Forschungsnetzwerk zur Früherkennung und Prävention- LiSyM-Krebs
Ein Netzwerk von Klinikern, Wissenschaftlern und Datenmanagern hat sich zur Aufgabe gemacht, Methoden zu entwickeln, um Patienten mit einem hohen Risiko für ein Leberkarzinom frühzeitig, in Vorstadien der Tumorentwicklung, identifizieren zu können. Gemeinsam bilden sie das „Systemmedizinische Forschungsnetzwerk zur Früherkennung und Prävention von Leberkrebs“, LiSym-Krebs, das vom Bundesministerium für Bildung und Forschung (BMBF) in den kommenden drei Jahren mit circa 10 Mio. Euro gefördert wird.
LiSyM-Krebs besteht aus den drei Forschungsverbünden : C-TIP-HCC, SMART-NAFLD und DEEP-HCC.
Programme: LiSyM-Krebs - Systemmedizinisches Forschungsnetz zur Früherkennung und Prävention von Leberkrebs
SEEK ID: https://seek.lisym.org/projects/16
Public web page: Not specified
Organisms: Homo sapiens, Mus musculus, Rattus norvegicus, Rattus rattus
FAIRDOM PALs: No PALs for this Project
Project created: 15th Jan 2021
Related items
- People (95)
- Programmes (1)
- Institutions (35)
- Investigations (2+2)
- Studies (8+2)
- Assays (13+11)
- Data files (7+1)
- Models (3)
- SOPs (4+6)
- Publications (42)
- Presentations (1+44)
- Events (8+4)
- Documents (8+12)
- Sample types (0+1)
- Samples (0+1)
Projects: LiSyM network, Forschungsnetzwerk LiSyM-Krebs, LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP), LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM Pillar III: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF), DEEP-HCC network
Institutions: HITS gGmbH
LiSyM-Krebs ist ein nationales Forschungsnetz zur Früherkennung und Prävention von Leberkrebs, das unter Verwendung des systemmedizinischen Forschungsansatzes die komplexen, dynamischen Prozesse der Krankheitsprogression analysiert, um ausgehend von den Erkenntnissen aus dem Forschungsnetz LiSyM die Entstehung von Leberkrebs besser zu verstehen, vorherzusagen und im besten Fall sogar zu verhindern. LiSyM-Krebs setzt die erfolgreichen Forschungsaktivitäten der BMBF-Vorgängerprogramme ...
Projects: LiSyM-Krebs Partnering, Forschungsnetzwerk LiSyM-Krebs, SMART-NAFLD, DEEP-HCC network, C-TIP-HCC network
Web page: https://www.lisym-cancer.org
Country: Germany
City: 69120 Heidelberg
Web page: https://www.dkfz.de/en/tumor-metabolismus-microenvironment/index.php
Macrophages play an important role in maintaining liver homeostasis and regeneration. Here we investigate how different macrophage populations of the liver differ in terms of their activation state and which other liver cell populations may play a role in regulating the same.
Submitter: Stephanie Wolf
Studies: Study changes in gene expressionand in the activation state of macrophag...
Assays: Hepatocytes induces properties of wound healing type and regulatory macr..., Transcriptomics : RNA Microarray, Transcriptomics: RNA-seq of coding RNA from single cells
Snapshots: No snapshots
LiSyM-Cancer project data for integration into public repositories based on
Submitter: Olga Krebs
Studies: GENOMICS/TRANSCRIPTOMICS, METABOLOMICS, OTHER OMICS DATA, Several proteomics experimental data
Assays: DNA sequence data, RNA sequence data, Western blot
Snapshots: No snapshots
Several proteomics experimental data
Submitter: Olga Krebs
Investigation: LiSyM-Cancer project data for integration into...
Assays: Western blot
Snapshots: No snapshots
Reverse transcription PCR, flow cytometry, transcriptome, proteome, secretome, single cell analysis, and immunohistochemical methods were used to study changes in gene expression as well as the activation state of macrophages in vitro and in vivo under homeostatic conditions and after partial hepatectomy.
Submitter: Stephanie Wolf
Investigation: Hepatocytes reprogram liver macrophages involvi...
Assays: Hepatocytes induces properties of wound healing type and regulatory macr..., Transcriptomics : RNA Microarray, Transcriptomics: RNA-seq of coding RNA from single cells
Snapshots: No snapshots
OTHER OMICS DATA
Submitter: Olga Krebs
Investigation: LiSyM-Cancer project data for integration into...
