Identification of genes and pathways involved in the development and progression of glomerular diseases

Chronic kidney disease (CKD) affects millions of people worldwide and is characterized by a reduction in glomerular filtration rate and albuminuria resulting in a gradual loss of kidney function. The high prevalence of the disease, along with the limited treatment options available, makes it a major burden to the health care systems around the world. Current treatment strategies are directed towards slowing the progression and delaying the complications. The glomerulus is the filtration unit of the kidney and a major target of injury, making glomerular diseases one of the leading causes of CKD. The kidney is a challenging organ to study due to tissue heterogeneity, complex disease phenotypes and morphologies. The lack of knowledge on the molecular mechanisms of disease pathogenesis limits the development of new diagnostic and treatment tools.

The main aim of this thesis was to gain a better understanding into genes and pathways involved in the development and progression of glomerular diseases. In a long run, our aim is to utilize the gained knowledge to develop new means to diagnose and treat CKD.

In the first part of the thesis (paper I and II), we used single cell RNA-sequencing (scRNAseq) to get insights into the glomerular environment in health and disease, as well as under drug therapy.

Paper I: By profiling the glomerulus, we defined the true transcriptomic signatures of specific cell types, gained better insight into their functionality, and identified molecular profiles of rare cell types. By comparing the expression profiles between mouse and human glomerulus, we revealed significant cross-species differences in the main glomerular cells.

Paper II: By profiling the molecular signatures of Angiotensin Converting Enzyme-inhibitor (ACEi) in diseased glomerular tissue, we revealed mesangial cells (MCs) to be the main early responder to the treatment. MCs showed downregulation of genes and pathways related to extracellular matrix (ECM) production. Only few transcriptomic changes were detected in the other glomerular cell types.

In the second part of the thesis (paper III and IV), we investigated two candidate genes identified through transcriptomic studies. Retinoic acid receptor responder 1 (Rarres1) and Natriuretic peptide receptor 3 (NPR3) were analysed through various in vitro and in vivo experiments.

Paper III: We investigated the role of Rarres1 in the glomerulus using various transgenic mouse lines, molecular profiling of patient material and in vitro models. We identified Rarres1 as a possible therapeutic target and biomarker of injury for glomerular diseases. In diseases, an up-regulation of Rarres1 expression was observed in endothelial cells, in which it aggravated the glomerular injury. This effect was potentially mediated by the activation of NFκB pathway via tyrosine kinase Axl.

Paper IV: We analysed the role of NPR3 in the glomerulus, and especially explored the possibility of manipulating glomerular natriuretic peptide (NP) system through NPR3. Pharmacological inhibition of NPR3 showed variable reno-protective effects when profiled in two rodent models of glomerular injury, suggesting that the modulation of the glomerular NP system could be a potential therapeutic target for CKD. However, more studies are needed to optimise the treatment strategy and to further understand the role of NPR3 in kidney tissue.

To summarise in this thesis, we have demonstrated the power of transcriptomic approach in gaining new knowledge on the molecular biology of the glomerulus. Moreover, our studies with Rarres1 and NPR3 contribute to identification of possible novel therapeutic approaches and biomarkers.

List of scientific papers

I. Bing He, Ping Chen, Sonia Zambrano, Dina Dabaghie, Yizhou Hu, Katja Möller-Hackbarth, David Unnersjö-Jess, Gül Gizem Korkut, Emmanuelle Charrin, Marie Jeansson, Maria Bintanel-Morcillo, Anna Witasp, Lars Wennberg, Annika Wernerson, Bernhard Schermer, Thomas Benzing, Patrik Ernfors, Christer Betsholtz, Mark Lal, Rickard Sandberg, Jaakko Patrakka. Single-cell RNA sequencing reveals the mesangial identity and species diversity of glomerular cell transcriptomes. Nature Communications. 12(1), p.2141.
https://doi.org/10.1038/s41467-021-22331-9

II. Dina Dabaghie, Liqun He, Emmanuelle Charrin, Katja Möller-Hackbarth, Gül Gizem Korkut, Christer Betsholtz, Jaakko Patrakka. Profiling glomeruloprotective mechanisms of angiotensin converting enzyme inhibitors (ACEi) using single cell RNA-sequencing. [Manuscript]

III. Katja Möller-Hackbarth, Dina Dabaghie, Emmanuelle Charrin, Sonia Zambrano, Guillem Genové, Xidan Li, Annika Wernerson, Mark Lal, and Jaakko Patrakka. Retinoic acid receptor responder1 promotes development of glomerular diseases via the Nuclear Factor-κB signaling pathway. Kidney International. 100, no. 4 (2021): 809-823.
https://doi.org/10.1016/j.kint.2021.05.036

IV. Dina Dabaghie*, Emmanuelle Charrin*, Pernilla Tonelius, Birgitta Rosengren, Anna Bjornson-Granqvist, Mark Lal, Jaakko Patrakka. Unravelling the role of natriuretic peptide clearance receptor (NPR3) in glomerular diseases. *Equal contribution. [Manuscript]