TP3 - SyMBoD

Identification of biomarkers for the early diagnosis and prognosis of the progression of bone defect healing with Type 2 Diabetes Mellitus (T2DM)

In line with the long-term vision of SyMBoD: the creation of a digital platform with the capability of theranostics, SP3’s main goal involves (i) the determination of an individual patient’s “blueprint” including a comprehensive, time-resolved and predictive molecular profile of metabolite, protein and RNA data and (ii) developing bioinformatics analysis pipelines to determine molecular biomarkers that may be used for early disease diagnosis (and prognosis or patient stratification) as well as checking the progress of bone defect healing patients with Non-union and T2DM.
Initially, samples from T2DM rat model generated in SP1 will be used to test the effect of different fracture treatment protocols extensively. We will collect blood plasma, regenerated tissue and wound fluids for omics analysis to gain comprehensive insights into the molecular profiles during the progression of fracture healing. Network-enhanced machine learning approaches and correlation with text mining will provide a list of potential mechanistic biomarkers that will serve for translation into analyses of human samples generated in SP2.
The quantitative metabolite, protein and transcriptome information of blood serum and exosomes will be determined for distinctive human patient groups (Kalkhof Lab at Fraunhofer IZI) to reveal and validate inherent biomarkers responsible for the observed phenotypes amongst patients diagnosed with non-union and T2DM. Additionally, the results from the integrative omics analyses shall be coupled with pathway- and network-based analysis (leveraging on The Baumbach Lab expertise) to enable a system-wide view of the molecular biomarkers at play in patients diagnosed with non-union and T2DM and with potential to guide the decision making for clinical treatment. The biomarkers generated from this subproject will then further be validated by targeted assays and be used as input features for the models that will be built in SP4 as well as the APIs and plugins to be developed in SP5.