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

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 sc...

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Autores principales: Talyan, Sweta, Filipów, Samantha, Ignarski, Michael, Smieszek, Magdalena, Chen, He, Kühne, Lucas, Butt, Linus, Göbel, Heike, Hoyer-Allo, K. Johanna R., Koehler, Felix C., Altmüller, Janine, Brinkkötter, Paul, Schermer, Bernhard, Benzing, Thomas, Kann, Martin, Müller, Roman-Ulrich, Dieterich, Christoph
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8003990/
https://www.ncbi.nlm.nih.gov/pubmed/33804736
http://dx.doi.org/10.3390/cells10030692
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author Talyan, Sweta
Filipów, Samantha
Ignarski, Michael
Smieszek, Magdalena
Chen, He
Kühne, Lucas
Butt, Linus
Göbel, Heike
Hoyer-Allo, K. Johanna R.
Koehler, Felix C.
Altmüller, Janine
Brinkkötter, Paul
Schermer, Bernhard
Benzing, Thomas
Kann, Martin
Müller, Roman-Ulrich
Dieterich, Christoph
author_facet Talyan, Sweta
Filipów, Samantha
Ignarski, Michael
Smieszek, Magdalena
Chen, He
Kühne, Lucas
Butt, Linus
Göbel, Heike
Hoyer-Allo, K. Johanna R.
Koehler, Felix C.
Altmüller, Janine
Brinkkötter, Paul
Schermer, Bernhard
Benzing, Thomas
Kann, Martin
Müller, Roman-Ulrich
Dieterich, Christoph
author_sort Talyan, Sweta
collection PubMed
description 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.
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spelling pubmed-80039902021-03-28 CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease Talyan, Sweta Filipów, Samantha Ignarski, Michael Smieszek, Magdalena Chen, He Kühne, Lucas Butt, Linus Göbel, Heike Hoyer-Allo, K. Johanna R. Koehler, Felix C. Altmüller, Janine Brinkkötter, Paul Schermer, Bernhard Benzing, Thomas Kann, Martin Müller, Roman-Ulrich Dieterich, Christoph Cells Article 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. MDPI 2021-03-20 /pmc/articles/PMC8003990/ /pubmed/33804736 http://dx.doi.org/10.3390/cells10030692 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ).
spellingShingle Article
Talyan, Sweta
Filipów, Samantha
Ignarski, Michael
Smieszek, Magdalena
Chen, He
Kühne, Lucas
Butt, Linus
Göbel, Heike
Hoyer-Allo, K. Johanna R.
Koehler, Felix C.
Altmüller, Janine
Brinkkötter, Paul
Schermer, Bernhard
Benzing, Thomas
Kann, Martin
Müller, Roman-Ulrich
Dieterich, Christoph
CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease
title CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease
title_full CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease
title_fullStr CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease
title_full_unstemmed CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease
title_short CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease
title_sort calinca—a novel pipeline for the identification of lncrnas in podocyte disease
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8003990/
https://www.ncbi.nlm.nih.gov/pubmed/33804736
http://dx.doi.org/10.3390/cells10030692
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