Assays: No Assays
Snapshots: No snapshots
METABOLOMICS
Submitter: Olga Krebs
Investigation: LiSyM-Cancer project data for integration into...
Assays: No Assays
Snapshots: No snapshots
GENOMICS/TRANSCRIPTOMICS
Submitter: Olga Krebs
Investigation: LiSyM-Cancer project data for integration into...
Assays: DNA sequence data, RNA sequence data
Snapshots: No snapshots
Project proposals
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: Documents submitted to BMBF
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Meeting minutes 2021
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: Meeting minutes
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Meeting minutes 2022
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: Meeting minutes
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Project deliverables 2021
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: Documents submitted to BMBF
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Project deliverables 2022
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: Documents submitted to BMBF
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Raw data of proteomic analysis of primary murine hepatocytes treated with Hedgehog-modulating compounds
Manuscript: "Impact of Hedgehog Modulators on Signaling Pathways in Primary Murine and Human Hepatocytes in vitro: Insights into Liver Metabolism" Journal Name: Archives of Toxicology Author Names: Fritzi Ott, Christiane Körner, Knut Krohn, Janett Fischer, Georg Damm, Daniel Seehofer, Thomas Berg, Madlen Matz-Soja Corresponding author: Madlen Matz-Soja (madlen.matz-soja@medizin.uni-leipzig.de) ...
Creator: Fritzi Ott
Submitter: Fritzi Ott
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Raw data of RNA-seq analysis of primary murine hepatocytes treated with Hh modulating compounds
Manuscript: "Impact of Hedgehog Modulators on Signaling Pathways in Primary Murine and Human Hepatocytes in vitro: Insights into Liver Metabolism" Journal Name: Archives of Toxicology Author Names: Fritzi Ott, Christiane Körner, Knut Krohn, Janett Fischer, Georg Damm, Daniel Seehofer, Thomas Berg, Madlen Matz-Soja Corresponding author: Madlen Matz-Soja (madlen.matz-soja@medizin.uni-leipzig.de)
Creators: None
Submitter: Fritzi Ott
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Supplementary Tables 1-7 of the Manuscript: "Multiomics and kinetic modeling reveal dominance of 12-hour rhythms in global liver metabolism"
for table headings please refer to Supplementary Material
Creator: Fritzi Ott
Submitter: Fritzi Ott
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Data deposited on the European Bioinformatics Insititute (EBI) database under accession number E-MTAB- 11727 (https://www.ebi.ac.uk/arrayexpress/experiments/ E-MTAB-11727)
Hepatocyte-controlled availability of activated TGFb reprograms macrophage polarization affecting liver injury and regeneration.
Samples in SEEK (ArrayExpress-compliant sample type https://seek.lisym.org/sample_types/21)
Creator: Stephanie Wolf
Submitter: Stephanie Wolf
Hepatocytes and macrophages from mono and co-culture were harvested and prepared for mass spectrometric analysis , samples were shortly separated in a polyacrylamide gel, silver-stained, reduced, alkylated and digested with trypsin.
Creators: None
Submitter: Stephanie Wolf
The model studies the influence of hepatocyte–sinusoid alignment (HSA), i.e. the orientation of the division plane such that daughter hepatocytes align with nearby sinusoids, on the shape of tumor nodules in liver lobules. It employs the structure of the model ‘Liver Regeneration from CCl4’ (https://seek.lisym.org/models/19).
Originally, Höhme et al. (https://doi.org/10.1007/s11538-017-0375-1) employed a center-based model. Here, the model is encoded in the standardized language MorpheusML. ...
Creators: Diego Jahn, Michael Kücken, Lutz Brusch
Submitter: Diego Jahn
Model type: Agent based modelling
Model format: MorpheusML
Environment: Morpheus
In the experimental paradigm of CCl4 intoxication of mice, hepatocytes around the central vein (located in the center of an idealized hexagonal liver lobule) are dying and are subsequently replaced by new hepatocytes, largely through activation of proliferation in the remaining hepatocytes.
Alignment of daughter hepatocytes along the orientation of the closest sinusoid, a process which is named hepatocyte-sinusoid alignment (HSA), was proposed by Höhme et al. (https://doi.org/10.1073/pnas.0909374107) ...
