SMART-NAFLD : A Systems Medicine Approach to Early Detection and Prevention of Hepatocellular Carcinoma in Non-Alcoholic Fatty Liver Disease
The massive increase in obesity is leading to an alarming rise in non-alcoholic liver disease (NAFLD). This development will lead to a dramatic increase in liver diseases such as hepatocellular carcinoma (HCC). A particular challenge is that NAFLD-associated HCCs, for reasons still unknown, not only occur in association with advanced liver fibrosis/cirrhosis, but one third of NAFLD-associated HCCs arise in non-cirrhotic liver tissue. As a result, the tumour is often not detected until it is in a late, incurable state. Innovative strategies for early detection of NAFLD patients at high risk of HCC are urgently needed. To address this clinical challenge, the interdisciplinary team consisting of physicians, clinical scientists, cell biologists, systems biologists, and physics and bioinformatics theorists in SMART-NAFLD is taking an integrative systems medicine approach. By providing longitudinal serum samples, imaging diagnostics with multiparametric MRI, tissue samples and primary hepatocytes used by the project partners for quantitative mass spectrometry, metabolic analyses and the use of artificial intelligence, a classifier will be developed that allows early detection of NAFLD patients at particularly high risk for HCC. The established tissue model of hepatic steatosis will be further developed into a multiclade model. By combining the results from serum and image data in combination with trained CNNS (artificial intelligence), the classification of patients is to be carried out, which can predict an early prognosis with regard to the dynamics of the disease progression to HCC and estimate the liver regeneration potential. The aim is to support decisions in the clinic and to contribute to the prevention of HCC development.
Programme: LiSyM-Krebs - Systemmedizinisches Forschungsnetz zur Früherkennung und Prävention von Leberkrebs
SEEK ID: https://seek.lisym.org/projects/17
Public web page: Not specified
Organisms: Mus musculus, Homo sapiens
FAIRDOM PALs: No PALs for this Project
Project created: 1st Dec 2021
Related items
- People (67)
- Programmes (1)
- Institutions (22)
- Investigations (1+1)
- Studies (6+1)
- Assays (10+6)
- Data files (3+1)
- SOPs (4+5)
- Publications (13)
- Presentations (1+25)
- Events (3+4)
- Documents (9+5)
- Sample types (0+3)
Projects: SMART-NAFLD, Forschungsnetzwerk LiSyM-Krebs
Institutions: Augsburg University, Institute of Computer Science
Program management team LiSyM-Cancer (project and communications manager)
Former PhD student in LiSyM, at DKFZ Heidelberg in the group of Ursula Klingmüller
(née Schmitt)
Projects: LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI), DEEP-HCC network, Forschungsnetzwerk LiSyM-Krebs, SMART-NAFLD, C-TIP-HCC network
Institutions: Universitätsklinikum Dresden - Medizinische Klinik I, Bereich Gastroenterologie & Hepatologie
Expertise: Genetics
Universitätsklinikum Dresden - Medizinische Klinik I, Bereich Gastroenterologie & Hepatologie
Projects: LiSyM-Krebs Partnering, The Hedgehog Signalling Pathway (LiSyM-JGMMS), SMART-NAFLD, DEEP-HCC network, Forschungsnetzwerk LiSyM-Krebs
Institutions: Universität Leipzig - Sächsischer Inkubator für Klinische Translation (SIKT)
https://orcid.org/0000-0002-2104-8076Expertise: Primary human hepatocytes, liver models, Steatosis, NPCs
Tools: Biobanking, Cell Isolation, REIMS
The clinical department of Prof. Dr. med Daniel Seehofer performs more than 200 surgical interventions on the liver annually. Therefore, the group has access to a broad variety of liver tissues as well as corresponding patient, clinical laboratory and characterization data. I lead the experimental work group which has a longstandind expertise in the isolation, characterization and application of primary human liver and hepatoma cells. These cells as well as data generated from established liver ...
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: 86159 Augsburg
Web page: https://www.uni-augsburg.de/en/fakultaet/fai/informatik/
Country: Germany
City: 69120 Heidelberg
Web page: https://www.dkfz.de/en/tumor-metabolismus-microenvironment/index.php
Country: Germany
City: 69120 Heidelberg
Web page: https://www.dkfz.de/genomics-proteomics/proteomics-core-facility
Country: Germany
City: 69120 Heidelberg
Web page: https://www.klinikum.uni-heidelberg.de/Willkommen.100293.0.html
Country: Germany
City: 69120 Heidelberg
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
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
Documents submitted to BMBF
Submitter: Olga Krebs
Investigation: 1 hidden item
Assays: Meeting minutes 2021, Meeting minutes 2022
Snapshots: No snapshots
Documents submitted to BMBF
Submitter: Olga Krebs
Investigation: 1 hidden item
Assays: Project deliverables 2021, Project deliverables 2022, Project proposals
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
DMPlaning 2021
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: 1 hidden item
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
DMPlaning 2022
Submitter: Olga Krebs
Biological problem addressed: Model Analysis Type
Investigation: 1 hidden item
Study: 1 hidden item
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
RNA sequence data
Submitter: Olga Krebs
Assay type: RNA-seq Profiling
Technology type: Technology Type
Investigation: LiSyM-Cancer project data for integration into...
