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MESI-STRAT

Overview

MESI-STRAT: Systems Medicine of Metabolic-Signaling Networks -A New Concept for Breast Cancer Patient Stratification.
Breast cancer is a complex disease with high prevalence in the European Union and world-wide. 75%-80 of the patients have estrogen receptor-positive (ER)-positive tumors and are treated with endocrine therapies. Endocrine therapies, which block ER-driven tumor growth, show high efficacy. Yet, a significant proportion of the patients will eventually relapse with metastatic breast cancer, and the recurrence rates remain almost constant for up to 20 years. MESI-STRAT develops metabolite marker panels measurable in biological fluids to enable patient stratification, resistance monitoring and clinical decision-making throughout endocrine therapy. This is a new concept as breast cancer metabolism is poorly explored for diagnostics and therapy. Upon successful validation in preclinical models, the predictive marker panels and related treatments will be jointly investigated by MESI-STRAT’s clinical and industrial partners. The MESI-STRAT consortium explores the interplay of breast cancer metabolism and oncogenic signaling (MEtabolic SIgnaling) by systems medicine approaches. MESI-STRAT develops new models for knowledge-based STRATification of patients into subgroups with different endocrine therapy resistance mechanisms.

Programme: This Project is not associated with a Programme

SEEK ID: https://fairdomhub.org/projects/99

Public web page: http://www.mesi-strat.eu

Organisms: Homo sapiens, Mus musculus, Rattus norvegicus

FAIRDOM PALs: No PALs for this Project

Project created: 26th Feb 2018

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Tobias Anzeneder

Projects: MESI-STRAT

Institutions: PATH - Patients' Tumor Bank of Hope

Barbara Bakker project_administrator

Projects: SilicoTryp, Multiscale modelling of state transitions in the host-microbiome-brain network, MESI-STRAT, PoLiMeR - Polymers in the Liver: Metabolism and Regulation

Institutions: University of Groningen

https://orcid.org/0000-0001-6274-3633
Dyah Dewi

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Institutions: German Cancer Research Center (DKFZ)

Petra Engele

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Institutions: University Of Innsbruck

Cornelia Gieseler

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Institutions: Charité University Medicine Berlin

Sushma Nagaraja Grellscheid

Projects: MESI-STRAT, Stress granules

Institutions: Durham University, University of Bergen

Sebastian Groothuis

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Institutions: University of Groningen

Alexander Heberle

Projects: MESI-STRAT

Institutions: University of Groningen

https://orcid.org/0000-0001-6414-8707
Ines Heiland project_administrator

Projects: MESI-STRAT, NAD COMPARTMENTATION, NAD phylogeny

Institutions: The Arctic University of Norway (UiT)

Karl-Heinz Kellner

Projects: MESI-STRAT

Institutions: Neuroimmun GmbH

Olga Krebs adminproject_administratorasset_housekeeperasset_gatekeeperprogramme_administrator

Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, ZucAt, SysMO-LAB, Kinetics on the move - Workshop 2016, Example use cases, FAIRDOM user meeting, ErasysApp Funders, EraCoBiotech 2 nd call proposal preparation, Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, Multiscale modelling of state transitions in the host-microbiome-brain network, BESTER, TRALAMINOL, Sustainable co-production, INDIE - Biotechnological production of sustainable indole, Extremophiles metabolsim, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, GB-XMap: Assessing the risk of gut-brain cross-diseases Investigating the gut-brain-axis, NAD COMPARTMENTATION, HOTSOLUTE, Stress granules

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH), FAIRDOM User meeting, Norwegian University of Science and Technology

https://orcid.org/0000-0003-3540-0402
Janina Leyk

Projects: MESI-STRAT

Institutions: University of Groningen

Wolfgang Müller project_administratorasset_housekeeperasset_gatekeeperprogramme_administrator

Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, de.NBI-SysBio, Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Kinetics on the move - Workshop 2016, Example use cases, SBEpo - Systems Biology of Erythropoietin, FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, EnzymeML, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, MS_DILI, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik"

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

https://orcid.org/0000-0002-4980-3512
Juliane Nees

Projects: MESI-STRAT

Institutions: University of Heidelberg

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Marc Niere project_administrator

Projects: MESI-STRAT, NAD COMPARTMENTATION, Bergen(Ziegler lab) project AF-NADase

Institutions: University of Bergen

Aysen Lisa Norte

Projects: MESI-STRAT

Institutions: SysBioSim

Christiane Opitz

Projects: MESI-STRAT

Institutions: German Cancer Research Center (DKFZ)

Marta Palafox

Projects: MESI-STRAT

Institutions: Vall d´Hebron Institute of Oncology (VHIO)

Mirja Tamara Prentzell

Projects: MESI-STRAT

Institutions: German Cancer Research Center (DKFZ)

https://orcid.org/0000-0002-9659-9825
Patricia Razquin Navas

Projects: MESI-STRAT

Institutions: University of Groningen

Charité University Medicine Berlin

Country:  Germany

City: Berlin

Web page: http://www.charite.de/

De Duve Institute

Country:  BE

City: Bruxelles

Web page: https://www.deduveinstitute.be

Durham University

Country:  GB

City: Durham

Web page: https://www.dur.ac.uk

German Cancer Research Center (DKFZ)