Creators: Diego Jahn, Michael Kücken, Lutz Brusch
Submitter: Diego Jahn
Model type: Agent based modelling
Model format: MorpheusML
Environment: Morpheus
Creator: Andreas Weidemann
Submitter: Andreas Weidemann
Model type: Stoichiometric model
Model format: SBML
Environment: Copasi
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Liver is the major site for glycogen storage. Glycogen content can be significantly altered upon disruption of glucose homeostasis in metabolic syndromes, such as diabetes.
Glycogen content can be determined by an acid-hydrolysis method . Basically, glucose, the hydrolysis product of glycogen, is converted into glucose-6- phosphate (G-6-P) by hexokinase in the presence of ATP.
With the supply of NADP, G-6-P is further converted into 6-phosphogluconic acid by G-6-P dehydrogenase (G-6-PDH), while ...
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: LiSyM-Cancer project data for integration into...
Studies: METABOLOMICS
Assays: 1 hidden item
This protocol details the RNAseq sample preparation starting with mRNA and ending with quality control of finished libraries. This protocol was used specifically for virus mRNA samples related to ORFeome lab group.
Creators: Olga Krebs, Marcia Sanders (marcia_sanders@unc.edu), Anne Beall (aebeall@email.unc.edu
Submitter: Olga Krebs
Investigations: LiSyM-Cancer project data for integration into...
Studies: GENOMICS/TRANSCRIPTOMICS
Assays: RNA sequence data
SOP Western diat mouse housing and feeding
Creator: Ina Biermayer
Submitter: Olga Krebs
Investigations: 1 hidden item
Studies: Proteomic alterations in Western Diet (WD) hepa...
Assays: 2 hidden items
Isolation of primary mouse hepatocytes
Creators: Ina Biermayer, Ursula Klingmüller
Submitter: Olga Krebs
Investigations: 1 hidden item
Studies: Proteomic alterations in Western Diet (WD) hepa...
Assays: 2 hidden items
Abstract (Expand)
Authors: Sophia Müller-Dott, Eric J. Jaehnig, Khoi Pham Munchic, Wen Jiang, Tomer M. Yaron-Barir, Sara R. Savage, Martin Garrido-Rodriguez, Jared L. Johnson, Alessandro Lussana, Evangelia Petsalaki, Jonathan T. Lei, Aurélien Dugourd, Karsten Krug, Lewis C. Cantley, D. R. Mani, Bing Zhang, Julio Saez-Rodriguez
Date Published: 2nd Jul 2024
Publication Type: Journal
DOI: 10.1101/2024.06.27.601117
Citation: biorxiv;2024.06.27.601117v1,[Preprint]
Abstract (Expand)
Authors: Valentin Blank, Thomas Karlas, Ulf Anderegg, Johannes Wiegand, Josi Arnold, Linnaeus Bundalian, Gabriela‐Diana Le Duc, Christiane Körner, Thomas Ebert, Anja Saalbach
Date Published: 4th May 2024
Publication Type: Journal
DOI: 10.1111/liv.15956
Citation: Liver International,liv.15956
Abstract (Expand)
Authors: Barbara Helm, Pauline Hansen, Li Lai, Luisa Schwarzmüller, Simone M. Clas, Annika Richter, Max Ruwolt, Fan Liu, Dario Frey, Lorenza A. D’Alessandro, Wolf-Dieter Lehmann, Marcel Schilling, Dominic Helm, Dorothea Fiedler, Ursula Klingmüller
Date Published: 21st Feb 2024
Publication Type: Journal
DOI: 10.1101/2024.02.19.580971
Citation:
All authors
Abstract (Expand)
Authors: Sebastian Burbano De Lara, Svenja Kemmer, Ina Biermayer, Svenja Feiler, Artyom Vlasov, Lorenza A D’Alessandro, Barbara Helm, Christina Mölders, Yannik Dieter, Ahmed Ghallab, Jan G Hengstler, Christiane Körner, Madlen Matz-Soja, Christina Götz, Georg Damm, Katrin Hoffmann, Daniel Seehofer, Thomas Berg, Marcel Schilling, Jens Timmer, Ursula Klingmüller
Date Published: 12th Jan 2024
Publication Type: Journal
DOI: 10.1038/s44320-023-00007-4
Citation: Mol Syst Biol
Abstract (Expand)
Authors: Felix Hiebinger, Aiste Kudulyte, Huanting Chi, Sebastian Burbano De Lara, Doroteja Ilic, Barbara Helm, Hendrik Welsch, Viet Loan Dao Thi, Ursula Klingmüller, Marco Binder
Date Published: 1st Dec 2023
Publication Type: Journal
DOI: 10.1186/s12935-023-03150-y
Citation: Cancer Cell Int 23(1),315
As a member of LiSyM-Cancer you already have a “profile” in LiSyM SEEK, i.e. your name and mail address is known to the system. You now have to register or in other words create a user name and a password. Download and watch the the short tutorial on how this works.
