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Yang LX, Li H, Cheng ZH, Sun HY, Huang JP, Li ZP, Li XX, Hu ZG, Wang J. The Application of Non-Coding RNAs as Biomarkers, Therapies, and Novel Vaccines in Diseases. Int J Mol Sci 2025; 26:3055. [PMID: 40243658 PMCID: PMC11988403 DOI: 10.3390/ijms26073055] [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: 01/31/2025] [Revised: 03/22/2025] [Accepted: 03/24/2025] [Indexed: 04/18/2025] Open
Abstract
Non-coding RNAs (ncRNAs) are a class of RNAs that largely lack the capacity to encode proteins. They have garnered significant attention due to their central regulatory functions across numerous cellular and physiological processes at transcriptional, post-transcriptional, and translational levels. Over the past decade, ncRNA-based therapies have gained considerable attention in the diagnosis, treatment, and prevention of diseases, and many studies have revealed a significant relationship between ncRNAs and diseases. At the same time, due to their tissue specificity, an increasing number of projects have focused on the application of ncRNAs as biomarkers in diseases, as well as the design and development of novel ncRNA-based vaccines and therapies for clinical use. These ncRNAs may also drive research into the potential molecular mechanisms and complex pathogenesis of related diseases. However, new biomarkers need to be validated for their clinical effectiveness. Additionally, to produce safe and stable RNA products, factors such as purity, precise dosage, and effective delivery methods must be ensured to achieve optimal bioactivity. These challenges remain key issues in the clinical application of ncRNAs. This review summarizes the prospects of ncRNAs as potential biomarkers, as well as the current research status and clinical applications of ncRNAs in therapies and vaccines, and discusses the challenges and expectations of ncRNAs in disease diagnosis and drug therapy.
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Affiliation(s)
- Lu-Xuan Yang
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (L.-X.Y.); (H.L.); (Z.-H.C.); (H.-Y.S.); (J.-P.H.); (Z.-P.L.)
| | - Hui Li
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (L.-X.Y.); (H.L.); (Z.-H.C.); (H.-Y.S.); (J.-P.H.); (Z.-P.L.)
| | - Zhi-Hui Cheng
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (L.-X.Y.); (H.L.); (Z.-H.C.); (H.-Y.S.); (J.-P.H.); (Z.-P.L.)
| | - He-Yue Sun
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (L.-X.Y.); (H.L.); (Z.-H.C.); (H.-Y.S.); (J.-P.H.); (Z.-P.L.)
| | - Jie-Ping Huang
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (L.-X.Y.); (H.L.); (Z.-H.C.); (H.-Y.S.); (J.-P.H.); (Z.-P.L.)
| | - Zhi-Peng Li
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (L.-X.Y.); (H.L.); (Z.-H.C.); (H.-Y.S.); (J.-P.H.); (Z.-P.L.)
| | - Xin-Xin Li
- Institute of Scientific Research, Guangxi University, Nanning 530004, China;
| | - Zhi-Gang Hu
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jian Wang
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (L.-X.Y.); (H.L.); (Z.-H.C.); (H.-Y.S.); (J.-P.H.); (Z.-P.L.)
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Shang Y, Zhang Q, Ding Y, Wang Y, Gu S, Zang X, Xu Z, Huang S, Li Z, Wu Z, Gu T, Hong L, Cai G. The Expression Pattern and Functional Analysis of Extracellular Vesicle Long Non-Coding RNAs from Uterine Fluid During Implantation in Pig. Animals (Basel) 2025; 15:245. [PMID: 39858245 PMCID: PMC11758334 DOI: 10.3390/ani15020245] [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: 12/08/2024] [Revised: 01/05/2025] [Accepted: 01/13/2025] [Indexed: 01/27/2025] Open
Abstract
Long non-coding RNAs (lncRNAs) act as competing endogenous RNAs and play significant roles in porcine embryo development. Extracellular vesicles (EVs) in the uterine fluid (UF) can target and deliver maternal endometrial signalling molecules to embryonic trophoblast cells, exerting crucial regulatory effects during embryo implantation. However, the specific roles of lncRNAs carried by UF-EVs during the embryo implantation period have not been thoroughly reported in the literature. In the present study, high-throughput sequencing and biological tools were applied to analyse lncRNAs in UF-EVs on days 9, 12, and 15 of pregnancy to identify key regulatory lncRNAs in UF-EVs during the porcine embryonic implantation period and to explore their expression patterns and functional roles. A total of 30,203 lncRNAs were identified and 7879 differentially expressed lncRNAs were screened, and qRT-PCR was used to verify the sequencing data. Days 9-12 of pregnancy represent a critical stage of embryo implantation characterised by substantial morphological changes in porcine embryos. During this period, we identified a total of 4348 differentially expressed lncRNAs. Through screening and validation, we discovered that LNC_026212 was highly expressed on day 12 of pregnancy and can promote the proliferation and migration of porcine trophoblast cells (PTr cells). These novel findings contribute to our understanding of the impact of lncRNAs on porcine reproductive processes, offering new research directions to improve the success rate of embryo implantation in pigs.
