Circular RNA expression and the competitive endogenous RNA network in pathological, age-related macular degeneration events: A cross-platform normalization study

Ruxu Sun; Hongjing Zhu; Ying Wang; Jianan Wang; Chao Jiang; Qiuchen Cao; Yeran Zhang; Yichen Zhang; Songtao Yuan; Qinghuai Liu

doi:10.7555/JBR.37.20230010

Article Contents

Article Navigation > The Journal of Biomedical Research > 2023 > Online Publication

Ruxu Sun, Hongjing Zhu, Ying Wang, Jianan Wang, Chao Jiang, Qiuchen Cao, Yeran Zhang, Yichen Zhang, Songtao Yuan, Qinghuai Liu. Circular RNA expression and the competitive endogenous RNA network in pathological, age-related macular degeneration events: A cross-platform normalization study[J]. The Journal of Biomedical Research. doi: 10.7555/JBR.37.20230010

Citation:

Ruxu Sun, Hongjing Zhu, Ying Wang, Jianan Wang, Chao Jiang, Qiuchen Cao, Yeran Zhang, Yichen Zhang, Songtao Yuan, Qinghuai Liu. Circular RNA expression and the competitive endogenous RNA network in pathological, age-related macular degeneration events: A cross-platform normalization study[J]. The Journal of Biomedical Research. doi: 10.7555/JBR.37.20230010

Citation:

Ruxu Sun, Hongjing Zhu, Ying Wang, Jianan Wang, Chao Jiang, Qiuchen Cao, Yeran Zhang, Yichen Zhang, Songtao Yuan, Qinghuai Liu. Circular RNA expression and the competitive endogenous RNA network in pathological, age-related macular degeneration events: A cross-platform normalization study[J]. The Journal of Biomedical Research. doi: 10.7555/JBR.37.20230010

PDF( 3676 KB)

Circular RNA expression and the competitive endogenous RNA network in pathological, age-related macular degeneration events: A cross-platform normalization study

doi: 10.7555/JBR.37.20230010

Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, Jiangsu, 211166, China

More Information

Corresponding author: Songtao Yuan and Qinghuai Liu, Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, 101 Longmian Avenue, Jiangning District, Nanjing, Jiangsu 211166, China. Tel/Fax: +86-25-68303110 and +86-25-68303160, E-mails: yuansongtao@vip.sina.com and liuqh@njmu.edu.cn;
Received: 2023-01-16
Revised: 2023-02-20
Accepted: 2023-02-20

Published: 2023-04-28

Abstract

Abstract

Age-related macular degeneration (AMD) causes irreversible blindness in people aged over 50 worldwide. The dysfunction of retinal pigment epithelium is the primary cause of atrophic AMD. In the current study, we used ComBat and Training Distribution Matching to integrate data obtained from the gene expression omnibus (GEO) database. Integrated sequencing data were analyzed by Gene Set Enrichment Analysis (GSEA). Peroxisome and tumor necrosis factor-α (TNF-α) signaling via nuclear factor kappa B (NF-κB) were among the top 10 pathways and were selected to construct AMD cell models to identify differentially expressed circular RNAs (circRNAs). A competing endogenous RNA network, related to differentially expressed circRNAs, was then constructed. This network included seven circRNAs, 15 microRNAs, and 82 mRNAs. The Kyoto Encyclopedia of Genes and Genomes analysis (KEGG) of mRNAs in this network showed that the hypoxia-inducible factor-1 (HIF-1) signaling pathway is a common downstream event. The results of the current study may provide insights into the pathological processes that cause atrophic AMD.
- age-related macular degeneration,
- retinal pigment epithelium,
- circular RNA,
- bioinformatics analysis,
- competing endogenous RNA

CLC number: R774.5, Document code: A
The authors reported no conflict of interests.
^△These authors contributed equally to this work.

FullText(HTML)

References(35)

