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Article

FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis

1
Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark
2
Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
3
Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
4
Bioinformatics Research Network, Atlanta, GA 30317, USA
5
Language Technologies Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
6
Osthus GmbH, 52068 Aachen, Germany
7
May’s Cancer Center, UT Health San Antonio, San Antonio, TX 78229, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Pieter-Jan Volders
Non-Coding RNA 2022, 8(1), 13; https://doi.org/10.3390/ncrna8010013
Received: 14 January 2022 / Revised: 25 January 2022 / Accepted: 27 January 2022 / Published: 28 January 2022
(This article belongs to the Special Issue Advances in Non-coding RNA Databases and Resources)
Most long non-coding RNAs (lncRNAs) are expressed at lower levels than protein-coding genes and their expression is often restricted to specific cell types, certain time points during development, and various stress and disease conditions, respectively. To revisit this long-held concept, we focused on fibroblasts, a common cell type in various organs and tissues. Using fibroblasts and changes in their expression profiles during fibrosis as a model system, we show that the overall expression level of lncRNA genes is significantly lower than that of protein-coding genes. Furthermore, we identified lncRNA genes whose expression is upregulated during fibrosis. Using dermal fibroblasts as a model, we performed loss-of-function experiments and show that the knockdown of the lncRNAs LINC00622 and LINC01711 result in gene expression changes associated with cellular and inflammatory responses, respectively. Since there are no lncRNA databases focused on fibroblasts and fibrosis, we built a web application, FibroDB, to further promote functional and mechanistic studies of fibrotic lncRNAs. View Full-Text
Keywords: fibroblast; fibrosis; gene expression; lncRNA; RNA-seq fibroblast; fibrosis; gene expression; lncRNA; RNA-seq
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Figure 1

  • Supplementary File 1:

    ZIP-Document (ZIP, 5404 KiB)

  • Externally hosted supplementary file 1
    Link: https://github.com/heartlncrna/Analysis_of_FB_Studies
    Description: Supplementary Table S1. RNA-seq data of fibroblasts from seven anatomical locales (abdomen, upper gingiva, lung, soft palate, scalp, trachea, and vocal fold; GEO accession number, GSE140523). The average CPM values of each anatomical locale are shown for each gene.; Sup-plementary Table S2. Differentially expressed genes in thrombus compared to pulmonary artery adventitia (control) of CTEPH patients at the threshold of 2-fold (logFC, fold change in logarithm of base 2) and p < 0.05 (PValue) (GEO accession number, GSE149413).; Supplementary Table S3. Differentially expressed genes in TGF-β treated MRC5 lung fibroblastic cell line compared to non-treated MRC5 cells at the threshold of 2-fold (logFC, fold change in logarithm of base 2) and FDR-adjusted p < 0.05 (FDR) (GEO accession number, GSE97829).; Supplementary Table S4. List of differentially expressed genes shared between two data sets: fibroblasts from CTEPH patients and MRC5 cells treated with TGF-β.; Supplementary Table S5. List of differentially expressed genes in pulmonary fibroblasts (CTEPH patients and MRC5 cells treated with TGF-β) and their expression changes in cardiac fibroblasts stimulated with TGF-β for 24 hours compared to the CFs before the TGF-β stimulation (baseline). The category column is based on the RNA-seq data of pulmonary fibroblasts. The logFC column shows the logarithm of base 2 of fold change, while the FDR column displays the FDR-adjusted p-values.; Supplementary Table S6. List of primers used in this study.; Supplementary Table S7. List of antibodies used in this study.
  • Externally hosted supplementary file 2
    Link: https://github.com/heartlncrna/Analysis_of_FB_Studies
    Description: Supplementary Figure S1. Gene expression of tissue-specific human fibroblasts normalized to gene lengths.
MDPI and ACS Style

Ilieva, M.; Miller, H.E.; Agarwal, A.; Paulus, G.K.; Madsen, J.H.; Bishop, A.J.R.; Kauppinen, S.; Uchida, S. FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis. Non-Coding RNA 2022, 8, 13. https://doi.org/10.3390/ncrna8010013

AMA Style

Ilieva M, Miller HE, Agarwal A, Paulus GK, Madsen JH, Bishop AJR, Kauppinen S, Uchida S. FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis. Non-Coding RNA. 2022; 8(1):13. https://doi.org/10.3390/ncrna8010013

Chicago/Turabian Style

Ilieva, Mirolyuba, Henry E. Miller, Arav Agarwal, Gabriela K. Paulus, Jens H. Madsen, Alexander J.R. Bishop, Sakari Kauppinen, and Shizuka Uchida. 2022. "FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis" Non-Coding RNA 8, no. 1: 13. https://doi.org/10.3390/ncrna8010013

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