathology), and subjected to histopathological analysis and RNA sequencing.
Finally, the established in vivo model systems will be a suitable testbed for novel therapeutic interventions, and hopefully contribute to a fast ‘from bench to bed’ transition of our research findings.
MYC family proteins have long been described as transcription factors that promote transformation and tumorigenic growth by promoting the expression of pro-proliferative genes. It is now becoming clear that an important oncogenic function of MYC proteins in vivo is being a key driver of immune evasion. Depletion of MYC protein in orthotopically transplanted PDAC tumors leads to tumor regression in syngeneic, immunocompetent BL6/J mice, whereas tumors in immunocompromised models such as nude mice, Rag1-deficient mice or NRG mice fail to regress after MYC interference.
To translate these findings, we aim to replace genetic models using shRNA-mediated depletion of MYC in KRASG12D and TP53R172H-driven pancreatic ductal adenocarcinoma (PDAC) in mice with systemic therapies. To this end, we exploited the observation that treatment with cardiac glycosides, clinically well-established drugs for patients with heart disease, strongly reduces MYC protein levels in culture as a consequence of interfering with core metabolic processes. Mirroring the effect of MYC depletion, systemic treatment with cardiac glycosides induced complete tumor remission in immunocompetent BL6/J mice. In contrast, the same treatment did not affect tumor growth in immunocompromised (NRG) mice. This underscores the critical role of a functioning immune system in PDAC tumor regression following MYC-targeted intervention using genetic tools or systemic treatment. To date, it is unclear which immune cell type is responsible for this rapid anti-tumor effect.
Using state-of-the-art multi-color flow cytometry and single-cell RNA sequencing methods, we will dissect the changes in the global tumor immune infiltrate in response to MYC depletion using a genetic model and systemic treatment. This will allow to study changes in the tumor microenvironment, in particular in lymphocyte states of cytotoxicity, dysfunction and exhaustion, but also maturation states of antigen presenting cells and polarization of macrophages.
Understanding and targeting the mechanisms of MYC-driven immune evasion may lead to novel therapeutic interventions in PDAC. In addition, it would allow for the combination of cell non-autonomous effects of therapies targeting MYC-driven dependencies and the vastly expanding field of immunotherapies such as (CAR-)T cell allografts and immune checkpoint inhibition.