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Ribeiro E. Silva A, Diallo MA, Sausset A, Robert T, Bach S, Bussière FI, Laurent F, Lacroix-Lamandé S, Silvestre A. Overexpression of Eimeria tenella Rhoptry Kinase 2 Induces Early Production of Schizonts. Microbiol Spectr 2023; 11:e0013723. [PMID: 37260371 PMCID: PMC10434272 DOI: 10.1128/spectrum.00137-23] [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: 01/10/2023] [Accepted: 05/04/2023] [Indexed: 06/02/2023] Open
Abstract
Eimeria tenella is an obligate intracellular parasite responsible for avian coccidiosis. Like other apicomplexan parasites, such as Toxoplasma gondii, cell invasion and intracellular development rely on apical organelle content discharge, named micronemes and rhoptries. Some rhoptry (ROP) kinases (ROPK) are key virulence factors in T. gondii. To date, among the 28 ropk genes carried by E. tenella, only two to four were confirmed by proteomic analysis or immunostaining to be expressed at the sporozoite stage. We have previously shown that EtROP1 is implicated in the inhibition of host cell apoptosis by interacting with the cellular p53. This work functionally described the second ROP kinase expressed at the sporozoite stage in E. tenella. EtROP2 is an active kinase that phosphorylates cell substrates of approximately 50 kDa. Its overexpression leads to the shortening of the prepatent period and to the early development of first-generation schizonts. Conduction of RNA sequencing analysis and reverse transcriptase quantitative PCR (RT-qPCR) on the host cell allowed us to identify the mitogen-activated protein kinase (MAPK) pathway and the transcription factor cFos to be upregulated by EtROP2. We also showed by immunofluorescence assay that the active kinase EtROP2 is implicated in the p38 MAPK pathway activation. We established here that EtROP2 activates the p38 MAPK pathway through a direct or indirect phosphorylation, leading to the overexpression of the master transcription factor cFos known to be implicated in E. tenella development. IMPORTANCE Rhoptries are specialized secretory organelles found in zoite stages of apicomplexan parasites. In addition to well-conserved rhoptry neck proteins, their protein consists mostly of kinase proteins, highly divergent from eukaryotic kinases. Some of those kinases are described as major virulence factors in Toxoplasma gondii, secreted into the host cell to hijack signaling pathways. Most of those kinases remain to be characterized in Eimeria tenella. Deciphering their cellular function is a prerequisite to supporting their relevance as a druggable target in development of new means of Eimeria tenella control. Secreted divergent kinases that interact with host cell partners to modulate pathways are good candidates, as they coevolve with their host targets to ensure their function within the host and are less prone to mutations that would lead to drug resistance. The absence of any orthologous kinase in host cells makes these parasite kinases a promising drug target candidate.
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Affiliation(s)
| | | | - Alix Sausset
- ISP, INRAE, Université de Tours, Nouzilly, France
| | - Thomas Robert
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models Laboratory (LBI2M), Station Biologique de Roscoff, Roscoff, France
- Sorbonne Université, CNRS, FR 2424, Plateforme de Criblage KISSf (Kinase Inhibitor Specialized Screening Facility), Station Biologique de Roscoff, Roscoff, France
| | - Stéphane Bach
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models Laboratory (LBI2M), Station Biologique de Roscoff, Roscoff, France
- Sorbonne Université, CNRS, FR 2424, Plateforme de Criblage KISSf (Kinase Inhibitor Specialized Screening Facility), Station Biologique de Roscoff, Roscoff, France
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, South Africa
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Yin YL, Yang X, Huang S, Hu GR, Yao Q, Song JK, Zhao GH. Circular RNA ciRS-7 affects the propagation of Cryptosporidium parvum in HCT-8 cells via regulating miR-135a-5p/stat1 axis. Acta Trop 2023; 243:106927. [PMID: 37080266 DOI: 10.1016/j.actatropica.2023.106927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/04/2023] [Accepted: 04/17/2023] [Indexed: 04/22/2023]
Abstract
Cryptosporidium spp. are protozoan parasites that mainly inhabit intestinal epithelial cells, causing diarrheal diseases in humans and a great number of animals. Cryptosporidium parvum is the most common zoonotic species, responsible for nearly 45% of human cryptosporidiosis worldwide. Understanding the interaction mechanisms between C. parvum and host gastrointestinal epithelial cells has significant implications to control cryptosporidiosis. One up-regulated circRNA ciRS-7 was found previously by our group to promote in vitro propagation of C. parvum in HCT-8 cells. In the present study, miR-135a-5p, was found to be a miRNA target of ciRS-7. Cryptosporidium parvum infection induced significantly down-regulation of miR-135a-5p and dramatic up-regulation of its potential target stat1 gene at mRNA and protein levels. Dual luciferase reporter assays validated the physical interactions between miR-135a-5p and stat1, and between ciRS-7 and miR-135a-5p. Further study revealed that ciRS-7 could sponge miR-135a-5p to positively regulate the protein levels of STAT1 and phosphorylated STAT1 (p-STAT1) and thus promote C. parvum propagation in HCT-8 cells. Our findings further reveal the mystery of regulatory roles of host circRNAs during Cryptosporidium infection, and provide a novel insight to develop strategies to control cryptosporidiosis.
