1
|
Yu Z, Ai N, Xu X, Zhang P, Jin Z, Li X, Ma H. Exploring the Molecular Mechanism of Skeletal Muscle Development in Ningxiang Pig by Weighted Gene Co-Expression Network Analysis. Int J Mol Sci 2024; 25:9089. [PMID: 39201775 PMCID: PMC11354759 DOI: 10.3390/ijms25169089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 08/18/2024] [Accepted: 08/20/2024] [Indexed: 09/03/2024] Open
Abstract
With the continuous improvement in living standards, people's demand for high-quality meat is increasing. Ningxiang pig has delicious meat of high nutritional value, and is loved by consumers. However, its slow growth and low meat yield seriously restrict its efficient utilization. Gene expression is the internal driving force of life activities, so in order to fundamentally improve its growth rate, it is key to explore the molecular mechanism of skeletal muscle development in Ningxiang pigs. In this paper, Ningxiang boars were selected in four growth stages (30 days: weaning period, 90 days: nursing period, 150 days: early fattening period, and 210 days: late fattening period), and the longissimus dorsi (LD) muscle was taken from three boars in each stage. The fatty acid content, amino acid content, muscle fiber diameter density and type of LD were detected by gas chromatography, acidolysis, hematoxylin eosin (HE) staining and immunofluorescence (IF) staining. After transcription sequencing, weighted gene co-expression network analysis (WGCNA) combined with the phenotype of the LD was used to explore the key genes and signaling pathways affecting muscle development. The results showed that 10 modules were identified by WGCNA, including 5 modules related to muscle development stage, module characteristics of muscle fiber density, 5 modules characteristic of muscle fiber diameter, and a module characteristic of palmitoleic acid (C16:1) and linoleic acid (C18:2n6C). Gene ontology (GO) enrichment analysis found that 52 transcripts relating to muscle development were enriched in these modules, including 44 known genes and 8 novel genes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that these genes were enriched in the auxin, estrogen and cyclic guanosine monophosphate-protein kinase G (cGMP-PKG) pathways. Twelve of these genes were transcription factors, there were interactions among 20 genes, and the interactions among 11 proteins in human, pig and mouse were stable. To sum up, through the integrated analysis of phenotype and transcriptome, this paper analyzed the key genes and possible regulatory networks of skeletal muscle development in Ningxiang pigs at various stages, to provide a reference for the in-depth study of skeletal muscle development.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (Z.Y.); (N.A.); (X.X.); (P.Z.); (Z.J.); (X.L.)
| |
Collapse
|
2
|
Li T, Zhang W, Wang J, Liu B, Gao Q, Zhang J, Qian H, Pan J, Liu M, Huang Q, Fang A, Zhang Q, Gong X, Cui R, Liang Y, Lu Q, Wu W, Chi Z. Circulating Small Extracellular Vesicles Involved in Systemic Regulation Respond to RGC Degeneration in Glaucoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309307. [PMID: 38923329 PMCID: PMC11348076 DOI: 10.1002/advs.202309307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/14/2024] [Indexed: 06/28/2024]
Abstract
Glaucoma is a leading cause of irreversible blindness worldwide and is characterized by progressive retinal ganglion cell (RGC) degeneration and vision loss. Since irreversible neurodegeneration occurs before diagnosable, early diagnosis and effective neuroprotection are critical for glaucoma management. Small extracellular vesicles (sEVs) are demonstrated to be potential novel biomarkers and therapeutics for a variety of diseases. In this study, it is found that intravitreal injection of circulating plasma-derived sEVs (PDEV) from glaucoma patients ameliorated retinal degeneration in chronic ocular hypertension (COH) mice. Moreover, it is found that PDEV-miR-29s are significantly upregulated in glaucoma patients and are associated with visual field defects in progressed glaucoma. Subsequently, in vivo and in vitro experiments are conducted to investigate the possible function of miR-29s in RGC pathophysiology. It is showed that the overexpression of miR-29b-3p effectively prevents RGC degeneration in COH mice and promotes the neuronal differentiation of human induced pluripotent stem cells (hiPSCs). Interestingly, engineered sEVs with sufficient miR-29b-3p delivery exhibit more effective RGC protection and neuronal differentiation efficiency. Thus, elevated PDEV-miR-29s may imply systemic regulation to prevent RGC degeneration in glaucoma patients. This study provides new insights into PDEV-based glaucoma diagnosis and therapeutic strategies for neurodegenerative diseases.