References

[1]	Mitchell P, Liew G, Gopinath B, et al. Age-related macular degeneration[J]. Lancet, 2018, 392(10153): 1147–1159. doi: 10.1016/S0140-6736(18)31550-2
[2]	Datta S, Cano M, Ebrahimi K, et al. The impact of oxidative stress and inflammation on RPE degeneration in non-neovascular AMD[J]. Prog Retin Eye Res, 2017, 60: 201–218. doi: 10.1016/j.preteyeres.2017.03.002
[3]	Zhao C, Yasumura D, Li X, et al. mTOR-mediated dedifferentiation of the retinal pigment epithelium initiates photoreceptor degeneration in mice[J]. J Clin Invest, 2011, 121(1): 369–383. doi: 10.1172/JCI44303
[4]	Liu B, Wei L, Meyerle C, et al. Complement component C5a promotes expression of IL-22 and IL-17 from human T cells and its implication in age-related macular degeneration[J]. J Transl Med, 2011, 9: 111. doi: 10.1186/1479-5876-9-111
[5]	Cousins SW, Espinosa-Heidmann DG, Csaky KG. Monocyte activation in patients with age-related macular degeneration: a biomarker of risk for choroidal neovascularization?[J]. Arch Ophthalmol, 2004, 122(7): 1013–1018. doi: 10.1001/archopht.122.7.1013
[6]	Yang L, Wilusz JE, Chen L. Biogenesis and regulatory roles of circular RNAs[J]. Annu Rev Cell Dev Biol, 2022, 38: 263–289. doi: 10.1146/annurev-cellbio-120420-125117
[7]	Chen X, Jiang C, Sun R, et al. Circular noncoding RNA NR3C1 acts as a miR-382–5p sponge to protect RPE functions via regulating PTEN/AKT/mTOR signaling pathway[J]. Mol Ther, 2020, 28(3): 929–945. doi: 10.1016/j.ymthe.2020.01.010
[8]	Dhirachaikulpanich D, Li X, Porter LF, et al. Integrated microarray and RNAseq transcriptomic analysis of retinal pigment epithelium/choroid in age-related macular degeneration[J]. Front Cell Dev Biol, 2020, 8: 808. doi: 10.3389/fcell.2020.00808
[9]	Thompson JA, Tan J, Greene CS. Cross-platform normalization of microarray and RNA-seq data for machine learning applications[J]. PeerJ, 2016, 4: e1621. doi: 10.7717/peerj.1621
[10]	Orozco LD, Chen HH, Cox C, et al. Integration of eQTL and a single-cell atlas in the human eye identifies causal genes for age-related macular degeneration[J]. Cell Rep, 2020, 30(4): 1246–1259.e6. doi: 10.1016/j.celrep.2019.12.082
[11]	Newman AM, Gallo NB, Hancox LS, et al. Systems-level analysis of age-related macular degeneration reveals global biomarkers and phenotype-specific functional networks[J]. Genome Med, 2012, 4(2): 16. doi: 10.1186/gm315
[12]	Gálvez JM, Castillo-Secilla D, Herrera LJ, et al. Towards improving skin cancer diagnosis by integrating microarray and RNA-Seq datasets[J]. IEEE J Biomed Health Inform, 2020, 24(7): 2119–2130. doi: 10.1109/JBHI.2019.2953978
[13]	Chen X, Sun R, Yang D, et al. LINC00167 regulates RPE differentiation by targeting the miR-203a-3p/SOCS3 axis[J]. Mol Ther Nucleic Acids, 2020, 19: 1015–1026. doi: 10.1016/j.omtn.2019.12.040
[14]	Kanehisa M, Furumichi M, Tanabe M, et al. KEGG: new perspectives on genomes, pathways, diseases and drugs[J]. Nucleic Acids Res, 2017, 45(D1): D353–D361. doi: 10.1093/nar/gkw1092
[15]	Zhang Y, Li J, Cui Q, et al. Circular RNA hsa_circ_0006091 as a novel biomarker for hepatocellular carcinoma[J]. Bioengineered, 2022, 13(2): 1988–2003. doi: 10.1080/21655979.2021.2006952
[16]	Kim KW, Kim K, Kim HJ, et al. Posttranscriptional modulation of KCNQ2 gene expression by the miR-106b microRNA family[J]. Proc Natl Acad Sci USA, 2021, 118(47): e2110200118. doi: 10.1073/pnas.2110200118
[17]	Müller C, Charniga C, Temple S, et al. Quantified F-actin morphology is predictive of phagocytic capacity of stem cell-derived retinal pigment epithelium[J]. Stem Cell Rep, 2018, 10(3): 1075–1087. doi: 10.1016/j.stemcr.2018.01.017
[18]	Foltz SM, Greene CS, Taroni JN. Cross-platform normalization enables machine learning model training on microarray and RNA-Seq data simultaneously[J]. Commun Biol, 2023, 6(1): 222. doi: 10.1038/s42003-023-04588-6