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Affiliation(s)
- Yan-Ling Yin
- Key Laboratory of Ruminant Disease Prevention and Control (West), College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China; Chongqing Three Gorges Vocational College, Chongqing 404155, China
| | - Xin Yang
- Key Laboratory of Ruminant Disease Prevention and Control (West), College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Shuang Huang
- Key Laboratory of Ruminant Disease Prevention and Control (West), College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Gui-Rong Hu
- Key Laboratory of Ruminant Disease Prevention and Control (West), College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Qian Yao
- Key Laboratory of Ruminant Disease Prevention and Control (West), College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Jun-Ke Song
- Key Laboratory of Ruminant Disease Prevention and Control (West), College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Guang-Hui Zhao
- Key Laboratory of Ruminant Disease Prevention and Control (West), College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
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Chen X, Wang Z, Chen Y, Akinci I, Luo W, Xu Y, Jebessa E, Blake D, Sparks N, Hanotte O, Nie Q. Transcriptome analysis of differentially expressed circRNAs miRNAs and mRNAs during the challenge of coccidiosis. Front Immunol 2022; 13:910860. [PMID: 36458003 PMCID: PMC9706185 DOI: 10.3389/fimmu.2022.910860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 10/24/2022] [Indexed: 09/23/2023] Open
Abstract
Avian coccidiosis is a common enzootic disease caused by infection of Eimeria species parasites. It causes huge economic losses in the global poultry industry. Current control using anticoccidial drugs or vaccination is limited due to drug resistance and the relatively high cost of vaccines. Improving host genetic resistance to Eimeria species is considered an effective strategy for improved control of coccidiosis. Circular RNAs (circRNAs) have been found to function as biomarkers or diagnoses of various kinds of diseases. The molecular biological functions of circRNAs, miRNAs, and mRNAs related to Sasso chicken have not yet been described during Eimeria species challenge. In this study, RNA-seq was used to profile the expression pattern of circRNAs, miRNAs, and mRNAs in spleens from Eimeria tenella-infected and non-infected commercial dual-purpose Sasso T445 breed chickens. Results showed a total of 40 differentially expressed circRNAs (DEcircRNAs), 31 differentially expressed miRNAs (DEmiRNAs), and 820 differentially expressed genes (DEmRNAs) between infected and non-infected chickens. Regulatory networks were constructed between differentially expressed circRNAs, miRNAs, and mRNAs to offer insights into the interaction mechanisms between chickens and Eimeria spp. Functional validation of a significantly differentially expressed circRNA, circMGAT5, revealed that circMGAT5 could sponge miR-132c-5p to promote the expression of the miR-132c-5p target gene monocyte to macrophage differentiation-associated (MMD) during the infection of E. tenella sporozoites or LPS stimulation. Pathologically, knockdown of circMGAT5 significantly upregulated the expression of macrophage surface markers and the macrophage activation marker, F4/80 and MHC-II, which indicated that circMGAT5 might inhibit the activation of macrophage. miR-132c-5p markedly facilitated the expression of F4/80 and MHC-II while circMGAT5 could attenuate the increase of F4/80 and MHC-II induced by miR-132c-5p, indicating that circMGAT5 exhibited function through the circMGAT5-miR-132c-5p-MMD axis. Together, our results indicate that circRNAs exhibit their resistance or susceptive roles during E. tenella infection. Among these, circMGAT5 may inhibit the activation of macrophages through the circMGAT5-miR-132c-5p-MMD axis to participate in the immune response induced by Eimeria infection.
