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View a Copy of This Licence, Visit Mmons​ .Org/Licen​ Ses/By/4.0/​ Ni et al. BMC Med Genomics (2021) 14:30 https://doi.org/10.1186/s12920-021-00875-5 RESEARCH ARTICLE Open Access Coding and non-coding RNA interactions reveal immune-related pathways in peripheral blood mononuclear cells derived from patients with proliferative vitreoretinopathy Yao Ni†, Fangyuan Liu†, Xiao Hu, Yingyan Qin and Zhaotian Zhang* Abstract Background: Peripheral immune response has been revealed to play a critical role in proliferative vitreoretinopathy (PVR). However, the reliable immune-related factors that are acting as prognostic indicators or therapeutic targets for PVR remain to explore further. Methods: In the current study, we applied whole-transcriptome sequencing to profle peripheral blood mononu- clear cells from PVR patients and also analyzed lncRNA-mRNA interactions in peripheral immune cells to explore the pathways that might mediate immunopathology and resultant retinal damage in PVR. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses and Ingenuity Pathway Analysis (IPA) were employed to classify the function of these diferentially expressed genes. Results: Compared to the controls, there were 319 genes upregulated, and 191 genes downregulated in PVR patients. GO, and KEGG enrichment analyses as well as IPA showed that these upregulated genes were signifcantly enriched in immune-related and infection-relate terms. Immune-related gene NFKBIA, CXCL2, and CXCL8 were detected as hub-genes in the co-expression network, while lncRNAs such as AC007032.1, AC037198.2, AL929472.2, and SLED1 were highly co-expressed with them. lncRNA-mRNA interactions analysis also showed that putative targeted genes of these diferentially expressed lncRNAs were also signifcantly enriched in immune-related or infection-relate pathways. Conclusion: Our study highlights the transformation of immune-related genes/pathways in PVR by comparing controls, and validates several critical genes and lncRNAs, which are serving as potential diagnostic markers for PVR patients. Keywords: Proliferative vitreoretinopathy, Gene expression profle, Long non-coding RNAs, Immune-related pathway Background Proliferative vitreoretinopathy (PVR) is a critically blind- ing complication that occurs during rhegmatogenous retinal detachment (RRD), before or after surgery. It is caused by the proliferation of glial cells or RPE cells to *Correspondence: [email protected] form a fbrous membrane at the neural retinal surface † Yao Ni and Fangyuan Liu have contributed equally to this work or even in the retina [1]. Immune cells involved in the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, 54S Xianlie Road, Guangzhou 510060, China pathogenesis of PVR, such as monocyte/macrophage © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creat iveco mmons .org/licen ses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/publi cdoma in/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Ni et al. BMC Med Genomics (2021) 14:30 Page 2 of 9 infltration and activity contributed to the progress of RNA extraction and cDNA library construction PVR [2]. And, some infammatory-related genes are iden- Using Ficoll-Paque™ PREMIUM Media (GE Health- tifed that can predict the susceptibility of PVR in popu- care Life Sciences, Massachusetts, America) and lations [3]. Recently, the interaction of long non-coding SepMate™-50 (STEMCELL Technologies, Vancou- RNAs (lncRNAs) and protein-coding RNAs (mRNAs) ver, Canada), approximately 5 mL of anticoagulated has been revealed playing a signifcant role in diseases peripheral blood was centrifuged at 500 g for 30 min, related to infammation and immunity [4, 5]. However, and the thin white layer was collected as PBMC. RNe- despite some lncRNAs, such as MALAT1 that had been asy Mini Kit (Qiagen Corporation, Hilden, Germany) unveiled by some publications [6, 7], there are no reliable was used to extract the total RNA from PBMC. After lncRNAs currently implicating in clinical practice acting using Agilent 4200 Bioanalyzer (Agilent Technologies, as prognostic indicators or therapeutic targets for PVR Santa Clara, CA, USA) to determine the RNA integrity patients. Tus, subsequent studies to identify more criti- number and quantity, the rRNA was removed by Epi- cal lncRNAs associated with PVR