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Mao S, Dong S, Hou B, Li Y, Sun B, Guo Y, Deng M, Liu D, Liu G. Transcriptome analysis reveals pituitary lncRNA, circRNA and mRNA affecting fertility in high- and low-yielding goats. Front Genet 2023; 14:1303031. [PMID: 38152654 PMCID: PMC10751935 DOI: 10.3389/fgene.2023.1303031] [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: 09/27/2023] [Accepted: 12/01/2023] [Indexed: 12/29/2023] Open
Abstract
The pituitary gland serves as the central endocrine regulator of growth, reproduction, and metabolism and plays a crucial role in the reproductive process of female animals. Transcriptome analysis was conducted using pituitary gland samples from Leizhou goats with varying levels of fecundity to investigate the effects of long noncoding RNA (lncRNA), circular RNA (circRNA), and mRNA regulation on pituitary hormone secretion and its association with goat fecundity. The analysis aimed to identify lncRNAs, circRNAs, and mRNAs that influence the fertility of Leizhou goats. GO and KEGG enrichment analyses were performed on differentially expressed lncRNAs, circRNAs, and mRNAs and revealed considerable enrichment in pathways, such as regulation of hormone secretion, germ cell development, and gonadotropin-releasing hormone secretion. The pituitary lncRNAs (ENSCHIT00000010293, ENSCHIT00000010304, ENSCHIT00000010306, ENSCHIT00000010290, ENSCHIT00000010298, ENSCHIT00000006769, ENSCHIT00000006767, ENSCHIT00000006921, and ENSCHIT00000001330) and circRNAs (chicirc_029285, chicirc_026618, chicirc_129655, chicirc_018248, chicirc_122554, chicirc_087101, and chicirc_078945) identified as differentially expressed regulated hormone secretion in the pituitary through their respective host genes. Additionally, differential mRNAs (GABBR2, SYCP1, HNF4A, CBLN1, and CDKN1A) influenced goat fecundity by affecting hormone secretion in the pituitary gland. These findings contribute to the understanding of the molecular mechanisms underlying pituitary regulation of fecundity in Leizhou goats.
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Affiliation(s)
| | | | | | | | | | | | | | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Guangbin Liu
- College of Animal Science, South China Agricultural University, Guangzhou, China
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Chen B, Tan L, Wang Y, Yang L, Liu J, Chen D, Huang S, Mao F, Lian J. LOC102549726/miR-760-3p network is involved in the progression of ISO-induced pathological cardiomyocyte hypertrophy via endoplasmic reticulum stress. J Mol Histol 2023; 54:675-687. [PMID: 37899367 PMCID: PMC10635935 DOI: 10.1007/s10735-023-10166-1] [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: 03/26/2023] [Accepted: 09/30/2023] [Indexed: 10/31/2023]
Abstract
Pathological cardiac hypertrophy (CH) is featured by myocyte enlargement and cardiac malfunction. Multiple signaling pathways have been implicated in diverse pathological and physiological processes in CH. However, the function of LOC102549726/miR-760-3p network in CH remains unclear. Here, we characterize the functional role of LOC102549726/miR-760-3p network in CH and delineate the underlying mechanism. The expression of LncRNA LOC102549726 and hypertrophic markers was significantly increased compared to the control, while the level of miR-760-3p was decreased. Next, we examined ER stress response in a hypertrophic cardiomyocyte model. The expression of ER stress markers was greatly enhanced after incubation with ISO. The hypertrophic reaction, ER stress response, and increased potassium and calcium ion channels were alleviated by genetic downregulation of LOC102549726. It has been demonstrated that LOC102549726 functions as a competitive endogenous RNA (ceRNA) of miR-760-3p. Overexpression of miR-760-3p decreased cell surface area and substantially mitigated ER stress response; protein levels of potassium and calcium channels were also significantly up-regulated compared to the NC control. In contrast, miR-760-3p inhibition increased cell size, aggravated CH and ER stress responses, and reduced ion channels. Collectively, in this study we demonstrated that the LOC102549726/miR-760-3p network was a crucial regulator of CH development. Ion channels mediate the ER stress response and may be a downstream sensor of the LOC102549726/miR-760-3p network. Therefore, these findings advance our understanding of pathological CH and provide new insights into therapeutic targets for cardiac remodeling.