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Affiliation(s)
- Xiaolan Chen
- Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Zhijun Wang
- Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Yangfeng Chen
- Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Ibrahim Akinci
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Department of Animal Breeding and Genetics, Poultry Research Institute, Ankara, Turkey
| | - Wei Luo
- State Key Laboratory of Livestock and Poultry Breeding & Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yibin Xu
- Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
| | - Endashaw Jebessa
- Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
- LiveGene – CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Damer Blake
- Pathobiology and Population Sciences, Royal Veterinary College, North Mymms, United Kingdom
| | - Nick Sparks
- Roslin Institute Building, Scotland’s Rural College, Edinburgh, United Kingdom
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- LiveGene – CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Qinghua Nie
- Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, Guangdong, China
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Zhao SS, Tao DL, Chen JM, Wu JP, Yang X, Song JK, Zhu XQ, Zhao GH. RNA sequencing reveals dynamic expression of lncRNAs and mRNAs in caprine endometrial epithelial cells induced by Neospora caninum infection. Parasit Vectors 2022; 15:297. [PMID: 35999576 PMCID: PMC9398501 DOI: 10.1186/s13071-022-05405-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/19/2022] [Indexed: 11/10/2022] Open
Abstract
Background The effective transmission mode of Neospora caninum, with infection leading to reproductive failure in ruminants, is vertical transmission. The uterus is an important reproductive organ that forms the maternal–fetal interface. Neospora caninum can successfully invade and proliferate in the uterus, but the molecular mechanisms underlying epithelial-pathogen interactions remain unclear. Accumulating evidence suggests that host long noncoding RNAs (lncRNAs) play important roles in cellular molecular regulatory networks, with reports that these RNA molecules are closely related to the pathogenesis of apicomplexan parasites. However, the expression profiles of host lncRNAs during N. caninum infection has not been reported. Methods RNA sequencing (RNA-seq) analysis was used to investigate the expression profiles of messenger RNAs (mRNAs) and lncRNAs in caprine endometrial epithelial cells (EECs) infected with N. caninum for 24 h (TZ_24h) and 48 h (TZ_48 h), and the potential functions of differentially expressed (DE) lncRNAs were predicted by using Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of their mRNA targets. Results RNA-seq analysis identified 1280.15 M clean reads in 12 RNA samples, including six samples infected with N. caninum for 24 h (TZ1_24h-TZ3_24h) and 48 h (TZ1_48h-TZ3_48h), and six corresponding control samples (C1_24h-C3_24h and C1_48h-C3_48h). Within the categories TZ_24h-vs-C_24h, TZ_48h-vs-C_48h and TZ_48h-vs-TZ_24h, there were 934 (665 upregulated and 269 downregulated), 1238 (785 upregulated and 453 downregulated) and 489 (252 upregulated and 237 downregulated) DEmRNAs, respectively. GO enrichment and KEGG analysis revealed that these DEmRNAs were mainly involved in the regulation of host immune response (e.g. TNF signaling pathway, MAPK signaling pathway, transforming growth factor beta signaling pathway, AMPK signaling pathway, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway), signaling molecules and interaction (e.g. cytokine-cytokine receptor interaction, cell adhesion molecules and ECM-receptor interaction). A total of 88 (59 upregulated and 29 downregulated), 129 (80 upregulated and 49 downregulated) and 32 (20 upregulated and 12 downregulated) DElncRNAs were found within the categories TZ_24h-vs-C_24h, TZ_48h-vs-C_48h and TZ_48h-vs-TZ_24h, respectively. Functional prediction indicated that these DElncRNAs would be involved in signal transduction (e.g. MAPK signaling pathway, PPAR signaling pathway, ErbB signaling pathway, calcium signaling pathway), neural transmission (e.g. GABAergic synapse, serotonergic synapse, cholinergic synapse), metabolism processes (e.g. glycosphingolipid biosynthesis-lacto and neolacto series, glycosaminoglycan biosynthesis-heparan sulfate/heparin) and signaling molecules and interaction (e.g. cytokine-cytokine receptor interaction, cell adhesion molecules and ECM-receptor interaction). Conclusions This is the first investigation of global gene expression profiles of lncRNAs during N. caninum infection. The results provide valuable information for further studies of the roles of lncRNAs during N. caninum infection. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05405-5.
