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Jiang S, Chen J, Li X, Ren W, Li F, Wang T, Li C, Dong Z, Tian X, Zhang L, Wang L, Lu C, Chi J, Feng L, Yan M. Identification and integrated analysis of lncRNAs and miRNAs in IPEC-J2 cells provide novel insight into the regulation of the innate immune response by PDCoV infection. BMC Genomics 2022; 23:486. [PMID: 35787252 PMCID: PMC9251034 DOI: 10.1186/s12864-022-08722-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 06/21/2022] [Indexed: 11/10/2022] Open
Abstract
Background Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), are pivotal regulators involved in the pathogenic mechanism of multiple coronaviruses. Porcine deltacoronavirus (PDCoV) has evolved multiple strategies to escape the innate immune response of host cells, but whether ncRNAs are involved in this process during PDCoV infection is still unknown. Results In this study, the expression profiles of miRNAs, lncRNAs and mRNAs in IPEC-J2 cells infected with PDCoV at 0, 12 and 24 hours postinfection (hpi) were identified through small RNA and RNA sequencing. The differentially expressed miRNAs (DEmiRNAs), lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were screened from the comparison group of IPEC-J2 cells at 0 and 12 hpi as well as the comparison group of IPEC-J2 cells at 12 and 24 hpi. The target genes of these DEncRNAs were predicted. The bioinformatics analysis of the target genes revealed multiple significantly enriched functions and pathways. Among them, the genes that were associated with innate immunity were specifically screened. The expression of innate immunity-related ncRNAs and mRNAs was validated by RT–qPCR. Competing endogenous RNA (ceRNA) regulatory networks among innate immunity-related ncRNAs and their target mRNAs were established. Moreover, we found that the replication of PDCoV was significantly inhibited by two innate immunity-related miRNAs, ssc-miR-30c-3p and ssc-miR-374b-3p, in IPEC-J2 cells. Conclusions This study provides a data platform to conduct studies of the pathogenic mechanism of PDCoV from a new perspective and will be helpful for further elucidation of the functional role of ncRNAs involved in PDCoV escaping the innate immune response. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08722-2.
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Affiliation(s)
- Shan Jiang
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Jianfei Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China
| | - Xiuli Li
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Weike Ren
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Fengxiang Li
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China
| | - Ting Wang
- Institute of Pathogenic Microorganism and College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China
| | - Cheng Li
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Zhimin Dong
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Xiangxue Tian
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Li Zhang
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Lili Wang
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Chao Lu
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Jingjing Chi
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150069, China.
| | - Minghua Yan
- Tianjin Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China. .,Tianjin Observation and Experimental Site of National Animal Health, Tianjin, 300381, China.
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Rajasekaran S, Soundararajan DCR, Nayagam SM, Tangavel C, Raveendran M, Thippeswamy PB, Djuric N, Anand SV, Shetty AP, Kanna RM. Modic changes are associated with activation of intense inflammatory and host defense response pathways - molecular insights from proteomic analysis of human intervertebral discs. Spine J 2022; 22:19-38. [PMID: 34303868 DOI: 10.1016/j.spinee.2021.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/08/2021] [Accepted: 07/02/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND CONTEXT Patients with modic changes (MC) form a distinct clinical subset with reports of higher intensity of pain, poor clinical and surgical outcomes and higher incidence of recurrence. MC also is an independent risk factor for increased post-operative surgical site infection. PURPOSE This study aimed to investigate the biological changes at molecular level, in discs with MCs. We also aim to identify biological biomarkers and potential targets for molecular therapy. STUDY DESIGN Experimental analysis MATERIALS AND METHODS: Nucleus pulposus (NP) from 24 patients undergoing microdiscectomy for disc herniation [14 discs with MC and 10 without modic changes (NMC)] were procured. The overall expression of proteins, biological processes, protein-protein and metabolite interactions were analysed and compared. Host defense response proteins (HDRPs) and immunological pathways activated in patients with MC were documented and analysed. RESULTS Label-free proteomic approach with stringent filters revealed a total of 208 proteins in MC and 193 in NMC groups. 45 proteins were specific to MC; 30 to NMC and 163 common to both. Downregulated proteins in MC belonged to components of extracellular matrix such as collagens (COL- 6A1, 6A2, 6A3, 11A1, 12A1, and 20A1), and proteoglycans (versican (VCAN), and biglycan (BGN)). Inflammatory molecules [plasminogen (PLG), angiogenin (ANG), fibroblast growth factor-binding protein 2 (FGFBP2), tetranectin (CLEC3B), cartilage acidic protein 1(CRTAC1), kininogen (KNG-1), chitinase-3-like protein 2 (CHI3L2), and ferritin (FTL) were expressed only in the MC group. The significantly altered pathways in MC included Fc Fragment of IgG Receptor IIIa (FCGR3A)-mediated phagocytosis, regulation of Toll-like receptors (TLR) by endogenous ligand, neutrophil and platelet degranulation. 50 HDRPs were identified in the study, 14 of which were specific to MC and included acute phase reactants, antimicrobial peptides, complement cascade proteins, inflammatory molecule and stress response proteins. Metabolite-protein interaction analysis revealed a significant interaction between 19 proteins, specifically involving ubiquitin mediating proteasome degradative pathway and an association with the metabolite-glutamic acid in the MC group. Accumulation of glutamic acid in MC discs was confirmed by quantitative amino acid analysis using High-performance liquid chromatography. CONCLUSION Our study confirms that MC represents an intense inflammatory status and activation of host defense response and immunological pathways. Downstream effects leading to ubiquitin mediated proteasomal degradation of ECM proteins and the resulting metabolites such as glutamic acid could cause excessive pain and needs further investigation. CLINICAL SIGNIFICANCE We have documented the expression of inflammatory molecules, immune mechanisms and host defense response proteins which throw molecular insights into the pathological mechanisms of MC. Further, ubiquitin mediated proteasomal degradation and accumulation of glutamate in discs with MC might serve as targets for molecular therapy.