are warranted. centre Ribo-zero rRNA Removal Kit (Epicentre, Madi- In the present study, we hypothesized that transcrip- son, WI, USA). Subsequently, the DNA was cleaned tomes of peripheral immune cells in PVR might be by DNase and then captured and purifed by magnet altered, which are the potential cause for the initiation beads (Vazyme, Nanjing, China). Te purifed RNA was or progression of PVR. Peripheral blood samples were interrupted into short fragments by adding fragmenta- taken from patients undergoing standard three-port pars tion bufer, then the frst-strand cDNA was synthesized plana vitrectomy for indications of PVR secondary to and double-strand cDNA was obtained thereafter with RRD and the entire transcriptome sequencing was per- VAHTS Universal V6 RNA-seq Library Prep Kit for formed. Patients with idiopathic epiretinal membrane Illumina (Vazyme, Nanjing, China). Adapters were then (iERM) underwent pars plana vitrectomy were used as connected to the cDNAs and Agilent 4200 Bioanalyzer, controls [8,9]. Patients were excluded from analysis if as well as qPCR, were used to verify the fragment size they were with systemic diseases (e.g., diabetes, immu- and amplify the templates. Te constructed library was nological diseases, infections, etc.) that could infuence then loaded on the Illumina HiSeq X Ten system for systemic infammation. With the sequencing data, we use sequencing. lncRNA associated genes to applied Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Ingenuity Pathway Analysis (IPA), Sequence analysis and functional annotation as well as gene-lncRNA co-expression analysis to see the We used FastQC frst to check the quality of raw reads diferences in genes and transcripts level between PVR and then processed with Cutadapt software to generate patients and controls. We also validated some selected clean reads by trim adaptor sequences and removed the diferentially expressed lncRNAs by quantitative real- low-quality sequences [11]. HISAT2 was used to align the time polymerase chain reaction (qPCR) assay. Te results clean reads to the hg38 human reference genome [12]. of the current study provide novel insights into PVR Mapped reads used the StringTie software and Ensembl pathogenesis and treatment therapeutic targets. GTF fle(release 90) to obtain gene expression profles [13–15], and then the diferential expression analysis was executed via the DESeq2 package on R programmer Methods [16]. |log2Fold Change|≥ 0.585 (Fold change ≥ 1.5 or Fold Ethics statement and clinical sample collection change ≤ 0.6667) and P value < 0.05 were decided upon as Tis study was approved by the ethics committees of the the signifcance of diferentially expressed genes. GO and Zhongshan Ophthalmic Center. Te peripheral blood KEGG enrichment analyses were then performed using samples were taken in accordance with the Declaration of the Clusterprofler R package.17 And then use WCGNA Helsinki and written consent was obtained from all par- package on R to calculate the person coefcient and Con- ticipants. Patients diagnosed as primary rhegmatogenous struction of hierarchical clustering trees by correlation retinal detachment (RRD) with serious PVR (≥ Grade coefcients between genes. Ten export to Cytoscape C) [10], and were scheduled to have pars plana vitrec- software to draw the network plot. For further functional tomy (PPV) from October 2018 to February 2019 were analysis, diferentially expressed genes and transcripts included (PVR group). Patients diagnosed as idiopathic between PVR and iERM patients, including gene symbols epiretinal membrane (iERM) and scheduled to have PPV and expression values were uploaded into IPA software during the same period were included as negative con- (Qiagen, Germany). Te canonical pathways, diseases trols (iERM group). Te blood samples were collected and biofunctions as well as gene networks analysis were from patients before surgery. processed. Ni et al. BMC Med Genomics (2021) 14:30 Page 3 of 9 QPCR validation Mann–Whitney U test between PVR and iERM groups. Total RNA was isolated as mentioned above, and the A P value ≤ 0.05 was considered statistically signifcant. cDNA was then synthesized with HiScript II Q Select RT SuperMix for qPCR (Vazyme, Nanjing, China). Results Roche lightcycler 96 was then used to perform qPCR.
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