Collapse
Affiliation(s)
- Tong Li
- State Key Laboratory of OphthalmologyOptometry and Visual ScienceEye Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Wen‐Meng Zhang
- State Key Laboratory of OphthalmologyOptometry and Visual ScienceEye Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Jie Wang
- State Key Laboratory of OphthalmologyOptometry and Visual ScienceEye Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Bai‐Jing Liu
- State Key Laboratory of OphthalmologyOptometry and Visual ScienceEye Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Qiao Gao
- State Key Laboratory of OphthalmologyOptometry and Visual ScienceEye Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Jing Zhang
- State Key Laboratory of OphthalmologyOptometry and Visual ScienceEye Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Hai‐Dong Qian
- State Key Laboratory of OphthalmologyOptometry and Visual ScienceEye Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Jun‐Yi Pan
- State Key Laboratory of OphthalmologyOptometry and Visual ScienceEye Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Ming Liu
- State Key Laboratory of OphthalmologyOptometry and Visual ScienceEye Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Qing Huang
- State Key Laboratory of OphthalmologyOptometry and Visual ScienceEye Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Ai‐Wu Fang
- National Clinical Research Center for Ocular DiseasesEye Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Qi Zhang
- National Clinical Research Center for Ocular DiseasesEye Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Xian‐Hui Gong
- National Clinical Research Center for Ocular DiseasesEye Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Ren‐Zhe Cui
- Department of OphthalmologyAffiliated Hospital of Yanbian UniversityYanji136200China
| | - Yuan‐Bo Liang
- State Key Laboratory of OphthalmologyOptometry and Visual ScienceEye Hospital of Wenzhou Medical UniversityWenzhou325027China
- National Clinical Research Center for Ocular DiseasesEye Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Qin‐Kang Lu
- Department of OphthalmologyYinzhou People's HospitalMedical School of Ningbo UniversityNingbo315040China
| | - Wen‐Can Wu
- State Key Laboratory of OphthalmologyOptometry and Visual ScienceEye Hospital of Wenzhou Medical UniversityWenzhou325027China
- National Clinical Research Center for Ocular DiseasesEye Hospital of Wenzhou Medical UniversityWenzhou325027China
| | - Zai‐Long Chi
- State Key Laboratory of OphthalmologyOptometry and Visual ScienceEye Hospital of Wenzhou Medical UniversityWenzhou325027China
- National Clinical Research Center for Ocular DiseasesEye Hospital of Wenzhou Medical UniversityWenzhou325027China
| |
Collapse
|
3
|
Kong K, Ding X, Wang Y, Xu S, Li G, Wang X, Zhang M, Ni Y, Xu G. Circular RNA expression profile and functional analysis of circUvrag in light-induced photoreceptor degeneration. Clin Exp Ophthalmol 2024; 52:558-575. [PMID: 38282307 DOI: 10.1111/ceo.14355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 11/18/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND Circular RNAs (circRNAs) are implicated in retinal pathophysiology; however, their expression profiles and functions in photoreceptor apoptosis are largely unknown. We explored circRNA-expression profiles and circUvrag (host gene: Uvrag, ultraviolet radiation resistance associated gene) function in light-induced photoreceptor apoptosis. METHODS Sprague-Dawley rats and 661 W photoreceptor cells were exposed to blue light to establish light-induced photoreceptor degeneration. Differentially expressed circRNAs were identified using microarrays. Potential functions of dysregulated circRNAs were analysed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. CircUvrag expression and localization were evaluated using quantitative RT-PCR and fluorescence in situ hybridization, respectively. CircUvrag overexpression and knockdown were induced using a plasmid and a small interfering RNA, respectively, and retinal function and structure were assessed using scotopic electroretinography, haematoxylin-eosin staining, and TUNEL staining. Microglial migration was assessed using IBA1 immunostaining. The apoptosis ratio of photoreceptor cells in vitro was detected using flow cytometry. RESULTS We identified 764 differentially expressed circRNAs, which were potentially related with the development of retinal structures, including neurons, dendrites, and synapses, and might participate in nervous-system pathophysiology. Light exposure enriched circUvrag in the cytoplasm of photoreceptors in the outer nuclear layer (ONL). CircUvrag knockdown decreased photoreceptor apoptosis and microglial migration to the ONL after light exposure, preserving ONL thickness and a-wave amplitude. In vitro, circUvrag knockdown inhibited photoreceptor apoptosis, although circUvrag overexpression slightly promoted photoreceptor apoptosis. CONCLUSIONS CircUvrag knockdown attenuated light-induced photoreceptor apoptosis, and might be a potential target in retinal degeneration.