Study: GENOMICS/TRANSCRIPTOMICS
Organisms: No organisms
SOPs: SOP for RNAseq sample preparation and 1 hidden item
Data files: 1 hidden item
Snapshots: No snapshots
Western blot
Submitter: Olga Krebs
Assay type: Immune Precipitation
Technology type: Technology Type
Investigation: LiSyM-Cancer project data for integration into...
Organisms: No organisms
SOPs: SOP template based on nature protocol format an...
Data files: No Data files
Snapshots: No snapshots
DNA sequence data
Submitter: Olga Krebs
Assay type: Transcriptomics
Technology type: Technology Type
Investigation: LiSyM-Cancer project data for integration into...
Study: GENOMICS/TRANSCRIPTOMICS
Organisms: No organisms
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Hepatocyte-controlled availability of activated TGFb reprograms macrophage polarization affecting liver injury and regeneration
Creator: Stephanie Wolf
Submitter: Olga Krebs
Primary hepatocytes from a preclinical mouse model fed with high-sugar and high-fat diet are used to develop a data-based mathematical model that identifies the basal phosphorylation rate of the tyrosine kinase receptor MET as the main dysregulated parameter driving fatty liver disease.
Creators: Ursula Klingmüller, Sebastian Burbano de Lara
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Wolf2023Hepatology Communications
Creator: Stephanie Wolf
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
SOP Western diet 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
Empty SOP template based on nature protocol format and reqiremeents
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: LiSyM-Cancer project data for integration into...
Studies: METABOLOMICS, Several proteomics experimental data
Assays: Western blot and 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
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: 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
Abstract (Expand)
Authors: Felix Hiebinger, Aiste Kudulyte, Huanting Chi, Sebastian Burbano De Lara, Barbara Helm, Hendrik Welsch, Viet Loan Dao Thi, Ursula Klingmüller, Marco Binder
Date Published: 24th Aug 2023
Publication Type: Journal
DOI: 10.21203/rs.3.rs-3276415/v1
Citation: [Preprint]
Abstract
Authors: Miquel Serra-Burriel, Adrià Juanola, Feliu Serra-Burriel, Maja Thiele, Isabel Graupera, Elisa Pose, Guillem Pera, Ivica Grgurevic, Llorenç Caballeria, Salvatore Piano, Laurens van Kleef, Mathias Reichert, Dominique Roulot, Juan M Pericàs, Jörn M Schattenberg, Emmanuel A Tsochatztis, Indra Neil Guha, Montserrat Garcia-Retortillo, Rosario Hernández, Jordi Hoyo, Matilde Fuentes, Carmen Expósito, Alba Martínez, Patricia Such, Anita Madir, Sönke Detlefsen, Marta Tonon, Andrea Martini, Ann T Ma, Judith Pich, Eva Bonfill, Marta Juan, Anna Soria, Marta Carol, Jordi Gratacós-Ginès, Rosa M Morillas, Pere Toran, J M Navarrete, Antoni Torrejón, Céline Fournier, Anne Llorca, Anita Arslanow, Harry J de Koning, Fernando Cucchietti, Michael Manns, Phillip N Newsome, Rubén Hernáez, Alina Allen, Paolo Angeli, Robert J de Knegt, Tom H Karlsen, Peter Galle, Vincent Wai-Sun Wong, Núria Fabrellas, Laurent Castera, Aleksander Krag, Frank Lammert, Patrick S Kamath, Pere Ginès, Marifé Alvarez, Peter Andersen, Paolo Angeli, Alba Ardèvol, Anita Arslanow, Luca Beggiato, Zahia Ben Abdesselam, Lucy Bennett, Bajiha Boutouria, Alessandra Brocca, M. Teresa Broquetas, Llorenç Caballeria, Valeria Calvino, Judith Camacho, Aura Capdevila, Marta Carol, Laurent Castera, Marta Cervera, Fernando Cucchietti, Anna de Fuentes, Rob de Knegt, Harry J de Koning, Sonke Detlefsen, Alba Diaz, José Diéguez Bande, Vanessa Esnault, Núria Fabrellas, Josep Lluis Falcó, Rosa Fernández, Céline Fournier, Matilde Fuentes, Peter Galle, Edgar García, Montserrat García-Retortillo, Esther Garrido, Pere Ginès, Rosa Gordillo Medina, Jordi Gratacós-Ginès, Isabel Graupera, Ivica Grgurevic, Indra Neil Guha, Eva Guix, Johanne Kragh Hansen, Rebecca Harris, Elena Hernández Boluda, Rosario Hernández-Ibañez, Jordi Hoyo, Arfan Ikram, Simone