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Research article
Expression Profile of Peripheral Immune Cells-derived Coding and Long Non-coding RNAs in Patients With Proliferative Vitreoretinopathy
Zhaotian Zhang
State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University Add: 54S Xianlie Road, Guangzhou, 510060, China
Corresponding Author
ORCiD: https://orcid.org/0000-0003-0436-3338
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Introduction: 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 profile peripheral blood mononuclear cells (PBMCs) 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 differentially expressed genes (DEGs).
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 significantly 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 differentially expressed lncRNAs were also significantly 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 profile, long non-coding RNAs, immune-related pathway
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Received 28 Dec, 2020
Editor assigned
On 27 Dec, 2020
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Editor invited
On 27 Dec, 2020
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Version 1
Posted 21 Sep, 2020
No community comments so far
Editorial decision: Minor revision
On 10 Dec, 2020
Reviewer #2 agreed
On 09 Dec, 2020
Review #2 received
Received 09 Dec, 2020
Review #1 received
Received 12 Oct, 2020
Reviewer #1 agreed
On 28 Sep, 2020
Editor assigned
On 24 Sep, 2020
Reviewers invited
Invitations sent on 24 Sep, 2020
Submission checks complete
On 18 Sep, 2020
Editor invited
On 18 Sep, 2020
First submitted
On 09 Sep, 2020
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Subject Areas
Epigenetics & Genomics
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This preprint is under consideration at BMC Medical Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Expression Profile of Peripheral Immune Cells-derived Coding and Long Non-coding RNAs in Patients With Proliferative Vitreoretinopathy
Zhaotian Zhang
State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University Add: 54S Xianlie Road, Guangzhou, 510060, China
Corresponding Author
ORCiD: https://orcid.org/0000-0003-0436-3338
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version (no preprint)
Posted 08 Jan, 2021
Submission checks complete
On 08 Jan, 2021
Editorial decision: Minor revision
On 06 Jan, 2021
This version was not preprinted
Version (no preprint)
Posted 28 Dec, 2020
Reviewer #2 agreed
On 28 Dec, 2020
Reviewers invited
Invitations sent on 28 Dec, 2020
Reviewer #1 agreed
On 28 Dec, 2020
Review #2 received
Received 28 Dec, 2020
Review #1 received
Received 28 Dec, 2020
Editor assigned
On 27 Dec, 2020
Submission checks complete
On 27 Dec, 2020
Editor invited
On 27 Dec, 2020
This version was not preprinted
Version 1
Posted 21 Sep, 2020
No community comments so far
Editorial decision: Minor revision
On 10 Dec, 2020
Reviewer #2 agreed
On 09 Dec, 2020
Review #2 received
Received 09 Dec, 2020
Review #1 received
Received 12 Oct, 2020
Reviewer #1 agreed
On 28 Sep, 2020
Editor assigned
On 24 Sep, 2020
Reviewers invited
Invitations sent on 24 Sep, 2020
Submission checks complete
On 18 Sep, 2020
Editor invited
On 18 Sep, 2020
First submitted
On 09 Sep, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Introduction: 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 profile peripheral blood mononuclear cells (PBMCs) 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 differentially expressed genes (DEGs).
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 significantly 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 differentially expressed lncRNAs were also significantly 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.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6