Research Information Infrastructure, Data Management and Bioinformatics Core
Research Focus
S03 will provide central bioinformatic analyses (Melanie Börries) and data management (Pooja Gupta) for reproducible omics analysis as well as support and consultation to the experimental researchers in the consortium. S03 will collaborate with the TRR researchers to adapt and develop analysis pipelines for specific projects, to set up their particular data management plans, and to create a knowledge platform to foster cross-area scientific synergies, e.g. by promoting and exchanging code repositories, analysis notebooks, standard data formats, general data management policies and overviews on publicly available data and software tools.
Main Collaborations
- P01 Greten: Modulating CAF plasticity to enable immunotherapy of colorectal cancer:
- P02 Büttner/Flinner: Multi modal prediction of therapy response for rectal cancer patients:
- P03 Briquez/Fichtner-Feigl/Reuten: Metastasis predisposing extracellular matrix architecture in colorectal cancer:
- P04 Farin/Stemmler: Mapping the CAF subtype-dependent reciprocal signaling in the CRC niche:
- P05 Neufert: The role of LIFR signaling in CAFs in CRC:
- P06 Günther/Naschberger: Impact of vascular plasticity on therapy responses in CRC:
- P07 Berlin/Groß: Specific role(s) of the inflammasome in the TME of primary and metastasized sporadic CRC:
- P08 Weigert: The role of IL-38 in shaping tumor-promoting versus protective inflammation in colorectal cancer:
- P09 Koop/Neurath: Unraveling the Role of Stromal IL-36R Signaling in Colorectal Tumorigenesis:
- P10 Bengsch/Feuerstein: Targeting the intra-metastatic microbiome in colorectal cancer:
- P11 Arkan/Tatarova: Role of microbial amino acid metabolism on chemotherapy response in CRC:
- P12 Rosshart: Identification of immunomodulatory microbial metabolites as novel therapeutics for advanced CRC:
- P13 Müller/Zundler: Modulation of CRC development and progression by GPR15L-dependent effects on lymphocyte infiltration and the intestinal microbiota:
- P14 Kesselring/Minguet: The role of γδ T cells in the tumor microenvironment of colorectal cancer:
- P15 Hildner: Tumor stroma-derived signals impair cDC1-dependent checkpoint inhibition as a potential resistance mechanism of colorectal cancer immunotherapy:
- P17 Ziegler: STAT3-controlled cross-dressing of dendritic cells in anti-tumor immunity:
- P18 Buchholz/Farin: Identifying and overcoming CAR T cell barriers in the colorectal carcinoma microenvironment:
- P19 Wiegering: Targeting colorectal liver metastasis by overcoming MYC-induced immune evasion:
- S01 Berlin/Greten/Naschberger: Human tumor organoid biobanks for preclinical validation:
- S02 Reiss/Ritter: Spatial profiling of the tumor microenvironment in CRC:
Core Team
Publications
Spatially confined sub-tumor microenvironments in pancreatic cancer.
Grünwald BT, Devisme A, Andrieux G, Vyas F, Aliar K, McCloskey CW, Macklin A, Jang GH, Denroche R, Romero JM, Bavi P, Bronsert P, Notta F, O'Kane G, Wilson J, Knox J, Tamblyn L, Udaskin M, Radulovich N, Fischer SE, Boerries M, Gallinger S, Kislinger T, Khokha R. Cell. 2021 Oct 28;184(22):5577-5592.e18. doi: 10.1016/j.cell.2021.09.022. Epub 2021 Oct 12. PMID: 34644529
The EMT transcription factor ZEB1 governs a fitness-promoting but vulnerable DNA replication stress response.
Schuhwerk H, Kleemann J, Gupta P, van Roey R, Armstark I, Kreileder M, Feldker N, Ramesh V, Hajjaj Y, Fuchs K, Mahapatro M, Hribersek M, Volante M, Groenewoud A, Engel FB, Ceppi P, Eckstein M, Hartmann A, Müller F, Kroll T, Stemmler MP, Brabletz S, Brabletz T. Cell Rep. 2022 Dec 13;41(11):111819. doi: 10.1016/j.celrep.2022.111819. PMID: 36516781