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Han R, Rao X, Zhou H, Lu L. Synergistic Immunoregulation: harnessing CircRNAs and PiRNAs to Amplify PD-1/PD-L1 Inhibition Therapy. Int J Nanomedicine 2024; 19:4803-4834. [PMID: 38828205 PMCID: PMC11144010 DOI: 10.2147/ijn.s461289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/12/2024] [Indexed: 06/05/2024] Open
Abstract
The utilization of PD-1/PD-L1 inhibitors marks a significant advancement in cancer therapy. However, the efficacy of monotherapy is still disappointing in a substantial subset of patients, necessitating the exploration of combinational strategies. Emerging from the promising results of the KEYNOTE-942 trial, RNA-based therapies, particularly circRNAs and piRNAs, have distinguished themselves as innovative sensitizers to immune checkpoint inhibitors (ICIs). These non-coding RNAs, notable for their stability and specificity, were once underrecognized but are now known for their crucial roles in regulating PD-L1 expression and bolstering anti-cancer immunity. Our manuscript offers a comprehensive analysis of selected circRNAs and piRNAs, elucidating their immunomodulatory effects and mechanisms, thus underscoring their potential as ICIs enhancers. In conjunction with the recent Nobel Prize-awarded advancements in mRNA vaccine technology, our review highlights the transformative implications of these findings for cancer treatment. We also discuss the prospects of circRNAs and piRNAs in future therapeutic applications and research. This study pioneers the synergistic application of circRNAs and piRNAs as novel sensitizers to augment PD-1/PD-L1 inhibition therapy, demonstrating their unique roles in regulating PD-L1 expression and modulating immune responses. Our findings offer a groundbreaking approach for enhancing the efficacy of cancer immunotherapy, opening new avenues for treatment strategies. This abstract aims to encapsulate the essence of our research and the burgeoning role of these non-coding RNAs in enhancing PD-1/PD-L1 inhibition therapy, encouraging further investigation into this promising field.
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Affiliation(s)
- Rui Han
- Department of Chinese Medicine Oncology, The First Affiliated Hospital of Naval Medical University, Shanghai, People’s Republic of China
- Department of Chinese Medicine, Naval Medical University, Shanghai, People’s Republic of China
| | - Xiwu Rao
- Department of Oncology, The First Hospital Affiliated to Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, People’s Republic of China
| | - Huiling Zhou
- Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, People’s Republic of China
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, Yale University, New Haven, CT, USA
- School of Medicine, Center for Biomedical Data Science, Yale University, New Haven, CT, USA
- Yale Cancer Center, Yale University, New Haven, CT, USA
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Ning XH, Han B, Peng Y, Yin SW. LncRNA pol-lnc78 as a ceRNA regulates antibacterial responses via suppression of pol-miR-n199-3p-mediated SARM down-regulation in Paralichthys olivaceus. Zool Res 2024; 45:25-35. [PMID: 38114430 PMCID: PMC10839655 DOI: 10.24272/j.issn.2095-8137.2022.520] [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: 04/27/2023] [Accepted: 09/07/2023] [Indexed: 12/21/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) function as key modulators in mammalian immunity, particularly due to their involvement in lncRNA-mediated competitive endogenous RNA (ceRNA) crosstalk. Despite their recognized significance in mammals, research on lncRNAs in lower vertebrates remains limited. In the present study, we characterized the first immune-related lncRNA (pol-lnc78) in the teleost Japanese flounder ( Paralichthys olivaceus). Results indicated that pol-lnc78 acted as a ceRNA for pol-miR-n199-3p to target the sterile alpha and armadillo motif-containing protein (SARM), the fifth discovered member of the Toll/interleukin 1 (IL-1) receptor (TIR) adaptor family. This ceRNA network regulated the antibacterial responses of flounder via the Toll-like receptor (TLR) signaling pathway. Specifically, SARM acted as a negative regulator and exacerbated bacterial infection by inhibiting the expression of inflammatory cytokines IL-1β and tumor necrosis factor-α (TNF-α). Pol-miR-n199-3p reduced SARM expression by specifically interacting with the 3' untranslated region (UTR), thereby promoting SARM-dependent inflammatory cytokine expression and protecting the host against bacterial dissemination. Furthermore, pol-lnc78 sponged pol-miR-n199-3p to ameliorate the inhibition of SARM expression. During infection, the negative regulators pol-lnc78 and SARM were significantly down-regulated, while pol-miR-n199-3p was significantly up-regulated, thus favoring host antibacterial defense. These findings provide novel insights into the mechanisms underlying fish immunity and open new horizons to better understand ceRNA crosstalk in lower vertebrates.
