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| Status |
Public on Sep 06, 2023 |
| Title |
Regional Gene Expression in the Retina, Optic Nerve Head, and Optic Nerve of Mice with Optic Nerve Crush and Experimental Glaucoma |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
A major risk factor for glaucomatous optic neuropathy is the level of intraocular pressure (IOP), which can lead to retinal ganglion cell axon injury and cell death. The optic nerve has a rostral unmyelinated portion at the optic nerve head followed by a caudal myelinated region. The unmyelinated region is differentially susceptible to IOP-induced damage in rodent models and in human glaucoma. While several studies have analyzed gene expression changes in the mouse optic nerve following optic nerve injury, few were designed to consider the regional gene expression differences that exist between these distinct areas. We performed bulk RNA-sequencing on the retina and on separately micro-dissected unmyelinated and myelinated optic nerve regions from naïve C57BL/6 mice, mice after optic nerve crush, and mice with microbead-induced experimental glaucoma (total = 36). Gene expression patterns in the naïve unmyelinated optic nerve showed significant enrichment of the Wnt, Hippo, PI3K-Akt, and transforming growth factor β pathways, as well as extracellular matrix–receptor and cell membrane signaling pathways, compared to the myelinated optic nerve and retina. Gene expression changes induced by both injuries were more extensive in the myelinated optic nerve than the unmyelinated region, and greater after nerve crush than glaucoma. Changes present three and fourteen days after injury largely subsided by six weeks. Gene markers of reactive astrocytes did not consistently differ between injury states. Overall, the transcriptomic phenotype of the mouse unmyelinated optic nerve was significantly different from immediately adjacent tissues, likely dominated by expression in astrocytes, whose junctional complexes are inherently important in responding to IOP elevation.
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| Overall design |
To characterize the region-specific transcriptome of mouse eyes in a naïve state and following optic nerve (ON) crush and experimental ocular hypertension injury models.
Tissue from mouse retinas and separately micro-dissected unmyelinated ON (UON) and myelinated ON (MON) were collected (n=4 replicate samples per experimental group, sexes pooled for n=2 RNA-seq libraries).
We then performed gene expression profiling analysis using data obtained from bulk RNA-seq of retina, UON, and MON tissue regions from naïve C57BL/6 mice (control, 0D), at two time points following ON crush (three days, 3D; two weeks, 2W), and at three time points following microbead-induced experimental glaucoma (three days, 3D; two weeks, 2W; six weeks, 6W).
Gene expression profiling analysis of RNA-seq data comparing tissue regions (retina, UON, and MON) and treatments/time points (naïve, crush, and glaucoma).
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| Web link |
https://www.mdpi.com/1422-0067/24/18/13719
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| Contributor(s) |
Keuthan CJ, Schaub JA, Wei M, Fang W, Quillen S, Kimball E, Johnson TV, Ji H, Zack DJ, Quigley HA |
| Citation(s) |
37762022 |
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| Submission date |
Aug 28, 2023 |
| Last update date |
Dec 06, 2023 |
| Contact name |
Casey Keuthan |
| E-mail(s) |
ckeutha1@jh.edu
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| Organization name |
Johns Hopkins University
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| Street address |
400 N Broadway, Smith Bldg, Rm 3001-N
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| City |
Baltimore |
| ZIP/Postal code |
21287 |
| Country |
USA |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (36)
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| GSM7743513 |
UON, 2W, Glaucoma, Female |
| GSM7743514 |
UON, 3D, Crush, Female |
| GSM7743515 |
UON, 3D, Crush, Male |
| GSM7743516 |
UON, 3D, Glaucoma, Male |
| GSM7743517 |
UON, 3D, Glaucoma, Female |
| GSM7743518 |
UON, 6W, Glaucoma, Female |
| GSM7743519 |
UON, 6W, Glaucoma, Male |
| GSM7743520 |
UON, 0D, Naïve, Female |
| GSM7743521 |
UON, 0D, Naïve, Male |
| GSM7743522 |
MON, 2W, Crush, Male |
| GSM7743523 |
MON, 2W, Crush, Female |
| GSM7743524 |
MON, 2W, Glaucoma, Male |
| GSM7743525 |
MON, 2W, Glaucoma, Female |
| GSM7743526 |
MON, 3D, Crush, Female |
| GSM7743527 |
MON, 3D, Crush, Male |
| GSM7743528 |
MON, 3D, Glaucoma, Male |
| GSM7743529 |
MON, 3D, Glaucoma, Female |
| GSM7743530 |
MON, 6W, Glaucoma, Male |
| GSM7743531 |
MON, 6W, Glaucoma, Female |
| GSM7743532 |
MON, 0D, Naïve, Female |
| GSM7743533 |
MON, 0D, Naïve, Male |
| GSM7743534 |
Retina, 2W, Crush, Female |
| GSM7743535 |
Retina, 2W, Crush, Male |
| GSM7743536 |
Retina, 2W, Glaucoma, Male |
| GSM7743537 |
Retina, 2W, Glaucoma, Female |
| GSM7743538 |
Retina, 3D, Crush, Male |
| GSM7743539 |
Retina, 3D, Crush, Female |
| GSM7743540 |
Retina, 3D, Glaucoma, Male |
| GSM7743541 |
Retina, 3D, Glaucoma, Female |
| GSM7743542 |
Retina, 6W, Glaucoma, Male |
| GSM7743543 |
Retina, 6W, Glaucoma, Female |
| GSM7743544 |
Retina, 0D, Naïve, Female |
| GSM7743545 |
Retina, 0D, Naïve, Male |
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| Relations |
| BioProject |
PRJNA1009858 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE241782_RAW.tar |
47.3 Mb |
(http)(custom) |
TAR (of TSV) |
| GSE241782_gene_count_matrix.csv.gz |
2.1 Mb |
(ftp)(http) |
CSV |
| GSE241782_transcript_count_matrix.csv.gz |
4.4 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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