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Affiliation(s)
- Bangsheng Chen
- Emergency Medical Center, Ningbo Yinzhou No. 2 Hospital, Ningbo, Zhejiang, 315192, China
| | - Lian Tan
- Intensive Care Unit, Ningbo Yinzhou No. 2 Hospital, Ningbo, Zhejiang, 315192, China
| | - Ying Wang
- Cadiovascular Department, Ningbo Medical Center LiHuiLi Hospital, Ningbo, Zhejiang, 315100, China
| | - Lei Yang
- Emergency Medical Center, Ningbo Yinzhou No. 2 Hospital, Ningbo, Zhejiang, 315192, China
| | - Jiequan Liu
- Emergency Medical Center, Ningbo Yinzhou No. 2 Hospital, Ningbo, Zhejiang, 315192, China
| | - Danqi Chen
- Intensive Care Unit, Ningbo Yinzhou No. 2 Hospital, Ningbo, Zhejiang, 315192, China
| | - Shuaishuai Huang
- Laboratory of Renal Carcinoma, Ningbo Yinzhou No. 2 Hospital, Ningbo, Zhejiang, 315192, China
| | - Feiyan Mao
- Department of General Surgery, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, 315100, China
| | - Jiangfang Lian
- Cadiovascular Department, Ningbo Medical Center LiHuiLi Hospital, Ningbo, Zhejiang, 315100, China.
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Wang S, Gu X, Ma J, Gu Z, Zhang R, Li R, Bai J, Li P, Wei L, Ye Y, Wang Y, Zhang L, Su L, Liang C. Selenium nanoparticles improve nickel-induced testosterone synthesis disturbance by down-regulating miR-708-5p/p38 MAPK pathway in Leydig cells. ENVIRONMENTAL TOXICOLOGY 2023. [PMID: 37126647 DOI: 10.1002/tox.23811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 03/29/2023] [Accepted: 04/16/2023] [Indexed: 05/03/2023]
Abstract
The present study was designed to investigate the role of miR-708-5p/p38 mitogen-activated protein kinase (MAPK) pathway during the mechanism of selenium nanoparticles (Nano-Se) against nickel (Ni)-induced testosterone synthesis disorder in rat Leydig cells. We conducted all procedures based on in vitro culture of rat primary Leydig cells. After treating Leydig cells with Nano-Se and NiSO4 alone or in combination for 24 h, we determined the cell viability, reactive oxygen species (ROS) levels, testosterone production, and the protein expression of key enzymes involved in testosterone biosynthesis: steroidogenic acute regulatory (StAR) and cytochrome P450 cholesterol side chain cleavage enzyme (CYP11A1). The results indicated that Nano-Se antagonized cytotoxicity and eliminated ROS generation induced by NiSO4 , suppressed p38 MAPK protein phosphorylation and reduced miR-708-5p expression. Importantly, we found that Nano-Se upregulated the expression of testosterone synthase and increased testosterone production in Leydig cells. Furthermore, we investigated the effects of p38 MAPK and miR-708-5p using their specific inhibitor during Nano-Se against Ni-induced testosterone synthesis disorder. The results showed that Ni-inhibited testosterone secretion was alleviated by Nano-Se co-treatment with p38 MAPK specific inhibitor SB203580 and miR-708-5p inhibitor, respectively. In conclusion, these findings suggested Nano-Se could inhibit miR-708-5p/p38 MAPK pathway, and up-regulate the key enzymes protein expression for testosterone synthesis, thereby antagonizing Ni-induced disorder of testosterone synthesis in Leydig cells.