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Affiliation(s)
- S Rajasekaran
- Department of Spine Surgery, Ganga Hospital, 313, Mettupalayam road, Coimbatore, India.
| | | | | | - Chitraa Tangavel
- Ganga Research Centre, No 91, Mettupalayam road, Coimbatore 641030, India
| | - M Raveendran
- Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003 India
| | | | - Niek Djuric
- Department of Neurosurgery, Leiden University Medical Center, Albinusdreef 2, 2300 RC Leiden, the Netherlands
| | - Sri Vijay Anand
- Department of Spine Surgery, Ganga Hospital, 313, Mettupalayam road, Coimbatore, India
| | - Ajoy Prasad Shetty
- Department of Spine Surgery, Ganga Hospital, 313, Mettupalayam road, Coimbatore, India
| | - Rishi Mugesh Kanna
- Department of Spine Surgery, Ganga Hospital, 313, Mettupalayam road, Coimbatore, India
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Abstract
Casein kinase 1α (CK1α) is a multifunctional protein belonging to the CK1 protein family that is conserved in eukaryotes from yeast to humans. It regulates signaling pathways related to membrane trafficking, cell cycle progression, chromosome segregation, apoptosis, autophagy, cell metabolism, and differentiation in development, circadian rhythm, and the immune response as well as neurodegeneration and cancer. Given its involvement in diverse cellular, physiological, and pathological processes, CK1α is a promising therapeutic target. In this review, we summarize what is known of the biological functions of CK1α, and provide an overview of existing challenges and potential opportunities for advancing theranostics.
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Affiliation(s)
- Shaojie Jiang
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Zhejiang, 310016, Hangzhou, China
| | - Miaofeng Zhang
- Department of Orthopaedics, Second Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, 310009, Hangzhou, China
| | - Jihong Sun
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Zhejiang, 310016, Hangzhou, China
| | - Xiaoming Yang
- Department of Radiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Zhejiang, 310016, Hangzhou, China. .,Image-Guided Bio-Molecular Intervention Research, Department of Radiology, University of Washington School of Medicine, Seattle, WA, 98109, USA.
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Guo S, Wong SM. Deep sequencing analysis reveals a TMV mutant with a poly(A) tract reduces host defense responses in Nicotiana benthamiana. Virus Res 2017; 239:126-135. [PMID: 28082213 DOI: 10.1016/j.virusres.2017.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/07/2017] [Accepted: 01/08/2017] [Indexed: 12/24/2022]
Abstract
Tobacco mosaic virus (TMV) possesses an upstream pseudoknotted domain (UPD), which is important for replication. After substituting the UPD with an internal poly(A) tract (43 nt), a mutant TMV-43A was constructed. TMV-43A replicated slower than TMV and induced a non-lethal mosaic symptom in Nicotiana benthamiana. In this study, deep sequencing was performed to detect the differences of small RNA profiles between TMV- and TMV-43A-infected N. benthamiana. The results showed that TMV-43A produced lesser amount of virus-derived interfering RNAs (vsiRNAs) than that of TMV. However, the distributions of vsiRNAs generation hotspots between TMV and TMV-43A were similar. Expression of genes related to small RNA biogenesis in TMV-43A-infected N. benthamiana was significantly lower than that of TMV, which leads to generation of lesser vsiRNAs. The expressions of host defense response genes were up-regulated after TMV infection, as compared to TMV-43A-infected plants. Host defense response to TMV-43A infection was lower than that to TMV. The absence of UPD might contribute to the reduced host response to TMV-43A. Our study provides valuable information in the role of the UPD in eliciting host response genes after TMV infection in N. benthamiana. (187 words).
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Affiliation(s)
- Song Guo
- Department of Biological Sciences, National University of Singapore, Republic of Singapore
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore, Republic of Singapore; Temasek Life Sciences Laboratory, Singapore, Republic of Singapore; National University of Singapore Research Institute in Suzhou, Jiangsu, People's Republic of China.
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