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CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease

Authors :
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
Source :
Cells, Vol 10, Iss 3, p 692 (2021)
Publication Year :
2021
Publisher :
MDPI AG, 2021.

Abstract

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.

Details

Language :
English
ISSN :
20734409
Volume :
10
Issue :
3
Database :
Directory of Open Access Journals
Journal :
Cells
Publication Type :
Academic Journal
Accession number :
edsdoj.76f8f517d9ed4986bae55e3138f26d5e
Document Type :
article
Full Text :
https://doi.org/10.3390/cells10030692