Country:  Germany

City: Heidelberg

Web page: http://www.dkfz.de/en/index.html

Heidelberg Institute for Theoretical Studies (HITS gGmbH)

Country:  Germany

City: Heidelberg

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

Neuroimmun GmbH

Country:  DE

City: Karlsruhe

Web page: https://www.neuroimmun.com/

PATH - Patients' Tumor Bank of Hope

Country:  DE

City: München

Web page: http://path-biobank.org/index.php/de/

SysBioSim

Country:  NL

City: Leiden

Web page: http://sysbiosim.com/

The Arctic University of Norway (UiT)

Country:  NO

City: Tromsø

Web page: https://en.uit.no/startsida

University Of Innsbruck

Country:  AT

City: Innsbruck

Web page: https://www.uibk.ac.at/

University of Bergen

Country:  Norway

City: Not specified

Web page: Not specified

University of Groningen

Country:  Netherlands

City: Groningen

Web page: http://www.rug.nl/corporate/index

University of Heidelberg

Country:  Germany

City: Heidelberg

Web page: http://www.uni-heidelberg.de/index_e.html

University of Newcastle

Country:  United Kingdom

City: Newcastle

Web page: http://www.ncl.ac.uk/camb/

Vall d´Hebron Institute of Oncology (VHIO)

Country:  ES

City: Barcelona

Web page: http://www.vhio.net/en

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MCF-7
MESI-STRAT

Contributor: Pamela Riemer

Provider Name: Opitz lab

Provider's strain ID: MCF-7

Organism: Homo sapiens

Genotypes: wild-type

Phenotypes: wild-type

Comment: The cells were sent to CHAB from Opitz lab and STR profiled to confirm their identity. Their mutational pattern was analysed by panel DNA sequencing as described in file "MESI-STRATcells.docx".

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Model of tryptophan metabolism, readily scalable using tissue-specific gene expression data.
MESI-STRAT

Abstract (Expand)

Tryptophan is utilized in various metabolic routes including protein synthesis, serotonin, and melatonin synthesis and the kynurenine pathway. Perturbations in these pathways have been associated with … neurodegenerative diseases and cancer. Here we present a comprehensive kinetic model of the complex network of human tryptophan metabolism based upon existing kinetic data for all enzymatic conversions and transporters. By integrating tissue-specific expression data, modeling tryptophan metabolism in liver and brain returned intermediate metabolite concentrations in the physiological range. Sensitivity and metabolic control analyses identified expected key enzymes to govern fluxes in the branches of the network. Combining tissue-specific models revealed a considerable impact of the kynurenine pathway in liver on the concentrations of neuroactive derivatives in the brain. Moreover, using expression data from a cancer study predicted metabolite changes that resembled the experimental observations. We conclude that the combination of the kinetic model with expression data represents a powerful diagnostic tool to predict alterations in tryptophan metabolism. The model is readily scalable to include more tissues, thereby enabling assessment of organismal tryptophan metabolism in health and disease.

Authors: A. K. Stavrum, Ines Heiland, S. Schuster, P. Puntervoll, Mathias Ziegler

Date Published: No date defined

Journal: J Biol Chem

Suppression of indoleamine-2,3-dioxygenase 1 expression by promoter hypermethylation in ER-positive breast cancer.
MESI-STRAT

Abstract (Expand)

Kynurenine formation by tryptophan-catabolic indoleamine-2,3-dioxygenase 1 (IDO1) plays a key role in tumor immune evasion and inhibition of IDO1 is efficacious in preclinical models of breast cancer. … As the response of breast cancer to immune checkpoint inhibitors may be limited, a better understanding of the expression of additional targetable immunomodulatory pathways is of importance. We therefore investigated the regulation of IDO1 expression in different breast cancer subtypes. We identified estrogen receptor alpha (ER) as a negative regulator of IDO1 expression. Serum kynurenine levels as well as tumoral IDO1 expression were lower in patients with ER-positive than ER-negative tumors and an inverse relationship between IDO1 and estrogen receptor mRNA was observed across 14 breast cancer data sets. Analysis of whole genome bisulfite sequencing, 450k, MassARRAY and pyrosequencing data revealed that the IDO1 promoter is hypermethylated in ER-positive compared with ER-negative breast cancer. Reduced induction of IDO1 was also observed in human ER-positive breast cancer cell lines. IDO1 induction was enhanced upon DNA demethylation in ER-positive but not in ER-negative cells and methylation of an IDO1 promoter construct reduced IDO1 expression, suggesting that enhanced methylation of the IDO1 promoter suppresses IDO1 in ER-positive breast cancer. The association of ER overexpression with epigenetic downregulation of IDO1 appears to be a particular feature of breast cancer as IDO1 was not suppressed by IDO1 promoter hypermethylation in the presence of high ER expression in cervical or endometrial cancer.