Incicco, Mads Israelsen, Marta Juan, Adrià Juanola, Ralf Kaiser, Patrick S Kamath, Tom H Karlsen, Maria Kjærgaard, Marko Korenjak, Aleksander Krag, Marcin Krawczyk, Philippe Laboulaye, Irina Lambert, Frank Lammert, Simon Langkjær Sørensen, Cristina Laserna-Jiménez, Sonia Lazaro Pi, Elsa Ledain, Vincent Levy, Katrine Prier Lindvig, Anne Llorca, Vanessa Londoño, Guirec Loyer, Ann T. Ma, Anita Madir, Michael Manns, Denise Marshall, M. Lluïsa Martí, Sara Martínez, Ricard Martínez Sala, Roser Masa-Font, Jane Møller Jensen, Rosa M Morillas, Laura Muñoz, Ruth Nadal, Laura Napoleone, JM Navarrete, Phillip N Newsome, Vibeke Nielsen, Martina Pérez, Juan Manuel Pericás-Pulido, Salvatore Piano, Judit Pich, Elisa Pose, Judit Presas Escobet, Matthias Reichert, Carlota Riba, Dominique Roulot, Ana Belén Rubio, Maria Sánchez-Morata, Jörn Schattenberg, Miquel Serra-Burriel, Feliu Serra-Burriel, Louise Skovborg Just, Milan Sonneveld, Anna Soria, Christiane Stern, Patricia Such, Maja Thiele, Marta Tonon, Pere Toran, Antoni Torrejón, Emmanuel A Tsochatzis, Laurens van Kleef, Paulien van Wijngaarden, Vanessa Velázquez, Ana Viu, Susanne Nicole Weber, Tracey Wildsmith
Date Published: 1st Aug 2023
Publication Type: Journal
DOI: 10.1016/S0140-6736(23)01174-1
Citation: The Lancet,S0140673623011741
Abstract (Expand)
Authors: Sebastian Burbano De Lara, Svenja Kemmer, Ina Biermayer, Svenja Feiler, Artyom Vlasov, Lorenza D'Alessandro, Barbara Helm, Yannik Dieter, Ahmed Ghallab, Jan Hengstler, Professor Dr. med. Katrin Hoffmann, Marcel Schilling, Jens Timmer, Ursula Klingmüller
Date Published: 4th Jul 2023
Publication Type: Journal
DOI: 10.1101/2023.07.04.547655
Citation: biorxiv;2023.07.04.547655v1,[Preprint]
Abstract (Expand)
Authors: L. Seidemann, S. Prinz, J. C. Scherbel, C. Gotz, D. Seehofer, G. Damm
Date Published: 20th Jan 2023
Publication Type: Journal
PubMed ID: 36660192
Citation: EXCLI J. 2023 Jan 4;22:12-34. doi: 10.17179/excli2022-5459. eCollection 2023.
Abstract (Expand)
Authors: A. Friebel, T. Johann, D. Drasdo, S. Hoehme
Date Published: 30th Sep 2022
Publication Type: Journal
PubMed ID: 35976110
Citation: Bioinformatics. 2022 Sep 30;38(19):4622-4628. doi: 10.1093/bioinformatics/btac547.
Abstract (Expand)
Authors: S. Chakraborty, G. Andrieux, P. Kastl, L. Adlung, S. Altamura, M. E. Boehm, L. E. Schwarzmuller, Y. Abdullah, M. C. Wagner, B. Helm, H. J. Grone, W. D. Lehmann, M. Boerries, H. Busch, M. U. Muckenthaler, M. Schilling, U. Klingmuller
Date Published: 20th Sep 2022
Publication Type: Journal
PubMed ID: 36130519
Citation: Cell Rep. 2022 Sep 20;40(12):111360. doi: 10.1016/j.celrep.2022.111360.
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
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
Young Scientists Retreat (YSR) will take place from September 7th to 9th in Hofgeismar (close to Kassel) (https://tagungsstaette-hofgeismar.de/). Participation is mandatory for all PhD students, MD students and Postdocs in SMART-NAFLD, C-TIP-HCC and DEEP-HCC
Start Date: 7th Sep 2022
End Date: 9th Sep 2022
Event Website: Not specified
Country: Germany
City: Not specified
Kickoff Meeting SMART- NAFLD 1.12.2021 - 2.12.2021
Heidelberg, Bioquant 7th Floor Greenier Room
Start Date: 1st Dec 2021
End Date: 2nd Dec 2021
Event Website: Not specified
Country: Germany
City: Heidelberg
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
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Agreement on the Use of Personal Data during LiSyM-Cancer Young Scientists Retreat Date: 07.09. -09.09.2022 Place: Ev. Tagungsstätte Hofgeismar
Creator: Olga Krebs
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Agenda for LiSyM-Cancer status seminar 2022
Creators: Olga Krebs, Wolfgang Müller, Ursula Klingmüller, Ina Biermayer
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Agenda Kickoff Meeting SMART-NAFLD 1-2 december 2021 in Heidelberg
Creators: Ursula Klingmüller, Ina Biermayer
Submitter: Olga Krebs
Investigations: No Investigations
Studies: No Studies
Assays: No Assays