Gene expression in retinal ischemic post-conditioning
The pathophysiology of retinal ischemia involves mechanisms including inflammation and apoptosis. Ischemic post-conditioning (Post-C), a brief non-lethal ischemia, induces a long-term ischemic tolerance, but the mechanisms of ischemic post-conditioning in the retina have only been described on a limited basis. Accordingly, we conducted this study to determine the molecular events in retinal ischemic post-conditioning and to identify targets for therapeutic strategies for retinal ischemia.
To determine global molecular events in ischemic post-conditioning, a comprehensive study of the transcriptome of whole retina was performed. We utilized RNA sequencing (RNA-Seq), a recently developed, deep sequencing technique enabling quantitative gene expression, with low background noise, dynamic detection range, and discovery of novel genes. Rat retina was subjected to ischemia in vivo by elevation of intraocular pressure above systolic blood pressure. At 24 h after ischemia, Post-C or sham Post-C was performed by another, briefer period of ischemia, and 24 h later, retinas were collected and RNA processed.
There were 71 significantly affected pathways in post-conditioned/ischemic vs. normals and 43 in sham post conditioned/ischemic vs. normals. Of these, 28 were unique to Post-C and ischemia. Seven biological pathways relevant to ischemic injury, in Post-C as opposed to sham Post-C, were examined in detail. Apoptosis, p53, cell cycle, JAK-STAT, HIF-1, MAPK and PI3K-Akt pathways significantly differed in the number as well as degree of fold change in genes between conditions.
Post-C is a complex molecular signaling process with a multitude of altered molecular pathways. We identified potential gene candidates in Post-C. Studying the impact of altering expression of these factors may yield insight into new methods for treating or preventing damage from retinal ischemic disorders.
KeywordsIschemia Post-conditioning Retina RNA-Seq
This study was supported by the National Institutes of Health (Rockville, MD, USA) grant EY10343 to Dr. Roth, UL1TR000050 to the Center for Clinical and Translational Sciences of the University of Illinois at Chicago, the Illinois Society for the Prevention of Blindness, Chicago, IL, USA (Ms. Stelman); the Craig Foundation (Chicago, IL, USA, Ms. Stelman), a medical student research fellowship grant from the Foundation for Anesthesia Education and Research (Schaumburg, IL, USA, Ms. Stelman), and Core Grant P30 EY001792 (to the Department of Ophthalmology, University of Illinois at Chicago from the National Institutes of Health, Rockville, MD, USA); There was no involvement of the funding bodies in the design of the study or in collection, analysis and interpretation of the data or the writing of the manuscript. None of the authors have any conflicts of interest.
Compliance with ethical standards
Ethical approval: All procedures performed in studies involving animals were in accordance with the ethical standards of and approved by the Institutional Animal Care and Use Committee of the University of Illinois at Chicago.
- 10.Brown J, Pirrung M, McCue LA (2017) FQC dashboard: integrates FastQC results into a web based interactive and extensible FastQ quality control tool. Bioinformatics. https://doi.org/10.1093/bioinformatics/btx373
- 15.Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B (Methodological) 57:289–300Google Scholar
- 16.Pathan M, Keerthikumar S, Ang CS, Gangoda L, Quek CY, Williamson NA, Mouradov D, Sieber OM, Simpson RJ, Salim A, Bacic A, Hill AF, Stroud DA, Ryan MT, Agbinya JI, Mariadason JM, Burgess AW, Mathivanan S (2015) FunRich: an open access standalone functional enrichment and interaction network analysis tool. Proteomics 15:2597–2601. https://doi.org/10.1002/pmic.201400515 CrossRefPubMedGoogle Scholar
- 17.Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25:25–29. https://doi.org/10.1038/75556 CrossRefPubMedPubMedCentralGoogle Scholar
- 23.Hussein SMI, Puri MC, Tonge PD, Benevento M, Corso AJ, Clancy JL, Mosbergen R, Li M, Lee D-S, Cloonan N, Wood DLA, Munoz J, Middleton R, Korn O, Patel HR, White CA, Shin J-Y, Gauthier ME, Cao K-AL, Kim J-I, Mar JC, Shakiba N, Ritchie W, Rasko JEJ, Grimmond SM, Zandstra PW, Wells CA, Preiss T, Seo J-S, Heck AJR, Rogers IM, Nagy A (2014) Genome-wide characterization of the routes to pluripotency. Nature 516:198–206. https://doi.org/10.1038/nature14046 CrossRefPubMedGoogle Scholar
