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Article

Lens Epithelial Explants Treated with Vitreous Humor Undergo Alterations in Chromatin Landscape with Concurrent Activation of Genes Associated with Fiber Cell Differentiation and Innate Immune Response

by
Anil Upreti
1,2,
Stephanie L. Padula
1,2,
Jared A. Tangeman
1,2,
Brad D. Wagner
2,
Michael J. O’Connell
3,
Tycho J. Jaquish
1,2,
Raye K. Palko
2,
Courtney J. Mantz
2,
Deepti Anand
4,
Frank J. Lovicu
5,
Salil A. Lachke
4,6 and
Michael L. Robinson
1,2,*
1
Cell, Molecular and Structural Biology Program, Miami University, Oxford, OH 45056, USA
2
Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
3
Department of Statistics, Miami University, Oxford, OH 45056, USA
4
Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
5
Molecular and Cellular Biomedicine, School of Medical Sciences, and Save Sight Institute, The University of Sydney, Sydney, NSW 2006, Australia
6
Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
*
Author to whom correspondence should be addressed.
Cells 2023, 12(3), 501; https://doi.org/10.3390/cells12030501
Submission received: 17 November 2022 / Revised: 31 January 2023 / Accepted: 31 January 2023 / Published: 3 February 2023
(This article belongs to the Special Issue New Advances in Lens Biology and Pathology)
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Abstract

Lens epithelial explants are comprised of lens epithelial cells cultured in vitro on their native basement membrane, the lens capsule. Biologists have used lens epithelial explants to study many different cellular processes including lens fiber cell differentiation. In these studies, fiber differentiation is typically measured by cellular elongation and the expression of a few proteins characteristically expressed by lens fiber cells in situ. Chromatin and RNA was collected from lens epithelial explants cultured in either un-supplemented media or media containing 50% bovine vitreous humor for one or five days. Chromatin for ATAC-sequencing and RNA for RNA-sequencing was prepared from explants to assess regions of accessible chromatin and to quantitatively measure gene expression, respectively. Vitreous humor increased chromatin accessibility in promoter regions of genes associated with fiber differentiation and, surprisingly, an immune response, and this was associated with increased transcript levels for these genes. In contrast, vitreous had little effect on the accessibility of the genes highly expressed in the lens epithelium despite dramatic reductions in their mRNA transcripts. An unbiased analysis of differentially accessible regions revealed an enrichment of cis-regulatory motifs for RUNX, SOX and TEAD transcription factors that may drive differential gene expression in response to vitreous.
Keywords: ATAC-seq; RNA-seq; lens; development; differentiation; explants; immune; motif; chromatin ATAC-seq; RNA-seq; lens; development; differentiation; explants; immune; motif; chromatin

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MDPI and ACS Style

Upreti, A.; Padula, S.L.; Tangeman, J.A.; Wagner, B.D.; O’Connell, M.J.; Jaquish, T.J.; Palko, R.K.; Mantz, C.J.; Anand, D.; Lovicu, F.J.; et al. Lens Epithelial Explants Treated with Vitreous Humor Undergo Alterations in Chromatin Landscape with Concurrent Activation of Genes Associated with Fiber Cell Differentiation and Innate Immune Response. Cells 2023, 12, 501. https://doi.org/10.3390/cells12030501

AMA Style

Upreti A, Padula SL, Tangeman JA, Wagner BD, O’Connell MJ, Jaquish TJ, Palko RK, Mantz CJ, Anand D, Lovicu FJ, et al. Lens Epithelial Explants Treated with Vitreous Humor Undergo Alterations in Chromatin Landscape with Concurrent Activation of Genes Associated with Fiber Cell Differentiation and Innate Immune Response. Cells. 2023; 12(3):501. https://doi.org/10.3390/cells12030501

Chicago/Turabian Style

Upreti, Anil, Stephanie L. Padula, Jared A. Tangeman, Brad D. Wagner, Michael J. O’Connell, Tycho J. Jaquish, Raye K. Palko, Courtney J. Mantz, Deepti Anand, Frank J. Lovicu, and et al. 2023. "Lens Epithelial Explants Treated with Vitreous Humor Undergo Alterations in Chromatin Landscape with Concurrent Activation of Genes Associated with Fiber Cell Differentiation and Innate Immune Response" Cells 12, no. 3: 501. https://doi.org/10.3390/cells12030501

APA Style

Upreti, A., Padula, S. L., Tangeman, J. A., Wagner, B. D., O’Connell, M. J., Jaquish, T. J., Palko, R. K., Mantz, C. J., Anand, D., Lovicu, F. J., Lachke, S. A., & Robinson, M. L. (2023). Lens Epithelial Explants Treated with Vitreous Humor Undergo Alterations in Chromatin Landscape with Concurrent Activation of Genes Associated with Fiber Cell Differentiation and Innate Immune Response. Cells, 12(3), 501. https://doi.org/10.3390/cells12030501

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