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Affiliation(s)
- Shuang Wang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Xueyan Gu
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Jianhua Ma
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Zhangyu Gu
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, China
- Key Laboratory of Materials Physics and Anhui Key Laboratory of Nanomaterials and Nanotechnology, Institute of Solid State Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Rui Zhang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Ruifen Li
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Jun Bai
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Peng Li
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Linyu Wei
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Yixing Ye
- Key Laboratory of Materials Physics and Anhui Key Laboratory of Nanomaterials and Nanotechnology, Institute of Solid State Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Yan Wang
- Reproductive Medicine Center, Gansu Provincial Maternity and Child-care Hospital, Lanzhou, China
| | - Li Zhang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Li Su
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Changhao Liang
- Key Laboratory of Materials Physics and Anhui Key Laboratory of Nanomaterials and Nanotechnology, Institute of Solid State Physics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
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Tomczyk-Socha M, Kręcicka J, Misiuk-Hojło M, Turno-Kręcicka A. MicroRNA Expression in Pseudoexfoliation Syndrome with the Use of Next-Generation Sequencing. Genes (Basel) 2022; 13:genes13040582. [PMID: 35456388 PMCID: PMC9031982 DOI: 10.3390/genes13040582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/12/2022] [Accepted: 03/23/2022] [Indexed: 02/01/2023] Open
Abstract
Pseudoexfoliation syndrome (PEX) is a clinically important and biologically intriguing systemic disorder of the extracellular matrix. PEX etiopathogenesis was proved to be connected to multiple genes and other factors. However, the exact etiopathogenesis remains unknown. The aim of this study was to analyze miR expression in PEX using next-generation sequencing. An attempt was made to find the most commonly occurring miR in PEX, to evaluate miR that may have an essential role in the etiology of PEX syndrome. In addition, the correlation between the selected miRs’ expressions and age was investigated. Anterior lens capsules were obtained during cataract surgery. Next-generation sequencing was conducted on Illumina MiSeq. The average age was 68.2 years (with standard deviation +/− 6.92 years). Ten miRs with the highest level of expression represent approx. 95% of all readings. Four miRs with statistically significant differences in expression between groups have been distinguished: miR-671-3p, miR374a-5p, miR-1307-5p and miR-708-5p. The relationship between the most frequent miRs’ expressions and age has been evaluated and no correlation has been detected. In view of the above, it seems reasonable to examine the influence of miR on the biogenesis of PEX. Further studies on miR-671-3p, miR-374a-5p, miR-1307-5p and miR-708-5p expression in PEX are needed.
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Affiliation(s)
- Martyna Tomczyk-Socha
- Department of Ophthalmology, Wroclaw Medical University, Borowska 213, 50-556 Wrocław, Poland; (M.M.-H.); (A.T.-K.)
- Correspondence: ; Tel.: +48-71-736-43-00; Fax: +48-71-736-43-09
| | - Julia Kręcicka
- Department and Clinic of Ophthalmology, Wroclaw University Hospital, Borowska 213, 50-556 Wrocław, Poland;
| | - Marta Misiuk-Hojło
- Department of Ophthalmology, Wroclaw Medical University, Borowska 213, 50-556 Wrocław, Poland; (M.M.-H.); (A.T.-K.)
| | - Anna Turno-Kręcicka
- Department of Ophthalmology, Wroclaw Medical University, Borowska 213, 50-556 Wrocław, Poland; (M.M.-H.); (A.T.-K.)