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Affiliation(s)
- Shan-Shan Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - De-Liang Tao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jin-Ming Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jiang-Ping Wu
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xin Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jun-Ke Song
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xing-Quan Zhu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China. .,Key Laboratory of Veterinary Public Health of Higher Education of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
| | - Guang-Hui Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Olajide JS, Olopade B, Cai J. Functional Intricacy and Symmetry of Long Non-Coding RNAs in Parasitic Infections. Front Cell Infect Microbiol 2021; 11:751523. [PMID: 34692567 PMCID: PMC8531492 DOI: 10.3389/fcimb.2021.751523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/20/2021] [Indexed: 12/11/2022] Open
Abstract
RNAs are a class of molecules and the majority in eukaryotes are arbitrarily termed non- coding transcripts which are broadly classified as short and long non-coding RNAs. Recently, knowledge of the identification and functions of long non-coding RNAs have continued to accumulate and they are being recognized as important molecules that regulate parasite-host interface, parasite differentiation, host responses, and disease progression. Herein, we present and integrate the functions of host and parasite long non-coding RNAs during infections within the context of epigenetic re-programming and molecular crosstalk in the course of host-parasite interactions. Also, the modular range of parasite and host long non-coding RNAs in coordinated parasite developmental changes and host immune dynamic landscapes are discussed. We equally canvass the prospects of long non-coding RNAs in disease diagnosis and prognosis. Hindsight and suggestions are offered with the aim that it will bolster our understanding for future works on host and parasite long non-coding RNAs.
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Affiliation(s)
- Joshua Seun Olajide
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Institute of Veterinary Research Chinese Academy of Agricultural Sciences, Lanzhou, China.,Centre for Distance Learning, Obafemi Awolowo University, Ile-Ife, Nigeria.,Jiangsu Co-Innovation Center for Prevention and Control of Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Bolatito Olopade
- Department of Medical Microbiology and Parasitology, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Jianping Cai
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Institute of Veterinary Research Chinese Academy of Agricultural Sciences, Lanzhou, China.,Jiangsu Co-Innovation Center for Prevention and Control of Animal Infectious Diseases and Zoonoses, Yangzhou, China
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Yuan J, Ni A, Li Y, Bian S, Liu Y, Wang P, Shi L, Isa AM, Ge P, Sun Y, Ma H, Chen J. Transcriptome Analysis Revealed Potential Mechanisms of Resistance to Trichomoniasis gallinae Infection in Pigeon ( Columba livia). Front Vet Sci 2021; 8:672270. [PMID: 34595226 PMCID: PMC8477972 DOI: 10.3389/fvets.2021.672270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022] Open
Abstract
Trichomoniasis gallinae (T. gallinae) is one of the most pathogenic parasites in pigeon, particularly in squabs. Oral cavity is the main site for the host-parasite interaction. Herein, we used RNA-sequencing technology to characterize lncRNA and mRNA profiles and compared transcriptomic dynamics of squabs, including four susceptible birds (S) from infected group, four tolerant birds (T) without parasites after T. gallinae infection, and three birds from uninfected group (N), to understand molecular mechanisms underlying host resistance to this parasite. We identified 29,809 putative lncRNAs and characterized their genomic features subsequently. Differentially expressed (DE) genes, DE-lncRNAs and cis/trans target genes of DE-lncRNAs were further compared among the three groups. The KEGG analysis indicated that specific intergroup DEGs were involved in carbon metabolism (S vs. T), metabolic pathways (N vs. T) and focal adhesion pathway (N vs. S), respectively. Whereas, the cis/trans genes of DE-lncRNAs were enriched in cytokine-cytokine receptor interaction, toll-like receptor signaling pathway, p53 signaling pathway and insulin signaling pathway, which play crucial roles in immune system of the host animal. This suggests T. gallinae invasion in pigeon mouth may modulate lncRNAs expression and their target genes. Moreover, co-expression analysis identified crucial lncRNA-mRNA interaction networks. Several DE-lncRNAs including MSTRG.82272.3, MSTRG.114849.42, MSTRG.39405.36, MSTRG.3338.5, and MSTRG.105872.2 targeted methylation and immune-related genes, such as JCHAIN, IL18BP, ANGPT1, TMRT10C, SAMD9L, and SOCS3. This implied that DE-lncRNAs exert critical influence on T. gallinae infections. The quantitative exploration of host transcriptome changes induced by T. gallinae infection broaden both transcriptomic and epigenetic insights into T. gallinae resistance and its pathological mechanism.