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Affiliation(s)
- Xian-Hui Ning
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
- CAS Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Bing Han
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Ye Peng
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Shao-Wu Yin
- College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu 210023, China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China. E-mail:
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Gao C, Cai X, Lymbery AJ, Ma L, Li C. The evolution of NLRC3 subfamily genes in Sebastidae teleost fishes. BMC Genomics 2023; 24:683. [PMID: 37964222 PMCID: PMC10648357 DOI: 10.1186/s12864-023-09785-5] [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: 04/16/2023] [Accepted: 11/05/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND With more than 36,000 valid fish species, teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. NLRC3 subfamily genes, which are specific to fishes, play vital roles in the immune system of teleosts. The evolution of teleosts has been impacted by several whole-genome duplication (WGD) events, which might be a key reason for the expansions of the NLRC3 subfamily, but detailed knowledge of NLRC3 subfamily evolution in the family Sebastidae is still limited. RESULTS Phylogenetic inference of NLRC3 subfamily protein sequences were conducted to evaluate the orthology of NLRC3 subfamily genes in black rockfish (Sebastes schlegilii), 13 other fish species from the families Sebastidae, Serranidae, Gasterosteidae and Cyclopteridae, and three species of high vertebrates (bird, reptile and amphibian). WGD analyses were used to estimate expansions and contractions of the NLRC3 subfamily, and patterns of expression of NLRC3 subfamily genes in black rockfish following bacterial infections were used to investigate the functional roles of these genes in the traditional and mucosal immune system of the Sebastidae. Different patterns of gene expansions and contractions were observed in 17 fish and other species examined, and one and two whole-genome duplication events were observed in two members of family Sebastidae (black rockfish and honeycomb rockfish, Sebastes umbrosus), respectively. Subsequently, 179 copy numbers of NLRC3 genes were found in black rockfish and 166 in honeycomb rockfish. Phylogenetic analyses corroborated the conservation and evolution of NLRC3 orthologues between Sebastidae and other fish species. Finally, differential expression analyses provided evidence of the immune roles of NLRC3 genes in black rockfish during bacterial infections and gene ontology analysis also indicated other functional roles. CONCLUSIONS We hypothesize that NLRC3 genes have evolved a variety of different functions, in addition to their role in the immune response, as a result of whole genome duplication events during teleost diversification. Importantly, this study had underscored the importance of sampling across taxonomic groups, to better understand the evolutionary patterns of the innate immunity system on which complex immunological novelties arose. Moreover, the results in this study could extend current knowledge of the plasticity of the immune system.
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Affiliation(s)
- Chengbin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, 266109, Qingdao, China
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, 6150, Murdoch, WA, Australia
| | - Xin Cai
- School of Marine Science and Engineering, Qingdao Agricultural University, 266109, Qingdao, China
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, 6150, Murdoch, WA, Australia
| | - Alan J Lymbery
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, 6150, Murdoch, WA, Australia
| | - Le Ma
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, 6150, Murdoch, WA, Australia
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, 266109, Qingdao, China.
