Identification of novel diagnostic, predictive and therapeutic strategies in chronic kidney disease

Project Information

TargetCKD

Grant agreement ID: 101043403

DOI

10.3030/101043403

EC signature date 23 June 2022

Start date 1 July 2022

End date 30 June 2028

Funded under

• European Research Council (ERC)

Total cost

€ 1 999 063,00

EU contribution

€ 1 999 063,00

Coordinated by

UNIVERSITAETSKLINIKUM AACHEN
Germany

Periodic Reporting for period 1 - TargetCKD (Identification of novel diagnostic, predictive and therapeutic strategies in chronic kidney disease)

Reporting period: 2022-07-01 to 2024-12-31

Summary of the context and overall objectives of the project

Chronic Kidney Disease (CKD) represents an important medical, social and economic burden with high morbidity and mortality. The prevalence of CKD has reached >10% in the developed world, and CKD globally accounts for more years lived with disability than all neoplasms combined. Therapeutic strategies to treat CKD or tools for risk stratification of patients are limited and the field has produced the fewest translational randomized clinical trials in medicine while diagnosis is still based on invasive tissue biopsies. TargetCKD aims to establish a holistic understanding of cellular and molecular mechanisms that drive disease to develop novel diagnostic, predictive and therapeutic options. Concrete objectives are: (1) the development of a platform for identification of novel predictive markers and therapeutic targets in kidney biopsies; (2) the identification of conserved spatio-temporal mechanisms and cellular cross-talk events driving CKD; (3) the validation of mechanisms and therapeutic targets in human 3D organoid systems and development of therapeutics and (4) the development of a non-invasive diagnostic platform from urine. TargetCKD will utilize different single cell and spatial genomic and computational technologies combined with transgenic mouse models and in vitro models. The combination of all these technologies with follow-up data and large validation cohorts will allow TargetCKD to transform nephrology towards an improved understanding of kidney diseases and the development of novel diagnostics, risk stratification tools, clinical testing as well as therapeutics for patients suffering from CKD.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We have generated snRNA-sequencing and snATAC sequencing from >100 kidney biopsies (objective 1) and have built the first spatial proteomics panels to validate findings. Our data indicates various potential predictive factors and novel mechanisms that we are currently validating in both mouse models and organoids. To scale up the single cell /nuclear sequencing we have initially tested split seq approaches as proposed. However, the data quality was not acceptable and thus we have developed a better pipeline for utilizing SNPs based demultiplexing, which we have termed SoupLadle. This wetlab and coputational pipeline allows us to increase throughput and precisely allign almost 100% of cells back to the actual patient.

In mice and organoids, we have generated first spatiotemporal datasets that unravel interesting novel mechanisms of kidney fibrosis (objective 2). Using iPSC derived kidney organoids and co-culture models with cell lines we have identified and validated several mechanisms of kidney fibrosis (objective 3). Among several new mechanisms we have identified the metalloprotease ADAMTS12 which is specifically expressed in perivascular fibroblasts. We have identified a novel substrate of this metalloprotease namely HMCN1 and demonstrated that cleavage of HMCN1 is critical for fibroblast migration. ADAMTS12 knockout mice are protected from kidney fibrosis.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

We have identified ADAMTS12 as a novel therapeutic target in fibrosis and have already submitted a patent application to secure IP. We are currently conducting market research for this therapeutic target in kidney fibrosis. We have identified a tool compound that binds ADAMTS12 and are aiming to develop this further as a novel therapy for kidney fibrosis and CKD.

The SoupLadle pipeline will be published open access and the code will be freely available. We believe that this pipeline will allow the scientific community to increase throughput in scRNA-seq and increase precision in demultiplexing of human scRNA-seq datasets.