Creator: Maja Rey
Submitter: Maja Rey
The “Computational Modeling in Biology” Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology and related fields. COMBINE 2024 is a workshop-style event with oral presentations, breakout sessions and tutorials. The three meeting days will include talks about the COMBINE standards and associated or related standardization efforts, presentations of tools using these standards, breakout sessions for detailed discussions as ...
Start Date: 1st Sep 2024 (1st Sep 2024 (Europe/Berlin))
End Date: 3rd Sep 2024 (3rd Sep 2024 (Europe/Berlin))
Event Website: https://co.mbine.org/author/combine-2024/
Country: Germany
City: Stuttgart
Sessions:
- From single cell analysis to clinical application
- Mechanistic modeling at the cellular scale proposing intervention strategies
- Tissue scale modeling and organ communication in systems medicine
- AI contributions to systems medicine - Diagnosis and therapy monitoring
- The future of systems biology
Start Date: 13th May 2024 (13th May 2024 (Etc/UTC))
End Date: 15th May 2024 (15th May 2024 (Etc/UTC))
Event Website: https://www.lisym-cancer.org/sbmc2024
Country: Germany
City: 04109 Leipzig
The “Computational Modeling in Biology” Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology, synthetic biology and related fields. HARMONY is a codefest-type meeting, with a focus on development of the standards, interoperability and infrastructure. There are generally not many general discussions or oral presentations during HARMONY; instead, the time is devoted to allowing hands-on hacking and interaction between ...
Start Date: 8th Apr 2024 (8th Apr 2024 (Europe/London))
End Date: 11th Apr 2024 (11th Apr 2024 (Europe/London))
Event Website: https://co.mbine.org/author/harmony-2024/
Country: United Kingdom
City: London
Just over 30 years ago, the cellular Potts model (CPM) was introduced to explain experimental observations of spontaneous cell sorting in embryonic tissue cultures. In the years since, the CPM evolved into a powerful model framework for simulating a wide range of physical and biological processes – from foam physics to tissue development, cancer growth, angiogenesis, plant development, evolution, immune responses, and cell migration. Having just celebrated the 30th birthday of the CPM, now is a ...
Start Date: 18th Dec 2023 (18th Dec 2023 (Europe/Amsterdam))
End Date: 22nd Dec 2023 (22nd Dec 2023 (Europe/Amsterdam))
Event Website: https://www.lorentzcenter.nl/simulating-tissue-dynamics-with-cellular-potts-models.html
Country: Netherlands
City: Leiden
The “Computational Modeling in Biology” Network (COMBINE) is an initiative to coordinate the development of the various community standards and formats in systems biology and related fields. COMBINE 2023 is a workshop-style event with oral presentations, breakout sessions and tutorials. The three meeting days will include talks about the COMBINE standards and associated or related standardization efforts, presentations of tools using these standards, breakout sessions for detailed discussions as ...
Start Date: 5th Oct 2023 (5th Oct 2023 (America/New_York))
End Date: 7th Oct 2023 (7th Oct 2023 (America/New_York))
Event Website: https://co.mbine.org/author/combine-2023/
Country: United States
City: Farmington, CT
Creators: Ina Biermayer, Susan Eckerle
Submitter: Maja Rey
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creators: Ina Biermayer, Susan Eckerle
Submitter: Maja Rey
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Workshop #1 LiSym status seminar March 2023, Dresden “Towards concordant multiomics of liver”
Creators: Andrej Shevchenko, Ursula Klingmüller
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Group picture from Lisym-Cancer Status Seminar 2023
Creators: Olga Krebs, Ina Biermayer, Susan Eckerle
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Creators: Ursula Klingmüller, Ina Biermayer, Susan Eckerle
Submitter: Ursula Klingmüller
Investigations: No Investigations
Studies: No Studies
Assays: No Assays