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Li Y, Yang P, Chen F, Tang J, He Z, Yang Z, Weng L, Guo J, Zeng L, Yin H. Ccrl2-centred immune-related lncRNA-mRNA co-expression network revealed the local skin immune activation mechanism of moxibustion on adjuvant arthritis mice. Life Sci 2023; 329:121910. [PMID: 37406766 DOI: 10.1016/j.lfs.2023.121910] [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: 01/29/2023] [Revised: 06/26/2023] [Accepted: 07/02/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND Moxibustion is an important external therapy of traditional medicine that operates on some acupoints on the skin and is usually used for immune-related diseases. However, whether the immune function of the skin, especially the immune-related lncRNAs, contributes to the mechanism of moxibustion remains unclear. METHODS Adjuvant arthritis (AA) was induced by injection of Complete Freund's adjuvant (CFA) into the right hind paw of mice. Moxibustion was administered on the Zusanli (ST36) acupoint for 3 weeks. The alteration of foot volume and cytokine concentration in serum was used to evaluate the anti-inflammation effect of moxibustion. CD83 expression in the local skin of ST36 was measured by immunofluorescence staining. Transcriptome RNA sequencing (RNA-seq) and lncRNA-mRNA network analysis were performed to construct a moxibustion-induced Immune-related lncRNA-mRNA co-expression network. qRT-PCR was used to validate the RNA-seq data. RESULTS Moxibustion at ST36 relieved the foot swelling, decreased the TNF-α and IL-1β concentrations in serum, and obviously increased the CD83 expression at the local skin of ST36. A total of 548 differentially expressed lncRNAs and 520 linked mRNAs were screened out. The significantly and predominately enriched Go term was inflammatory and immune response, and the main pathways related to inflammatory and immune responses include Toll-like receptor, cytokine-cytokine receptor, and MAPK signaling. The immune-related lncRNA-mRNA co-expression network showed 88 lncRNAs and 36 mRNAs, and Ccrl2 is the central hub of this network. CONCLUSION Local immune activation is significantly triggered by moxibustion in ST36 of AA mice. The Ccrl2-centered immune-related lncRNA-mRNA co-expression network would be a promising target for decoding the mechanism of moxibustion for immune-related diseases.
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Affiliation(s)
- Yifan Li
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China.
| | - Peng Yang
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Fenglin Chen
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Jinfan Tang
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China.
| | - Zhaoxuan He
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China.
| | - Zhonghao Yang
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China.
| | - Li Weng
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China.
| | - Jing Guo
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China.
| | - Li Zeng
- Department of Rehabilitation, Medical Center Hospital of Qionglai City, Chengdu 611530, China
| | - Haiyan Yin
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China; Acupuncture and Chronobiology Key Laboratory of Sichuan Province, Chengdu 610075, China.
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Integration Analysis of circRNA–miRNA–mRNA and Identification of Critical Networks in Valgus-Varus Deformity (Gallus gallus). Genes (Basel) 2023; 14:genes14030622. [PMID: 36980895 PMCID: PMC10048443 DOI: 10.3390/genes14030622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/17/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
Valgus-valgus deformity (VVD) is a common leg deformity in broilers with inward or outward deviation of the tibiotarsus and tarsometatarsus. The competing endogenous RNA (ceRNA) network plays an essential role in the study of leg disease. However, its role in the etiology and pathogenesis of VVD remains unclear. Here, based on case (VVD) and control (normal) group design, we performed analyses of differentially expressed circRNAs (DEcircRNAs), differentially expressed miRNAs (DEmiRNAs) and differentially expressed mRNAs (DEmRNAs). Transcriptome data derived 86 DEcircRNAs, 13 DEmiRNAs and 410 DEmRNAs. Functional analysis showed that DEmRNAs were significantly enriched in cell cycle, apoptosis, ECM-receptor interaction, FoxO signaling pathway and protein processing synthesis. DEcirc/miRNA-associated DEmRNAs were associated with skeletal and muscle growth and development pathways, including mTOR, Wnt, and VEGF signaling pathways. Subsequently, a circRNA–miRNA–mRNA regulatory network was constructed based on the ceRNA hypothesis, including 8 circRNAs, 6 miRNAs, and 31 mRNAs, which were significantly enriched in the skeletal developmental pathway. Finally, two key mRNAs (CDC20 and CTNNB1) and their regulatory axes were screened by the PPI network and cytohubba. The expression levels of CDC20 and CTNNB1 in cartilage and seven other tissues were also quantified by qPCR. In conclusion, we analyzed the functions of DEmRNA, DEcircRNA and DEmiRNA and constructed the hub ceRNA regulatory axis, and obtained two hub genes, CDC20 and CTNNB1. The study more deeply explored the etiology and pathogenesis of VVD and lays the foundation for further study of the role of the ceRNA network on skeletal development.
