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Saeinasab M, Iranpour S, Hosseini-Giv N, Saljooghi AS, Matin MM. Tumor-targeted delivery of SNHG15 siRNA using a ZIF-8 nanoplatform: Towards a more effective prostate cancer therapy. Int J Biol Macromol 2024; 259:129233. [PMID: 38184035 DOI: 10.1016/j.ijbiomac.2024.129233] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/08/2024]
Abstract
Small interfering RNAs (siRNAs) can be used as a powerful tool in gene therapy to downregulate the expression of specific disease related genes. Some properties however, such as instability, and low penetration into cells can limit their efficacy, and thus reduce their therapeutic potential. Metal-organic frameworks (MOFs) such as zeolitic imidazolate framework-8 (ZIF-8), which consist of organic bridging ligands and metal cations (Zn), have a very high binding affinity with nucleic acids including siRNAs. In this study, we designed a PEGylated ZIF-8 platform that was equipped with epithelial cell adhesion molecule (EpCAM) aptamer for the targeted delivery of siRNA molecules, in order to knockdown SNHG15 in both a prostate cancer (PC) cell line, and a human PC xenograft mouse model. SNHG15 is a long noncoding RNA, with oncogenic roles in different cancers including PC. The results indicated that the depletion of SNHG15 by Apt-PEG-siRNA@ZIF-8 nanoplatfrom inhibited cell proliferation and colony formation, and increased apoptosis in PC cells. This nanoparticle facilitated the release of siRNAs into the tumor environment in vivo, and subsequently reduced the tumor growth, with no side effects observed in vital organs. We have therefore developed a novel siRNA nano-delivery system for targeted prostate cancer treatment; however further studies are required before it can be tested in clinical trials.
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Affiliation(s)
- Morvarid Saeinasab
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sonia Iranpour
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Niloufar Hosseini-Giv
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Amir Sh Saljooghi
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran; Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Maryam M Matin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran; Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.
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Lu Z, Zhong H, Tang L, Luo J, Zhou W, Liu L. Predicting lncRNA-disease associations based on heterogeneous graph convolutional generative adversarial network. PLoS Comput Biol 2023; 19:e1011634. [PMID: 38019786 PMCID: PMC10686445 DOI: 10.1371/journal.pcbi.1011634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
There is a growing body of evidence indicating the crucial roles that long non-coding RNAs (lncRNAs) play in the development and progression of various diseases, including cancers, cardiovascular diseases, and neurological disorders. However, accurately predicting potential lncRNA-disease associations remains a challenge, as existing methods have limitations in extracting heterogeneous association information and handling sparse and unbalanced data. To address these issues, we propose a novel computational method, called HGC-GAN, which combines heterogeneous graph convolutional neural networks (GCN) and generative adversarial networks (GAN) to predict potential lncRNA-disease associations. Specifically, we construct a lncRNA-miRNA-disease heterogeneous network by integrating multiple association data and sequence information. The GCN-based generator is then employed to aggregate neighbor information of nodes and obtain node embeddings, which are used to predict lncRNA-disease associations. Meanwhile, the GAN-based discriminator is trained to distinguish between real and fake lncRNA-disease associations generated by the generator, enabling the generator to improve its ability to generate accurate lncRNA-disease associations gradually. Our experimental results demonstrate that HGC-GAN performs better in predicting potential lncRNA-disease associations, with AUC and AUPR values of 0.9591 and 0.9606, respectively, under 10-fold cross-validation. Moreover, our case study further confirms the effectiveness of HGC-GAN in predicting potential lncRNA-disease associations, even for novel lncRNAs without any known lncRNA-disease associations. Overall, our proposed method HGC-GAN provides a promising approach to predict potential lncRNA-disease associations and may have important implications for disease diagnosis, treatment, and drug development.
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Affiliation(s)
- Zhonghao Lu
- School of Information, Yunnan Normal University, Yunnan, People’s Republic of China
| | - Hua Zhong
- School of Information, Yunnan Normal University, Yunnan, People’s Republic of China
| | - Lin Tang
- Key Laboratory of Educational Information for Nationalities Ministry of Education, Yunnan Normal University, Yunnan, People’s Republic of China
| | - Jing Luo
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, School of Life Sciences and School of Ecology and Environment, Yunnan University, Kunming, People’s Republic of China
| | - Wei Zhou
- School of Software, Yunnan University, Kunming, People’s Republic of China
| | - Lin Liu
- School of Information, Yunnan Normal University, Yunnan, People’s Republic of China
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Xiao H, Feng X, Liu M, Gong H, Zhou X. SnoRNA and lncSNHG: Advances of nucleolar small RNA host gene transcripts in anti-tumor immunity. Front Immunol 2023; 14:1143980. [PMID: 37006268 PMCID: PMC10050728 DOI: 10.3389/fimmu.2023.1143980] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/03/2023] [Indexed: 03/17/2023] Open
Abstract
The small nucleolar RNA host genes (SNHGs) are a group of genes that can be transcript into long non-coding RNA SNHG (lncSNHG) and further processed into small nucleolar RNAs (snoRNAs). Although lncSNHGs and snoRNAs are well established to play pivotal roles in tumorigenesis, how lncSNHGs and snoRNAs regulate the immune cell behavior and function to mediate anti-tumor immunity remains further illustrated. Certain immune cell types carry out distinct roles to participate in each step of tumorigenesis. It is particularly important to understand how lncSNHGs and snoRNAs regulate the immune cell function to manipulate anti-tumor immunity. Here, we discuss the expression, mechanism of action, and potential clinical relevance of lncSNHGs and snoRNAs in regulating different types of immune cells that are closely related to anti-tumor immunity. By uncovering the changes and roles of lncSNHGs and snoRNAs in different immune cells, we aim to provide a better understanding of how the transcripts of SNHGs participate in tumorigenesis from an immune perspective.
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Affiliation(s)
- Hao Xiao
- Department of Clinical Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Clinical Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Xin Feng
- Department of Clinical Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Clinical Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Mengjun Liu
- Department of Clinical Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Clinical Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Hanwen Gong
- Department of Clinical Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Clinical Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Xiao Zhou
- Department of Clinical Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Clinical Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- *Correspondence: Xiao Zhou,
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