Collapse
Affiliation(s)
- Kangjie Kong
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Xinyi Ding
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Yingchao Wang
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Sisi Xu
- Department of Ophthalmology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Gang Li
- Research Center, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Xin Wang
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Meng Zhang
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Yingqin Ni
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| | - Gezhi Xu
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Eye and ENT Hospital of Fudan University, Shanghai, China
| |
Collapse
|
4
|
Sun L, Cen Y, Liu X, Wei J, Ke X, Wang Y, Liao Q, Chang M, Zhou M, Wu W. Systemic whole transcriptome analysis identified underlying molecular characteristics and regulatory networks implicated in the retina following optic nerve injury. Exp Eye Res 2024; 244:109929. [PMID: 38750783 DOI: 10.1016/j.exer.2024.109929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 04/18/2024] [Accepted: 05/12/2024] [Indexed: 06/02/2024]
Abstract
Optic nerve injuries are severely disrupt the structural and functional integrity of the retina, often leading to visual impairment or blindness. Despite the profound impact of these injuries, the molecular mechanisms involved remain poorly understood. In this study, we performed a comprehensive whole-transcriptome analysis of mouse retina samples after optic nerve crush (ONC) to elucidate changes in gene expression and regulatory networks. Transcriptome analysis revealed a variety of molecular alterations, including 256 mRNAs, 530 lncRNAs, and 37 miRNAs, associated with metabolic, inflammatory, signaling, and biosynthetic pathways in the injured retina. The integrated analysis of co-expression and protein-protein interactions identified an active interconnected module comprising 5 co-expressed proteins (Fga, Serpina1a, Hpd, Slc38a4, and Ahsg) associated with the complement and coagulation cascades. Finally, 5 mRNAs (Fga, Serpinala, Hpd, Slc38a4, and Ahsg), 2 miRNAs (miR-671-5p and miR-3057-5p), and 6 lncRNAs (MSTRG. 1830.1, Gm10814, A530013C23Rik, Gm40634, MSTRG.9514.1, A330023F24Rik) were identified by qPCR in the injured retina, and some of them were validated as critical components of a ceRNA network active in 661W and HEK293T cells through dual-luciferase reporter assays. In conclusion, our study provides comprehensive insight into the complex and dynamic biological mechanisms involved in retinal injury responses and highlights promising potential targets to enhance neuroprotection and restore vision.
Collapse
Affiliation(s)
- Lanfang Sun
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Yixin Cen
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Xiaojiang Liu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jinfei Wei
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Xiaoyu Ke
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Yanan Wang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Qianling Liao
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Mengchun Chang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Meng Zhou
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
| | - Wencan Wu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
| |
Collapse
|
5
|
Zhang L, Liu X, Li W, Liu K, Zhang J, Liu X, Wang J. Integrative transcriptomic profiling of ncRNAs and mRNAs in developing mouse lens. Front Genet 2024; 15:1405715. [PMID: 38933921 PMCID: PMC11199715 DOI: 10.3389/fgene.2024.1405715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
In recent years, burgeoning research has underscored the pivotal role of non-coding RNA in orchestrating the growth, development, and pathogenesis of various diseases across organisms. However, despite these advances, our understanding of the specific contributions of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) to lens development remains notably limited. Clarifying the intricate gene regulatory networks is imperative for unraveling the molecular underpinnings of lens-related disorders. In this study, we aimed to address this gap by conducting a comprehensive analysis of the expression profiles of messenger RNAs (mRNAs), lncRNAs, and circRNAs at critical developmental time points of the mouse lens, encompassing both embryonic (E10.5, E12.5, and E16.5) and postnatal stages (P0.5, P10.5, and P60). Leveraging RNA-sequencing technology, we identified key transcripts pivotal to lens development. Our analysis revealed differentially expressed (DE) mRNAs, lncRNAs, and circRNAs across various developmental stages. Particularly noteworthy, there were 1831 co-differentially expressed (CO-DE) mRNAs, 150 CO-DE lncRNAs, and 13 CO-DE circRNAs identified during embryonic stages. Gene Ontology (GO) enrichment analysis unveiled associations primarily related to lens development, DNA conformational changes, and angiogenesis among DE mRNAs and lncRNAs. Furthermore, employing protein-protein interaction networks, mRNA-lncRNA co-expression networks, and circRNA-microRNA-mRNA networks, we predicted candidate key molecules implicated in lens development. Our findings underscore the pivotal roles of lncRNAs and circRNAs in this process, offering fresh insights into the pathogenesis of lens-related disorders and paving the way for future exploration in this field.
Collapse
Affiliation(s)
- Liyun Zhang
- Department of Ophthalmology, General Hospital of Central Theater Command, Wuhan, China
| | - Xin Liu
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, Guangdong, China
| | - Wei Li
- Department of Pediatric Respiratory Medicine, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kaiqing Liu
- The Department of Urology, The Third Affiliated Hospital of Shenzhen University, Shenzhen, Guangdong, China
| | - Jing Zhang
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, Guangdong, China
| | - Xinhua Liu
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, Guangdong, China
| | - Jiantao Wang
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, Guangdong, China
| |
Collapse
|
6
|
Chen A, Ji C, Li C, Brand-Saberi B, Zhang S. Multiple transcriptome analyses reveal mouse testis developmental dynamics. BMC Genomics 2024; 25:395. [PMID: 38649810 PMCID: PMC11036721 DOI: 10.1186/s12864-024-10298-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
The testes are the organs of gamete production and testosterone synthesis. Up to date, no model system is available for mammalian testicular development, and only few studies have characterized the mouse testis transcriptome from no more than three postnatal ages. To describe the transcriptome landscape of the developing mouse testis and identify the potential molecular mechanisms underlying testis maturation, we examined multiple RNA-seq data of mouse testes from 3-week-old (puberty) to 11-week-old (adult). Sperm cells appeared as expected in 5-week-old mouse testis, suggesting the proper sample collection. The principal components analysis revealed the genes from 3w to 4w clustered away from other timepoints, indicating they may be the important nodes for testicular development. The pairwise comparisons at two adjacent timepoints identified 7,612 differentially expressed genes (DEGs), resulting in 58 unique mRNA expression patterns. Enrichment analysis identified functions in tissue morphogenesis (3-4w), regulation of peptidase activity (4-5w), spermatogenesis (7-8w), and antigen processing (10-11w), suggesting distinct functions in different developmental periods. 50 hub genes and 10 gene cluster modules were identified in the testis maturation process by protein-protein interaction (PPI) network analysis, and the miRNA-lncRNA-mRNA, miRNA-circRNA-mRNA and miRNA-circRNA-lncRNA-mRNA competing endogenous RNA (ceRNA) networks were constructed. The results suggest that testis maturation is a complex developmental process modulated by various molecules, and that some potential RNA-RNA interactions may be involved in specific developmental stages. In summary, this study provides an update on the molecular basis of testis development, which may help to understand the molecular mechanisms of mouse testis development and provide guidance for mouse reproduction.