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Affiliation(s)
- Yijun Shang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Qiuping Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Yue Ding
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Yongzhong Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Shengchen Gu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Xupeng Zang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zheng Xu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Sixiu Huang
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zicong Li
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zhenfang Wu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527300, China
- National Regional Gene Bank of Livestock and Poultry (Gene Bank of Guangdong Livestock and Poultry), Guangzhou 510642, China
| | - Ting Gu
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- National Regional Gene Bank of Livestock and Poultry (Gene Bank of Guangdong Livestock and Poultry), Guangzhou 510642, China
| | - Linjun Hong
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- National Regional Gene Bank of Livestock and Poultry (Gene Bank of Guangdong Livestock and Poultry), Guangzhou 510642, China
| | - Gengyuan Cai
- State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527300, China
- National Regional Gene Bank of Livestock and Poultry (Gene Bank of Guangdong Livestock and Poultry), Guangzhou 510642, China
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Elskens J, Madder A. Crosslinker-modified nucleic acid probes for improved target identification and biomarker detection. RSC Chem Biol 2021; 2:410-422. [PMID: 34458792 PMCID: PMC8341421 DOI: 10.1039/d0cb00236d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/11/2021] [Indexed: 01/02/2023] Open
Abstract
Understanding the intricate interaction pattern of nucleic acids with other molecules is essential to gain further insight in biological processes and disease mechanisms. To this end, a multitude of hybridization-based assays have been designed that rely on the non-covalent recognition between complementary nucleic acid sequences. However, the ephemeral nature of these interactions complicates straightforward analysis as low efficiency and specificity are rule rather than exception. By covalently locking nucleic acid interactions by means of a crosslinking agent, the overall efficiency, specificity and selectivity of hybridization-based assays could be increased. In this mini-review we highlight methodologies that exploit the use of crosslinker-modified nucleic acid probes for interstrand nucleic acid crosslinking with the objective to study, detect and identify important targets as well as nucleic acid sequences that can be considered relevant biomarkers. We emphasize on the usefulness and advantages of crosslinking agents and elaborate on the chemistry behind the crosslinking reactions they induce.
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Affiliation(s)
- Joke Elskens
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 Building S4 9000 Ghent Belgium +32-9-264-49-98 +32-9-264-44-72
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University Krijgslaan 281 Building S4 9000 Ghent Belgium +32-9-264-49-98 +32-9-264-44-72
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Sztuba-Solinska J, Rausch JW, Smith R, Miller JT, Whitby D, Le Grice SFJ. Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA: a structural scaffold for nuclear, cytoplasmic and viral proteins. Nucleic Acids Res 2017; 45:6805-6821. [PMID: 28383682 PMCID: PMC5499733 DOI: 10.1093/nar/gkx241] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/30/2017] [Indexed: 01/04/2023] Open
Abstract
Kaposi's sarcoma-associated herpes virus (KSHV) polyadenylated nuclear (PAN) RNA facilitates lytic infection, modulating the cellular immune response by interacting with viral and cellular proteins and DNA. Although a number nucleoprotein interactions involving PAN have been implicated, our understanding of binding partners and PAN RNA binding motifs remains incomplete. Herein, we used SHAPE-mutational profiling (SHAPE-MaP) to probe PAN in its nuclear, cytoplasmic or viral environments or following cell/virion lysis and removal of proteins. We thus characterized and put into context discrete RNA structural elements, including the cis-acting Mta responsive element and expression and nuclear retention element (1,2). By comparing mutational profiles in different biological contexts, we identified sites on PAN either protected from chemical modification by protein binding or characterized by a loss of structure. While some protein binding sites were selectively localized, others were occupied in all three biological contexts. Individual binding sites of select KSHV gene products on PAN RNA were also identified in in vitro experiments. This work constitutes the most extensive structural characterization of a viral lncRNA and interactions with its protein partners in discrete biological contexts, providing a broad framework for understanding the roles of PAN RNA in KSHV infection.
