Ina Biermayer

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About Ina Biermayer:

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)

SEEK ID: https://seek.lisym.org/people/115

Location: Germany

ORCID: Not specified

Joined: 29th Nov 2018

Expertise: Molecular Biology, Primary human hepatocytes, Systems Biology, wet lab, Signal transduction, Proteomics

Tools: Cell and tissue culture, Cell Isolation, Isolation and cultivation of mouse hepatocyte, Molecular Biology

Their tags

Hepatocytes Proteome TGFb

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Advanced Programmes list for this Person with search and filtering

LiSyM-Krebs - Systemmedizinisches Forschungsnetz zur Früherkennung und Prävention von Leberkrebs

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

LiSyM: Liver Systems Medicine

Liver Systems Medicine : striving to develop non-invasive methods for diagnosing and treating NAFLD by combining mathematical modeling and biological research. LiSyM, is a multidisciplinary research network, in which molecular and cell biologists, clinical researchers, pharmacologists and experts in mathematical modeling examine the liver in its entirety. LiSyM research focuses on the metabolic liver disease non-alcoholic fatty liver disease (NAFLD), which includes non-alcoholic steatohepatitis ...

Projects: LiSyM Core Infrastructure and Management (LiSyM-PD), LiSyM Pillar I: Early Metabolic Injury (LiSyM-EMI), LiSyM Pillar II: Chronic Liver Disease Progression (LiSyM-DP), LiSyM Pillar III: Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF), LiSyM Pillar IV: Liver Function Diagnostics (LiSyM-LiFuDi), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), LiSyM PALs, Project Management PTJ, LiSyM network, LiSyM Scientific Leadership Team (LiSyM-LT)

Web page: https://www.lisym.org/

Showing 5 out of a possible 6 Projects Advanced Projects list for this Person with search and filtering

C-TIP-HCC network

C-TIP-HCC- Mechanism-based Multiscale Model to Dissect the Tipping Point from Liver Cirrhosis to Hepatocellular Carcinoma

The ultimate goal of the C-TIP-HCC is a „mechanistic multiscale model to describe dynamic changes in regenerative nodes across a tipping point (TIP) towards development in patients with cirrhosis to facilitate early monitoring and intervention“ and facilitate intervention“. To achieve this, we will conduct in-depth studies on cirrhotic regenerative nodes.

Programme: LiSyM-Krebs - Systemmedizinisches Forschungsnetz zur Früherkennung und Prävention von Leberkrebs

Public web page: Not specified

Organisms: Homo sapiens, Mus musculus

SMART-NAFLD

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, ...

Programme: LiSyM-Krebs - Systemmedizinisches Forschungsnetz zur Früherkennung und Prävention von Leberkrebs

Public web page: Not specified

Organisms: Mus musculus, Homo sapiens

Forschungsnetzwerk LiSyM-Krebs

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 ...

Programme: LiSyM-Krebs - Systemmedizinisches Forschungsnetz zur Früherkennung und Prävention von Leberkrebs

Public web page: Not specified

Organisms: Homo sapiens, Mus musculus, Rattus norvegicus, Rattus rattus

DEEP-HCC network

DEEP-HCC - Detailed Analysis of the Spatial Organization of the Development of Hepatocellular Carcinoma

Programme: LiSyM-Krebs - Systemmedizinisches Forschungsnetz zur Früherkennung und Prävention von Leberkrebs

Public web page: Not specified

Organisms: Homo sapiens, Mus musculus

LiSyM network

This comprises the whole LiSyM network

Programme: LiSyM: Liver Systems Medicine

Public web page: http://www.lisym.org

Start date: 1st Jan 2016

Organisms: Rattus norvegicus, Rattus rattus, Mus musculus, Homo sapiens

View all 6 Projects

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German Cancer Research Center (DKFZ), Division of Systems Biology of Signal Transduction

Country: Germany

City: 69120 Heidelberg

Web page: https://www.dkfz.de/en/systembiologie/index.php

HITS gGmbH

Country: Germany

City: 69118 Heidelberg

Web page: https://www.h-its.org/

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Proteomic alterations in Western Diet (WD) hepatocytes

Forschungsnetzwerk LiSyM-Krebs

In this study, we characterize Western diet-induced phenotypic changes in murine 392 hepatocytes and employ dynamic pathway modelling to resolve the underlying molecular 393 mechanisms resulting in altered intracellular signal transduction and enhanced proliferation 394 of WD hepatocytes.

Submitter: Olga Krebs

Investigation: 1 hidden item

Assays: No Assays

Snapshots: No snapshots

Created: 16th Aug 2023 at 09:26, Last updated: 16th Aug 2023 at 09:28

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SOP : Western diat mouse housing and feeding

Forschungsnetzwerk LiSyM-Krebs, SMART-NAFLD

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

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Created: 16th Aug 2023 at 10:08, Last updated: 16th Aug 2023 at 10:18

SOP : Isolation of primary mouse hepatocytes

Forschungsnetzwerk LiSyM-Krebs, SMART-NAFLD

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

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Created: 16th Aug 2023 at 10:17

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Showing 5 out of a possible 44 Publications Advanced Publications list for this Person with search and filtering

Comprehensive evaluation of phosphoproteomic-based kinase activity inference (preprint)

Forschungsnetzwerk LiSyM-Krebs, C-TIP-HCC network

Abstract (Expand)