[19]	Saddala MS, Lennikov A, Mukwaya A, et al. Transcriptome-wide analysis of differentially expressed chemokine receptors, SNPs, and SSRs in the age-related macular degeneration[J]. Hum Genomics, 2019, 13(1): 15. doi: 10.1186/s40246-019-0199-1
[20]	Perez VL, Caspi RR. Immune mechanisms in inflammatory and degenerative eye disease[J]. Trends Immunol, 2015, 36(6): 354–363. doi: 10.1016/j.it.2015.04.003
[21]	Vogt SD, Curcio CA, Wang L, et al. Retinal pigment epithelial expression of complement regulator CD46 is altered early in the course of geographic atrophy[J]. Exp Eye Res, 2011, 93(4): 413–423. doi: 10.1016/j.exer.2011.06.002
[22]	Ebrahimi KB, Fijalkowski N, Cano M, et al. Decreased membrane complement regulators in the retinal pigmented epithelium contributes to age-related macular degeneration[J]. J Pathol, 2013, 229(5): 729–742. doi: 10.1002/path.4128
[23]	Kozumi K, Kodama T, Murai H, et al. Transcriptomics identify thrombospondin-2 as a biomarker for NASH and advanced liver fibrosis[J]. Hepatology, 2021, 74(5): 2452–2466. doi: 10.1002/hep.31995
[24]	Baek JH, Lim D, Park KH, et al. Quantitative proteomic analysis of aqueous humor from patients with drusen and reticular pseudodrusen in age-related macular degeneration[J]. BMC Ophthalmol, 2018, 18(1): 289. doi: 10.1186/s12886-018-0941-9
[25]	Gadaleta RM, Garcia-Irigoyen O, Cariello M, et al. Fibroblast Growth Factor 19 modulates intestinal microbiota and inflammation in presence of Farnesoid X Receptor[J]. EBioMedicine, 2020, 54: 102719. doi: 10.1016/j.ebiom.2020.102719
[26]	Choudhary M, Ismail EN, Yao P, et al. LXRs regulate features of age-related macular degeneration and may be a potential therapeutic target[J]. JCI Insight, 2020, 5(1): e131928. doi: 10.1172/jci.insight.131928
[27]	Lu H, Yang Y, Kuang D, et al. Expression profile of circRNA in peripheral blood mononuclear cells of patients with rheumatoid arthritis[J]. BMC Med Genomics, 2022, 15(1): 77. doi: 10.1186/s12920-022-01225-9
[28]	Wen J, Liu J, Wan L, et al. Triptolide inhibits cell growth and inflammatory response of fibroblast-like synoviocytes by modulating hsa-circ-0003353/microRNA-31–5p/CDK1 axis in rheumatoid arthritis[J]. Int Immunopharmacol, 2022, 106: 108616. doi: 10.1016/j.intimp.2022.108616
[29]	Iparraguirre L, Muñoz-Culla M, Prada-Luengo I, et al. Circular RNA profiling reveals that circular RNAs from ANXA2 can be used as new biomarkers for multiple sclerosis[J]. Hum Mol Genetics, 2017, 26(18): 3564–3572. doi: 10.1093/hmg/ddx243
[30]	Duan X, Yu X, Li Z. Circular RNA hsa_circ_0001658 regulates apoptosis and autophagy in gastric cancer through microRNA-182/Ras-related protein Rab-10 signaling axis[J]. Bioengineered, 2022, 13(2): 2387–2397. doi: 10.1080/21655979.2021.2024637
[31]	Lei Q, Liang Z, Lei Q, et al. Analysis of circRNAs profile in TNF-α treated DPSC[J]. BMC Oral Health, 2022, 22(1): 269. doi: 10.1186/s12903-022-02267-2
[32]	Kuschel A, Simon P, Tug S. Functional regulation of HIF‐1α under normoxia—is there more than post‐translational regulation?[J]. J Cell Physiol, 2012, 227(2): 514–524. doi: 10.1002/jcp.22798
[33]	Dong S, Liang S, Cheng Z, et al. ROS/PI3K/Akt and Wnt/β-catenin signalings activate HIF-1α-induced metabolic reprogramming to impart 5-fluorouracil resistance in colorectal cancer[J]. J Exp Clin Cancer Res, 2022, 41(1): 15. doi: 10.1186/s13046-021-02229-6
[34]	Chen G, Liu T, Yu B, et al. CircRNA-UBE2G1 regulates LPS-induced osteoarthritis through miR-373/HIF-1a axis[J]. Cell Cycle, 2020, 19(13): 1696–1705. doi: 10.1080/15384101.2020.1772545
[35]	Kurihara T, Westenskow PD, Gantner ML, et al. Hypoxia-induced metabolic stress in retinal pigment epithelial cells is sufficient to induce photoreceptor degeneration[J]. eLife, 2016, 5: e14319. doi: 10.7554/eLife.14319