Authors: D. L. Dewi, S. R. Mohapatra, S. Blanco Cabanes, I. Adam, L. F. Somarribas Patterson, B. Berdel, M. Kahloon, L. Thurmann, S. Loth, K. Heilmann, D. Weichenhan, O. Mucke, Ines Heiland, P. Wimberger, J. D. Kuhlmann, Karl-Heinz Kellner, Sarah Schott, C. Plass, M. Platten, C. Gerhauser, S. Trump, Christiane Opitz

Date Published: No date defined

Journal: Oncoimmunology

Gene expression profiling of primary male breast cancers reveals two unique subgroups and identifies N-acetyltransferase-1 (NAT1) as a novel prognostic biomarker.
MESI-STRAT

Abstract (Expand)

INTRODUCTION: Male breast cancer (MBC) is a rare and inadequately characterized disease. The aim of the present study was to characterize MBC tumors transcriptionally, to classify them into comprehensive … subgroups, and to compare them with female breast cancer (FBC). METHODS: A total of 66 clinicopathologically well-annotated fresh frozen MBC tumors were analyzed using Illumina Human HT-12 bead arrays, and a tissue microarray with 220 MBC tumors was constructed for validation using immunohistochemistry. Two external gene expression datasets were used for comparison purposes: 37 MBCs and 359 FBCs. RESULTS: Using an unsupervised approach, we classified the MBC tumors into two subgroups, luminal M1 and luminal M2, respectively, with differences in tumor biological features and outcome, and which differed from the intrinsic subgroups described in FBC. The two subgroups were recapitulated in the external MBC dataset. Luminal M2 tumors were characterized by high expression of immune response genes and genes associated with estrogen receptor (ER) signaling. Luminal M1 tumors, on the other hand, despite being ER positive by immunohistochemistry showed a lower correlation to genes associated with ER signaling and displayed a more aggressive phenotype and worse prognosis. Validation of two of the most differentially expressed genes, class 1 human leukocyte antigen (HLA) and the metabolizing gene N-acetyltransferase-1 (NAT1), respectively, revealed significantly better survival associated with high expression of both markers (HLA, hazard ratio (HR) 3.6, P = 0.002; NAT1, HR 2.5, P = 0.033). Importantly, NAT1 remained significant in a multivariate analysis (HR 2.8, P = 0.040) and may thus be a novel prognostic marker in MBC. CONCLUSIONS: We have detected two unique and stable subgroups of MBC with differences in tumor biological features and outcome. They differ from the widely acknowledged intrinsic subgroups of FBC. As such, they may constitute two novel subgroups of breast cancer, occurring exclusively in men, and which may consequently require novel treatment approaches. Finally, we identified NAT1 as a possible prognostic biomarker for MBC, as suggested by NAT1 positivity corresponding to better outcome.

Authors: I. Johansson, C. Nilsson, P. Berglund, M. Lauss, M. Ringner, H. Olsson, L. Luts, E. Sim, S. Thorstensson, M. L. Fjallskog, I. Hedenfalk

Date Published: No date defined

Journal: Breast Cancer Res

Copy number profiling by array comparative genomic hybridization identifies frequently occurring BRCA2-like male breast cancer.
MESI-STRAT

Abstract (Expand)

Genomic aberrations can be used to subtype breast cancer. In this study, we investigated DNA copy number (CN) profiles of 69 cases of male breast cancer (MBC) by array comparative genomic hybridization … (aCGH) to detect recurrent gains and losses in comparison with female breast cancers (FBC). Further, we classified these profiles as BRCA1-like, BRCA2-like or non-BRCA-like profiles using previous classifiers derived from FBC, and correlated these profiles with pathological characteristics. We observed large CN gains on chromosome arms 1q, 5p, 8q, 10p, 16p, 17q, and chromosomes 20 and X. Large losses were seen on chromosomes/chromosome arms 1p, 6p, 8p, 9, 11q, 13, 14q, 16q, 17p, and 22. The pattern of gains and losses in estrogen receptor positive (ER+) MBC was largely similar to ER+ FBC, except for gains on chromosome X in MBC, which were uncommon in FBC. Out of 69 MBC patients, 15 patients (22%) had a BRCA2-like profile, of which 2 (3%) were also BRCA1-like. One patient (1%) was only BRCA1-like; the remaining 53 (77%) patients were classified as non-BRCA-like. BRCA2-like cases were more often p53 accumulated than non-BRCA-like cases (P = 0.014). In conclusion, the pattern of gains and losses in ER+ MBC was largely similar to that of its ER+ FBC counterpart, except for gains on chromosome X in MBC, which are uncommon in FBC. A significant proportion of MBC has a BRCA2-like aCGH profile, pointing to a potentially hereditary nature, and indicating that they could benefit from a drug regimen targeting BRCA defects as in FBC.

Authors: H. D. Biesma, P. C. Schouten, M. M. Lacle, J. Sanders, W. Brugman, R. Kerkhoven, I. Mandjes, P. van der Groep, P. J. van Diest, S. C. Linn

Date Published: No date defined

Journal: Genes Chromosomes Cancer

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