Kinases play a central role in regulating cellular processes, making their study essential for understanding cellular function and disease mechanisms. To investigate the regulatory state of a kinase, … numerous methods have been, and continue to be, developed to infer kinase activities from phosphoproteomics data. These methods usually rely on a set of kinase targets collected from various kinase-substrate libraries. However, only a small percentage of measured phosphorylation sites can usually be attributed to an upstream kinase in these libraries, limiting the scope of kinase activity inference. In addition, the inferred activities from different methods can vary making it crucial to evaluate them for accurate interpretation. Here, we present a comprehensive evaluation of kinase activity inference methods using multiple kinase-substrate libraries combined with different inference algorithms. Additionally, we try to overcome the coverage limitations for measured targets in kinase substrate libraries by adding predicted kinase-substrate interactions for activity inference. For the evaluation, in addition to classical cell-based perturbation experiments, we introduce a tumor-based benchmarking approach that utilizes multi-omics data to identify highly active or inactive kinases per tumor type. We show that while most computational algorithms perform comparably regardless of their complexity, the choice of kinase-substrate library can highly impact the inferred kinase activities. Hereby, manually curated libraries, particularly PhosphoSitePlus, demonstrate superior performance in recapitulating kinase activities from phosphoproteomics data. Additionally, in the tumor-based evaluation, adding predicted targets from NetworKIN further boosts the performance, while normalizing sites to host protein levels reduces kinase activity inference performance. We then showcase how kinase activity inference can help in characterizing the response to kinase inhibitors in different cell lines. Overall, the selection of reliable kinase activity inference methods is important in identifying deregulated kinases and novel drug targets. Finally, to facilitate the evaluation of novel methods in the future, we provide both benchmarking approaches in the R package benchmarKIN.

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]

Created: 5th Jul 2024 at 07:42

Thy‐1 restricts steatosis and liver fibrosis in steatotic liver disease

Forschungsnetzwerk LiSyM-Krebs, SMART-NAFLD, DEEP-HCC network

Abstract (Expand)

Abstract Background and Aims Steatotic liver disease (SLD) is generally considered to represent a hepatic manifestation of metabolic syndrome and includes a disease spectrum comprising isolated steatosis, …ludes a disease spectrum comprising isolated steatosis, metabolic dysfunction‐associated steatohepatitis, liver fibrosis and ultimately cirrhosis. A better understanding of the detailed underlying pathogenic mechanisms of this transition is crucial for the design of new and efficient therapeutic interventions. Thymocyte differentiation antigen (Thy‐1, also known as CD90) expression on fibroblasts controls central functions relevant to fibrogenesis, including proliferation, apoptosis, cytokine responsiveness, and myofibroblast differentiation. Methods The impact of Thy‐1 on the development of SLD and progression to fibrosis was investigated in high‐fat diet (HFD)‐induced SLD wild‐type and Thy‐1‐deficient mice. In addition, the serum soluble Thy‐1 (sThy‐1) concentration was analysed in patients with metabolic dysfunction‐associated SLD stratified according to steatosis, inflammation, or liver fibrosis using noninvasive markers. Results We demonstrated that Thy‐1 attenuates the development of fatty liver and the expression of profibrogenic genes in the livers of HFD‐induced SLD mice. Mechanistically, Thy‐1 directly inhibits the profibrotic activation of nonparenchymal liver cells. In addition, Thy‐1 prevents palmitic acid‐mediated amplification of the inflammatory response of myeloid cells, which might indirectly contribute to the pronounced development of liver fibrosis in Thy‐1‐deficient mice. Serum analysis of patients with metabolically associated steatotic liver disease syndrome revealed that sThy‐1 expression is correlated with liver fibrosis status, as assessed by liver stiffness, the Fib4 score, and the NAFLD fibrosis score. Conclusion Our data strongly suggest that Thy‐1 may function as a fibrosis‐protective factor in mouse and human SLD.

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

Created: 10th Jul 2024 at 13:31, Last updated: 10th Jul 2024 at 13:32

Lysis buffer selection guidance for mass spectrometry-based global proteomics including studies on the intersection of signal transduction and metabolism (preprint)

LiSyM network, Forschungsnetzwerk LiSyM-Krebs, SMART-NAFLD, C-TIP-HCC network

Abstract (Expand)

Prerequisite for a successful proteomics experiment is a high-quality lysis of the sample of interest, resulting in a large number of identified proteins as well as a high coverage of protein sequences. …

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:

Created: 1st Mar 2024 at 13:14, Last updated: 8th Mar 2024 at 07:44

Basal MET phosphorylation is an indicator of hepatocyte dysregulation in liver disease

Forschungsnetzwerk LiSyM-Krebs, SMART-NAFLD

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Abstract (Expand)

Abstract Chronic liver diseases are worldwide on the rise. Due to the rapidly increasing incidence, in particular in Western countries, metabolic dysfunction-associated steatotic liver disease (MASLD) …

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

Created: 19th Jan 2024 at 12:34, Last updated: 8th Mar 2024 at 07:44

Tumour cells can escape antiproliferative pressure by interferon-β through immunoediting of interferon receptor expression

LiSyM network, Forschungsnetzwerk LiSyM-Krebs, SMART-NAFLD, C-TIP-HCC network

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Abstract (Expand)

Abstract Type I interferons (IFNs) play a central role not only in innate immunity against viral infection, but also in the antitumour response, e.g. through a direct impact on cell proliferation. …

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