Collapse
Affiliation(s)
- Anqi Chen
- Institute of Forensic Science, Fudan University, 200032, Shanghai, China
| | - Chaoneng Ji
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Chengtao Li
- Institute of Forensic Science, Fudan University, 200032, Shanghai, China
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Ministry of Justice, Academy of Forensic Science, 200063, Shanghai, China
| | - Beate Brand-Saberi
- Department of Anatomy and Molecular Embryology, Institute of Anatomy, Medical Faculty, Ruhr University Bochum, 44801, Bochum, Germany.
| | - Suhua Zhang
- Institute of Forensic Science, Fudan University, 200032, Shanghai, China.
| |
Collapse
|
7
|
Zhang X, Zhang M, Li Y, Jiang Y. Comprehensive transcriptional analysis of early dorsal skin development in pigs. Gene 2024; 899:148141. [PMID: 38184019 DOI: 10.1016/j.gene.2024.148141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/11/2023] [Accepted: 01/03/2024] [Indexed: 01/08/2024]
Abstract
Porcine skin is similar to human skin in physiology, anatomy and histology and is often used as a model animal for human skin research. There are few studies on the transcriptome aspects of pig skin during the embryonic period. In this study, RNA sequencing was performed on the dorsal skin of Chenghua sows at embryonic day 56 (E56), embryonic day 76 (E76), embryonic day 105 (E105), and 3 days after birth (D3) to explore RNA changes in pig dorsal skin at four ages. A number of skin-related differential genes were identified by intercomparison between RNAs at four time points, and KEGG functional analysis showed that these differential genes were mainly enriched in metabolic and developmental, immune, and disease pathways, and the pathways enriched in GO analysis were highly overlapping. Collagen is an important part of the skin, with type I collagen making up the largest portion. In this study, collagen type I alpha 1 (COL1A1) and collagen type I alpha 2 (COL1A2) were significantly upregulated at four time points. In addition, lncRNA-miRNA-mRNA and miRNA-circRNA coexpression networks were constructed. The data obtained may help to explain age-related changes in transcriptional patterns during skin development and provide further references for understanding human skin development at the molecular level.
Collapse
Affiliation(s)
- Xinyue Zhang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an 625014, Sichuan, China
| | - Mei Zhang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an 625014, Sichuan, China
| | - Yujing Li
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an 625014, Sichuan, China
| | - Yanzhi Jiang
- Department of Zoology, College of Life Science, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
| |
Collapse
|
8
|
Bai Y, He H, Ren B, Ren J, Zou T, Chen X, Liu Y. Sstr2 Defines the Cone Differentiation-Competent Late-Stage Retinal Progenitor Cells in the Developing Mouse Retina. Stem Cells Transl Med 2024; 13:83-99. [PMID: 37935630 PMCID: PMC10785222 DOI: 10.1093/stcltm/szad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 10/06/2023] [Indexed: 11/09/2023] Open
Abstract
Cone cell death is a characteristic shared by various retinal degenerative disorders, such as cone-rod dystrophy, Stargardt disease, achromatopsia, and retinitis pigmentosa. This leads to conditions like color blindness and permanently impaired visual acuity. Stem cell therapy focused on photoreceptor replacement holds promise for addressing these conditions. However, identifying surface markers that aid in enriching retinal progenitor cells (RPCs) capable of differentiating into cones remains a complex task. In this study, we employed single-cell RNA sequencing to scrutinize the transcriptome of developing retinas in C57BL/6J mice. This revealed the distinctive expression of somatostatin receptor 2 (Sstr2), a surface protein, in late-stage RPCs exhibiting the potential for photoreceptor differentiation. In vivo lineage tracing experiments verified that Sstr2+ cells within the late embryonic retina gave rise to cones, amacrine and horizontal cells during the developmental process. Furthermore, Sstr2+ cells that were isolated from the late embryonic mouse retina displayed RPC markers and exhibited the capability to differentiate into cones in vitro. Upon subretinal transplantation into both wild-type and retinal degeneration 10 (rd10) mice, Sstr2+ cells survived and expressed cone-specific markers. This study underscores the ability of Sstr2 to enrich late-stage RPCs primed for cone differentiation to a large extent. It proposes the utility of Sstr2 as a biomarker for RPCs capable of generating cones for transplantation purposes.
