Transcriptome Profiling of Trabecular Meshwork Progenitor Cells

Xiaochen Fan; Stephanie Kennedy; Emine K Bilir; Brian Lane; Olivia A Kingston; Xu Chen; Victoria R Kearns; Colin E Willoughby; Carl M Sheridan

doi:10.1007/s12015-025-10900-0

Transcriptome Profiling of Trabecular Meshwork Progenitor Cells

Xiaochen Fan, Stephanie Kennedy, Emine K Bilir, Brian Lane, Olivia A Kingston, Xu Chen, Victoria R Kearns, Colin E Willoughby, Carl M Sheridan

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Abstract

The loss and dysfunction of trabecular meshwork (TM) cells are implicated in aging and primary open-angle glaucoma. TM progenitor cells (TMPCs) contribute to the population and function of the TM, but their identity is not well elucidated. This study aimed to identify the expression profile of differentially expressed genes (DEGs) in human TM cell cultures, TM-derived spheres, and their differentiated progeny. Primary normal human TM cells (PTM) from three donors were cultured, de-differentiated into spheres, and re-differentiated into TM cells (DTM). RNA-Seq was performed using Illumina NGS, and bioinformatics analysis was conducted with Tuxedo, Bowtie2, Tophat, Cufflinks, and Ingenuity Pathway Analysis (IPA). DEGs were validated via Nanostring, RT-qPCR (in five independent donors), immunocytochemistry, and western blotting. RNA-seq identified significant DEGs in PTM, TM progenitor cells (TMPCs), and DTM cells. Gene expression in TMPCs differed significantly from PTM and DTM cells. Nanostring and RT-qPCR confirmed 70 DEGs upregulated in TMPCs (P

Original language	English
Pages (from-to)	1-22
Number of pages	22
Journal	Stem cell reviews and reports
Early online date	27 May 2025
DOIs	https://doi.org/10.1007/s12015-025-10900-0
Publication status	Published online - 27 May 2025

Bibliographical note

Publisher Copyright:
© The Author(s) 2025.

Data Access Statement

The datasets generated and analyzed during this study are available from the corresponding author upon reasonable request.

Keywords

Trabecular Meshwork
RNA-Seq
Primary open-angle glaucoma
Progenitor Cells
Cell Differentiation

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1007/s12015-025-10900-0

s12015-025-10900-0Final published version, 2.44 MBLicence: CC BY

Cite this

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title = "Transcriptome Profiling of Trabecular Meshwork Progenitor Cells",

abstract = "The loss and dysfunction of trabecular meshwork (TM) cells are implicated in aging and primary open-angle glaucoma. TM progenitor cells (TMPCs) contribute to the population and function of the TM, but their identity is not well elucidated. This study aimed to identify the expression profile of differentially expressed genes (DEGs) in human TM cell cultures, TM-derived spheres, and their differentiated progeny. Primary normal human TM cells (PTM) from three donors were cultured, de-differentiated into spheres, and re-differentiated into TM cells (DTM). RNA-Seq was performed using Illumina NGS, and bioinformatics analysis was conducted with Tuxedo, Bowtie2, Tophat, Cufflinks, and Ingenuity Pathway Analysis (IPA). DEGs were validated via Nanostring, RT-qPCR (in five independent donors), immunocytochemistry, and western blotting. RNA-seq identified significant DEGs in PTM, TM progenitor cells (TMPCs), and DTM cells. Gene expression in TMPCs differed significantly from PTM and DTM cells. Nanostring and RT-qPCR confirmed 70 DEGs upregulated in TMPCs (P ",

keywords = "Trabecular Meshwork, RNA-Seq, Primary open-angle glaucoma, Progenitor Cells, Cell Differentiation",

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doi = "10.1007/s12015-025-10900-0",

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AU - Fan, Xiaochen

AU - Kennedy, Stephanie

AU - Bilir, Emine K

AU - Lane, Brian

AU - Kingston, Olivia A

AU - Chen, Xu

AU - Kearns, Victoria R

AU - Willoughby, Colin E

AU - Sheridan, Carl M

PY - 2025/5/27

Y1 - 2025/5/27

N2 - The loss and dysfunction of trabecular meshwork (TM) cells are implicated in aging and primary open-angle glaucoma. TM progenitor cells (TMPCs) contribute to the population and function of the TM, but their identity is not well elucidated. This study aimed to identify the expression profile of differentially expressed genes (DEGs) in human TM cell cultures, TM-derived spheres, and their differentiated progeny. Primary normal human TM cells (PTM) from three donors were cultured, de-differentiated into spheres, and re-differentiated into TM cells (DTM). RNA-Seq was performed using Illumina NGS, and bioinformatics analysis was conducted with Tuxedo, Bowtie2, Tophat, Cufflinks, and Ingenuity Pathway Analysis (IPA). DEGs were validated via Nanostring, RT-qPCR (in five independent donors), immunocytochemistry, and western blotting. RNA-seq identified significant DEGs in PTM, TM progenitor cells (TMPCs), and DTM cells. Gene expression in TMPCs differed significantly from PTM and DTM cells. Nanostring and RT-qPCR confirmed 70 DEGs upregulated in TMPCs (P

AB - The loss and dysfunction of trabecular meshwork (TM) cells are implicated in aging and primary open-angle glaucoma. TM progenitor cells (TMPCs) contribute to the population and function of the TM, but their identity is not well elucidated. This study aimed to identify the expression profile of differentially expressed genes (DEGs) in human TM cell cultures, TM-derived spheres, and their differentiated progeny. Primary normal human TM cells (PTM) from three donors were cultured, de-differentiated into spheres, and re-differentiated into TM cells (DTM). RNA-Seq was performed using Illumina NGS, and bioinformatics analysis was conducted with Tuxedo, Bowtie2, Tophat, Cufflinks, and Ingenuity Pathway Analysis (IPA). DEGs were validated via Nanostring, RT-qPCR (in five independent donors), immunocytochemistry, and western blotting. RNA-seq identified significant DEGs in PTM, TM progenitor cells (TMPCs), and DTM cells. Gene expression in TMPCs differed significantly from PTM and DTM cells. Nanostring and RT-qPCR confirmed 70 DEGs upregulated in TMPCs (P

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Transcriptome Profiling of Trabecular Meshwork Progenitor Cells

Abstract

Bibliographical note

Data Access Statement

Keywords

UN SDGs

Access to Document

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