Biomarker in observational prospective studies
BEAt-DKD harmonized clinical cohorts, validated biomarkers previously identified in pilot studies and discovered novel markers. A novel stress score associated with long-term decline of eGFR in both early and late DKD was developed based on a comprehensive characterization of mRNA transcriptomes from urinary extracellular vesicles (uEVs). We demonstrated technical quality and reproducibility of the mRNAseq pipeline and feasibility in the clinical setting, establishing uEVs as promising non-invasive liquid biopsies in DKD.
Efficacy biomarkers in intervention studies
By integrating omics data from cell- and animal models, and samples from clinical trials, two promising pharmacodynamic markers that can predict the response to atrasentan and canagliflozin have been discovered and validated. Clinical implementation is currently assessed in new prospective clinical trials across Europe within a new EU Horizon RIA grant PRIME-CKD (
https://prime-ckd.com(si apre in una nuova finestra)). We validated TNF receptor markers that can be used to monitor the response to SGLT2 inhibitors and can predict the long-term risk of kidney endpoints, thus supporting decision making in clinical practice. Against the background of the discovered correlation between insulin resistance and increased DKD risk, existing treatments are being re-evaluated, possibly leading to new disease indications.
Mechanisms and pathways
A comprehensive cell encyclopaedia of the kidney was established to unravel the molecular changes of the epigenome, transcriptome, proteome and post-translational modifications in different renal cells (podocytes, parietal epithelial cells, glomerular endothelial cells, mesangial cells, proximal tubular cells). Integration of cell and animal data identified common and cell-specific insulin resistance and DKD molecular programs. Single nucleus RNA-sequencing to identify molecular mechanisms of SGLT2 inhibitors and AI-based image analysis pipelines for biomarker validation were established, as well as novel imaging to quantify glomerular endothelial glycocalyx damage. Some of the more recent discoveries are based on extensive single-cell transcriptomics work, experimental work to gain further mechanistic insight with regards to insulin and leptin resistance, to explore epigenetic regulation in kidney organoids, to test the role of endothelial glycocalyx in DKD.
Development, identification and validation of prognostic and predictive imaging biomarkers
The iBEAt study, a prospective multi-centre observational cohort study in 608 patients with early stage DKD, explores associations between imaging biomarkers and renal function, and tests if imaging biomarkers can better predict DKD progression. Ancillary studies aim to: (1) validate imaging biomarkers against renal histopathology; (2) validate MRI measured renal blood flow against positron-emission tomography (PET); (3) validate methods for (semi-)automated processing of renal MRI; (4) examine longitudinal changes in imaging biomarkers; (5) examine if glycocalyx and microvascular measures are associated with imaging biomarkers and eGFR decline; (6) explore if findings in type 2 diabetes can be extrapolated to type 1. We established a central repository of biofluids with generous volumes to allow extensive targeted and untargeted omics analyses in serum, plasma, whole blood, urine, urinary vesicles and urinary sediment. Study protocols including standard operating procedures have been published (PMID: 32600374).
Integration and prioritization of DKD biomarkers and targets (systems medicine)
BEAt-DKD applied systems biology analyses of human, rodent and cell line data to identify predictive and dynamic biomarkers. Integration of multi-omics data from cell lines was used to identify pathways and mechanisms underlying DKD, as well as integrative analysis of metabolomics and lipidomics profiling and assessment of predictive power in early stage DKD. To ensure sustainability of resources generated by BEAt-DKD and according to FAIRification principles, results have been stored in a central repository, visualized and shared via the European Platform for Diabetes and Complications.
Optimization of trial design and preparation of implementation in the regulatory process
BEAt-DKD collaborated with key stakeholders including patient and physician groups, regulators, health technology assessors, and scientists from academia, pharmaceutical and biotech companies to develop an optimized blueprint for clinical studies. Recent highlights are the submission of the PRE-score document to the EMA for a Qualification Opinion, resulting in a Letter of Support from EMA, as well as several review articles on the biomarker qualification process and use in personalised medicine.