Collapse
Affiliation(s)
- Yihan Bai
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, People’s Republic of China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, People’s Republic of China
| | - Han He
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, People’s Republic of China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, People’s Republic of China
| | - Bangqi Ren
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, People’s Republic of China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, People’s Republic of China
| | - Jiayun Ren
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, People’s Republic of China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, People’s Republic of China
| | - Ting Zou
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, People’s Republic of China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, People’s Republic of China
| | - Xi Chen
- Department of Ophthalmology, Beijing Friendship Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Yong Liu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, People’s Republic of China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, People’s Republic of China
- Jinfeng Laboratory, Chongqing, China
| |
Collapse
|
9
|
Wang Y, Liu Y, Cai J, Zong T, Zhang Z, Xie T, Mu T, Wu M, Yang Q, Wang Y, Wang X, Yao Y. Differentially expressed genes in orbital adipose/connective tissue of thyroid-associated orbitopathy. PeerJ 2023; 11:e16569. [PMID: 38130930 PMCID: PMC10734407 DOI: 10.7717/peerj.16569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Background Thyroid-associated orbitopathy (TAO) is a disease associated with autoimmune thyroid disorders and it can lead to proptosis, diplopia, and vision-threatening compressive optic neuropathy. To comprehensively understand the molecular mechanisms underlying orbital adipogenesis in TAO, we characterize the intrinsic molecular properties of orbital adipose/connective tissue from patients with TAO and control individuals. Methods RNA sequencing analysis (RNA-seq) was performed to measure the gene expression of orbital adipose/connective tissues of TAO patients. Differentially expressed genes (DEGs) were detected and analyzed through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and Gene Set Enrichment Analysis (GSEA). The protein-protein interaction (PPI) network was constructed using the STRING database, and hub genes were identified by the Cytoscape plug-in, cytoHubba. We validated several top DEGs through quantitative real-time polymerase chain reaction (qRT-PCR). Results We identified 183 DEGs in adipose tissue between TAO patients (n = 3) and control patients (n = 3) through RNA sequencing, including 114 upregulated genes and 69 downregulated genes. The PPI network of these DEGs had 202 nodes and 743 edges. PCR-based validation results of orbital adipose tissue showed multiple top-ranked genes in TAO patients (n = 4) are immune and inflammatory response genes compared with the control individual (n = 4). They include ceruloplasmin isoform x3 (CP), alkaline tissue-nonspecific isozyme isoform x1 (ALPL), and angiotensinogen (AGT), which were overrepresented by 2.27- to 6.40-fold. Meanwhile, protein mab-21-like 1 (MAB21L1), phosphoinositide 3-kinase gamma-subunit (PIK3C2G), and clavesin-2 (CLVS2) decreased by 2.6% to 32.8%. R-spondin 1 (RSPO1), which is related to oogonia differentiation and developmental angiogenesis, was significantly downregulated in the orbital muscle tissues of patients with TAO compared with the control groups (P = 0.024). Conclusions Our results suggest that there are genetic differences in orbital adipose-connective tissues derived from TAO patients. The upregulation of the inflammatory response in orbital fat of TAO may be consistent with the clinical phenotype like eyelid edema, exophthalmos, and excess tearing. Downregulation of MAB21L1, PIK3C2G, and CLVS2 in TAO tissue demonstrates dysregulation of differentiation, oxidative stress, and developmental pathways.
