CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease
Sweta Talyan,
Samantha Filipów,
Michael Ignarski,
Magdalena Smieszek,
He Chen,
Lucas Kühne,
Linus Butt,
Heike Göbel,
K. Johanna R. Hoyer-Allo,
Felix C. Koehler,
Janine Altmüller,
Paul Brinkkötter,
Bernhard Schermer,
Thomas Benzing,
Martin Kann,
Roman-Ulrich Müller,
Christoph Dieterich
Affiliations
Sweta Talyan
German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
Samantha Filipów
Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
Michael Ignarski
Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
Magdalena Smieszek
Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
He Chen
Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
Lucas Kühne
Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
Linus Butt
Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
Heike Göbel
Institute for Pathology, Diagnostic and Experimental Nephropathology Unit, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
K. Johanna R. Hoyer-Allo
Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
Felix C. Koehler
Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
Janine Altmüller
Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
Paul Brinkkötter
Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
Bernhard Schermer
Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
Thomas Benzing
Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
Martin Kann
Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
Roman-Ulrich Müller
Department II of Internal Medicine and Center for Molecular Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50931 Cologne, Germany
Christoph Dieterich
German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Im Neuenheimer Feld 669, 69120 Heidelberg, Germany
Diseases of the renal filtration unit—the glomerulus—are the most common cause of chronic kidney disease. Podocytes are the pivotal cell type for the function of this filter and focal-segmental glomerulosclerosis (FSGS) is a classic example of a podocytopathy leading to proteinuria and glomerular scarring. Currently, no targeted treatment of FSGS is available. This lack of therapeutic strategies is explained by a limited understanding of the defects in podocyte cell biology leading to FSGS. To date, most studies in the field have focused on protein-coding genes and their gene products. However, more than 80% of all transcripts produced by mammalian cells are actually non-coding. Here, long non-coding RNAs (lncRNAs) are a relatively novel class of transcripts and have not been systematically studied in FSGS to date. The appropriate tools to facilitate lncRNA research for the renal scientific community are urgently required due to a row of challenges compared to classical analysis pipelines optimized for coding RNA expression analysis. Here, we present the bioinformatic pipeline CALINCA as a solution for this problem. CALINCA automatically analyzes datasets from murine FSGS models and quantifies both annotated and de novo assembled lncRNAs. In addition, the tool provides in-depth information on podocyte specificity of these lncRNAs, as well as evolutionary conservation and expression in human datasets making this pipeline a crucial basis to lncRNA studies in FSGS.