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Zhao R, Song J, Jin Y, Liu Y. Long noncoding RNA HOXC-AS3 enhances the progression of cervical cancer via activating ErbB signaling pathway. J Mol Histol 2021; 52:991-1006. [PMID: 34387789 DOI: 10.1007/s10735-021-10007-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/06/2021] [Indexed: 11/25/2022]
Abstract
Emerging evidence reveals that long noncoding RNAs (lncRNAs) contribute to human tumorigenesis. Nevertheless, the function of HOXC cluster antisense RNA 3 (HOXC-AS3) in human cervical cancer (CC) remains largely unknown. The levels of HOXC-AS3, miR-105-5p and SOS1 in CC tissues and cells were monitored by reverse transcription-polymerase chain reaction (RT-PCR) and western blot (WB). Gain- and loss-of-function experiments were conducted to verify the function of HOXC-AS3 and miR-105-5p in CC cells. Meanwhile, cell proliferation, apoptosis, migration and invasion were examined by the cell counting kit-8 (CCK8) experiment, colony formation assay, flow cytometry and Transwell assay. Dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assay were carried out to test the regulatory interaction of HOXC-AS3, miR-105-5p and SOS1. In addition, in vivo experiment was performed to certain the role of HOXC-AS3 in tumorigenesis of CC. HOXC-AS3 was overexpressed in CC tissues (vs. adjacent normal tissues) and CC cells. Besides, the higher HOXC-AS3 profile was associated with the poorer clinical prognosis of CC patients. Overexpression of HOXC-AS3 promoted cell growth, migration and invasion, hampered apoptosis, whereas knocking down HOXC-AS3 exhibited the reverse effects. MiR-105-5p was a downstream target of HOXC-AS3, and it mediated the HOXC-AS3-induced oncogenic effects. Mechanistically, the bioinformatic analysis illustrated that SOS1 was targeted by miR-105-5p. Up-regulating SOS1 heightened the growth, migration and invasion of CC cells by enhancing the ErbB signaling pathway, which was reversed by miR-105-5p. Up-regulated HOXC-AS3 aggravates CC by promoting SOS1 expression via targeting miR-105-5p.
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Affiliation(s)
- Runsheng Zhao
- Department of Oncology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, No.136 Jingzhou Street, Xiangcheng, Xiangyang, 441000, Hubei, China
| | - Jing Song
- Department of Oncology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, No.136 Jingzhou Street, Xiangcheng, Xiangyang, 441000, Hubei, China
| | - Yiqiang Jin
- Department of Oncology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, No.136 Jingzhou Street, Xiangcheng, Xiangyang, 441000, Hubei, China.
| | - Yingying Liu
- Department of Oncology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, No.136 Jingzhou Street, Xiangcheng, Xiangyang, 441000, Hubei, China.
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Liu Y, Liu Y, Wang J, Huang F, Du P, Wu L, Guo F, Song Y, Qin G. LncRNA FENDRR promotes apoptosis of Leydig cells in late-onset hypogonadism by facilitating the degradation of Nrf2. Cell Tissue Res 2021; 386:379-389. [PMID: 34278519 DOI: 10.1007/s00441-021-03497-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/23/2021] [Indexed: 12/23/2022]
Abstract
This study aimed to investigate the role of lncRNA FENDRR in apoptosis of Leydig cells and the further mechanism. The apoptosis of Leydig cells (TM3 cell line) was induced by H2O2-treatment and detected by flow cytometry. The function of FENDRR was determined by in vitro and in vivo silencing experiments. The mechanism of FENDRR in regulating the expression of nuclear factor erythroid 2-related factor 2 (Nrf2) was assessed by RNA immunoprecipitation, RNA pull-down, and ubiquitination assays. FENDRR expression was up-regulated in H2O2-treated TM3 cells. Knockdown of FENDRR augmented Nrf2 and HO-1 protein levels and testosterone production in H2O2-treated TM3 cells, whereas the apoptosis rate and caspase 3 activity were decreased. Mechanically, FENDRR bound to Nrf2 and promoted its ubiquitination and degradation. Nrf2 overexpression reversed the effects FENDRR overexpression on apoptosis, caspase 3 activity, and testosterone concentration in H2O2-treated TM3 cells. The in vivo experiments showed that FENDRR silence increased serum testosterone level and improved testosterone-related anti-depression behaviors of late-onset hypogonadism (LOH) mice. Our findings suggested that FENDRR could promote apoptosis of Leydig cells in LOH partly through facilitating Nrf2 degradation.