Collapse
Affiliation(s)
- Yan Wang
- Department of Ophthalmology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Yanqiu Liu
- Department of Ophthalmology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Jiping Cai
- Department of Ophthalmology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Tianyi Zong
- Department of Ophthalmology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Ziyin Zhang
- Department of Ophthalmology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Tianhua Xie
- Department of Ophthalmology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Tong Mu
- Department of Ophthalmology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Meili Wu
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Qian Yang
- Department of Ophthalmology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Yangningzhi Wang
- Department of Ophthalmology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Xiaolu Wang
- Center of Clinical Research, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| | - Yong Yao
- Department of Ophthalmology, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi, China
| |
Collapse
|
10
|
Fu W, Gu H, Ye Y. Long Noncoding RNA MIAT Modulates Chronic Retinal Ischemia-Reperfusion Injury in Mice via the microRNA-203-3p/SNAI2 Axis. Chem Res Toxicol 2023; 36:1683-1692. [PMID: 37870436 DOI: 10.1021/acs.chemrestox.3c00129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Retinal ischemia-reperfusion injury (RIRI) is a vital pathological process of multiple ocular diseases. This study aimed at investigating the effects of the MIAT/miR-203-3p/SNAI2 axis on RIRI. RIRI was produced by inducing an exceedingly high intraocular pressure (IOP) in mice. Mouse retinal ganglion cells (RGCs) were subjected to oxygen-glucose deprivation/reoxygenation (OGD/R) to mimic in vitro models. Relevant oligonucleotides or plasmids were transfected into OGD/R-induced RGCs in vitro or injected into RIRI mice models in vivo via a vitreous cavity. The findings of our paper indicated that MIAT and SNAI2 were highly expressed and miR-203-3p was lowly expressed in mouse RIRI tissues and OGD/R-induced RGCs. Interfering MIAT promoted the viability of OGD/R-induced RGCs, decreased apoptosis, and reduced oxidative stress in vitro. Silencing MIAT increased retinal neuronal cell numbers and decreased retinal neuronal cell apoptosis in mouse RIRI tissues in vivo. MIAT sponged miR-203-3p, and miR-203-3p targeted and inhibited SNAI2 expression. SNAI2 up-regulation or miR-203-3p down-regulation reversed the protective effects of MIAT down-regulation on RIRI in mice and OGD/R-induced RGCs. MIAT sponges miR-203-3p upregulated the expression of SNAI2, thereby promoting RIRI in mice. In summary, MIAT may be a therapeutic target for the treatment of chronic RIRI.
Collapse
Affiliation(s)
- Weina Fu
- Department of Ophthalmology, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315040, China
| | - Hong Gu
- Department of Ophthalmology, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315040, China
| | - Yunyan Ye
- Department of Ophthalmology, Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315040, China
| |
Collapse
|
11
|
Kong K, Wang P, Xie Z, Wang L, Jiang J, Liu Y, Du S, Jiang J, Song Y, Lin F, Wang W, Fang X, Shi Z, Zhang X, Chen S. Integrated Transcriptome Analysis of Long Noncoding RNA and mRNA in Developing and Aging Mouse Retina. Sci Data 2023; 10:653. [PMID: 37741836 PMCID: PMC10518015 DOI: 10.1038/s41597-023-02562-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023] Open
Abstract
Mice have emerged as a widely employed model for investigating various retinal diseases. However, the availability of comprehensive datasets capturing the entire developmental and aging stages of the mouse retina, particularly during the elderly period, encompassing integrated lncRNA and mRNA expression profiles, is limited. In this study, we assembled a total of 18 retina samples from mice across 6 distinct stages of development and aging (5 days, 3 weeks, 6 weeks, 10 weeks, 6 months, and 15 months) to conduct integrated lncRNA and mRNA sequencing analysis. This invaluable dataset offers a comprehensive transcriptomic resource of mRNA and lncRNA expression profiles during the natural progression of retinal development and aging. The discoveries stemming from this investigation will significantly contribute to the elucidation of the underlying molecular mechanisms associated with various retinal diseases, such as congenital retinal dysplasia and retinal degenerative diseases.
Collapse
Affiliation(s)
- Kangjie Kong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Peiyuan Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Zihong Xie
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou, 510060, China
| | - Lu Wang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510060, China
| | - Jiaxuan Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Yaoming Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Shaolin Du
- Dongguan Tungwah Hospital, Dongguan, 523000, China
| | - Jingwen Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Yunhe Song
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Fengbin Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Wei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Xiuli Fang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China
| | - Zhuoxing Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China.
| | - Xiulan Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China.
| | - Shida Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Center for Ocular Diseases, Guangzhou, 510060, China.