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Zhou Z, Leng C, Wang Z, Long L, Lv Y, Gao Z, Wang Y, Wang S, Li P. The potential regulatory role of the lncRNA-miRNA-mRNA axis in teleost fish. Front Immunol 2023; 14:1065357. [PMID: 36895573 PMCID: PMC9988957 DOI: 10.3389/fimmu.2023.1065357] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/06/2023] [Indexed: 02/23/2023] Open
Abstract
Research over the past two decades has confirmed that noncoding RNAs (ncRNAs), which are abundant in cells from yeast to vertebrates, are no longer "junk" transcripts but functional regulators that can mediate various cellular and physiological processes. The dysregulation of ncRNAs is closely related to the imbalance of cellular homeostasis and the occurrence and development of various diseases. In mammals, ncRNAs, such as long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), have been shown to serve as biomarkers and intervention targets in growth, development, immunity, and disease progression. The regulatory functions of lncRNAs on gene expression are usually mediated by crosstalk with miRNAs. The most predominant mode of lncRNA-miRNA crosstalk is the lncRNA-miRNA-mRNA axis, in which lncRNAs act as competing endogenous RNAs (ceRNAs). Compared to mammals, little attention has been given to the role and mechanism of the lncRNA-miRNA-mRNA axis in teleost species. In this review, we provide current knowledge about the teleost lncRNA-miRNA-mRNA axis, focusing on its physiological and pathological regulation in growth and development, reproduction, skeletal muscle, immunity to bacterial and viral infections, and other stress-related immune responses. Herein, we also explored the potential application of the lncRNA-miRNA-mRNA axis in the aquaculture industry. These findings contribute to an enhanced understanding of ncRNA and ncRNA-ncRNA crosstalk in fish biology to improve aquaculture productivity, fish health and quality.
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Affiliation(s)
- Zhixia Zhou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Cuibo Leng
- The Affiliated Qingdao Central Hospital of Qingdao University, The Second Affiliated Hospital of Medical College of Qingdao University, Qingdao, China
| | - Zhan Wang
- The Affiliated Qingdao Central Hospital of Qingdao University, The Second Affiliated Hospital of Medical College of Qingdao University, Qingdao, China
| | - Linhai Long
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yiju Lv
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Ziru Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Shoushi Wang
- The Affiliated Qingdao Central Hospital of Qingdao University, The Second Affiliated Hospital of Medical College of Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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Zhao L, Huang J, Wu S, Li Y, Pan Y. Integrative analysis of miRNA and mRNA expression associated with the immune response in the intestine of rainbow trout (Oncorhynchus mykiss) infected with infectious hematopoietic necrosis virus. FISH & SHELLFISH IMMUNOLOGY 2022; 131:54-66. [PMID: 36174908 DOI: 10.1016/j.fsi.2022.09.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Rainbow trout (Oncorhynchus mykiss), an economically important cold-water fish cultured worldwide, suffers from infectious hematopoietic necrosis virus (IHNV) infection, resulting in huge financial losses. In order to understand the immune response of rainbow trout during virus infection, we explored trout intestine transcriptome profiles following IHNV challenge, and identified 3355 differentially expressed genes (DEGs) and 80 differentially expressed miRNAs (DEMs). Transcriptome analysis revealed numerous DEGs involved in immune responses, such as toll-like receptor 3 (TLR3), toll-like receptor 7/8 (TLR7/8), tripartite motif-containing 25 (TRIM25), DExH-Box helicase 58 (DHX58), interferon-induced with helicase C domain 1 (IFIH1), interferon regulatory factor 3 (IRF3/7), signal transducer and activator of transcription 1 (STAT1) and heat shock protein 90-alpha 1 (HSP90A1). Integrated analysis identified five key miRNAs (miR-19-y, miR-181-z, miR-203-y, miR-143-z and miR-206-y) targeting at least two important immune genes (TRIM25, DHX58, STAT1, TLR7/8 and HSP90A1). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that DEGs and target genes were significantly enriched in various immune-related terms including immune system process, binding, cell part and pathways of Toll-like receptor signalling, RIG-I-like receptor signalling, NOD-like receptor signalling, JAK-STAT signalling, PI3K-Akt signalling, NF-kappa B signalling, IL-17 signalling and AGE-RAGE signalling. In addition, protein-protein interaction networks (PPI) was used to display highly interactive DEG networks involving eight immune-related pathways. The expression trends of 12 DEGs and 10 DEMs were further verified by quantitative real-time PCR, which confirmed the reliability of the transcriptome sequencing results. This study expands our understanding of the immune response of rainbow trout infected with IHNV, and provides valuable resources for future studies on the immune molecular mechanism and disease resistance breeding.
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Affiliation(s)
- Lu Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jinqiang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Shenji Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yongjuan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China; College of Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yucai Pan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
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