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Affiliation(s)
- Yanling Liu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Yanxia Liu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jiao Wang
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Fengjiao Huang
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Peijie Du
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Lina Wu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Feng Guo
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Yi Song
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Guijun Qin
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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Counteracting effects of heavy metals and antioxidants on male fertility. Biometals 2021; 34:439-491. [PMID: 33761043 DOI: 10.1007/s10534-021-00297-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/04/2021] [Indexed: 01/06/2023]
Abstract
Infertility is regarded as a global health problem affecting 8-12% of couples. Male factors are regarded as the main cause of infertility in 40% of infertile couples and contribute to this condition in combination with female factors in another 20% of cases. Abnormal sperm parameters such as oligospermia, asthenospermia, and teratozoospermia result in male factor infertility. Several studies have shown the deteriorative impact of heavy metals on sperm parameters and fertility in human subjects or animal models. Other studies have pointed to the role of antioxidants in counteracting the detrimental effects of heavy metals. In the currents study, we summarize the main outcomes of studies that assessed the counteracting impacts of heavy metal and antioxidants on male fertility. Based on the provided data from animal studies, it seems rational to administrate appropriate antioxidants in persons who suffer from abnormal sperm parameters and infertility due to exposure to toxic elements. Yet, further human studies are needed to approve the beneficial effects of these antioxidants.
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CeNet Omnibus: an R/Shiny application to the construction and analysis of competing endogenous RNA network. BMC Bioinformatics 2021; 22:75. [PMID: 33602117 PMCID: PMC7890952 DOI: 10.1186/s12859-021-04012-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/08/2021] [Indexed: 01/01/2023] Open
Abstract
Background The competing endogenous RNA (ceRNA) regulation is a newly discovered post-transcriptional regulation mechanism and plays significant roles in physiological and pathological progress. CeRNA networks provide global views to help understand the regulation of ceRNAs. CeRNA networks have been widely used to detect survival biomarkers, select candidate regulators of disease genes, and predict long noncoding RNA functions. However, there is no software platform to provide overall functions from the construction to analysis of ceRNA networks. Results To fill this gap, we introduce CeNet Omnibus, an R/Shiny application, which provides a unified framework for the construction and analysis of ceRNA network. CeNet Omnibus enables users to select multiple measurements, such as Pearson correlation coefficient (PCC), mutual information (MI), and liquid association (LA), to identify ceRNA pairs and construct ceRNA networks. Furthermore, CeNet Omnibus provides a one-stop solution to analyze the topological properties of ceRNA networks, detect modules, and perform gene enrichment analysis and survival analysis. CeNet Omnibus intends to cover comprehensiveness, high efficiency, high expandability, and user customizability, and it also offers a web-based user-friendly interface to users to obtain the output intuitionally. Conclusion CeNet Omnibus is a comprehensive platform for the construction and analysis of ceRNA networks. It is highly customizable and outputs the results in intuitive and interactive. We expect that CeNet Omnibus will assist researchers to understand the property of ceRNA networks and associated biological phenomena. CeNet Omnibus is an R/Shiny application based on the Shiny framework developed by RStudio. The R package and detailed tutorial are available on our GitHub page with the URL https://github.com/GaoLabXDU/CeNetOmnibus.
