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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...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2021
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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. |
format | Online Article Text |
id | pubmed-8003990 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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