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Affiliation(s)
- Jingwei Yuan
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Aixin Ni
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Yunlei Li
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Shixiong Bian
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Yunjie Liu
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Panlin Wang
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Lei Shi
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Adamu Mani Isa
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China.,Department of Animal Science, Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Pingzhuang Ge
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Yanyan Sun
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Hui Ma
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
| | - Jilan Chen
- Institute of Animal Science, China Academy of Agricultural Science, Beijing, China
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Gao Y, Suding Z, Wang L, Liu D, Su S, Xu J, Hu J, Tao J. Full-length transcriptome analysis and identification of transcript structures in Eimeria necatrix from different developmental stages by single-molecule real-time sequencing. Parasit Vectors 2021; 14:502. [PMID: 34579769 PMCID: PMC8474931 DOI: 10.1186/s13071-021-05015-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 09/14/2021] [Indexed: 03/08/2023] Open
Abstract
Background Eimeria necatrix is one of the most pathogenic parasites, causing high mortality in chickens. Although its genome sequence has been published, the sequences and complete structures of its mRNA transcripts remain unclear, limiting exploration of novel biomarkers, drug targets and genetic functions in E. necatrix. Methods Second-generation merozoites (MZ-2) of E. necatrix were collected using Percoll density gradients, and high-quality RNA was extracted from them. Single-molecule real-time (SMRT) sequencing and Illumina sequencing were combined to generate the transcripts of MZ-2. Combined with the SMRT sequencing data of sporozoites (SZ) collected in our previous study, the transcriptome and transcript structures of E. necatrix were studied. Results SMRT sequencing yielded 21,923 consensus isoforms in MZ-2. A total of 17,151 novel isoforms of known genes and 3918 isoforms of novel genes were successfully identified. We also identified 2752 (SZ) and 3255 (MZ-2) alternative splicing (AS) events, 1705 (SZ) and 1874 (MZ-2) genes with alternative polyadenylation (APA) sites, 4019 (SZ) and 2588 (MZ-2) fusion transcripts, 159 (SZ) and 84 (MZ-2) putative transcription factors (TFs) and 3581 (SZ) and 2039 (MZ-2) long non-coding RNAs (lncRNAs). To validate fusion transcripts, reverse transcription-PCR was performed on 16 candidates, with an accuracy reaching up to 87.5%. Sanger sequencing of the PCR products further confirmed the authenticity of chimeric transcripts. Comparative analysis of transcript structures revealed a total of 3710 consensus isoforms, 815 AS events, 1139 genes with APA sites, 20 putative TFs and 352 lncRNAs in both SZ and MZ-2. Conclusions We obtained many long-read isoforms in E. necatrix SZ and MZ-2, from which a series of lncRNAs, AS events, APA events and fusion transcripts were identified. Information on TFs will improve understanding of transcriptional regulation, and fusion event data will greatly improve draft versions of gene models in E. necatrix. This information offers insights into the mechanisms governing the development of E. necatrix and will aid in the development of novel strategies for coccidiosis control. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-05015-7.
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Affiliation(s)
- Yang Gao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Zeyang Suding
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Lele Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Dandan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Shijie Su
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Jinjun Xu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
| | - Junjie Hu
- Biology Department, Yunnan University, Kunming, 650500, China
| | - Jianping Tao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China. .,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China. .,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China.
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Yin YL, Liu TL, Yao Q, Wang YX, Wu XM, Wang XT, Yang X, Song JK, Zhao GH. Circular RNA ciRS-7 affects the propagation of Cryptosporidium parvum in HCT-8 cells by sponging miR-1270 to activate the NF-κB signaling pathway. Parasit Vectors 2021; 14:238. [PMID: 33957927 PMCID: PMC8101149 DOI: 10.1186/s13071-021-04739-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/21/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Cryptosporidium is an important zoonotic pathogen responsible for severe enteric diseases in humans and animals. However, the molecular mechanisms underlying host and Cryptosporidium interactions are still not clear. METHODS To study the roles of circRNAs in host cells during Cryptosporidium infection, the expression profiles of circRNAs in HCT-8 cells infected with C. parvum were investigated using a microarray assay, and the regulatory role of a significantly upregulated circRNA, ciRS-7, was investigated during C. parvum infection. RESULTS C. parvum infection caused notable alterations in the expression profiles of circRNAs in HCT-8 cells, and a total of 178 (including 128 up- and 50 downregulated) circRNAs were significantly differentially expressed following C. parvum infection. Among them, ciRS-7 was significantly upregulated and regulated the NF-κB signaling pathway by sponging miR-1270 during C. parvum infection. Furthermore, the ciRS-7/miR-1270/relA axis markedly affected the propagation of C. parvum in HCT-8 cells. CONCLUSIONS Our results revealed that ciRS-7 would promote C. parvum propagation by regulating the miR-1270/relA axis and affecting the NF-κB pathway. To the best of our knowledge, this is the first study to investigate the role of circRNA during Cryptosporidium infection, and the findings provide a novel view for implementing control strategies against Cryptosporidium infection.