- 25.Wang C, Gong B, Bushel PR, Thierry-Mieg J, Thierry-Mieg D, Xu J, Fang H, Hong H, Shen J, Su Z, Meehan J, Li X, Yang L, Li H, Labaj PP, Kreil DP, Megherbi D, Gaj S, Caiment F, van Delft J, Kleinjans J, Scherer A, Devanarayan V, Wang J, Yang Y, Qian H-R, Lancashire LJ, Bessarabova M, Nikolsky Y, Furlanello C, Chierici M, Albanese D, Jurman G, Riccadonna S, Filosi M, Visintainer R, Zhang KK, Li J, Hsieh J-H, Svoboda DL, Fuscoe JC, Deng Y, Shi L, Paules RS, Auerbach SS, Tong W (2014) The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nat Biotechnol 32:926–932. https://doi.org/10.1038/nbt.3001 CrossRefPubMedPubMedCentralGoogle Scholar
- 31.Kuan CY, Schloemer AJ, Lu A, Burns KA, Weng WL, Williams MT, Strauss KI, Vorhees CV, Flavell RA, Davis RJ, Sharp FR, Rakic P (2004) Hypoxia-ischemia induces DNA synthesis without cell proliferation in dying neurons in adult rodent brain. J Neurosci 24:10763–10772. https://doi.org/10.1523/jneurosci.3883-04.2004 CrossRefPubMedPubMedCentralGoogle Scholar
- 40.Langley B, D'Annibale MA, Suh K, Ayoub I, Tolhurst A, Bastan B, Yang L, Ko B, Fisher M, Cho S, Beal MF, Ratan RR (2008) Pulse inhibition of histone deacetylases induces complete resistance to oxidative death in cortical neurons without toxicity and reveals a role for cytoplasmic p21(waf1/cip1) in cell cycle-independent neuroprotection. J Neurosci 28:163–176. https://doi.org/10.1523/jneurosci.3200-07.2008 CrossRefPubMedPubMedCentralGoogle Scholar
- 41.Babapoor-Farrokhran S, Jee K, Puchner B, Hassan SJ, Xin X, Rodrigues M, Kashiwabuchi F, Ma T, Hu K, Deshpande M, Daoud Y, Solomon S, Wenick A, Lutty GA, Semenza GL, Montaner S, Sodhi A (2015) Angiopoietin-like 4 is a potent angiogenic factor and a novel therapeutic target for patients with proliferative diabetic retinopathy. Proc Natl Acad Sci U S A 112:E3030–E3039. https://doi.org/10.1073/pnas.1423765112 CrossRefPubMedPubMedCentralGoogle Scholar
- 46.Vogler M, Zieseniss A, Hesse AR, Levent E, Tiburcy M, Heinze E, Burzlaff N, Schley G, Eckardt KU, Willam C, Katschinski DM (2015) Pre- and post-conditional inhibition of prolyl-4-hydroxylase domain enzymes protects the heart from an ischemic insult. Pflugers Arch 467:2141–2149. https://doi.org/10.1007/s00424-014-1667-z CrossRefPubMedGoogle Scholar
- 49.Kim HC, Kim E, Bae JI, Lee KH, Jeon YT, Hwang JW, Lim YJ, Min SW, Park HP (2017) Sevoflurane Postconditioning reduces apoptosis by activating the JAK-STAT pathway after transient global cerebral ischemia in rats. J Neurosurg Anesthesiol 29:37–45. https://doi.org/10.1097/ana.0000000000000331 CrossRefPubMedGoogle Scholar
- 55.Machida N, Umikawa M, Takei K, Sakima N, Myagmar BE, Taira K, Uezato H, Ogawa Y, Kariya K (2004) Mitogen-activated protein kinase kinase kinase kinase 4 as a putative effector of Rap2 to activate the c-Jun N-terminal kinase. J Biol Chem 279:15711–15714. https://doi.org/10.1074/jbc.C300542200 CrossRefPubMedGoogle Scholar
- 56.Roth Flach RJ, Skoura A, Matevossian A, Danai LV, Zheng W, Cortes C, Bhattacharya SK, Aouadi M, Hagan N, Yawe JC, Vangala P, Menendez LG, Cooper MP, Fitzgibbons TP, Buckbinder L, Czech MP (2015) Endothelial protein kinase MAP4K4 promotes vascular inflammation and atherosclerosis. Nat Commun 6:8995. https://doi.org/10.1038/ncomms9995 CrossRefPubMedPubMedCentralGoogle Scholar
- 57.Rowley SM, Kuriakose T, Dockery LM, Tran-Ngyuen T, Gingerich AD, Wei L, Watford WT (2014) Tumor progression locus 2 (Tpl2) kinase promotes chemokine receptor expression and macrophage migration during acute inflammation. J Biol Chem 289:15788–15797. https://doi.org/10.1074/jbc.M114.559344 CrossRefPubMedPubMedCentralGoogle Scholar
- 63.Ishikawa K, Yoshida S, Kobayashi Y, Zhou Y, Nakama T, Nakao S, Sassa Y, Oshima Y, Niiro H, Akashi K, Kono T, Ishibashi T (2015) Microarray analysis of gene expression in Fibrovascular membranes excised from patients with proliferative diabetic retinopathy. Invest Ophthalmol Vis Sci 56:932–946. https://doi.org/10.1167/iovs.14-15589 CrossRefPubMedGoogle Scholar