A network-based approach to modelling cell-niche interactions and its application to studying salamander limb regeneration

• Applicant: Professorin Elly Margaret Tanaka, Ph.D.
• Subject Area: Developmental Biology ; Bioinformatics and Theoretical Biology
• Term: from 2016 to 2019
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 283697158

• Final Report Year: 2019

Final Report Abstract

This project aimed to use expression profiling of regenerating fibroblasts during limb regeneration to identify key nodes and niche signals involved in the conversion from adult phenotype to blastema cell phenotype. The Tanaka laboratory performed the expression profiling and developed the methods for testing gene candidates. The del Sol Mesa lab developed the algorithms for analysis and performed analysis of the data. Candidate honing and testing is still ongoing. Beyond the premise of the original grant, single cell sequencing was applied to identify additional candidates. Furthermore, these methods were applied to analyze candidate signaling pathways involved in spinal cord regeneration. Lysophosphatadic acid acting through rho kinase and SRF was shone to be involved in lumen enlargement in neural stem cells.

Publications

• (2018) Application and optimization of CRISPR-Cas9-mediated genome engineering in axolotl (Ambystoma mexicanum). Nat Protoc. 13:2908-2943
  Fei JF, Lou WP, Knapp D, Murawala P, Gerber T, Taniguchi Y, Nowoshilow S, Khattak S, Tanaka EM
  (See online at https://doi.org/10.1038/s41596-018-0071-0)
• (2018) Signaling-Dependent Control of Apical Membrane Size and Self-Renewal in Rosette-Stage Human Neuroepithelial Stem Cells. Stem Cell Reports. 10:1751-1765.
  Medelnik JP, Roensch K, Okawa S, Del Sol A, Chara O, Mchedlishvili L, Tanaka EM
  (See online at https://doi.org/10.1016/j.stemcr.2018.04.018)
• (2018) Single-cell analysis uncovers molecular convergence of cell identities during axolotl limb regeneration. Science, 362(6413)
  Gerber T, Murawala P, Knapp D, Masselink W, Schuez M, Hermann S, Gac-Santel M, Nowoshilow S, Kagejama J, Khattak S, Currie J, Camp JG, Tanaka EM, Treutlein B
  (See online at https://doi.org/10.1126/science.aaq0681)
• (2019) Broad applicability of a streamlined ethyl cinnamatebased clearing procedure. Development. 146:dev166884
  Masselink W, Reumann D, Murawala P, Pasierbek P, Taniguchi Y, Bonnay F,Meixner K, Knoblich JA, Tanaka EM
  (See online at https://doi.org/10.1242/dev.166884)