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Affiliation(s)
- Yan-Ling Yin
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Ting-Li Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Qian Yao
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yu-Xin Wang
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xue-Mei Wu
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xue-Ting Wang
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xin Yang
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jun-Ke Song
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Guang-Hui Zhao
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, China.
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9
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Yu H, Mi C, Wang Q, Zou W, Dai G, Zhang T, Zhang G, Xie K, Wang J, Shi H. Comprehensive Analyses of circRNA Expression Profiles and Function Prediction in Chicken Cecums After Eimeria tenella Infection. Front Cell Infect Microbiol 2021; 11:628667. [PMID: 33777841 PMCID: PMC7988198 DOI: 10.3389/fcimb.2021.628667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/01/2021] [Indexed: 01/01/2023] Open
Abstract
Coccidiosis is an important intestinal parasitic disease that causes great economic losses to the global poultry production industry. Circular RNAs (circRNAs) are long non-coding RNAs that play important roles in various infectious diseases and inflammatory responses. However, the expression profiles and functions of circRNAs during Eimeria tenella (E. tenella) infection remain unclear. In this study, high-throughput sequencing was carried out to detect circRNAs in chicken cecal tissues from the control (JC), resistant (JR), and susceptible (JS) groups on day 4.5 postinfection (pi), respectively. A total of 104 circRNAs were differentially expressed, including 47 circRNAs between the JS and JC groups, 38 between the JR and JS groups, and 19 between the JR and JC groups. Functional analyses indicated that these differentially expressed circRNAs were involved in pathways related to E. tenella infection; the adaptive immune response was enriched in the JS vs JC group, the NF-kappa B signaling and natural killer cell-mediated cytotoxicity pathways were enriched in the JS vs JC and JR vs JC groups, while the B cell receptor signaling pathway was enriched in only the JR vs JC group. Moreover, the coexpression network of differentially expressed circRNAs and mRNAs suggested that circRNA2202 and circRNA0759 associated with DTX1 in the JS vs JC group, circRNA4338 associated with VPREB3 and CXCL13L3 in the JR vs JC group, and circRNA2612 associated with IL8L1 and F2RL2 in the JR vs JS group were involved in the immune response upon E. tenella infection. In conclusion, our results provide valuable information on the circRNAs involved in the progression of chicken E. tenella infection and advance our understanding of the circRNA regulatory mechanisms of host resistance and susceptibility to E. tenella infection in chickens.
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Affiliation(s)
- Hailiang Yu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Changhao Mi
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Qi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Wenbin Zou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guojun Dai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Tao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Kaizhou Xie
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Huiqiang Shi
- Technical Research Department, Jiangsu Jinghai Poultry Group Co. Ltd., Haimen, China
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10
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Epigenetic Regulation by Non-Coding RNAs in the Avian Immune System. Life (Basel) 2020; 10:life10080148. [PMID: 32806547 PMCID: PMC7459779 DOI: 10.3390/life10080148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/20/2022] Open
Abstract
The identified non-coding RNAs (ncRNAs) include circular RNAs, long non-coding RNAs, microRNAs, ribosomal RNAs, small interfering RNAs, small nuclear RNAs, piwi-interacting RNAs, and transfer RNAs, etc. Among them, long non-coding RNAs, circular RNAs, and microRNAs are regulatory RNAs that have different functional mechanisms and were extensively participated in various biological processes. Numerous research studies have found that circular RNAs, long non-coding RNAs, and microRNAs played their important roles in avian immune system during the infection of parasites, virus, or bacterium. Here, we specifically review and expand this knowledge with current advances of circular RNAs, long non-coding RNAs, and microRNAs in the regulation of different avian diseases and discuss their functional mechanisms in response to avian diseases.
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