| |
Collapse
|
12
|
Liang J, Fang D, Yao F, Chen L, Zou Z, Tang X, Feng L, Zhuang Y, Xie T, Wei P, Li P, Zheng H, Zhang S. Analysis of shared ceRNA networks and related-hub genes in rats with primary and secondary photoreceptor degeneration. Front Neurosci 2023; 17:1259622. [PMID: 37811327 PMCID: PMC10552924 DOI: 10.3389/fnins.2023.1259622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Photoreceptor degenerative diseases are characterized by the progressive death of photoreceptor cells, resulting in irreversible visual impairment. However, the role of competing endogenous RNA (ceRNA) in photoreceptor degeneration is unclear. We aimed to explore the shared ceRNA regulation network and potential molecular mechanisms between primary and secondary photoreceptor degenerations. Methods We established animal models for both types of photoreceptor degenerations and conducted retina RNA sequencing to identify shared differentially expressed long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs). Using ceRNA regulatory principles, we constructed a shared ceRNA network and performed function enrichment and protein-protein interaction (PPI) analyses to identify hub genes and key pathways. Immune cell infiltration and drug-gene interaction analyses were conducted, and hub gene expression was validated by quantitative real-time polymerase chain reaction (qRT-PCR). Results We identified 37 shared differentially expressed lncRNAs, 34 miRNAs, and 247 mRNAs and constructed a ceRNA network consisting of 3 lncRNAs, 5 miRNAs, and 109 mRNAs. Furthermore, we examined 109 common differentially expressed genes (DEGs) through functional annotation, PPI analysis, and regulatory network analysis. We discovered that these diseases shared the complement and coagulation cascades pathway. Eight hub genes were identified and enriched in the immune system process. Immune infiltration analysis revealed increased T cells and decreased B cells in both photoreceptor degenerations. The expression of hub genes was closely associated with the quantities of immune cell types. Additionally, we identified 7 immune therapeutical drugs that target the hub genes. Discussion Our findings provide new insights and directions for understanding the common mechanisms underlying the development of photoreceptor degeneration. The hub genes and related ceRNA networks we identified may offer new perspectives for elucidating the mechanisms and hold promise for the development of innovative treatment strategies.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Shaochong Zhang
- Shenzhen Eye Hospital, Shenzhen Eye Institute, Jinan University, Shenzhen, Guangdong, China
| |
Collapse
|
13
|
Zou L, Wang X, Han X. LncRNA MALAT 1/miR-625-3p/HIF-1α axis regulates the EMT of hypoxia-induced RPE cells by activating NF-κB/snail signaling. Exp Cell Res 2023; 429:113650. [PMID: 37209990 DOI: 10.1016/j.yexcr.2023.113650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/03/2023] [Accepted: 05/14/2023] [Indexed: 05/22/2023]
Abstract
The retina may undergo structural and functional damage as a result of hypoxia, which could lead to permanent blindness. As competing endogenous RNAs (ceRNAs), lncRNAs are essential in eye disorders. The biological function of lncRNA MALAT 1 and its potential mechanisms in hypoxic-ischemic retinal diseases are still unknown. MALAT 1 and miR-625-3p expression alterations in hypoxia-treated RPE cells were examined using qRT-PCR. The target binding relationships between MALAT 1 and miR-625-3p, as well as between miR-625-3p and HIF-1α, were identified utilizing bioinformatics analysis and dual luciferase reporter assay. We observed that si-MALAT 1 and miR-625-3p mimic both reduced apoptosis and epithelial-mesenchymal transition (EMT) in hypoxic RPE cells, whereas si-MALAT 1 was reversed by miR-625-3p inhibitor. Further, we carried out a mechanistic investigation, and rescue assays demonstrated that MALAT 1 sponging miR-625-3p influenced HIF-1α expression and consequently took part in the NF-κB/Snail signaling pathway, which regulated apoptosis and EMT. In conclusion, our research had shown that the MALAT 1/miR-625-3p/HIF-1α axis drove the progression of hypoxic-ischemic retinal disorders and may serve as a promising predictive biomarker for their therapeutic and diagnostic targets.
Collapse
Affiliation(s)
- Lirong Zou
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Eye Hospital of China Medical University, Key Lens Research Laboratory of Liaoning Province, Shenyang City, Liaoning Province, 110005, PR China
| | - Xinling Wang
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Eye Hospital of China Medical University, Key Lens Research Laboratory of Liaoning Province, Shenyang City, Liaoning Province, 110005, PR China.
| | - Xiao Han
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Eye Hospital of China Medical University, Key Lens Research Laboratory of Liaoning Province, Shenyang City, Liaoning Province, 110005, PR China.
| |
Collapse
|
14
|
Yu D, Wu Y, Zhu L, Wang Y, Sheng D, Zhao X, Liang G, Gan L. The landscape of the long non-coding RNAs in developing mouse retinas. BMC Genomics 2023; 24:252. [PMID: 37165305 PMCID: PMC10173636 DOI: 10.1186/s12864-023-09354-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 05/03/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND The long non-coding RNAs (lncRNAs) are critical regulators of diverse biological processes. Nevertheless, a global view of its expression and function in the mouse retina, a crucial model for neurogenesis study, still needs to be made available. RESULTS Herein, by integrating the established gene models and the result from ab initio prediction using short- and long-read sequencing, we characterized 4,523 lncRNA genes (MRLGs) in developing mouse retinas (from the embryonic day of 12.5 to the neonatal day of P28), which was so far the most comprehensive collection of retinal lncRNAs. Next, derived from transcriptomics analyses of different tissues and developing retinas, we found that the MRLGs were highly spatiotemporal specific in expression and played essential roles in regulating the genesis and function of mouse retinas. In addition, we investigated the expression of MRLGs in some mouse mutants and revealed that 97 intergenic MRLGs might be involved in regulating differentiation and development of retinal neurons through Math5, Isl1, Brn3b, NRL, Onecut1, or Onecut2 mediated pathways. CONCLUSIONS In summary, this work significantly enhanced our knowledge of lncRNA genes in mouse retina development and provided valuable clues for future exploration of their biological roles.
Collapse
Affiliation(s)
- Dongliang Yu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China.