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Affiliation(s)
- Joanna Sztuba-Solinska
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Jason W Rausch
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Rodman Smith
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jennifer T Miller
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Denise Whitby
- Viral Oncology Section, AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Stuart F J Le Grice
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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Niu ZS, Niu XJ, Wang WH. Long non-coding RNAs in hepatocellular carcinoma: Potential roles and clinical implications. World J Gastroenterol 2017; 23:5860-5874. [PMID: 28932078 PMCID: PMC5583571 DOI: 10.3748/wjg.v23.i32.5860] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 05/10/2017] [Accepted: 07/22/2017] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are a subgroup of non-coding RNA transcripts greater than 200 nucleotides in length with little or no protein-coding potential. Emerging evidence indicates that lncRNAs may play important regulatory roles in the pathogenesis and progression of human cancers, including hepatocellular carcinoma (HCC). Certain lncRNAs may be used as diagnostic or prognostic markers for HCC, a serious malignancy with increasing morbidity and high mortality rates worldwide. Therefore, elucidating the functional roles of lncRNAs in tumors can contribute to a better understanding of the molecular mechanisms of HCC and may help in developing novel therapeutic targets. In this review, we summarize the recent progress regarding the functional roles of lncRNAs in HCC and explore their clinical implications as diagnostic or prognostic biomarkers and molecular therapeutic targets for HCC.
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MESH Headings
- Antineoplastic Agents/therapeutic use
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/antagonists & inhibitors
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinogenesis/genetics
- Carcinoma, Hepatocellular/diagnosis
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/mortality
- Disease Progression
- Early Detection of Cancer/methods
- Epigenesis, Genetic
- Gene Expression Regulation, Neoplastic
- Humans
- Liver Neoplasms/diagnosis
- Liver Neoplasms/drug therapy
- Liver Neoplasms/genetics
- Liver Neoplasms/mortality
- Molecular Targeted Therapy/methods
- Prognosis
- RNA, Long Noncoding/analysis
- RNA, Long Noncoding/antagonists & inhibitors
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
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Affiliation(s)
- Zhao-Shan Niu
- Laboratory of Micromorphology, School of Basic Medicine, Medical Department of Qingdao University, Qingdao 266071, Shandong Province, China
| | - Xiao-Jun Niu
- Oncology Specialty, Medical Department of Qingdao University, Qingdao 266071, Shandong Province, China
| | - Wen-Hong Wang
- Department of Pathology, School of Basic Medicine, Medical Department of Qingdao University, Qingdao 266071, Shandong Province, China
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Qin N, Tong GF, Sun LW, Xu XL. Long Noncoding RNA MEG3 Suppresses Glioma Cell Proliferation, Migration, and Invasion by Acting as a Competing Endogenous RNA of miR-19a. Oncol Res 2017; 25:1471-1478. [PMID: 28276316 PMCID: PMC7841124 DOI: 10.3727/096504017x14886689179993] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Glioma, with varying malignancy grades and histological subtypes, is the most common primary brain tumor in adults. Long noncoding RNAs (lncRNAs) are non-protein-coding transcripts and have been proven to play an important role in tumorigenesis. Our study aims to elucidate the combined effect of lncRNA maternally expressed gene 3 (MEG3) and microRNA-19a (miR-19a) in human glioma U87 and U251 cell lines. Real-time PCR revealed that MEG3 was downregulated and miR-19a was upregulated in malignant glioma tissues and cell lines. Bioinformatics analyses (TargetScan, miRanda, and starBase V2.0) showed that phosphatase and tensin homolog (PTEN) is a target of miR-19a with complementary binding sites in the 3'-UTR. As expected, luciferase results verified the putative target site and also revealed the complementary binding between miR-19a and MEG3. miR-19a represses the expression of PTEN and promotes glioma cell proliferation, migration, and invasion. However, MEG3 could directly bind to miR-19a and effectively act as a competing endogenous RNA (ceRNA) for miR-19a to suppress tumorigenesis. Our study is the first to demonstrate that lncRNA MEG3 suppresses glioma cell proliferation, migration, and invasion by acting as a ceRNA of miR-19a, which provides a novel insight about the pathogenesis of glioma.
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