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Integrated Transcriptome and Proteome Analyses Reveal the Regulatory Role of miR-146a in Human Limbal Epithelium via Notch Signaling

MiR-146a is upregulated in the stem cell-enriched limbal region vs. central human cornea and can mediate corneal epithelial wound healing. The aim of this study was to identify miR-146a targets in human primary limbal epithelial cells (LECs) using genomic and proteomic analyses. RNA-seq combined wit...

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Autores principales: Poe, Adam J., Kulkarni, Mangesh, Leszczynska, Aleksandra, Tang, Jie, Shah, Ruchi, Jami-Alahmadi, Yasaman, Wang, Jason, Kramerov, Andrei A., Wohlschlegel, James, Punj, Vasu, Ljubimov, Alexander V., Saghizadeh, Mehrnoosh
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7650592/
https://www.ncbi.nlm.nih.gov/pubmed/32993109
http://dx.doi.org/10.3390/cells9102175
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author Poe, Adam J.
Kulkarni, Mangesh
Leszczynska, Aleksandra
Tang, Jie
Shah, Ruchi
Jami-Alahmadi, Yasaman
Wang, Jason
Kramerov, Andrei A.
Wohlschlegel, James
Punj, Vasu
Ljubimov, Alexander V.
Saghizadeh, Mehrnoosh
author_facet Poe, Adam J.
Kulkarni, Mangesh
Leszczynska, Aleksandra
Tang, Jie
Shah, Ruchi
Jami-Alahmadi, Yasaman
Wang, Jason
Kramerov, Andrei A.
Wohlschlegel, James
Punj, Vasu
Ljubimov, Alexander V.
Saghizadeh, Mehrnoosh
author_sort Poe, Adam J.
collection PubMed
description MiR-146a is upregulated in the stem cell-enriched limbal region vs. central human cornea and can mediate corneal epithelial wound healing. The aim of this study was to identify miR-146a targets in human primary limbal epithelial cells (LECs) using genomic and proteomic analyses. RNA-seq combined with quantitative proteomics based on multiplexed isobaric tandem mass tag labeling was performed in LECs transfected with miR-146a mimic vs. mimic control. Western blot and immunostaining were used to confirm the expression of some targeted genes/proteins. A total of 251 differentially expressed mRNAs and 163 proteins were identified. We found that miR-146a regulates the expression of multiple genes in different pathways, such as the Notch system. In LECs and organ-cultured corneas, miR-146a increased Notch-1 expression possibly by downregulating its inhibitor Numb, but decreased Notch-2. Integrated transcriptome and proteome analyses revealed the regulatory role of miR-146a in several other processes, including anchoring junctions, TNF-α, Hedgehog signaling, adherens junctions, TGF-β, mTORC2, and epidermal growth factor receptor (EGFR) signaling, which mediate wound healing, inflammation, and stem cell maintenance and differentiation. Our results provide insights into the regulatory network of miR-146a and its role in fine-tuning of Notch-1 and Notch-2 expressions in limbal epithelium, which could be a balancing factor in stem cell maintenance and differentiation.
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spelling pubmed-76505922020-11-10 Integrated Transcriptome and Proteome Analyses Reveal the Regulatory Role of miR-146a in Human Limbal Epithelium via Notch Signaling Poe, Adam J. Kulkarni, Mangesh Leszczynska, Aleksandra Tang, Jie Shah, Ruchi Jami-Alahmadi, Yasaman Wang, Jason Kramerov, Andrei A. Wohlschlegel, James Punj, Vasu Ljubimov, Alexander V. Saghizadeh, Mehrnoosh Cells Article MiR-146a is upregulated in the stem cell-enriched limbal region vs. central human cornea and can mediate corneal epithelial wound healing. The aim of this study was to identify miR-146a targets in human primary limbal epithelial cells (LECs) using genomic and proteomic analyses. RNA-seq combined with quantitative proteomics based on multiplexed isobaric tandem mass tag labeling was performed in LECs transfected with miR-146a mimic vs. mimic control. Western blot and immunostaining were used to confirm the expression of some targeted genes/proteins. A total of 251 differentially expressed mRNAs and 163 proteins were identified. We found that miR-146a regulates the expression of multiple genes in different pathways, such as the Notch system. In LECs and organ-cultured corneas, miR-146a increased Notch-1 expression possibly by downregulating its inhibitor Numb, but decreased Notch-2. Integrated transcriptome and proteome analyses revealed the regulatory role of miR-146a in several other processes, including anchoring junctions, TNF-α, Hedgehog signaling, adherens junctions, TGF-β, mTORC2, and epidermal growth factor receptor (EGFR) signaling, which mediate wound healing, inflammation, and stem cell maintenance and differentiation. Our results provide insights into the regulatory network of miR-146a and its role in fine-tuning of Notch-1 and Notch-2 expressions in limbal epithelium, which could be a balancing factor in stem cell maintenance and differentiation. MDPI 2020-09-26 /pmc/articles/PMC7650592/ /pubmed/32993109 http://dx.doi.org/10.3390/cells9102175 Text en © 2020 by the authors. 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/).
spellingShingle Article
Poe, Adam J.
Kulkarni, Mangesh
Leszczynska, Aleksandra
Tang, Jie
Shah, Ruchi
Jami-Alahmadi, Yasaman
Wang, Jason
Kramerov, Andrei A.
Wohlschlegel, James
Punj, Vasu
Ljubimov, Alexander V.
Saghizadeh, Mehrnoosh
Integrated Transcriptome and Proteome Analyses Reveal the Regulatory Role of miR-146a in Human Limbal Epithelium via Notch Signaling
title Integrated Transcriptome and Proteome Analyses Reveal the Regulatory Role of miR-146a in Human Limbal Epithelium via Notch Signaling
title_full Integrated Transcriptome and Proteome Analyses Reveal the Regulatory Role of miR-146a in Human Limbal Epithelium via Notch Signaling
title_fullStr Integrated Transcriptome and Proteome Analyses Reveal the Regulatory Role of miR-146a in Human Limbal Epithelium via Notch Signaling
title_full_unstemmed Integrated Transcriptome and Proteome Analyses Reveal the Regulatory Role of miR-146a in Human Limbal Epithelium via Notch Signaling
title_short Integrated Transcriptome and Proteome Analyses Reveal the Regulatory Role of miR-146a in Human Limbal Epithelium via Notch Signaling
title_sort integrated transcriptome and proteome analyses reveal the regulatory role of mir-146a in human limbal epithelium via notch signaling
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7650592/
https://www.ncbi.nlm.nih.gov/pubmed/32993109
http://dx.doi.org/10.3390/cells9102175
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