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Lin Y, Lin M, Liu Y, Zhang J, Lai W, Xu Q, Zheng Y. Predicting miRNA-lncRNA-mRNA network in ultraviolet A-induced human skin photoaging. J Cosmet Dermatol 2020; 20:1875-1884. [PMID: 33025709 DOI: 10.1111/jocd.13760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/11/2020] [Accepted: 09/25/2020] [Indexed: 01/05/2023]
Abstract
BACKGROUND/OBJECTIVE Recent researches had reported that microRNAs (miRNAs) played a role in skin photoaging. Our previous study found that long noncoding RNA (lncRNA) expression was changed in the UVA-irradiated skin fibroblasts, but the regulating network of noncoding RNA in UV-induced skin changes has not been elucidated well. Here, we investigated the interactions of miRNA-lncRNA-mRNAs in skin photoaging mechanisms. METHODS Human dermal fibroblasts (HDFs) were irradiated with UVA at 10 J/cm2 once a day lasting for 14 days. miRNA expression profiles were detected by high-throughput sequencing. miRNAs changed significantly were identified by qRT-PCR. Functional annotation analysis and pathway enrichment were carried out using Gene Ontology and KEGG, and predicted miRNA-lncRNA-mRNA interactions were performed via bioinformatic analysis. RESULTS 34 differentially expressed miRNAs (>1.5-fold changes, P < .05) after UVA irradiation were identified to interact with distinct lncRNAs. miRNA-lncRNA-mRNA network prediction and regulatory role analysis showed that the gene expression of cellular process, cell part, and binding was mainly coordinated in UVA-irradiated fibroblasts. miRNA-lncRNA-mRNA-signal transduction pathway analysis showed that TNF signaling pathway, thyroid hormone signaling pathway, and lysosome were mainly affected after UVA irradiation. CONCLUSION miRNA-lncRNA-mRNA network played a critical part in skin photoaging. Our research provided novel insights into the repeated UVA-induced skin damage in noncoding RNA regulatory field and might help to further understand the delicate interplay of gene regulation at the noncoding RNA level in photoaged skin and UV-induced skin cancers in future researching and provide novel insights into the repeated UVA-damaging pathology and potential targets for preventing human skin photoaging.
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Affiliation(s)
- Yao Lin
- Department of Dermatology and Venereology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Mengbi Lin
- Department of Dermatology and Venereology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yufang Liu
- Department of Dermatology and Venereology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jie Zhang
- Department of Dermatology and Venereology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wei Lai
- Department of Dermatology and Venereology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qingfang Xu
- Department of Dermatology and Venereology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yue Zheng
- Department of Dermatology and Venereology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Yan L, Yue C, Xu Y, Jiang X, Zhang L, Wu J. Identification of Potential Diagnostic and Prognostic Pseudogenes in Hepatocellular Carcinoma Based on Pseudogene-miRNA-mRNA Competitive Network. Med Sci Monit 2020; 26:e921895. [PMID: 32457285 PMCID: PMC7249743 DOI: 10.12659/msm.921895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background It is widely known that hepatocellular carcinoma (HCC) has high rates of morbidity and mortality. A large number of studies have indicated that pseudogenes have an important effect on the carcinogenesis of HCC. Pseudogenes can play a role through the ceRNA network. There have been numerous studies on lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA networks. However, the pseudogene-miRNA-mRNA network in HCC has rarely been researched or reported on. Material/Methods The Cancer Genome Atlas (TCGA) database was researched and differences between selected genes were studied. A pseudogene-miRNA-mRNA network was then constructed and clustering of pseudogenes was studied. The diagnostic value of the selected pseudogenes, their functions, and pathways were investigated using available databases to understand their possible pathogenic mechanism in HCC. The protein-protein interaction network of target genes was found and the top 10 hub genes were identified. Expression of hub genes in HCC tissues was then detected by RT-qPCR. Results By analyzing the gene difference and clinical data of HCC, we constructed a ceRNA network composed of 4 pseudogenes, 8 miRNAs, and 30 mRNAs. The pseudogenes AP000769.1, KRT16P1, KRT16P3, and RPLP0P2 were all correlated with the diagnosis and prognosis of HCC. Functional analyses through the Kyoto Encyclopedia of Genes and Genomes and the Gene Ontology databases indicated that pseudogenes can affect the physiological process of HCC through the p53 pathway. The top 10 hub genes identified were all highly expressed in HCC tissues and affected the patient survival rate. Conclusions In this study, 4 pseudogenes related to the diagnosis and prognosis of liver cancer were found through the construction of a ceRNA network. These 4 pseudogenes might constitute new therapeutic targets for liver cancer patients.
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Affiliation(s)
- Lijun Yan
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
| | - Chaosen Yue
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
| | - Yingchen Xu
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
| | - Xincen Jiang
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
| | - Lijun Zhang
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
| | - Jixiang Wu
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
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