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China.
| | - Yuqing Wu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China
| | - Leilei Zhu
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Yuying Wang
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Donglai Sheng
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Xiaofeng Zhao
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China
| | - Guoqing Liang
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 310036, China.
| | - Lin Gan
- Department of Neuroscience & Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.
| |
Collapse
|
15
|
Navarro-Calvo J, Esquiva G, Gómez-Vicente V, Valor LM. MicroRNAs in the Mouse Developing Retina. Int J Mol Sci 2023; 24:ijms24032992. [PMID: 36769311 PMCID: PMC9918188 DOI: 10.3390/ijms24032992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The retina is among the highest organized tissues of the central nervous system. To achieve such organization, a finely tuned regulation of developmental processes is required to form the retinal layers that contain the specialized neurons and supporting glial cells to allow precise phototransduction. MicroRNAs are a class of small RNAs with undoubtful roles in fundamental biological processes, including neurodevelopment of the brain and the retina. This review provides a short overview of the most important findings regarding microRNAs in the regulation of retinal development, from the developmental-dependent rearrangement of the microRNA expression program to the key roles of particular microRNAs in the differentiation and maintenance of retinal cell subtypes.
Collapse
Affiliation(s)
- Jorge Navarro-Calvo
- Unidad de Investigación, Hospital General Universitario Dr. Balmis, ISABIAL, 03010 Alicante, Spain
| | - Gema Esquiva
- Department of Optics, Pharmacology and Anatomy, University of Alicante, 03690 Alicante, Spain
| | - Violeta Gómez-Vicente
- Department of Optics, Pharmacology and Anatomy, University of Alicante, 03690 Alicante, Spain
| | - Luis M. Valor
- Unidad de Investigación, Hospital General Universitario Dr. Balmis, ISABIAL, 03010 Alicante, Spain
- Correspondence: ; Tel.: +34-965-913-988
| |
Collapse
|
16
|
He H, Zhang J, Gong W, Liu M, Liu H, Li X, Wu Y, Lu Q. Involvement of CircRNA Expression Profile in Diabetic Retinopathy and Its Potential Diagnostic Value. Front Genet 2022; 13:833573. [PMID: 35251136 PMCID: PMC8891611 DOI: 10.3389/fgene.2022.833573] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/27/2022] [Indexed: 12/14/2022] Open
Abstract
Background: Circular RNAs (circRNAs), a class of non-coding and undegradable RNAs, play many pathological functions by acting as miRNA sponges, interacting with RNA-binding proteins, and others. The recent literature indicates that circRNAs possess the advanced superiority for the early screening of diabetic retinopathy (DR). Methods: CircRNA sources of peripheral blood mononuclear cells (PBMCs) from healthy controls (n = 4), diabetes mellitus patients (DM) (n = 4), and DR patients (n = 4) were extracted for circular RNA microarray analysis. Enriched biological modules and signaling pathways were analyzed by Gene Ontology Enrichment and Kyoto Encyclopedia of Genes and Genomes analysis, respectively. Real-time quantitative reverse transcription PCR (RT-qPCR) was performed to validate differentiated levels of several circRNAs (fold change ≥2, p < .05) in different groups of healthy control subjects (n = 20), DM patients (n = 60), and DR patients (n = 42). Based on our clinical data from DR, the diagnostic performance of candidate circRNAs was measured by operating characteristic curves (ROCs). Subsequently, their circRNA–miRNA networks were constructed by bioinformatics analysis. Results: Circular RNA microarray analysis was performed, and 2,452 and 289 circRNAs were screened with differential expression in DR patients compared to healthy controls and DM patients, respectively. Enrichment analyses showed that circRNAs in DR patients were enriched in extracellular matrix (ECM)–receptor interaction and focal adhesion pathways. The top 5 differential circRNAs in circRNA microarray analysis were subsequently quantified and verified by RT-qPCR. Consistently, a significant 2.2-fold reduction of hsa_circ_0095008 and 1.7-fold increase in hsa_circ_0001883 were identified in DR patients compared to DM patients. Meanwhile, the area under curves of hsa_circ_0095008 and hsa_circ_0001883 were 0.6710 (95% CI, 0.5646–0.7775) (p = 0.003399) and 0.6071 (95% CI, 0.4953–0.7189) (p = 0.06644), respectively, indicating a good diagnostic value. Conclusion: Our study provided a new sight for the pathological mechanism of DR and revealed the potential value of hsa_circ_0095008 and hsa_circ_0001883 as diagnostic biomarkers for the early diagnosis of DR patients.
Collapse
Affiliation(s)
- Hengqian He
- Department of Ophthalmology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
| | - Juntao Zhang
- Department of Ophthalmology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
| | - Weikun Gong
- Department of Ophthalmology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
| | - Mengyun Liu
- Department of Ophthalmology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
| | - Hao Liu
- Department of Ophthalmology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
| | - Xiaoyong Li
- Center for Disease Control and Prevention of Yinzhou District, Ningbo, China
| | - Yufei Wu
- Department of Ophthalmology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
| | - Qinkang Lu
- Department of Ophthalmology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
- *Correspondence: Qinkang Lu,
| |
Collapse
|