Molecular mechanisms of mechanotransduction during tumor progression

• Applicant: Professorin Dr. Mirka Uhlirova
• Subject Area: Cell Biology ; General Genetics and Functional Genome Biology
• Term: from 2014 to 2018
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 253567115

• Final Report Year: 2019

Final Report Abstract

In conclusion, our transcriptome profiling produced a comprehensive and reliable dataset providing a foundation for the identification of novel tumor-promoting and -suppressing genes. Their functional characterization may guide identification of novel cancer biomarkers and development of therapeutic interventions targeting tumors and/or associated immune cells. The methodology describing the generation of genetically defined and visually marked clones in Drosophila EADs, including the protocols for the dissection and imaging of Drosophila larval EADs, quantification of tumor invasiveness and RNA isolation from dissected tissue suitable for downstream applications such as qRT-PCR and mRNA-seq profiling has been published. The protocols accompanied by videos provide guidelines on how to create, handle and analyze Drosophila epithelial tumors to achieve reproducible and robust results. Moreover, the article has been aimed to support teaching, guiding undergraduate and graduate students during practical courses that utilize the Drosophila model. Within this project, the following state-of-the-art methodological approaches have been established with help of national and international collaborations and pursued in the laboratory: 1) Protocols for the comparative gene expression and TF motif analyses based on mRNA-seq and ChIP-seq in collaboration with Bioinformatics facility (CECAD, Cologne) and Bianca Habermann (Institut de Biologie du Developpement de Marseille, France). 2) Protocols for affinity purification of proteins from Drosophila tissues followed by comparative proteomics in collaboration with Hendrik Nolte (CECAD, Cologne) and Proteomic facility (CECAD, Cologne). 3) Protocol for Fluorescence-activated cell sorting (FACS) of various live cell populations labeled with transgenic fluorescent proteins in collaboration with Kat Folz-Donahue (The FACS & Imaging Core Facility, MPI-Age, Cologne) followed by mRNA isolation and transcriptome analysis.

Publications

• (2015) Atf3 bridges the gap between cell polarity and the nucleus. PhD Thesis, University of Cologne, USB Köln
  Donohoe CD
  
• (2015). Interplay among Drosophila transcription factors Ets21c, Fos and Ftz-F1 drives JNK-mediated tumor malignancy. Dis Model Mech 8, 1279-1293
  Külshammer, E., Mundorf, J., Kilinc, M., Frommolt, P., Wagle, P., and Uhlirova, M.
  
• (2016). The Drosophila Imaginal Disc Tumor Model: Visualization and Quantification of Gene Expression and Tumor Invasiveness Using Genetic Mosaics. J Vis Exp 116, e54585
  Mundorf, J., and Uhlirova, M.
  
• (2017) Ets21c – A novel regulator of epithelial homeostasis downstream of JNK. PhD Thesis, University of Cologne, USB Köln
  Mundorf J.
  
• (2018) Learning from the fly: Oncogenic JNK signaling is linked to Hippo pathway via its downstream effectors Cheerio and Ftz-F1. PhD Thesis, University of Cologne, USB Köln
  Kilinc M.
  
• (2018). Atf3 links loss of epithelial polarity to defects in cell differentiation and cytoarchitecture. PLoS Genet 14, e1007241
  Donohoe, C.D., Csordas, G., Correia, A., Jindra, M., Klein, C., Habermann, B., and Uhlirova, M.