Fraunhofer Institute for Translational Medicine and Pharmacology ITMP
Fraunhofer Institute for Translational Medicine and Pharmacology ITMP

© Fraunhofer ITMP | Sonja Luckhardt

OMICS-Technologies

By now, omics technologies and multi-omics analyses are fundamental methods in preclinical and clinical research as well as in drug development.

The focus is on understanding the molecular basis of disease development and progression as well as on the identification of biomarkers for diagnosis, prognosis and potential treatment response.

By combining different datasets and integrating clinical parameters, the aim is to derive disease and patient profiles and to make them available for use in patient care.

We are focusing on the analysis of secreted molecules (proteins, lipids, metabolites), particularly in blood samples, as they are easily accessible and therefore represent optimal candidates for broad application as biomarkers. However, the methods used are also applied for the analysis of other biological matrices (e.g., other body fluids, tissue or cell samples).

 

Core competencies:

Proteomics: PEA-based (Olink)

  • Olink Panel: Target 96, Target 48, Flex, Focus
    Further information about the technology and products can be found here.
  • Single samples, single- and multi-plate projects, longitudinal studies
  • Human and murine samples
  • Various matrices: e.g., plasma, serum, tissue- and cell lysates, cell supernatants, ISF, DBS, ascites fluid, synovial fluid, breath condensate, liquor, extracellular vesicles
  • Analysis of minimum volumes

Lipidomics & Metabolomics: Mass Spectrometry

  • Mass spectrometry coupled to liquid or gas chromatography
  • Imaging mass spectrometry for tissue samples
  • Screening methods for abundant lipids and metabolites as well as specified methods for low concentrated signaling molecules (e.g. oxylipins, sphingolipids, endocannabinoids, tryptophan and related metabolites)
  • Various matrices of different origin (human, murine etc.): e.g. plasma, serum, tissue- and cell samples, cell organelles, cell supernatants, ISF, DBS, synovial fluid, liquor, extracellular vesicles
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Preclinical and Clinical studies

  • Identification of diagnostic, prognostic and predictive biomarkers
  • Identification of surrogate markers for efficacy and safety
  • Patient stratification

Research Projects

  • Biomarker analyses in different in vitro-, ex vivo and in vivo model systems
  • Validation studies
  • Mechanistic analyses

Services Offered

  • Single- or Multi-Omics analyses
  • Analysis of single samples up to big cohorts (high-throughput analyses) in longitudinal studies
  • Preparation of protocols for sample collection and preanalytical sample processing
  • Project/study support from preparation to data processing
  • Support for data analysis and evaluation

COVIMMUN - "Omics"-based immunome analysis for prediction of acute COVID-19 disease progression and early detection of long-term effects

What is the risk of developing a severe COVID-19 disease after SARS-CoV-2 infection? Can possible long-term damage and subsequent diseases be detected at an early stage and prevented therapeutically? The Fraunhofer ITMP project »COVIMMUN» deals with these questions in close cooperation with the University Hospital Frankfurt and Fraunhofer IAIS and IGD. The patient-individual immunome of COVID-19 patients in the acute disease phase and during subsequent long-term observation is analyzed in detail using OMICS technologies. The aim is to identify molecular biomarkers that indicate whether there is a particular risk of COVID-19 disease progression or the development of long-term damage and secondary complications, in order to be able to initiate early and purposefully preventive or therapeutic measures, if necessary.

Partner: University Hospital Frankfurt, Fraunhofer IAIS, Fraunhofer IGD

Additional information

4D Clinic - Identification of biomarker profiles of patients with immune-mediated diseases for the development of individualized therapies

The combination of omics-bases data and clinical parameters of patients with various immune-mediated diseases will be used to create so-called „immunological maps. The information they contain will be used as diagnostic, prognostic and predictive biomarkers as well as for patient stratification. Based on common characteristics, therapy concepts that can be integrated into clinical routine across all disciplines will be derived.

Further information: 4D Clinic

COVend – A new therapy to prevent progression to severe ARDS

Data from proteomics and lipidomic/metabolomic analyses will be incorporated into the study and contribute to a better understanding of the molecular mechanisms underlying the mode of action of FX06 and the therapeutic effects on the cellular level.

Further information: COVend – A new therapy to prevent the progression of COVID-19

HIPPOCRATES – Early detection and therapy optimization for the treatment of psoriatic arthritis

The complex datasets consisting of clinical parameters, imaging data and different omics analyses of patients with psoriasis and psoriatic arthritis will be processed with the help of machine learning and artificial intelligence. The resulting models will then be used for diagnostics, the prediction of patient-specific disease progression and the identification of individualized therapies.

Further information: HIPPOCRATES


Rischke S, Gurke R, Bennett A, Behrens F, Geisslinger G, Hahnefeld L
ALISTER – Application for lipid stability evaluation and research.
Clin Chim Acta. 2024 Mar 15:557:117858
doi: 10.1016/j.cca.2024.117858

Kugler S, Hahnefeld L, Kloka JA, Ginzel S, Nürenberg-Goloub E, Zinn S, Vehreschild MJ, Zacharowski K, Lindau S, Ullrich E, Burmeister J, Kohlhammer J, Schwäble J, Gurke R, Dorochow E, Bennett A, Dauth S, Campe J, Knape T, Laux V, Kannt A, Köhm M, Geisslinger G, Resch E, Behrens F
Short-term predictor for COVID-19 severity from a longitudinal multi-omics study for practical application in intensive care units.
Talanta. 2024 Feb 1;268(Pt 1):125295
doi: 10.1016/j.talanta.2023.125295

Rischke S, Hahnefeld L, Burla B, Behrens F, Gurke R, Garrett TJ
Small molecule biomarker discovery: Proposed workflow for LC-MS-based clinical research projects.
J Mass Spectrom Adv Clin Lab. 2023 Feb 17:28:47-55
doi: 10.1016/j.jmsacl.2023.02.003

Sens A, Rischke S, Hahnefeld L, Dorochow E, Schäfer SMG, Thomas D, Köhm M, Geisslinger G, Behrens F, Gurke R
Pre-analytical sample handling standardization for reliable measurement of metabolites and lipids in LC-MS-based clinical research.
J Mass Spectrom Adv Clin Lab. 2023 Feb 17:28:35-46
doi: 10.1016/j.jmsacl.2023.02.002

Gurke R, Bendes A, Bowes J, Koehm M, Twyman RM, Barton A, Elewaut D, Goodyear C, Hahnefeld L, Hillenbrand R, Hunter E, Ibberson M, Ioannidis V, Kugler S, Lories RJ, Resch E, Rüping S, Scholich K, Schwenk JM, Waddington JC, Whitfield P, Geisslinger G, FitzGerald O, Behrens F, Pennington SR; HIPPOCRATES Consortium
Omics and Multi-Omics Analysis for the Early Identification and Improved Outcome of Patients with Psoriatic Arthritis.
Biomedicines 2022 Sep 24;10(10):2387
doi: 10.3390/biomedicines10102387

Nieraad H, de Bruin N, Arne O, Hofmann MCJ, Pannwitz N, Resch E, Luckhardt S, Schneider AK, Trautmann S, Schreiber Y, Gurke R, Parnham MJ, Till U, Geisslinger G
The Roles of Long-Term Hyperhomocysteinemia and Micronutrient Supplementation in the AppNL-G-F Model of Alzheimer’s Disease.
Front Aging Neurosci. 2022 Apr 26:14:876826
doi: 10.3389/fnagi.2022.876826