High-Throughput Transcriptomics of <i>Celf1</i> Conditional Knockout Lens Identifies Downstream Networks Linked to Cataract Pathology
Defects in the development of the ocular lens can cause congenital cataracts. To understand the various etiologies of congenital cataracts, it is important to characterize the genes linked to this developmental defect and to define their downstream pathways that are relevant to lens biology and path...
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| Format: | Article |
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MDPI AG
2023-04-01
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| Series: | Cells |
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| Online Access: | https://www.mdpi.com/2073-4409/12/7/1070 |
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| author | Archana D. Siddam Matthieu Duot Sarah Y. Coomson Deepti Anand Sandeep Aryal Bailey A. T. Weatherbee Yann Audic Luc Paillard Salil A. Lachke |
| author_facet | Archana D. Siddam Matthieu Duot Sarah Y. Coomson Deepti Anand Sandeep Aryal Bailey A. T. Weatherbee Yann Audic Luc Paillard Salil A. Lachke |
| author_sort | Archana D. Siddam |
| collection | DOAJ |
| description | Defects in the development of the ocular lens can cause congenital cataracts. To understand the various etiologies of congenital cataracts, it is important to characterize the genes linked to this developmental defect and to define their downstream pathways that are relevant to lens biology and pathology. Deficiency or alteration of several RNA-binding proteins, including the conserved RBP Celf1 (CUGBP Elav-like family member 1), has been described to cause lens defects and early onset cataracts in animal models and/or humans. Celf1 is involved in various aspects of post-transcriptional gene expression control, including regulation of mRNA stability/decay, alternative splicing and translation. <i>Celf1</i> germline knockout mice and lens conditional knockout (<i>Celf1</i><sup>cKO</sup>) mice develop fully penetrant cataracts in early postnatal stages. To define the genome-level changes in RNA transcripts that result from <i>Celf1</i> deficiency, we performed high-throughput RNA-sequencing of <i>Celf1</i><sup>cKO</sup> mouse lenses at postnatal day (P) 0. <i>Celf1</i><sup>cKO</sup> lenses exhibit 987 differentially expressed genes (DEGs) at cut-offs of >1.0 log2 counts per million (CPM), ≥±0.58 log2 fold-change and <0.05 false discovery rate (FDR). Of these, 327 RNAs were reduced while 660 were elevated in <i>Celf1</i><sup>cKO</sup> lenses. The DEGs were subjected to various downstream analyses including iSyTE lens enriched-expression, presence in Cat-map, and gene ontology (GO) and representation of regulatory pathways. Further, a comparative analysis was done with previously generated microarray datasets on <i>Celf1</i><sup>cKO</sup> lenses P0 and P6. Together, these analyses validated and prioritized several key genes mis-expressed in <i>Celf1</i><sup>cKO</sup> lenses that are relevant to lens biology, including known cataract-linked genes (e.g., <i>Cryab</i>, <i>Cryba2</i>, <i>Cryba4</i>, <i>Crybb1</i>, <i>Crybb2</i>, <i>Cryga</i>, <i>Crygb</i>, <i>Crygc</i>, <i>Crygd</i>, <i>Cryge</i>, <i>Crygf</i>, <i>Dnase2b</i>, <i>Bfsp1</i>, <i>Gja3</i>, <i>Pxdn</i>, <i>Sparc</i>, <i>Tdrd7</i>, etc.) as well as novel candidates (e.g., <i>Ell2</i> and <i>Prdm16</i>). Together, these data have defined the alterations in lens transcriptome caused by Celf1 deficiency, in turn uncovering downstream genes and pathways (e.g., structural constituents of eye lenses, lens fiber cell differentiation, etc.) associated with lens development and early-onset cataracts. |
| first_indexed | 2024-03-11T05:40:27Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4409 |
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| last_indexed | 2024-03-11T05:40:27Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cells |
