Identification of the transcriptional regulated gene networks at the single nucleus level in mice and humans and in males and females, that control cachexia onset and survival.

• Applicant: Dr. Lea Geßler
• Subject Area: Cell Biology ; Molecular and Cellular Neurology and Neuropathology
• Term: since 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 550408047

One third of cancer deaths are due to cachexia, a metabolic syndrome characterized by loss of fat and lean mass. Loss of muscle mass is the major clinical feature of cachexia, and a key predictor of poor outcome. Marco Sandri’s lab found that preventing muscle wasting in tumor-bearing animals prolonged lifespan. Several attempts to develop therapeutic or treatment approaches for cachexia have failed due to a lack of understanding of the insights of this syndrome. Recently, Marco Sandri’s lab started to address the complexity of cachexia by comparing muscle biopsies from patients and controls. The combination of data from mice and humans leads to exiting observations that inspire my proposal. My plan is to define the transcriptionally regulated gene networks at the single nucleus level that control cachexia onset and survival. First, I will use cancer cachexia mice implanted with colon or pancreatic cancer cell lines. I will simultaneously determine the transcriptional and chromatin signatures of the different cell types in the muscles of pre-cachectic and cachectic mice at the single nucleus level using RNA seq and ATAC seq. Subsequent bioinformatic analysis of the promoter regions of the differentially expressed genes will identify transcription factors (TFs) that are activated or inhibited during cachexia onset in the different cell types. The cellular and cytokine receptor landscapes in muscle tissue are controlled by transcription-dependent programs in myonuclei. The TFs that are required to induce specific atrophy- and cachexia-related genes are still unknown. Second, I will genetically modulate the top hits of TFs that will be identified in my first task to be activated/engaged in myonuclei during tumor growth in muscles of tumor-bearing mice. Using a combination of spatial transcriptomic and snRNA/ATAC multiome techniques, I will dissect the contribution of each TF and their combination to the pro-cachectic gene signature and cellular landscape. I will also monitor the effects of systemic inhibition of TFs on muscle mass, muscle strength, metabolism/bioenergetics, tumor growth, and animal survival. Cachexic mice are useful for studying pathogenetics and for intervention studies, but they are an imperfect represention of cancer patients. Therefore, third, I will perform and compare snRNA/ATAC-seq multiome analyses of nuclei from muscle biopsies of pancreatic and colon cancer patients in pre-cachexia and cachexia states and compare them with matched control patients. Sections from the same biopsies will be processed for spatial transcriptomics. The cellular and cytokine receptor landscapes and the transcriptional signatures of the different cell types will be compared with the cachexic mice to identify overlap or divergence between human and mouse. The identification of the key players will be fundamental for the development of an RNA-based therapeutic approach to preserve muscle mass and prevent cachexia in patients.

• DFG Programme: WBP Fellowship
• International Connection: Italy
• Host: Professor Marco Sandri, Ph.D.