Multiplexed Deconvolution of metastasis in vivo

• Applicant: Professorin Dr. Barbara Grüner
• Subject Area: Gastroenterology ; Hematology, Oncology ; Cell Biology
• Term: from 2017 to 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 341532333

Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer deaths in the Western World with a median survival of only 6 months and a 5 year-survival rate below 5%. The ability of cancer cells to leave the primary tumors and establish inoperable metastases is a major impediment to successful therapy. Metastasis thus represents a major clinical challenge that is driven by as yet poorly understood cell state alterations. We have developed a multiplexed small molecule screening platform that allows interrogating small molecules in vivo in an efficient high-throughput manner. This approach integrates molecular cell barcoding, in vitro compound pretreatment, and in vivo selection to allow multiplexed compound screening in mice. We used this platform to screen a library of FDA-approved inhibitors and identified the cholesterol-pathway as a regulator of cancer cell plasticity and inducers of a mesenchymal phenotype (EMT). We discovered that the cancer cells’ response to this induction of EMT is depending on their ability to activate ERK signaling. Either they become apoptotic due to this forced shift in cell state, or they activate ERK signaling and survive, but are then stuck in this state. Therefore, one aim of this project focuses on investigating cellular plasticity of metastatic cancer cells upon cholesterol-pathway inhibition. For this, we will utilize patient-derived model systems representing these two distinct cellular responses and perform transcriptome and proteome analyses to dissect in detail which molecular signaling pathways determine the ability to activate ERK. Candidate regulators will be functionally validated using siRNA technology followed by in vitro assays as well as in in vivo translational model systems and in patient-derived samples. In the second part, we will focus on the changes in the lipidome that might regulate pancreatic cancer metastasis. In preliminary findings, we determined that particularly unsaturated lipids as well as genes regulating unsaturated fatty acid metabolism are differentially regulated between primary tumors and metastases. Therefore, we will expand our analyses to patient-derived cell line models and samples and perform lipidome as well as transcriptome analyses. Focusing on the fatty acid desaturases 1 and 2, we will uncover what mechanistic impact these genes have on PDAC metastasis. Validation experiments in vitro and in vivo using genetic knockdowns as well as chemical inhibition will complete our analyses. Taken together, by combining quantitative methods and powerful in vivo tools, we hope to uncover general principles that govern tumor progression and metastatic spread. Given the immense clinical impact of metastatic cancer and the current gap in understanding the molecular underpinnings of this disease, both clinical practice and patient outcome would be greatly impacted by any new therapies that might result from the fundamental knowledge gained from the proposed analyses.

• DFG Programme: Independent Junior Research Groups