| spelling | doaj.art-0cf37258f0814ba39811a89a6d23ad072023-11-17T16:28:52ZengMDPI AGCells2073-44092023-04-01127107010.3390/cells12071070High-Throughput Transcriptomics of <i>Celf1</i> Conditional Knockout Lens Identifies Downstream Networks Linked to Cataract PathologyArchana D. Siddam0Matthieu Duot1Sarah Y. Coomson2Deepti Anand3Sandeep Aryal4Bailey A. T. Weatherbee5Yann Audic6Luc Paillard7Salil A. Lachke8Department of Biological Sciences, University of Delaware, Newark, DE 19716, USADepartment of Biological Sciences, University of Delaware, Newark, DE 19716, USADepartment of Biological Sciences, University of Delaware, Newark, DE 19716, USADepartment of Biological Sciences, University of Delaware, Newark, DE 19716, USADepartment of Biological Sciences, University of Delaware, Newark, DE 19716, USADepartment of Biological Sciences, University of Delaware, Newark, DE 19716, USACNRS, IGDR (Institut de Génétique et Développement de Rennes), Univ. Rennes, UMR 6290, Rennes, F-35000 Rennes, FranceCNRS, IGDR (Institut de Génétique et Développement de Rennes), Univ. Rennes, UMR 6290, Rennes, F-35000 Rennes, FranceDepartment of Biological Sciences, University of Delaware, Newark, DE 19716, USADefects in the development of the ocular lens can cause congenital cataracts. To understand the various etiologies of congenital cataracts, it is important to characterize the genes linked to this developmental defect and to define their downstream pathways that are relevant to lens biology and pathology. Deficiency or alteration of several RNA-binding proteins, including the conserved RBP Celf1 (CUGBP Elav-like family member 1), has been described to cause lens defects and early onset cataracts in animal models and/or humans. Celf1 is involved in various aspects of post-transcriptional gene expression control, including regulation of mRNA stability/decay, alternative splicing and translation. <i>Celf1</i> germline knockout mice and lens conditional knockout (<i>Celf1</i><sup>cKO</sup>) mice develop fully penetrant cataracts in early postnatal stages. To define the genome-level changes in RNA transcripts that result from <i>Celf1</i> deficiency, we performed high-throughput RNA-sequencing of <i>Celf1</i><sup>cKO</sup> mouse lenses at postnatal day (P) 0. <i>Celf1</i><sup>cKO</sup> lenses exhibit 987 differentially expressed genes (DEGs) at cut-offs of >1.0 log2 counts per million (CPM), ≥±0.58 log2 fold-change and <0.05 false discovery rate (FDR). Of these, 327 RNAs were reduced while 660 were elevated in <i>Celf1</i><sup>cKO</sup> lenses. The DEGs were subjected to various downstream analyses including iSyTE lens enriched-expression, presence in Cat-map, and gene ontology (GO) and representation of regulatory pathways. Further, a comparative analysis was done with previously generated microarray datasets on <i>Celf1</i><sup>cKO</sup> lenses P0 and P6. Together, these analyses validated and prioritized several key genes mis-expressed in <i>Celf1</i><sup>cKO</sup> lenses that are relevant to lens biology, including known cataract-linked genes (e.g., <i>Cryab</i>, <i>Cryba2</i>, <i>Cryba4</i>, <i>Crybb1</i>, <i>Crybb2</i>, <i>Cryga</i>, <i>Crygb</i>, <i>Crygc</i>, <i>Crygd</i>, <i>Cryge</i>, <i>Crygf</i>, <i>Dnase2b</i>, <i>Bfsp1</i>, <i>Gja3</i>, <i>Pxdn</i>, <i>Sparc</i>, <i>Tdrd7</i>, etc.) as well as novel candidates (e.g., <i>Ell2</i> and <i>Prdm16</i>). Together, these data have defined the alterations in lens transcriptome caused by Celf1 deficiency, in turn uncovering downstream genes and pathways (e.g., structural constituents of eye lenses, lens fiber cell differentiation, etc.) associated with lens development and early-onset cataracts.https://www.mdpi.com/2073-4409/12/7/1070lenseyecataractsRNA-binding proteinCugbp1development |
| spellingShingle | Archana D. Siddam Matthieu Duot Sarah Y. Coomson Deepti Anand Sandeep Aryal Bailey A. T. Weatherbee Yann Audic Luc Paillard Salil A. Lachke High-Throughput Transcriptomics of <i>Celf1</i> Conditional Knockout Lens Identifies Downstream Networks Linked to Cataract Pathology Cells lens eye cataracts RNA-binding protein Cugbp1 development |
| title | High-Throughput Transcriptomics of <i>Celf1</i> Conditional Knockout Lens Identifies Downstream Networks Linked to Cataract Pathology |
| title_full | High-Throughput Transcriptomics of <i>Celf1</i> Conditional Knockout Lens Identifies Downstream Networks Linked to Cataract Pathology |
| title_fullStr | High-Throughput Transcriptomics of <i>Celf1</i> Conditional Knockout Lens Identifies Downstream Networks Linked to Cataract Pathology |
| title_full_unstemmed | High-Throughput Transcriptomics of <i>Celf1</i> Conditional Knockout Lens Identifies Downstream Networks Linked to Cataract Pathology |
| title_short | High-Throughput Transcriptomics of <i>Celf1</i> Conditional Knockout Lens Identifies Downstream Networks Linked to Cataract Pathology |
| title_sort | high throughput transcriptomics of i celf1 i conditional knockout lens identifies downstream networks linked to cataract pathology |
| topic | lens eye cataracts RNA-binding protein Cugbp1 development |
| url | https://www.mdpi.com/2073-4409/12/7/1070 |
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